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January 2018

Penn Bioinformatics Forum – Jeff Barrett, PhD

January 25 @ 3:00 pm - 4:00 pm
Austrian Auditorium, CRB, 415 Curie Blvd.
Philadelphia, 19104
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Expanding the genetic architecture of neurodevelopment and autism Dr. Jeff Barrett Director, Open Targets Wellcome Trust Sanger Institute Abstract: Recent advances in scale and speed of DNA sequencing have transformed our understanding of a range of neurodevelopmental disorders, from autism spectrum disorders to profound intellectual disability with a wide range of physical comorbidities. I will describe two efforts that are beginning to shed light on the differences and similarities of genetic architecture across these disorders. The Deciphering Developmental Disorders study…

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February 2018

IBI Seminar: Danielle Mowery PhD, MS, MS

February 1 @ 3:00 pm - 4:00 pm
Reunion Hall, John Morgan Building, 3620 Hamilton Walk
Philadelphia, 19104
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"Supporting Clinical and Population Health Research with Natural Language Processing" Danielle Mowery PhD, MS, MS Post-doctoral Fellow | Department of Biomedical Informatics | University of Utah Health Science Officer | Informatics, Decision-Enhancement and Analytic Sciences Center (IDEAS 2.0) | George E Wahlen Veterans Affairs Medical Center Thursday, February 1, 2018 JMB Reunion Auditorium 3:00pm - 4:00pm Seminar Abstract: Textual data sources including clinical notes from electronic health records and posts from public social media platforms (e.g., Twitter and Reddit) provide…

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IBI/CIS Invited Seminar – Munmun De Choudhury, PhD

February 6 @ 3:00 pm - 4:30 pm
Wu & Chen Auditorium, Levine Hall, 3330 Walnut St
Philadelphia, PA 19104 United States
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Munmun De Choudhury, Ph.D. Assistant Professor, School of Interactive Computing Georgia Institute of Technology Transforming Mental Health Care with Social Media Abstract: Social media platforms continue to deeply intertwine with our lives. In this talk I will present a body of work demonstrating how social media can serve two purposes supporting our mental wellbeing. First, employing social media as a passive “sensor” of behaviors, emotion, socialization, and linguistic expression, I will highlight a series of projects that enable fine-grained and proactive…

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IBI Seminar: Dokyoon Kim, PhD

February 26 @ 11:00 am - 12:00 pm
Class of ’62 Auditorium, John Morgan Building, 3620 Hamilton Walk
Philadelphia, 19104
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"Multi-omics data integration for translational bioinformatics" Dokyoon Kim, PhD Assistant Professor, Biomedical & Translational Informatics Institute Geisinger Health System February 26, 2018 JMB Auditorium Class of 62' 11:00 a.m. -12:00 a.m. Seminar Abstract: Recent multi-omics data and clinical information emerging from a large-scale collaborative initiative, such as The Cancer Genome Atlas (TCGA), have provided exceptional opportunities to investigate the complex genetic basis of disease for improving the ability to diagnose, treat, and prevent cancer. The ultimate utility of our significant…

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IBI/CIS Invited Seminar -Eric Xing, PhD

February 27 @ 11:00 am - 12:30 pm
Glandt Forum, Singh Center for Nanotechnology, 3205 Walnut St
Philadelphia, PA 19104 United States
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Eric Xing, Ph.D. Professor, School of Computer Science Carnegie Mellon University PetuumMed: algorithm and system for EHR-based medical decision-making With the rapid growth of electronic health records (EHRs) and the advancement of machine learning technologies, needs for AI-enabled clinical decision-making support is emerging. In this talk, I will present some recent work toward these needs at Petuum Inc. where an integrative system that distills insights from large-scale and heterogeneous patient data, as well as learns and integrates medical knowledge from…

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Penn Bioinformatics Forum – Ryan Gutenkunst, PhD

February 28 @ 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 @ 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 @ 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 @ 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 @ 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 @ 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 @ 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
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 @ 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 @ 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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