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.
Monday, October 28, 2019
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.
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