dc-short

Keynotes

Mona Singh, PhD - Princeton University

Title: Sequence, structure and network methods to uncover cancer genes
Abstract: A major aim of cancer genomics is to pinpoint which somatically mutated genes are involved in tumor initiation and progression. This is a difficult task, as numerous somatic mutations are typically observed in each cancer genome, only a subset of which are cancer-relevant, and very few genes are found to be somatically mutated across large numbers of individuals. In this talk, I will overview three methods my group has introduced for identifying cancer genes. First, I will present a framework for uncovering cancer genes, differential mutation analysis, that compares the mutational profiles of genes across cancer genomes with their natural germline variation across healthy individuals. Next, I will show how to leverage per-individual mutational profiles within the context of protein-protein interaction networks in order to identify small connected subnetworks of genes that, while not individually frequently mutated, comprise pathways that are altered across (i.e., “cover”) a large fraction of individuals. Finally, I will demonstrate that cancer genes can be discovered by identifying genes whose interaction interfaces are enriched in somatic mutations. Overall, these methods recapitulate known cancer driver genes, and discover novel, and sometimes rarely-mutated, genes with likely roles in cancer.

Biography: Mona Singh obtained her AB and SM degrees at Harvard University, and her PhD at MIT, all three in Computer Science. She did postdoctoral work at the Whitehead Institute for Biomedical Research. She has been on the faculty at Princeton since 1999, and currently she is Professor of Computer Science in the Department of Computer Science and the Lewis-Sigler Institute for Integrative Genomics. Her group works broadly in computational molecular biology, as well as its interface with machine learning and algorithms. Her group is especially interested in developing methods for predicting and characterizing protein specificity, interactions, and networks. She is currently a Methods Editor at PLOS Computational Biology, has been program committee chair for several major computational biology conferences, including ISMB (2010), WABI (2010), ACM-BCB (2012), and RECOMB (2016), and has been Chair of the NIH Modeling and Analysis of Biological Systems Study Section (2012-2014). She received the Presidential Early Career Award for Scientists and Engineers (PECASE) in 2001, and is an ISCB Fellow.

Joshua C. Denny, MD, MS, FACMI - Vanderbilt University Medical Center

Title: Huge cohorts, genomics, and clinical data to personalize medicine
Abstract: Precision medicine offers the promise of improved diagnosis and for more effective, patient-specific therapies. Typically, such studies have been pursued using research cohorts. At Vanderbilt, we have linked de-identified electronic health records (EHRs), to a DNA repository, called BioVU, which has nearly 250,000 samples. Through BioVU and a NHGRI-funded network using EHRs for discovery, the Electronic Medical Records and Genomics (eMERGE) network, we have used clinical data of genomic basis of disease and drug response using real-world clinical data. The EHR also enables the inverse experiment – starting with a genotype and discovering all the phenotypes with which it is associated – a phenome-wide association study. By looking for clusters of diseases and symptoms through phenotype risk scores, we find unrecognized genetic variants associated with common disease. The era of huge international cohorts such as the UK Biobank, Million Veteran Program, and the newly started All of Us Research Program will make millions of individuals available with dense molecular and phenotypic data. All of Us launched May 6, 2018 and will engage one million diverse individuals across the US who will contribute data and also receive results back.

Biography: Dr. Joshua Denny is Professor of Biomedical Informatics and Medicine, Director of the Center for Precision Medicine and Vice President of Personalized Medicine at Vanderbilt University Medical Center. He is a Fellow of the American College of Medical Informatics and a member of the National Academy of Medicine. He has substantial experience in the design, development, and implementation of electronic health record (EHR) data mining algorithms and was the primary author of several natural language processing systems to support phenotype extraction algorithms for genomic research projects, including development of the phenome-wide association study (PheWAS) method. He is principal investigator (PI) of nodes in the Electronic Medical Records and Genomics (eMERGE) Network, Pharmacogenomics Research Network (PGRN), and the Implementing Genomics into Practice (IGNITE) Network. Dr. Denny is PI of the Data and Research Center of the Precision Medicine Initiative All of Us Research Program (previously called the Precision Medicine Initiative Cohort Program), which will eventually enroll at least 1 million Americans in an effort to understand the genetic, environmental, and behavioral factors that influence human health and disease. To date, he has led >100 genome-wide and candidate gene association studies using EHR data linked to genetic data. Dr. Denny serves on a number of mentoring committees and has trained >30 postdoctoral and predoctoral trainees.

