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ACM-BCB '17- Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology,and Health Informatics

ACM-BCB '17- Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology,and Health Informatics

Full Citation in the ACM Digital Library

SESSION: Session 1: Cancer Genomics and Inferring Phylogenies and Haplotypes

  • Kevin Liu

Beyond Perfect Phylogeny: Multisample Phylogeny Reconstruction via ILP

  • Paola Bonizzoni
  • Simone Ciccolella
  • Gianluca Della Vedova
  • Mauricio Soto

A Compatibility Approach to Identify Recombination Breakpoints in Bacterial and Viral Genomes

  • Yi-Pin Lai
  • Thomas R. Ioerger

Phylogenetic Tree based Method for Uncovering Co-mutational Site-pairs in Influenza Viruses

  • Fransiskus Xaverius Ivan
  • Xinrui Zhou
  • Akhila Deshpande
  • Rui Yin
  • Jie Zheng
  • Chee Keong Kwoh

SESSION: Session 2: Text Mining and Classification

  • Eva Lee

Mapping Free Text into MedDRA by Natural Language Processing: A Modular Approach in Designing and Evaluating Software Extensions

  • Margherita Zorzi
  • Carlo Combi
  • Gabriele Pozzani
  • Ugo Moretti

Dependency and AMR Embeddings for Drug-Drug Interaction Extraction from Biomedical Literature

  • Yanshan Wang
  • Sijia Liu
  • Majid Rastegar-Mojarad
  • Liwei Wang
  • Feichen Shen
  • Fei Liu
  • Hongfang Liu

Leveraging Sentiment Analysis for Classifying Patient Complaints

  • Adel ElMessiry
  • Zhe Zhang
  • William O. Cooper
  • Thomas F. Catron
  • Jan Karrass
  • Munindar P. Singh

Identifying Harm Events in Clinical Care through Medical Narratives

  • Arman Cohan
  • Allan Fong
  • Raj M. Ratwani
  • Nazli Goharian

SESSION: Session 3: Proteins and RNA Structure, Dynamics, and Analysis I

  • Filip Jagodzinski

GOstruct 2.0: Automated Protein Function Prediction for Annotated Proteins

  • Indika Kahanda
  • Asa Ben-Hur

Identification and Prediction of Intrinsically Disordered Regions in Proteins Using n-grams

  • Mauricio Oberti
  • Iosif I. Vaisman

Deep Recurrent Conditional Random Field Network for Protein Secondary Prediction

  • Alexander Rosenberg Johansen
  • Casper Kaae Sønderby
  • Søren Kaae Sønderby
  • Ole Winther

SESSION: Session 4: Genomic Variation and Disease

  • Anna Ritz

CERENKOV: Computational Elucidation of the Regulatory Noncoding Variome

  • Yao Yao
  • Zheng Liu
  • Satpreet Singh
  • Qi Wei
  • Stephen A. Ramsey

Exploring Frequented Regions in Pan-Genomic Graphs

  • Alan Cleary
  • Indika Kahanda
  • Brendan Mumey
  • Joann Mudge
  • Thiruvarangan Ramaraj

Bayesian Hyperparameter Optimization for Machine Learning Based eQTL Analysis

  • Andrew Quitadadmo
  • James Johnson
  • Xinghua Shi

Coal-Miner: A Statistical Method for GWA Studies of Quantitative Traits with Complex Evolutionary Origins

  • Hussein A. Hejase
  • Natalie Vande Pol
  • Gregory M. Bonito
  • Patrick P. Edger
  • Kevin J. Liu

SESSION: Session 5: Clinical Databases and Information Systems

  • Carlo Combi

Learning Deep Representations from Heterogeneous Patient Data for Predictive Diagnosis

  • Chongyu Zhou
  • Yao Jia
  • Mehul Motani
  • Jingwei Chew

Winnow: Interactive Visualization of Temporal Changes in Multidimensional Clinical Data

  • Hsueh-Chien Cheng
  • Rainer von Coelln
  • Ann L. Gruber-Baldini
  • Lisa M. Shulman
  • Amitabh Varshney

Associating Genomics and Clinical Information by Means of Semantic Based Ranking

  • Francesca Cristiano
  • Giuseppe Tradigo
  • Pierangelo Veltri

Tailoring Training for Obese Individuals with Case-Based Reasoning

  • Fabiana Lorenzi
  • Rodrigo G. da Rosa
  • Alessandra Peres
  • Gilson Pires Dorneles
  • Andre Peres
  • Francesco Ricci

