PROGRAM


Keynote Talks

  1. Alfonso Valencia.The Landscape of Disease Comorbidities
  2. Franziska Michor.Evolutionary mathematical modeling enables optimization of glioblastoma treatment strategies
  3. Eytan Ruppin.Harnessing genetic interactions to advance whole-exome precision cancer treatment
  4. Rachel Kolodny.Evolution-CSI: hunting for evidence in the protein universe
  5. Carlos Bustamante.Innovating in Biomedical Data Science for Precision Health
  6. Mihai Pop.Uncovering heterogeneity in microbial communities

Accepted Papers

  1. Fatemeh Almodaresi, Prashant Pandey, Michael Ferdman, Rob Johnson and Rob Patro.An Efficient and Scalable Representation of High-Dimensional Color Information Enabled via de Bruijn Graph Search
  2. Aryan Arbabi, David Adams, Sanja Fidler and Michael Brudno. Identifying clinical terms in free-text notes using ontology-guided machine learning
  3. Metin Balaban, Shahab Sarmashghi and Siavash Mirarab. APPLES: Fast Distance Based Phylogenetic Placement
  4. Bahar Behsaz, Hosein Mohimani, Alexey Gurevich, Andrey Prjibelski, Mark F Fisher, Larry Smarr, Pieter C. Dorrestein, Joshua S. Mylne and Pavel A. Pevzner. De Novo Peptide Sequencing Reveals a Vast Cyclopeptidome in Human Gut and Other Environments
  5. Philipp Benner and Martin Vingron. ModHMM: A modular supra-Bayesian genome segmentation method
  6. Lodewijk Brand, Xue Yang, Liu Kai, Saad Elbeleidy, Hua Wang and Hao Zhang. Learning Robust Multi-Label Sample Specific Distances for Identifying HIV-1 Drug Resistance
  7. Dexiong Chen, Laurent Jacob and Julien Mairal. Biological Sequence Modeling with Convolutional Kernel Networks
  8. Van Hoan Do, Mislav Blažević, Pablo Monteagudo, Luka Borozan, Khaled Elbassioni, Soeren Laue, Francisca Rojas Ringeling, Domagoj Matijevic and Stefan Canzar. Dynamic pseudo-time warping of complex single-cell trajectories
  9. Rebecca Elyanow, Bianca Dumitrascu, Barbara E. Engelhardt, and Benjamin J. Raphael. netNMF: A network regularization algorithm for dimensionality reduction and imputation of single-cell expression data
  10. Boying Gong and Elizabeth Purdom. MethCP: Differentially Methylated Region Detection with Change Point Models
  11. Brian Hie, Hyunghoon Cho, Benjamin DeMeo, Bryan Bryson and Bonnie Berger. Geometric sketching of single-cell data preserves transcriptional structure
  12. Chirag Jain, Haowen Zhang, Yu Gao and Srinivas Aluru. On the Complexity of Sequence to Graph Alignment
  13. Jonathan Jou, Graham Holt, Anna Lowegard and Bruce Donald. Minimization-Aware Recursive K* (MARK*): A Novel, Provable Algorithm that Accelerates Ensemble-based Protein Design and Provably Approximates the Energy Landscape
  14. Mikhail Karasikov, Harun Mustafa, Amir Joudaki, Sara Javadzadeh No, Gunnar Rätsch and André Kahles. Sparse Binary Relation Representations for Genome Graph Annotation
  15. Younhun Kim, Frederic Koehler, Ankur Moitra, Elchanan Mossel and Govind Ramnarayan. How Many Subpopulations is Too Many? Exponential Lower Bounds for Inferring Population Histories
  16. Can Kockan, Kaiyuan Zhu, Natnatee Dokmai, Nikolai Karpov, Oguzhan Kulekci, David Woodruff and Cenk Sahinalp. Sketching Algorithms for Genomic Data Analysis and Querying in a Secure Enclave
  17. Alan Kuhnle, Taher Mun, Christina Boucher, Travis Gagie, Ben Langmead and Giovanni Manzini. Efficient Construction of a Complete Index for Pan-Genomics Read Alignment
  18. Haoyun Lei, Bochuan Lyu, E. Michael Gertz, Alejandro A. Schaffer, Xulian Shi, Kui Wu, Guibo Li, Liquin Xu, Yong Hu, Michael Dean and Russell Schwartz. Tumor Copy Number Deconvolution Integrating Bulk and Single-Cell Sequencing Data
  19. Yunan Luo, Jianzhu Ma, Xiaoming Zhao, Yufeng Su, Yang Liu, Trey Ideker and Jian Peng. Mitigating Data Scarcity in Protein Binding Prediction Using Meta-Learning
  20. Joel Mefford, Danny Park, Zhili Zheng, Arthur Ko, Mika Ala-Korpela, Markku Laakso, Paivi Pajukanta, Jian Yang, John Witte and Noah Zaitlen. Efficient estimation and applications of cross-validated genetic predictions