Avi Ma'ayan, PhD - Icahn School of Medicine at Mount Sinai

Title: The Art of Connectivity Mapping
Abstract: Motivation: The powerful idea of the Connectivity Mapping proposes the creation of a library of drug induced gene expression signatures. Such a resource can facilitate finding small molecules to mimic or reverse disease signatures, identifying drug targets, discovering the mechanisms of action for novel small molecules, elucidating off-target effect mechanisms, and directing cellular differentiation and reprogramming. A related concept is Gene Set Enrichment Analysis.
Problem statement: In my presentation I will discuss how these two transformative ideas can be expanded in various creative ways to unify knowledge representation in system biology.
Approach: I will demonstrate how expanded Connectivity Mapping and Gene Set Enrichment Analyses combined with Machine Learning can enable imputing and illuminating new biological and pharmacological knowledge.

Biography: The Ma’ayan laboratory applies computational methods to study the complexity of regulatory networks in mammalian cells. We develop software tools to study how molecular intracellular regulatory networks control cellular processes such as differentiation, proliferation, and apoptosis. Our main focus is in developing methods that link changes in genome-wide gene and protein expression to transcriptional regulators and cell signaling pathways. So far we published several popular web-based software tools and databases that enable biologists to perform enrichment analyses and build networks using their own data. By employing the tools we have developed, we work closely with experimental biologists on projects that utilize high-throughput experiments to understand cell regulation at a global scale. So far we published over 130 peer-reviewed articles where several of them are in top-tier journals and are highly cited. In addition, we have mentored over 80 trainees, including postdoctoral fellows, graduate and medical students, undergraduates and high school students. We also contribute to educational and outreach activities of these initiatives including teaching two MOOCs on the Coursera platform. In the past four years we have served as an integral part of the BD2K-LINCS Data Coordination and Integration Center (DCIC), and the Knowledge Management Center (KMC) for the Illuminating the Druggable Genome (KMC-IDG) project, where we are centrally involved in the development of computational methods, databases and web-based software tools for LINCS, IDG and BD2K. Recently, we also became involved with the construction and design of the NIH Data Commons pilot project.

Schedule at a Glance

Tuesday, August 28, 2018
6-8 P.M. Registration at Capital Foyer
Wednesday, August 29, 2018
7-8 A.M. Continental Breakfast at Capital Foyer Registration at Capital Foyer
8 A.M.-5 P.M.
Wednesday, August 29, 2018 - Workshops and Satellite Meetings
8-10 A.M. CNB-MAC 2018, 5th International Workshop on Computational Network Biology: Modeling, Analysis, and Control

Venue: Salon G (H-J)
CSBW: Computational Structural Bioinformatics Workshop

Venue: Salon D (A-B)
CAME 2018: 7th Workshop on Computational Advances in Molecular Epidemiology

Venue: Salon E
ParBIO: 7th Workshop on Parallel and Cloud-based Bioinformatics and Biomedicine

Venue: Rus/Hart/Cannon
BioC: BioCreative Satellite Meeting

Venue: Salon F
10-10:30 A.M. Coffee Break at Capital Foyer
10:30 A.M.-12 P.M.
12-1:00 P.M. Lunch at Penn Avenue Terrace
1:00-3:00 P.M. NCI Could Resources

