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June 2016

Penn Bioinformatics Forum – Ben Raphael, PhD

June 8, 2016 @ 3:00 pm - 4:00 pm
BRB Auditorium, 421 Curie Blvd
Philadelphia, PA 19104 United States
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Penn Bioinformatics Forum – Ben Raphael, PhD

June 8, 2016 @ 3:00 pm - 4:00 pm
BRB Auditorium, 421 Curie Blvd
Philadelphia, PA 19104 United States
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Algorithms for Cancer Genome Interpretation and Evolution

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2016 Institute for Biomedical Informatics/Genomics and Computational Biology Retreat

June 13, 2016 @ 8:00 am - 5:00 pm

Click here to register for the 2016 Retreat.

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September 2016

Penn Bioinformatics Forum – Mark Gerstein, PhD

September 7, 2016 @ 3:00 pm - 4:00 pm
Austrian Auditorium, CRB, 415 Curie Blvd.
Philadelphia, 19104
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Analysis of Personal Genomics

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October 2016

Penn Bioinformatics Forum – Debora Marks, PhD

October 5, 2016 @ 3:00 pm - 4:00 pm
Austrian Auditorium, CRB, 415 Curie Blvd.
Philadelphia, 19104
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Molecular structure and organism fitness from genomic sequences Debora Marks, PhD Assistant Professor, Department of Systems Biology Director, Raymond and Beverly Sackler Laboratory of Computational Biology Harvard Medical School Abstract: The evolutionary trajectories of biological sequences are propelled by mutation and whittled away by selection to maintain function. Present day sequences can therefore be regarded as the outcomes of millions of evolutionary experiments that record functional constraints in the genotype-phenotype map. In this talk I will introduce computational methods that,…

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IBI Seminar- Matthew K. Breitenstein, Ph.D.

October 10, 2016 @ 10:00 am - 11:00 am
Class of ’62 Auditorium, John Morgan Building, 3620 Hamilton Walk
Philadelphia, 19104
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" Informatics in the translational science of metformin repurposing" Matthew K. Breitenstein, Ph.D. Research Fellow - Cancer Genetic Epidemiology Training Program Department of Health Sciences Research Mayo Clinic October 10, 2016 10:00 a.m. JMB Class of 62 Abstract: Medication exposure events occurring in populations serve as powerful molecular probes to develop precision medicine knowledge and elucidate novel biological insights. The rapid advancement and increasing scale of electronic health records (EHR) and biorepository resources create an exciting environment with an increasing…

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November 2016

Penn Bioinformatics Forum – Molly Przeworksi, PhD

November 16, 2016 @ 3:00 pm - 4:00 pm
BRB Auditorium, 421 Curie Blvd
Philadelphia, PA 19104 United States
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Of mice, men, and birds: mechanisms and evolution of recombination hotspots

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Health Informatics Speaker Series – Terry Fairbanks, MD, MS and Raj Ratwani, PhD

November 29, 2016 @ 12:00 pm - 1:00 pm
Stokes Auditorium, Children’s Hospital of Philadelphia, 34th Street and Civic Center Blvd
Philadelphia, PA 19104 United States
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Human Factors is focused on understanding human capabilities and designing the technology, systems, and processes around us to meet these capabilities. While many other high-risk industries have embraced human factors the application of human factors in healthcare is in its infancy. The speakers will describe the importance of human factors and safety science, describe human factors principles with examples, and address the culture of safety. The speakers will also focus on the application of human factors to health information technology…

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December 2016

Penn Bioinformatics Forum – Rachel Karchin, PhD

December 7, 2016 @ 3:00 pm - 4:00 pm
BRB Auditorium, 421 Curie Blvd
Philadelphia, PA 19104 United States
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Evaluating the Evaluation of Cancer Driver Genes Dr. Rachel Karchin Associate Professor, William R. Brody Faculty Scholar Johns Hopkins University Abstract: Numerous methods have been developed to identify driver genes, but evaluation of the performance of these methods is hindered by the lack of a gold standard.  I will discuss an evaluation framework that can be applied to driver gene prediction methods.  Most current methods do not adequately account for heterogeneity in the number of mutations expected by chance and…

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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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