  21. Matthew Myers, Gryte Satas and Benjamin Raphael. Inferring tumor evolution from longitudinal samples
  22. Weihua Pan, Tao Jiang and Stefano Lonardi. OMGS: Optical Map-based Genome Scaffolding
  23. Ali Pazokitoroudi, Yue Wu, Kathryn S. Burch, Kangcheng Hou, Bogdan Pasaniuc and Sriram Sankararaman. Scalable multi-component linear mixed models with application to SNP heritability estimation
  24. Leonardo Pellegrina, Cinzia Pizzi and Fabio Vandin. Fast Approximation of Frequent k-mers and Applications to Metagenomics
  25. Kristoffer Sahlin and Paul Medvedev. De novo clustering of long-read transcriptome data using a greedy, quality-value based algorithm
  26. Shahab Sarmashghi and Vineet Bafna. A Note on Computing Interval Overlap Statistics
  27. Itay Sason, Damian Wojtowicz, Welles Robinson, Mark Leiserson, Teresa Przytycka and Roded Sharan. A sticky multinomial mixture model of strand-coordinated mutational processes in cancer
  28. Mike Thompson, Zeyuan Johnson Chen, Elior Rahmani and Eran Halperin. Recovery of cell-type composition in methylation data using canonical correlation analysis
  29. Sheng Wang, Emily Flynn and Russ Altman. GRep: Gene Set Representation via Gaussian Embedding
  30. Yijie Wang, Jan Hoinka and Teresa M. Przytycka. Accurate sub-population detection and mapping across single cell experiments with PopCorn
  31. Ziheng Wang, Grace Ht Yeo, Richard Sherwood and David Gifford. Disentangled Representations of Cellular Identity
  32. Ye Wu, Ruibang Luo, Henry C.M. Leung, Hing-Fung Ting and Tak-Wah Lam. RENET: A Deep Learning Approach for Extracting Gene-Disease Associations from Literature
  33. Yue Wu, Anna Yaschenko, Mohammadreza Hajy Heydary, and Sriram Sankararaman. Fast estimation of genetic correlation for Biobank-scale data
  34. Jinbo Xu. Distance-based Protein Folding Powered by Deep Learning
  35. Yang Yang, Yang Zhang, Bing Ren, Jesse Dixon and Jian Ma. Comparing 3D Genome Organization in Multiple Species using Phylo-HMRF
  36. Jesse Zhang, Govinda Kamath and David Tse. Towards a post-clustering test for differential expression
  37. Martin Zhang, Fei Xia and James Zou. AdaFDR: a Fast, Powerful and Covariate-Adaptive Approach for Multiple Hypothesis Testing

Highlight Talks

  1. Daifeng Wang, Shuang Liu, Jonathan Warrell, Hyejung Won, Xu Shi, Fabio Navarro, Declan Clarke, Mengting Gu, Prashant Emani, Daniel Geschwind, James Knowles and Mark Gerstein.Interpretable deep learning modeling embedding gene regulatory network for understanding functional genomics in neuropsychiatric disorders
  2. Rachel M. Sherman, Juliet Forman, Valentin Antonescu, Daniela Puiu, Michelle Daya, Nicholas Rafaels, Meher Preethi Boorgula, Sameer Chavan, Candelaria Vergara, Victor E. Ortega, Albert M. Levin, Celeste Eng, Maria Yazdanbakhsh, James G. Wilson, Javier Marrugo, Leslie A. Lange, L. Keoki Williams, Harold Watson, Lorraine B. Ware, Christopher O. Olopade, Olufunmilayo Olopade, Ricardo R. Oliveira, Carole Ober, Dan L. Nicolae, Deborah A. Meyers, Alvaro Mayorga, Jennifer Knight-Madden, Tina Hartert, Nadia N. Hansel, Marilyn G. Foreman, Jean G. Ford, Mezbah U. Faruque, Georgia M. Dunston, Luis Caraballo, Esteban G. Burchard, Eugene R. Bleecker, Maria I. Araujo, Edwin F. Herrera-Paz, Monica Campbell Cassandra Foster, Margaret A. Taub, Terri H. Beaty, Ingo Ruczinski, Rasika A. Mathias, Kathleen C. Barnes and Steven L. Salzberg.Assembly of a pan-genome from deep sequencing of 910 humans of African descent
  3. Tom Aharon Hait, David Amar, Ron Shamir and Ran Elkon.FOCS: a novel method for analyzing enhancer and gene activity patterns infers an extensive enhancer–promoter map
  4. Jack Kuipers, Thomas Thurnherr, Giusi Moffa, Polina Suter, Jonas Behr, Ryan Goosen, Gerhard Christofori and Niko Beerenwinkel.Mutational interactions define novel cancer subgroups
  5. Yaniv Erlich, Tal Shor, Itsik Pe’Er and Shai Carmi.Identity inference of genomic data using long-range familial searches
  6. Brian Hie, Hyunghoon Cho and Bonnie Berger.Realizing private and practical pharmacological collaboration
