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GLBIO 2017 | May 15- 17, 2017 | Univ. of Illinois at Chicago |Accepted Papers and Abstracts for Talks


Link within this page: Abstracts for Oral Presentations

De-novo transcriptome analysis provides novel insight to the biology of giant intestinal fluke Fasciolopsis buski Devendra Biswal, Tanmoy Roychowdhury, Priyatama Pandey, Alok Bhattacharya and Veena Tandon
Minimum variance rooting of phylogenetic trees and implications for species tree reconstruction Uyen Mai, Erfan Sayyari and Siavash Mirarab
Parametric Studies of Metabolic Cooperativity in Escherichia coli Colonies: Strain and Geometric Confinement Effects Joseph Peterson, John Cole and Zaida Luthey-Schulten
CRISPRpred: A flexible and efficient tool for sgRNAs on-target activity prediction in CRISPR/Cas9 systems Md. Khaledur Rahman and M. Sohel Rahman
Uncovering Robust Patterns of MicroRNA Co-Expression across Cancers Using Bayesian Relevance Networks Parameswaran Ramachandran, Daniel Sanchez-Taltavull and Theodore Perkins
Identification of Potential Antimicrobials against Salmonella typhimurium and Listeria monocytogenes using Quantitative Structure-Activity Relation Modeling Ethan Rath, Hunter Gill and Yongsheng Bai
The Breast Cancer Microbiome and Host Biology Kevin J. Thompson, James N. Ingle, Xiaojia Tang, Nicholas Chia, Patricio R. Jeraldo, Marina R. Walther-Antonio, Karunya K. Kandimalla, Stephen Johnson, Janet Z. Yao, Sean C. Harrington, Vera J. Suman, Liewei Wang, Richard L. Weinshilboum, Judy C. Boughey, Jean-Pierre Kocher, Heidi Nelson, Matthew P. Goetz and Krishna R. Kalari
Clust: automatic identification and optimisation of consensus clusters of co-expressed genes from multiple heterogeneous transcriptomic datasets Basel Abu-Jamous and Steve Kelly
Method for region-specific population health prediction using virtual populations based on a simulation model of individual health Charul Aggarwal, Pallavi Grover, Mahesh Dadhich, Joydeep Sarkar, Samuel Burns and Gaurav Dwivedi
TBA Frank Alber
In sickness and in health: Gene regulation via 3D chromatin organization Ferhat Ay
The role of viral transmission between wild and domestic animals in the spread emerging infectious diseases Justin Bahl, Xueting Qiu, Joseph Hicks and Truc Pham
Integrative analysis to evaluate similarity between ‘BRCAness’ tumors and BRCA tumors Weston Bodily and Stephen Piccolo
One Library’s Focus on Visualization Services and Guiding Principles Marci Brandenburg
Virtual Lock Masses: an algorithmic method to enable mass spectra comparison in untargeted studies Francis Brochu, Pier-Luc Plante, Alexandre Drouin, Mario Marchand, Jacques Corbeil and François Laviolette
Seten: A tool for systematic identification and comparison of processes, phenotypes and diseases associated with RNA-binding proteins from condition-specific CLIP-seq profiles Gungor Budak, Rajneesh Srivastava and Sarath Chandra Janga
Simple Computational Tools for RNA-seq Isoform Analysis Ben Busby
A versatile pipeline to simulate Hi-C data with genomic rearrangements (AVeSim) Abhijit Chakraborty and Ferhat Ay
Integrating Genomics and Clinical Outcomes Data to Optimize Patient Matching James Chen
Modeling the Microbiome in Colorectal Cancer: emerging approaches to an old problem Nicholas Chia
Novel inferences from Hi-C data with protein-coding gene data Davide Chicco, Sarah Bi, Jüri Reimand and Michael Hoffman
Network science inspires tree shape statistics informative of viral phylogeography Leonid Chindelevitch, Art Poon and Caroline Colijn
vKLAT: A High-Throughput Alignment Tool for Mapping Shotgun Reads to Reference Database with Variants Jeremy Cox and Alexey Porollo
Using metabolic networks to probe the symbiosis between Wolbachia and filarial nematodes David Curran, Nirvana Nursimulu, Alexandra Grote, Elodie Ghedin and John Parkinson