Venue: Rus/Hart/Cannon
3:00-3:30 P.M. Coffee Break at Capital Foyer
3:30-5:00 P.M.
Wednesday, August 29, 2018 - Tutorials
8-10 A.M. MMS:Modeling Macromolecular Structures and Motions: Computational Methods for Sampling and Analysis of Energy Landscapes

Venue:Salon G (K)
MDL: Making Deep Learning Understandable for Analyzing Sequential Data about Gene Regulation

Venue: Salon D (C)
10-10:30 A.M. Coffee Break at Capital Foyer IMLH: Interpretable Machine Learning in Healthcare

Venue: Salon G (K)
10:30 A.M.-12 P.M. BWD: Using BioDepot-workflow-Builder to create and execute reproducible bioinformatics workflows

Venue: Salon D (C)
12-1:00 P.M. Lunch at Penn Avenue Terrace
1:00-3:00 P.M. ASD: Analysis of Sequencing Data

Venue: The Congressional Room
ACDS: Agile Clinical Decision Support Development and Implementation

Venue: Salon G(K)
RIDS: Rapidly identifying disease-associated rare variants using annotation and machine learning at whole-genome scale online

Venue:Salon D (C)
3:00-3:30 P.M. Coffee Break at Capital Foyer SSE: Student Social Event
Venue: Capitol Foyer (meet here at 3 PM)
Session Chairs: Nasrin Akhter, George Mason University &
Riza Bautista, University of Delaware
3:30-5:00 P.M.
Thursday, August 30
Registration 07:30 A.M.-5:00 P.M. at Capitol Foyer
8:45-9 A.M. Opening and Welcome Remarks: Cathy Wu, University of Delaware & Amarda Shehu, George Mason University
Session Chairs: Cathy Wu & Amarda Shehu
Keynote Introduction: Amarda Shehu
9-10 A.M. Keynote: Mona Singh
Ttitle: Sequence, structure and network methods to uncover cancer genes
Venue: Salons E, F, G
10-10:30 A.M. Coffee Break at Capitol Foyer
10:30 A.M.-12 P.M. Network Analysis
Venue: Salon D
Session Chair: Jing Li, Case Western Reserve University

Highlight
Title: Aligning dynamic networks with DynaWAVE
Authors: Vijayan V, Milenkovic T.

Long
Title: Target gene prediction of transcription factor using a new neighborhood-regularized tri-factorization one-class collaborative filtering algorithm
Authors: Hansaim Lim and Lei Xie

Long
Title: A Decomposition-based Approach towards the Control of Boolean Networks
Authors: Soumya Paul, Cui Su, Jun Pang and Andrzej Mizera

Short
Title: ANCA- Alignment-based Network Construction Algorithm
Authors: Kevin Chow, Ahmet Ay, Rasha Elhesha and Tamer Kahveci
Sequence Analysis
Venue: Salon E
Session Chair: Tamer Kahveci, University of Florida

Highlight
Title: ROP: dumpster diving in RNA-sequencing to find the source of 1 trillion reads across diverse adult human tissues
Authors: Serghei Mangul

Long
Title: Towards selective-alignment: Bridging the accuracy gap between alignment-based and alignment-free transcript quantification
Authors: Hirak Sarkar, Mohsen Zakeri, Laraib Malik and Rob Patro

Long
Title: ULTRA: A Model Based Tool to Detect Tandem Repeats
Authors: Daniel Olson and Travis Wheeler

Short
Title: Measuring the mappability spectrum of reference genome assemblies
Authors: Zachary Stephens and Ravishankar Iyer
Genetics and Evolution
Venue: Salon F
Session Chair: Hongfang Liu, Mayo Clinic

Highlight
Title: CrossPlan: Systematic Planning of Genetic Crosses to Validate Mathematical Models
Authors: Pratapa A, Adames N, Kraikivski P, Franzese N, Tyson JJ, Peccoud J, Murali TM, Berger B

Long
Title: Efficient Synthesis of Mutants Using Genetic Crosses
Authors: Aditya Pratapa, Amogh Jalihal, S. S. Ravi and T. M. Murali