SESSION: Session 6: Big Data in Bioinformatics I

  • Ananth Kalyanaraman

SparkGA: A Spark Framework for Cost Effective, Fast and Accurate DNA Analysis at Scale

  • Hamid Mushtaq
  • Frank Liu
  • Carlos Costa
  • Gang Liu
  • Peter Hofstee
  • Zaid Al-Ars

Fast and Highly Scalable Bayesian MDP on a GPU Platform

  • He Zhou
  • Sunil P. Khatri
  • Jiang Hu
  • Frank Liu
  • Cliff Sze

Inferring Microbial Interactions from Metagenomic Time-series Using Prior Biological Knowledge

  • Chieh Lo
  • Radu Marculescu

Secure Cloud Computing for Pairwise Sequence Alignment

  • Sergio Salinas
  • Pan Li

SESSION: Session 7: Advancing Algorithms and Methods I

  • Mukul Bansal

Rich Chromatin Structure Prediction from Hi-C Data

  • Laraib Malik
  • Rob Patro

Cophenetic Median Trees Under the Manhattan Distance

  • Alexey Markin
  • Oliver Eulenstein

DeepCCI: End-to-end Deep Learning for Chemical-Chemical Interaction Prediction

  • Sunyoung Kwon
  • Sungroh Yoon

SESSION: Session 8: Automated Diagnosis and Prediction I

  • May Wang

A Multi-view Deep Learning Method for Epileptic Seizure Detection using Short-time Fourier Transform

  • Ye Yuan
  • Guangxu Xun
  • Kebin Jia
  • Aidong Zhang

TUCUXI: An Intelligent System for Personalized Medicine from Individualization of Treatments to Research Databases and Back

  • Alevtina Dubovitskaya
  • Thierry Buclin
  • Michael Schumacher
  • Karl Aberer
  • Yann Thoma

Interpretable Predictions of Clinical Outcomes with An Attention-based Recurrent Neural Network

  • Ying Sha
  • May D. Wang

Confused or not Confused?: Disentangling Brain Activity from EEG Data Using Bidirectional LSTM Recurrent Neural Networks

  • Zhaoheng Ni
  • Ahmet Cem Yuksel
  • Xiuyan Ni
  • Michael I. Mandel
  • Lei Xie

SESSION: Session 9: Protein and RNA Structure, Dynamics, and Analysis II

  • Henry van den Bedem

Predicting the Effect of Point Mutations on Protein Structural Stability

  • Roshanak Farhoodi
  • Max Shelbourne
  • Rebecca Hsieh
  • Nurit Haspel
  • Brian Hutchinson
  • Filip Jagodzinski

SESSION: Session 10: Advancing Algorithms and Methods II

  • Oliver Eulenstein

Synthesizing Species Trees from Unrooted Gene Trees: A Parameterized Approach

  • Jucheol Moon
  • Oliver Eulenstein

Fleximer: Accurate Quantification of RNA-Seq via Variable-Length k-mers

  • Chelsea J.-T. Ju
  • Ruirui Li
  • Zhengliang Wu
  • Jyun-Yu Jiang
  • Zhao Yang
  • Wei Wang

A Sparse Latent Regression Approach for Integrative Analysis of Glycomic and Glycotranscriptomic Data

  • Xuefu Wang
  • Sujun Li
  • Wenjing Peng
  • Yehia Mechref
  • Haixu Tang

Use of Structural Properties of Underlying Graphs in Pathway Enrichment Analysis of Genomic Data

  • Pourya Naderi Yeganeh
  • M. Taghi Mostafavi

SESSION: Session 11: Applications to Microbes and Imaging Genetics

  • Adam Wright

Seq2seq Fingerprint: An Unsupervised Deep Molecular Embedding for Drug Discovery

  • Zheng Xu
  • Sheng Wang
  • Feiyun Zhu
  • Junzhou Huang

Detection of Differential Abundance Intervals in Longitudinal Metagenomic Data Using Negative Binomial Smoothing Spline ANOVA

  • Ahmed A. Metwally
  • Patricia W. Finn
  • Yang Dai
  • David L. Perkins

Cell Neighbor Determination in the Metazoan Embryo System

  • Zi Wang
  • Dali Wang
  • Husheng Li
  • Zhirong Bao

Predictive and Comparative Network Analysis of the Gut Microbiota in Type 2 Diabetes

  • Mostafa Abbas
  • Yasser EL-Manzalawy

SESSION: Session 12: Systems Biology I

  • Jérôme Waldispühl

Bayesian Collective Markov Random Fields for Subcellular Localization Prediction of Human Proteins

