Paul Medvedev

Publication Activity (10 Years)

Years Active: 2001-2024
Publications (10 Years): 48

Top Topics

Preprocessing Steps

International Conference

Top Venues

J. Comput. Biol.

Publications

Md. Hasin Abrar, Paul Medvedev
PLA-index: A k-mer Index Exploiting Rank Curve Linearity. WABI (2024)
Askar Gafurov, Tomás Vinar, Paul Medvedev, Brona Brejová
Efficient Analysis of Annotation Colocalization Accounting for Genomic Contexts. RECOMB (2024)
Sebastian S. Schmidt, Santeri Toivonen, Paul Medvedev, Alexandru I. Tomescu
Applying the Safe-And-Complete Framework to Practical Genome Assembly. WABI (2024)
Tizian Schulz, Paul Medvedev
ESKEMAP: exact sketch-based read mapping. Algorithms Mol. Biol. 19 (1) (2024)
Amatur Rahman, Yoann Dufresne, Paul Medvedev
Compression algorithm for colored de Bruijn graphs. Algorithms Mol. Biol. 19 (1) (2024)
Paul Medvedev
Theoretical Analysis of Sequencing Bioinformatics Algorithms and Beyond. Commun. ACM 66 (7) (2023)
Tizian Schulz, Paul Medvedev
Exact Sketch-Based Read Mapping. WABI (2023)
Paul Medvedev
Theoretical Analysis of Edit Distance Algorithms. Commun. ACM 66 (12) (2023)
Amatur Rahman, Yoann Dufresne, Paul Medvedev
Compression Algorithm for Colored de Bruijn Graphs. WABI (2023)
Amatur Rahman, Paul Medvedev
Uncovering Hidden Assembly Artifacts: When Unitigs are not Safe and Bidirected Graphs are not Helpful (ABSTRACT). RECOMB (2022)
Paul Medvedev
Theoretical analysis of edit distance algorithms: an applied perspective. CoRR (2022)
Paul Medvedev
The limitations of the theoretical analysis of applied algorithms. CoRR (2022)
Yoann Dufresne, Teo Lemane, Pierre Marijon, Pierre Peterlongo, Amatur Rahman, Marek Kokot, Paul Medvedev, Sebastian Deorowicz, Rayan Chikhi
-mers. Bioinform. 38 (18) (2022)
Antonio Blanca, Robert S. Harris, David Koslicki, Paul Medvedev
The Statistics of k-mers from a Sequence Undergoing a Simple Mutation Process Without Spurious Matches. J. Comput. Biol. 29 (2) (2022)
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
GYAN: Accelerating Bioinformatics Tools in Galaxy with GPU-Aware Computation Mapping. IPDPS Workshops (2021)
Paul Medvedev, Mihai Pop
What do Eulerian and Hamiltonian cycles have to do with genome assembly? PLoS Comput. Biol. 17 (5) (2021)
Amatur Rahman, Rayan Chikhi, Paul Medvedev
Disk compression of k-mer sets. Algorithms Mol. Biol. 16 (1) (2021)
Rayan Chikhi, Jan Holub, Paul Medvedev
-long DNA Sequences. ACM Comput. Surv. 54 (1) (2021)
Kristoffer Sahlin, Paul Medvedev
De Novo Clustering of Long-Read Transcriptome Data Using a Greedy, Quality Value-Based Algorithm. J. Comput. Biol. 27 (4) (2020)
Paul Medvedev
Ten Simple Rules for writing algorithmic bioinformatics conference papers. PLoS Comput. Biol. 16 (4) (2020)
Amatur Rahman, Paul Medvedev
Representation of k-mer Sets Using Spectrum-Preserving String Sets. RECOMB (2020)
Robert S. Harris, Paul Medvedev
Improved representation of sequence bloom trees. Bioinform. 36 (3) (2020)
Amatur Rahman, Rayan Chikhi, Paul Medvedev
Disk Compression of k-mer Sets. WABI (2020)
Rayan Chikhi, Vladan Jovicic, Stefan Kratsch, Paul Medvedev, Martin Milanic, Sofya Raskhodnikova, Nithin Varma
Bipartite graphs of small readability. Theor. Comput. Sci. 806 (2020)
Paul Medvedev
Modeling biological problems in computer science: a case study in genome assembly. Briefings Bioinform. 20 (4) (2019)