Long
Title: A Consensus Approach to Infer Tumor Evolutionary Histories
Authors: Kiya Govek, Camden Sikes and Layla Oespe

Short
Title: Phenotyping Immune Cells in Tumor and Healthy Tissue Using Flow Cytometry Data
Authors: Ye Chen, Ryan Calvert, Ariful Azad, Bartek Rajwa, James Fleet, Timothy Ratliff and Alex Pothen
Gene Expression Analysis
Venue: Salon G
Session Chair: Amarda Shehu, George Mason University

Long
Title: TEMPO: Detecting pathway-specific temporal dysregulation of gene expression in disease
Authors: Christopher Pietras, Faith Ocitti and Donna Slonim

Long
Title: Deep Learning Convolutional Neural Network for Cancer Diagnosis using Gene Expression Pattern
Authors: Nan Deng

Long
Title: Deep Learning Based Tumor Type Classification Using Gene Expression Data
Authors: Boyu Lyu and Anamul Haque

Short
Title: A Distributed Constrained Non-negative Matrix Factorization Algorithm for Time-Series Gene Expression Data
Authors: Matthew Dyer and Julian Dymacek
12-1:30 P.M. Lunch at Penn Avenue Terrace Funding Agency Panel at Russel/Hart/Cannon
Session Chairs: Amarda Shehu, George Mason University & Cathy Wu, University of Delaware
1:30-2 P.M. Hands-on NIH Grant Writing Workshop
Venue: Salon G
Session Chairs: Veerasamy Ravichandran, NIH & Wenchi Liang, NIH
2-3:30 P.M. Medical Informatics
Venue: Salon D
Session Chair: Naveen Ashish, Fredhutch

Highlight
Title: Co-occurrence of medical conditions: Exposing patterns through probabilistic topic modeling of snomed codes.
Authors: Bhattacharya M, Jurkovitz C, Shatkay H.

Long
Title: Weakly-supervised Deep Learning for Thoracic Disease Classification and Localization on Chest X-rays
Authors: Chaochao Yan, Jiawen Yao, Ruoyu Li, Zheng Xu and Junzhou Huang

Long
Title: XGBoost-Based Instantaneous Drowsiness Detection Framework Using Multitaper Spectral Information of Electroencephalography
Authors: Hyun-Soo Choi, Siwon Kim, Jung Eun Oh, Jee Eun Yoon, Jung Ah Park, Chang-Ho Yun and Sungroh Yoon
Sequence Analysis
Venue: Salon E
Session Chair: Ananth Kalyanaraman, Washington State University

Highlight
Title: An integrative model for alternative polyadenylation, IntMAP, delineates mTOR-modulated endoplasmic reticulum stress response
Authors: Chang J-W, Zhang W, Yeh H-S, Park M, Yao C, Shi Y, Kuang R, Yong J.

Long
Title: Bioinformatic analysis of nucleotide cyclase functional centers and development of ACPred webserver
Authors: Nuo Xu, Changjiang Zhang, Leng Leng Lim and Aloysius Wong

Long
Title: Identification of cell types based on word embedding and nonparametric methods in single-cell RNA sequencing data
Authors: Tianyu Wang and Sheida Nabavi

Short
Title: The PepSeq Pipeline: software for antimicrobial motif discovery in randomly-generated peptide libraries
Authors: Tanner Jensen, Kristi Bresciano, Emma Dallon, M. Stanley Fujimoto, Cole Lyman, Enoch Stewart, Joel Griffitts and Mark Clement
Phenotypes and Diseases
Venue: Salon F
Session Chair: Mukul Bansal, University of Connecticut

Long
Title: RegMIL: Phenotype Classification From Metagenomic Data
Authors: Mohammad Arifur Rahman and Huzefa Rangwala

Long
Title: Detecting divergent subpopulations in phenomics data using interesting flares
Authors: Methun Kamruzzaman, Ananth Kalyanaraman and Bala Krishnamoorthy

