| 2019 | On the Complexity of Sequence to Graph Alignment. | Chirag Jain, Haowen Zhang, Yu Gao, Srinivas Aluru |
| 2019 | Geometric Sketching of Single-Cell Data Preserves Transcriptional Structure. | Brian Hie, Hyunghoon Cho, Benjamin Demeo, Bryan Bryson, Bonnie Berger |
| 2019 | MethCP: Differentially Methylated Region Detection with Change Point Models. | Boying Gong, Elizabeth Purdom |
| 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 | Dynamic Pseudo-time Warping of Complex Single-Cell Trajectories. | Van Hoan Do, Mislav Blazevic, Pablo Monteagudo, Luka Borozan, Khaled M. Elbassioni, Sren Laue, Francisca Rojas Ringeling, Domagoj Matijevic, Stefan Canzar |
| 2019 | Biological Sequence Modeling with Convolutional Kernel Networks. | Dexiong Chen, Laurent Jacob, Julien Mairal |
| 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 | ModHMM: A Modular Supra-Bayesian Genome Segmentation Method. | Philipp Benner, Martin Vingron |
| 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 | APPLES: Fast Distance-Based Phylogenetic Placement. | Metin Balaban, Shahab Sarmashghi, Siavash Mirarab |
| 2019 | Identifying Clinical Terms in Free-Text Notes Using Ontology-Guided Machine Learning. | Aryan Arbabi, David R. Adams, Sanja Fidler, Michael Brudno |
| 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 |
| 2018 | Deep Learning Reveals Many More Inter-protein Residue-Residue Contacts than Direct Coupling Analysis. | Tianming Zhou, Sheng Wang, Jinbo Xu |
| 2018 | Accurate Reconstruction of Microbial Strains from Metagenomic Sequencing Using Representative Reference Genomes. | Zhemin Zhou, Nina Luhmann, Nabil-Fareed Alikhan, Christopher Quince, Mark Achtman |
| 2018 | Speciation and Rate Variation in a Birth-and-Death Account of WGD and Fractionation; the Case of Solanaceae. | Yue Zhang, Chunfang Zheng, David Sankoff |
| 2018 | Estimation of the True Evolutionary Distance Under the INFER Model. | Alexey Zabelkin, Nikita Alexeev |
| 2018 | Continuous-Trait Probabilistic Model for Comparing Multi-species Functional Genomic Data. | Yang Yang, Quanquan Gu, Takayo Sasaki, Julianna Crivello, Rachel O'Neill, David M. Gilbert, Jian Ma |
| 2018 | Characterizing Protein-DNA Binding Event Subtypes in ChIP-Exo Data. | Naomi Yamada, William K. M. Lai, Nina Farrell, B. Franklin Pugh, Shaun Mahony |
| 2018 | A Unifying Framework for Summary Statistic Imputation. | Yue Wu, Eleazar Eskin, Sriram Sankararaman |
| 2018 | Linear-Time Tree Containment in Phylogenetic Networks. | Mathias Weller |
| 2018 | Non-parametric and Semi-parametric Support Estimation Using SEquential RESampling Random Walks on Biomolecular Sequences. | Wei Wang, Jack Smith, Hussein A. Hejase, Kevin J. Liu |
| 2018 | AptaBlocks: Accelerating the Design of RNA-Based Drug Delivery Systems. | Yijie Wang, Jan Hoinka, Piotr Swiderski, Teresa M. Przytycka |
| 2018 | Algorithmic Framework for Approximate Matching Under Bounded Edits with Applications to Sequence Analysis. | Sharma V. Thankachan, Chaitanya Aluru, Sriram P. Chockalingam, Srinivas Aluru |
| 2018 | Context-Specific Nested Effects Models. | Yuriy Sverchkov, Yi-Hsuan Ho, Audrey P. Gasch, Mark Craven |
| 2018 | A Nested 2-Level Cross-Validation Ensemble Learning Pipeline Suggests a Negative Pressure Against Crosstalk snoRNA-mRNA Interactions in Saccharomyces Cerevisae. | Antoine Soul, Jean-Marc Steyaert, Jrme Waldisphl |