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X-WR-CALNAME:UCLA | Bioinformatics
X-ORIGINAL-URL:https://bioinformatics.ucla.edu
X-WR-CALDESC:Events for UCLA | Bioinformatics
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BEGIN:VTIMEZONE
TZID:UTC
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TZOFFSETFROM:+0000
TZOFFSETTO:+0000
TZNAME:UTC
DTSTART:20150101T000000
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END:VTIMEZONE
BEGIN:VEVENT
DTSTART;TZID=UTC:20160524T170000
DTEND;TZID=UTC:20160524T180000
DTSTAMP:20160524T231629Z
CREATED:20160524T231629Z
LAST-MODIFIED:20160524T231629Z
UID:1842-1464109200-1464112800@bioinformatics.ucla.edu
SUMMARY:UCLA Undergraduate Bioinformatics Minor Information Session
DESCRIPTION:The UCLA Undergraduate Bioinformatics Minor program encourages all students currently enrolled as program minors as well as those who may be interested in learning more about the Bioinformatics minor as well as research opportunities in Bioinformatics to attend our quarterly information session on Tuesday\, May 24th at 5-6pm in Boelter Hall 4760. \nProgram faculty as well as current Bioinformatics undergraduate students involved in research will host this town hall style meeting to provide information about the bioinformatics minor and information on how to get involved in Bioinformatics research projects at UCLA. \nLight refreshments will be provided.
URL:https://bioinformatics.ucla.edu/event/ucla-undergraduate-bioinformatics-minor-information-session/
LOCATION:Boelter Hall 4760
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=UTC:20160523T160000
DTEND;TZID=UTC:20160523T170000
DTSTAMP:20160518T162844Z
CREATED:20160518T162844Z
LAST-MODIFIED:20160518T162844Z
UID:1736-1464019200-1464022800@bioinformatics.ucla.edu
SUMMARY:Su-In Lee Seminar
DESCRIPTION:Su-In Lee\, Ph.D. \nAssistant Professor of Computer Science and Engineering\, and Genome Sciences\, University of Washington \n“Learning the human chromatin network from all ENCODE ChIP-seq data” \nAbstract: \nIntroduction: A cell’s epigenome arises from interactions among regulatory factors — transcription factors\, histone modifications\, and other DNA-associated proteins — co-localized at particular genomic regions.  Identifying the network of interactions among regulatory factors\, the chromatin network\, is of paramount importance in understanding epigenome regulation. \nMethods: We developed a novel computational approach\, ChromNet\, to infer the chromatin network from a set of ChIP-seq datasets.  ChromNet has four key features that enable its use on large collections of ChIP-seq data.  First\, rather than using pairwise co-localization of factors along the genome\, ChromNet identifies conditional dependence relationships that better discriminate direct and indirect interactions.  Second\, our novel statistical technique\, the group graphical model\, improves inference of conditional dependence on highly correlated datasets.  Such datasets are common because some transcription factors form a complex and the same transcription factor is often assayed in different laboratories or cell types.  Third\, ChromNet’s computationally efficient method allows joint network learning across across 115 cell types\, which greatly increases the scope of possible interactions. Finally\, the genomic context causing any network edge can be inferred to aid understanding. \nResults: We applied ChromNet to all available ChIP-seq data from the ENCODE Project\, consisting of 1\,451 ChIP-seq datasets\, which revealed previously known physical interactions better than alternative approaches.  ChromNet also identified previously unreported regulatory factor interactions.  We experimentally validated one of these interactions\, between the MYC and HCFC1 transcription factors. \nDiscussion: ChromNet provides a useful tool for understanding the interactions among regulatory factors and identifying novel interactions.  