Paul Medvedev

According to our database, Paul Medvedev authored at least 53 papers between 2001 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2023

Theoretical Analysis of Edit Distance Algorithms.

Paul Medvedev

Commun. ACM, December, 2023

Theoretical Analysis of Sequencing Bioinformatics Algorithms and Beyond.

Paul Medvedev

Commun. ACM, July, 2023

Exact Sketch-Based Read Mapping.

Tizian Schulz, Paul Medvedev

Proceedings of the 23rd International Workshop on Algorithms in Bioinformatics, 2023

Compression Algorithm for Colored de Bruijn Graphs.

Amatur Rahman, Yoann Dufresne, Paul Medvedev

Proceedings of the 23rd International Workshop on Algorithms in Bioinformatics, 2023

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

Data Structures to Represent a Set of <i>k</i>-long DNA Sequences.

Rayan Chikhi, Jan Holub, Paul Medvedev

ACM Comput. Surv., 2022

The limitations of the theoretical analysis of applied algorithms.

Paul Medvedev

CoRR, 2022

Theoretical analysis of edit distance algorithms: an applied perspective.

Paul Medvedev

CoRR, 2022

The K-mer File Format: a standardized and compact disk representation of sets of <i>k</i>-mers.

Yoann Dufresne, Téo Lemane, Pierre Marijon, Pierre Peterlongo, Amatur Rahman, Marek Kokot, Paul Medvedev, Sebastian Deorowicz, Rayan Chikhi

Bioinform., 2022

Uncovering Hidden Assembly Artifacts: When Unitigs are not Safe and Bidirected Graphs are not Helpful (ABSTRACT).

Amatur Rahman, Paul Medvedev

Proceedings of the Research in Computational Molecular Biology, 2022

2021

What do Eulerian and Hamiltonian cycles have to do with genome assembly?

Paul Medvedev, Mihai Pop

PLoS Comput. Biol., 2021

Disk compression of k-mer sets.

Amatur Rahman, Rayan Chikhi, Paul Medvedev

Algorithms Mol. Biol., 2021

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

Proceedings of the IEEE International Parallel and Distributed Processing Symposium Workshops, 2021

2020

Bipartite graphs of small readability.

Rayan Chikhi, Vladan Jovicic, Stefan Kratsch, Paul Medvedev, Martin Milanic, Sofya Raskhodnikova, Nithin Varma

Theor. Comput. Sci., 2020

Ten Simple Rules for writing algorithmic bioinformatics conference papers.

Paul Medvedev

PLoS Comput. Biol., 2020

De Novo Clustering of Long-Read Transcriptome Data Using a Greedy, Quality Value-Based Algorithm.

Kristoffer Sahlin, Paul Medvedev

J. Comput. Biol., 2020

Improved representation of sequence bloom trees.

Robert S. Harris, Paul Medvedev

Bioinform., 2020

Representation of k-mer Sets Using Spectrum-Preserving String Sets.

Amatur Rahman, Paul Medvedev

Proceedings of the Research in Computational Molecular Biology, 2020

2019

An Optimal <i>O</i>(<i>nm</i>) 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

Data structures to represent sets of k-long DNA sequences.

Rayan Chikhi, Jan Holub, Paul Medvedev

CoRR, 2019

Toward fast and accurate SNP genotyping from whole genome sequencing data for bedside diagnostics.

Chen Sun, Paul Medvedev

Bioinform., 2019

Modeling biological problems in computer science: a case study in genome assembly.

Paul Medvedev

Briefings Bioinform., 2019

2018

AllSome Sequence Bloom Trees.

Chen Sun, Robert S. Harris, Rayan Chikhi, Paul Medvedev

J. Comput. Biol., 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

Introduction to HiCOMB 2018.

Srinivas Aluru, David A. Bader, Paul Medvedev

Proceedings of the 2018 IEEE International Parallel and Distributed Processing Symposium Workshops, 2018

Parallel Read Partitioning for Concurrent Assembly of Metagenomic Data.

Vasudevan Rengasamy, Mahmut T. Kandemir, Paul Medvedev, Kamesh Madduri

Proceedings of the 25th IEEE International Conference on High Performance Computing, 2018

2017

Safe and Complete Contig Assembly Through Omnitigs.