Rayan Chikhi, Jan Holub, Paul Medvedev
Data structures to represent sets of k-long DNA sequences. CoRR (2019)
Massimo Cairo, Paul Medvedev, Nidia Obscura Acosta, Romeo Rizzi, Alexandru I. Tomescu
) Algorithm for Enumerating All Walks Common to All Closed Edge-covering Walks of a Graph. ACM Trans. Algorithms 15 (4) (2019)
Chen Sun, Paul Medvedev
Toward fast and accurate SNP genotyping from whole genome sequencing data for bedside diagnostics. Bioinform. 35 (3) (2019)
Kristoffer Sahlin, Paul Medvedev
De Novo Clustering of Long-Read Transcriptome Data Using a Greedy, Quality-Value Based Algorithm. RECOMB (2019)
Samarth Rangavittal, Robert S. Harris, Monika Cechova, Marta Tomaszkiewicz, Rayan Chikhi, Kateryna D. Makova, Paul Medvedev
RecoverY: k-mer-based read classification for Y-chromosome-specific sequencing and assembly. Bioinform. 34 (7) (2018)
Vasudevan Rengasamy, Mahmut T. Kandemir, Paul Medvedev, Kamesh Madduri
Parallel Read Partitioning for Concurrent Assembly of Metagenomic Data. HiPC (2018)
Srinivas Aluru, David A. Bader, Paul Medvedev
Introduction to HiCOMB 2018. IPDPS Workshops (2018)
Chen Sun, Robert S. Harris, Rayan Chikhi, Paul Medvedev
AllSome Sequence Bloom Trees. J. Comput. Biol. 25 (5) (2018)
Rayan Chikhi, Vladan Jovicic, Stefan Kratsch, Paul Medvedev, Martin Milanic, Sofya Raskhodnikova, Nithin Varma
Bipartite Graphs of Small Readability. COCOON (2018)
Rayan Chikhi, Vladan Jovicic, Stefan Kratsch, Paul Medvedev, Martin Milanic, Sofya Raskhodnikova, Nithin Varma
Bipartite Graphs of Small Readability. CoRR (2018)
Chen Sun, Robert S. Harris, Rayan Chikhi, Paul Medvedev
AllSome Sequence Bloom Trees. RECOMB (2017)
Ilya Minkin, Son K. Pham, Paul Medvedev
TwoPaCo: an efficient algorithm to build the compacted de Bruijn graph from many complete genomes. Bioinform. 33 (24) (2017)
Paul Medvedev
Modeling Biological Problems in Computer Science: A Case Study in Genome Assembly. CoRR (2017)
Chen Sun, Paul Medvedev
VarMatch: robust matching of small variant datasets using flexible scoring schemes. Bioinform. 33 (9) (2017)
Vasudevan Rengasamy, Paul Medvedev, Kamesh Madduri
Parallel and Memory-Efficient Preprocessing for Metagenome Assembly. IPDPS Workshops (2017)
Alexandru I. Tomescu, Paul Medvedev
Safe and Complete Contig Assembly Through Omnitigs. J. Comput. Biol. 24 (6) (2017)
Massimo Cairo, Paul Medvedev, Nidia Obscura Acosta, Romeo Rizzi, Alexandru I. Tomescu
Optimal Omnitig Listing for Safe and Complete Contig Assembly. CPM (2017)
Alexandru I. Tomescu, Paul Medvedev
Safe and complete contig assembly via omnitigs. CoRR (2016)
Farhad Hormozdiari, Fereydoun Hormozdiari, Carl Kingsford, Paul Medvedev, Fabio Vandin
The Second Decade of the International Conference on Research in Computational Molecular Biology (RECOMB). RECOMB (2016)
Rayan Chikhi, Antoine Limasset, Paul Medvedev
Compacting de Bruijn graphs from sequencing data quickly and in low memory. Bioinform. 32 (12) (2016)
Alexandru I. Tomescu, Paul Medvedev
Safe and Complete Contig Assembly Via Omnitigs. RECOMB (2016)
Rayan Chikhi, Paul Medvedev, Martin Milanic, Sofya Raskhodnikova
On the readability of overlap digraphs. Discret. Appl. Math. 205 (2016)
Ilya Minkin, Son K. Pham, Paul Medvedev
TwoPaCo: An efficient algorithm to build the compacted de Bruijn graph from many complete genomes. CoRR (2016)