  • Lu Zhu
  • Martin Ester

Differential Community Detection in Paired Biological Networks

  • Raghvendra Mall
  • Ehsan Ullah
  • Khalid Kunji
  • Fulvio D'Angelo
  • Halima Bensmail
  • MIchele Ceccarelli

TINTIN: Exploiting Target Features for Signaling Network Similarity Computation and Ranking

  • Huey Eng Chua
  • Sourav S. Bhowmick
  • Lisa Tucker-Kellogg

SESSION: Session 13: Knowledge Representation Applications

  • Pierangelo Veltri

Determining Optimal Features for Predicting Type IV Secretion System Effector Proteins for Coxiella burnetii

  • Zhila Esna Ashari Esfahani
  • Kelly A. Brayton
  • Shira L. Broschat

Knowledge Rich Natural Language Queries over Structured Biological Databases

  • Hasan M. Jamil

Discovering Inconsistencies in PubMed Abstracts through Ontology-Based Information Extraction

  • Nisansa de Silva
  • Dejing Dou
  • Jingshan Huang

TRuML: A Translator for Rule-Based Modeling Languages

  • Ryan Suderman
  • William S. Hlavacek

SESSION: Session 14: Integrative Methods for Genomic Data

  • Marco Masseroli

HEMnet: Integration of Electronic Medical Records with Molecular Interaction Networks and Domain Knowledge for Survival Analysis

  • Edward W. Huang
  • Sheng Wang
  • Bingxue Li
  • Ran Zhang
  • Baoyan Liu
  • Runshun Zhang
  • Jie Liu
  • Xuezhong Zhou
  • Hongsheng Lin
  • ChengXiang Zhai

A Novel Approach for Classifying Gene Expression Data using Topic Modeling

  • Soon Jye Kho
  • Hima Bindu Yalamanchili
  • Michael L. Raymer
  • Amit P. Sheth

Differential Compound Prioritization via Bi-Directional Selectivity Push with Power

  • Junfeng Liu
  • Xia Ning

SESSION: Session 15: Sdequence Analysis and Genome Assembly

  • Christina Boucher

Understanding Sequence Conservation With Deep Learning

  • Yi Li
  • Daniel Quang
  • Xiaohui Xie

SeqyClean: A Pipeline for High-throughput Sequence Data Preprocessing

  • Ilya Y. Zhbannikov
  • Samuel S. Hunter
  • James A. Foster
  • Matthew L. Settles

Distributed Memory Partitioning of High-Throughput Sequencing Datasets for Enabling Parallel Genomics Analyses

  • Nagakishore Jammula
  • Sriram P. Chockalingam
  • Srinivas Aluru

Scalable Genomic Assembly through Parallel de Bruijn Graph Construction for Multiple K-mers

  • Kanak Mahadik
  • Christopher Wright
  • Milind Kulkarni
  • Saurabh Bagchi
  • Somali Chaterji

SESSION: Session 16: Applications to Healthcare Processes

  • Alistair Johnson

Co-MEAL: Cost-Optimal Multi-Expert Active Learning Architecture for Mobile Health Monitoring

  • Ramyar Saeedi
  • Keyvan Sasani
  • Assefaw H. Gebremedhin

Antidote Application: An Educational System for Treatment of Common Toxin Overdose

  • Jon B. Long
  • Yingyuan Zhang
  • Vladimir Brusic
  • Lou Chitkushev
  • Guanglan Zhang

Automated Off-label Drug Use Detection from User Generated Content

  • Mengnan Zhao
  • Christopher C. Yang

SESSION: Session 17: Biological Modeling

  • Naveena Yanamala

Circadian Rhythms in Neurospora Exhibit Biologically Relevant Driven and Damped Harmonic Oscillations

  • Hannah De los Santos
  • Emily J. Collins
  • Jennifer M. Hurley
  • Kristin P. Bennett

Hybrid ODE/SSA Model of the Budding Yeast Cell Cycle Control Mechanism with Mutant Case Study

  • Mansooreh Ahmadian
  • Shuo Wang
  • John Tyson
  • Young Cao

RBFNN-based Modelling and Analysis for the Signal Reconstruction of Peripheral Nerve Tissue

  • Qichun Zhang
  • Francisco Sepulveda

SESSION: Session 18: Systems Biology II

  • Xinghua (Mindy) Shi

Reverse Engineering Gene Networks: A Comparative Study at Genome-scale

  • Sriram P. Chockalingam
  • Maneesha Aluru
  • Hongqing Guo
  • Yanhai Yin
  • Srinivas Aluru

