Dr. Casey Mueller
Assistant Professor, CSUSM, Biology
Lab Website
Thermal physiology: exploring themes of development and variability in different animal models
Tuesday, Dec. 3, 12 PM, AHF 153 (Torrey Webb Room)
Abstract: Dr. Mueller will present some of her lab’s data on copepods, as well as some work on chorus frogs and possibly rainbow trout. Many of the ideas can be applied to marine organisms.
Monday, December 2, 2019
QCB Colloquium | Dr. Shilpa Kobren
Dr. Shilpa Kobren
Research Fellow in Biomedical Informatics, Harvard Medical School
Research Profile
Uncovering genes with significantly perturbed functionalities in cancer
Thursday, Dec. 5, 2 PM, RRI 101
Abstract: A major challenge in cancer genomics is to identify genes with functional roles in cancer and uncover their mechanisms of action. This is a difficult task as there is substantial mutational heterogeneity across tumors, and only a small subset of the numerous mutations in a given tumor may be functionally relevant for the disease. In my talk, I will introduce our newly developed, unified analytical framework that enables rapid integration of multiple sources of information in order to identify cancer-relevant genes by pinpointing those whose interaction or other functional sites are enriched in somatic mutations across tumors. Our method PertInInt combines knowledge about sites participating in interactions with DNA, RNA, peptides, ions or small molecules with domain, evolutionary conservation and gene-level mutation data. When applied to 10,037 tumor samples across 33 cancer types, PertInInt efficiently uncovers both known and newly predicted cancer genes. Importantly, our analytical integration of data allows PertInInt to simultaneously reveal whether interaction potential or other molecular functionalities are disrupted, thereby enabling valuable insights that may help guide personalized cancer treatments. PertInInt’s analysis demonstrates that somatic mutations are frequently enriched in binding residues and functional domains in cancer genes, and implicates interaction perturbation as a pervasive cancer driving event.
Research Fellow in Biomedical Informatics, Harvard Medical School
Research Profile
Uncovering genes with significantly perturbed functionalities in cancer
Thursday, Dec. 5, 2 PM, RRI 101
Abstract: A major challenge in cancer genomics is to identify genes with functional roles in cancer and uncover their mechanisms of action. This is a difficult task as there is substantial mutational heterogeneity across tumors, and only a small subset of the numerous mutations in a given tumor may be functionally relevant for the disease. In my talk, I will introduce our newly developed, unified analytical framework that enables rapid integration of multiple sources of information in order to identify cancer-relevant genes by pinpointing those whose interaction or other functional sites are enriched in somatic mutations across tumors. Our method PertInInt combines knowledge about sites participating in interactions with DNA, RNA, peptides, ions or small molecules with domain, evolutionary conservation and gene-level mutation data. When applied to 10,037 tumor samples across 33 cancer types, PertInInt efficiently uncovers both known and newly predicted cancer genes. Importantly, our analytical integration of data allows PertInInt to simultaneously reveal whether interaction potential or other molecular functionalities are disrupted, thereby enabling valuable insights that may help guide personalized cancer treatments. PertInInt’s analysis demonstrates that somatic mutations are frequently enriched in binding residues and functional domains in cancer genes, and implicates interaction perturbation as a pervasive cancer driving event.
QCB Colloquium | Dr. Pei Wang
Dr. Pei Wang
Professor, Icahn School of Medicine at Mount Sinai, Genetics and Genomic Sciences
Lab Website
Constructing tumor-specific gene regulatory networks based on samples with tumor purity heterogeneity
Monday, Dec. 2, 2 PM, RRI 101
Abstract: Tumor tissue samples often contain an unknown fraction of normal cells. This problem well known as tumor purity heterogeneity (TPH) was recently recognized as a severe issue in omics studies. Specifically, if TPH is ignored when inferring co-expression networks, edges are likely to be estimated among genes with mean shift between normal and tumor cells rather than among gene pairs interacting with each other in tumor cells. To address this issue, we propose TSNet a new method which constructs tumor-cell specific gene/protein co-expression networks based on gene/protein expression profiles of tumor tissues. TSNet treats the observed expression profile as a mixture of expressions from different cell types and explicitly models tumor purity percentage in each tumor sample. The advantage of TSNet over existing methods ignoring TPH is illustrated through extensive simulation examples. We then apply TSNet to estimate tumor specific co-expression networks based on ovarian cancer expression profiles. We identify novel co-expression modules and hub structure specific to tumor cells
Professor, Icahn School of Medicine at Mount Sinai, Genetics and Genomic Sciences
Lab Website
Constructing tumor-specific gene regulatory networks based on samples with tumor purity heterogeneity
Monday, Dec. 2, 2 PM, RRI 101
Abstract: Tumor tissue samples often contain an unknown fraction of normal cells. This problem well known as tumor purity heterogeneity (TPH) was recently recognized as a severe issue in omics studies. Specifically, if TPH is ignored when inferring co-expression networks, edges are likely to be estimated among genes with mean shift between normal and tumor cells rather than among gene pairs interacting with each other in tumor cells. To address this issue, we propose TSNet a new method which constructs tumor-cell specific gene/protein co-expression networks based on gene/protein expression profiles of tumor tissues. TSNet treats the observed expression profile as a mixture of expressions from different cell types and explicitly models tumor purity percentage in each tumor sample. The advantage of TSNet over existing methods ignoring TPH is illustrated through extensive simulation examples. We then apply TSNet to estimate tumor specific co-expression networks based on ovarian cancer expression profiles. We identify novel co-expression modules and hub structure specific to tumor cells
Monday, November 18, 2019
QCB Colloquium | Dr. Neda Bagheri
Dr. Neda Bagheri
Adjunct Professor of Chemical and Biological Engineering, Northwestern University
Lab Website
Modeling toward systems medicine: predicting how context impacts cell population dynamics
Thursday, Nov. 21, 2 PM, RRI 101
Abstract: Computational models are essential tools that can be used to simultaneously explain and guide biological intuition. My lab employs machine learning, dynamical systems, and agent-based modeling strategies to help explain biological observations, and to uncover fundamental principles that drive both individual cellular decisions and cell populations. We are interested in the inherent multiscale nature of cells—how “the whole is greater than the sum of its parts”—and in predicting cell population dynamics from the composition of simpler biological modules to advance basic science and medicine.
Adjunct Professor of Chemical and Biological Engineering, Northwestern University
Lab Website
Modeling toward systems medicine: predicting how context impacts cell population dynamics
Thursday, Nov. 21, 2 PM, RRI 101
Abstract: Computational models are essential tools that can be used to simultaneously explain and guide biological intuition. My lab employs machine learning, dynamical systems, and agent-based modeling strategies to help explain biological observations, and to uncover fundamental principles that drive both individual cellular decisions and cell populations. We are interested in the inherent multiscale nature of cells—how “the whole is greater than the sum of its parts”—and in predicting cell population dynamics from the composition of simpler biological modules to advance basic science and medicine.
HEB Seminar | Dr. Caitlin O'Connell
Dr. Caitlin O'Connell
Post-Doctoral Scholar/Teaching Fellow, USC, Dept. of Biological Sciences
Research Profile
The Costs and Benefits of Sociality Explored in the Semi-Solitary Orangutan
Monday, Nov. 18, 12 PM, AHF 153 (Torrey Webb Room)
Abstract: Social relationships are an integral part of primate life for humans and nonhumans
alike, but the extent to which a primate devotes its time and energy to
socializing can vary tremendously within and between species. With a semisolitary
social system, orangutans present a unique opportunity to examine both
social and solitary conditions within a single population to test predictions
regarding the costs and benefits of sociality. While the socioecological model
predicts that orangutans display reduced sociality compared to other apes, this
should affect individuals differently across life history stages. This research
examines the variation in social behavior among age-sex classes in wild
orangutans using social interactions, behavioral and hormonal indicators of stress,
and intestinal parasites to evaluate the reasons orangutans socialize or remain
solitary at different times. Adolescent females were found to socialize the most, to
suffer the lowest physiological cost from socializing, and to employ unique
behavioral strategies to mitigate potentially risky social situations. My findings
highlight the adolescent period as behaviorally distinct and socially rich for
female orangutans who face unique challenges as members of a socially dispersed
species with high levels of sexual coercion.
Post-Doctoral Scholar/Teaching Fellow, USC, Dept. of Biological Sciences
Research Profile
The Costs and Benefits of Sociality Explored in the Semi-Solitary Orangutan
Monday, Nov. 18, 12 PM, AHF 153 (Torrey Webb Room)
Abstract: Social relationships are an integral part of primate life for humans and nonhumans
alike, but the extent to which a primate devotes its time and energy to
socializing can vary tremendously within and between species. With a semisolitary
social system, orangutans present a unique opportunity to examine both
social and solitary conditions within a single population to test predictions
regarding the costs and benefits of sociality. While the socioecological model
predicts that orangutans display reduced sociality compared to other apes, this
should affect individuals differently across life history stages. This research
examines the variation in social behavior among age-sex classes in wild
orangutans using social interactions, behavioral and hormonal indicators of stress,
and intestinal parasites to evaluate the reasons orangutans socialize or remain
solitary at different times. Adolescent females were found to socialize the most, to
suffer the lowest physiological cost from socializing, and to employ unique
behavioral strategies to mitigate potentially risky social situations. My findings
highlight the adolescent period as behaviorally distinct and socially rich for
female orangutans who face unique challenges as members of a socially dispersed
species with high levels of sexual coercion.
Sunday, November 10, 2019
Green Corps is hiring for next year’s class of environmental organizers!
Green Corps is looking for college graduates who are ready to take on the biggest environmental challenges of our day.
Our year-long program puts you in an intensive classroom training with people like Bill McKibben and other guest speakers. Then, you move to hands-on experience working with groups like Oceana, Corporate Accountability, The Wilderness Society and Mighty Earth to fight climate change, protect public lands and reform our food system. And when you graduate we will help you find a career with one of the nation’s leading environmental and social change groups.
The planet needs all the help it can get, especially now with so many protections under attack. To win now and build a strong foundation for lasting progress, we need people who know how to organize: to run organizations and campaigns that will inspire the support and action we need to save our planet.
We’re accepting the top 25 out of more than 1000 applicants for our 2020-2021 program. If you’re passionate about the environment and ready to learn and practice the craft of organizing, click here to apply.
Green Corps’ year long program begins in August 2019 with Introductory Classroom Training, and continues with field placements in multiple locations across the U.S. Candidates must be willing to relocate.
For more information, click here.
Our year-long program puts you in an intensive classroom training with people like Bill McKibben and other guest speakers. Then, you move to hands-on experience working with groups like Oceana, Corporate Accountability, The Wilderness Society and Mighty Earth to fight climate change, protect public lands and reform our food system. And when you graduate we will help you find a career with one of the nation’s leading environmental and social change groups.
The planet needs all the help it can get, especially now with so many protections under attack. To win now and build a strong foundation for lasting progress, we need people who know how to organize: to run organizations and campaigns that will inspire the support and action we need to save our planet.
We’re accepting the top 25 out of more than 1000 applicants for our 2020-2021 program. If you’re passionate about the environment and ready to learn and practice the craft of organizing, click here to apply.
Green Corps’ year long program begins in August 2019 with Introductory Classroom Training, and continues with field placements in multiple locations across the U.S. Candidates must be willing to relocate.
For more information, click here.
Deepfake Detection: Methods for Combatting and Detecting Deepfakes
Elizabeth Galoozis, Associate University Librarian and Head, Information Literacy
Curtis Fletcher, Director, Ahmanson Lab
Samir Ghosh, Project Coordinator, Ahmanson Lab
November 12, 3:00-4:30pm
Ahmanson Lab | LVL 301 (Map)
RSVP for this event
The term deepfake, a combination of “deep learning” and “fake,” designates a new class of hyper-realistic, fake media - images, video, and audio generated leveraging machine-learning algorithms to, primarily, superimpose faces and/or voices on people in order to manufacture their saying and doing things they have not said or done.
While there are real artistic benefits to such techniques, much has recently been made about the great social harm the technology can unleash in an increasingly polarized and fragmented social media ecosystem.
In this workshop, we’ll discuss with participants the troubling nature of truth in an era of deepfakes. We’ll survey the history of visual evidence and media manipulation; introduce participants to current large-scale media forensic efforts to combat deepfakes; talk about the methods, techniques, and technology behind the creation of deepfakes; and, finally, offer some best practices for researching and spotting AI-generated fake media online.
Curtis Fletcher, Director, Ahmanson Lab
Samir Ghosh, Project Coordinator, Ahmanson Lab
November 12, 3:00-4:30pm
Ahmanson Lab | LVL 301 (Map)
RSVP for this event
The term deepfake, a combination of “deep learning” and “fake,” designates a new class of hyper-realistic, fake media - images, video, and audio generated leveraging machine-learning algorithms to, primarily, superimpose faces and/or voices on people in order to manufacture their saying and doing things they have not said or done.
While there are real artistic benefits to such techniques, much has recently been made about the great social harm the technology can unleash in an increasingly polarized and fragmented social media ecosystem.
In this workshop, we’ll discuss with participants the troubling nature of truth in an era of deepfakes. We’ll survey the history of visual evidence and media manipulation; introduce participants to current large-scale media forensic efforts to combat deepfakes; talk about the methods, techniques, and technology behind the creation of deepfakes; and, finally, offer some best practices for researching and spotting AI-generated fake media online.
QCB Colloquium | Dr. Alison Hill
Dr. Alison Hill
Research Fellow, Harvard Univ., Prog. for Evolutionary Dynamics
Research Profile
Countdown to a cure? Mathematical approaches to designing better HIV treatments
Thursday, Nov. 14, 2 PM, RRI 101
Abstract: HIV infection can be effectively treated with combination antiretroviral therapy, but new classes of drugs are needed to permanently cure the infection. In this talk I will discuss our work developing mathematical and computational methods to better understand the mechanisms of HIV persistence and evaluate new methods to cure the disease. Firstly, I will show how models have helped us understand how much the pool of latent virus must be reduced to delay or prevent the viral rebound when drugs are stopped. We explain why existing anti-latency drugs have had negligible benefit, and why we have seen multiple cases of apparent (but false) “cures” of HIV. Secondly, I will discuss how longitudinal studies of viral genetics during antiretroviral therapy can be used to help elucidate the dominant cause of long-term persistence. This includes a new method we have developed to quantify how important the proliferation of latently-infected cells is to driving long-term viral persistence, which also suggests that therapies to target this process could be highly effective. Finally, I will describe a series of studies using new immunotherapy strategies to cure HIV, and our work using mathematical models to uncover the mechanism of action of these interventions. Overall, this work highlights the role that simulation, analysis, and inference using mathematical models can play in informing new potentially-curative treatments for HIV.