Rayan Chikhi, Paul Medvedev, Martin Milanic, Sofya Raskhodnikova
On the readability of overlap digraphs. CoRR (2015)
Rayan Chikhi, Paul Medvedev, Martin Milanic, Sofya Raskhodnikova
On the Readability of Overlap Digraphs. CPM (2015)
Rayan Chikhi, Antoine Limasset, Shaun Jackman, Jared T. Simpson, Paul Medvedev
On the Representation of De Bruijn Graphs. J. Comput. Biol. 22 (5) (2015)
Rayan Chikhi, Paul Medvedev
-mer size selection for genome assembly. Bioinform. 30 (1) (2014)
Rayan Chikhi, Antoine Limasset, Shaun Jackman, Jared T. Simpson, Paul Medvedev
On the representation of de Bruijn graphs. CoRR (2014)
Rayan Chikhi, Antoine Limasset, Shaun Jackman, Jared T. Simpson, Paul Medvedev
On the Representation of de Bruijn Graphs. RECOMB (2014)
David Golan, Paul Medvedev
Using state machines to model the Ion Torrent sequencing process and to improve read error rates. Bioinform. 29 (13) (2013)
Marcin Kaminski, Paul Medvedev, Martin Milanic
Complexity of independent set reconfigurability problems. Theor. Comput. Sci. 439 (2012)
Marcin Kaminski, Paul Medvedev, Martin Milanic
Shortest paths between shortest paths. Theor. Comput. Sci. 412 (39) (2011)
Paul Medvedev, Son K. Pham, Mark Chaisson, Glenn Tesler, Pavel A. Pevzner
Paired de Bruijn Graphs: A Novel Approach for Incorporating Mate Pair Information into Genome Assemblers. J. Comput. Biol. 18 (11) (2011)
Paul Medvedev, Eric Scott, Boyko Kakaradov, Pavel A. Pevzner
Error correction of high-throughput sequencing datasets with non-uniform coverage. Bioinform. 27 (13) (2011)
Marcin Kaminski, Paul Medvedev, Martin Milanic
The plane-width of graphs. J. Graph Theory 68 (3) (2011)
Paul Medvedev, Son K. Pham, Mark Chaisson, Glenn Tesler, Pavel A. Pevzner
Paired de Bruijn Graphs: A Novel Approach for Incorporating Mate Pair Information into Genome Assemblers. RECOMB (2011)
Marcin Kaminski, Paul Medvedev, Martin Milanic
Shortest Paths between Shortest Paths and Independent Sets. IWOCA (2010)
Anne Bergeron, Paul Medvedev, Jens Stoye
Rearrangement Models and Single-Cut Operations. J. Comput. Biol. 17 (9) (2010)
Marcin Kaminski, Paul Medvedev, Martin Milanic
Shortest paths between shortest paths and independent sets CoRR (2010)
Paul Medvedev, Michael Brudno
Maximum Likelihood Genome Assembly. J. Comput. Biol. 16 (8) (2009)
Paul Medvedev, Jens Stoye
Rearrangement Models and Single-Cut Operations. RECOMB-CG (2009)
Michael Brudno, Paul Medvedev, Jens Stoye, Francisco M. de la Vega
A report on the 2009 SIG on short read sequencing and algorithms (Short-SIG). Bioinform. 25 (21) (2009)
Marcin Kaminski, Paul Medvedev, Martin Milanic
On the Plane-Width of Graphs. Electron. Notes Discret. Math. 34 (2009)
Paul Medvedev, Michael Brudno
Ab Initio Whole Genome Shotgun Assembly with Mated Short Reads. RECOMB (2008)
Joan Boyar, Paul Medvedev
The relative worst order ratio applied to seat reservation. ACM Trans. Algorithms 4 (4) (2008)
Marcin Kaminski, Paul Medvedev, Martin Milanic
The Plane-Width of Graphs CoRR (2008)
Paul Medvedev, Konstantinos Georgiou, Gene Myers, Michael Brudno
Computability of Models for Sequence Assembly. WABI (2007)
Joan Boyar, Paul Medvedev
The Relative Worst Order Ratio Applied to Seat Reservation. SWAT (2004)
Haiyun Luo, Paul Medvedev, Jerry Cheng, Songwu Lu
A Self-Coordinating Approach to Distributed Fair Queueing in Ad Hoc Wireless Networks. INFOCOM (2001)