EClerize: A Customized Force-Directed Layout Algorithm for Biological Networks with EC Attributes Hasan F. Danaci, Rengul Atalay and Volkan Atalay
Computational Prediction of Novel Drug Candidate Compound – Target Protein Interactions and Their Verification on PI3K/AKT/mTOR Signalling Pathway Tunca Dogan, Ece Akhan, Marcus Baumann, Andrew Nightingale, Ian Baxendale, Maria Martin and Rengul Cetin-Atalay
Rule-based machine learning algorithms for antimicrobial resistance prediction Alexandre Drouin, Frédéric Raymond, Gaël Letarte St-Pierre, Mario Marchand, Jacques Corbeil and François Laviolette
Epidemiologists who use the ‘Omics: A case in point' Lara Dugas, Amy Luke, Brian Layden, Jack Gilbert, Julia Goedecke, Vicki Lambert, Jacob Plange-Rhule and Beatrice Penalver
How trauma affects the fate of Pseudomonas aeurginosa in blood Moamen Elmassry, Nithya Mudaliar, Rao Kottapalli, Sharmila Dissanaike, John Griswold, Michael San Francisco, Jane Colmer-Hamood and Abdul Hamood
High-resolution tracking of microbial colonization in Fecal Microbiota Transplantation experiments via metagenome-assembled genomes A. Murat Eren
Metapangenomics: Linking the genomic traits and niche partitioning of microbial populations A. Murat Eren
Improving biomass compositions across 70.000 phylogenetically diverse genome-scale metabolic models José P. Faria, Janaka N. Edirisinghe, Samuel M. D. Seaver, James G. Jeffryes, Pamela Weisenhorn, Tian Gu, Qizh Zhang and Christopher S. Henry
From high school to postdoc: lessons from a decade of bioinformatics education Mallory Freeberg
The National Center for Genome Analysis Support Carrie Ganote, Thomas Doak, Philip Blood and Sheri Sanders
Chromosome scale de novo assembly of mammalian genomes using chromatin interaction data Jay Ghurye, Mihai Pop, Sergey Koren, Derek Bickhart and Chen-Shan Chin
Compositionally-appropriate linear association in high-throughput sequencing data   
Greg Gloor, Vera Pawlowsky-Glahn and Juan Jose Egozcue
From Homogeneous to Heterogeneous Network Alignment Shawn Gu and Tijana Milenkovic
Bacteriocin Detection with Autoencoder and  Support Vector Machines Md Nafiz Hamid and Iddo Friedberg
Linking intracellular metabolism to microbial ecosystem dynamics in structured environments William Harcombe
Phylo-PFP: Highly accurate phylogenomics based protein function prediction method Aashish Jain and Daisuke Kihara
The dark matter of the human gut microbiome follows neutral ecological assembly rules Patricio Jeraldo, Lisa Boardman, Bryan A. White, Heidi Nelson, Nigel Goldenfeld and Nicholas Chia
Assessment of intra-tumor genetic heterogeneity and evolutionary dynamics in lung cancer Chuan Jiang, Anchal Sharma, Greg Riedlinger, Jyoti Malhotra, Lorna Rodriguez and Subhajyoti De
Phenome-wide association studies of Polycystic Ovary Syndrome (PCOS) Yoonjung Yoonie Joo, M Geoffrey Hayes, Jennifer Allen Pacheco, Margrit Urbanek and Abel N Kho
Statistical methods for profiling long range chromatin interactions from repetitive regions of the genome Sunduz Keles
Variant calling by assembly for detection of transposable element movement in Glycine max Matthew Kendzior, Junyu Li, Luidmila Mainzer and Matthew Hudson
Computational Immunology: new computational approaches to understand immune function Aly Khan
geneXtendeR: R/Bioconductor package for functional annotation of histone modification ChIP-seq data in a 3D genome world Bohdan Khomtchouk, Derek Van Booven and Claes Wahlestedt
Evolution of modular organization of chromatin states Sara Knaack, Lina Antounians, Alejandra Medina-Rivera, Azad Alizada, Sushmita Roy and Michael Wilson
Visualizing and exploring chromatin interactions using the self-organizing map Tim Kunz and Shaun Mahony
Integrating metagenomics and metatranscriptomics to understand microbial communities Jason Kwan
Assessment of methods for finding regulatory sites based on ChIP-seq experiments Istvan Ladunga, Avi Knecht, Adam Caprez, Natasha Pavlovikj, Timothy L. Bailey, Tao Liu and David Swanson
