| 2018 | SCIΦ: Single-Cell Mutation Identification via Phylogenetic Inference. | Jochen Singer, Jack Kuipers, Katharina Jahn, Niko Beerenwinkel |
| 2018 | A General Framework for Genome Rearrangement with Biological Constraints. | Pijus Simonaitis, Annie Chateau, Krister M. Swenson |
| 2018 | ModulOmics: Integrating Multi-Omics Data to Identify Cancer Driver Modules. | Dana Silverbush, Simona Cristea, Gali Yanovich, Tamar Geiger, Niko Beerenwinkel, Roded Sharan |
| 2018 | Latent Variable Model for Aligning Barcoded Short-Reads Improves Downstream Analyses. | Ariya Shajii, Ibrahim Numanagic, Bonnie Berger |
| 2018 | Assembly-Free and Alignment-Free Sample Identification Using Genome Skims. | Shahab Sarmashghi, Kristine Bohmann, M. Thomas P. Gilbert, Vineet Bafna, Siavash Mirarab |
| 2018 | Circular Networks from Distorted Metrics. | Sebastien Roch, Kun-Chieh Wang |
| 2018 | On the Variance of Internode Distance Under the Multispecies Coalescent. | Sbastien Roch |
| 2018 | Tensor Composition Analysis Detects Cell-Type Specific Associations in Epigenetic Studies. | Elior Rahmani, Regev Schweiger, Saharon Rosset, Sriram Sankararaman, Eran Halperin |
| 2018 | On the Non-uniqueness of Solutions to the Perfect Phylogeny Mixture Problem. | Dikshant Pradhan, Mohammed El-Kebir |
| 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 | Reverse de Bruijn: Utilizing Reverse Peptide Synthesis to Cover All Amino Acid k-mers. | Yaron Orenstein |
| 2018 | NJMerge: A Generic Technique for Scaling Phylogeny Estimation Methods and Its Application to Species Trees. | Erin K. Molloy, Tandy J. Warnow |
| 2018 | The Rooted SCJ Median with Single Gene Duplications. | Aniket C. Mane, Manuel Lafond, Pedro Feijo, Cdric Chauve |
| 2018 | Integrative Inference of Subclonal Tumour Evolution from Single-Cell and Bulk Sequencing Data. | Salem Malikic, Katharina Jahn, Jack Kuipers, Sleyman Cenk Sahinalp, Niko Beerenwinkel |
| 2018 | Deciphering Signaling Specificity with Deep Neural Networks. | Yunan Luo, Jianzhu Ma, Yang Liu, Qing Ye, Trey Ideker, Jian Peng |
| 2018 | Constrained De Novo Sequencing of neo-Epitope Peptides Using Tandem Mass Spectrometry. | Sujun Li, Alex DeCourcy, Haixu Tang |
| 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 | Modeling Dependence in Evolutionary Inference for Proteins. | Gary Larson, Jeffrey L. Thorne, Scott C. Schmidler |
| 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 Mkinen |
| 2018 | Assembly of Long Error-Prone Reads Using Repeat Graphs. | Mikhail Kolmogorov, Jeffrey Yuan, Yu Lin, Pavel A. Pevzner |
| 2018 | Inference of Population Structure from Ancient DNA. | Tyler A. Joseph, Itsik Pe'er |
| 2018 | Contribution of Structural Variation to Genome Structure: TAD Fusion Discovery and Ranking. | Linh Huynh, Fereydoun Hormozdiari |
| 2018 | FastNet: Fast and Accurate Statistical Inference of Phylogenetic Networks Using Large-Scale Genomic Sequence Data. | Hussein A. Hejase, Natalie Vande Pol, Gregory M. Bonito, Kevin J. Liu |
| 2018 | mClass: Cancer Type Classification with Somatic Point Mutation Data. | Md. Abid Hasan, Stefano Lonardi |
| 2018 | Fixed-Parameter Tractable Sampling for RNA Design with Multiple Target Structures. | Stefan Hammer, Yann Ponty, Wei Wang, Sebastian Will |