Long
Title: Neuroinformatics and analysis of connectomic alterations due to cerebral microhemorrhages in geriatric mild neurotrauma
Authors: Alexander Maher, Kenneth A. Rostowsky, Nahian F. Chowdhury and Andrei Irimia

Short
Title: Microbiomarkers Discovery in Inflammatory Bowel Diseases using Network-Based Feature Selection
Authors: Mostafa Abbas, Thanh Le, Halima Bensmail, Vasant Honavar and Yasser El-Manzalawy
3:30-4 P.M. Coffee Break at Capitol Foyer
Setup posters in Salons E, F
4-5:30 P.M. ACM SIGBio General Meeting
Venue: Salon G
6-8:30 P.M. Poster Session
Venue: Salons E, F
Setup posters between 5:00-6:00 P.M.
Pick up posters by 9:00 P.M.
Reception
Venue: Capitol Foyer
Friday, August 31
Registration 07:30 A.M.-5:00 P.M. at Capitol Foyer
8:45-9 A.M. Opening and Welcome Remarks
Session Chair: Amarda Shehu, George Mason University
Keynote Introduction: Hongfang Liu, Mayo Clinic
9-10 A.M. Keynote: Joshua C Denny
Ttitle: Huge cohorts, genomics, and clinical data to personalize medicine
Venue: Salons E, F, G
10-10:30 A.M. Coffee Break at Capitol Foyer
10:30 A.M.-12 P.M. Medical Informatics
Venue: Salon D
Session Chair: Hagit Shatkay, University of Delaware

Highlight
Title: Literature Mining to Improve the Prioritization, Curation, and Integration of Knowledge for Clinically Relevant Variants.
Authors: Wei C-H, Phan L, Allot A, Peng Y, Lee K, Maiti R, Hefferon T, Feltz J, Lu, Zhiyong L

Long
Title: Improving Validity of Cause of Death on Death Certificates
Authors: Ryan Hoffman, Janani Venugopalan, Li Qu, Hang Wu and May D. Wang

Long
Title: CausalTriad: Toward Pseudo Causal Relation Discovery and Hypotheses Generation from Medical Text Data
Authors: Sendong Zhao, Meng Jiang, Ming Liu, Bing Qin and Ting Liu

Short
Title: Melanoma Risk Prediction with Structured Electronic Health Records
Authors: Aaron Richter and Taghi Khoshgoftaar
Protein Analysis
Venue: Salon E
Session Chair: Sheida Nabavi, University of Connecticut

Highlight
Title: Choosing non-redundant representative subsets of protein sequence data sets using submodular optimization
Authors: Libbrecht MW, Bilmes JA, Noble WS

Long
Title: Splice-Aware Multiple Sequence Alignment of Protein Isoforms
Authors: Alex Nord, Peter Hornbeck, Kaitlin Carey and Travis Wheeler

Long
Title: Ensemble Voting Schemes that Improve Machine Learning Models for Predicting the Effects of Protein Mutations
Authors: Sarah Gunderson and Filip Jagodzinski

Short
Title: Convolutional Neural Networks for Predicting Molecular Binding Affinity to HIV-1 Proteins
Authors: Paul Morris, Yahchayil Dasilva, Evan Clark, William Edward Hahn and Elan Barenholtz
Deep Learning and Applications
Venue: Salon F
Session Chair: Xiaoqian Jiang, UT Health

Long
Title: Cost-Sensitive Deep Active Learning for Epileptic Seizure Detection
Authors: Xuhui Chen, Jinlong Ji, Tianxi Ji and Pan Li

Long
Title: Automated Mouse Organ Segmentation: A Deep Learning Based Solution
Authors: Naveen Ashish and Mi-Youn Brusniak

Long
Title: A Distributed Semi-Supervised Platform for DNase-Seq Data Analytics using Deep Generative Convolutional Networks
Authors: Shayan Shams, Richard Platania, Joohyun Kim, Jian Zhang, Kisung Lee, Seungwon Yang and Seung-Jong Park

