DETAILED AGENDA
| Go directly to: Friday - December 7 | Saturday - December 8 | ||
| WEDNESDAY – December 5, 2018 | ||
| START TIME | END TIME | SESSION TYPE |
| 04:00 pm | 06:00 pm | REGISTRATION |
| THURSDAY – December 6, 2018 | ||
| START TIME | END TIME | SESSION TYPE |
| 08:00 am | 06:00 pm | Registration |
| 08:00 am | 09:00 am | Breakfast |
| 09:00 am | 09:45 am | Keynote 1 ZHIYONG LU, Ph.D. Deputy Director for Literature Search National Center for Biotechnology Information (NCBI) Senior Investigator, NCBI/NLM/NIH Machine Learning in Biomedicine: from PubMed Search to Autonomous Disease Diagnosis |
| 09:45 am | 09:55 am | OP01 Proteomics of natural bacterial isolates powered by deep learning-based de novo identification Presenting Author: Samuel Payne, Brigham Young University |
| 09:55 am | 10:05 am | OP02 A platform for community-scale transcriptome-wide association studies Presenting Author: YoSon Park, Perelman School of Medicine University of Pennsylvania |
| 10:05 am | 10:15 am | OP03 Harmonizing and Analyzing Clinical Trials Data in the AHA Precision Medicine Platform Presenting Author: Carsten Goerg, University of Colorado |
| 10:15 am | 10:25 am | OP04 anexVis: visual analytics framework for analysis of RNA expression Presenting Author: Diem-Trang Tran, University of Utah |
| 10:25 am | 10:45 am | Break |
| 10:45 am | 11:15 am | Keynote 2 AARON VON HOOSER, PhD Principal Scientist Computational Biology PatientsLikeMe, Inc. Building a Learning System that Helps Individuals to Thrive by Connecting Their Experiences and Goals with Molecular Measures of Health |
| 11:15 am | 11:25 am | OP05 The characterization of different cell types using the Benford law Presenting Author: Sne Morag, Ariel University |
| 11:25 am | 11:35 am | OP06 Use of metadata and Bag-of-words to map measurements across observational study data Presenting Author: Laura Stevens, University of Colorado Anschutz Medical Campus |
| 11:35 am | 11:45 am | OP07 ExtRamp: A novel algorithm for extracting the ramp sequence based on the tRNA adaptation index or relative codon adaptiveness Presenting Author: Justin Miller, Brigham Young University |
| 11:45 am | 11:55 am | OP08 Using machine learning algorithms for classification of medulloblastoma subgroups based on gene expression data Presenting Author: Sivan Gershanov, Ariel University |
| 12:00 pm | 04:00 pm | -->Ski Break |
| 04:00 pm | 04:30 pm | Keynote 3 JOSLYNN S. LEE, Ph.D. Science Education Fellow Howard Hughes Medical Institute Training and Engaging URM Undergraduate Students in Genomics Research Through a Place-based Microbiome Research Project |
| 04:30 pm | 04:40 pm | OP09 A human disease network from gene-publication relationships on PubMed Presenting Author: Edward Lau, Stanford University |
| 04:40 pm | 04:50 pm | OP10 Transcriptome analysis of cancer adjacent normal tissues reveal genes co-expressed with LINE elements Presenting Author: Mira Han, University of Nevada Las Vegas |
| 04:50 pm | 05:00 pm | OP11 Highly Accurate Computational Characterization of Protein Kinase Family-specific Phosphorylation Sites Presenting Author: Chen Li, ETH Zürich |
| 05:00 pm | 05:10 pm | OP12 ORCHID: a method for detecting short-range chromatin interactions in high-resolution 5C and Hi-C datasets Presenting Author: Fei Ji, Massachusetts General Hospital |
| 05:10 pm | 05:30 pm | Break |
| 05:30 pm | 05:40 pm | OP13 Using Adversarial Deep Neural Networks to Remove Nonlinear Batch Effects from Expression Data Presenting Author: Jonathan Dayton, Brigham Young University |