Research Fellow, Harvard Univ., Prog. for Evolutionary Dynamics
Research Profile
Countdown to a cure? Mathematical approaches to designing better HIV treatments
Thursday, Nov. 14, 2 PM, RRI 101
Abstract: HIV infection can be effectively treated with combination antiretroviral therapy, but new classes of drugs are needed to permanently cure the infection. In this talk I will discuss our work developing mathematical and computational methods to better understand the mechanisms of HIV persistence and evaluate new methods to cure the disease. Firstly, I will show how models have helped us understand how much the pool of latent virus must be reduced to delay or prevent the viral rebound when drugs are stopped. We explain why existing anti-latency drugs have had negligible benefit, and why we have seen multiple cases of apparent (but false) “cures” of HIV. Secondly, I will discuss how longitudinal studies of viral genetics during antiretroviral therapy can be used to help elucidate the dominant cause of long-term persistence. This includes a new method we have developed to quantify how important the proliferation of latently-infected cells is to driving long-term viral persistence, which also suggests that therapies to target this process could be highly effective. Finally, I will describe a series of studies using new immunotherapy strategies to cure HIV, and our work using mathematical models to uncover the mechanism of action of these interventions. Overall, this work highlights the role that simulation, analysis, and inference using mathematical models can play in informing new potentially-curative treatments for HIV.
Monday, November 4, 2019
MEB Seminar | Dr. Jeff Bowman
Dr. Jeff Bowman
Assistant Professor, UCSD, Scripps Institute of Oceanography, Integrative Oceanography Division
Lab Website
Trials, tribulations, and transcriptomes: Understanding microbial ecosystem processes along the western Antarctic Peninsula
Tuesday, Nov. 5, 12 PM, AHF 153 (Torrey Webb Room)
Abstract: The western Antarctic Peninsula (WAP) is a dynamic marine environment defined by contrasting onshore and offshore water masses, rapidly shifting sea ice conditions, and strong season cycles of light and temperature. The region is well known for its charismatic megafauna, but the charisma of its marine microbes is just beginning to emerge. I’ll describe some of our efforts over the last several years to understand the dynamics of marine microbial communities along the WAP, culminating in our ongoing effort to use metatranscriptomics to understand the carbon and energy transfers associated with the winter-spring seasonal transition. This transitional period is dominated by lipid metabolisms among a surprisingly diverse group of marine phytoplankton. Given the variability in timing of the annual sea ice retreat, and the importance of lipid-rich phytoplankton in regional foodwebs, we anticipate implications for metabolic energy budgets across trophic levels.
Assistant Professor, UCSD, Scripps Institute of Oceanography, Integrative Oceanography Division
Lab Website
Trials, tribulations, and transcriptomes: Understanding microbial ecosystem processes along the western Antarctic Peninsula
Tuesday, Nov. 5, 12 PM, AHF 153 (Torrey Webb Room)
Abstract: The western Antarctic Peninsula (WAP) is a dynamic marine environment defined by contrasting onshore and offshore water masses, rapidly shifting sea ice conditions, and strong season cycles of light and temperature. The region is well known for its charismatic megafauna, but the charisma of its marine microbes is just beginning to emerge. I’ll describe some of our efforts over the last several years to understand the dynamics of marine microbial communities along the WAP, culminating in our ongoing effort to use metatranscriptomics to understand the carbon and energy transfers associated with the winter-spring seasonal transition. This transitional period is dominated by lipid metabolisms among a surprisingly diverse group of marine phytoplankton. Given the variability in timing of the annual sea ice retreat, and the importance of lipid-rich phytoplankton in regional foodwebs, we anticipate implications for metabolic energy budgets across trophic levels.
Monday, October 28, 2019
QCB Colloquium | Dr. Matthew J. Simpson
Dr. Matthew J. Simpson
Professor, Queensland University of Technology, Science & Engineering, Mathematical Sciences, Applied & Computational Mathematics
Research Website
Mathematical and experimental models of cell invasion with fluorescent cell cycle indicators
Thursday, Oct. 31, 2 PM, RRI 101
Abstract: Fluorescent cell cycle indicators, such as FUCCI, allow us to visualize the cell cycle in individual cells. FUCCI reveals real-time information about cell cycle dynamics in individual cells, and can be used to explore how the cell cycle relates to the location of cells, local cell density, and different microenvironments. In this talk I will describe how FUCCI technology can be incorporated into continuum and discrete models of cell invasion. Using experimental data from two-dimensional cell invasion assays with FUCCI-transduced melanoma cells, we show how mathematical models can be used to predict key features of the experiments. The models we present are also amenable to travelling wave analysis, and some key highlights of this analysis will also be presented and discussed.
Professor, Queensland University of Technology, Science & Engineering, Mathematical Sciences, Applied & Computational Mathematics
Research Website
Mathematical and experimental models of cell invasion with fluorescent cell cycle indicators
Thursday, Oct. 31, 2 PM, RRI 101
Abstract: Fluorescent cell cycle indicators, such as FUCCI, allow us to visualize the cell cycle in individual cells. FUCCI reveals real-time information about cell cycle dynamics in individual cells, and can be used to explore how the cell cycle relates to the location of cells, local cell density, and different microenvironments. In this talk I will describe how FUCCI technology can be incorporated into continuum and discrete models of cell invasion. Using experimental data from two-dimensional cell invasion assays with FUCCI-transduced melanoma cells, we show how mathematical models can be used to predict key features of the experiments. The models we present are also amenable to travelling wave analysis, and some key highlights of this analysis will also be presented and discussed.
Survey of Christian, Muslim, Jewish, or Atheist Students in Science
I am a professor in the School of Life Sciences at Arizona State University and my research group is interested in understanding the experiences of graduate students from diverse religious backgrounds. We are conducting scholarly interviews with biology graduate students who identify as Christian, Muslim, Jewish, or Atheist about their experiences in the biology community. We would like to understand the range of experiences students have with these identities to improve the training of scientists from many different backgrounds.
We are offering students a $15 gift card to conduct a one-hour Skype interview with our researchers. All information will remain completely confidential. If you are interested in participating, please follow this link and fill out our short survey and our research team will contact you shortly to schedule your interview: https://tinyurl.com/y5ocuj38
If you have any questions or concerns about the research, you can contact my postdoctoral researcher Elizabeth Barnes at liz.barnes@asu.edu
Sincerely,
Sara Brownell, PhD
Associate Professor
School of Life Science
Arizona State University
sara.brownell@asu.edu
M. Elizabeth Barnes, PhD
Postdoctoral scholar
School of Life Science
Arizona State University
Liz.barnes@asu.edu
We are offering students a $15 gift card to conduct a one-hour Skype interview with our researchers. All information will remain completely confidential. If you are interested in participating, please follow this link and fill out our short survey and our research team will contact you shortly to schedule your interview: https://tinyurl.com/y5ocuj38
If you have any questions or concerns about the research, you can contact my postdoctoral researcher Elizabeth Barnes at liz.barnes@asu.edu
Sincerely,
Sara Brownell, PhD
Associate Professor
School of Life Science
Arizona State University
sara.brownell@asu.edu
M. Elizabeth Barnes, PhD
Postdoctoral scholar
School of Life Science
Arizona State University
Liz.barnes@asu.edu
QCB Colloquium | Dr. John H. Maddocks
Dr. John H. Maddocks
Professor, EPFL Lausanne, Switzerland, Laboratory for Computation & Visualization in Mathematics & Mechanics
Lab Website
The cgDNA sequence-dependent coarse-grain model of dsDNA: Bridging the scales from Molecular Dynamics to Bioinformatics
Tuesday, Oct. 29, 3:15 PM, MCB 102
Abstract: The cgDNA+ coarse-grain model of DNA (lcvmwww.epfl.ch/research/cgDNA/) can now accurately predict the sequence-dependent statistical mechanics properties, for example shape and stiffness (or equivalently first and second moments of the equilibrium distributions), of double-stranded DNA fragments of arbitrary sequence. At scales of tens of base pairs these predictions can be compared with Molecular Dynamics simulations and they agree very well. However the efficiency of the cgDNA+ model allows genome length scales to be scanned in order to identify mechanically exceptional sequence fragments, including in an epigenetically modified sequence alphabet.
Professor, EPFL Lausanne, Switzerland, Laboratory for Computation & Visualization in Mathematics & Mechanics
Lab Website
The cgDNA sequence-dependent coarse-grain model of dsDNA: Bridging the scales from Molecular Dynamics to Bioinformatics
Tuesday, Oct. 29, 3:15 PM, MCB 102
Abstract: The cgDNA+ coarse-grain model of DNA (lcvmwww.epfl.ch/research/cgDNA/) can now accurately predict the sequence-dependent statistical mechanics properties, for example shape and stiffness (or equivalently first and second moments of the equilibrium distributions), of double-stranded DNA fragments of arbitrary sequence. At scales of tens of base pairs these predictions can be compared with Molecular Dynamics simulations and they agree very well. However the efficiency of the cgDNA+ model allows genome length scales to be scanned in order to identify mechanically exceptional sequence fragments, including in an epigenetically modified sequence alphabet.
Monday, October 21, 2019
Post-doc and Bioinformatician positions available in NYC
The Bunyavanich Lab welcomes talented, self-motivated individuals who can fulfill the responsibilities and requirements below to apply for positions in our lab at the Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY. The successful applicant will be part of an interdisciplinary team led by Dr. Supinda Bunyavanich that applies computational analysis and bioinformatics to interpret multi-scale data generated from subjects with asthma and allergic diseases. Our researchers receive generous packages, including robust salaries and a wealth of opportunities to participate in academic activities here at the Institute for Data Science and Genomic Technology and more broadly at regional and national workshops and conferences. We are located in the heart of Manhattan, and Mount Sinai is one of the oldest and largest teaching hospitals in the US.
Responsibilities:
• Analyze high-throughput sequence data.
• Develop and implement methods to analyze these data.
• Maintain large datasets linked to clinical data.
• Communicate progress with PI regularly and contribute to the success of the research team.
• Develop and maintain productive collaborations within Mount Sinai and with outside researchers in academia and industry.
• Publish and present novel research findings in academic journals and conferences
• Some supervision of trainees and technical staff may also be required.
Requirements:
• Degree in bioinformatics, computer science, computational biology, genomics, or a related field.
• Outstanding programming skills in R, Python, and Unix shell scripting.
• Excellent track record of analyzing sequence data. Experience with clinical cohorts and microbiome analysis a plus.
• Demonstrated knowledge of statistics and statistical genetics. Familiarity with genomic data tools, repositories, and databases.
• Strong attention to detail and solid analytical skills.
• Ability to work hard and independently while contributing to the team effort and adhering to deadlines.
• Excellent oral and written communication skills with track record of productive collaborations.
• Demonstrated ability to work concurrently on several projects, and good understanding of analytic complexities to do independent research as well as assist other researchers.
The Institute for Data Science and Genomic Technology at the Icahn School of Medicine at Mount Sinai seeks to comprehensively integrate the digital universe of information into research, training, and patient care and to develop programs that advance the future of healthcare and data science.
Interested and qualified candidates should submit a CV and detailed letter of interest to Dr. Supinda Bunyavanich (Supinda.Bunyavanich at mssm.edu).
Responsibilities:
• Analyze high-throughput sequence data.
• Develop and implement methods to analyze these data.
• Maintain large datasets linked to clinical data.
• Communicate progress with PI regularly and contribute to the success of the research team.
• Develop and maintain productive collaborations within Mount Sinai and with outside researchers in academia and industry.
• Publish and present novel research findings in academic journals and conferences
• Some supervision of trainees and technical staff may also be required.
Requirements:
• Degree in bioinformatics, computer science, computational biology, genomics, or a related field.
• Outstanding programming skills in R, Python, and Unix shell scripting.
• Excellent track record of analyzing sequence data. Experience with clinical cohorts and microbiome analysis a plus.
• Demonstrated knowledge of statistics and statistical genetics. Familiarity with genomic data tools, repositories, and databases.
• Strong attention to detail and solid analytical skills.
• Ability to work hard and independently while contributing to the team effort and adhering to deadlines.
• Excellent oral and written communication skills with track record of productive collaborations.
• Demonstrated ability to work concurrently on several projects, and good understanding of analytic complexities to do independent research as well as assist other researchers.
The Institute for Data Science and Genomic Technology at the Icahn School of Medicine at Mount Sinai seeks to comprehensively integrate the digital universe of information into research, training, and patient care and to develop programs that advance the future of healthcare and data science.
Interested and qualified candidates should submit a CV and detailed letter of interest to Dr. Supinda Bunyavanich (Supinda.Bunyavanich at mssm.edu).
Research and Fellowships Week
Research and Fellowships Week is an annual event hosted by USC’s Academic Honors and Fellowships, the Graduate School and the Office of Postdoctoral Affairs. The goal of the week is to discuss opportunities that support research, graduate study, language learning, teaching and internships within the U.S. and abroad. The sessions are open to students of all academic levels, staff and faculty, attendees participate in interactive panels and workshops to explore USC programs and external post-graduate possibilities.
The following activities are geared towards graduate students:
Monday, November 4
Fellowships for PhD Students in Health Fields, 12:00-12:50pm, HSC Norris Medical Library, West Conference Room
“The Novelty Moves”: How to Pitch Your Research to Potential Funders….and Beyond, 1:00-1:50pm, Doheny Library (DML) 241
Tuesday, November 5
Fellowships for International PhD Students, 1:00-1:50pm, Doheny Library (DML) 241
USC Advanced PhD Fellowships, 2:00-2:50pm, Doheny Library (DML) 241
Wednesday, November 6
Research with Impact: Data and Bibliometrics, 2:00-2:50pm, Doheny Library (DML) 241
Thursday, November 7
Focus on the NSF Graduate Research Fellowship Program, 1:00-1:50pm, Doheny Library (DML) 241
Friday, November 8
Fulbright U.S. Student Program,11:00-11:50am, Hedco Neurosciences Building (HNB 100)
More information about Research and Fellowships Week is available here: https://ahf.usc.edu/events/rfw/
The following activities are geared towards graduate students:
Monday, November 4
Fellowships for PhD Students in Health Fields, 12:00-12:50pm, HSC Norris Medical Library, West Conference Room
“The Novelty Moves”: How to Pitch Your Research to Potential Funders….and Beyond, 1:00-1:50pm, Doheny Library (DML) 241
Tuesday, November 5
Fellowships for International PhD Students, 1:00-1:50pm, Doheny Library (DML) 241
USC Advanced PhD Fellowships, 2:00-2:50pm, Doheny Library (DML) 241
Wednesday, November 6
Research with Impact: Data and Bibliometrics, 2:00-2:50pm, Doheny Library (DML) 241
Thursday, November 7
Focus on the NSF Graduate Research Fellowship Program, 1:00-1:50pm, Doheny Library (DML) 241
Friday, November 8
Fulbright U.S. Student Program,11:00-11:50am, Hedco Neurosciences Building (HNB 100)
More information about Research and Fellowships Week is available here: https://ahf.usc.edu/events/rfw/
QCB Colloquium | Dr. Yinglei Lai
Dr. Yinglei Lai
Professor, The George Washington University, Dept. of Statistics
Professional Website
Assessing the discovery reproducibility from a large-scale association analysis
Wednesday, Oct. 23, 3 PM, RRI 421
Abstract: Reproducibility plays essential roles in scientific research. Magnetic Resonance Imaging (MRI) and genomic/proteomic high-throughput technologies have been widely used in brain and health research. The Dice Similarity Coefficient (DSC) has been commonly used for assessing the reproducibility of discoveries in a large-scale association analysis. However, in the current assessment of reproducibility, there is a lack of efficiency in the use of all available samples. More importantly, there is a lack of consistency with the reported discoveries identified based on all available samples. We have developed a probabilistic framework to assess discovery reproducibility based on all available samples. In our results, we demonstrated the usefulness of our approach and its advantages over DSC. We identified the minimal sample size required to achieve a given reproducibility rate, which provides an informative guidance for planning large-scale association studies.