Unsupervised Multi-View Feature Selection for Tumor Subtype Identification

  • Sultan Imangaliyev
  • Evgeni Levin

Computational Intractability Generates the Topology of Biological Networks

  • Ali Atiia
  • Corbin Hopper
  • Jérôme Waldispühl

A Flexible and Robust Multi-Source Learning Algorithm for Drug Repositioning

  • Huiyuan Chen
  • Jing Li

SESSION: Session 19: Automated Diagnosys and Prediction II

  • Dong Si

Tensor-Factorization-Based Phenotyping using Group Information: Case Study on the Efficacy of Statins

  • Jingyun Choi
  • Yejin Kim
  • Hun-Sung Kim
  • In Young Choi
  • Hwanjo Yu

Infer Cause of Death for Population Health Using Convolutional Neural Network

  • Hang Wu
  • May D. Wang

Automated Breast Cancer Diagnosis Using Deep Learning and Region of Interest Detection (BC-DROID)

  • Richard Platania
  • Shayan Shams
  • Seungwon Yang
  • Jian Zhang
  • Kisung Lee
  • Seung-Jong Park

A Physiological Thermal Regulation Model with Application to the Diagnosis of Diabetic Peripheral Neuropathy

  • Viktor Chekh
  • Peter Soliz
  • Mark Burge
  • Shuang Luan

SESSION: Session 20: Big Data in Bioinformatics II

  • Tom Pollard

An Out-of-Core GPU based Dimensionality Reduction Algorithm for Big Mass Spectrometry Data and Its Application in Bottom-up Proteomics

  • Muaaz Gul Awan
  • Fahad Saeed

Building Applications for Interactive Data Exploration in Systems Biology

  • Bjørn Fjukstad
  • Vanessa Dumeaux
  • Karina Standahl Olsen
  • Eiliv Lund
  • Michael Hallett
  • Lars Ailo Bongo

Mining Faces from Biomedical Literature using Deep Learning

  • Mitchell Dawson
  • Andrew Zisserman
  • Christoffer Nellåker

A Correlation Network Model Utilizing Gait Parameters for Evaluating Health Levels

  • Elham Rastegari
  • Hesham Ali

POSTER SESSION: Poster Session

Study of Antidepressant Molecular Structure Leading to Safer Dosing

  • Meera Garg

Supervised Machine Learning Approaches Predict and Characterize Nanomaterial Exposures: MWCNT Markers in Lung Lavage Fluid.

  • Naveena Yanamala
  • Marlene S. Orandle
  • Vamsi K. Kodali
  • Lindsey M. Bishop
  • Patti C. Zeidler-Erdely
  • Jenny R. Roberts
  • Vincent Castranova
  • Aaron Erdely

Prokaryotic Autolysin Database Construction

  • Brandon A. Saiz
  • Padmanabhan Mahadevan

The Fate of Retrotransposed Processed Genes in Arabidopsis Thaliana

  • Basma Abdelkarim
  • Vincent Maranda
  • Guy Drouin

Super-enhancer Dynamics Throughout Myogenesis

  • Basma Abdelkarim
  • Theodore Perkins

Varsimlab: A Docker-based Pipeline to Automatically Synthesize Short Reads with Genomic Aberrations

  • Abdelrahman Hosny
  • Fatima Zare
  • Sheida Nabavi

An Advanced Workflow for Metabolite Annotation

  • Neda Hassanpour
  • Nicholas Alden
  • Kyongbum Lee
  • Soha Hassoun

Development of a Polymer-Theoretic Approach to Describing Constraints on Reactions Between Antipeptide Antibodies and Intrinsically Disordered Peptide Antigens: Implications for B-Cell Epitope Prediction

  • Salvador Eugenio C. Caoili

Development of Nicotinic Acetylcholine Receptor nAChR α7 Binding Activity Prediction Model: Coupling Machine Learning with Competitive Molecular Docking

  • Huixiao Hong
  • Carmine Leggett
  • Suguna Sakkiah

Automated Next Generation Sequencing Bioinformatics Pipelines for Pathogen Discovery and Surveillance

  • Margaret Okomo-Adhiambo
  • Edward Ramos
  • Reagan Kelly
  • Yatish Jain
  • Roman Tatusov
  • Anna Montmayeur
  • Gregory Doho
  • Rachel L. Marine
  • Terry Fei Fan Ng
  • Adam Retchless
  • Steve Oberste
  • Paul Rota
  • Xin Wang
  • Agha N. Khan

Protein Classification using Modified N-Gram and Skip-Gram Models: Extended Abstract

  • SM Ashiqul Islam
  • Christopher Michel Kearney
  • Ankan Choudhury
  • Erich J. Baker

Self-Tuning Spectral Clustering for Full-length Viral Quasispecies Reconstruction with PacBio Long Reads

  • Xiaoli Jiao
  • Hiromi Imamichi
  • Tauseef Rehman
  • Rishub Nahar
  • Robin L. Dewar
  • H. Clifford Lane
  • Tomozumi Imamichi
  • Brad T. Sherman

Best Setting of Model Parameters in Applying Topic Modeling on Textual Documents.

