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February 2018

Penn Bioinformatics Forum – Ryan Gutenkunst, PhD

February 28, 2018 @ 3:00 pm - 4:30 pm
BRB Auditorium, 421 Curie Blvd
Philadelphia, PA 19104 United States
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Ryan Gutenkunst, PhD Associate Professor, Molecular and Cellular Biology & of Ecology and Evolutionary Biology University of Arizona Mutation fitness effects across populations and proteins Abstract: The distribution of fitness effects (DFE) among new mutations quantifies how likely a mutation is to have severe, moderate, or minor effect. The DFE is a key determinant of how functional genetic variation is distributed among and within populations, and much research has focused on inferring the DFE from population genetic data. Here, we extend the…

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March 2018

IBI Seminar: H. Robert Frost, PhD

March 12, 2018 @ 2:00 pm - 3:00 pm
Reunion Hall, John Morgan Building, 3620 Hamilton Walk
Philadelphia, 19104
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"Analyzing high-dimensional genomic data through the lens of prior knowledge" March 12, 2018 JMB Reunion Hall Auditorium 2:00 p.m. -3:00 p.m. Seminar Abstract: Gene set testing, or pathway analysis, is an important bioinformatics technique that lets researchers step back from the level of individual genomic variables and explore associations for biologically meaningful groups of genes, e.g., genes involved in a single metabolic pathway. By focusing the analysis on a smaller number of functional gene sets, this approach can substantially improve…

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Penn Bioinformatics Forum – Christina Curtis, PhD

March 14, 2018 @ 3:00 pm - 4:30 pm
BRB Auditorium, 421 Curie Blvd
Philadelphia, PA 19104 United States
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Christina Curtis, PhD Assistant Professor of Medicine and Genetics Stanford University Co-Director of the Molecular Tumor Board, Stanford Cancer Institute Title: Quantifying the evolutionary dynamics of tumor progression and metastasis Abstract: Cancer results from the acquisition of somatic alterations in an evolutionary process that typically occurs over many years, much of which is occult. Understanding the evolutionary dynamics that are operative at different stages of progression in individual tumors might inform the earlier detection, diagnosis, and treatment of cancer. Although…

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IBI/CIS Invited Seminar – Greg Cooper, MD, PhD

March 20, 2018 @ 3:00 pm - 4:30 pm
337 Towne Building, 220 S. 33rd St.
Philadelphia, PA 19104 United States
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Greg Cooper, MD, PhD Professor, Department of Biomedical Informatics and of Intelligent Systems University of Pittsburgh Causal Network Discovery from Biomedical and Clinical Data Abstract: This talk will provide an introduction to concepts and methods for learning causal relationships in the form of causal networks from biomedical and clinical data, including solely observational data. Examples will be given of applying these methods to biomedical data. The talk will also provide pointers to software for learning causal networks from data, including…

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April 2018

Penn Bioinformatics Forum – Suchi Saria, PhD

April 11, 2018 @ 3:00 pm - 4:30 pm
Austrian Auditorium, CRB, 415 Curie Blvd.
Philadelphia, 19104
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Suchi Saria, PhD John C. Malone Assistant Professor of Computer Science Johns Hopkins University Individualizing Healthcare with Machine Learning Abstract: Healthcare is rapidly becoming a data-intensive discipline, driven by increasing digitization of health data, novel measurement technologies, and new policy-based incentives. Critical decisions about whom and how to treat can be made more precisely by layering an individual’s data over that from a population. In this talk, I will begin by summarizing open challenges associated with learning models from these data. Next, I will…

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May 2018

Penn Bioinformatics Forum – Peter Kharchenko, PhD

May 2, 2018 @ 3:00 pm - 4:30 pm
BRB Auditorium, 421 Curie Blvd
Philadelphia, PA 19104 United States
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Peter Kharchenko, Ph.D. Assistant Professor of Biomedical Informatics Harvard University Exploring human brain with single-cell transcriptional and epigenetic measurements Abstract: Single-cell genomic protocols provide powerful means for characterization of cell type and cell state composition in complex biological tissues. Human brain is by far the most complex organ, consisting of 100 billion spatially organized and functionally connected neurons, complemented by over a trillion other cells. In an effort to characterize major cell types of the human brain we used single-cell…

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2018 Institute for Biomedical Informatics/Genomics and Computational Biology Retreat

May 30, 2018 @ 8:00 am - 5:00 pm
College of Physicians of Philadelphia, 19 S. 22nd St.
Philadelphia, PA 19103 United States
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  Registration is closed.

