PhD Pathways Career Series_Spring 2020 by uscbiscgrad on Scribd
Monday, January 13, 2020
Stanford PRISM - Stanford Postdoc Recruitment Now Accepting Applications
The application is now open for our fifth PRISM cohort. Stanford PRISM is a recruitment opportunity for late-stage graduate students from diverse backgrounds to explore postdoctoral training at Stanford.
Please forward the following message to your colleagues and any graduate students planning to complete their PhDs by June 2021 who might be interested in considering postdoctoral training at Stanford.
Stanford PRISM
PRISM (Postdoctoral Recruitment Initiative in Sciences and Medicine) is an opportunity for select late-stage graduate students from broadly diverse backgrounds to come to Stanford for a recruitment weekend, interview with potential mentors, and get the inside scoop on postdoctoral training at Stanford. The purpose of this program is to encourage those who might not currently consider a postdoctoral position at Stanford to get a first-hand look at whether Stanford might be a good fit for them. Our goal is to match excellent trainees to excellent mentors at Stanford.
This opportunity is open to all. We especially encourage those from backgrounds underrepresented in academia to apply, including but not limited to: African Americans, Latinos, Native Americans, Pacific Islanders, Filipinos, those with disabilities, first generation college-goers, those from disadvantaged socio-economic backgrounds, and those underrepresented on the basis of gender identity or expression or sexual orientation. Applications consist of an application form, a CV, a research statement, a recommendation from your graduate advisor, and the names of up to 6 potential mentors at Stanford.
For more information or to apply, go to http://postdocs.stanford.edu/PRISM
PRISM Spring 2020 dates: May 20-23, 2020
Deadline: March 2, 2020
Please forward the following message to your colleagues and any graduate students planning to complete their PhDs by June 2021 who might be interested in considering postdoctoral training at Stanford.
Stanford PRISM
PRISM (Postdoctoral Recruitment Initiative in Sciences and Medicine) is an opportunity for select late-stage graduate students from broadly diverse backgrounds to come to Stanford for a recruitment weekend, interview with potential mentors, and get the inside scoop on postdoctoral training at Stanford. The purpose of this program is to encourage those who might not currently consider a postdoctoral position at Stanford to get a first-hand look at whether Stanford might be a good fit for them. Our goal is to match excellent trainees to excellent mentors at Stanford.
This opportunity is open to all. We especially encourage those from backgrounds underrepresented in academia to apply, including but not limited to: African Americans, Latinos, Native Americans, Pacific Islanders, Filipinos, those with disabilities, first generation college-goers, those from disadvantaged socio-economic backgrounds, and those underrepresented on the basis of gender identity or expression or sexual orientation. Applications consist of an application form, a CV, a research statement, a recommendation from your graduate advisor, and the names of up to 6 potential mentors at Stanford.
For more information or to apply, go to http://postdocs.stanford.edu/PRISM
PRISM Spring 2020 dates: May 20-23, 2020
Deadline: March 2, 2020
Marine biology field course in South Africa
Are you looking for an exciting opportunity to study biodiversity and further your marine biology skills this year in the kelp forests of South Africa? Cape RADD facilitates a 2 week and 4 week field course for students who want to learn more about the marine environment, conservation and research through hands on field experience and diver development. The Cape RADD course runs every month and includes training in multiple data collection and field operation techniques, theoretical workshops on analysis techniques and tools like R and GIS. Come spend a month abroad, scuba diving and freediving in one of the most beautiful parts of the world.
Visit www.caperadd.com or email info@caperadd.com for more details.
Visit www.caperadd.com or email info@caperadd.com for more details.
QCB Colloquium | Dr. Serghei Mangul
Dr. Serghei Mangul
Assistant Professor, USC School of Pharmacy
Lab Website
Dumpster diving in RNA-sequencing to study the immune receptor repertoires and microbial communities
Thursday, January 16, 2 PM, RRI 101
Abstract: Assay-based approaches provide a detailed view of the adaptive immune system by profiling T- and B-cell receptor (TCR/BCR) repertoires. However, these methods are costly, time-consuming, and lack the scale of RNA sequencing (RNA-seq). The seminar will introduce bioinformatic methods that mine discarded sequences and produce rich research level data including T and B cell receptor sequences, microbiome, genome-wide germline genotypes, and rDNA and mtDNA copy number. We have applied our methods to GTEx multi-tissue RNA-Seq data (n=8,555) and Profile OncoPanel cancer sequencing data (n=20,000). We validated the accuracy of our methods and showed their utility through replication of known genetic associations. The presented systematic atlas of immunological sequences data contains one of the largest collections of immune receptor sequencing across a broad range of tissue. Additionally, we investigated the functional mechanisms underlying connections between the immune system, microbiome, and disease.
Assistant Professor, USC School of Pharmacy
Lab Website
Dumpster diving in RNA-sequencing to study the immune receptor repertoires and microbial communities
Thursday, January 16, 2 PM, RRI 101
Abstract: Assay-based approaches provide a detailed view of the adaptive immune system by profiling T- and B-cell receptor (TCR/BCR) repertoires. However, these methods are costly, time-consuming, and lack the scale of RNA sequencing (RNA-seq). The seminar will introduce bioinformatic methods that mine discarded sequences and produce rich research level data including T and B cell receptor sequences, microbiome, genome-wide germline genotypes, and rDNA and mtDNA copy number. We have applied our methods to GTEx multi-tissue RNA-Seq data (n=8,555) and Profile OncoPanel cancer sequencing data (n=20,000). We validated the accuracy of our methods and showed their utility through replication of known genetic associations. The presented systematic atlas of immunological sequences data contains one of the largest collections of immune receptor sequencing across a broad range of tissue. Additionally, we investigated the functional mechanisms underlying connections between the immune system, microbiome, and disease.
Monday, December 2, 2019
MEB Seminar | Dr. Casey Mueller
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.
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.
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
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