  • Wen Zou
  • Weizhong Zhao
  • James J. Chen
  • Roger Perkins

Neopepsee: Accurate Genome-level Prediction of Neoantigens by Harnessing Sequence and Amino Acid Immunogenicity Information

  • Sora Kim
  • Han Sang Kim
  • Sangwoo Kim

Novel Unsupervised Named Entity Recognition Used in Text Annotation Tool (OntoMate) At Rat Genome Database

  • Omid Ghiasvand
  • Mary Shimoyama

Bias and Noise Cancellation for Robust Copy Number Variation Detection

  • Fatima Zare
  • Sardar Ansari
  • Kayvan Najarian
  • Sheida Nabavi

Applying Bayesian Changepoint Model and Hierarchical Divisive Model for Detecting Anomalies in Clinical Decision Support Alert Firing

  • Soumi Ray
  • Adam Wright

Preconditioned Random Forest Regression: Application to Genome-Wide Study for Radiotherapy Toxicity Prediction

  • Sangkyu Lee
  • Sarah Kerns
  • Barry Rosenstein
  • Harry Ostrer
  • Joseph O. Deasy
  • Jung Hun Oh

Outlier Genes as Biomarkers of Breast Cancer Survivability in Time-Series Data

  • Naveen Mangalakumar
  • Abed Alkhateeb
  • Huy Quang Pham
  • Luis Rueda
  • Alioune Ngom

Pisces: An Accurate and Versatile Single Sample Somatic and Germline Variant Caller

  • Tamsen Dunn
  • Gwenn Berry
  • Dorothea Emig-Agius
  • Yu Jiang
  • Anita Iyer
  • Nitin Udar
  • Michael Strömberg

Nirvana: Clinical Grade Variant Annotator

  • Michael Stromberg
  • Rajat Roy
  • Julien Lajugie
  • Yu Jiang
  • Haochen Li
  • Elliott Margulies

Streptomyces Clavuligerus Constraint-Based Modeling and Gene Expression Analysis for Clavulanic Acid Production

  • León F. Toro
  • Laura Pinilla-Mendoza
  • Rigoberto Ríos-Estepa

Notch Signaling Plays an Important Role in mTEC Specification during Fetal Thymus Development

  • Dong Liu
  • Anastasia I. Kousa
  • Simon R. Tomlinson
  • C. Clare Blackburn

Analysis of 16S Genomic Data using Graphical Databases

  • Olivia M. Ahern
  • Rebecca J. Stevick
  • Li Yuan
  • Noah M. Daniels

High Dimensional Ensemble Neuronal Activity Pattern Analysis: Visualization and Wave Detection Focused

  • Varshini Guddanti
  • Shawn Horvatic
  • Jie Zhou
  • Yujia Hu
  • Bing Ye

Tumor Neoantigens Derived from RNA Sequencing Analysis

  • Shaojun Tang
  • Suthee Rapisuwon
  • Anton Wellstein
  • Subha Madhavan

Challenges in Prediction of different Cancer Stages using Gene Expression Profile of Cancer Patients

  • Sherry Bhalla
  • Suresh Sharma
  • Gajendra Pal Singh Raghava

NGSPipes: Fostering Reproducibility and Scalability in Biosciences

  • Bruno Dantas
  • Calmenelias Fleitas
  • Alexandre Almeida
  • João Forja
  • Alexandre P. Francisco
  • José Simão
  • Cátia Vaz

Dynamic Phylogenetic Inference for Sequence-based Typing Data

  • Alexandre P. Francisco
  • Marta Nascimento
  • Cátia Vaz

Classification and Prediction of Antimicrobial Peptides Using N-gram Representation and Machine Learning

  • Manal Othman
  • Sujay Ratna
  • Anant Tewari
  • Anthony M. Kang
  • Katherine Du
  • Iosif I. Vaisman

Network Analysis Identifies Regulatory Hotspots in Regions of Chromosome Interactions

  • Anastasiya Belyaeva
  • Saradha Venkatachalapathy
  • Mallika Nagarajan
  • G.V. Shivashankar
  • Caroline Uhler

Machine Learning Model for Identifying Gene Biomarkers for Breast Cancer Treatment Survival