Short
Title: DeepAnnotator: Genome Annotation with Deep Learning
Authors: Mohammad Ruhul Amin, Alisa Yurovsky, Yingtao Tian and Steven Skiena
Genome Rearrangements and Genetic Variation
Venue: Salon G
Session Chair: Layla Oesper, Carleton College

Highlight
Title: Implicit Transpositions in DCJ Scenarios
Authors: Avdeyev P, Jiang S, Alekseyev MA

Long
Title: On the Minimum Copy Number Generation Problem in Cancer Genomics
Authors: Letu Qingge and Binhai Zhu

Long
Title: Detecting Chromosomal Inversions from Dense SNPs by Combining PCA and Association Tests
Authors: Ronald Nowling and Scott Emrich

Short
Title: Disease Subtyping using Somatic Variant Data
Authors: Suzan Arslanturk and Sorin Draghici
12-12:30 P.M. Grab Boxed Lunch at Penn Avenue Terrace
12:30-1:30 P.M. Women in Bioinformatics (WiB) at Salons F, G
Session Chair: May D. Wang, Georgia Institute of Technology and Emory University
1:30-2 P.M.
2-3:30 P.M. Medical Informatics
Venue: Salon D
Session Chair: Zhiyong Lu, NIH/NCBI

Highlight
Title: The National Sleep Research Resource: towards a sleep data commons
Authors: Zhang G-Q, Cui L, Mueller R, Tao S, Kim M, Rueschman M, Mariani S, Mobley D, Redline S.

Long
Title: Leveraging Treatment Patterns to Predict Survival of Patients with Advanced Non-Small-Cell Lung Cancer
Authors: Kyle Haas, Malika Mahoui, Simone Gupta and Stuart Morto

Long
Title: Open Information Extraction with Meta-pattern Discovery in Biomedical Literature
Authors: Xuan Wang, Yu Zhang, Qi Li, Yinyin Chen and Jiawei Han

Short
Title: What Happens When? Interpreting Schedule of Activity Tables in Clinical Trial Documents
Authors: Murtaza Dhuliawala, Nicholas Fay, Daniel Gruen and Amar Das
Protein Structure and Molecular Dynamics
Venue: Salon E
Session Chair:Amarda Shehu, George Mason University

Highlight
Title: DeepSF: Deep convolutional neural network for mapping protein sequences to folds
Authors: Hou J, Adhikari B, Cheng J.

Long
Title: clustQ: Efficient protein decoy clustering using superposition-free weighted internal distance comparisons
Authors: Rahul Alapati and Debswapna Bhattacharya

Long
Title: Graphic Encoding of Macromolecules for Efficient High-Throughput Analysis
Authors: Trilce Estrada, Jeremy Benson, Hector Carrillo-Cabada, Asghar Razavi, Michel Cuendet, Harel Weinstein, Ewa Deelman and Michela Taufer

Short
Title: Hybrid Spectral/Subspace Clustering of Molecular Dynamics Simulations
Authors: Ivan Syzonenko and Joshua Phillips
Biomarker and Cancer
Venue: Salon F
Session Chair: Tamer Kahveci, University of Florida

Long
Title: Biomarker Discovery via Optimal Bayesian Feature Filtering for Structured Multiclass Data
Authors: Ali Foroughi Pour and Lori A. Dalton

Long
Title: Integration of Cancer Data through Multiple Mixed Graphical Model
Authors: Christopher Ma, Tina Gui, Xin Dang, Yixin Chen and Dawn Wilkins

Long
Title: TFmeta: Uncovering Transcription Factors Governing Metabolic Reprogramming in Lung Cancer Using Paired Human Benign and Lung Cancer Tissues
Authors: Yi Zhang, Xiaofei Zhang, Andrew Lane, Teresa Fan and Jinze Liu