Professor, The George Washington University, Dept. of Statistics
Professional Website
Assessing the discovery reproducibility from a large-scale association analysis
Wednesday, Oct. 23, 3 PM, RRI 421
Abstract: Reproducibility plays essential roles in scientific research. Magnetic Resonance Imaging (MRI) and genomic/proteomic high-throughput technologies have been widely used in brain and health research. The Dice Similarity Coefficient (DSC) has been commonly used for assessing the reproducibility of discoveries in a large-scale association analysis. However, in the current assessment of reproducibility, there is a lack of efficiency in the use of all available samples. More importantly, there is a lack of consistency with the reported discoveries identified based on all available samples. We have developed a probabilistic framework to assess discovery reproducibility based on all available samples. In our results, we demonstrated the usefulness of our approach and its advantages over DSC. We identified the minimal sample size required to achieve a given reproducibility rate, which provides an informative guidance for planning large-scale association studies.
QCB Colloquium | Dr. Siavash Mirarab
Dr. Siavash Mirarab
Assistant Professor, UCSD, Dept. of Electrical & Computer Engineering
Faculty Profile
Assembly-free and alignment-free sample identification and phylogenetic placement using genome skims
Thursday, Oct. 24, 2 PM, RRI 101
Abstract: The ability to inexpensively describe taxonomic diversity is critical in this era of rapid climate and biodiversity changes. The recent genome-skimming approach extends current barcoding practices beyond short markers by applying low-pass sequencing and recovering whole organelle genomes computationally. This approach discards the nuclear DNA, which constitutes the vast majority of the data. In contrast, we suggest using all unassembled reads. We introduce an assembly-free and alignment-free tool, Skmer, to compute genomic distances between the query and reference genome skims. Skmer is based on a fast computation of Jaccard index and appropriate corrections for lack of coverage. Skmer shows excellent accuracy in estimating distances and identifying the closest match in reference datasets. When paired with our new phylogenetic placement tool, APPLES, it can perform distance-based phylogenetics.
Assistant Professor, UCSD, Dept. of Electrical & Computer Engineering
Faculty Profile
Assembly-free and alignment-free sample identification and phylogenetic placement using genome skims
Thursday, Oct. 24, 2 PM, RRI 101
Abstract: The ability to inexpensively describe taxonomic diversity is critical in this era of rapid climate and biodiversity changes. The recent genome-skimming approach extends current barcoding practices beyond short markers by applying low-pass sequencing and recovering whole organelle genomes computationally. This approach discards the nuclear DNA, which constitutes the vast majority of the data. In contrast, we suggest using all unassembled reads. We introduce an assembly-free and alignment-free tool, Skmer, to compute genomic distances between the query and reference genome skims. Skmer is based on a fast computation of Jaccard index and appropriate corrections for lack of coverage. Skmer shows excellent accuracy in estimating distances and identifying the closest match in reference datasets. When paired with our new phylogenetic placement tool, APPLES, it can perform distance-based phylogenetics.
Monday, October 14, 2019
Need lecturer to teach Landscape Ecology
We are looking for a lecturer to teach our Landscape Ecology class next semester (Spring, 2020). It is upper division class taken by a mix of upperclassmen and Master’s students.
Anyone (grad students, postdocs, junior scientists) who might be interested in teaching such a class should contact me directly.
I would be happy to discuss pay and schedule with any interested parties.
Thank you.
H. K. Choi, Ph.D.
Associate Professor and Chair, Department of Biology
California State University, Dominguez Hills
1000 East Victoria Street, Carson CA 90747
Tel: (310) 243-3382 (Office)
Fax: (310) 243-2350
Email: hchoi@csudh.edu
Anyone (grad students, postdocs, junior scientists) who might be interested in teaching such a class should contact me directly.
I would be happy to discuss pay and schedule with any interested parties.
Thank you.
H. K. Choi, Ph.D.
Associate Professor and Chair, Department of Biology
California State University, Dominguez Hills
1000 East Victoria Street, Carson CA 90747
Tel: (310) 243-3382 (Office)
Fax: (310) 243-2350
Email: hchoi@csudh.edu
Stanford Science Fellows Postdoctoral Training Program
Stanford University is launching a new fellows program for postdoctoral researchers. I welcome your help in encouraging promising candidates to apply. The deadline for application is November 1, 2019.
The Stanford Science Fellows program is focused on incubating new directions in foundational scientific research through an interdisciplinary community of exceptional postdoctoral scholars from around the world who are driven by a sense of wonder about the natural world. The goals of this new postdoctoral training program are:
• To deepen our understanding of the natural world by advancing and bridging disciplines in the physical, mathematical, and life sciences.
• To provide opportunities for exceptionally qualified early-career scientists to develop academic leadership skills focused on fostering scientific discovery, acquire interdisciplinary approaches to foundational scientific research, and broaden science communication skills.
• To recognize and support scholars who bring a diversity of perspectives, identities, and backgrounds, including those from groups who are underrepresented in the sciences.
• To build community at Stanford around frontier research challenges.
• To provide flexibility and resources for bold, independent thinkers to pursue their own scientific research visions.
Stanford Science Fellowships are intended for exceptional early-career postdoctoral scholars who have recently been awarded their PhD or will be awarded their PhD by the start of the fellowship and who want to pursue research and training in any natural science discipline. International scholars are welcome to apply.
Between 4 to 8 fellows will be selected to start appointments between July 1 and September 1, 2020. Prospective fellows will be considered by a committee of Stanford faculty from departments and schools across the natural sciences at Stanford. An explicit goal of these selection committees, in addition to selecting candidates with tremendous intellectual strength, will be the enhancement of demographic and intellectual diversity in the scientific community at Stanford.
Learn more about the Stanford Science Fellows and the application at stanfordsciencefellows.stanford.edu.
Stanford Science Fellow appointments will be for three-year terms. Fellows will receive an annual stipend of $83,000 per year, benefits, and up to $8,000 per year supplemental funds to support research and professional development.
Interested applicants must apply online (stanfordsciencefellows.stanford.edu) by November 1, 2019.
Inquiries may be directed to stanfordsciencefellows@stanford.edu.
The Stanford Science Fellows program is focused on incubating new directions in foundational scientific research through an interdisciplinary community of exceptional postdoctoral scholars from around the world who are driven by a sense of wonder about the natural world. The goals of this new postdoctoral training program are:
• To deepen our understanding of the natural world by advancing and bridging disciplines in the physical, mathematical, and life sciences.
• To provide opportunities for exceptionally qualified early-career scientists to develop academic leadership skills focused on fostering scientific discovery, acquire interdisciplinary approaches to foundational scientific research, and broaden science communication skills.
• To recognize and support scholars who bring a diversity of perspectives, identities, and backgrounds, including those from groups who are underrepresented in the sciences.
• To build community at Stanford around frontier research challenges.
• To provide flexibility and resources for bold, independent thinkers to pursue their own scientific research visions.
Stanford Science Fellowships are intended for exceptional early-career postdoctoral scholars who have recently been awarded their PhD or will be awarded their PhD by the start of the fellowship and who want to pursue research and training in any natural science discipline. International scholars are welcome to apply.
Between 4 to 8 fellows will be selected to start appointments between July 1 and September 1, 2020. Prospective fellows will be considered by a committee of Stanford faculty from departments and schools across the natural sciences at Stanford. An explicit goal of these selection committees, in addition to selecting candidates with tremendous intellectual strength, will be the enhancement of demographic and intellectual diversity in the scientific community at Stanford.
Learn more about the Stanford Science Fellows and the application at stanfordsciencefellows.stanford.edu.
Stanford Science Fellow appointments will be for three-year terms. Fellows will receive an annual stipend of $83,000 per year, benefits, and up to $8,000 per year supplemental funds to support research and professional development.
Interested applicants must apply online (stanfordsciencefellows.stanford.edu) by November 1, 2019.
Inquiries may be directed to stanfordsciencefellows@stanford.edu.
“2019 R for Bioinformatics" Workshop – USC Libraries Bioinformatics
The USC Libraries Bioinformatics Service is pleased to present the 2019 R for Bioinformatics workshop. Knowing how to use R is a valuable skillset as numerous open access and cutting-edge tools for various genomic data analyses are written in R. This full-day workshop is aimed at training participants to achieve basic competency in using R for simple bioinformatics tasks, which will form the foundation for other more specialized and advanced R analysis packages. This is a beginner workshop and no prior R knowledge is required.
Topics Covered
• Introduction to R and learning R for bioinformatics
• Using RStudio – an integrated development environment for R
• The general context and concepts of R programming
• Commonly used functions for wrangling bioinformatics data
• Practical examples of wrangling bioinformatics data
• Visualization – creating plots using R
• Bioinformatics Package Repositories: CRAN and Bioconductor
The workshops will be conducted at both UPC and HSC. You will be required to bring your own laptops.
UPC: 9am to 4.30pm, Wednesday, October 30th, 2019
Learning Center, Wilson Dental Library (DEN21)
HSC: 9am to 4.30pm, Tuesday, November 19th, 2019
Computer Classroom (2nd Level), Norris Medical Library
Limited to 20 participants per workshop. Due to high demand, please register only if you are sure you would be able to attend. Attendance will be checked and no-shows may be subjected to restriction of future bioinformatics services.
Please register at:
https://usc.qualtrics.com/jfe/form/SV_835wUPfkfMXvY1L
Also, we understand that the demand and popularity of R workshops is extremely high and many of you may not be successful in your registration. We have specially packaged last year’s R workshop into a series of online videos where you can learn the same R workshop contents at your own pace. The videos and training materials are available at https://libguides.usc.edu/c.php?g=913498.
Topics Covered
• Introduction to R and learning R for bioinformatics
• Using RStudio – an integrated development environment for R
• The general context and concepts of R programming
• Commonly used functions for wrangling bioinformatics data
• Practical examples of wrangling bioinformatics data
• Visualization – creating plots using R
• Bioinformatics Package Repositories: CRAN and Bioconductor
The workshops will be conducted at both UPC and HSC. You will be required to bring your own laptops.
UPC: 9am to 4.30pm, Wednesday, October 30th, 2019
Learning Center, Wilson Dental Library (DEN21)
HSC: 9am to 4.30pm, Tuesday, November 19th, 2019
Computer Classroom (2nd Level), Norris Medical Library
Limited to 20 participants per workshop. Due to high demand, please register only if you are sure you would be able to attend. Attendance will be checked and no-shows may be subjected to restriction of future bioinformatics services.
Please register at:
https://usc.qualtrics.com/jfe/form/SV_835wUPfkfMXvY1L
Also, we understand that the demand and popularity of R workshops is extremely high and many of you may not be successful in your registration. We have specially packaged last year’s R workshop into a series of online videos where you can learn the same R workshop contents at your own pace. The videos and training materials are available at https://libguides.usc.edu/c.php?g=913498.
Overcoming Research Anxiety: A Mindful Approach to Literature Review Searching
Presented by Kevin Klipfel, Instructional Design & Assessment Librarian, and Elizabeth Galoozis, Head of Information Literacy
This workshop will discuss psychological strategies for approaching literature reviews, such as adopting a process-oriented “growth” mindset toward research, as well as several practical search techniques that will help you feel confident both getting started with your research and knowing when your literature review is complete. Though this workshop is intended for graduate students, all are welcome.
In-person: Thursday, November 7, 3:30-4:30, Leavey Library 113J: More information and RSVP
Online: Tuesday, November 19, 3:00, 4:00: More information and RSVP
This workshop will discuss psychological strategies for approaching literature reviews, such as adopting a process-oriented “growth” mindset toward research, as well as several practical search techniques that will help you feel confident both getting started with your research and knowing when your literature review is complete. Though this workshop is intended for graduate students, all are welcome.
In-person: Thursday, November 7, 3:30-4:30, Leavey Library 113J: More information and RSVP
Online: Tuesday, November 19, 3:00, 4:00: More information and RSVP
Using Zotero to Organize Your Research
At this workshop, get an introduction to, and hands-on practice using, the free, open-source software Zotero, which can help you organize and cite sources. Zotero is particularly good at capturing web content and for creating group and public "libraries" of sources. Bring a laptop or tablet that you normally use for research.
Presented by Elizabeth Galoozis, Head of Information Literacy, USC Libraries
In-person:
• Tuesday, October 22, 12:00-1:00, Leavey Library 113H: More information and RSVP
• Thursday, November 21, 12:30-1:30, VKC Library B40E - Multi-Media Room: More information and RSVP
Online:
• Tuesday, October 29, 2:00-3:00: More information and RSVP
• Monday, November 18, 3:30-4:30: More information and RSVP
Presented by Elizabeth Galoozis, Head of Information Literacy, USC Libraries
In-person:
• Tuesday, October 22, 12:00-1:00, Leavey Library 113H: More information and RSVP
• Thursday, November 21, 12:30-1:30, VKC Library B40E - Multi-Media Room: More information and RSVP
Online:
• Tuesday, October 29, 2:00-3:00: More information and RSVP
• Monday, November 18, 3:30-4:30: More information and RSVP
QCB Colloquium | Dr. Jill Gallaher
Dr. Jill Gallaher
Research Scientist, Moffit Cancer Center
Google Scholar Profile
Systemic dynamics of multiple metastases during adaptive therapy
Tuesday, October 15
2 PM
RRI 101
Abstract: Although metastatic disease is thought to be responsible for about 90% of cancer deaths, there has been relatively little improvement in the understanding and treatment of cancer at this advanced stage. Increasingly, data point toward intra- and inter-tumor heterogeneity as a major driver of treatment failure in metastatic cancer. We have recently shown that disseminated disease may be better managed using evolutionary-designed maintenance therapies as opposed to maximum tolerated dose, treat-to-kill strategies. Adaptive therapy is one such evolutionary treatment strategy that exploits sensitive and resistant cell competition; a lower dose is given to a shrinking tumor and a higher dose to a growing tumor. From clinical and pre-clinical data, we are learning how the total tumor burden (for example, PSA in prostate cancer) can be used to control disease using this strategy, but details on how multiple distinct heterogeneous metastatic lesions contribute to systemic measures of burden are not fully understood or well documented. We use an off-lattice agent-based computational model to simulate different treatment schedules of an anti-proliferative drug applied systemically to multiple individual micro-metastases. We assume that there is a tradeoff between fast proliferation and drug resistance, and use the total tumor burden from all metastases to make treatment decisions for adaptive therapy. We simulate how intra- and inter- tumor heterogeneity and seeding dynamics affect the best treatment strategy between a maximum continuous dose or an adaptive therapy schedule. When adaptive therapy is optimal, we investigate how tumor composition and number of metastases change the treatment cycling times and indicate future treatment failure. We examine how using different biomarkers that only measure a subset of the tumor phenotypes versus the total tumor burden affect the dose schedule and overall disease control. With these trends in mind, we aim to identify which which patients are best suited for an adaptive therapy strategy, and for those that qualify, identify metrics to assess ongoing treatment response.
