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CALSCALE:GREGORIAN
METHOD:PUBLISH
X-ORIGINAL-URL:https://bioinformatics.ucla.edu
X-WR-CALDESC:Events for UCLA | Bioinformatics
REFRESH-INTERVAL;VALUE=DURATION:PT1H
X-Robots-Tag:noindex
X-PUBLISHED-TTL:PT1H
BEGIN:VTIMEZONE
TZID:UTC
BEGIN:STANDARD
TZOFFSETFROM:+0000
TZOFFSETTO:+0000
TZNAME:UTC
DTSTART:20150101T000000
END:STANDARD
END:VTIMEZONE
BEGIN:VEVENT
DTSTART;TZID=UTC:20170123T160000
DTEND;TZID=UTC:20170123T170000
DTSTAMP:20170109T220607Z
CREATED:20170109T220607Z
LAST-MODIFIED:20170109T220607Z
UID:2327-1485187200-1485190800@bioinformatics.ucla.edu
SUMMARY:Anshul Kundaje Seminar
DESCRIPTION:
URL:https://bioinformatics.ucla.edu/event/anshul-kundaje-seminar/
LOCATION:Boyer Hall 159
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=UTC:20170119T040000
DTEND;TZID=UTC:20170119T170000
DTSTAMP:20170119T181929Z
CREATED:20170119T181929Z
LAST-MODIFIED:20170119T181929Z
UID:2330-1484798400-1484845200@bioinformatics.ucla.edu
SUMMARY:Undergraduate Bioinformatics Info Session
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 Thursday January 19th from 4-5pm in Boelter Hall 4760.\n\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.\n\nIn addition\, if you are an undergraduate student and want to present a poster\, there will be an opportunity to present posters. If you have already made one in the past please bring it with you to the event.  Please contact eeskin@cs.ucla.edu if you are bringing a poster so we can have an easel for you.\n\nLight refreshments will be provided.
URL:https://bioinformatics.ucla.edu/event/undergraduate-bioinformatics-info-session/
LOCATION:Boelter Hall 4760
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=UTC:20170109T160000
DTEND;TZID=UTC:20170109T170000
DTSTAMP:20170109T220531Z
CREATED:20161220T191558Z
LAST-MODIFIED:20170109T220531Z
UID:2323-1483977600-1483981200@bioinformatics.ucla.edu
SUMMARY:David Heckerman Seminar
DESCRIPTION:
URL:https://bioinformatics.ucla.edu/event/david-heckerman-seminar/
LOCATION:Boyer Hall 159
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=UTC:20161128T160000
DTEND;TZID=UTC:20161128T170000
DTSTAMP:20161121T163942Z
CREATED:20161103T165427Z
LAST-MODIFIED:20161121T163942Z
UID:2241-1480348800-1480352400@bioinformatics.ucla.edu
SUMMARY:Jessica Wu Seminar
DESCRIPTION:
URL:https://bioinformatics.ucla.edu/event/jessica-wu-seminar/
LOCATION:Boyer Hall 159
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=UTC:20161121T160000
DTEND;TZID=UTC:20161121T170000
DTSTAMP:20161108T190257Z
CREATED:20161103T165221Z
LAST-MODIFIED:20161108T190257Z
UID:2240-1479744000-1479747600@bioinformatics.ucla.edu
SUMMARY:Lauren Weiss Seminar
DESCRIPTION:
URL:https://bioinformatics.ucla.edu/event/lauren-weiss-seminar/
LOCATION:Boyer Hall 159
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=UTC:20161114T160000
DTEND;TZID=UTC:20161114T170000
DTSTAMP:20161109T202754Z
CREATED:20161019T233725Z
LAST-MODIFIED:20161109T202754Z
UID:2136-1479139200-1479142800@bioinformatics.ucla.edu
SUMMARY:Bin Zhang Seminar
DESCRIPTION:Abstract: Network biology has been increasingly utilized to model large-scale Omics data for its great potential to identify novel key variables and interacting pathways underlying a biological function\, system or state under examination. Often a single type of molecular networks (gene coexpression network\, gene causal network\, protein interaction network) is used for a particular Omics study. For complex biological systems or diseases\, any single type of networks may be insufficient to fully characterize the underlying Omics data. Multiscale network modeling emerges as a more powerful way to dissect complex molecular interactions and regulations in such complex systems or diseases for identification of novel pathways and targets that are essential to maintain biological functions\, initiate disease process or drive disease progression. In this talk\, I will introduce our latest progresses on constructing and analyzing multiscale molecular networks including weighted interaction network analysis (WINA)\, multiscale embedded gene coexpression network analysis (MEGENA) and differential gene correlation analysis (DGCA)\, and highlight their applications to cancer\, diabetes and neurodegenerative diseases.
