Table of Contents

• Computing the Rearrangement Distance of Natural GenomesLeonard Bohnenkämper, Marília D. V. Braga, Daniel Doerr, Jens Stoye. 3-18 [doi]
• Deep Large-Scale Multi-task Learning Network for Gene Expression InferenceKamran Ghasedi Dizaji, Wei Chen, Heng Huang. 19-36 [doi]
• A Randomized Parallel Algorithm for Efficiently Finding Near-Optimal Universal Hitting SetsBaris Ekim, Bonnie Berger, Yaron Orenstein. 37-53 [doi]
• Multiple Competition-Based FDR Control and Its Application to Peptide DetectionKristen Emery, Syamand Hasam, William Stafford Noble, Uri Keich. 54-71 [doi]
• Supervised Adversarial Alignment of Single-Cell RNA-seq DataSongwei Ge, Haohan Wang, Amir Alavi, Eric P. Xing, Ziv Bar-Joseph. 72-87 [doi]
• Bagging MSA Learning: Enhancing Low-Quality PSSM with Deep Learning for Accurate Protein Structure Property PredictionYuzhi Guo, Jiaxiang Wu, Hehuan Ma, Sheng Wang, JunZhou Huang. 88-103 [doi]
• AStarix: Fast and Optimal Sequence-to-Graph AlignmentPesho Ivanov, Benjamin Bichsel, Harun Mustafa, André Kahles, Gunnar Rätsch, Martin T. Vechev. 104-119 [doi]
• Polynomial-Time Statistical Estimation of Species Trees Under Gene Duplication and LossBrandon Legried, Erin K. Molloy, Tandy J. Warnow, Sébastien Roch. 120-135 [doi]
• RoboCOP: Multivariate State Space Model Integrating Epigenomic Accessibility Data to Elucidate Genome-Wide Chromatin OccupancySneha Mitra, Jianling Zhong, David M. MacAlpine, Alexander J. Hartemink. 136-151 [doi]
• Representation of k-mer Sets Using Spectrum-Preserving String SetsAmatur Rahman, Paul Medvedev. 152-168 [doi]
• NetMix: A Network-Structured Mixture Model for Reduced-Bias Estimation of Altered SubnetworksMatthew A. Reyna, Uthsav Chitra, Rebecca Elyanow, Benjamin J. Raphael. 169-185 [doi]
• Stochastic Sampling of Structural Contexts Improves the Scalability and Accuracy of RNA 3D Module IdentificationRoman Sarrazin-Gendron, Hua-Ting Yao, Vladimir Reinharz, Carlos G. Oliver, Yann Ponty, Jérôme Waldispühl. 186-201 [doi]
• Lower Density Selection Schemes via Small Universal Hitting Sets with Short Remaining Path LengthHongyu Zheng, Carl Kingsford, Guillaume Marçais. 202-217 [doi]
• Strain-Aware Assembly of Genomes from Mixed Samples Using Flow Variation GraphsJasmijn A. Baaijens, Leen Stougie, Alexander Schönhuth. 221-222 [doi]
• Spectral Jaccard Similarity: A New Approach to Estimating Pairwise Sequence AlignmentsTavor Z. Baharav, Govinda M. Kamath, David N. C. Tse, Ilan Shomorony. 223-225 [doi]
• MosaicFlye: Resolving Long Mosaic Repeats Using Long ReadsAnton Bankevich, Pavel A. Pevzner. 226-228 [doi]
• Bayesian Non-parametric Clustering of Single-Cell Mutation ProfilesNico Borgsmüller, Jose Bonet, Francesco Marass, Abel Gonzalez-Perez, Núria López-Bigas, Niko Beerenwinkel. 229-230 [doi]
• RL: Designing Anticancer Drugs From Transcriptomic Data via Reinforcement LearningJannis Born, Matteo Manica, Ali Oskooei, Joris Cadow, María Rodríguez Martínez. 231-233 [doi]