Research Scientist, Moffit Cancer Center
Google Scholar Profile
Systemic dynamics of multiple metastases during adaptive therapy
Tuesday, October 15
2 PM
RRI 101
Abstract: Although metastatic disease is thought to be responsible for about 90% of cancer deaths, there has been relatively little improvement in the understanding and treatment of cancer at this advanced stage. Increasingly, data point toward intra- and inter-tumor heterogeneity as a major driver of treatment failure in metastatic cancer. We have recently shown that disseminated disease may be better managed using evolutionary-designed maintenance therapies as opposed to maximum tolerated dose, treat-to-kill strategies. Adaptive therapy is one such evolutionary treatment strategy that exploits sensitive and resistant cell competition; a lower dose is given to a shrinking tumor and a higher dose to a growing tumor. From clinical and pre-clinical data, we are learning how the total tumor burden (for example, PSA in prostate cancer) can be used to control disease using this strategy, but details on how multiple distinct heterogeneous metastatic lesions contribute to systemic measures of burden are not fully understood or well documented. We use an off-lattice agent-based computational model to simulate different treatment schedules of an anti-proliferative drug applied systemically to multiple individual micro-metastases. We assume that there is a tradeoff between fast proliferation and drug resistance, and use the total tumor burden from all metastases to make treatment decisions for adaptive therapy. We simulate how intra- and inter- tumor heterogeneity and seeding dynamics affect the best treatment strategy between a maximum continuous dose or an adaptive therapy schedule. When adaptive therapy is optimal, we investigate how tumor composition and number of metastases change the treatment cycling times and indicate future treatment failure. We examine how using different biomarkers that only measure a subset of the tumor phenotypes versus the total tumor burden affect the dose schedule and overall disease control. With these trends in mind, we aim to identify which which patients are best suited for an adaptive therapy strategy, and for those that qualify, identify metrics to assess ongoing treatment response.
Monday, October 7, 2019
MCB Seminar | Dr. Bérénice Benayoun
Dr. Bérénice Benayoun
Assistant Professor, USC, Leonard Davis School of Gerontology
Lab Website
Genomic regulation of Vertebrate aging
Friday, October, 11
12 PM
RRI 101
Abstract: The overarching goal of the Benayoun laboratory is to understand how aging influences the epigenome, and in return, how modulation of the epigenome can influence the aging process. We want to understand how this interaction is modulated in response to environmental stimuli and in the context of specific endogenous factors, specifically sex, invertebrate organisms. Aging is accompanied by striking changes in chromatin and gene expression across cell types and species. Yet, how chromatin landscapes change with age and regulate transcription, and how epigenomic changes in turn influence aging in response to external or internal cues, is largely unknown.
Such knowledge will be critical to counteract the functional decline associated with physiological aging, and its exacerbation in age-related disease. A critical aspect of our research is the use of multiple vertebrate model organisms. The short lifespan of non-vertebrate model systems (e.g. yeasts, worms, and flies) makes their use in experimental aging research very attractive, and they have been widely used to explore genetic and environmental underpinnings of aging. However, as a result of this experimental pragmatism, our understanding of mechanisms that regulate vertebrate aging, including the role of vertebrate-specific genes, organs, and tissues (e.g. bones and blood), and physiological processes (e.g. adaptive immunity), significantly lags behind.
These considerations led us to spearhead the de novo sequencing, assembly, and annotation of the African turquoise killifish genome, the shortest-lived vertebrate that can be bred in captivity. Despite this compressed lifespan, the African turquoise killifish display all key age-related phenotypes, including age-related cognitive decline. Our work has transformed the use of this organism as a vertebrate model, and we now are able to leverage this powerful new model organism in conjunction to established traditional models to rapidly identify novel pathways regulating aging and longevity in vertebrates.
Our main cell model of study are key components of the innate immune system and the inflammatory response: macrophages, which accomplish key tasks such as phagocytosis, antigen presentation, and cytokine production. Consistently, aging is associated with increased macrophage infiltration into tissues. Macrophages have two main origins: tissue-resident macrophages differentiate from specific embryonic progenitors, whereas monocyte-derived macrophages differentiate from bone-marrow progenitors throughout life.
Resident macrophage populations exist across tissues. Because of their key role in inflammation and damage repair, macrophages are a key cell type in age-related inflammatory diseases. Specific ongoing research directions in the Benayoun lab focus on (i) identifying transcriptional and epigenomic changes with age and upon interventions which extend vertebrate longevity, (ii) dissecting transcriptional regulation changes throughout life, as well as underlying molecular mechanisms for these changes, and (iii) understanding the regulation of aspects of aging by sex, an important, yet very much understudied, factor in aging and longevity.
Assistant Professor, USC, Leonard Davis School of Gerontology
Lab Website
Genomic regulation of Vertebrate aging
Friday, October, 11
12 PM
RRI 101
Abstract: The overarching goal of the Benayoun laboratory is to understand how aging influences the epigenome, and in return, how modulation of the epigenome can influence the aging process. We want to understand how this interaction is modulated in response to environmental stimuli and in the context of specific endogenous factors, specifically sex, invertebrate organisms. Aging is accompanied by striking changes in chromatin and gene expression across cell types and species. Yet, how chromatin landscapes change with age and regulate transcription, and how epigenomic changes in turn influence aging in response to external or internal cues, is largely unknown.
Such knowledge will be critical to counteract the functional decline associated with physiological aging, and its exacerbation in age-related disease. A critical aspect of our research is the use of multiple vertebrate model organisms. The short lifespan of non-vertebrate model systems (e.g. yeasts, worms, and flies) makes their use in experimental aging research very attractive, and they have been widely used to explore genetic and environmental underpinnings of aging. However, as a result of this experimental pragmatism, our understanding of mechanisms that regulate vertebrate aging, including the role of vertebrate-specific genes, organs, and tissues (e.g. bones and blood), and physiological processes (e.g. adaptive immunity), significantly lags behind.
These considerations led us to spearhead the de novo sequencing, assembly, and annotation of the African turquoise killifish genome, the shortest-lived vertebrate that can be bred in captivity. Despite this compressed lifespan, the African turquoise killifish display all key age-related phenotypes, including age-related cognitive decline. Our work has transformed the use of this organism as a vertebrate model, and we now are able to leverage this powerful new model organism in conjunction to established traditional models to rapidly identify novel pathways regulating aging and longevity in vertebrates.
Our main cell model of study are key components of the innate immune system and the inflammatory response: macrophages, which accomplish key tasks such as phagocytosis, antigen presentation, and cytokine production. Consistently, aging is associated with increased macrophage infiltration into tissues. Macrophages have two main origins: tissue-resident macrophages differentiate from specific embryonic progenitors, whereas monocyte-derived macrophages differentiate from bone-marrow progenitors throughout life.
Resident macrophage populations exist across tissues. Because of their key role in inflammation and damage repair, macrophages are a key cell type in age-related inflammatory diseases. Specific ongoing research directions in the Benayoun lab focus on (i) identifying transcriptional and epigenomic changes with age and upon interventions which extend vertebrate longevity, (ii) dissecting transcriptional regulation changes throughout life, as well as underlying molecular mechanisms for these changes, and (iii) understanding the regulation of aspects of aging by sex, an important, yet very much understudied, factor in aging and longevity.
MEB Seminar | Dr. Alyson Santoro
Dr. Alyson Santoro
Assistant Professor, UCSB, EEMB
Lab Website
Nitrification as a window on the mesopelagic
Tuesday, October 7
12 PM
AHF 153 (Torrey Webb Room)
Abstract: The mesopelagic ocean--often called the “twilight zone”--is a critical area for the microbial processing of sinking organic matter. Our lab studies some of the most abundant members of the mesopelagic microbial community, the ammonia-oxidizing archaea and nitrite-oxidizing bacteria. Together, these organisms carry out the biogeochemical process of nitrification and are responsible for producing the vast deep ocean nitrate reservoir. They also play an underappreciated role in carbon and trace metal cycling. My talk will describe combining laboratory cultures with field rate measurements to understand the critical role of nitrifiers in the intertwined geochemical cycles of carbon, nitrogen, and trace metals in the dark ocean.
Assistant Professor, UCSB, EEMB
Lab Website
Nitrification as a window on the mesopelagic
Tuesday, October 7
12 PM
AHF 153 (Torrey Webb Room)
Abstract: The mesopelagic ocean--often called the “twilight zone”--is a critical area for the microbial processing of sinking organic matter. Our lab studies some of the most abundant members of the mesopelagic microbial community, the ammonia-oxidizing archaea and nitrite-oxidizing bacteria. Together, these organisms carry out the biogeochemical process of nitrification and are responsible for producing the vast deep ocean nitrate reservoir. They also play an underappreciated role in carbon and trace metal cycling. My talk will describe combining laboratory cultures with field rate measurements to understand the critical role of nitrifiers in the intertwined geochemical cycles of carbon, nitrogen, and trace metals in the dark ocean.
Monday, September 30, 2019
QCB Colloquium | Dr. Kai Tan
Dr. Kai Tan
Associate Professor of Pediatrics, University of Pennsylvania, Perelman School of Medicine
Lab Website
Systematic Analysis of Noncoding Genetic Variants
Thursday, October 3
2 PM
RRI 101
Abstract: The vast majority of genetic variants in the human genome are located in the noncoding region. Functional interpretation of causal noncoding variants has remained a major challenge in human genetics. In this talk, I will present a couple of computational algorithms for predicting causal noncoding variants by integrating large scale omics datasets. I will also present a couple of case studies on identifying and validating germline variants in type 1 diabetes and somatic variants in pediatric cancers. Our work established a much-needed systemic approach to identifying and characterizing noncoding causal variants in human diseases.
Associate Professor of Pediatrics, University of Pennsylvania, Perelman School of Medicine
Lab Website
Systematic Analysis of Noncoding Genetic Variants
Thursday, October 3
2 PM
RRI 101
Abstract: The vast majority of genetic variants in the human genome are located in the noncoding region. Functional interpretation of causal noncoding variants has remained a major challenge in human genetics. In this talk, I will present a couple of computational algorithms for predicting causal noncoding variants by integrating large scale omics datasets. I will also present a couple of case studies on identifying and validating germline variants in type 1 diabetes and somatic variants in pediatric cancers. Our work established a much-needed systemic approach to identifying and characterizing noncoding causal variants in human diseases.
MEB Seminar | Dr. Rebecca Albright
Dr. Rebecca Albright
California Academy of Sciences, Invertebrate Zoology
Research Profile
Coral Reefs in a Changing Climate: Challenges and Reasons for Hope
Tuesday, October 1
12 PM
AHF 153 (Torrey Webb Room)
Abstract: Already under severe pressure from a number of stressors, including overfishing and pollution, coral reefs are also among the most vulnerable ecosystems to climate change and ocean acidification: We have lost an estimated 50% of the world's coral reefs over the last several decades and are projected to lose more than 90% by 2050. While acute disturbances such as temperature-induced coral bleaching are largely responsible for accelerated reef decline in recent years, chronic disturbances like ocean acidification erode a reef’s capacity to recover by slowing growth and reproduction. In this talk, I will give an overview to the challenges that reefs are currently facing, focusing on the impacts of changing seawater chemistry on various aspects of coral reef biology, ecology, and biogeochemistry. We will also explore some of the novel and exciting ideas that are emerging to address the coral reef crisis. We'll highlight strengths and limitations of current approaches and discuss next steps towards saving these valuable ecosystems.
California Academy of Sciences, Invertebrate Zoology
Research Profile
Coral Reefs in a Changing Climate: Challenges and Reasons for Hope
Tuesday, October 1
12 PM
AHF 153 (Torrey Webb Room)
Abstract: Already under severe pressure from a number of stressors, including overfishing and pollution, coral reefs are also among the most vulnerable ecosystems to climate change and ocean acidification: We have lost an estimated 50% of the world's coral reefs over the last several decades and are projected to lose more than 90% by 2050. While acute disturbances such as temperature-induced coral bleaching are largely responsible for accelerated reef decline in recent years, chronic disturbances like ocean acidification erode a reef’s capacity to recover by slowing growth and reproduction. In this talk, I will give an overview to the challenges that reefs are currently facing, focusing on the impacts of changing seawater chemistry on various aspects of coral reef biology, ecology, and biogeochemistry. We will also explore some of the novel and exciting ideas that are emerging to address the coral reef crisis. We'll highlight strengths and limitations of current approaches and discuss next steps towards saving these valuable ecosystems.
Monday, September 23, 2019
MEB Seminar | Dr. Eric Boyd
Dr. Eric Boyd
Associate Professor, Montana State Univ., Microbiology and Immunology
Lab Website
Tuesday, September 24
12 PM
AHF 153 (Torrey Webb Room)
Abstract: Feedbacks between biological and geological processes drove the co-evolution of life and the environment. Yet, little is known of the nature of these feedbacks and the time scales over which they occurred. Here we describe a series of geobiological feedbacks that have played out over the past ~1.1 to 0.8 Ga and that shaped the co-evolution of thermoacidophiles and their acidic hot spring habitats. Future experimentation will evaluate kinetic controls on the acid-generating reactions and the physiological adaptations that allowed microbes to exploit these reactions to fuel their metabolisms.
Associate Professor, Montana State Univ., Microbiology and Immunology
Lab Website
Tuesday, September 24
12 PM
AHF 153 (Torrey Webb Room)
Abstract: Feedbacks between biological and geological processes drove the co-evolution of life and the environment. Yet, little is known of the nature of these feedbacks and the time scales over which they occurred. Here we describe a series of geobiological feedbacks that have played out over the past ~1.1 to 0.8 Ga and that shaped the co-evolution of thermoacidophiles and their acidic hot spring habitats. Future experimentation will evaluate kinetic controls on the acid-generating reactions and the physiological adaptations that allowed microbes to exploit these reactions to fuel their metabolisms.
Register now for the BCLA Fall Networking mixer and 2019 BCLA Biotech Summit!
Fall Networking mixer and Fireside chat
At the first networking mixer of the academic year, we have the pleasure of welcoming Anna Skaya, CEO of BasePaws for an exciting fireside chat. Having successfully navigated through the jaws of the hit TV show Shark Tank, Anna has an exciting and interesting story of raising money for successful scaling of her start-up. After the fireside chat, attendees have the opportunity to mingle and network over drinks and appetizers at the wonderful Studio 55, ADP’s innovation center.