URL:https://bioinformatics.ucla.edu/event/bin-zhang-seminar/
LOCATION:Boyer Hall 159
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=UTC:20161107T160000
DTEND;TZID=UTC:20161107T170000
DTSTAMP:20161025T193716Z
CREATED:20161019T233554Z
LAST-MODIFIED:20161025T193716Z
UID:2135-1478534400-1478538000@bioinformatics.ucla.edu
SUMMARY:Wenyi Wang Seminar
DESCRIPTION:
URL:https://bioinformatics.ucla.edu/event/wenyi-wang-seminar/
LOCATION:Boyer Hall 159
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=UTC:20161031T160000
DTEND;TZID=UTC:20161031T170000
DTSTAMP:20161018T234845Z
CREATED:20160926T233913Z
LAST-MODIFIED:20161018T234845Z
UID:2080-1477929600-1477933200@bioinformatics.ucla.edu
SUMMARY:Graham McVicker Seminar
DESCRIPTION:
URL:https://bioinformatics.ucla.edu/event/graham-mcvicker-seminar/
LOCATION:Boyer Hall 159
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=UTC:20161024T160000
DTEND;TZID=UTC:20161024T170000
DTSTAMP:20161010T171130Z
CREATED:20161010T171130Z
LAST-MODIFIED:20161010T171130Z
UID:2109-1477324800-1477328400@bioinformatics.ucla.edu
SUMMARY:Kimberly Siegmund Seminar
DESCRIPTION:
URL:https://bioinformatics.ucla.edu/event/kimberly-siegmund-seminar/
LOCATION:Boyer Hall 159
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=UTC:20161010T170000
DTEND;TZID=UTC:20161010T180000
DTSTAMP:20161005T235350Z
CREATED:20161005T235350Z
LAST-MODIFIED:20161005T235350Z
UID:2104-1476118800-1476122400@bioinformatics.ucla.edu
SUMMARY:Bioinformatics Minor Information Session
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 Monday October 10th from 5-6pm in Boelter Hall 4760.\n\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.\n\nIn addition\, there will be an opportunity to present posters. If you have already made one in the past please bring it with you to the event.\n\nLight refreshments will be provided.
