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

TUTORIAL SESSION: Tutorials

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