| 05:40 pm | 05:50 pm | OP14 Med2Mech: Neural-Symbolic Representation of Molecular Mechanisms Underlying Pediatric Disease Presenting Author: Tiffany Callahan, University of Colorado Anschutz Medical Campus |
| 05:50 pm | 06:00 pm | OP15 A Machine Learning Classifier for Assigning Individual Patients with Systemic Sclerosis to Intrinsic Molecular Subsets Presenting Author: Jennifer Franks, Geisel School of Medicine at Dartmouth |
| 06:30 pm | 09:30 pm | Dinner - Il Poggio |
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| FRIDAY – December 7, 2018 | ||
| START TIME | END TIME | SESSION TYPE |
| 08:00 am | 06:00 pm | Registration |
| 08:00 am | 09:00 am | Breakfast |
| 09:00 am | 09:45 am | Keynote 4 DEBORAH L. MCGUINNESS, PhD Tetherless World Senior Constellation Chair Professor of Computer Science and Cognitive Science Rensselaer Polytechnic Institute Semantic Data Resources Enabling Science: Building, Using, and Maintaining Ontology-Enabled Biology Data Resources |
| 09:45 am | 09:55 am | OP16 A Data Quality Testing Tool for Cross-institutional OMOP Electronic Health Record Data Repositories Presenting Author: Timothy Bergquist, University of Washington |
| 09:55 am | 10:05 am | OP17 Comparative Analysis of Germline Microsatellites in the 1,000 Genomes Project Presenting Author: Nicholas Kinney, Virginia College of Osteopathic Medicine |
| 10:05 am | 10:15 am | OP18 Unbiased Pathway Detection Expands Cancer Pathways Presenting Author: Chih-Hsu Lin, Baylor College of Medicine |
| 10:15 am | 10:25 am | OP19 A systems biology approach to define essential kinases in small cell lung cancer Presenting Author: Jihye Kim, University of Colorado Anschutz Medical Campus |
| 10:25 am | 10:45 am | Break |
| 10:45 am | 11:15 am | Keynote 5 DAVID ASTLING, PhD Scientist, Bioinformatics SomaLogic Inc. Beyond Genomics: Deriving Actionable Health Insights from the Human Proteome |
| 11:15 am | 11:25 am | OP20 Clustering of Protein Conformations using Parallelized Dimensionality Reduction Presenting Author: Arpita Joshi, University of Massachusetts, Boston |
| 11:25 am | 11:35 am | OP21 PredHPI: an integrated web-server platform for the prediction and visualization of host-pathogen interactions Presenting Author: Rakesh Kaundal, Utah State University |
| 11:35 am | 11:45 am | OP22 Searching for translatable alternative splice isoforms in the human proteome Presenting Author: Maggie Pui Yu Lam, University of Colorado Anschutz Medical Campus |
| 11:45 am | 11:55 am | OP23 Text Mining Novel Disease- and Drug-Specific Pathways Presenting Author: Minh Pham, Baylor College of Medicine |
| 12:00 pm | 04:00 pm | -->Ski Break |
| 04:00 pm | 04:30 pm | Keynote 6 NICOLE A. VASILEVSKY, Ph.D. Research Assistant Professor Department of Medical Informatics and Clinical Epidemiology (DMICE) Oregon Health & Science University LOINC2HPO: Improving Translational Informatics by Standardizing EHR Phenotypic Data Using the Human Phenotype Ontology |
| 04:30 pm | 04:40 pm | OP24 Optimizing nontuberculous mycobacteria (NTM) de novo genome assemblies for application in clinical case studies Presenting Author: Sara Kammlade, National Jewish Health |
| 04:40 pm | 04:50 pm | OP25 REAL-neo, a comprehensive neoantigen prediction and prioritization pipeline using tumor sequencing data Presenting Author: Yesesri Cherukuri, Mayo Clinic |
| 04:50 pm | 05:00 pm | OP26 Measuring chromosome conformation Presenting Author: Brian Ross, University of Colorado Anschutz Medical Campus |