Short
Title: MIA: A Multi-cohort Integrated Analysis for biomarker identification
Authors: Brian Marks, Nina Hees, Hung Nguyen and Tin Nguyen
Phylogenetics
Venue: Salon G
Session Chair: Scott Emrich, University of Tennessee

Long
Title: Phylogenetic Consensus for Exact Median Trees
Authors: Pawel Tabaszewski, Pawel Gorecki and Oliver Eulenstein

Long
Title: Species tree and reconciliation estimation under a duplication-loss-coalescence model
Authors: Peng Du and Luay Nakhleh

Long
Title: An Integer Linear Programming Solution for the Domain-Gene-Species Reconciliation Problem
Authors: Lei Li and Mukul S. Bansal

Short
Title: A Network Science Approach for Determining the Ancestral Phylum of Bacteria
Authors: Ehdie Khaledian, Assefaw Gebremedhin, Kelly Brayton and Shira Broschat
TCBB editorial board meeting
Venue: State Room
Session Chair: Aidong Zhang, State University of New York at Buffalo
3:30-4 P.M. Coffee Break at Capitol Foyer
4-6 P.M. NSF-sponsored Student Research Forum
Venue: Salon D
Session Chair: May D. Wang, Georgia Institute of Technology and Emory University
6-8 P.M. Dinner Banquet
Venue: Salons E, F, G
Saturday, September 1
Registration 7:30 A.M.-2:00 P.M. at Capitol Foyer
8:45-9 A.M. Opening and Welcome Remarks
Session Chair: Cathy Wu, University of Delaware
Keynote Introduction: Jing Li, Case Western Reserve University
9-10 A.M. Keynote: Avi May’an
Ttitle: The Art of Connectivity Mapping
Venue: Salons E, F, G
10-10:30 A.M. Coffee Break at Capitol Foyer
10:30 A.M.-12:15 P.M. Drug Discovery and Docking
Venue: Salon G
Session Chair: Yuji Zhang, University of Maryland

Highlight
Title: General Prediction of Peptide-MHC Binding Modes Using Incremental Docking: A Proof of Concept
Authors: Antunes DA, Devaurs D, Moll M, Lizée G, Kavraki LE

Long
Title: Seq3seq Fingerprint: Towards End-to-end Semi-supervised Deep Drug Discovery
Authors: Xiaoyu Zhang, Sheng Wang, Feiyun Zhu, Zheng Xu, Yuhong Wang and Junzhou Huang

Long
Title: Identifying Experimental Evidence from Biomedical Abstracts Relevant to Drug-Drug Interactions
Authors: Gongbo Zhang, Debarati Roychowdhury, Pengyuan Li, Heng-Yi Wu, Shijun Zhang, Lang Li and Hagit Shatkay

Long
Title: Feature Selection to Predict Compound's Effect on Aging
Authors: Hafez Eslami Manoochehri, Susmitha Sri Kadiyala and Mehrdad Nourani
Algorithms
Venue: Salon E
Session Chair: Byung-Jun, Texas A&M University

Long
Title: A Practical and Efficient Algorithm for the k-mismatch Shortest Unique Substring Finding Problem
Authors: Daniel R. Allen, Sharma V. Thankachan and Bojian Xu

Long
Title: kmerEstimate: A Streaming Algorithm for Estimating k-mer Counts with Optimal Space Usage
Authors: Sairam Behera, Sutanu Gayen, Jitender S Deogun and Vinodchandran Variyam

Long
Title: Are Profile Hidden Markov Models Identifiable?
Authors: Srilakshmi Pattabiraman and Tandy Warnow

Long
Title: Applying Stochastic Process Model to Imputation of Censored Longitudinal Data
Authors: Ilya Zhbannikov, Liang He, Konstantin Arbeev and Anatoliy Yashin
mHealth
Venue: Salon F
Session Chair: GQ Zhang, University of Kentucky

Long
Title: Automatic Autism Spectrum Disorder Detection Using Everyday Vocalizations Captured by Smart Devices
Authors: Yuan Gong, Hasini Yatawatte, Christian Poellabauer, Sandra Schneider and Susan Latham

