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December 2016

IBI Seminar: Mary Regina Boland, MA

December 13, 2016 @ 3:00 pm - 4:00 pm
Reunion Hall, John Morgan Building, 3620 Hamilton Walk
Philadelphia, 19104
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"A Systems-Level Approach to Understand the Seasonal Factors of Early Development with Clinical and Pharmacological Applications" Mary Regina Boland, MA Pre-doctoral Precision Medicine Fellow Department of Biomedical Informatics, Columbia University December 13, 2016 3:00 p.m. JMB Reunion Hall Auditorium   Abstract: Developmental defects occur in 100,000 to 200,000 children born each year in the United States of America. 97% of these defects are from unidentified causes. Many fetal outcomes (e.g., developmental defects), result from interactions between genetic and environmental factors. The lifetime effects from prenatal exposures with low…

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January 2017

Penn Bioinformatics Forum – Chris Cotsapas

January 18 @ 3:00 pm - 4:00 pm
BRB Auditorium, 421 Curie Blvd
Philadelphia, PA 19104 United States
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Dr. Chris Cotsapas Associate Professor of Neurology and of Genetics, Yale School of Medicine Visiting Scientist, Broad Institute of Harvard and MIT Visiting Scholar, Massachusetts General Hospital Identifying Causal Genes Driving Autoimmune Disease Abstract: Large-scale genetic studies have uncovered thousands of loci mediating risk to a wide variety of diseases, including the autoimmune diseases, where lack of self-tolerance leads to debilitating and often fatal destruction of specific organs and tissues by the immune system in ~8% of the population. The…

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IBI Seminar: Po-Yin Yen, PhD, RN

January 25 @ 10:00 am - 11:00 am
Class of ’62 Auditorium, John Morgan Building, 3620 Hamilton Walk
Philadelphia, 19104
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"Applied Clinical Informatics Research: Improve Clinical Practice in the Health IT Era via Clinical Workflow Analysis, Socio-Technical Evaluation, and Article Network Visualization​" Po-Yin Yen, PhD, RN Assistant Professor - Clinical, Department of Biomedical Informatics (BMI) Clinical Nurse Scientist, Wexner Medical Center Adjunct Assistant Professor, College of Nursing Director, BMI Summer Internship Program The Ohio State University January 25, 2017 10:00 a.m. JMB Class of 62' Abstract: With the accelerated Health Information Technology (Health IT) implementation across the nation, it is important to understand the usage and the impact of…

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February 2017

Penn Bioinformatics Forum – Goncalo Abecasis, PhD

February 8 @ 3:00 pm - 4:00 pm
BRB Auditorium, 421 Curie Blvd
Philadelphia, PA 19104 United States
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Sequencing and Analysis of 10,000s of Human Genomes: Challenges and Opportunities Dr. Goncalo Abecasis Felix E. Moore Collegiate Professor of Biostatistics Chair of the Department of Biostatistics University of Michigan School of Public Health Abstract: Rapid advances in genome sequencing and genotyping technology are enabling increasingly detailed analysis of human genetic variation. In the next year, we expect to analyze >50,000 deeply sequenced human genomes, corresponding to ~5 million billion bases of raw sequence data. The generation, transfer and analysis…

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March 2017

Penn Bioinformatics Forum – Alexis Battle, PhD

March 15 @ 3:00 pm - 4:00 pm
BRB Auditorium, 421 Curie Blvd
Philadelphia, PA 19104 United States
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Predicting the impact of rare regulatory variation The enormous increase in availability of full human genomic sequences presents great opportunity for understanding the impact of rare genetic variants. Based on current knowledge, however, we are still limited in our ability to interpret or predict regulatory consequences of rare variants. Association methods are inherently limited for variants observed in only one or a few individuals. Diverse genomic annotations such as growing resources of epigenetic data and have been shown to be…

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April 2017

Penn Bioinformatics Forum – Christina Kendziorski, PhD

April 19 @ 3:00 pm - 4:00 pm
Austrian Auditorium, CRB, 415 Curie Blvd.
Philadelphia, 19104
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Statistical methods for single-cell RNA-seq experiments Dr. Christina Kendziorski Professor, Department of Biostatistics & Medical Informatics University of Wisconsin - Madison Abstract: Single-cell RNA-sequencing (scRNA-seq) has emerged as a revolutionary tool that allows us to address scientific questions that were elusive just a few years ago. With the advantages of scRNA-seq come computational challenges that are just beginning to be addressed. In this talk, I will review statistical methods our group has developed for scRNA-seq experiments with a focus on…

