| 2019 | A Note on Computing Interval Overlap Statistics. Shahab Sarmashghi, Vineet Bafna |
| 2019 | A Sticky Multinomial Mixture Model of Strand-Coordinated Mutational Processes in Cancer. Itay Sason, Damian Wójtowicz, Welles Robinson, Mark D. M. Leiserson, Teresa M. Przytycka, Roded Sharan |
| 2019 | APPLES: Fast Distance-Based Phylogenetic Placement. Metin Balaban, Shahab Sarmashghi, Siavash Mirarab |
| 2019 | Accurate Sub-population Detection and Mapping Across Single Cell Experiments with PopCorn. Yijie Wang, Jan Hoinka, Teresa M. Przytycka |
| 2019 | AdaFDR: A Fast, Powerful and Covariate-Adaptive Approach to Multiple Hypothesis Testing. Martin J. Zhang, Fei Xia, James Zou |
| 2019 | An Efficient, Scalable and Exact Representation of High-Dimensional Color Information Enabled via de Bruijn Graph Search. Fatemeh Almodaresi, Prashant Pandey, Michael Ferdman, Rob Johnson, Rob Patro |
| 2019 | Biological Sequence Modeling with Convolutional Kernel Networks. Dexiong Chen, Laurent Jacob, Julien Mairal |
| 2019 | Comparing 3D Genome Organization in Multiple Species Using Phylo-HMRF. Yang Yang, Yang Zhang, Bing Ren, Jesse R. Dixon, Jian Ma |
| 2019 | De Novo Clustering of Long-Read Transcriptome Data Using a Greedy, Quality-Value Based Algorithm. Kristoffer Sahlin, Paul Medvedev |
| 2019 | De Novo Peptide Sequencing Reveals a Vast Cyclopeptidome in Human Gut and Other Environments. Bahar Behsaz, Hosein Mohimani, Alexey A. Gurevich, Andrey D. Prjibelski, Mark F. Fisher, Larry Smarr, Pieter C. Dorrestein, Joshua S. Mylne, Pavel A. Pevzner |
| 2019 | Disentangled Representations of Cellular Identity. Ziheng Wang, Grace H. T. Yeo, Richard Sherwood, David Gifford |
| 2019 | Distinguishing Biological from Technical Sources of Variation Using a Combination of Methylation Datasets. Mike Thompson, Zeyuan Johnson Chen, Elior Rahmani, Eran Halperin |
| 2019 | Dynamic Pseudo-time Warping of Complex Single-Cell Trajectories. Van Hoan Do, Mislav Blazevic, Pablo Monteagudo, Luka Borozan, Khaled M. Elbassioni, Sören Laue, Francisca Rojas Ringeling, Domagoj Matijevic, Stefan Canzar |
| 2019 | Efficient Construction of a Complete Index for Pan-Genomics Read Alignment. Alan Kuhnle, Taher Mun, Christina Boucher, Travis Gagie, Ben Langmead, Giovanni Manzini |
| 2019 | Efficient Estimation and Applications of Cross-Validated Genetic Predictions. Joel Mefford, Danny S. Park, Zhili Zheng, Arthur Ko, Mika Ala-Korpela, Markku Laakso, Paivi Pajukanta, Jian Yang, John S. Witte, Noah Zaitlen |
| 2019 | Fast Approximation of Frequent k-mers and Applications to Metagenomics. Leonardo Pellegrina, Cinzia Pizzi, Fabio Vandin |
| 2019 | Fast Estimation of Genetic Correlation for Biobank-Scale Data. Yue Wu, Anna Yaschenko, Mohammadreza Hajy Heydary, Sriram Sankararaman |
| 2019 | GRep: Gene Set Representation via Gaussian Embedding. Sheng Wang, Emily R. Flynn, Russ B. Altman |
| 2019 | Geometric Sketching of Single-Cell Data Preserves Transcriptional Structure. Brian Hie, Hyunghoon Cho, Benjamin Demeo, Bryan Bryson, Bonnie Berger |