We have provided an interactive web-based visualization of the full ENCODE chromatin network and the ability to incorporate custom datasets at http://chromnet.cs.washington.edu. \nBio:  Professor Su-In Lee is an Assistant Professor in the Departments of Computer Science & Engineering and Genome Sciences at the University of Washington. She received her Ph.D. degree in Electrical Engineering from Stanford University in 2009. Before joining the UW in 2010\, she was a Visiting Assistant Professor in the Computational Biology Department at Carnegie Mellon University. \nHer interest is in developing advanced machine learning (ML) algorithms to analyze high-throughput molecular data 1) to discover molecular mechanisms of disease initiation and progression\, 2) to identify therapeutic targets\, and 3) to develop personalized therapy based on individual patients’ molecular profiles. She has been named an American Cancer Society Research Scholar in 2015 and received the NSF CAREER award in 2016. Her lab is currently funded by the American Cancer Society\, the National Institutes of Health\, the National Science Foundation\, the Institute of Translational Health Sciences and the Solid Tumor Translational Research. \n  \n 
URL:https://bioinformatics.ucla.edu/event/su-in-lee-seminar/
LOCATION:Boyer Hall 159
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=UTC:20160516T160000
DTEND;TZID=UTC:20160516T170000
DTSTAMP:20160524T231528Z
CREATED:20160524T231528Z
LAST-MODIFIED:20160524T231528Z
UID:1123-1463414400-1463418000@bioinformatics.ucla.edu
SUMMARY:Hongkai Ji Seminar
DESCRIPTION:Hongkai Ji\, Ph.D. \nAssociate Professor\, Department of Biostatistics\, John Hopkins University \n\nTitle: Genome-wide Prediction of DNase I Hypersensitivity Using Gene Expression\n\nAbstract: We evaluate the feasibility of using a biological sample’s transcriptome to predict its genome-wide regulatory element activities measured by DNase I hypersensitivity (DH). We develop BIRD\, Big Data Regression for predicting DH\, to handle this high-dimensional problem. Applying BIRD to the Encyclopedia of DNA Element (ENCODE) data\, we found that gene expression to a large extent predicts DH\, and information useful for prediction is contained in the whole transcriptome rather than limited to a regulatory element’s neighboring genes. We show that the predicted DH predicts transcription factor binding sites (TFBSs)\, prediction models trained using ENCODE data can be applied to gene expression samples in Gene Expression Omnibus (GEO) to predict regulome\, and one can use predictions as pseudo-replicates to improve the analysis of high-throughput regulome profiling data. Besides improving our understanding of the regulome-transcriptome relationship\, this study suggests that transcriptome-based prediction can provide a useful new approach for regulome mapping.\n 
URL:https://bioinformatics.ucla.edu/event/hongkai-ji-seminar/
LOCATION:Boyer Hall 159
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=UTC:20160502T160000
DTEND;TZID=UTC:20160502T170000
DTSTAMP:20160428T235937Z
CREATED:20160428T235937Z
LAST-MODIFIED:20160428T235937Z
UID:1060-1462204800-1462208400@bioinformatics.ucla.edu
SUMMARY:Liang Chen Seminar
DESCRIPTION:Liang Chen\, Ph.D. \nAssociate Professor\, Department of Biological Sciences\, University of Southern California \n“Tackling overdispersion in RNA-seq data analysis” \nThe rapid advances in high-throughput sequencing technologies provide us an opportunity to dissect transcriptomes with unprecedented resolution. However transcriptome quantification is still hindered by non-uninform read sampling. Existing methods assume a constant bias factor for each relative position of genes or simply correct the sequence-specific bias caused by random hexamer priming. However\, the overall bias is complicated and caused by multiple factors including many unknown ones\, and the bias pattern can vary significantly across different regions and different protocols. In light of these facts\, we proposed to use the generalized-Poisson (GP) model to estimate the bias in a data-adaptive way without any presumption. We further incorporated this data-adaptive bias correction in the deconvolution of isoform expression. Our methods significantly improve the quantification of isoform and gene expression as well as the derived exon inclusion rates. For single-cell RNA-seq data\, our method distinguishes bias heterogeneity from true biological heterogeneity and uncovers smaller cell-to-cell expression variability. \n  \n  \n 
