| 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 |