Alexandru I. Tomescu, Paul Medvedev

J. Comput. Biol., 2017

VarMatch: robust matching of small variant datasets using flexible scoring schemes.

Chen Sun, Paul Medvedev

Bioinform., 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

Parallel and Memory-Efficient Preprocessing for Metagenome Assembly.

Vasudevan Rengasamy, Paul Medvedev, Kamesh Madduri

Proceedings of the 2017 IEEE International Parallel and Distributed Processing Symposium Workshops, 2017

Optimal Omnitig Listing for Safe and Complete Contig Assembly.

Massimo Cairo, Paul Medvedev, Nidia Obscura Acosta, Romeo Rizzi, Alexandru I. Tomescu

Proceedings of the 28th Annual Symposium on Combinatorial Pattern Matching, 2017

2016

On the readability of overlap digraphs.

Rayan Chikhi, Paul Medvedev, Martin Milanic, Sofya Raskhodnikova

Discret. Appl. Math., 2016

Compacting de Bruijn graphs from sequencing data quickly and in low memory.

Rayan Chikhi, Antoine Limasset, Paul Medvedev

Bioinform., 2016

Safe and Complete Contig Assembly Via Omnitigs.

Alexandru I. Tomescu, Paul Medvedev

Proceedings of the Research in Computational Molecular Biology - 20th Annual Conference, 2016

The Second Decade of the International Conference on Research in Computational Molecular Biology (RECOMB).

Farhad Hormozdiari, Fereydoun Hormozdiari, Carl Kingsford, Paul Medvedev, Fabio Vandin

Proceedings of the Research in Computational Molecular Biology - 20th Annual Conference, 2016

2015

On the Representation of De Bruijn Graphs.

Rayan Chikhi, Antoine Limasset, Shaun Jackman, Jared T. Simpson, Paul Medvedev

J. Comput. Biol., 2015

2014

Informed and automated <i>k</i>-mer size selection for genome assembly.

Rayan Chikhi, Paul Medvedev

Bioinform., 2014

2013

Using state machines to model the Ion Torrent sequencing process and to improve read error rates.

David Golan, Paul Medvedev

Bioinform., 2013

2012

Complexity of independent set reconfigurability problems.

Marcin Kaminski, Paul Medvedev, Martin Milanic

Theor. Comput. Sci., 2012

2011

Genome Graphs.

Paul Medvedev

PhD thesis, 2011

Shortest paths between shortest paths.

Marcin Kaminski, Paul Medvedev, Martin Milanic

Theor. Comput. Sci., 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

Error correction of high-throughput sequencing datasets with non-uniform coverage.

Paul Medvedev, Eric Scott, Boyko Kakaradov, Pavel A. Pevzner

Bioinform., 2011

2010

Rearrangement Models and Single-Cut Operations.

Anne Bergeron, Paul Medvedev, Jens Stoye

J. Comput. Biol., 2010

Shortest Paths between Shortest Paths and Independent Sets.

Marcin Kaminski, Paul Medvedev, Martin Milanic

Proceedings of the Combinatorial Algorithms - 21st International Workshop, 2010

2009

Maximum Likelihood Genome Assembly.

Paul Medvedev, Michael Brudno

J. Comput. Biol., 2009

On the Plane-Width of Graphs.

Marcin Kaminski, Paul Medvedev, Martin Milanic

Electron. Notes Discret. Math., 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

Rearrangement Models and Single-Cut Operations.

Paul Medvedev, Jens Stoye

Proceedings of the Comparative Genomics, International Workshop, 2009

2008

The relative worst order ratio applied to seat reservation.

Joan Boyar, Paul Medvedev

ACM Trans. Algorithms, 2008

Ab Initio Whole Genome Shotgun Assembly with Mated Short Reads.

Paul Medvedev, Michael Brudno

Proceedings of the Research in Computational Molecular Biology, 2008

2007

Computability of Models for Sequence Assembly.

Paul Medvedev, Konstantinos Georgiou, Gene Myers, Michael Brudno

Proceedings of the Algorithms in Bioinformatics, 7th International Workshop, 2007

2001

A Self-Coordinating Approach to Distributed Fair Queueing in Ad Hoc Wireless Networks.

Haiyun Luo, Paul Medvedev, Jerry Cheng, Songwu Lu

Proceedings of the Proceedings IEEE INFOCOM 2001, 2001