Where: Studio 55, ADP innovation center, 55 S Lake Ave Drive, Pasadena, CA 91101
When: September 24th, 5.30-8.30pm
RSVP: https://www.eventbrite.com/e/bcla-fall-networking-mixer-fireside-chat-tickets-70976270937
The 2019 BCLA Biotech Summit
The largest BCLA event of the year is coming up! Following the theme of this summit, ‘Mapping out LA’s biotech landscape’, we will delve into the intricate network of how Los Angeles is working towards becoming the next biotech hub. Following the huge success of the 2018 summit, which attracted over 250 people, we are making the 2019 summit even bigger and better! Thank you to our platinum sponsors UCLA CTSI, IndieBio, LA Biolabs! Only a few more spots are left for exhibiting sponsors, so contact us now at team@bc-la.org for more information on how to participate! Finally, RSVP using the link below!
Where: CNSI at UCLA, 570 Westwood Plaza Building 114, Los Angeles, CA 90095
When: Saturday October 26th, 9 - 5pm
RSVP: https://www.eventbrite.com/e/5th-annual-bcla-biotech-summit-tickets-70977424387
The future of drug development Panel Discussion at Amgen
BCLA has partnered with the biggest biotech company in LA (and the world!) to bring you a fascinating panel discussion on the future of the drug development process. With some of the main drivers in R&D and innovation at Amgen, this event is poised to be one of the best panels of the year. We have also partnered with various university organizations to secure free transportation to and from Amgen campus for students and postdocs at UCLA, USC and Caltech! Space is limited, so make sure you RSVP now! This will be a sell-out event!
Where: Amgen Conference Center B24, Thousand Oaks, 91320
When: November 6th, 5.15-8.30pm
RSVP: https://www.eventbrite.com/e/the-future-of-drug-development-panel-mixer-tickets-72042030653
AILA & MIT Hackathon
Our close partner AILA will be holding a hackathon for Oncology and Mental Health between October 18-20th! This event will connect the best minds across the healthcare ecosystem to catalyze affordable medical technology, business models and process innovations to transform cancer prevention, diagnosis, and care. Space is limited, so if you want to sign up to be considered to be a participant, click the link below to RSVP!
When: October 18th - 20th
RSVP: https://docs.google.com/forms/d/e/1FAIpQLScPLOVPAN89ss34Wkq8ANtVbxk2zXcHAGbT93d-K3y00kWDZw/viewform
At the first networking mixer of the academic year, we have the pleasure of welcoming Anna Skaya, CEO of BasePaws for an exciting fireside chat. Having successfully navigated through the jaws of the hit TV show Shark Tank, Anna has an exciting and interesting story of raising money for successful scaling of her start-up. After the fireside chat, attendees have the opportunity to mingle and network over drinks and appetizers at the wonderful Studio 55, ADP’s innovation center.
Where: Studio 55, ADP innovation center, 55 S Lake Ave Drive, Pasadena, CA 91101
When: September 24th, 5.30-8.30pm
RSVP: https://www.eventbrite.com/e/bcla-fall-networking-mixer-fireside-chat-tickets-70976270937
The 2019 BCLA Biotech Summit
The largest BCLA event of the year is coming up! Following the theme of this summit, ‘Mapping out LA’s biotech landscape’, we will delve into the intricate network of how Los Angeles is working towards becoming the next biotech hub. Following the huge success of the 2018 summit, which attracted over 250 people, we are making the 2019 summit even bigger and better! Thank you to our platinum sponsors UCLA CTSI, IndieBio, LA Biolabs! Only a few more spots are left for exhibiting sponsors, so contact us now at team@bc-la.org for more information on how to participate! Finally, RSVP using the link below!
Where: CNSI at UCLA, 570 Westwood Plaza Building 114, Los Angeles, CA 90095
When: Saturday October 26th, 9 - 5pm
RSVP: https://www.eventbrite.com/e/5th-annual-bcla-biotech-summit-tickets-70977424387
The future of drug development Panel Discussion at Amgen
BCLA has partnered with the biggest biotech company in LA (and the world!) to bring you a fascinating panel discussion on the future of the drug development process. With some of the main drivers in R&D and innovation at Amgen, this event is poised to be one of the best panels of the year. We have also partnered with various university organizations to secure free transportation to and from Amgen campus for students and postdocs at UCLA, USC and Caltech! Space is limited, so make sure you RSVP now! This will be a sell-out event!
Where: Amgen Conference Center B24, Thousand Oaks, 91320
When: November 6th, 5.15-8.30pm
RSVP: https://www.eventbrite.com/e/the-future-of-drug-development-panel-mixer-tickets-72042030653
AILA & MIT Hackathon
Our close partner AILA will be holding a hackathon for Oncology and Mental Health between October 18-20th! This event will connect the best minds across the healthcare ecosystem to catalyze affordable medical technology, business models and process innovations to transform cancer prevention, diagnosis, and care. Space is limited, so if you want to sign up to be considered to be a participant, click the link below to RSVP!
When: October 18th - 20th
RSVP: https://docs.google.com/forms/d/e/1FAIpQLScPLOVPAN89ss34Wkq8ANtVbxk2zXcHAGbT93d-K3y00kWDZw/viewform
QCB Colloquium | Dr. Aaron Smargon
Dr. Aaron Smargon
Postdoctoral Scholar, University of California, San Diego, School of Medicine, Department of Cellular and Molecular Medicine
Research Profile
RNA-targeting CRISPR systems: from metagenomic discovery to transcriptomic engineering
Thursday, September 26
2 PM
RRI 101
Abstract: The deployment of RNA-guided DNA endonuclease CRISPR-Cas technology has led to radical advances in biology. As the functional diversity of CRISPR-Cas and other prokaryotic defense systems is further explored, RNA manipulation has emerged as a powerful new mode of CRISPR-based engineering. In this seminar I chart the most recent progress in the RNA-targeting CRISPR-Cas (RCas) field and illustrate how a continuing evolution in scientific discovery translates into applications for RNA biology and insights into the mysteries, obstacles, and alternative technologies that lie ahead.
Postdoctoral Scholar, University of California, San Diego, School of Medicine, Department of Cellular and Molecular Medicine
Research Profile
RNA-targeting CRISPR systems: from metagenomic discovery to transcriptomic engineering
Thursday, September 26
2 PM
RRI 101
Abstract: The deployment of RNA-guided DNA endonuclease CRISPR-Cas technology has led to radical advances in biology. As the functional diversity of CRISPR-Cas and other prokaryotic defense systems is further explored, RNA manipulation has emerged as a powerful new mode of CRISPR-based engineering. In this seminar I chart the most recent progress in the RNA-targeting CRISPR-Cas (RCas) field and illustrate how a continuing evolution in scientific discovery translates into applications for RNA biology and insights into the mysteries, obstacles, and alternative technologies that lie ahead.
This Week On Campus | Sept. 23-29, 2019
Below is a curated list of events on campus that may be of interest to BISC students.
Tuesday, September 24, 2019
Work it Series | Pitch it: Share your story in 60 seconds
The Princeton Review - Introduction to GRE Exams
Thursday, September 26, 2019
Fall Career Fair
Tuesday, September 24, 2019
DSS - Jaiswal Flyer Final.pdf by uscbiscgrad on Scribd
Work it Series | Pitch it: Share your story in 60 seconds
The Princeton Review - Introduction to GRE Exams
Thursday, September 26, 2019
Fall Career Fair
2019 09 26 ShelleyBillik by uscbiscgrad on Scribd
Sunday, September 8, 2019
TENURE-TRACK FACULTY POSITION | BIOTECHNOLOGY
California State Polytechnic University, Pomona
Biological Sciences Department
College of Science
The Biological Sciences Department at California State Polytechnic University, Pomona (Cal Poly Pomona) invites applications for a tenure-track, ASSISTANT PROFESSOR position in Biotechnology, beginning in the 2020-2021 academic year. A Ph.D. in Biology, Bioengineering, Biotechnology, Genetics, Molecular Biology or related science discipline or a related science discipline is required. In addition, Post-doctoral experience, demonstrated potential to establish an independent and active research program with students and a demonstrated potential to contribute to the diversity and excellence of the academic community are required. Previous teaching experience, experience or familiarity with teaching techniques that promote equitable student learning and evidence of conducting scholarly research activities involving students are preferred. The successful candidate will have the potential for excellence in undergraduate teaching, and for developing an externally-funded research program that will involve undergraduate and Master's students. Teaching responsibilities will include courses with a focus in innovations in Biotechnology. Other teaching responsibilities may include introductory biology, genetics, cell & molecular biology, microbiology, molecular biology techniques or specialty courses in the candidate’s area of expertise. The successful candidate is expected to develop an extramurally funded research program involving undergraduate and Master’s level students. The candidate's area of specialty is open to agriculture, bioengineering, biofuels and renewable energy, biomedical applications, genetic engineering, or any other research area within the broad umbrella of biotechnology. The applicant will be expected to assist in curriculum development, advise students, serve on department, college, and university committees, and engage in professional activities. Cal Poly Pomona is a comprehensive Master’s university with a diverse student body. The successful candidate will have demonstrated an ability to be responsive to the educational equity goals of the University and its increasing ethnic diversity and international character. Applicants should submit (1) cover letter that describes how the candidate’s teaching and research experience have prepared the applicant to meet the duties and qualifications articulated in the position description; (2) curriculum vitae; (3) 1-page statement of teaching philosophy; (4) 1-page student success statement about the candidate’s teaching or other experiences, successes, and challenges in working with a diverse student population; (5) 2-page max proposed plan of research; (6) three representative publication reprints; (7) the names and contact information of five references; and (8) completed University application form. Review of applications begins on November 15, 2019. Full position description and application procedure: http://www.cpp.edu/~faculty-affairs/open-positions/.
Inquiries can be made to Chair, Biotechnology Search Committee, Biological Sciences Department, California State Polytechnic University, 3801 West Temple Avenue, Pomona, CA 91768 or to biotech_search@cpp.edu. Official transcripts and three letters of reference will be required of all semifinalists. For further information, visit the Department web site at: http://www.cpp.edu/~biology.
California State Polytechnic University, Pomona is an Equal Opportunity, Affirmative Action Employer.
Biological Sciences Department
College of Science
The Biological Sciences Department at California State Polytechnic University, Pomona (Cal Poly Pomona) invites applications for a tenure-track, ASSISTANT PROFESSOR position in Biotechnology, beginning in the 2020-2021 academic year. A Ph.D. in Biology, Bioengineering, Biotechnology, Genetics, Molecular Biology or related science discipline or a related science discipline is required. In addition, Post-doctoral experience, demonstrated potential to establish an independent and active research program with students and a demonstrated potential to contribute to the diversity and excellence of the academic community are required. Previous teaching experience, experience or familiarity with teaching techniques that promote equitable student learning and evidence of conducting scholarly research activities involving students are preferred. The successful candidate will have the potential for excellence in undergraduate teaching, and for developing an externally-funded research program that will involve undergraduate and Master's students. Teaching responsibilities will include courses with a focus in innovations in Biotechnology. Other teaching responsibilities may include introductory biology, genetics, cell & molecular biology, microbiology, molecular biology techniques or specialty courses in the candidate’s area of expertise. The successful candidate is expected to develop an extramurally funded research program involving undergraduate and Master’s level students. The candidate's area of specialty is open to agriculture, bioengineering, biofuels and renewable energy, biomedical applications, genetic engineering, or any other research area within the broad umbrella of biotechnology. The applicant will be expected to assist in curriculum development, advise students, serve on department, college, and university committees, and engage in professional activities. Cal Poly Pomona is a comprehensive Master’s university with a diverse student body. The successful candidate will have demonstrated an ability to be responsive to the educational equity goals of the University and its increasing ethnic diversity and international character. Applicants should submit (1) cover letter that describes how the candidate’s teaching and research experience have prepared the applicant to meet the duties and qualifications articulated in the position description; (2) curriculum vitae; (3) 1-page statement of teaching philosophy; (4) 1-page student success statement about the candidate’s teaching or other experiences, successes, and challenges in working with a diverse student population; (5) 2-page max proposed plan of research; (6) three representative publication reprints; (7) the names and contact information of five references; and (8) completed University application form. Review of applications begins on November 15, 2019. Full position description and application procedure: http://www.cpp.edu/~faculty-affairs/open-positions/.
Inquiries can be made to Chair, Biotechnology Search Committee, Biological Sciences Department, California State Polytechnic University, 3801 West Temple Avenue, Pomona, CA 91768 or to biotech_search@cpp.edu. Official transcripts and three letters of reference will be required of all semifinalists. For further information, visit the Department web site at: http://www.cpp.edu/~biology.
California State Polytechnic University, Pomona is an Equal Opportunity, Affirmative Action Employer.
QCB Colloquium | Dr. Aafke van den Berg
Dr. Aafke van den Berg
Post-Doctoral Fellow, Massachusetts Institute of Technology (MIT), Institute for Medical Engineering and Science
Lab Website (Dr. Leonid Mirny)
Transcription shapes 3D organization of mammalian chromatin
Thursday, September 12, 2019
2 PM
RRI 101
Abstract: Recent theoretical and experimental studies indicate that the process of loop extrusion is one of the main mechanisms underlying chromosome organization during interphase. According to the model for loop extrusion, a cohesin complex is loaded onto chromatin and extrudes loops until it dissociates or encounters an obstacle such as CTCF. We aim to understand what genomic elements other than CTCF sites, and what processes on DNA can act as extrusion barriers, thus shaping chromosome organization.
We analyzed data from new experiments that remove CTCF and extend cohesin residence time and found profound changes of chromosome folding near active genes. To explain these changes we propose the moving barrier model where cohesin cannot bypass an elongating PolII. As a result cohesin traces PolII at its low speed in the direction of transcription, while a cohesin approaching PolII in the opposite direction is shoveled back to the end of the gene.
The moving barrier model recapitulates both ChIP-seq patterns of cohesin accumulation and patterns in Hi-C around active genes. Interestingly, the model also provides a long-sought mechanism for dynamic enhancer-PolII tracking during transcription elongation. I will discuss how future in vitro and time course experiments can further test the moving barrier model.
Post-Doctoral Fellow, Massachusetts Institute of Technology (MIT), Institute for Medical Engineering and Science
Lab Website (Dr. Leonid Mirny)
Transcription shapes 3D organization of mammalian chromatin
Thursday, September 12, 2019
2 PM
RRI 101
Abstract: Recent theoretical and experimental studies indicate that the process of loop extrusion is one of the main mechanisms underlying chromosome organization during interphase. According to the model for loop extrusion, a cohesin complex is loaded onto chromatin and extrudes loops until it dissociates or encounters an obstacle such as CTCF. We aim to understand what genomic elements other than CTCF sites, and what processes on DNA can act as extrusion barriers, thus shaping chromosome organization.
We analyzed data from new experiments that remove CTCF and extend cohesin residence time and found profound changes of chromosome folding near active genes. To explain these changes we propose the moving barrier model where cohesin cannot bypass an elongating PolII. As a result cohesin traces PolII at its low speed in the direction of transcription, while a cohesin approaching PolII in the opposite direction is shoveled back to the end of the gene.