URL:https://bioinformatics.ucla.edu/event/liang-chen-seminar/
LOCATION:Boyer Hall 159
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=UTC:20160425T160000
DTEND;TZID=UTC:20160425T170000
DTSTAMP:20160419T161528Z
CREATED:20160414T211206Z
LAST-MODIFIED:20160419T161528Z
UID:1061-1461600000-1461603600@bioinformatics.ucla.edu
SUMMARY:Sunduz Keles Seminar
DESCRIPTION:Sunduz Keles\, Ph.D. \nProfessor\, Department of Biostatistics & Medical Informatics\, University of Wisconsin \n“Integrative Models of Genomic and Epigenomic Data“ \nConsortium projects such as ENCODE and NIH Roadmap Epigenomics generated a wealth of genomic and epigenomic data. We will present two general modeling frameworks for efficiently utilizing these data in genome-wide inference problems. Specifically\, we will present integrative models to (i) identify protein-DNA and long-range interactions involving repetitive genomic DNA; (ii) integrate functional annotation information into genome-wide association studies. \n  \n 
URL:https://bioinformatics.ucla.edu/event/sunduz-keles-seminar/
LOCATION:Boyer Hall 159
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=UTC:20160425T110000
DTEND;TZID=UTC:20160425T120000
DTSTAMP:20160420T235528Z
CREATED:20160420T235528Z
LAST-MODIFIED:20160420T235528Z
UID:1783-1461582000-1461585600@bioinformatics.ucla.edu
SUMMARY:Shao-Shan Carol Huang\, Special Seminar
DESCRIPTION:Shao-Shan Carol Huang\, Ph.D. \nGenomic Analysis Laboratory & Plant Biology Laboratory\nThe Salk Institute for Biological Studies\n“Efficient mapping of genome-wide regulatory elements for biological insights” \nWe developed a high-throughput sequencing assay for rapid transcription factor binding site (TFBS) discovery\, DNA affinity purification sequencing (DAP-seq)\, that uses in vitro prepared transcription factors (TFs) to capture native genomic DNA. We applied DAPseq to 1\,812 Arabidopsis thaliana TFs to resolve motifs for 529 factors and genome-wide enrichment maps for 349 factors. Cumulatively\, the ~2.7 million experimentally determined TFBSs captured the Arabidopsis cistrome and predicted thousands of TF target genes enriched for known and novel functions. Base-resolution epicistrome maps were established by comparison of TF-binding to genomic DNA with native cytosinemethylation patterns and genomic DNA that had been synthetically demethylated. This revealed methylcytosine inhibited binding of ~72% of factors and promoted binding of 4.3% of factors. Lastly\, we showed DAP-seq binding sites provided a way to annotate genomic and epigenomic variations in natural populations and interpret results from genome-wide association studies. Overall\, DAP-seq enables rapid development of base-resolution cistrome and epicistrome atlases for a wide-array of applications for eukaryotic genomes.
URL:https://bioinformatics.ucla.edu/event/shao-shan-carol-huang-special-seminar/
LOCATION:158 Hershey Hall
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=UTC:20160418T100000
DTEND;TZID=UTC:20160418T110000
DTSTAMP:20160404T165123Z
CREATED:20160404T165123Z
LAST-MODIFIED:20160404T165123Z
UID:1737-1460973600-1460977200@bioinformatics.ucla.edu
SUMMARY:Editorial Decision Making at Nature Genetics Talk
DESCRIPTION:Editorial decision making at Nature Genetics \nBrooke LaFlamme\, PhD\, Associate Editor\, Nature Genetics \nLocation: 10-11am\, 13-105 CHS\, Monday April 18\, 2016 \nAbstract: The editorial and publication process at high impact journals\, such as Nature Genetics\, is often perceived as confusing and difficult to navigate for researchers. My presentation will provide an overview of the editorial process at Nature Genetics\, including how we prioritize papers in our current focus areas and how the publication process works. I will then discuss how to best organize and present your manuscript prior to submission\, from an editor’s perspective. Finally\, I will briefly discuss some of the current and ongoing initiatives at Nature journals that are aimed at providing the highest quality author and referee services. \n  \nHost: Bogdan Pasaniuc (pasaniuc@ucla.edu)