Modeling Emergent Properties of the Mouse Gut Microbiome and Their Effects on Host Obesity Peter Larsen and Yang Dai
Disease gene prioritization by integrating and visualizing multiple genomic data Xing Li, Timothy Nelson and Jean-Pierre Kocher
An integrative approach for ChIP-exo identifies previously unrecognized direct binding of a transcription factor Hee-Woong Lim and Kyoung-Jae Won
New framework for classification in biological networks Jose Lugo-Martinez and Predrag Radivojac
Stochastic Simulations of Cellular Processes: From Single Cells to Colonies Zan Luthey-Schulten
A Logical Approach to Modelling the Three-Dimensional Genome Kimberly MacKay, Christopher Eskiw and Anthony Kusalik Kimberly MacKay, Christopher Eskiw and Anthony Kusalik
How robust are our semantic similarity measurements? Prashanti Manda, James Balhoff and Todd Vision
Chromatin Accessibility Analysis for Biological/Clinical Applications Ewy Mathe
Time Series Analysis of Microbiome Associations with Disease Outcomes Ahmed Metwally, Patricia Finn, David Perkins and Yang Dai
Optimizing predictors of gene expression within and across diverse populations using the Multiethnic Study of Atherosclerosis Lauren Mogil and Heather Wheeler
How reliable are protein structures determined by electron microscopy? Lyman Monroe, Genki Terashi and Daisuke Kihara
NIBLSE: A network to fully integrate bioinformatics into undergraduate life science education William Morgan, Elizabeth Dinsdale, Anne Rosenwald, Eric Triplett and Mark Pauley
Reformulating confidence substantially improves taxonomic classification of DNA sequences Adithya Murali, Aniruddha Bhargava and Erik Wright
Systematic Exploration of Single-Cell Morphological Phenotypes from Transcriptomic Profile Isar Nassiri and Matthew McCall
A novel computational framework to identify novel drug targets: a case study of kinase inhibitors Hammad Naveed
HIPPI (Hierarchical Profile Hidden Markov Models for Protein family Identification) Nam Nguyen, Michael Nute, Siavash Mirarab and Tandy Warnow
The Genetic Basis of Cross-Tissue Protein Expression Variability in Humans Meritxell Oliva, Fernando Marian, Linke Caroline, Wu Fan, Andrew Skol and Barbara E. Stranger
Functional signatures and impact of loss-of-function genetic variants Kymberleigh Pagel, Vikas Pejaver, Guan Ning Lin, Hyunjun Nam, Matthew Mort, David N. Cooper, Jonathan Sebat, Lilia M. Iakoucheva, Sean D. Mooney and Predrag Radivojac
Towards More Robust Metagenome Profiling Ravi Shanker Pandey, David Burks and Rajeev Azad
Predicting topological domains from ChIP-seq data using pairwise feature extraction Rohan Paul, Jianlin Shao and Ferhat Ay
Microbes Everywhere David Perkins, Ahmed Metwally and Patricia Finn
Experiences teaching bioinformatics skills to novices and to advanced undergraduates Stephen Piccolo
ADAR footprints: insights into molecular evolution of the Zika virus (ZIKV; Flaviviridae) Helen Piontkivska, Madeline Frederick, Michael Miyamoto and Marta Wayne
Human protein-RNA interaction network is highly stable across vertebrates and exhibits extensive conservation of mRNA targets on 3' regions of genes Aarthi Ramakrishnan and Sarath Chandra Janga
Inferring horizontal gene transfer by pangenome analysis Frederic Raymond, Maxime Deraspe, Maurice Boissinot and Jacques Corbeil
A Convolutional Neural Network Approach to Analysing Association of Microbiome and Phenotype Derek Reiman, Yang Dai and Ahmed Metwally
De Novo Assembly of Lucina pectinata Genome Using Ion Semiconductor Sequence Reads Alexander Ropelewski, Ingrid Montes-Rodriguez, Ricardo Gonzalez Mendez, Carmen Cadilla and Juan Lopez-Garriga
Bioinformatics Professional Development Needs of Faculty at Minority Serving Institutions. Alexander Ropelewski, Ricardo Gonzalez Mendez, Jimmy Torres, Hugh Nicholas and Pallavi Ishwad
Computational methods to study dynamics of long-range gene regulation Sushmita Roy