  7. Ngoc-Hieu Tran, Rui Qiao, Lei Xin, Xin Chen, Chuyi Liu, Xianglilan Zhang, Baozhen Shan, Ali Ghodsi and Ming Li.Deep learning enables de novo peptide sequencing from data-independent-acquisition mass spectrometry
  8. David Danko, Dmitrii Meleshko, Daniela Bezdan, Christopher Mason and Iman Hajirasouliha.Minerva: An Alignment and Reference Free Approach to Deconvolve Linked-Reads for Metagenomics
  9. Ali Sinan Köksal, Kirsten Beck, Dylan R Cronin, Aaron McKenna, Nathan D Camp, Saurabh Srivastava, Matthew E MacGilvray, Rastislav Bodík, Alejandro Wolf-Yadlin, Ernest Fraenkel, Jasmin Fisher and Anthony Gitter.Synthesizing Signaling Pathways from Temporal Phosphoproteomic Data
  10. Mahsa Ghanbari, Julia Lasserre and Martin Vingron.The Distance Precision Matrix: computing networks from non-linear relationships
  11. Martin Zhang, Fei Xia and James Zou.AdaFDR: a Fast, Powerful and Covariate-Adaptive Approach for Multiple Hypothesis Testing

Accepted Posters


IDTitleAuthors
1Accelerating sequence alignment to graphsChirag Jain, Sanchit Misra, Haowen Zhang, Alexander Dilthey and Srinivas Aluru
2Scalable multiple whole-genome alignment and locally collinearblock construction with SibeliaZIlia Minkin and Paul Medvedev
3Locality sensitive hashing for the edit distanceGuillaume Marcais, Dan DeBlasio, Prashant Pandey and Carl Kingsford
5A Network Theory Approach to Identifying Synthetic Lethal Combinations of Pre-Existing Therapeutics in Chemoresistant Cancer ContextsJonathon Gast, Matthew Bartolowits, Tony Pedley, Sridar Chittur and Vincent Jo Davisson
6Reconstructing haplotype-specific cancer genome karyotypes with multiple sequencing technologiesSergey Aganezov, Fritz Sedlazeck, Sara Goodwin, Gayatri Arun, Isac Lee, Sam Kovaka, Michael Kirsche, Rachel Sherman, Robert Wappel, Melissa Kramer, Karen Kostroff, David Spector, Winston Timp, Michael Schatz and Richard McCombie
7Identifying Retroviral Remnants that Drive an Immune Response to CancerJames I McDonald, Alejandro Velasquez, Xiaoyun Xing, Michael J Topper, Stephen B Baylin, Ting Wang and Katherine B Chiappinelli
8Investigating how DNA Methylation Shapes the Immune Response to Epigenetic Cancer TherapiesAlejandro Velasquez, James McDonald and Katherine Chiappinelli
9pathCHEMO: Uncovering (epi) genomic pathways of chemoresistance in lung adenocarcinomaNusrat Epsi, Antonina Mitrofanova, Sukanya Panja and Sharon Pine
10An Integer Programing Model for Identification of Cancer-Responsive SubnetworkBayarbaatar Amgalan and Makhgal Ganbold
11Neoantigen Clonal Balance Predicts Immunotherapy Outcomes and PrognosisTianshi Lu
12The Clinical Implications of Subclonal Copy Number Alterations in Chronic Lymphocytic LeukemiaMark Zucker and Kevin Coombes
13Heterogeneity in refractory acute myeloid leukemiaSachi Horibata, Gege Gui, Justin Lack, Christin DeStefano, Michael Gottesman and Christopher Hourigan
14Comparing Regulatory Networks between Breast Cancer Cell Line MCF-7 and Human Breast Cancer TissuesVy Tran, Alexandra Maertens and Thomas Hartung
15Genome-wide alteration of CTCF bindings in multiple cancersZhenjia Wang, Celestia Fang, Panagiotis Ntziachristos and Chongzhi Zang
16Target gene prediction of a frequently mutated regulatory element in epithelial ovarian cancerRosario Corona, Ji-Heui Seo, Xianzhi Lin, Dennis Hazelett, Paulette Mhawech-Fauceglia, Jenny Lester, Sohrab Shah, David Huntsman, Alexander Gusev, Beth Karlan, Benjamin Berman, Matthew Freedman, Simon Gayther and Kate Lawrenson
17Copy number phylogenetics for single cellsJack Kuipers, Mustafa Tuncel, Katharina Jahn and Niko Beerenwinkel
18Heterogeneous Imaging Genetics Data Classification via Strictly Orthogonal Nonnegative Matrix Tri-Factorization for Early Detecting Alzheimer's DiseaseKai Liu, Lodewijk Brand, Matthew Miller and Hua Wang
19Convergence of healthcare records and genetic evidence links cardiovascular dysfunction and Alzheimer’s diseaseHyojung Paik, Junehawk Lee, Chan-Seok Jeong, Jun Sung Park, Jeong Ho Lee, Nadav Rappoport, Atul Butte and Seong Beom Cho
20Assessing prognostic and diagnostic features of (epi)genomics data for neuroblastomaKatarzyna Wreczycka, Joern Toedling, Falk Hertwig, Johannes Schulte and Altuna Akalin