Long
Title: Prediction of Clinical Outcomes of Spinal Muscular Atrophy Using Motion Tracking Data and Elastic Net Regularized Regression
Authors: David Chen, Steve Rust, En-Ju Lin, Simon Lin, Leslie Nelson, Lindsay Alfano and Linda Lowes

Long
Title: Cohesion-driven Online Actor-Critic Reinforcement Learning for mHealth Intervention
Authors: Feiyun Zhu, Peng Liao, Xinliang Zhu, Jiawen Yao and Junzhou Huang

Long
Title: Robust Actor-Critic Contextual Bandit for Mobile Health (mHealth) Interventions
Authors: Feiyun Zhu, Jun Guo, Ruoyu Li and Junzhou Huang
12:15-1:45 P.M. Lunch Buffet at Capitol Foyer
1:45-2 P.M. Closing Remarks
Venue: Salon F

Funding Agencies Panel

Topics: Major initiatives and funding opportunities from NSF, NIH and DOE relating to support for research and education in Bioinformatics, Computational Biology and Biomedical Informatics; covering opportunities for early-career investigators, inter-agency initiatives.

Panelists:

Mitra Basu
Program Director, Division of Computing and Communication Foundations (CCF)
Directorate for Computer & Information Science & Engineering (CISE)
National Science Foundation (NSF)

Wendy Nielsen
Program Director, Division of Information and Intelligent Systems (IIS)
Directorate for Computer & Information Science & Engineering (CISE)
National Science Foundation (NSF)

Jennifer Couch
Chief, Structural Biology and Molecular Applications Branch
Division of Cancer Biology (DCB)
National Cancer Institute (NCI)
National Institutes of Health (NIH)

Susan Gregurick
Director, Division of Biophysics, Biomedical Technology, and Computational Biosciences (BBCB)
National Institute of General Medical Sciences (NIGMS)
National Institutes of Health (NIH)

Daniel Drell
Program Manager, Biological Systems Science Division (BSSD)
Office of Biological & Environmental Research (OBER)
Department of Energy (DOE)

NIH Grant Writing Workshop

Topics: Hands-on grant writing for early-career investigators, covering both the program and funding opportunity aspect and the grant review aspect.

Speakers:

Veerasamy “Ravi” Ravichandran
Program Director
Division of Biophysics, Biomedical Technology, and Computational Biology (BBCB)
National Institute of General Medical Sciences (NIGMS)
National Institutes of Health (NIH)

Wenchi Liang
Scientific Review Officer
Biodata Management and Analysis (BDMA) Study Section
Center for Scientific Review (CSR)
National Institutes of Health (NIH)
Important Dates
Call for Submission Deadline Notification of Acceptance
Papers May 20 June 11
Workshops March 31 April 7
Tutorials March 31 April 7
Highlights June 1 June 11
Posters June 13 June 20
Hotel Reservation cutoff date August 10

News

ACM-BCB room rate at JW Marriot is available till August 10th

August 6, 2018

Accepted Posters list

July 27, 2018

Full schedule posted

June 24, 2018

Day 1 schedule posted

June 8, 2018

Updated Camera Ready Deadline- June 30

June 8, 2018

Program Committee listed

June 4, 2018

Accepted Workshops' links added

May 22, 2018

Registration Open

May 21, 2018

Revised Highlights deadline- June 1

May 11, 2018

Accepted Workshops are listed

April 29, 2018

Accepted Tutorials are listed

April 29, 2018

Updated Paper submission deadline- May 20

April 22, 2018

Sponsorship Benefits information available

April 18, 2018

Revised Workshop proposal deadline- March 31

March 22, 2018

Revised Tutorial submission deadline- March 31

March 22, 2018

Venue information is available

February 18, 2018

Call for Papers, Workshops, Posters, Tutorials, Highlights

February 12, 2018


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