URL:https://bioinformatics.ucla.edu/event/editorial-decision-making-at-nature-genetics-talk/
LOCATION:CHS 13-105
END:VEVENT
BEGIN:VEVENT
DTSTART;VALUE=DATE:20160416
DTEND;VALUE=DATE:20160422
DTSTAMP:20160328T181304Z
CREATED:20160328T181203Z
LAST-MODIFIED:20160328T181304Z
UID:1729-1460764800-1461283199@bioinformatics.ucla.edu
SUMMARY:RECOMB Conference 2016
DESCRIPTION:RECOMB 2016 is the twentieth in a series of well-established scientific conferences bridging the areas of computational\, mathematical\, statistical and biological sciences. The conference features keynote talks by preeminent scientists in life sciences\, proceeding presentations of peer-reviewed research papers in computational biology\, and poster sessions on the latest research progress. \nThe conference series aims at attracting research contributions in all areas of computational molecular biology\, including but not limited to: molecular sequence analysis; recognition of genes and regulatory elements; molecular evolution; protein structure; structural genomics; analysis of gene expression; biological networks; sequencing and genotyping technologies; drug design; probabilistic and combinatorial algorithms; systems biology; computational proteomics; structural and functional genomics; information systems for computational biology and imaging. \nThe origins of the conference are in the mathematical and computational side of the field\, and there remains a certain focus on computational advances. However\, effective applications of computational techniques to achieve biological innovation remain a central aspect of the conference. \nThe RECOMB Conference Series (http://www.recomb.org/) was founded in 1997 to provide a scientific forum for theoretical advances in computational biology and their applications in molecular biology and medicine. \n  \nSchedule At-a-Glance \nApril 16th & 17th\, 2016- UCLA Campus\nSatellite Workshops:\nRECOMB-CCB\nRECOMB-Seq\nRECOMB-Genetics \nApril 17th\, 2016- Loews\, Santa Monica\n1:30 p.m. to 6 p.m.\nMike Waterman Symposium \nApril 17th\, 2016- Loews\, Santa Monica\n2:00pm – 5:00pm\nBioinformatics Flipped Course \nApril 17th\, 2016- Loews\, Santa Monica\n6:00 p.m. to 9 p.m.\nRECOMB 2016 Welcome Reception \nApril 18th-21st\, 2016- Loews\, Santa Monica\nRECOMB 2016 Conference
URL:https://bioinformatics.ucla.edu/event/recomb-2016/
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=UTC:20160411T160000
DTEND;TZID=UTC:20160411T170000
DTSTAMP:20160405T183803Z
CREATED:20160405T183803Z
LAST-MODIFIED:20160405T183803Z
UID:1734-1460390400-1460394000@bioinformatics.ucla.edu
SUMMARY:Eran Halperin Seminar
DESCRIPTION:Eran Halperin\, Ph.D. \nAssociate Professor of Computer Science\, and Molecular Microbiology and Biotechnology\, Tel Aviv University \n“Finding hidden signals in whole-genome genetic and epigenetic data” \nAbstract: Whole-genome genetic and epigenetic data sets the promise of detecting statistical correlations between phenotypes and genetic variants or epigenetic markers via genome-wide association studies (GWAS) and epigenome-wide association studies (EWAS). These correlations are useful for the generation of new hypotheses regarding the mechanisms involved\, and they can be used for disease prediction and prediction of treatment outcomes. GWAS and EWAS studies\, however\, are complicated by the fact that correlations between the phenotype and confounders such as age\, sex\, batch effects\, etc.\, may result in a large number of false positives. I will describe different approaches that deal with these confounders by directly predicting them from the data. Specifically\, I will show how one can predict cell type composition and ancestry from either genotype or methylation data\, using different variations of principal components analysis. These variations utilize the specific nature of each of the data types\, resulting in a better performance than standard PCA. I will demonstrate how these approaches can be useful in specific studies of whole-genome genetic and epigenetic data.
