| 2025 | ESA | Efficiency of Learned Indexes on Genome Spectra. | Md. Hasin Abrar, Paul Medvedev, Giorgio Vinciguerra |
| 2025 | WABI | Estimation of Substitution and Indel Rates via k-mer Statistics. | Mahmudur Rahman Hera, Paul Medvedev, David Koslicki, Antonio Blanca |
| 2025 | WABI | A k-mer-Based Estimator of the Substitution Rate Between Repetitive Sequences. | Haonan Wu, Antonio Blanca, Paul Medvedev |
| 2024 | RECOMB | Efficient Analysis of Annotation Colocalization Accounting for Genomic Contexts. | Askar Gafurov, Toms Vinar, Paul Medvedev, Brona Brejov |
| 2024 | WABI | PLA-index: A k-mer Index Exploiting Rank Curve Linearity. | Md. Hasin Abrar, Paul Medvedev |
| 2024 | WABI | Applying the Safe-And-Complete Framework to Practical Genome Assembly. | Sebastian S. Schmidt, Santeri Toivonen, Paul Medvedev, Alexandru I. Tomescu |
| 2023 | WABI | Compression Algorithm for Colored de Bruijn Graphs. | Amatur Rahman, Yoann Dufresne, Paul Medvedev |
| 2023 | WABI | Exact Sketch-Based Read Mapping. | Tizian Schulz, Paul Medvedev |
| 2022 | RECOMB | Uncovering Hidden Assembly Artifacts: When Unitigs are not Safe and Bidirected Graphs are not Helpful (ABSTRACT). | Amatur Rahman, Paul Medvedev |
| 2020 | RECOMB | Representation of k-mer Sets Using Spectrum-Preserving String Sets. | Amatur Rahman, Paul Medvedev |
| 2020 | WABI | Disk Compression of k-mer Sets. | Amatur Rahman, Rayan Chikhi, Paul Medvedev |
| 2019 | RECOMB | De Novo Clustering of Long-Read Transcriptome Data Using a Greedy, Quality-Value Based Algorithm. | Kristoffer Sahlin, Paul Medvedev |
| 2018 | COCOON | Bipartite Graphs of Small Readability. | Rayan Chikhi, Vladan Jovicic, Stefan Kratsch, Paul Medvedev, Martin Milanic, Sofya Raskhodnikova, Nithin Varma |
| 2018 | HiPC | Parallel Read Partitioning for Concurrent Assembly of Metagenomic Data. | Vasudevan Rengasamy, Mahmut T. Kandemir, Paul Medvedev, Kamesh Madduri |
| 2017 | CPM | Optimal Omnitig Listing for Safe and Complete Contig Assembly. | Massimo Cairo, Paul Medvedev, Nidia Obscura Acosta, Romeo Rizzi, Alexandru I. Tomescu |
| 2017 | RECOMB | AllSome Sequence Bloom Trees. | Chen Sun, Robert S. Harris, Rayan Chikhi, Paul Medvedev |
| 2016 | RECOMB | The Second Decade of the International Conference on Research in Computational Molecular Biology (RECOMB). | Farhad Hormozdiari, Fereydoun Hormozdiari, Carl Kingsford, Paul Medvedev, Fabio Vandin |
| 2016 | RECOMB | Safe and Complete Contig Assembly Via Omnitigs. | Alexandru I. Tomescu, Paul Medvedev |
| 2015 | CPM | On the Readability of Overlap Digraphs. | Rayan Chikhi, Paul Medvedev, Martin Milanic, Sofya Raskhodnikova |
| 2014 | RECOMB | On the Representation of de Bruijn Graphs. | Rayan Chikhi, Antoine Limasset, Shaun Jackman, Jared T. Simpson, Paul Medvedev |
| 2011 | RECOMB | Paired de Bruijn Graphs: A Novel Approach for Incorporating Mate Pair Information into Genome Assemblers. | Paul Medvedev, Son K. Pham, Mark Chaisson, Glenn Tesler, Pavel A. Pevzner |
| 2010 | IWOCA | Shortest Paths between Shortest Paths and Independent Sets. | Marcin Kaminski, Paul Medvedev, Martin Milanic |
| 2009 | RECOMB | Rearrangement Models and Single-Cut Operations. | Paul Medvedev, Jens Stoye |
| 2008 | RECOMB | Ab Initio Whole Genome Shotgun Assembly with Mated Short Reads. | Paul Medvedev, Michael Brudno |
| 2007 | WABI | Computability of Models for Sequence Assembly. | Paul Medvedev, Konstantinos Georgiou, Gene Myers, Michael Brudno |
| 2001 | INFOCOM | A Self-Coordinating Approach to Distributed Fair Queueing in Ad Hoc Wireless Networks. | Haiyun Luo, Paul Medvedev, Jerry Cheng, Songwu Lu |