• CluStrat: A Structure Informed Clustering Strategy for Population StratificationAritra Bose, Myson C. Burch, Agniva Chowdhury, Peristera Paschou, Petros Drineas. 234-236 [doi]
• PWAS: Proteome-Wide Association StudyNadav Brandes, Nathan Linial, Michal Linial. 237-239 [doi]
• Estimating the Rate of Cell Type Degeneration from Epigenetic Sequencing of Cell-Free DNAChrista Caggiano, Barbara Celona, Fleur Garton, Joel Mefford, Brian Black, Catherine Lomen-Hoerth, Andrew Dahl, Noah Zaitlen. 240-242 [doi]
• Potpourri: An Epistasis Test Prioritization Algorithm via Diverse SNP SelectionGizem Caylak, A. Ercument Cicek. 243-244 [doi]
• Privacy-Preserving Biomedical Database Queries with Optimal Privacy-Utility Trade-OffsHyunghoon Cho, Sean Simmons 0001, Ryan Kim, Bonnie Berger. 245-247 [doi]
• Iterative Refinement of Cellular Identity from Single-Cell Data Using Online LearningChao Gao, Joshua D. Welch. 248-250 [doi]
• A Guided Network Propagation Approach to Identify Disease Genes that Combines Prior and New InformationBorislav H. Hristov, Bernard Chazelle, Mona Singh 0001. 251-252 [doi]
• A Scalable Method for Estimating the Regional Polygenicity of Complex TraitsRuth Johnson, Kathryn S. Burch, Kangcheng Hou, Mario Paciuc, Bogdan Pasaniuc, Sriram Sankararaman. 253-254 [doi]
• Efficient and Accurate Inference of Microbial Trajectories from Longitudinal Count DataTyler A. Joseph, Amey P. Pasarkar, Itsik Pe'er. 255-256 [doi]
• Identifying Causal Variants by Fine Mapping Across Multiple StudiesNathan Lapierre, Kodi Taraszka, Helen Huang, Rosemary He, Farhad Hormozdiari, Eleazar Eskin. 257-258 [doi]
• MONN: A Multi-objective Neural Network for Predicting Pairwise Non-covalent Interactions and Binding Affinities Between Compounds and ProteinsShuya Li, Fangping Wan, Hantao Shu, Tao Jiang, Dan Zhao, Jianyang Zeng. 259-260 [doi]
• Evolutionary Context-Integrated Deep Sequence Modeling for Protein EngineeringYunan Luo, Lam Vo, Hantian Ding, Yufeng Su, Yang Liu 0097, Wesley Wei Qian, Huimin Zhao, Jian Peng 0001. 261-263 [doi]
• Log Transformation Improves Dating of PhylogeniesUyen Mai, Siavash Mirarab. 264-265 [doi]
• Reconstructing Genotypes in Private Genomic Databases from Genetic Risk ScoresBrooks Paige, James Bell, Aurélien Bellet, Adrià Gascón, Daphne Ezer. 266-268 [doi]
• d-PBWT: Dynamic Positional Burrows-Wheeler TransformAhsan Sanaullah, Degui Zhi, Shaojie Zhang. 269-270 [doi]
• A Mixture Model for Signature Discovery from Sparse Mutation DataItay Sason, Yuexi Chen, Mark D. M. Leiserson, Roded Sharan. 271-272 [doi]
• Single-Cell Tumor Phylogeny Inference with Copy-Number Constrained Mutation LossesGryte Satas, Simone Zaccaria, Geoffrey Mon, Benjamin J. Raphael. 273 [doi]
• Reconstruction of Gene Regulatory Networks by Integrating Biological Model and a Recommendation SystemYijie Wang, Justin M. Fear, Isabelle Berger, Hangnoh Lee, Brian Oliver, Teresa M. Przytycka. 274-275 [doi]
• Probing Multi-way Chromatin Interaction with Hypergraph Representation LearningRuochi Zhang, Jian Ma 0004. 276-277 [doi]