| 2018 | A Multi-species Functional Embedding Integrating Sequence and Network Structure. Mark D. M. Leiserson, Jason Fan, Anthony Cannistra, Inbar Fried, Tim Lim, Thomas Schaffner, Mark Crovella, Benjamin J. Hescott |
| 2018 | A Nested 2-Level Cross-Validation Ensemble Learning Pipeline Suggests a Negative Pressure Against Crosstalk snoRNA-mRNA Interactions in Saccharomyces Cerevisae. Antoine Soulé, Jean-Marc Steyaert, Jérôme Waldispühl |
| 2018 | A Unifying Framework for Summary Statistic Imputation. Yue Wu, Eleazar Eskin, Sriram Sankararaman |
| 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 | Algorithmic Framework for Approximate Matching Under Bounded Edits with Applications to Sequence Analysis. Sharma V. Thankachan, Chaitanya Aluru, Sriram P. Chockalingam, Srinivas Aluru |
| 2018 | AptaBlocks: Accelerating the Design of RNA-Based Drug Delivery Systems. Yijie Wang, Jan Hoinka, Piotr Swiderski, Teresa M. Przytycka |
| 2018 | Assembly of Long Error-Prone Reads Using Repeat Graphs. Mikhail Kolmogorov, Jeffrey Yuan, Yu Lin, Pavel A. Pevzner |
| 2018 | Assembly-Free and Alignment-Free Sample Identification Using Genome Skims. Shahab Sarmashghi, Kristine Bohmann, M. Thomas P. Gilbert, Vineet Bafna, Siavash Mirarab |
| 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 | Chromatyping: Reconstructing Nucleosome Profiles from NOMe Sequencing Data. Shounak Chakraborty, Stefan Canzar, Tobias Marschall, Marcel H. Schulz |
| 2018 | Circular Networks from Distorted Metrics. Sebastien Roch, Kun-Chieh Wang |
| 2018 | Constrained De Novo Sequencing of neo-Epitope Peptides Using Tandem Mass Spectrometry. Sujun Li, Alex DeCourcy, Haixu Tang |
| 2018 | Context-Specific Nested Effects Models. Yuriy Sverchkov, Yi-Hsuan Ho, Audrey P. Gasch, Mark Craven |
| 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 | Contribution of Structural Variation to Genome Structure: TAD Fusion Discovery and Ranking. Linh Huynh, Fereydoun Hormozdiari |
| 2018 | Deciphering Signaling Specificity with Deep Neural Networks. Yunan Luo, Jianzhu Ma, Yang Liu, Qing Ye, Trey Ideker, Jian Peng |
| 2018 | Deep Learning Reveals Many More Inter-protein Residue-Residue Contacts than Direct Coupling Analysis. Tianming Zhou, Sheng Wang, Jinbo Xu |
| 2018 | Designing RNA Secondary Structures Is Hard. Édouard Bonnet, Pawel Rzazewski, Florian Sikora |
| 2018 | Efficient Algorithms to Discover Alterations with Complementary Functional Association in Cancer. Rebecca Sarto Basso, Dorit S. Hochbaum, Fabio Vandin |
| 2018 | Fixed-Parameter Tractable Sampling for RNA Design with Multiple Target Structures. Stefan Hammer, Yann Ponty, Wei Wang, Sebastian Will |
| 2018 | GTED: Graph Traversal Edit Distance. Ali Ebrahimpour Boroojeny, Akash Shrestha, Ali Sharifi-Zarchi, Suzanne Renick Gallagher, Süleyman Cenk Sahinalp, Hamidreza Chitsaz |
| 2018 | Generalizable Visualization of Mega-Scale Single-Cell Data. Hyunghoon Cho, Bonnie Berger, Jian Peng |
| 2018 | Inference of Population Structure from Ancient DNA. Tyler A. Joseph, Itsik Pe'er |
| 2018 | Integrative Inference of Subclonal Tumour Evolution from Single-Cell and Bulk Sequencing Data. Salem Malikic, Katharina Jahn, Jack Kuipers, Süleyman Cenk Sahinalp, Niko Beerenwinkel |
| 2018 | Latent Variable Model for Aligning Barcoded Short-Reads Improves Downstream Analyses. Ariya Shajii, Ibrahim Numanagic, Bonnie Berger |
| 2018 | Long Reads Enable Accurate Estimates of Complexity of Metagenomes. Anton Bankevich, Pavel A. Pevzner |
| 2018 | Loss-Function Learning for Digital Tissue Deconvolution. Franziska Görtler, Stefan Solbrig, Tilo Wettig, Peter J. Oefner, Rainer Spang, Michael Altenbuchinger |
| 2018 | Mantis: A Fast, Small, and Exact Large-Scale Sequence-Search Index. Prashant Pandey, Fatemeh Almodaresi, Michael A. Bender, Michael Ferdman, Rob Johnson, Rob Patro |
| 2018 | Modeling Dependence in Evolutionary Inference for Proteins. Gary Larson, Jeffrey L. Thorne, Scott C. Schmidler |
| 2018 | ModulOmics: Integrating Multi-Omics Data to Identify Cancer Driver Modules. Dana Silverbush, Simona Cristea, Gali Yanovich, Tamar Geiger, Niko Beerenwinkel, Roded Sharan |
| 2018 | Positive-Unlabeled Convolutional Neural Networks for Particle Picking in Cryo-electron Micrographs. Tristan Bepler, Andrew Morin, Alex J. Noble, Julia Brasch, Lawrence Shapiro, Bonnie Berger |
| 2018 | Probabilistic Count Matrix Factorization for Single Cell Expression Data Analysis. Ghislain Durif, Laurent Modolo, Jeff E. Mold, Sophie Lambert-Lacroix, Franck Picard |
| 2018 | Research in Computational Molecular Biology - 22nd Annual International Conference, RECOMB 2018, Paris, France, April 21-24, 2018, Proceedings Benjamin J. Raphael |
| 2018 | Reverse de Bruijn: Utilizing Reverse Peptide Synthesis to Cover All Amino Acid k-mers. Yaron Orenstein |
| 2018 | SCIΦ: Single-Cell Mutation Identification via Phylogenetic Inference. Jochen Singer, Jack Kuipers, Katharina Jahn, Niko Beerenwinkel |
| 2018 | Statistical Inference of Peroxisome Dynamics. Cyril Galitzine, Pierre M. Jean Beltran, Ileana M. Cristea, Olga Vitek |
| 2018 | Targeted Genotyping of Variable Number Tandem Repeats with AdVNTR. Mehrdad Bakhtiari, Sharona Shleizer-Burko, Melissa Gymrek, Vikas Bansal, Vineet Bafna |
| 2018 | Tensor Composition Analysis Detects Cell-Type Specific Associations in Epigenetic Studies. Elior Rahmani, Regev Schweiger, Saharon Rosset, Sriram Sankararaman, Eran Halperin |
| 2018 | Using Minimum Path Cover to Boost Dynamic Programming on DAGs: Co-linear Chaining Extended. Anna Kuosmanen, Topi Paavilainen, Travis Gagie, Rayan Chikhi, Alexandru I. Tomescu, Veli Mäkinen |