KEYNOTE SPEAKER

Dr. David Fenstermacher is currently the Vice President R&D-Bioinformatics at Medimmune, LLC. With more than 30 years of research experience as a molecular biologist and bioinformaticist, he has held several academic appointments at multiple universities and participated in several national and international informatics projects.

During his eighteen years in biomedical informatics, David has designed and directed the implementation of numerous bioinformatics and biomedical informatics distributed computing systems to support basic, translational and clinical research, including multiple institution research projects. He has also designed data warehouses that integrate patient-level clinical data, genomics (genome-wide association studies, massively parallel sequencing, array-based technologies) and other ‘omics data to support studies focused on cancer and other human diseases. Data management systems designed by David have included: collection and integration of subject clinical data; data quality methodologies, development of web-based forms for input, storage and retrieval of clinical and research data, customized data representations using data governance principles and data sharing technologies. Most recent academic research focused on developing informatics resources that span the informatics continuum of Bioinformatics, Biomedical Informatics and Clinical/Medical Informatics specifically for precision medicine including clinical decision support, and health outcomes research.

Before joining MedImmune, David served as the Chief Research Information Officer for Virginia Commonwealth University (VCU) and was Founding Chair of the Department of Biomedical Informatics at the H. Lee Moffitt Cancer Center.

David received his B.S. in Biology from Bloomsburg University of Pennsylvania and his PhD in Molecular Biology and Genetics from the University of North Carolina at Chapel Hill.

- top -

LOCATION & PARKING

Click here to download PDF of the George Mason University map.

Parking: There is about a 5-10 minute walk from Mason Pond Parking Deck to Innovation Hall. Please plan accordingly.

- top -

THE STORY BEHIND THE SYMPOSIUM

Please check back soon for updates.

- top -

ISCB Hosts the Second Youth Bioinformatics Symposium

The International Society for Computational Biology (ISCB) in partnership with George Mason University, will host the Youth Bioinformatics Symposium (YBS), Exploring Computational Biology at George Mason University in winter 2019.

At our first YBS, in 2016, nearly 100 students from the greater Washington DC area gathered for this event. This engaging one-day event introduces students to the amazing world of computational biology, allowing them to engage with and learn about three popular tools used in research in our hands-on workshop, inform them of the many career areas that bioinformatics is now appearing in, and spark the spirit of competition in our team-based mini science challenges.

We hope you join us to make YBS 2019 just as successful!

REGISTRATION IS NOW CLOSED

Click here to see the 2016 symposium photos.

What IS computational Biology?! Watch this video to find out and click here for additional resources.

- top -

TECHNOLOGY TALKS

Bioinformatics as the main protagonist of the microbiome field

Speaker: Dr. Daniel Almonacid

The human microbiome, the microorganisms that live in and on the human body, is one of the most diverse ecosystems on Earth. Our mission at uBiome is to advance the science of the microbiome and make useful products that improve human life. The company’s technological platform is based on the largest microbial dataset in the world (over 300,000 samples), allowing us unprecedented coverage of the microbial diversity across multiple sites of the human body. Using nucleotide sequencing, including our own approach called Precision Sequencing TM, bioinformatics, and machine learning methods, we are developing precision medicine solutions based on microbiome information, empowering doctors, patients, and citizen scientists to improve their quality of life.

Our current portfolio goes from tools for citizens scientists to study their own microbial communities (Explorer TM), to screening tests that can inform doctors of conditions associated with intestinal health (SmartGut TM) and vaginal health (SmartJane TM). The information generated with these analyses allow us continuous improvement of these products.  Additionally, we continually monitor the scientific literature to add new targets as well as novel correlations in our tests. Moreover, the sequencing information combined with the metadata collected from patients has allowed us to discover novel correlations between the microbiome and host conditions, some of which we have been able to understand mechanistically. This knowledge has presented uBiome with the opportunity to in silico design and test drugs that target the microbiome (drugs for bugs), drugs that are naturally produced by the microbiota to modulate the host (drugs from bugs), in addition to identifying and testing potential live biotherapeutics for different health conditions (bugs as drugs).

In this talk I will provide an overview of the work that we are currently doing at uBiome, emphasizing the use of reproducible approaches (both in the laboratory and bioinformatics).  This talk will also highlight the road that uBiome is taking from the research and implementation of clinical tests, toward the development of therapeutics products, having bioinformatics as the main protagonist.

- top -

TOP 10 PAPERS READING LIST, 2016-2017

As selected at RECOMB/ISCB Regulatory systems Genomics 2017
(Papers are listed alphabetically by title.  Due to a draw, this year's list contains 11 papers.)

A prior-based integrative framework for functional transcriptional regulatory network inference, Siahpirani A, Roy S. Nucleic Acids Res 45(4):e21

chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data, Schep AN, Wu B, Buenrostro JD, Greenleaf WJ. Nat Methods 14(10):975-978

Denoising genome-wide histone ChIP-seq with convolutional neural networks, Koh PW, Pierson E, Kundaje A. Bioinformatics 33(14):i225-i233

Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions, Ernst J, Melnikov A, Zhang X, Wang L, Rogov P, Mikkelsen T, Kellis M. Nat Biotechnol 34(11):1180-1190

Genome-Wide Association between Transcription Factor Expression and Chromatin Accessibility Reveals Regulators of Chromatin Accessibility, Lamparter D, Marbach D, Rueedi R, Bergmann S, Kutalik Z. PLoS Comput Biol 13(1):e1005311

Identification of novel prostate cancer drivers using RegNetDriver: a framework for integration of genetic and epigenetic alterations with tissue-specific regulatory network, Dhingra P, Martinez-Fundichely A, Berger A, Huang FW, Forbes AN, Liu EM, Liu D, Sboner A, Tamayo P, Rickman DS, Rubin MA, Khurana E. Genome Biol 18:141

Is a super-enhancer greater than the sum of its parts?, Dukler N, Gulko B, Huang YF, Siepel A. Nat Genet 49:2-3

Quantifying the impact of non-coding variants on transcription factor-DNA binding, Zhao J, Li D, Seo J, Allen AS, Gordan R. Res Comput Mol Biol 10229:336-352

Reconstruction of enhancer-target networks in 935 samples of human primary cells, tissues and cell lines, Cao Q, Anyansi C, Hu X, Xu L, Xiong L, Tang W, Mok MTS, Cheng C, Fan X, Gerstein M, Cheng ASL, Yip KY. Nat Genet 49(10):1428-1436

SMiLE-seq identifies binding motifs of single and dimeric transcription factors, Isakova A, Groux R, Imbeault M, Rainer P, Alpern D, Dainese R, Ambrosini G, Trono D, Bucher P, Deplancke B. Nat Methods 14(3):316-322

Transcription factor family-specific DNA shape readout revealed by quantitative specificity models, Yang L, Orenstein Y, Jolma A, Yin Y, Taipale J, Shamir R, Rohs R. Mol Syst Biol 13(2):910

CONGRATULATIONS TO ALL AUTHORS!

- top -

PROMOTION

Click here to download flyer (pdf)

- top -