| 2019 | How Many Subpopulations Is Too Many? Exponential Lower Bounds for Inferring Population Histories. Younhun Kim, Frederic Koehler, Ankur Moitra, Elchanan Mossel, Govind Ramnarayan |
| 2019 | Identifying Clinical Terms in Free-Text Notes Using Ontology-Guided Machine Learning. Aryan Arbabi, David R. Adams, Sanja Fidler, Michael Brudno |
| 2019 | Inferring Tumor Evolution from Longitudinal Samples. Matthew A. Myers, Gryte Satas, Benjamin J. Raphael |
| 2019 | Learning Robust Multi-label Sample Specific Distances for Identifying HIV-1 Drug Resistance. Lodewijk Brand, Xue Yang, Kai Liu, Saad El Beleidy, Hua Wang, Hao Zhang |
| 2019 | MethCP: Differentially Methylated Region Detection with Change Point Models. Boying Gong, Elizabeth Purdom |
| 2019 | Minimization-Aware Recursive K^* K ∗ ( MARK^* MARK ∗ ): A Novel, Provable Algorithm that Accelerates Ensemble-Based Protein Design and Provably Approximates the Energy Landscape. Jonathan D. Jou, Graham T. Holt, Anna U. Lowegard, Bruce Randall Donald |
| 2019 | Mitigating Data Scarcity in Protein Binding Prediction Using Meta-Learning. Yunan Luo, Jianzhu Ma, Xiaoming Zhao, Yufeng Su, Yang Liu, Trey Ideker, Jian Peng |
| 2019 | ModHMM: A Modular Supra-Bayesian Genome Segmentation Method. Philipp Benner, Martin Vingron |
| 2019 | OMGS: Optical Map-Based Genome Scaffolding. Weihua Pan, Tao Jiang, Stefano Lonardi |
| 2019 | On the Complexity of Sequence to Graph Alignment. Chirag Jain, Haowen Zhang, Yu Gao, Srinivas Aluru |
| 2019 | RENET: A Deep Learning Approach for Extracting Gene-Disease Associations from Literature. Ye Wu, Ruibang Luo, Henry C. M. Leung, Hing-Fung Ting, Tak Wah Lam |
| 2019 | Research in Computational Molecular Biology - 23rd Annual International Conference, RECOMB 2019, Washington, DC, USA, May 5-8, 2019, Proceedings Lenore J. Cowen |
| 2019 | Scalable Multi-component Linear Mixed Models with Application to SNP Heritability Estimation. Ali Pazokitoroudi, Yue Wu, Kathryn S. Burch, Kangcheng Hou, Bogdan Pasaniuc, Sriram Sankararaman |
| 2019 | Sketching Algorithms for Genomic Data Analysis and Querying in a Secure Enclave. Can Kockan, Kaiyuan Zhu, Natnatee Dokmai, Nikolai Karpov, M. Oguzhan Külekci, David P. Woodruff, Süleyman Cenk Sahinalp |
| 2019 | Sparse Binary Relation Representations for Genome Graph Annotation. Mikhail Karasikov, Harun Mustafa, Amir Joudaki, Sara Javadzadeh-No, Gunnar Rätsch, André Kahles |
| 2019 | Towards a Post-clustering Test for Differential Expression. Jesse M. Zhang, Govinda M. Kamath, David N. C. Tse |
| 2019 | Tumor Copy Number Deconvolution Integrating Bulk and Single-Cell Sequencing Data. Haoyun Lei, Bochuan Lyu, E. Michael Gertz, Alejandro A. Schäffer, Xulian Shi, Kui Wu, Guibo Li, Liqin Xu, Yong Hou, Michael Dean, Russell Schwartz |
| 2019 | netNMF-sc: A Network Regularization Algorithm for Dimensionality Reduction and Imputation of Single-Cell Expression Data. Rebecca Elyanow, Bianca Dumitrascu, Barbara E. Engelhardt, Benjamin J. Raphael |
| 2019 | stance-Based Protein Folding Powered by Deep Learning. Jinbo Xu |