URL:https://bioinformatics.ucla.edu/event/eran-halperin-seminar/
LOCATION:Boyer Hall 159
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=UTC:20160404T160000
DTEND;TZID=UTC:20160404T170000
DTSTAMP:20160331T161142Z
CREATED:20160324T222728Z
LAST-MODIFIED:20160331T161142Z
UID:1053-1459785600-1459789200@bioinformatics.ucla.edu
SUMMARY:David Goldstein Seminar
DESCRIPTION:David Goldstein\, Ph.D. \nProfessor of Genetics and Development and Director of Institute of Genomic Medicine\, Columbia University \n“Precision Genetics for Precision Medicine” \n  \n 
URL:https://bioinformatics.ucla.edu/event/david-goldstein-seminar/
LOCATION:Boyer Hall 159
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=UTC:20160318T130000
DTEND;TZID=UTC:20160318T150000
DTSTAMP:20160321T164321Z
CREATED:20160209T160333Z
LAST-MODIFIED:20160321T164321Z
UID:1678-1458306000-1458313200@bioinformatics.ucla.edu
SUMMARY:CAREER PANEL AND NETWORKING EVENT
DESCRIPTION:  \nFor Graduate Students and Postdoctoral Scholars in the Quantitative and Computational Biosciences \n  \nFEATURED PANELISTS: \n\n\n\n\n BARKEN\, Exagen Diagnostics  \n\n\n\n\nLUZ OROZCO\, Genentech \n\n\n\n\nJASON CHEN\, Verge Genomics \n\n\n\n\n\n\n\n\nKRISHNA CHODAVARAPU\, Gilead Sciences  \n\n\n\n\n\n\n\n\nNICK FURLOTTE\, 23andMe 
URL:https://bioinformatics.ucla.edu/event/career-panel-and-networking-event/
LOCATION:Boyer Hall 159
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=UTC:20160308T050000
DTEND;TZID=UTC:20160308T180000
DTSTAMP:20160308T165924Z
CREATED:20160308T165924Z
LAST-MODIFIED:20160308T165924Z
UID:1700-1457413200-1457460000@bioinformatics.ucla.edu
SUMMARY:Bioinformatics Minor information meeting
DESCRIPTION:The UCLA Bioinformatics Minor program encourages all students currently enrolled as program minors as well as those who may be interested in learning more about the Bioinformatics minor as well as research opportunities in Bioinformatics to attend our quarterly information session on Tuesday\, March 8th at 5-6pm in Boelter Hall 4760. \nProgram faculty as well as current Bioinformatics undergraduate students involved in research will host this town hall style meeting to provide information about the bioinformatics minor and information on how to get involved in Bioinformatics research projects at UCLA. \nLight refreshments will be provided.
URL:https://bioinformatics.ucla.edu/event/bioinformatics-minor-information-meeting/
LOCATION:Boelter Hall 4760
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=UTC:20160307T160000
DTEND;TZID=UTC:20160307T170000
DTSTAMP:20160304T230351Z
CREATED:20160304T230351Z
LAST-MODIFIED:20160304T230351Z
UID:1055-1457366400-1457370000@bioinformatics.ucla.edu
SUMMARY:Elissa Chesler Seminar
DESCRIPTION:Elissa Chesler\, Ph.D. \nAssociate Professor\, Department of Bioinformatics and Computational Biology\, The Jackson Laboratory \n“Refining classification and characterization of behavior with integrative genetics and genomics” \n  \n 
URL:https://bioinformatics.ucla.edu/event/elissa-chesler-seminar/
LOCATION:Boyer Hall 159
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=UTC:20160229T160000
DTEND;TZID=UTC:20160229T170000
DTSTAMP:20160223T161347Z
CREATED:20160223T161347Z
LAST-MODIFIED:20160223T161347Z
UID:1051-1456761600-1456765200@bioinformatics.ucla.edu
SUMMARY:Jianzhi (George) Zhang Seminar
DESCRIPTION:Jianzhi (George) Zhang\, Ph.D. \nProfessor\, Department of Ecology and Evolutionary Biology\, University of Michigan \n“What determines the rate of protein sequence evolution and why” \n 