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Informatics Day 2018

May 31, 2018
BRB Auditorium, 421 Curie Blvd
Philadelphia, PA 19104 United States
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Registration is open, but space is limited. To register, click here. Keynote lecture: Hamish Fraser, MBChB, MSc Associate Professor of Medical Science Brown University “Challenges and strategies in effective scale up OpenMRS and other eHealth systems in resource poor environments” Other speakers include: Mary Regina Boland, PhD, Assistant Professor of Informatics, PSOM Kathy Bowles, PhD, RN, FAAN, FACMI, Professor of Nursing Bimal R. Desai, MD, MBI, FAAP, Assistant Vice President & Chief Health Informatics Officer, CHOP Michael Draugelis, Chief Data…

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September 2018

Penn Bioinformatics Forum – Nir Yosef, PhD

September 21, 2018 @ 8:00 am - 5:00 pm

Nir Yosef, Ph.D. Assistant Professor of Electrical Engineering & Computer Science University of California Berkeley Details TBA

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October 2018

Penn Bioinformatics Forum – Gill Bejerano, PhD

October 3, 2018 @ 3:00 pm - 4:30 pm
Austrian Auditorium, CRB, 415 Curie Blvd.
Philadelphia, 19104
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Gill Bejerano, Ph.D. Associate Professor of Developmental Biology, Computer Science, Pediatrics, Biomedical Data Science Stanford University Automating and democratizing the future of genetic diagnosis Abstract: I will describe a number of works from our lab, focusing on Mendelian/monogenic disease diagnosis. The works combine elements from medical genetics, genomics, machine learning, natural language processing, cryptography and more. Taken together, these works start to paint a compelling picture for the future of genetic diagnosis. The talk will be aimed at both practicing…

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November 2018

Penn Bioinformatics Forum – Melissa Gymrek, PhD

November 28, 2018 @ 3:00 pm - 4:30 pm
BRB Auditorium, 421 Curie Blvd
Philadelphia, PA 19104 United States
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Melissa Gymrek, Ph.D. Assistant Professor of Computer Science and Engineering, Medicine University of California San Diego Dissecting the contribution of repetitive genetic variation to human traits Recent studies have made substantial progress in identifying genetic variants associated with disease and molecular phenotypes in humans. However, these studies have primarily focused on single nucleotide polymorphisms (SNPs), ignoring more complex variants that have been shown to play important functional roles. Here, I focus on short tandem repeats (STRs), one of the most…

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December 2018

CANCELED: Penn Bioinformatics Forum – Joel Dudley, PhD

December 5, 2018 @ 3:00 pm - 4:30 pm
Austrian Auditorium, CRB, 415 Curie Blvd.
Philadelphia, 19104
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This event has been canceled due to scheduling conflicts.

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January 2019

Penn Bioinformatics Forum – Sarah Pendergrass, PhD, MS

January 23 @ 3:00 pm - 4:30 pm
Austrian Auditorium, CRB, 415 Curie Blvd.
Philadelphia, 19104
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Sarah Pendergrass, Ph.D., M.S. Assistant Professor of Biomedical & Translational Informatics Geisinger Redefining our Understanding of Disease, Outcome, Phenotype and the Impact of Genetic Architecture through Electronic Health Records Disease is the sum of many parts, and risk, progression, and severity is not the same for each person. Working with large, phenotypically rich datasets, such as electronic health records (EHRs), we can leverage complexity to redefine our understanding of disease, outcome, and phenotype. Advancing how we use ever-expanding EHR data…

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February 2019

Penn Bioinformatics Forum – Tandy Warnow, PhD

February 13 @ 3:00 pm - 4:30 pm
BRB Auditorium, 421 Curie Blvd
Philadelphia, PA 19104 United States
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Tandy Warnow, PhD Professor of Computer Science, Bioengineering University of Illinois Improving Bioinformatics Analyses using Ensembles of Hidden Markov Models Abstract: Profile Hidden Markov Models (HMMs) are statistical models that are in wide use in bioinformatics. In this talk I will present a novel way of using HMMs that improves many bioinformatics analyses. The key approach is to represent a multiple sequence alignment using a collection of profile HMMs, and then use this complex model to analyze new sequences. As…

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March 2019

Penn Bioinformatics Forum – Kelly Frazer, PhD

March 12 @ 8:00 am - 5:00 pm
BRB Auditorium, 421 Curie Blvd
Philadelphia, PA 19104 United States
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Kelly Frazer, PhD Professor of Pediatrics Division Chief, Genome Information Sciences Director, Institute for Genomic Medicine University of California, San Diego Using iPS cells and derived cell types to functionally annotate human genetic variants Abstract: Over the past six years, Dr. Frazer’s lab has systematically derived and characterized a unique collection of iPSC lines from 222 individuals – referred to as iPSCORE (iPSC Collection for Omic Research). iPSCORE is currently being used to analyze genotype – molecular phenotype associations in…

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