  • Ashraf Abou Tabl
  • Abed Alkhateeb
  • Waguih ElMaraghy
  • Alioune Ngom

Genome-Wide Association Study (GWAS) for the Infliximab Responsiveness in Korean Inflammatory Bowel Disease Patients

  • Zewon Park
  • Ko-Woon Choi
  • Doo Won Seo
  • Sunae Ryu
  • Jong Gu Lee
  • Woo Yong Oh

Integrating Prior Information with Bayesian Feature Selection

  • Ali Foroughi pour
  • Lori A. Dalton

An Integrated Reconciliation Framework for Domain, Gene, and Species Level Evolution

  • Lei Li
  • Mukul S. Bansal

Assessing the Impact of Uncertain Gene Tree Rooting on Phylogenetic Reconciliation Using a Simulation Framework

  • Soumya Kundu
  • Mukul S. Bansal

Overlap Graph Reduction for Genome Assembly using Apache Spark

  • Alexander J. Paul
  • Dylan Lawrence
  • Tae-Hyuk Ahn

A Cross-Platform System Architecture for Form Design and Data Analytics for Public Health

  • Blake Camp
  • Jaya Mandivarapu
  • Jay Mehta
  • Nagashayana Ramamurthy
  • James Wingo
  • Anu G. Bourgeois
  • Xiaojun Cao
  • Rajshekhar Sunderraman

Deep Residual Nets for Improved Alzheimer's Diagnosis

  • Aly Valliani
  • Ameet Soni

Integrative Sufficient Dimension Reduction Methods for Multi-Omics Data Analysis

  • Yashita Jain
  • Shanshan Ding

Predicting Breast Cancer Outcome under Different Treatments by Feature Selection Approaches

  • Huy Quang Pham
  • Luis Rueda
  • Alioune Ngom

Breaking Ties in Weighted Interactomes

  • Ibrahim Youssef
  • Anna Ritz

Microbiome Dynamics as Predictors of Lung Transplant Rejection

  • Ahmed Metwally
  • Christian Ascoli
  • Kalista Andropolis
  • Ravi Ranjan
  • Yang Dai
  • Thomas Ferkol
  • Patricia Finn
  • David Perkins

Analysis of Controls in ChIP-seq

  • Aseel Awdeh
  • Theodore J. Perkins

SeqAnt: Cloud-Based Whole-Genome Annotation and Search

  • Alex V. Kotlar
  • Cristina E. Trevino
  • Michael E. Zwick
  • David J. Cutler
  • Thomas S. Wingo

A Tool for Predicting the Dark Side of Enzymes

  • Linfeng Liu
  • Soha Hassoun

Pathway Enrichment Analysis for Untargeted Metabolomics

  • Vladimir Porokhin
  • Xinmeng Li
  • Soha Hassoun

Towards the Design of Matrix Metalloproteinases (MMP) Antibody Sequences

  • Xinmeng Li
  • James Van Deventer
  • Soha Hassoun

ProSol DB: A Protein Solubility Database

  • Sara A. Amin
  • Venkatesh Endalur Gopinarayanan
  • Nikhil U. Nair
  • Soha Hassoun

Building a Molecular Taxonomy of Disease

  • Jisoo Park
  • Benjamin J. Hescott
  • Donna K. Slonim

Network Analysis of Correlated Mutations in Influenza

  • Uday Yallapragada
  • Iosif I. Vaisman


ACM-BCB '17 Tutorial: Robotics-inspired Algorithms for Modeling Protein Structures and Motions

  • Kevin Molloy
  • David Morris
  • Amarda Shehu

Computational Modeling of Protein-RNA Interactions

  • Yaron Orenstein

Stochastic Process Model and Its Applications to Analysis of Longitudinal Data

  • Ilya Y. Zhbannikov
  • Konstantin G. Arbeev

Analyzing the eICU Collaborative Research Database

  • Alistair E.W. Johnson
  • Tom J. Pollard
  • Leo A. Celi
  • Roger G. Mark

SESSION: Invited Keynote Talks

Instrumenting the Health Care Enterprise for Discovery in the Course of Clinical Care

  • Shawn Murphy

Challenges of Drug Design

  • Dagmar Ringe

Genome-scale Estimation of the Tree of Life

  • Tandy Warnow

SESSION: Highlights

Highlights Talks at ACM BCB 2017

  • Amarda Shehu
  • Tamer Kahveci
  • Giuseppe Pozzi

Model-based Transcriptome Engineering

  • Michael Brent

Analysis of Single Cells on a Pseudotime Scale along Postnatal Pancreatic Beta Cell Development