21Cross-study ensembling for epigenomic prediction of cardiovascular riskKenneth Westerman and José M. Ordovás
22Pathway-based meta-analysis for partially paired transcriptomics analysis in psoriasisWing Tung Fung, Joseph T. Wu, Wai Man Mandy Chan, Henry H. Chan and Herbert Pang
23Predicting Disease Progression of Colorectal Cancer via Unsupervised Learning Methods
Zorian Thornton and Allison Tegge
25Identifying Transcription Factors as Drug Targets for Prostate Carcinoma Considering Protein Moonlighting BehaviorAshmita Dey, Sagnik Sen, Ramkrishna Mitra and Ujjwal Maulik
26A Genome-wide Landscape of the Functional Basis of Complex Traits and DiseasesAlexander McKim and Arjun Krishnan
27Predicting ALZ-associated protein biomarkers from multiple evidence sourcesAnna Yannakopoulos, Alison Bernstein, Irving Vega and Arjun Krishnan
28MetaPGN: a pipeline for construction and graphical visualization of annotated pangenome networksJunhua Li
29Web-based Database System to Detect Fluctuating Selection in a Microbial MutualismHoi Yan Wu, Conard Faraon, Lisa Kim, Sheng Lin, Wai Kwan Shum, Yee Mey Seah, Kristina Hillesland and Wooyoung Kim
31Surveying bacteriophages of the human gutBalázs Ligeti, Ágnes Kata Hőnich, Janos Juhasz and Sándor Pongor
32Fast Approximation of Frequent k-mers and Applications to MetagenomicsLeonardo Pellegrina, Cinzia Pizzi and Fabio Vandin
33MetaCompass: Reference-guided Assembly of MetagenomesVictoria Cepeda-Espinoza, Bo Liu, Mathieu Almeida, Christopher Hill, Sergey Koren, Todd Treangen and Mihai Pop
34Comparing State-Of-The-Art Denoising Algorithms and Traditional Clustering Algorithms in Microbiome AnalysisRohan Patil
35Simultaneous metatranscriptomic and host transcriptional profiling to elucidate signatures of host-pathogen-microbiome interactionsHayden Brochu, Catherine O'Connell, Jenna Girardi, Erin Harrell, Aiden Jones, Toni Darville, Arlene Seña and Xinxia Peng
36Cedar: scalable, accurate and fast metagenomic abundance estimationFatemeh Almodaresi, Mohsen Zakeri and Rob Patro
38Genes with high network connectivity are enriched for disease heritabilitySamuel Kim, Chengzhen Dai, Farhad Hormozdiari, Bryce van de Geijn, Steven Gazal, Yongjin Park, Luke O’connor, Tiffany Amariuta, Po-Ru Loh, Hilary Finucane, Soumya Raychaudhuri and Alkes Price
39Identifying Phenotype-Associated SubnetworksYoo-Ah Kim, Rebecca Sarto Basso, Damian Wójtowicz, Dorit S. Hochbaum, Fabio Vandin and Teresa Przytycka
40Network Methods for Identifying Regulators of Influenza A Virus InfectionEmily Ackerman and Jason Shoemaker
41Classification in biological networks with hypergraphlet kernelsJose Lugo-Martinez and Predrag Radivojac
42TreeFix-TP: Phylogenetic Error-Correction for Infectious Disease Transmission Network InferenceSamuel Sledzieski, Chengchen Zhang, Ion Mandoiu and Mukul Bansal
43Building Robust Gene Co-expression Networks from RNA-seq DataKayla Johnson and Arjun Krishnan
44Integrative Network Analysis Discovers Causal RegulatoryNetwork of System Level MeasurementsDongze He, Arda Durmaz, Jean-Eudes Dazard and Gurkan Bebek
45Locating ligand binding sites in G-protein coupled receptors using combined information from docking and sequence conservationAshley Ryan Vidad, Stephen Macaspac and Ho Leung Ng
47PhoglyStruct: Prediction of phosphoglycerylated lysine residues using structural properties of amino acidsAbel Chandra, Alok Sharma, Abdollah Dehzangi, Shoba Ranganathan, Anjeela Jokhan, Kuo-Chen Chou and Tatsuhiko Tsunoda
50De-novo predictions of binding positions within protein domainsAnat Etzion-Fuchs, David A. Todd and Mona Singh
51Extending protein-DNA binding models to a 16-letter DNA alphabetHarshit Sahay, Ariel Afek and Raluca Gordan
52Classification of neurotoxic peptides in spider venom using convolutional neural networkByungjo Lee, In-Wook Hwang, Seung-Tae Kim, Jung-Suk Sung and Wonhee Jang
53Neural network-based approach for detecting G-quadruplexesMira Barshai, Desiree Tillo, Nima Assad, Sreejana Ray, Charles Vinson and Yaron Orenstein
