A Self-Coordinating Approach to Distributed Fair Queueing in Ad Hoc Wireless Networks. - Haiyun Luo; Paul Medvedev; Jerry Cheng; Songwu Lu (INFOCOM, 2001)

Computability of Models for Sequence Assembly. - Paul Medvedev; Konstantinos Georgiou; Gene Myers; Michael Brudno (WABI, 2007)

Ab Initio Whole Genome Shotgun Assembly with Mated Short Reads. - Paul Medvedev; Michael Brudno (RECOMB, 2008)

The relative worst order ratio applied to seat reservation. - Joan Boyar; Paul Medvedev (ACM Trans. Algorithms, 2008)

Rearrangement Models and Single-Cut Operations. - Paul Medvedev; Jens Stoye (RECOMB-CG, 2009)

A report on the 2009 SIG on short read sequencing and algorithms (Short-SIG). - Michael Brudno; Paul Medvedev; Jens Stoye; Francisco M. de la Vega (Bioinform., 2009)

Maximum Likelihood Genome Assembly. - Paul Medvedev; Michael Brudno (J. Comput. Biol., 2009)

Shortest Paths between Shortest Paths and Independent Sets. - Marcin Kaminski 001; Paul Medvedev; Martin Milanic (IWOCA, 2010)

Rearrangement Models and Single-Cut Operations. - Anne Bergeron; Paul Medvedev; Jens Stoye (J. Comput. Biol., 2010)

Error correction of high-throughput sequencing datasets with non-uniform coverage. - Paul Medvedev; Eric Scott; Boyko Kakaradov; Pavel A. Pevzner (Bioinform., 2011)

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 (J. Comput. Biol., 2011)

The plane-width of graphs. - Marcin Kaminski 001; Paul Medvedev; Martin Milanic (J. Graph Theory, 2011)

Shortest paths between shortest paths. - Marcin Kaminski 001; Paul Medvedev; Martin Milanic (Theor. Comput. Sci., 2011)

Genome Graphs. - Paul Medvedev (2011)

Complexity of independent set reconfigurability problems. - Marcin Kaminski 001; Paul Medvedev; Martin Milanic (Theor. Comput. Sci., 2012)

Using state machines to model the Ion Torrent sequencing process and to improve read error rates. - David Golan; Paul Medvedev (Bioinform., 2013)

Informed and automated k-mer size selection for genome assembly. - Rayan Chikhi; Paul Medvedev (Bioinform., 2014)

On the Representation of De Bruijn Graphs. - Rayan Chikhi; Antoine Limasset; Shaun Jackman; Jared T. Simpson; Paul Medvedev (J. Comput. Biol., 2015)

The Second Decade of the International Conference on Research in Computational Molecular Biology (RECOMB). - Farhad Hormozdiari; Fereydoun Hormozdiari; Carl Kingsford; Paul Medvedev; Fabio Vandin (RECOMB, 2016)

Safe and Complete Contig Assembly Via Omnitigs. - Alexandru I. Tomescu; Paul Medvedev (RECOMB, 2016)

Compacting de Bruijn graphs from sequencing data quickly and in low memory. - Rayan Chikhi; Antoine Limasset; Paul Medvedev (Bioinform., 2016)

On the readability of overlap digraphs. - Rayan Chikhi; Paul Medvedev; Martin Milanic; Sofya Raskhodnikova (Discret. Appl. Math., 2016)

Optimal Omnitig Listing for Safe and Complete Contig Assembly. - Massimo Cairo; Paul Medvedev; Nidia Obscura Acosta; Romeo Rizzi; Alexandru I. Tomescu (CPM, 2017)

Parallel and Memory-Efficient Preprocessing for Metagenome Assembly. - Vasudevan Rengasamy; Paul Medvedev; Kamesh Madduri (IPDPS Workshops, 2017)

TwoPaCo: an efficient algorithm to build the compacted de Bruijn graph from many complete genomes. - Ilya Minkin; Son K. Pham; Paul Medvedev (Bioinform., 2017)

VarMatch: robust matching of small variant datasets using flexible scoring schemes. - Chen Sun 014; Paul Medvedev (Bioinform., 2017)

Safe and Complete Contig Assembly Through Omnitigs. - Alexandru I. Tomescu; Paul Medvedev (J. Comput. Biol., 2017)

Parallel Read Partitioning for Concurrent Assembly of Metagenomic Data. - Vasudevan Rengasamy; Mahmut T. Kandemir; Paul Medvedev; Kamesh Madduri (HiPC, 2018)

Introduction to HiCOMB 2018. - Srinivas Aluru; David A. Bader; Paul Medvedev (IPDPS Workshops, 2018)

RecoverY: k-mer-based read classification for Y-chromosome-specific sequencing and assembly. - Samarth Rangavittal; Robert S. Harris; Monika Cechova; Marta Tomaszkiewicz; Rayan Chikhi; Kateryna D. Makova; Paul Medvedev (Bioinform., 2018)

AllSome Sequence Bloom Trees. - Chen Sun 014; Robert S. Harris; Rayan Chikhi; Paul Medvedev (J. Comput. Biol., 2018)

Modeling biological problems in computer science: a case study in genome assembly. - Paul Medvedev (Briefings Bioinform., 2019)

Toward fast and accurate SNP genotyping from whole genome sequencing data for bedside diagnostics. - Chen Sun 014; Paul Medvedev (Bioinform., 2019)