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May 2017

WEBINAR – Introduction to Cytoscape: network visualization software

May 4 @ 12:00 pm - 1:30 pm

Introduction to Cytoscape: network visualization software   Date: Thursday May 4th, 12:00-1:30 PM   Description: Cytoscape is an open source network visualization tool that can be used to explore complex networks of genes, author co-publications, social networks, and more. This webinar will provide an introduction to some of the core functionality of Cytoscape, including the loading and manipulation of experimental data. For example, you will learn how to change visual properties to easily distinguish biologically significant relationships. Many of the…

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IBI Seminar: Bin Chen, PhD

May 11 @ 10:00 am - 11:00 am
Reunion Hall, John Morgan Building, 3620 Hamilton Walk
Philadelphia, 19104
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"Leveraging molecular and clinical data to transform cancer drug discovery in the era of precision medicine" Bin Chen, PhD Assistant Professor Department of Pediatrics and Institute for Computational Health Sciences University of California, San Francisco Thursday, May 11, 2017 JMB Reunion 10:00AM-11:00AM Seminar Abstract: Rapidly decreasing costs of molecular measurement technologies not only enable profiling of disease sample molecular features at different levels (e.g., transcriptome, proteome, metabolome), but also enable measuring of cellular signatures of individual drugs in clinically relevant…

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IBI Seminar: Li Shen, PhD

May 30 @ 10:00 am - 11:00 am
Class of ’62 Auditorium, John Morgan Building, 3620 Hamilton Walk
Philadelphia, 19104
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" Bioinformatics Strategies for Multidimensional Brain Imaging Genomics" Li Shen, PhD Associate Professor, Center for Neuroimaging, Department of Radiology and Imaging Sciences Associate Director, Center for Computational Biology and Bioinformatics Indiana University School of Medicine Tuesday, May 30, 2017 JMB Class of 62' 10:00am -11:00am Seminar Abstract: Imaging genomics is an emerging data science field, where integrative analysis of imaging and omics data is performed to provide new insights into the phenotypic characteristics and genetic mechanisms of normal or disordered…

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June 2017

IBI Seminar: Ryan J. Urbanowicz, Ph.D.

June 1 @ 10:00 am - 11:00 am
Reunion Hall, John Morgan Building, 3620 Hamilton Walk
Philadelphia, 19104
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"A new paradigm for data mining in bioinformatics: Embracing genetic heterogeneity" Ryan J. Urbanowicz, Ph.D. Research Associate, Department of Biostatistics, Epidemiology and Informatics University of Pennsylvania Thursday, June 1, 2017 JMB Reunion Auditorium 10:00am-11:00am Seminar Abstract: The goals for data mining in bioinformatics are to detect, model, interpret, and make predictions.  In genomics, this typically involves connecting predictive genotypes with a disease phenotype. However, this task is regularly confounded by the complexity of underlying patterns of association as well as…

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2017 Institute for Biomedical Informatics/Genomics and Computational Biology Retreat

June 8 @ 8:00 am - 5:00 pm
College of Physicians of Philadelphia, 19 S. 22nd St.
Philadelphia, PA 19103 United States
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Click here to register for the 2017 Retreat.

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August 2017

IBI Seminar: Melissa A. Haendel, Ph.D.

August 8 @ 10:00 am - 11:00 am
Class of ’62 Auditorium, John Morgan Building, 3620 Hamilton Walk
Philadelphia, 19104
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“Crossing the semantic chasm of despair: semantics for translational research” Melissa A. Haendel, Ph.D. Associate Professor, Dept. of Medical Informatics and Clinical Epidemiology Oregon Health and Science University Tuesday, August 8th JMB Class of 62’ Auditorium 10:00am – 11:00am Seminar Abstract: Deep phenotyping is the precise and comprehensive analysis of phenotypic abnormalities in which the individual components of the phenotype are observed and described. However, one of the biggest challenges is that the languages used to describe phenotypes are notoriously…

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September 2017

IBI Seminar: Mathias Brochhausen Ph.D.

September 27 @ 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 @ 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 @ 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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