54Comparative Assessment of 6 Docking Software on an Exclusive Metalloprotein-ligand Benchmark with Metal Ions Closely Located at the Binding SiteSüleyman Selim Çınaroğlu and Emel Timuçin
55Exploratory data analysis and interactive visualization of FTICR-MS dataLee Ann McCue, Lisa Bramer, Amanda White, Kelly Stratton, Allison Thompson, Daniel Claborne and Kirsten Hofmockel
58Using Clustering Algorithms to Merge Multi-Sample Histone Modification RegionsDaniela Perry and Bogdan Pasaniuc
59Exploring the Role of Ribosomal Gene Repeats in the Context of RegenerationSofia Barreira and Andreas Baxevanis
60Computational Enhancer Prediction: Evaluation and ImprovementHasiba Asma and Marc S. Halfon
61HebbPlot: an intelligent tool for learning and visualizing chromatin mark signaturesHani Z Girgis, Alfredo Velasco and Zachary Reyes
62Reconstructing regulatory networks from multi-omics data using prior informationJohann Hawe, Benjamin Lehne, Melanie Waldenberger, Christian Gieger, John Chambers and Matthias Heinig
63Analysis of the structural variability of topologically associated domains as revealed by Hi-CNatalie Sauerwald, Akshat Singhal and Carl Kingsford
64Method to characterize how transcription factors influence development integrating RNA and ChIP-seqAshley Conard, Erica Larschan and Charles Lawrence
65Comparing chromatin accessibility profiles with maximal cliques in temporal graphsCoby Viner and Michael M. Hoffman
66GGmend: A Mendelian randomization method for finding gene-on-gene regulatory effects in the presence of unobserved confoundersJunghyun Jung, Robert Brown, Wonhee Jang, Bogdan Pasaniuc, Jong Wha Joo and Eleazar Eskin
67Integrated Probe Design and Quality Control for Capture Hi-C ExperimentsPeter Hansen, Salaheddine Ali, Hannah Blau, Daniel Danis, Jochen Hecht, Uwe Kornak, Darío Lupiáñez, Stefan Mundlos, Robin Steinhaus and Peter N. Robinson
68Inferring causal bayesian networks of epigenetic regulationAshwini Kumar Sharma
70Multivariate state space model integrating high precision epigenomic data to elucidate genome-wide chromatin occupancySneha Mitra, Jianling Zhong and Alexander Hartemink
71Integrating MNase-seq and RNA-seq Time Series Data to Study Dynamic Chromatin and Transcriptional Regulation Under Cadmium StressTrung Tran, Vinay Tripuraneni, Heather MacAlpine, Sneha Mitra, Yulong Li, Greg Crawford, David MacAlpine and Alexander Hartemink
72Evolutionary analysis of sequence divergence of cis-regulatory modules associated with changes in chromatin and gene expression in brain tissue of primates.Abusaid Shaimardanov and Dmitry Svetlichnyy
73Comparative analysis of HiChIP with HiC and ChIP-seqYifan Zhang and Chongzhi Zang
74BARTweb: a web server for functional transcription factor predictionWenjing Ma, Zhenjia Wang, Neal E. Magee, Byoung-Do Kim, Yang Chen and Chongzhi Zang
75Cell-type-specific resolution epigenetics without the need for cell sorting or single-cell biologyElior Rahmani, Regev Schweiger, Brooke Rhead, Lindsey Criswell, Lisa Barcellos, Eleazar Eskin, Saharon Rosset, Sriram Sankararaman and Eran Halperin
76SICER 2.0: A ChIP-seq broad peak identification tool redesignedJin Yong Yoo, Yiren Wang and Chongzhi Zang
77Modeling and correcting intrinsic biases in DNase-seq and ATAC-seq dataShengen Hu, Lin Liu, Wenjing Ma, Clifford Meyer, Michael Guertin, Tingting Zhang and Chongzhi Zang
78A Hidden Markov Model-based approach to reconstructing double minute chromosome ampliconsRuslan Mardugalliamov, Kamal Al Nasr and Matthew Hayes
79soMaCX: A pathway based somatic genome generation frameworkTimothy Becker, Andrew Koob and Dong-Guk Shin
80A toolkit for accelerating genomic analysis using NGS index formatsJohn Didion
82MeShClust: an intelligent tool for clustering DNA sequencesBenjamin James, Brian Luczak and Hani Zakaria Girgis
83A secure analysis of environmental and clinical samples using a hybrid cloud profilerRachid Ounit, Chris Mason, Stefano Lonardi and Niamh O'Hara
84In silico identification of novel genetic factors associated with longevity in DrosophilaBethany Hall, Nadia Chuzhanova, Jonathan Crofts and Yvonne Barnett