The moving barrier model recapitulates both ChIP-seq patterns of cohesin accumulation and patterns in Hi-C around active genes. Interestingly, the model also provides a long-sought mechanism for dynamic enhancer-PolII tracking during transcription elongation. I will discuss how future in vitro and time course experiments can further test the moving barrier model.
Graduate Research Opportunities at DOE National Laboratories
The Department of Energy’s (DOE) Office of Science is pleased to announce that the Office of Science Graduate Student Research (SCGSR) program is now accepting applications for the 2019 Solicitation 2. Applications are due 5:00pm Eastern Time on Thursday, November 14, 2019.
Detailed information about the program, including eligibility requirements and access to the online application system, can be found at: https://science.osti.gov/wdts/scgsr/.
The SCGSR program supports supplemental awards to outstanding U.S. graduate students to conduct part of their graduate thesis research at a DOE national laboratory/facility in collaboration with a DOE laboratory scientist for a period of 3 to 12 consecutive months—with the goal of preparing graduate students for scientific and technical careers critically important to the DOE Office of Science mission.
The SCGSR program is open to current Ph.D. students in qualified graduate programs at accredited U.S. academic institutions, who are conducting their graduate thesis research in targeted areas of importance to the DOE Office of Science. The research opportunity is expected to advance the graduate students’ overall doctoral thesis/dissertation while providing access to the expertise, resources, and capabilities available at the host DOE laboratories/facilities. The supplemental award provides for additional, incremental costs for living and travel expenses directly associated with conducting the SCGSR research project at the DOE host laboratory/facility during the award period.
The Office of Science expects to make approximately 70 awards in 2019 Solicitation 2 cycle, for project periods beginning anytime between June 15, 2020 and October 5, 2020.
Since its inception in 2014, the SCGSR program has provided support to over 480 graduate awardees from 135 different U.S. universities to conduct thesis research at 18 DOE national laboratories/facilities across the nation.
The SCGSR program is sponsored and managed by the DOE Office of Science’s Office of Workforce Development for Teachers and Scientists (WDTS), in collaboration with the six Office of Science research programs offices and the DOE national laboratories/facilities, and program administration support is provided by the Oak Ridge Institute of Science and Education (ORISE).
For any questions, please contact the SCGSR Program Manager, Dr. Ping Ge, at sc.scgsr@science.doe.gov.
U.S. Department of Energy, Office of Science
Detailed information about the program, including eligibility requirements and access to the online application system, can be found at: https://science.osti.gov/wdts/scgsr/.
The SCGSR program supports supplemental awards to outstanding U.S. graduate students to conduct part of their graduate thesis research at a DOE national laboratory/facility in collaboration with a DOE laboratory scientist for a period of 3 to 12 consecutive months—with the goal of preparing graduate students for scientific and technical careers critically important to the DOE Office of Science mission.
The SCGSR program is open to current Ph.D. students in qualified graduate programs at accredited U.S. academic institutions, who are conducting their graduate thesis research in targeted areas of importance to the DOE Office of Science. The research opportunity is expected to advance the graduate students’ overall doctoral thesis/dissertation while providing access to the expertise, resources, and capabilities available at the host DOE laboratories/facilities. The supplemental award provides for additional, incremental costs for living and travel expenses directly associated with conducting the SCGSR research project at the DOE host laboratory/facility during the award period.
The Office of Science expects to make approximately 70 awards in 2019 Solicitation 2 cycle, for project periods beginning anytime between June 15, 2020 and October 5, 2020.
Since its inception in 2014, the SCGSR program has provided support to over 480 graduate awardees from 135 different U.S. universities to conduct thesis research at 18 DOE national laboratories/facilities across the nation.
The SCGSR program is sponsored and managed by the DOE Office of Science’s Office of Workforce Development for Teachers and Scientists (WDTS), in collaboration with the six Office of Science research programs offices and the DOE national laboratories/facilities, and program administration support is provided by the Oak Ridge Institute of Science and Education (ORISE).
For any questions, please contact the SCGSR Program Manager, Dr. Ping Ge, at sc.scgsr@science.doe.gov.
U.S. Department of Energy, Office of Science
MEB Seminar | Dr. Randie Bundy
Dr. Randie Bundy
Assistant Professor, University of Washington, Chemical Oceanography
Lab Website
The impact of organic compounds on the cycling of trace metals in the ocean
Tuesday, September 10, 2019
12 PM
AHF 153 (Torrey Webb Room)
Abstract: Trace metals such as iron are essential nutrients for phytoplankton and bacteria, impacting primary productivity in many regions of the ocean. Our understanding of the iron cycle has improved dramatically since the dawn of the international GEOTRACES program, with the chemical speciation of iron emerging as a key control on the oceanic inventory of iron. The speciation of dissolved iron in seawater is dominated by complexation to a diverse pool of organic compounds which impact the bioavailability and reactivity of this scarce nutrient, yet the identity of these compounds are largely unknown. In this talk I will discuss how we determine the identity of these compounds in seawater with novel analytical tools, and why these organic ligands are important for trace metal cycling.
Assistant Professor, University of Washington, Chemical Oceanography
Lab Website
The impact of organic compounds on the cycling of trace metals in the ocean
Tuesday, September 10, 2019
12 PM
AHF 153 (Torrey Webb Room)
Abstract: Trace metals such as iron are essential nutrients for phytoplankton and bacteria, impacting primary productivity in many regions of the ocean. Our understanding of the iron cycle has improved dramatically since the dawn of the international GEOTRACES program, with the chemical speciation of iron emerging as a key control on the oceanic inventory of iron. The speciation of dissolved iron in seawater is dominated by complexation to a diverse pool of organic compounds which impact the bioavailability and reactivity of this scarce nutrient, yet the identity of these compounds are largely unknown. In this talk I will discuss how we determine the identity of these compounds in seawater with novel analytical tools, and why these organic ligands are important for trace metal cycling.
Tuesday, September 3, 2019
Tutoring Opportunity!
Looking for a grad student that is interested in tutoring an SMC student in molecular biology and general chemistry for an SMC student living in West LA. Please contact Dr. Michal Sela-Amit at msamit@att.net
Michal Sela-Amit, PhD
Clinical Associate Professor
USC Suzanne Dworak-Peck School of Social Work
University of Southern California
Social Work Center 230
Phone: 213 821-4402
Michal Sela-Amit, PhD
Clinical Associate Professor
USC Suzanne Dworak-Peck School of Social Work
University of Southern California
Social Work Center 230
Phone: 213 821-4402
Topping Board seeking student reps
We are looking for 5 new student representatives to join the Norman Topping Student Aid Fund's administrative body this year; both undergraduates and graduate students are welcome.
This is a great opportunity for professional development for non-profit, planning, public administration, education, and policy students! Please share! We want more students involved. Both grads and undergrads are encouraged to apply.
As you may be aware, the Topping Fund is administered by a Governing Board composed of a majority of current students who recruit and select fund recipients, and oversee the long-term policies of the Topping Scholarship. Benefits of being a student representative include service to the university and local community, organizational leadership experience, and networking with student leaders, faculty, and staff. Appointed by the Vice Provost for Undergraduate Programs, student representatives serve a two-year term and participate in 6-8 meetings per semester. Students interested in serving on the Governing Board in 2019-20 should apply by September 5th.
The following link leads to the application form, and can absolutely be distributed to interested students.
Link to Application: https://drive.google.com/file/d/1SqbwNvFfrSsrAVnC_02XIYAZVgARBsZH/view?usp=sharing
Thank you very much for your time.
Sincerely,
Trista Beard, Ed.D.
This is a great opportunity for professional development for non-profit, planning, public administration, education, and policy students! Please share! We want more students involved. Both grads and undergrads are encouraged to apply.
As you may be aware, the Topping Fund is administered by a Governing Board composed of a majority of current students who recruit and select fund recipients, and oversee the long-term policies of the Topping Scholarship. Benefits of being a student representative include service to the university and local community, organizational leadership experience, and networking with student leaders, faculty, and staff. Appointed by the Vice Provost for Undergraduate Programs, student representatives serve a two-year term and participate in 6-8 meetings per semester. Students interested in serving on the Governing Board in 2019-20 should apply by September 5th.
The following link leads to the application form, and can absolutely be distributed to interested students.
Link to Application: https://drive.google.com/file/d/1SqbwNvFfrSsrAVnC_02XIYAZVgARBsZH/view?usp=sharing
Thank you very much for your time.
Sincerely,
Trista Beard, Ed.D.
Gilliam 2020 Competition
I am pleased to invite you to nominate colleagues from your university for the Howard Hughes Medical Institute’s 2020 Gilliam Fellowships for Advanced Study. These three-year fellowships will be awarded to adviser-student pairs, with each pair comprising an eligible graduate student engaged in her/his PhD dissertation research and the thesis adviser. In 2020 we anticipate making 40-45 awards. The program announcement that provides details about the program, including eligibility criteria, can be downloaded from http://www.hhmi.org/gilliam.
You may nominate a total of 2 adviser-student pairs from University of Southern California.
Prospective fellows must be U.S. citizens, permanent residents, or other immigrants to the U.S., from racial, ethnic, or other groups recognized in the U.S. as underrepresented in the sciences or Alumni of the HHMI EXROP, be at the appropriate program stage of their PhD training and in an eligible discipline.
We expect the nominator to work with others to identify nominees and gather information to respond to the prompts listed below. Please forward the program information to all appropriate departments and programs.
The nomination initiates the application process and all the materials and information provided will shape the judgments of the reviewers. The nomination will include responses to three questions about how the adviser-student pair fits the eligibility criteria and requirements specific to this fellowship. The questions must be completed by a knowledgeable senior institutional representative who can speak and commit on the institution’s behalf.
1. How and why was the specific adviser-student pair internally selected?
2. What is the evidence that the adviser’s department is committed to advancing diversity and inclusion in science?
3. What is the evidence that the graduate program and/or department values career and professional development in the sciences?
4. How has/will HHMI's Gilliam Fellowship for Advanced Study help to improve the quality of the graduate program and create an inclusive environment?
In addition, the nominator will be asked to complete a table on doctoral enrollment/degree attainment and support the data with a statement about the institution’s context-specific commitment to advancing diversity and inclusion in the sciences. The nominator must also provide a letter of support that describes that adviser’s interest, demonstrated ability, and commitment to develop the talents of students, especially those from underrepresented groups.
The competition system will open for nominee submissions in early September. The nominator identified in this letter will be provided with login information and instructions via email on how to access the system at that time. The deadline for submission of your nominations is 2:00 p.m. ET, October 18, 2019.
This year, the Pathway system requires that the nominated thesis adviser confirm his/her participation before the nomination form can be submitted. After the nominator inputs the adviser name, the system will generate an email prompting the adviser to confirm participation.
After HHMI has received and reviewed the information for each adviser-student pair, we will contact eligible nominees directly with instructions for submitting an online application. It is the responsibility of the nominated pair to submit a complete application to HHMI by the January 3, 2020, deadline. Institutions and applicants will be notified of the outcome of the competition via email in June 2020.
Questions may be directed to gilliam@hhmi.org. For technical questions related to the electronic nominee submission, a toll-free number and online help service will be available when the designated individual logs into the electronic nomination system.
You may nominate a total of 2 adviser-student pairs from University of Southern California.
Prospective fellows must be U.S. citizens, permanent residents, or other immigrants to the U.S., from racial, ethnic, or other groups recognized in the U.S. as underrepresented in the sciences or Alumni of the HHMI EXROP, be at the appropriate program stage of their PhD training and in an eligible discipline.
We expect the nominator to work with others to identify nominees and gather information to respond to the prompts listed below. Please forward the program information to all appropriate departments and programs.
The nomination initiates the application process and all the materials and information provided will shape the judgments of the reviewers. The nomination will include responses to three questions about how the adviser-student pair fits the eligibility criteria and requirements specific to this fellowship. The questions must be completed by a knowledgeable senior institutional representative who can speak and commit on the institution’s behalf.
1. How and why was the specific adviser-student pair internally selected?
2. What is the evidence that the adviser’s department is committed to advancing diversity and inclusion in science?
3. What is the evidence that the graduate program and/or department values career and professional development in the sciences?
4. How has/will HHMI's Gilliam Fellowship for Advanced Study help to improve the quality of the graduate program and create an inclusive environment?
In addition, the nominator will be asked to complete a table on doctoral enrollment/degree attainment and support the data with a statement about the institution’s context-specific commitment to advancing diversity and inclusion in the sciences. The nominator must also provide a letter of support that describes that adviser’s interest, demonstrated ability, and commitment to develop the talents of students, especially those from underrepresented groups.
The competition system will open for nominee submissions in early September. The nominator identified in this letter will be provided with login information and instructions via email on how to access the system at that time. The deadline for submission of your nominations is 2:00 p.m. ET, October 18, 2019.
This year, the Pathway system requires that the nominated thesis adviser confirm his/her participation before the nomination form can be submitted. After the nominator inputs the adviser name, the system will generate an email prompting the adviser to confirm participation.
After HHMI has received and reviewed the information for each adviser-student pair, we will contact eligible nominees directly with instructions for submitting an online application. It is the responsibility of the nominated pair to submit a complete application to HHMI by the January 3, 2020, deadline. Institutions and applicants will be notified of the outcome of the competition via email in June 2020.
Questions may be directed to gilliam@hhmi.org. For technical questions related to the electronic nominee submission, a toll-free number and online help service will be available when the designated individual logs into the electronic nomination system.
Thank you.
David J. Asai
Senior Director, Science Education
Howard Hughes Medical Institute
MEB Seminar | Dr. Matthew Church
Dr. Matthew Church
Associate Professor, University of Montana, Flathead Lake Biological Station
Lab Website | Abstract
Eddy-driven variability in nitrification in the subtropical North Pacific Ocean
Tuesday, September 3
12 PM
AHF 153 (Torrey Webb Room)
Abstract: Nitrification is a key step in the marine nitrogen cycle, controlling oxidation of reduced nitrogen in the ocean. Mesoscale eddies, which vertically perturb isopycnal surfaces within the main pycnocline, are thought to play important roles in upper ocean biogeochemical processes; however, potential impacts of eddies on microbial nitrogen cycling in the dimly-lit mesopelagic waters remains largely unknown. In this talk I will summarize on-going work examining how eddies influence the export of particulate nitrogen (PN), rates of nitrification, and the abundances and spatial distributions of nitrifying Archaea (using the ammonia-monooxygenase gene [amoA] as a biomarker) in the oligotrophic waters of the North Pacific Ocean. Eddies influence upper ocean nutrient pools and fluxes, shape the distributions of nitrifying microorganisms and rates of nitrification in the mesopelagic waters. These results suggest that eddy-mediated changes to the upper ocean can have important roles in modifying nitrogen transformation in the interior waters of the ocean.