URL:https://bioinformatics.ucla.edu/event/bioinformatics-minor-information-session/
LOCATION:Boelter Hall 4760
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=UTC:20161010T160000
DTEND;TZID=UTC:20161010T170000
DTSTAMP:20161005T235533Z
CREATED:20160926T193945Z
LAST-MODIFIED:20161005T235533Z
UID:2078-1476115200-1476118800@bioinformatics.ucla.edu
SUMMARY:Saket Navlakha Seminar
DESCRIPTION:Dr. Saket Navlakha\nAssistant Professor\, Center for Integrative Biology\nSalk Institute for Biological Studies \n  \nTalk title: “Network design principles from developing brains and plants”
URL:https://bioinformatics.ucla.edu/event/saket-navlakha-seminar/
LOCATION:Boyer Hall 159
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=UTC:20160926T160000
DTEND;TZID=UTC:20160926T170000
DTSTAMP:20160923T170046Z
CREATED:20160921T232717Z
LAST-MODIFIED:20160923T170046Z
UID:2037-1474905600-1474909200@bioinformatics.ucla.edu
SUMMARY:Semyon Kruglyak Seminar
DESCRIPTION: 
URL:https://bioinformatics.ucla.edu/event/semyon-kruglyak-seminar/
LOCATION:Boyer Hall 159
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=UTC:20160920T080000
DTEND;TZID=UTC:20160920T190000
DTSTAMP:20160923T165405Z
CREATED:20160630T233737Z
LAST-MODIFIED:20160923T165405Z
UID:1911-1474358400-1474398000@bioinformatics.ucla.edu
SUMMARY:QCB Annual Retreat
DESCRIPTION:
URL:https://bioinformatics.ucla.edu/event/qcb-annual-retreat/
LOCATION:Skirball Cultural Center\, 2701 N Sepulveda Blvd.\, Los Angeles\, 90049\, United States
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=UTC:20160901T120000
DTEND;TZID=UTC:20160901T140000
DTSTAMP:20160815T232355Z
CREATED:20160815T232313Z
LAST-MODIFIED:20160815T232355Z
UID:1929-1472731200-1472738400@bioinformatics.ucla.edu
SUMMARY:Larry Lam Dissertation Defense
DESCRIPTION:DISSERTATION DEFENSE \nLarry Lam \n\nTitle: Computational Methods for the Analysis of DNA Methylations and Gene Expression Data \n\nCommittee:  \nMatteo Pellegrini\, Committee Chair\nThomas Graeber\nJason Ernst\nDaniel Ruderman
URL:https://bioinformatics.ucla.edu/event/larry-lam-dissertation-defense/
LOCATION:Boyer Hall 130
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=UTC:20160812T110000
DTEND;TZID=UTC:20160812T130000
DTSTAMP:20160812T224442Z
CREATED:20160810T235529Z
LAST-MODIFIED:20160812T224442Z
UID:1967-1470999600-1471006800@bioinformatics.ucla.edu
SUMMARY:B.I.G. Summer 2016 Poster Session
DESCRIPTION: 
URL:https://bioinformatics.ucla.edu/event/b-i-g-summer-2016-poster-session/
LOCATION:Boyer Hall 159
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=UTC:20160810T160000
DTEND;TZID=UTC:20160810T170000
DTSTAMP:20160810T191028Z
CREATED:20160809T192903Z
LAST-MODIFIED:20160810T191028Z
UID:1962-1470844800-1470848400@bioinformatics.ucla.edu
SUMMARY:Kin Fai Au Seminar
DESCRIPTION:Kin Fai Au\, Ph.D. \nAssistant Professor of Internal Medicine and Biostatistics\, University of Iowa \n“Transcriptome analysis by hybrid sequencing” \n 
URL:https://bioinformatics.ucla.edu/event/kin-fai-au-seminar/
LOCATION:Boelter Hall 4760
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=UTC:20160802T110000
DTEND;TZID=UTC:20160802T120000
DTSTAMP:20160801T164929Z
CREATED:20160801T164929Z
LAST-MODIFIED:20160801T164929Z
UID:1961-1470135600-1470139200@bioinformatics.ucla.edu
SUMMARY:QCBio/Big Summer Special Seminar: Richard A. Long Seminar
DESCRIPTION:Richard A. Long\, Ph.D.  \nAssociate Professor of Biological Sciences\, College of Science and Technology \nFlorida A&M University \n  \nMoving Towards an (Eco)Systems Approach of Understanding Vibrio cholerae \nThe fields of aquatic microbial ecology and data analytics developed in parallel and often intertwined. Vibrio cholerae\, a waterborne pathogen\, arguably is the most studied aquatic bacterium. Yet we lack an integrated wholistic understanding of the bacterium as it navigates between two complex and contrasting ecosystems.  Will Big Data Analytics pull all together?