85Jetski: Faster Assemblies with Minimizer-Based Removal of Contained ReadsMichael Kirsche and Michael Schatz
86Generalized intra-sequence k-mer distances as an alignment-free sequence-analysis metricBenjamin Lee and Paul Gamble
87Bioinformatics Analyses of Next Generation Sequencing Hepatitis C virus samples.Myrto Kremyda - Vlachou, Andrew Hayward, Laura Shallcross, Stephane Hue, Dan Frampton, Eleni Nastouli and Deenan Pillay
88LtrDetector: A tool-suite for detecting long terminal repeat retrotransposons de-novoJoseph D Valencia and Hani Z Girgis
89Predicting primer off-target rate using a sensitive homology search algorithm and deep neural networksChang Xu, Frank Reinecke, Raghavendra Padmanabhan, John DiCarlo and Yexun Wang
90Improved Personal Genome Inference Benefits Downstream AnalysisTaher Mun and Benjamin Langmead
91Refining orthology determination for whole-genome and whole-transcriptome phylogeneticsMadison H. Hansen and Ward C. Wheeler
92Evidence of transcription in novel human genomic sequencesRachel Sherman and Steven Salzberg
93Integrative analysis of pooled CRISPR genetic screens using MAGeCKFluteBingin Wang, Mei Wang, Wubing Zhang, Wei Li and Xiaole Liu
94AptaSUITE - A Bioinformatics Framework for the comprehensive Analysis of HT-SELEX ExperimentsJan Hoinka, Rolf Backofen and Teresa Przytycka
95Credibility of Horizontal Gene Transfer EventsAgnieszka Mykowiecka, Anna Muszewska and Pawel Gorecki
96Transcriptomic Analysis of Notch Signaling PerturbationGrace Solini and Margaret Saha
97Single-cell Phylogenetic Inference with Copy-number Supported Mutation LossesGryte Satas, Simone Zaccaria, Geoffrey Mon and Ben Raphael
98PEPATAC: A portable, optimized ATAC-seq pipelineJason Smith, Nathan Sheffield, Vince Reuter, Ryan Corces, Jin Xu, Yuning Wei and Howard Chang
99Implementation of a high-throughput NGS pipeline: How Amyris scaled from one molecule to dozensReshmi Chowdhury and Amoolya Singh
100Glycosylation Flux Analysis: A flux analysis tool to study protein glycosylationRudiyanto Gunawan and Sandro Hutter
101SKmDB: an integrated database of next generation sequencing information in skeletal muscleJie Yuan, Jiajian Zhou, Huating Wang and Hao Sun
102A computational analysis of spatial correlations of neural stem cell divisions in the zebrafish brainValerio Lupperger, Prisca Chapouton and Carsten Marr
103Sub-lethal effects of anthropogenic stressors on the cognitive abilities of bumblebee foragers drive population decline and loss of biodiversityKevin Heath
104A Comparative Genomics Study of NYC Legionella pneumophila serogroup 1 using Whole Genome Single Nucleotide Polymorphism (wgSNP) Analysis PipelinesJade Wang, Edimarlyn Gonzalez, Scott Hughes and Jennifer Rakeman
105PopVar: population variant detection with false discovery rate (FDR) controlZhengyuan Wang and Leo Wang-Kit Cheung
106Leveraging allelic heterogeneity to increase power of association testingFarhad Hormozdiari, Junghyun Jung, Eleazar Eskin and Jong Wha Joo
107Coordinate Covariation Analysis (COCOA): Understanding Interindividual Variation in Data with Genomic CoordinatesJohn Lawson, Jason Smith, Francine Garrett-Bakelman, Stefan Bekiranov and Nathan Sheffield
108Meta-analysis of polymyositis and dermatomyositis microarray data setsJaeseung Song, Wonhee Jang, Junghyun Jung, Da Eun Kim and Ju Yeon Hong
109Modular, part-based control of gene expression response time using protein degradation tagsEthan Jones, Callan Monette, John Marken, Sejal Dhawan, Theresa Gibney, Christine Li, Wukun Liu, Alyssa Luz-Ricca, Xida Ren, Xingyu Zheng and Margaret Saha
110Nested Tree Probabilistic Graphical Models Characterize Evolutionary and Spatial changes in Neural Cell TypesMichael Kleyman, Jing He, Bilge Esin Ozturk, Leah Byrne, William Stauffer and Andreas Pfenning
111The PAICE Suite: Using Extended Harmonic Oscillators to Identify and Understand Circadian Rhythms in Large DatasetsHannah De Los Santos, Emily J. Collins, Catherine Mann, April W. Sagan, Meaghan S. Jankowski, Kristin P. Bennett and Jennifer M. Hurley