Data structures to represent sets of k-long DNA sequences. - Rayan Chikhi; Jan Holub 001; Paul Medvedev (CoRR, 2019)

An Optimal O(nm) Algorithm for Enumerating All Walks Common to All Closed Edge-covering Walks of a Graph. - Massimo Cairo; Paul Medvedev; Nidia Obscura Acosta; Romeo Rizzi; Alexandru I. Tomescu (ACM Trans. Algorithms, 2019)

Representation of k-mer Sets Using Spectrum-Preserving String Sets. - Amatur Rahman; Paul Medvedev (RECOMB, 2020)

Improved representation of sequence bloom trees. - Robert S. Harris; Paul Medvedev (Bioinform., 2020)

De Novo Clustering of Long-Read Transcriptome Data Using a Greedy, Quality Value-Based Algorithm. - Kristoffer Sahlin; Paul Medvedev (J. Comput. Biol., 2020)

Ten Simple Rules for writing algorithmic bioinformatics conference papers. - Paul Medvedev (PLoS Comput. Biol., 2020)

Bipartite graphs of small readability. - Rayan Chikhi; Vladan Jovicic; Stefan Kratsch; Paul Medvedev; Martin Milanic; Sofya Raskhodnikova; Nithin Varma 001 (Theor. Comput. Sci., 2020)

GYAN: Accelerating Bioinformatics Tools in Galaxy with GPU-Aware Computation Mapping. - Gulsum Gudukbay; Jashwant Raj Gunasekaran; Yilin Feng; Mahmut T. Kandemir; Anton Nekrutenko; Chita R. Das; Paul Medvedev; Björn A. Grüning; Nate Coraor; Nathan Roach; Enis Afgan (IPDPS Workshops, 2021)

Disk compression of k-mer sets. - Amatur Rahman; Rayan Chikhi; Paul Medvedev (Algorithms Mol. Biol., 2021)

What do Eulerian and Hamiltonian cycles have to do with genome assembly? - Paul Medvedev; Mihai Pop (PLoS Comput. Biol., 2021)

Uncovering Hidden Assembly Artifacts: When Unitigs are not Safe and Bidirected Graphs are not Helpful (ABSTRACT). - Amatur Rahman; Paul Medvedev (RECOMB, 2022)

The minimizer Jaccard estimator is biased and inconsistent. - Mahdi Belbasi; Antonio Blanca; Robert S. Harris; David Koslicki; Paul Medvedev (Bioinform., 2022)

The K-mer File Format: a standardized and compact disk representation of sets of k-mers. - Yoann Dufresne; Téo Lemane; Pierre Marijon; Pierre Peterlongo; Amatur Rahman; Marek Kokot; Paul Medvedev; Sebastian Deorowicz; Rayan Chikhi (Bioinform., 2022)

Markov chains improve the significance computation of overlapping genome annotations. - Askar Gafurov; Brona Brejová; Paul Medvedev (Bioinform., 2022)

Theoretical analysis of edit distance algorithms: an applied perspective. - Paul Medvedev (CoRR, 2022)

The limitations of the theoretical analysis of applied algorithms. - Paul Medvedev (CoRR, 2022)

Data Structures to Represent a Set of k-long DNA Sequences. - Rayan Chikhi; Jan Holub 001; Paul Medvedev (ACM Comput. Surv., 2022)

The Statistics of k-mers from a Sequence Undergoing a Simple Mutation Process Without Spurious Matches. - Antonio Blanca; Robert S. Harris; David Koslicki; Paul Medvedev (J. Comput. Biol., 2022)

Exact Sketch-Based Read Mapping. - Tizian Schulz; Paul Medvedev (WABI, 2023)

Theoretical Analysis of Sequencing Bioinformatics Algorithms and Beyond. - Paul Medvedev (Commun. ACM, 2023)

Theoretical Analysis of Edit Distance Algorithms. - Paul Medvedev (Commun. ACM, 2023)

Efficient Analysis of Annotation Colocalization Accounting for Genomic Contexts. - Askar Gafurov; Tomás Vinar; Paul Medvedev; Brona Brejová (RECOMB, 2024)

PLA-index: A k-mer Index Exploiting Rank Curve Linearity. - Md. Hasin Abrar; Paul Medvedev (WABI, 2024)

Applying the Safe-And-Complete Framework to Practical Genome Assembly. - Sebastian S. Schmidt; Santeri Toivonen; Paul Medvedev; Alexandru I. Tomescu (WABI, 2024)

Fast Context-Aware Analysis of Genome Annotation Colocalization. - Askar Gafurov; Tomás Vinar; Paul Medvedev; Brona Brejová (J. Comput. Biol., 2024)

pla-index. - Md. Hasin Abrar; Paul Medvedev (DROPS Artifacts, 2024)

Compression algorithm for colored de Bruijn graphs. - Amatur Rahman; Yoann Dufresne; Paul Medvedev (Algorithms Mol. Biol., 2024)

ESKEMAP: exact sketch-based read mapping. - Tizian Schulz; Paul Medvedev (Algorithms Mol. Biol., 2024)

Estimation of Substitution and Indel Rates via k-mer Statistics. - Mahmudur Rahman Hera; Paul Medvedev; David Koslicki; Antonio Blanca (WABI, 2025)

A k-mer-Based Estimator of the Substitution Rate Between Repetitive Sequences. - Haonan Wu; Antonio Blanca; Paul Medvedev (WABI, 2025)