Paul Medvedev

Haiyun Luo, Paul Medvedev, Songwu Lu, 2001, Proceedings IEEE INFOCOM 2001. Conference on Computer Communications. Twentieth Annual Joint Conference of the IEEE Computer and Communications Society (Cat. No.01CH37213).

AllSome Sequence Bloom Trees

Chen Sun, Paul Medvedev, Rayan Chikhi, 2018, J. Comput. Biol..

AllSome Sequence Bloom Trees

Chen Sun, Paul Medvedev, Rayan Chikhi, 2016, bioRxiv.

An Optimal O(nm) Algorithm for Enumerating All Walks Common to All Closed Edge-covering Walks of a Graph

Alexandru I. Tomescu, Paul Medvedev, Romeo Rizzi, 2019, ACM Trans. Algorithms.

Data structures based on k-mers for querying large collections of sequencing data sets

Christina Boucher, Simon J. Puglisi, Paul Medvedev, 2019, bioRxiv.

Assembly of Big Genomic Data

Paul Medvedev, 2017 .

On the Readability of Overlap Digraphs pdf

Martin Milanič, Sofya Raskhodnikova, Paul Medvedev, 2015, CPM.

Computational Pan-Genomics: Status, Promises and Challenges

Jan O. Korbel, Ying Zhang, Eleazar Eskin, 2016 .

Rearrangement Models and Single-Cut Operations

Jens Stoye, Anne Bergeron, Paul Medvedev, 2010, J. Comput. Biol..

Representation of k-mer sets using spectrum-preserving string sets

Amatur Rahman, Paul Medvedev, P. Medvedev, 2020, bioRxiv.

Scalable Pairwise Whole-Genome Homology Mapping of Long Genomes with BubbZ

Paul Medvedev, Ilia Minkin, Ilia Minkin, 2020, iScience.

Computational methods for discovering structural variation with next-generation sequencing

Paul Medvedev, Michael Brudno, Monica Stanciu, 2009, Nature Methods.

Shortest paths between shortest paths

Martin Milanic, Marcin Kaminski, Paul Medvedev, 2011, Theor. Comput. Sci..

On the readability of overlap digraphs

Martin Milanič, Sofya Raskhodnikova, Paul Medvedev, 2015, Discret. Appl. Math..

The Relative Worst Order Ratio Applied to Seat Reservation

Joan Boyar, Paul Medvedev, 2004, SWAT.

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

Paul Medvedev, Pavel A. Pevzner, Boyko Kakaradov, 2011, Bioinform..

The plane‐width of graphs

Martin Milanič, Paul Medvedev, Marcin Kamiński, 2008, J. Graph Theory.

Ten Simple Rules for writing algorithmic bioinformatics conference papers

Paul Medvedev, 2020, PLoS Comput. Biol..

Disk compression of k-mer sets

Amatur Rahman, Paul Medvedev, Rayan Chikhi, 2021, WABI.

A report on the 2009 SIG on short read sequencing and algorithms (Short-SIG)

Jens Stoye, Paul Medvedev, Michael Brudno, 2009, Bioinform..

RecoverY: K-mer based read classification for Y-chromosome specific sequencing and assembly

Kateryna D. Makova, Paul Medvedev, Rayan Chikhi, 2017, bioRxiv.

Paired de Bruijn Graphs: A Novel Approach for Incorporating Mate Pair Information into Genome Assemblers

Paul Medvedev, Pavel A. Pevzner, Glenn Tesler, 2011, J. Comput. Biol..

Shortest Paths between Shortest Paths and Independent Sets

Martin Milanic, Marcin Kaminski, Paul Medvedev, 2010, IWOCA.

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

Paul Medvedev, Kristoffer Sahlin, 2019, RECOMB.

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

Paul Medvedev, Carl Kingsford, Fabio Vandin, 2016, RECOMB.

Bipartite Graphs of Small Readability pdf

Stefan Kratsch, Sofya Raskhodnikova, Martin Milanic, 2018, COCOON.

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

Paul Medvedev, David Golan, David Golan, 2013, Bioinform..

The plane-width of graphs pdf

Martin Milanič, Paul Medvedev, Marcin Kamiński, 2011, J. Graph Theory.