  • Francesca Mulas
  • Chun Zeng
  • Yinghui Sui
  • Tiffany Guan
  • Nathanael Miller
  • Yuliang Tan
  • Fenfen Liu
  • Wen Jin
  • Andrea C. Carrano
  • Mark O. Huising
  • Orian Shirihai
  • Gene W. Yeo
  • Maike Sander

Drug Response Prediction as a Link Prediction Problem

  • Zachary Stanfield
  • Mustafa Coskun
  • Mehmet Koyuturk

Fast, Clash-Free RNA Conformational Morphing using Molecular Junctions

  • A. Heliou
  • Dominik Budday
  • Rasmus Fonseca
  • Henry van den Bedem

Network-based Interpretation of Diverse High-Throughput Datasets through the Omics Integrator Software Package

  • Amanda J. Kedaigle

3D Genome Structure Modeling by Lorentzian Objective Function

  • Tuan Trieu
  • Jianlin Cheng

Folding Large Proteins by Ultra-Deep Learning

  • Jinbo Xu

SESSION: Computational Structural Bioinformatics Workshop (CSBW)

The 2017 Computational Structural Bioinformatics Workshop: CSBW 2017

  • Nurit Haspel
  • Amarda Shehu
  • Kevin Molloy

Computational Modeling of pH-dependent gp120-CD4 Interactions in Founder and Chronic HIV Strains

  • Jonathan Howton
  • Joshua L. Phillips

Analysis of ß-strand Twist from the 3-dimensional Image of a Protein

  • Tunazzina Islam
  • Michael Poteat
  • Jing He

ProMuteHT: A High Throughput Compute Pipeline for Generating Protein Mutants in silico

  • Erik Andersson
  • Filip Jagodzinski

String-Based Models for Predicting RNA-Protein Interaction

  • Donald Adjeroh
  • Maen Allaga
  • Jun Tan
  • Jie Lin
  • Yue Jiang
  • Ahmed Abbasi
  • Xiaobo Zhou

Ranking Protein-Protein Binding Using Evolutionary Information and Machine Learning

  • Roshanak Farhoodi
  • Bahar Akbal-Delibas
  • Nurit Haspel

Evolving Conformation Paths to Model Protein Structural Transitions

  • Emmanuel Sapin
  • Kenneth De Jong
  • Amarda Shehu

Statistical Analysis of Computed Energy Landscapes to Understand Dysfunction in Pathogenic Protein Variants

  • Wanli Qiao
  • Tatiana Maximova
  • Erion Plaku
  • Amarda Shehu

Automated Protein Chain Isolation from 3D Cryo-EM Data and Volume Comparison Tool

  • Michael Nissenson
  • Dong Si

A Graph Based Method for the Prediction of Backbone Trace from Cryo-EM Density Maps

  • Peter Collins
  • Dong Si

Investigating Rigidity Properties of Protein Cavities

  • Stephanie Mason
  • Tim Woods
  • Brian Chen
  • Filip Jagodzinski

Geometric Sampling Framework for Exploring Molecular Walker Energetics and Dynamics

  • Bruna Jacobson
  • Jon Christian L. David
  • Mitchell C. Malone
  • Kasra Manavi
  • Susan R. Atlas
  • Lydia Tapia

Gaussian Mixture Models with Constrained Flexibility for Fitting Tomographic Tilt Series

  • Kasra Manavi
  • Sahba Tashakkori
  • Lydia Tapia

Geometry Analysis for Protein Secondary Structures Matching Problem

  • Kamal Al Nasr
  • Feras Yousef
  • Christopher Jones
  • Ruba Jebril

WORKSHOP SESSION: 6th Workshop on Parallel and Cloud-based Bioinformatics and Biomedicine (ParBio)

ParBio'17: 6th Workshop on Parallel and Cloud-based Bioinformatics and Biomedicine

  • Mario Cannataro
  • John A. Springer

GPU-PCC: A GPU Based Technique to Compute Pairwise Pearson's Correlation Coefficients for Big fMRI Data

  • Taban Eslami
  • Muaaz Gul Awan
  • Fahad Saeed

Ensemble Convolution Neural Network with a Simple Voting Method for Lung Tumor Detection

  • Allison M. Rossetto
  • Wenjin Zhou

Fuzzy Prediction of Incipient Alzheimer's Disease cases from Mild Cognitive Impaired cases

  • Oriehi E.D. Anyaiwe
  • Gautam B. Singh

Using GenotypeAnalytics to Analyze Pharmacogenomic Datasets

  • Giuseppe Agapito
  • Pietro Hiram Guzzi
  • Mario Cannataro

Discovery of Regular Domains in Large DNA Data Sets

  • Francesca Bertacchini
  • Eleonora Bilotta
  • Pietro Pantano

WORKSHOP SESSION: 4th International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC)