112GREIN: An Interactive Web Platform for Re-analyzing GEO RNA-seq DataNaim Mahi
113Integrative Transcriptome Analysis of Zebra Finch Brain Tissue Exposed to Physiological Levels of MercuryKathryn Murphy, Hannah Paros, Margaret Saha and Eric Bradley
114Accurate estimation of transcriptome-wide differential allelic expressionAsia Mendelevich, Svetlana Vinogradova, Saumya Gupta, Andrey Mironov and Alexander Gimelbrant
115Detecting anomalies in RNA-seq quantificationCong Ma and Carl Kingsford
116TEMPO: Temporal Modeling of Pathway OutliersChristopher Pietras, Faith Ocitti and Donna Slonim
117Alevin efficiently estimates accurate gene abundances from dscRNA-seq dataAvi Srivastava, Laraib Iqbal Malik, Tom Smith, Ian Sudbery and Robert Patro

Accepted Late Breaking Posters


IDTitleAuthors
41ADynamic interaction network inference from longitudinal microbiome dataJose Lugo-Martinez, Daniel Ruiz Perez, Giri Narasimhan and Ziv Bar-Joseph
119Simulation-based comparative evaluation of isoform-level quantification for RNA-Seq dataDimitra Sarantopoulou, Soumyashant Nayak, Nicholas F. Lahens, Thomas G. Brooks and Gregory R. Grant
120NITECAP: A novel method for the identification of circadian behavior in time-course dataThomas G. Brooks, Cris W. Lawrence, Soumyashant Nayak, Dimitra Sarantopoulou, Nicholas F. Lahens, Tilo Grosser, Garret A. Fitzgerald and Gregory R. Grant
121TEQILA - A tool enabling queries for investigation of latent associationsSoumyashant Nayak, Eric McGivney, Thomas Brooks, Garret Fitzgerald and Gregory Grant
122BEERS 2.0: The Next Generation of RNA-Seq SimulatorNicholas Lahens, Thomas Brooks, Dimitra Sarantopoulou, Soumyashant Nayak, Cris Lawrence, Anand Srinivasan, Jonathan Schug, John Hogenesch and Gregory Grant
123Adaptive Monte Carlo Multiple Testing via Multi-Armed BanditsMartin Zhang, James Zou and David Tse
124Hera-T: an efficient and accurate approach for quantifying gene abundances from 10X-Chromium data with high rates of non-exonic readsThang Tran, Thao Truong, Hy Vuong and Son Pham
125A revisit of RSEM generative model and its EM algorithm for quantifying transcript abundancesHy Vuong, Thao Truong, Thang Tran and Son Pham
126BELLA: Berkeley Efficient Long-Read to Long-Read Aligner and OverlapperGiulia Guidi, Marquita Ellis, Daniel Rokhsar, Katherine Yelick and Aydın Buluç
127Unified Cox model based multifactor dimensionality reduction method for gene-gene analysis of the survival phenotypeSeungyeoun Lee, Donghee Son, Yongkang Kim, Wenbao Yu and Taesung Park
129Dissecting the Characteristics and Functions of Transcribed EnhancersMario Flores and Ivan Ovcharenko
130Deep Convolutional Neural Networks for Protein Contact PredictionBadri Adhikari
131nanotatoR: An annotation tool for Optical MappingSurajit Bhattacharya, Hayk Barseghyan, Emmanuèle C. Délot and Eric Vilain
132Computational modeling of stem cell kinetics identifies plausible hematopoietic lineage hierarchiesLisa Bast, Michele Kyncl, Robert Oostendorp, Katharina Götze, Carsten Marr and Lynette Henkel
133Decomposing Inexact Flows with Application to RNA Transcript AssemblyLucia Williams and Brendan Mumey
134An Optimal Combination of Computational Systems Biology Predictions: the MOCA algorithmMehmet Eren Ahsen, Gustavo Stolovitzky and Robert Vogel
135PU-Caller: Sensitive Somatic Variant Calling Using Positive-Unlabeled LearningElham Sherafat and Ion Mandoiu
136MALVA: genotyping by Mapping-free ALlele detection of known VariantsGiulia Bernardini, Paola Bonizzoni, Luca Denti, Marco Previtali and Alexander Schönhuth
137GenMap: Fast and Exact Computation of Genome MappabilityChristopher Pockrandt, Mai Alzamel, Costas Iliopoulos and Knut Reinert
138Using Deep Learning to understand the grammar of enhancers.Sanjarbek Hudaiberdiev and Ivan Ovcharenko
139Aberrant splicing and isoform production of kinase proteins is prevalent in metastatic melanomaDavid Holland and Laura Elnitski
140Biclustering analysis of transcriptome big data identifies cancer suppressing microRNAsDougu Nam
141Selene: a PyTorch-based deep learning library for sequence dataKathleen Chen, Evan Cofer, Jian Zhou and Olga Troyanskaya