Chromosome Conformation in Context Michael Sauria, Teresa Luperchio, Karen Reddy and James Taylor
Fast Coalescent-Based Branch Support Using Local Quartet Frequencies Erfan Sayyari and Siavash Mirarab
Nucleotide sequence and DNaseI sensitivity are predictive of 3D chromatin architecture Jacob Schreiber, Maxwell Libbrecht, Jeffrey Bilmes and William Noble
Evolving Standards for Graduate Education in Computational Biology Russell Schwartz
Linking geospatial mentions in journal articles to GenBank records for virus phylogeography Matthew Scotch and Graciela Gonzalez
Half-Sibling Reconstruction Using Forbidden Subgraphs Nick Shaskevich, Dhruv Mubayi, Aayush Kataria, Jordan Torf and Tanya Berger-Wolf
Molecular Surface-based screening methods for repurposing drugs: application to find novel NAD binders in the E. Coli proteome Woong-Hee Shin, Lingfei Zeng, Xiaolei Zhu, Chiwook Park, W. Andy Tao and Daisuke Kihara
Data Imputation for Phylogeny-Based Cell Lineage Reconstruction Alan Shteyman and Russell Schwartz
Highly performant inference for infectious disease evolution Marc Suchard
Exploring Vitamin D Receptor and Gut Microbiota: Push the Envelope Jun Sun
A closer look at cross-validation approaches for assessing the accuracy of gene regulatory networks and models Shayan Tabe Bordbar, Amin Emad, Dave Zhao and Saurabh Sinha
The percolation model of fusion protein-protein interaction networks reveals multi-interface hubs as potential drug targets Somnath Tagore and Milana Frenkel-Morgenstern
MAINMAST: Building main-chain models for medium resolution electron microscopy maps Genki Terashi and Daisuke Kihara
Feed-Forward Loop Network Motif As a Mediator of Phenotypic Switch in Cells Anna Terebus, Youfang Cao and Jie Liang
Towards high resolution structure prediction of Beta-barrel membrane proteins Wei Tian, Jie Liang and Hammad Naveed
Integrative Modeling of the Tumor Specific Structural Networks in Human Cancers Nurcan Tuncbag
FastRFS: fast and accurate Robinson-Foulds Supertrees using constrained exact optimization Pranjal Vachaspati and Tandy Warnow
Multi-scale modeling of microbial eco-evolutionary dynamics Kalin Vetsigian
3D Genome Browser: a web-based browser for visualizing 3D genome organization and long-range chromatin interactions Yanli Wang, Bo Zhang, Lijun Zhang, Ting Wang and Feng Yue
A general method for predicting amino acid residues that experience hydrogen-exchanges Boshen Wang, Alan Perez-Rathke and Jie Liang
Finding the centre: corrections for asymmetry in high-throughput sequencing datasets Jia Wu, Jean Macklaim and Greg Gloor
Predicting Protein Folding by Ultra-Deep Learning Jinbo Xu
HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient Tao Yang, Feipeng Zhang, Galip Gurkan Yardimci, Ross Hardison, William Noble, Feng Yue and Qunhua Li
Regulatory DNA motif identification by integrating DNA shape in a deep learning framework Jinyu Yang and Qin Ma
pHMM-tree: Phylogeny of Profile Hidden Markov Models Yanbin Yin, Luyang Huo, Han Zhang, Xueting Huo, Yasong Yang and Xueqiong Li
HiCPlus: a deep convolutional neural network for Hi-C interaction matrix enhancement Feng Yue, Yan Zhang, Lin An, Ming Hu and Jijun Tang
In silico prediction of high-resolution Hi-C interaction matrices Shilu Zhang, Deborah Chasman, Sara Knaack and Sushmita Roy
Systematic mapping of genomic-interaction loci for hundreds of non-coding RNAs Sheng Zhong
The usage of local ancestry to inform eQTL mapping in African Americans Yizhen Zhong, Minoli Perera and Eric Gamazon
The Critical Assessment of Protein Function Annotation: The Road Ahead Naihui Zhou, Yuxiang Jiang, Timothy Bergquist, Sean D. Mooney, Casey S. Greene, Predrag Radivojac and Iddo Friedberg
The Role of Selective Breeding in Chicken Genetics and Health
Angela Zou, John Parkinson, John Brumell, Doug Korver, Shayan Sharif and David Guttman
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