URL:https://bioinformatics.ucla.edu/event/qcbiobig-summer-special-seminar-richard-a-long-seminar/
LOCATION:Boyer Hall 130
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=UTC:20160727T160000
DTEND;TZID=UTC:20160727T170000
DTSTAMP:20160725T180502Z
CREATED:20160725T180502Z
LAST-MODIFIED:20160725T180502Z
UID:1947-1469635200-1469638800@bioinformatics.ucla.edu
SUMMARY:Erez Levanon Seminar
DESCRIPTION:Erez Levanon\, Ph.D. \nThe Mina & Everard Faculty of Life Sciences\, Bar-Ilan University Ramat Gan\, Israel \n“DNA and RNA Editing of Retrotransposons Accelerate Mammalian Genome Evolution” \nHost: Dr. Grace Xiao \n  \n  \n 
URL:https://bioinformatics.ucla.edu/event/erez-levanon-seminar/
LOCATION:Boyer Hall 159
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=UTC:20160725T130000
DTEND;TZID=UTC:20160725T153000
DTSTAMP:20160728T182233Z
CREATED:20160728T182233Z
LAST-MODIFIED:20160728T182233Z
UID:1953-1469451600-1469460600@bioinformatics.ucla.edu
SUMMARY:GPB CSU Summer Symposium & Graduate Fair
DESCRIPTION:  \nThe Graduate Programs in Bioscience is proud to host the first CSU Summer Symposium at UCLA! At this event\, UCLA Home Areas / Departments\, Faculty and campus resource centers will be advertising their programs / services to local CSU students and UCLA Summer Program participants. Following the Grad Fair\, the CSU Symposium poster session will highlight research being conducted by Cal State Students who participate in capstone research programs. \nEvent Details\nDate: July 25\, 2016\nTime: 1:00 – 3:30 PM\nLocation: Ackerman Grand Ball Room \n 
URL:https://bioinformatics.ucla.edu/event/gpb-csu-summer-symposium-graduate-fair/
LOCATION:Ackerman Grand Ballroom
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=UTC:20160720T080000
DTEND;TZID=UTC:20160812T170000
DTSTAMP:20160623T170655Z
CREATED:20160623T164937Z
LAST-MODIFIED:20160623T170655Z
UID:1862-1469001600-1471021200@bioinformatics.ucla.edu
SUMMARY:UCLA B.I.G. Summer 2016
DESCRIPTION:Overview \nThe UCLA Institute for Quantitative and Computational Biosciences (QCB)\, is committed to training undergraduates who are interested in learning about Bioinformatics and Genomics – skillets that are critical for 21st century Biomedical research and Precision Medicine. \nThe Bruins in Genomics (B.I.G.) Summer program includes next generation sequencing analysis workshops\, weekly science talks by researchers\, a weekly student journal club\, professional development seminars\, social activities\, concluding poster sessions\, and an optional GRE test prep course. \n  \nMore information can be found here: http://qcb.ucla.edu/big-summer/
URL:https://bioinformatics.ucla.edu/event/ucla-b-i-g-summer-2016/
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=UTC:20160718T080000
DTEND;TZID=UTC:20160812T170000
DTSTAMP:20160524T231050Z
CREATED:20160524T231050Z
LAST-MODIFIED:20160524T231050Z
UID:1839-1468828800-1471021200@bioinformatics.ucla.edu
SUMMARY:UCLA Computational Genomics Summer Institute
DESCRIPTION:Overview \nBiological sciences have been transformed over the past two decades by the development of technologies capable of performing large-scale measurements of cellular states. In particular\, DNA sequencing instruments have undergone an extraordinary increase in efficiency during the past few years that has reduced the time and cost required to sequence billions of bases by several orders of magnitude. This is revolutionizing the scale and potential applications of genomic studies\, and creating an enormous need to develop mathematical and computational infrastructures to meet emerging data analysis challenges. To name just a few examples\, applications requiring the development of novel mathematical and statistical frameworks include the reconstruction of RNA transcript populations\, identifying sequence variations (both single-nucleotide and segmental) and exploring their disease associations\, locating the sites of protein-DNA interactions\, elucidating population histories\, and reconstructing microbial communities that colonize particular hosts or environmental niches. The goal of this long program is to bring together