Associate Professor, University of Montana, Flathead Lake Biological Station
Lab Website | Abstract
Eddy-driven variability in nitrification in the subtropical North Pacific Ocean
Tuesday, September 3
12 PM
AHF 153 (Torrey Webb Room)
Abstract: Nitrification is a key step in the marine nitrogen cycle, controlling oxidation of reduced nitrogen in the ocean. Mesoscale eddies, which vertically perturb isopycnal surfaces within the main pycnocline, are thought to play important roles in upper ocean biogeochemical processes; however, potential impacts of eddies on microbial nitrogen cycling in the dimly-lit mesopelagic waters remains largely unknown. In this talk I will summarize on-going work examining how eddies influence the export of particulate nitrogen (PN), rates of nitrification, and the abundances and spatial distributions of nitrifying Archaea (using the ammonia-monooxygenase gene [amoA] as a biomarker) in the oligotrophic waters of the North Pacific Ocean. Eddies influence upper ocean nutrient pools and fluxes, shape the distributions of nitrifying microorganisms and rates of nitrification in the mesopelagic waters. These results suggest that eddy-mediated changes to the upper ocean can have important roles in modifying nitrogen transformation in the interior waters of the ocean.
QCB Colloquium | Dr. Hannah Carter
Dr. Hannah Carter
Assistant Professor, UCSD, Health Sciences
Lab Website
MHC genotype shapes the oncogenic landscape
Thursday, September 5
2 PM
RRI 101
Abstract: Significant insights into tumorigenesis have been gained by characterizing the extensive somatic alterations that arise during cancer and uncovering rare inherited mutations that lead to early onset cancer syndromes. However, little is understood about the role of genetic background in ‘sporadic’ adulthood cancers. Mounting evidence suggests that the somatic evolution of a tumor is influenced by inherited polymorphisms. We investigated this phenomenon in the context of the immune system, which is a major source of selective pressure during tumor development. The genomic region encoding the Major Histocompatibility Complex Class (MHC) is one of the most variable regions in the human population. MHC molecules expose peptide fragments on the cell surface, allowing T-Cell elimination of cells contaminated by foreign peptide. Although this system has evolved as a defense against microbial and viral agents, MHC can also trigger elimination of cells harboring mutant peptides (neoantigens) in cancer. Each individual carries multiple MHC alleles that define the set of peptides that can be effectively presented for immune surveillance. We hypothesized that individual variation in MHC could create personal gaps in immune surveillance, generating individual-specific susceptibility for cells to acquire specific oncogenic mutations. To test this hypothesis, we developed residue-centric patient presentation scores for MHC class I and II molecules and applied them to 1,018 recurrent oncogenic mutations in 9,176 cancer patients. This analysis uncovered a clear signature of immune selection acting on tumors with implications for age at diagnosis, driver occurrence in tumors and frequency of driver mutations in cancer cohorts. Thus, the landscape of oncogenic mutations observed in clinically diagnosed tumors is shaped by MHC genotype-restricted immunoediting during tumor formation, and individual MHC genotype provides information about the mutations likely to emerge in tumors that develop later in life.
Host: Dr. Michael Waterman
Assistant Professor, UCSD, Health Sciences
Lab Website
MHC genotype shapes the oncogenic landscape
Thursday, September 5
2 PM
RRI 101
Abstract: Significant insights into tumorigenesis have been gained by characterizing the extensive somatic alterations that arise during cancer and uncovering rare inherited mutations that lead to early onset cancer syndromes. However, little is understood about the role of genetic background in ‘sporadic’ adulthood cancers. Mounting evidence suggests that the somatic evolution of a tumor is influenced by inherited polymorphisms. We investigated this phenomenon in the context of the immune system, which is a major source of selective pressure during tumor development. The genomic region encoding the Major Histocompatibility Complex Class (MHC) is one of the most variable regions in the human population. MHC molecules expose peptide fragments on the cell surface, allowing T-Cell elimination of cells contaminated by foreign peptide. Although this system has evolved as a defense against microbial and viral agents, MHC can also trigger elimination of cells harboring mutant peptides (neoantigens) in cancer. Each individual carries multiple MHC alleles that define the set of peptides that can be effectively presented for immune surveillance. We hypothesized that individual variation in MHC could create personal gaps in immune surveillance, generating individual-specific susceptibility for cells to acquire specific oncogenic mutations. To test this hypothesis, we developed residue-centric patient presentation scores for MHC class I and II molecules and applied them to 1,018 recurrent oncogenic mutations in 9,176 cancer patients. This analysis uncovered a clear signature of immune selection acting on tumors with implications for age at diagnosis, driver occurrence in tumors and frequency of driver mutations in cancer cohorts. Thus, the landscape of oncogenic mutations observed in clinically diagnosed tumors is shaped by MHC genotype-restricted immunoediting during tumor formation, and individual MHC genotype provides information about the mutations likely to emerge in tumors that develop later in life.
Host: Dr. Michael Waterman
Monday, August 26, 2019
Lab Research Assistant Position Available
I have a Laboratory Research Assistant position open in my lab. Apply if you might have an interest in working with us on our vaginal microbiome projects. We can adjust the position to a wide variety of experience and training.
LINK to apply is online: https://umb.taleo.net/careersection/jobdetail.ftl?job=1900013V&lang=en
Please feel free to contact me directly if you have any questions.
Thanks!
LINK to apply is online: https://umb.taleo.net/careersection/jobdetail.ftl?job=1900013V&lang=en
Please feel free to contact me directly if you have any questions.
Thanks!
Rebecca M. Brotman, PhD, MPH
Associate Professor
Department of Epidemiology and Public Health
Institute for Genome Sciences
University of Maryland School of Medicine
670 West Baltimore Street, Room #3175
Baltimore, MD 21201
phone: (410) 706-6767
fax: (410) 706-1482
email: rbrotman@som.umaryland.edu
Sunday, August 25, 2019
MEB Seminar | Dr. Sheila Kitchen
Dr. Sheila Kitchen
Post-Doc, California Institute of Technology, PI: Dr. Joseph Parker
Research Website
Adaptive potential and limits in Caribbean acroporid corals
Tuesday, August 27
12 PM
AHF 153 (Torrey Webb Room)
Abstract: Reef-building corals are currently threatened by rapid changes in local and global stressors, and hybridization offers a potential shortcut for rapid adaptation and evolutionary rescue in these species. The sympatric corals Acropora palmata and A. cervicornis form the hybrid, A. prolifera, whose abundance has continued to increase while the parental species decline. Previous work indicates that weakened prezygotic isolation mechanisms in A. cervicornis but not A. palmata could allow for continuous unidirectional gene flow between the two species. Furthermore, asymmetric introgression from A. palmata to A. cervicornis has been recorded in three nuclear loci. In contrast, we found evidence for bidirectional introgession across three hybrid zones, although the frequency of hybrids and backcrosses differs across the range. Genome assemblies of A. palmataand A. cervicornis were compared to other corals to identify orthologs uniquely shared by the Caribbean acroporids. Genomic sequence data from the two parental species and their hybrids was used to further characterize the patterns of genomic synteny, divergence and introgression across hybrid zones. Combined, these approaches elucidate genomic hotspots of introgression and parallel evolution with implications for how hybridization may shape adaptation in these important foundation species across the Caribbean and North-West Atlantic.
Host: Dr. Carly Kenkel
Post-Doc, California Institute of Technology, PI: Dr. Joseph Parker
Research Website
Adaptive potential and limits in Caribbean acroporid corals
Tuesday, August 27
12 PM
AHF 153 (Torrey Webb Room)
Abstract: Reef-building corals are currently threatened by rapid changes in local and global stressors, and hybridization offers a potential shortcut for rapid adaptation and evolutionary rescue in these species. The sympatric corals Acropora palmata and A. cervicornis form the hybrid, A. prolifera, whose abundance has continued to increase while the parental species decline. Previous work indicates that weakened prezygotic isolation mechanisms in A. cervicornis but not A. palmata could allow for continuous unidirectional gene flow between the two species. Furthermore, asymmetric introgression from A. palmata to A. cervicornis has been recorded in three nuclear loci. In contrast, we found evidence for bidirectional introgession across three hybrid zones, although the frequency of hybrids and backcrosses differs across the range. Genome assemblies of A. palmataand A. cervicornis were compared to other corals to identify orthologs uniquely shared by the Caribbean acroporids. Genomic sequence data from the two parental species and their hybrids was used to further characterize the patterns of genomic synteny, divergence and introgression across hybrid zones. Combined, these approaches elucidate genomic hotspots of introgression and parallel evolution with implications for how hybridization may shape adaptation in these important foundation species across the Caribbean and North-West Atlantic.
Host: Dr. Carly Kenkel
QCB Colloquium | Dr. Charleston Chiang
Dr. Charleston Chiang
Assistant Professor, USC Keck School of Medicine, Center for Genetic Epidemiology, Preventive Medicine
Lab Website
The impact of demographic history and natural selection on human complex traits: examples from Sardinia and Finland
Thursday, August 29, 2019
2 PM
RRI 101
Abstract: How complex traits change through time is a central question in evolutionary biology and genetics. Two of the major evolutionary forces that shaped the distribution of human complex traits are the demographic and adaptive histories of a population. Therefore, in order for human genetics to provide a compelling context to study complex trait evolution, it is necessary to integrate genetic mapping with a detailed knowledge of population history. A well-known example of demographic impact on complex traits is a population bottleneck followed by long-term isolations. I will use examples from European populations of Sardinia and Finland to illustrate the impact of the demographic history on patterns of genetic variation and human complex traits. By utilizing large-scale whole-genome or whole-exome sequencing datasets, I will describe our findings in delineating the population structure and history of these populations, and how the special population history empowered association studies. Moreover, natural selection through polygenic adaptation is also thought to be an important force in shaping the complex traits of extant populations. Adult height differences across European populations had been thought of as the prime example of polygenic adaptation in humans, until recent papers demonstrated that the differences across Europe might have been over-estimated due to uncorrected biases in genome-wide association studies (GWAS). I will show that by using GWAS summary statistics ascertained from an East Asian population, we continue to see signature consistent with polygenic adaptation at height-associated loci in at least some European populations.
Host: Andrew Smith
Assistant Professor, USC Keck School of Medicine, Center for Genetic Epidemiology, Preventive Medicine
Lab Website
The impact of demographic history and natural selection on human complex traits: examples from Sardinia and Finland
Thursday, August 29, 2019
2 PM
RRI 101
Abstract: How complex traits change through time is a central question in evolutionary biology and genetics. Two of the major evolutionary forces that shaped the distribution of human complex traits are the demographic and adaptive histories of a population. Therefore, in order for human genetics to provide a compelling context to study complex trait evolution, it is necessary to integrate genetic mapping with a detailed knowledge of population history. A well-known example of demographic impact on complex traits is a population bottleneck followed by long-term isolations. I will use examples from European populations of Sardinia and Finland to illustrate the impact of the demographic history on patterns of genetic variation and human complex traits. By utilizing large-scale whole-genome or whole-exome sequencing datasets, I will describe our findings in delineating the population structure and history of these populations, and how the special population history empowered association studies. Moreover, natural selection through polygenic adaptation is also thought to be an important force in shaping the complex traits of extant populations. Adult height differences across European populations had been thought of as the prime example of polygenic adaptation in humans, until recent papers demonstrated that the differences across Europe might have been over-estimated due to uncorrected biases in genome-wide association studies (GWAS). I will show that by using GWAS summary statistics ascertained from an East Asian population, we continue to see signature consistent with polygenic adaptation at height-associated loci in at least some European populations.
Host: Andrew Smith
Monday, May 6, 2019
Post-Doc @ Univ. of Maryland School of Medicine
A postdoctoral position is available in the laboratory of Dr. David Serre at the Institute for Genome Sciences at the University of Maryland School of Medicine. Our laboratory is interested in developing and applying novel genomic approaches to better understand the biology of malaria parasites and the vectors that transmit them.
We are seeking a highly motivated individual to take the lead on analyses of single-cell RNA-seq data generated from Plasmodiumparasites at different life stages of their development and under various conditions. This postdoctoral position is supported by NIH awards and involves collaborations with researchers at NIAID, Johns Hopkins School of Public Health and in malaria-endemic countries. There are also opportunities for the successful candidate to develop her/his own independent projects within the framework of this research.
A PhD in biology, bioinformatics, genomics or a related field is required. The work involves custom bioinformatic analyses of large amount of data and proficiency in one programming language and knowledge of statistics would be an advantage. Previous knowledge of parasitology is not required.
Interested candidates should send a cover letter and CV to David Serre (dserre@som.umaryland.edu)
We are seeking a highly motivated individual to take the lead on analyses of single-cell RNA-seq data generated from Plasmodiumparasites at different life stages of their development and under various conditions. This postdoctoral position is supported by NIH awards and involves collaborations with researchers at NIAID, Johns Hopkins School of Public Health and in malaria-endemic countries. There are also opportunities for the successful candidate to develop her/his own independent projects within the framework of this research.
A PhD in biology, bioinformatics, genomics or a related field is required. The work involves custom bioinformatic analyses of large amount of data and proficiency in one programming language and knowledge of statistics would be an advantage. Previous knowledge of parasitology is not required.
Interested candidates should send a cover letter and CV to David Serre (dserre@som.umaryland.edu)
QCB Colloquium Series | Dr. Hongyu Zhao
Dr. Hongyu Zhao
Department Chair and Ira V. Hiscock Professor of Biostatistics, Professor of Genetics and Professor of Statistics and Data Science, Yale University, School of Public Health
Lab Website
Dissecting Genetic Architecture of Complex Diseases From Genome Wide Association Studies
Wednesday, May 8, 2019
2 PM
RRI 301
Abstract: Genome-wide association study (GWAS) has been a great success in the past decade, with thousands of regions in the human genome implicated for hundreds of complex diseases. However, significant challenges remain in both identifying new risk loci and interpreting results, even for samples with tens of thousands of subjects. In this presentation, we describe our recent efforts to infer the genetic architecture of complex disease through random effects models, the development of functional annotations of the human genome, and the integrated analysis of these annotations with GWAS results. The effectiveness of our methods will be demonstrated through their applications to a large number of GWASs to identify tissues/cell types that are relevant to a specific disease, to infer shared genetic contributions to several diseases, and to improve genetic disease risk predictions. This is joint work with Qiongshi Lu, Yiming Hu, Jiming Jiang, Can Yang, Ryan Powels, Yixuan Ye, and others.
Department Chair and Ira V. Hiscock Professor of Biostatistics, Professor of Genetics and Professor of Statistics and Data Science, Yale University, School of Public Health
Lab Website
Dissecting Genetic Architecture of Complex Diseases From Genome Wide Association Studies
Wednesday, May 8, 2019
2 PM
RRI 301
Abstract: Genome-wide association study (GWAS) has been a great success in the past decade, with thousands of regions in the human genome implicated for hundreds of complex diseases. However, significant challenges remain in both identifying new risk loci and interpreting results, even for samples with tens of thousands of subjects. In this presentation, we describe our recent efforts to infer the genetic architecture of complex disease through random effects models, the development of functional annotations of the human genome, and the integrated analysis of these annotations with GWAS results. The effectiveness of our methods will be demonstrated through their applications to a large number of GWASs to identify tissues/cell types that are relevant to a specific disease, to infer shared genetic contributions to several diseases, and to improve genetic disease risk predictions. This is joint work with Qiongshi Lu, Yiming Hu, Jiming Jiang, Can Yang, Ryan Powels, Yixuan Ye, and others.
