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September 2017

IBI Seminar: Mathias Brochhausen Ph.D.

September 27, 2017 @ 3:00 pm - 4:00 pm
Reunion Hall, John Morgan Building, 3620 Hamilton Walk
Philadelphia, 19104
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"Advanced Knowledge Management for Biomedicine using Semantic Web Technologies" Mathias Brochhausen Ph.D., Associate Professor Department of Biomedical Informatics University of Arkansas for Biomedical Sciences September 27, 2017 JMB Reunion Auditorium 3:00p.m.-4:00p.m. Abstract: Recent years have seen an explosion of data available for biomedical research. Tackling big data has created a call for advanced knowledge management approaches in this field. Semantic Web Technologies, a set of methodologies allowing schema-free data representation and logical inference, provide huge opportunities to foster using computers…

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October 2017

Penn Bioinformatics Forum – Eytan Ruppin, MD, PhD

October 11, 2017 @ 3:00 pm - 4:00 pm
Austrian Auditorium, CRB, 415 Curie Blvd.
Philadelphia, 19104
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Genome wide identification of genes mediating cancer resistance to targeted and immune therapy Dr. Eytan Ruppin Professor, Center for Bioinformatics and Computational Biology & Dept. of Computer Science, the University of Maryland University of Maryland Abstract: Most patients with advanced cancer eventually acquire resistance to targeted therapies, spurring extensive efforts to identify molecular events mediating therapy resistance. Many of these events involve synthetic rescue (SR) interactions, where the reduction in cancer cell viability caused by targeted gene inactivation is rescued by the adaptive…

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November 2017

Penn Bioinformatics Forum – Will Noble, PhD

November 8, 2017 @ 3:00 pm - 4:00 pm
Austrian Auditorium, CRB, 415 Curie Blvd.
Philadelphia, 19104
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Machine learning and statistical challenges in protein mass spectrometry Dr. Will Noble Professor, Department of Genome Sciences &  Director, Computational Molecular Biology Program University of Washington Abstract: Bioinformatics is driven in large part by technological innovation, such as the advances in DNA sequencing for genomics. The field of proteomics is undergoing a similar, technology-driven transformation, as the field begins to switch from data-dependent acquisition to data-independent acquisition. I will explain this transformation and its implications for our understanding of the…

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December 2017

Penn Bioinformatics Forum – Eimear Kenny, PhD

December 6, 2017 @ 3:00 pm - 4:00 pm
Austrian Auditorium, CRB, 415 Curie Blvd.
Philadelphia, 19104
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Population Genomics in an Era of Precision Medicine Eimear Kenny, Ph.D. Assistant Professor in Genetics and Genomic Sciences Icahn School of Medicine at Mount Sinai Abstract: Achieving confidence in the causality of a disease locus is a complex task that often requires supporting data from both statistical genetics and clinical genomics. Here we describe approaches leveraging population-scale statistical genetics to identify and characterize genetic disorders in a large health system in New York City. First we utilize genomic data to uncover…

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January 2018

IBI/CIS Invited Seminar – Howard Chizeck, PhD

January 16 @ 3:00 pm - 4:30 pm
Wu & Chen Auditorium, Levine Hall, 3330 Walnut St
Philadelphia, PA 19104 United States
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Howard Jay Chizeck, PhD Professor of Electrical Engineering University of Washington Telerobotics: In Surgery, Underwater and in Space Abstract: Whenever tasks need to be done in environments that are too hostile or difficult for humans, but that require human judgement, telerobots provide a solution. Telerobots are appropriate for situations involving unsafe temperatures, chemical or biological hazards, radioactivity, lack of atmosphere or pressure extremes. They are also useful for manipulating very small objects, very large objects, or in situations where the…

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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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