mathematical and computational scientists\, sequencing technology developers in both industry and academia\, and the biologists who use the instruments for particular research applications. This presents a unique opportunity to foster interactions between these three communities over an extended period of time and advance the mathematical foundations of this exciting field. \nThe development of high-throughput genomic technology has transformed biomedical sciences and provides limitless potential for developing new treatments for disease. However\, analyzing the data generated by these technologies requires tremendous computational resources and significant computational expertise by the researchers. \nThe UCLA Computational Genomics Summer Institute (CGSI) will provide two programs in the summer of 2016. \nCGSI Short Course: July 18 – 22 \nThe short course provides didactic training in computational and statistical genomic methods development and is relevant to a wide range of trainees who are interested in developing or enhancing the methodology development aspect of their research program.  The course is taught by program faculty who are world leading experts in computational and statistical genomics methodology development.  The program consists of full days of lectures covering a wide variety of techniques are cutting edge methodology. \nCGSI Long Course July 18- August 12 \nThe long course provides additional training to more senior trainees including senior graduate students and post-docs through a research residence program at UCLA where they will have the opportunity to interact with world leading researchers while at UCLA.  The program consists of a mix of structured training programs as well as flexible time to interact and collaborate with other participants and program faculty. \nDeadline to apply is March 1\, 2016. Early applications are encouraged and applicants will be admitted on a rolling basis. If you are interested in participating in the program\, please complete the UCLA CGSI Application Form. The registration fee for the program will be $550 and applicants who are accepted will be asked to pay the fee at the time of registration. \nMore information can be found here: http://computationalgenomics.bioinformatics.ucla.edu
URL:https://bioinformatics.ucla.edu/event/ucla-computational-genomics-summer-institute/
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=UTC:20160705T133000
DTEND;TZID=UTC:20160705T153000
DTSTAMP:20160622T171016Z
CREATED:20160622T170848Z
LAST-MODIFIED:20160622T171016Z
UID:1861-1467725400-1467732600@bioinformatics.ucla.edu
SUMMARY:Diego Ortega Del Vecchyo Dissertation Defense
DESCRIPTION:DISSERTATION DEFENSE \nDiego Ortega Del Vecchyo \n  \nTitle: Demography-aware inference of the strength of natural selection \n  \nCommittee:  \nKirk Lohmueller\, Committee Co-chair\nJohn Novembre\, Committee Co-chair\nKenneth Lange\nJanet Sinsheimer\nRobert Wayne \n 
URL:https://bioinformatics.ucla.edu/event/diego-ortega-del-vecchyo-dissertation-defense/
LOCATION:Boyer Hall 159
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=UTC:20160701T170000
DTEND;TZID=UTC:20160701T190000
DTSTAMP:20160630T232057Z
CREATED:20160630T232057Z
LAST-MODIFIED:20160630T232057Z
UID:1908-1467392400-1467399600@bioinformatics.ucla.edu
SUMMARY:QCB Social Hour
DESCRIPTION:
URL:https://bioinformatics.ucla.edu/event/qcb-social-hour/
LOCATION:Boyer Hall Patio
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=UTC:20160601T090000
DTEND;TZID=UTC:20160601T161500
DTSTAMP:20160601T203846Z
CREATED:20160601T203846Z
LAST-MODIFIED:20160601T203846Z
UID:1846-1464771600-1464797700@bioinformatics.ucla.edu
SUMMARY:QCB Annual Symposium 2016
DESCRIPTION:2016 Annual Symposium \nExploring the Frontiers of Biomedical Big Data\n \nhosted by The Institute for Quantitative and Computational Biosciences \n 
URL:https://bioinformatics.ucla.edu/event/qcb-annual-symposium-2016/
END:VEVENT
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
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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
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