Improving the Power of Structural Variation Detection by Augmenting the Reference

Paul Medvedev, Anthony T. Papenfuss, Santhosh Girirajan, 2015 .

Safe and Complete Contig Assembly Via Omnitigs

Alexandru I. Tomescu, Paul Medvedev, P. Medvedev, 2016, RECOMB.

Genome Graphs

Paul Medvedev, P. Medvedev, 2010 .

Computational pan-genomics: status, promises and challenges

Ying Zhang, Eleazar Eskin, Knut Reinert, 2016, bioRxiv.

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

Amatur Rahman, Paul Medvedev, 2020, RECOMB.

Scalable multiple whole-genome alignment and locally collinear block construction with SibeliaZ

Paul Medvedev, Ilia Minkin, 2020, Nature communications.

Accelerating SNP genotyping from whole genome sequencing data for bedside diagnostics

Paul Medvedev, Chen Sun, 2017 .

Modeling Biological Problems in Computer Science: A Case Study in Genome Assembly

Paul Medvedev, P. Medvedev, 2017, Briefings Bioinform..

Improved representation of sequence bloom trees

Paul Medvedev, Robert S. Harris, 2020, Bioinform..

Maximum Likelihood Genome Assembly

Paul Medvedev, Michael Brudno, M. Brudno, 2009, J. Comput. Biol..

AllSome Sequence Bloom Trees

Paul Medvedev, Rayan Chikhi, Chen Sun, 2016 .

Bipartite graphs of small readability

Stefan Kratsch, Sofya Raskhodnikova, Martin Milanic, 2020, Theor. Comput. Sci..

Computability of Models for Sequence Assembly

Eugene W. Myers, Konstantinos Georgiou, Paul Medvedev, 2007, WABI.

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

Chen Sun, Paul Medvedev, Chen Sun, 2016, bioRxiv.

Rearrangement Models and Single-Cut Operations

Jens Stoye, Paul Medvedev, J. Stoye, 2009, RECOMB-CG.

GYAN: Accelerating Bioinformatics Tools in Galaxy with GPU-Aware Computation Mapping

Mahmut T. Kandemir, Chita R. Das, Anton Nekrutenko, 2021, 2021 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW).

Disk compression of k-mer sets

Amatur Rahman, Paul Medvedev, Rayan Chikhi, 2021, Algorithms Mol. Biol..

A time- and cost-effective strategy to sequence mammalian Y Chromosomes: an application to the de novo assembly of gorilla Y

Paul Medvedev, Rebeca Campos Sánchez, Rayan Chikhi, 2016, Genome research.

Deciphering highly similar multigene family transcripts from Iso-Seq data with IsoCon

Kateryna D. Makova, Paul Medvedev, Kristoffer Sahlin, 2018, Nature Communications.

RecoverY: K-mer based read classification for Y-chromosome specific sequencing and assembly

Kateryna D. Makova, Paul Medvedev, Rayan Chikhi, 2017, bioRxiv.

Error correction enables use of Oxford Nanopore technology for reference-free transcriptome analysis

Paul Medvedev, Kristoffer Sahlin, Botond Sipos, 2020, Nature Communications.

Reprever: resolving low-copy duplicated sequences using template driven assembly

Vineet Bafna, Paul Medvedev, T. Paton, 2013, Nucleic acids research.

Towards complete and error-free genome assemblies of all vertebrate species

Sergey Koren, Adam M. Phillippy, Eugene W. Myers, 2020, Nature.

Correcting palindromes in long reads after whole-genome amplification

Paul Medvedev, Dick de Ridder, Kateryna D Makova, 2018, BMC Genomics.

DiscoverY: a classifier for identifying Y chromosome sequences in male assemblies

Kateryna D. Makova, Paul Medvedev, Kristoffer Sahlin, 2019, BMC Genomics.

Accurate typing of short tandem repeats from genome-wide sequencing data and its applications

Paul Medvedev, Guruprasad Ananda, Kateryna D Makova, 2015, Genome research.

Improving the Power of Structural Variation Detection by Augmenting the Reference

Jan Schröder, Paul Medvedev, Anthony T. Papenfuss, 2015, bioRxiv.