| 05:00 pm | 05:10 pm | OP27 Modeling the Structure of BioGRID PPI Networks Presenting Author: Sridevi Maharaj, University of California-Irvine |
| 05:10 pm | 05:30 pm | Break |
| 05:30 pm | 05:40 pm | OP28 Addressing the compositional data problem in sequencing with a novel, robust normalization method Presenting Author: James St. Pierre, University of Toronto |
| 05:40 pm | 05:50 pm | OP29 A Case Study on the Effects of Noisy, Long-read Correction Approaches on Assembly Contiguity Presenting Author: Brandon Pickett, Brigham Young University |
| 05:50 pm | 06:00 pm | OP30 Integrative analysis of transcriptomics and proteomics to detect novel protein isoforms from alternatively spliced transcripts induced by SF3B1 spliceosomal mutations Presenting Author: Kelsey Nassar, University of Colorado Anschutz Medical Campus |
| 06:30 pm | 08:30 pm | Poster Session |
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| SATURDAY – December 8, 2018 | ||
| START TIME | END TIME | SESSION TYPE |
| 08:00 am | 11:00 am | Registration |
| 08:00 am | 09:00 am | Breakfast |
| 09:00 am | 09:30 am | Keynote 7 BENJAMIN M. GOOD, PhD Consultant Lawerence Berkeley National Labs Integrating Pathway Databases with Gene Ontology Causal Activity Models |
| 09:30 am | 09:40 am | OP31 Exploring the Fabric of Breast Cancer Using Gene Sets Presenting Author: Judith Blake, The Jackson Laboratory |
| 09:40 am | 09:50 am | OP32 Measuring and Protecting the Sensitive Linking Information Leakage Across Epigenetic and Transcriptomics Datasets Through Genotype and Assay Prediction Presenting Author: Arif Harmanci, University of Texas Health Science Center |
| 09:50 am | 10:00 am | OP33 Education, Networking and Building Next Generation Prototypes -- Hackathons and Analyzeathons for Bioinformaticians, Biomedical Informaticians and Computational Biologists! Presenting Author: Ben Busby, NCBI |
| 10:00 am | 10:10 am | OP34 Alternative Splicing of Single Cells in Squamous Cell Lung Cancer Premalignancy Presenting Author: Hyunmin Kim, University of Colorado Anschutz Medical Campus |
| 10:10 am | 10:20 am | OP35 Inferring trade-offs in protein folding networks Presenting Author: Sebastian Pechmann, Université de Montréal |
| 10:20 am | 10:40 am | Break |
| 10:40 am | 10:50 am | OP36 Fully Bayesian model for non-random missing data in qPCR Presenting Author: Valeriia Sherina, University of Rochester Medical Center |
| 10:50 am | 11:00 am | OP37 Homologous Inter-Domain Segments in Protein Families Presenting Author: Dylan Barth, University of Nevada Las Vegas |
| 11:00 am | 11:10 am | OP38 Integrating extracted relations into existing knowledge bases Presenting Author: Harrison Pielke-Lombardo, University of Colorado |
| 11:10 am | 11:20 am | OP39 The Use of Scientific Ignorance to Drive Literature-Based Discovery in Prenatal Nutrition Across Disciplinary Boundaries Presenting Author: Mayla Boguslav, University of Colorado Anschutz Medical Campus |
| 11:20 am | 11:30 am | OP40 Governance Innovations for Promoting Cross-institutional Electronic Health Data Sharing Presenting Author: Kari A. Stephens, University of Washington |
| 11:30 am | 12:00 pm | Keynote 8 KIRK E. JORDAN, PhD IBM Distinguished Engineer Data Centric Solutions IBM T.J. Watson Research & Chief Science Officer Algorithm Exploitation & Evolving AI/Cognitive Examples on IBM’s Data Centric Systems |
| 12:00 pm | 12:15 pm | Closing Raffle and Awards |