Monday, April 29, 2019
MBBO Ph.D. Dissertation Defense | Erin McParland
Erin McParland
Ph.D. Candidate, MBBO Graduate Program (PI: Dr. Naomi Levine)
The dynamic regulation of DMSP production by marine phytoplankton
Wednesday, May 8, 2019
10 AM
AHF 153 (Torrey Webb Room)
Abstract: Dimethylsulfoniopropionate (DMSP) is a labile sulfur and carbon metabolite that significantly contributes to both the cycling of marine dissolved organic carbon and the balance of Earth’s albedo. DMSP is produced by the majority of eukaryotic marine phytoplankton and by many prokaryotes, but despite decades of research, the cellular mechanism and environmental drivers of DMSP production remain unknown. My thesis confirms that the cellular mechanism of DMSP is differentiated by the cellular concentrations of DMSP in different producers, where high DMSP producers (e.g. dinoflagellates and haptophytes) constitutively produce DMSP and low DMSP producers (e.g. cyanobacteria and diatoms) actively regulate DMSP production in response to environmental stress. However, with natural community experiments and global model predictions, my thesis demonstrates that variability of in situ DMSP production is driven by the biomass of high producers. My thesis highlights the potential for predicting in situ DMSP concentrations with a high DMSP producer marker gene and demonstrates the importance of accurately capturing the sub-dominant community for prediction of DMSP, or other similar metabolites produced by a small fraction of the marine microbial community.
Ph.D. Candidate, MBBO Graduate Program (PI: Dr. Naomi Levine)
The dynamic regulation of DMSP production by marine phytoplankton
Wednesday, May 8, 2019
10 AM
AHF 153 (Torrey Webb Room)
Abstract: Dimethylsulfoniopropionate (DMSP) is a labile sulfur and carbon metabolite that significantly contributes to both the cycling of marine dissolved organic carbon and the balance of Earth’s albedo. DMSP is produced by the majority of eukaryotic marine phytoplankton and by many prokaryotes, but despite decades of research, the cellular mechanism and environmental drivers of DMSP production remain unknown. My thesis confirms that the cellular mechanism of DMSP is differentiated by the cellular concentrations of DMSP in different producers, where high DMSP producers (e.g. dinoflagellates and haptophytes) constitutively produce DMSP and low DMSP producers (e.g. cyanobacteria and diatoms) actively regulate DMSP production in response to environmental stress. However, with natural community experiments and global model predictions, my thesis demonstrates that variability of in situ DMSP production is driven by the biomass of high producers. My thesis highlights the potential for predicting in situ DMSP concentrations with a high DMSP producer marker gene and demonstrates the importance of accurately capturing the sub-dominant community for prediction of DMSP, or other similar metabolites produced by a small fraction of the marine microbial community.
MBBO Ph.D. Dissertation Defense | Pingping Qu
Pingping Qu
Ph.D. Candidate, MBBO Graduate Program (PI: Dr. David Hutchins)
Thermal Acclimation and Adaptation of Key Phytoplankton Groups and Interactions with Other Global Change Variables
Wednesday, May 1, 2019
11 AM
AHF 153 (Torrey Webb Room)
Abstract: Marine phytoplankton play critical roles in global primary productivity, carbon export and biogeochemistry. The relationships between environmental forcing and key phytoplankton groups in marine ecosystems need more attention, especially under global change scenarios. Among many other environmental changes, phytoplankton communities in the euphotic zone are anticipated to be most sensitive to concurrent ocean acidification, warming, more thermal variability and reduced nutrient supplies.
Marine diatoms play critical roles in global primary productivity, carbon export and the food web. Marine diazotrophic cyanobacteria are equally important as a source of new nitrogen through nitrogen fixation. In order to better understand the possible responses of marine diatoms and diazotrophs to a changing ocean environment, my studies focused on the synergistic effects of multiple climate change variables on an important diatom, as well as the responses of two keystone diazotrophs to thermal variability and to long-term selection by warming.
In my first chapter, the physiological responses of the widespread centric diatom Coscinodiscus sp. to interactions between three climate-change variables (elevated CO2, warming, and nitrate availability) were investigated to better understand the interactions of multiple global changes on large, carbon-exporting diatoms. The second one examined how short-term thermal variability affects the growth and physiology of the diazotrophic cyanobacterium Trichodesmium erythraeum GBRTRLI101, as well as the interaction between temperature variation and phosphate availability. The third chapter tested the physiological responses and compared and contrasted acclimation and adaptation of Trichodesmium erythraeum IMS101 and Crocosphaera WH0005 under long-term experimental selection at different temperatures, exploring possible ecological and biogeochemical implications of ways that these two representative diazotrophic cyanobacteria may cope with future warmer conditions.
Ph.D. Candidate, MBBO Graduate Program (PI: Dr. David Hutchins)
Thermal Acclimation and Adaptation of Key Phytoplankton Groups and Interactions with Other Global Change Variables
Wednesday, May 1, 2019
11 AM
AHF 153 (Torrey Webb Room)
Abstract: Marine phytoplankton play critical roles in global primary productivity, carbon export and biogeochemistry. The relationships between environmental forcing and key phytoplankton groups in marine ecosystems need more attention, especially under global change scenarios. Among many other environmental changes, phytoplankton communities in the euphotic zone are anticipated to be most sensitive to concurrent ocean acidification, warming, more thermal variability and reduced nutrient supplies.
Marine diatoms play critical roles in global primary productivity, carbon export and the food web. Marine diazotrophic cyanobacteria are equally important as a source of new nitrogen through nitrogen fixation. In order to better understand the possible responses of marine diatoms and diazotrophs to a changing ocean environment, my studies focused on the synergistic effects of multiple climate change variables on an important diatom, as well as the responses of two keystone diazotrophs to thermal variability and to long-term selection by warming.
In my first chapter, the physiological responses of the widespread centric diatom Coscinodiscus sp. to interactions between three climate-change variables (elevated CO2, warming, and nitrate availability) were investigated to better understand the interactions of multiple global changes on large, carbon-exporting diatoms. The second one examined how short-term thermal variability affects the growth and physiology of the diazotrophic cyanobacterium Trichodesmium erythraeum GBRTRLI101, as well as the interaction between temperature variation and phosphate availability. The third chapter tested the physiological responses and compared and contrasted acclimation and adaptation of Trichodesmium erythraeum IMS101 and Crocosphaera WH0005 under long-term experimental selection at different temperatures, exploring possible ecological and biogeochemical implications of ways that these two representative diazotrophic cyanobacteria may cope with future warmer conditions.
Monday, April 22, 2019
MEB Graduate Student Seminars
Yi-Chun Yeh (PI: Dr. Jed Fuhrman)
Long-term dynamics of free-living and particle-associated prokaryotic communities at the San Pedro Ocean Time-series
Abstract: The free-living and particle-associated marine prokaryotes have been proved to differ in their diversity and composition, but drivers of their long-term dynamics are poorly understood. We thus investigated surface to bottom dynamics of free-living (0.2-1.2 µm) and particle-associated (1.2-80 µm) prokaryotes at the San Pedro Ocean Time Series (SPOT) during 2000-2018 by using ssu rRNA tag sequencing. We assessed factors influencing the temporal variation of community composition by canonical correspondence analysis (CCA), and community turnover by the β-nearest taxon index (βNTI), a measure designed to assess the extent of stochastic vs. deterministic drivers. The results showed free-living and particle-associated prokaryotic communities both have strong seasonality at the surface and the deep chlorophyll maximum (DCM), though seasonal variation decreased in warm years, notably after 2012. Moreover, the free-living fraction exhibited a relatively stable dynamic without decreasing in average similarity over time, whereas the particle-associated fraction was undergoing directional change.
Melissa DellaTorre (PI: Dr. Donal Manahan)
Mechanisms of food and temperature impacts on growth in the ocean
Abstract: Variations in sources of energy and temperature have major impacts on the survival and growth of organisms. For marine larval forms, the degree to which food availability can alter physiological tolerances to thermal stress remains unknown. In this presentation, the physiological mechanisms of growth that are impacted by food quantity and temperature will be analyzed, in addition to food-temperature interactions. The goal of these studies is to understand resilience potential to future scenarios of ocean change.
Ariel Levi Simons (PI: Dr. Sergey Nuzhdin)
Using 𝞪, 𝞫, and 𝞯 diversity in describing the health of stream-based benthic macroinvertebrate communities
Abstract: Ecological monitoring of streams has frequently focused on measures describing the taxonomic, and sometimes functional, α diversity of benthic macroinvertebrates (BMIs) within a single sampled community. However, as many ecological processes effectively link BMI stream communities there is a need to describe groups of communities using measures of regional diversity. Here we demonstrate a role for incorporating both a traditional pairwise measure of community turnover, β diversity, in assessing community health as well as ζ diversity, a more generalized framework for describing similarity between multiple communities. Using 4395 samples of BMI stream communities in California, we constructed a model using measures of α, β, and ζ diversity which could account for most of the among-watershed variation in the mean health of communities, as described by the California Streams Condition Index (CSCI).
Tuesday, April 23, 2019
12 PM
AHF 153 (Torrey Webb Room)
Long-term dynamics of free-living and particle-associated prokaryotic communities at the San Pedro Ocean Time-series
Abstract: The free-living and particle-associated marine prokaryotes have been proved to differ in their diversity and composition, but drivers of their long-term dynamics are poorly understood. We thus investigated surface to bottom dynamics of free-living (0.2-1.2 µm) and particle-associated (1.2-80 µm) prokaryotes at the San Pedro Ocean Time Series (SPOT) during 2000-2018 by using ssu rRNA tag sequencing. We assessed factors influencing the temporal variation of community composition by canonical correspondence analysis (CCA), and community turnover by the β-nearest taxon index (βNTI), a measure designed to assess the extent of stochastic vs. deterministic drivers. The results showed free-living and particle-associated prokaryotic communities both have strong seasonality at the surface and the deep chlorophyll maximum (DCM), though seasonal variation decreased in warm years, notably after 2012. Moreover, the free-living fraction exhibited a relatively stable dynamic without decreasing in average similarity over time, whereas the particle-associated fraction was undergoing directional change.
Melissa DellaTorre (PI: Dr. Donal Manahan)
Mechanisms of food and temperature impacts on growth in the ocean
Abstract: Variations in sources of energy and temperature have major impacts on the survival and growth of organisms. For marine larval forms, the degree to which food availability can alter physiological tolerances to thermal stress remains unknown. In this presentation, the physiological mechanisms of growth that are impacted by food quantity and temperature will be analyzed, in addition to food-temperature interactions. The goal of these studies is to understand resilience potential to future scenarios of ocean change.
Ariel Levi Simons (PI: Dr. Sergey Nuzhdin)
Using 𝞪, 𝞫, and 𝞯 diversity in describing the health of stream-based benthic macroinvertebrate communities
Abstract: Ecological monitoring of streams has frequently focused on measures describing the taxonomic, and sometimes functional, α diversity of benthic macroinvertebrates (BMIs) within a single sampled community. However, as many ecological processes effectively link BMI stream communities there is a need to describe groups of communities using measures of regional diversity. Here we demonstrate a role for incorporating both a traditional pairwise measure of community turnover, β diversity, in assessing community health as well as ζ diversity, a more generalized framework for describing similarity between multiple communities. Using 4395 samples of BMI stream communities in California, we constructed a model using measures of α, β, and ζ diversity which could account for most of the among-watershed variation in the mean health of communities, as described by the California Streams Condition Index (CSCI).
Tuesday, April 23, 2019
12 PM
AHF 153 (Torrey Webb Room)
MCB Colloquium Series | Dr. Susan Strome
Dr. Susan Strome
Distinguished Professor, UC Santa Cruz, MCD Biology
Lab Website
Passing an epigenetic “memory of germline" from parents to offspring
Friday, April 26, 2019
12 PM
RRI 101
Abstract: The Strome lab investigates the molecular mechanisms used by germ cells to establish and maintain their identity, immortality, and totipotency. They study germ cells in C. elegans using a variety of approaches, including genetics, genomics, and imaging. Their current focus is on regulation of chromatin states and the involvement of those states in transmitting an epigenetic “memory of germline” from parent germ cells to germ cells in offspring.
Distinguished Professor, UC Santa Cruz, MCD Biology
Lab Website
Passing an epigenetic “memory of germline" from parents to offspring
Friday, April 26, 2019
12 PM
RRI 101
Abstract: The Strome lab investigates the molecular mechanisms used by germ cells to establish and maintain their identity, immortality, and totipotency. They study germ cells in C. elegans using a variety of approaches, including genetics, genomics, and imaging. Their current focus is on regulation of chromatin states and the involvement of those states in transmitting an epigenetic “memory of germline” from parent germ cells to germ cells in offspring.
Monday, April 15, 2019
MEB Seminar Series | Dr. Shana Goffredi
Dr. Shana Goffredi
Associate Professor, Occidental College, Biology/Biochemistry
Lab Website
Extreme Alliances: Relationships between deep-sea animals and bacteria
Tuesday, April 16, 2019
12 PM
AHF 153 (Torrey Webb Room)
Abstract: Forty years ago, scientists discovered invertebrates at the bottom of the ocean that forever changed how we view life on this planet. Abundant, thriving communities were not expected in the deep-sea, due to the very low levels of organic carbon that arrive at these depths from above. Certain worms, bivalves, and others, however, have forged relationships with bacteria, in order to harness inorganic sources of energy, typically foreign to animals. Symbiosis is the best of both worlds -- Morphological diversity of animals, and the Physiological diversity of bacteria. This seminar will highlight examples of deep-sea animal-bacterial symbioses from a variety of animal groups - some recently discovered, revealing surprising new relationships between animals and bacteria, and some among the oldest known.
Associate Professor, Occidental College, Biology/Biochemistry
Lab Website
Extreme Alliances: Relationships between deep-sea animals and bacteria
Tuesday, April 16, 2019
12 PM
AHF 153 (Torrey Webb Room)
Abstract: Forty years ago, scientists discovered invertebrates at the bottom of the ocean that forever changed how we view life on this planet. Abundant, thriving communities were not expected in the deep-sea, due to the very low levels of organic carbon that arrive at these depths from above. Certain worms, bivalves, and others, however, have forged relationships with bacteria, in order to harness inorganic sources of energy, typically foreign to animals. Symbiosis is the best of both worlds -- Morphological diversity of animals, and the Physiological diversity of bacteria. This seminar will highlight examples of deep-sea animal-bacterial symbioses from a variety of animal groups - some recently discovered, revealing surprising new relationships between animals and bacteria, and some among the oldest known.
Watershed Stewards Program now accepting applications for Year 26
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