URL:https://bioinformatics.ucla.edu/event/jianzhi-george-zhang-seminar/
LOCATION:Boyer Hall 159
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=UTC:20160222T160000
DTEND;TZID=UTC:20160222T170000
DTSTAMP:20160216T212737Z
CREATED:20160216T212737Z
LAST-MODIFIED:20160216T212737Z
UID:1059-1456156800-1456160400@bioinformatics.ucla.edu
SUMMARY:Barbara Engelhardt Seminar
DESCRIPTION:Barbara Engelhardt\, Ph.D. \nAssistant Professor\, Department of Computer Science\, Princeton University \n“Context-specific gene co-expression networks and expression QTLs” \n  \n 
URL:https://bioinformatics.ucla.edu/event/barbara-engelhardt-seminar/
LOCATION:Boyer Hall 159
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=UTC:20160208T160000
DTEND;TZID=UTC:20160208T170000
DTSTAMP:20160208T161727Z
CREATED:20160208T161727Z
LAST-MODIFIED:20160208T161727Z
UID:1052-1454947200-1454950800@bioinformatics.ucla.edu
SUMMARY:Avi Ma'ayan Seminar
DESCRIPTION:Avi Ma’ayan\, Ph.D. \nProfessor\, Department of Pharmacology and Systems Therapeutics\, Mount Sinai \n“Data Integration for Systems Pharmacology” \n 
URL:https://bioinformatics.ucla.edu/event/avi-maayan-seminar/
LOCATION:Boyer Hall 159
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=UTC:20160203T120000
DTEND;TZID=UTC:20160203T140000
DTSTAMP:20160127T220936Z
CREATED:20160127T220936Z
LAST-MODIFIED:20160127T220936Z
UID:1658-1454500800-1454508000@bioinformatics.ucla.edu
SUMMARY:CTSI Seminar - Atul Butte
DESCRIPTION:
URL:https://bioinformatics.ucla.edu/event/ctsi-seminar-atul-butte/
LOCATION:NRB 132 Auditorium
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=UTC:20160202T080000
DTEND;TZID=UTC:20160301T170000
DTSTAMP:20160202T210444Z
CREATED:20160202T205954Z
LAST-MODIFIED:20160202T210444Z
UID:1667-1454400000-1456851600@bioinformatics.ucla.edu
SUMMARY:Bioinformatics T-Shirt Design Competition
DESCRIPTION:The Bioinformatics IDP is holding a T-shirt design contest.\nThe winning design will communicate the breadth\, creativity and excellence of Bioinformatics at UCLA. \nThe individual or team submitting the winning T-shirt design will win a $500 prize.\nThe winning design will be printed as T-shirts for the UCLA Bioinformatics community. \nAll members of the UCLA community are eligible to participate.\nThe design cannot include copyrighted images\, and should include the campus-approved logo\, either long or short (attached).\nThe design may include front and back of the T-shirt and may specify T-shirt style and color. \nEntries should be submitted as pdfs to Allison Taka (ataka@lifesci.ucla.edu).  The deadline is March 1.
URL:https://bioinformatics.ucla.edu/event/bioinformatics-t-shirt-design-competition/
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=UTC:20160201T160000
DTEND;TZID=UTC:20160201T170000
DTSTAMP:20160127T220543Z
CREATED:20160127T220543Z
LAST-MODIFIED:20160127T220543Z
UID:1054-1454342400-1454346000@bioinformatics.ucla.edu
SUMMARY:Erik Ingelsson Seminar
DESCRIPTION:Erik Ingelsson\, Ph.D. \nVisiting Professor\, Department of Medicine\, Stanford University \nProfessor\, Department of Medical Sciences\, Uppsala University\, Sweden \n“Human genomics and molecular epidemiology: Using large-scale methods to advance cardiovascular medicine” \n  \n 
URL:https://bioinformatics.ucla.edu/event/erik-ingelsson-seminar/
LOCATION:Boyer Hall 159
END:VEVENT
END:VCALENDAR