142Identifying sample assignment errors in pedigreesMarteinn Hardarson, Gunnar Palsson, Bjarni Halldorsson, Gisli Masson, Florian Zink and Kári Stefánsson
143Characterizing mutagenic effects of recombinations through a sequence level genetic mapBjarni Halldorsson, Gunnar Palsson, Ólafur Andri Stefánsson, Hákon Jónsson, Marteinn Hardarson, Hannes P. Eggertsson, Bjarni Gunnarsson, Asmundur Oddsson, Gisli H. Halldorsson, Florian Zink, Sigurjon Gudjonsson, Michael Frigge, Gudmar Thorleifsson, Asgeir Sigurdsson, Simon Stacey, Patrick Sulem, Gisli Masson, Agnar Helgason, Daniel F. Gudbjartsson, Unnur Thorsteinsdottir and Kári Stefánsson
144HumanBase: A portal for data-driven predictions of gene expression, function, regulation and interactionsAaron Wong, Julien Funk, Kevin Yao, Chandra Theesfeld and Olga Troyanskaya
145Sharing DNA-binding information across structurally similar proteins enables accurate specificity determinationJoshua Wetzel and Mona Singh
146Distance Measures for Tumor Evolutionary TreesZach DiNardo, Kiran Tomlinson, Anna Ritz and Layla Oesper
147Modeling Clinical and Molecular Covariates of Mutational Process Activity in CancerWelles Robinson, Roded Sharan and Mark Leiserson
148INFERRING ALLELE-SPECIFIC COPY NUMBERS IN SINGLE-CELL SEQUENCING DATASimone Zaccaria and Ben Raphael
149Two classes of enhancer stability: stable enhancers active in development and fragile enhancers contributing to evolutionary adaptationShan Li, Evgeny Kvon, Axel Visel, Len Pennacchio and Ivan Ovcharenko
150The first enhancer in an enhancer chain safeguards subsequent enhancer-promoter contacts from a distanceWei Song, Roded Sharan and Ivan Ovcharenko
151BitMapperBS: a fast and accurate read aligner for whole-genome bisulfite sequencingHaoyu Cheng and Yun Xu
152metaFlye: accurate and fast long-read metagenome assemblerMikhail Kolmogorov and Pavel Pevzner
153Integration of Mouse and Human Single-cell RNA Sequencing Infers Spatial Cell-type Composition in Human BrainsTravis Johnson, Zachary Abrams, Bryan Helm, Peter Neidecker, Raghu Machiraju, Yan Zhang, Kun Huang and Jie Zhang
154Validating family pedigrees using shared DNA segmentsLadan Doroud, Luong Nguyen, Shiya Song, Jingwen Pei, Harendra Guturu, Keith Noto, Eurie Hong, Ken Chahine and Catherine Ball
155Simulation study of ancestral genome reconstruction from pedigreesJingwen Pei, Shiya Song, Ross Curtis, Ladan Doroud, Julie Granka, Keith Noto, Eurie Hong, Ken Chahine and Catherine Ball
156Identification of copy number variations and translocations in cancer cells from Hi-C dataAbhijit Chakraborty and Ferhat Ay
157FitHiChIP: Identification of significant chromatin contacts from HiChIP/PLAC-seq dataSourya Bhattacharyya, Vivek Chandra, Vijay Pandurangan and Ferhat Ay
158CHIP-seq analysis of multiple sclerosis-related differentially expressed genes in circulating B-cells.Samira Rahimi Rad and Shima Rahimi Rad
159Computational Analysis of Single-Cell Transcriptomics in Ciona Intestinalis Reveals Formation of Novel Neuronal Cell Types with Hybrid PropertiesPrakriti Paul, Michael Levine and Mona Singh
160Batch Effects Correction with Unknown SubtypesXiangyu Luo and Yingying Wei
161Selective neuronal vulnerability in Alzheimer's disease: an integrative network-based analysisVictoria Yao, Jean-Pierre Roussarie, Olga Troyanskaya and Paul Greengard
162Tissue-aware framework for unraveling rare and complex diseases using biomedical literatureRuth Dannenfelser, Ran Zhang, Alicja Tadych, Arjun Krishnan and Olga Troyanskaya
163Understanding microglia functional rewiring and disease association through developmental stage specific networksRan Zhang, Jose Ledo, Paul Greengard and Olga Troyanskaya
165Systematic modeling of pan-cancer drug responses using Bayesian multi-source regressionMehreen Ali, Tero Aittokallio and Suleiman Ali Khan
166Rotation Equivariant and Invariant Networks for Microscopy Image AnalysisBenjamin Chidester, Tianming Zhou, That-Vinh Ton, Minh N. Do and Jian Ma
167Bayesian modeling of RNA-Seq gene expression count dataEdin Salkovic and Halima Bensmail