ACCEPTED PAPERS & ABSTRACTS FOR TALKS
Link within this page: Abstracts for Oral Presentations
| FULL PAPERS FOR ORAL PRESENTATION |
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| TITLE | AUTHORS |
| 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 |
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| ABSTRACTS FOR ORAL PRESENTATIONS | |
| TITLE | AUTHORS |
| 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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