CNB-MAC'17: The Fourth International Workshop on Computational Network Biology: Modeling, Analysis, and Control

  • Byung-Jun Yoon
  • Xiaoning Qian
  • Tamer Kahveci

Bayesian Graphical Models for Computational Network Biology

  • Yang Ni
  • Peter Müller
  • Lin Wei
  • Yuan Ji

Detangling PPI Networks to Uncover Functionally Meaningful Clusters

  • Sarah Hall-Swan
  • Jake Crawford
  • Rebecca Newman
  • Lenore J. Cowen

SMILE: A Novel Procedure for Subcellular Module Identification with Localization Expansion

  • Lixin Cheng
  • Pengfei Liu
  • Kwong-Sak Leung

Overlapping Functional Modules Detection in PPI Network with Pairwise Constrained Nonnegative Matrix Tri-Factorization

  • Guangming Liu
  • Bianfang Chai
  • Kuo Yang
  • Xuezhong Zhou
  • Jian Yu

Heuristic Algorithms for Feature Selection under Bayesian Models with Block-diagonal Covariance Structure

  • Ali Foroughi pour
  • Lori A. Dalton

Feature Selection with Interactions in Logistic Regression Models using Multivariate Synergies for a GWAS Application

  • Easton Li Xu
  • Xiaoning Qian
  • Qilian Yu
  • Han Zhang
  • Shuguang Cui

Simulating Variance Heterogeneity in Quantitative Genome Wide Association Studies

  • Ahmad Al Kawam
  • Mustafa Alshawaqfeh
  • James Cai
  • Erchin Serpedin
  • Aniruddha Datta

Sparse Tensor Decomposition for Haplotype Assembly of Diploids and Polyploids

  • Abolfazl Hashemi
  • Banghua Zhu
  • Haris Vikalo

Intrinsically Bayesian Robust Classifier for Single-Cell Gene Expression Time Series in Gene Regulatory Networks

  • Alireza Karbalayghareh
  • Ulisses Braga-Neto
  • Edward R. Dougherty

Constraints On Signaling Networks Logic Reveal Functional Subgraphs On Multiple Myeloma OMIC Data

  • Bertrand Miannay
  • Stéphane Minvielle
  • Olivier Roux
  • Florence Magrangeas
  • Carito Guziolowski

Protein-Protein Interaction Extraction Using Attention-Based Convolution Neural Networks

  • Hao Zhang
  • Mary Qu Yang
  • Xiaoyue Feng
  • William Yang
  • Weida Tong
  • Renchu Guan

Investigation of Model Stacking for Drug Sensitivity Prediction

  • Kevin Matlock
  • Carlos De Niz
  • Raziur Rahman
  • Souparno Ghosh
  • Ranadip Pal

A Bayesian Approach to Determine the Composition of Heterogeneous Cancer Tissue

  • Ashish Katiyar
  • Anwoy Mohanty
  • Chao Sima
  • Jianping Hua
  • Rosana Lopes
  • Aniruddha Datta
  • Michael L. Bittner

WORKSHOP SESSION: 6th Workshop on Computational Advances in Molecular Epidemiology (CAME 2017)

CAME 2017: 6th Workshop on Computational Advances in Molecular Epidemiology

  • Yury Khudyakov
  • Ion Mandoiu
  • Pavel Skums
  • Alexander Zelikovsky

WORKSHOP SESSION: Workshop on Microbiomics, Metagenomics, and Metabolomics

A Workshop on Microbiomics, Metagenomics, and Metabolomics

  • Soha Hassoun
  • Curtis Huttenhower
Important Dates
Call for Submission Deadline Notification of Acceptance
Papers April 24 June 7
Workshops March 17 March 20
Tutorials March 17 March 20
Highlights May 8 June 7
Posters June 11 June 19


ACM-BCB 2017 papers now available through ACM DL

August 17, 2017

ACM-BCB 2017 tutorials are now posted

August 11, 2017

Preliminary program booklet posted

June 22, 2017

Poster submission deadline extended to June 11

May 25, 2017

Registration is open

May 17, 2017

Paper submission deadline extended to April 24

April 8, 2017

ACM-BCB 2017 Call for Posters dates updated

April 8, 2017

ACM-BCB 2017 Call for Highlights is now posted

March 13, 2017

Workshop proposal deadline extended to March 17

March 10, 2017

Venue information is available

January 18, 2017

ACM-BCB 2017 Call for Papers is now posted

January 5, 2017