Paul Medvedev - RankMe

81 papers A* 1A 1B 12C 9Misc 2Journal 50Unranked 5

Year	Rank	Type	Title / Venue / Authors
2025	C	`conf`	A k-mer-Based Estimator of the Substitution Rate Between Repetitive Sequences. WABI Haonan Wu, Antonio Blanca, Paul Medvedev
2025	A	`conf`	Efficiency of Learned Indexes on Genome Spectra. ESA Md. Hasin Abrar, Paul Medvedev, Giorgio Vinciguerra
2025	C	`conf`	Estimation of Substitution and Indel Rates via k-mer Statistics. WABI Mahmudur Rahman Hera, Paul Medvedev, David Koslicki, Antonio Blanca
2024	C	`conf`	Applying the Safe-And-Complete Framework to Practical Genome Assembly. WABI Sebastian S. Schmidt, Santeri Toivonen, Paul Medvedev, Alexandru I. Tomescu
2024	J	`jnl`	Compression algorithm for colored de Bruijn graphs. Algorithms Mol. Biol. Amatur Rahman, Yoann Dufresne, Paul Medvedev
2024	J	`jnl`	ESKEMAP: exact sketch-based read mapping. Algorithms Mol. Biol. Tizian Schulz, Paul Medvedev
2024	B	`conf`	Efficient Analysis of Annotation Colocalization Accounting for Genomic Contexts. RECOMB Askar Gafurov, Tomás Vinar, Paul Medvedev, Brona Brejová
2024	J	`jnl`	Fast Context-Aware Analysis of Genome Annotation Colocalization. J. Comput. Biol. Askar Gafurov, Tomás Vinar, Paul Medvedev, Brona Brejová
2024	C	`conf`	PLA-index: A k-mer Index Exploiting Rank Curve Linearity. WABI Md. Hasin Abrar, Paul Medvedev
2023	C	`conf`	Compression Algorithm for Colored de Bruijn Graphs. WABI Amatur Rahman, Yoann Dufresne, Paul Medvedev
2023	C	`conf`	Exact Sketch-Based Read Mapping. WABI Tizian Schulz, Paul Medvedev
2023	J	`jnl`	Theoretical Analysis of Edit Distance Algorithms. Commun. ACM Paul Medvedev
2023	J	`jnl`	Theoretical Analysis of Sequencing Bioinformatics Algorithms and Beyond. Commun. ACM Paul Medvedev
2022	J	`jnl`	Data Structures to Represent a Set of ACM Comput. Surv. Rayan Chikhi, Jan Holub, Paul Medvedev
2022	J	`jnl`	Markov chains improve the significance computation of overlapping genome annotations. Bioinform. Askar Gafurov, Brona Brejová, Paul Medvedev
2022	J	`jnl`	The K-mer File Format: a standardized and compact disk representation of sets of Bioinform. Yoann Dufresne, Téo Lemane, Pierre Marijon, Pierre Peterlongo, Amatur Rahman, Marek Kokot, Paul Medvedev, Sebastian Deorowicz, Rayan Chikhi
2022	J	`jnl`	The Statistics of k-mers from a Sequence Undergoing a Simple Mutation Process Without Spurious Matches. J. Comput. Biol. Antonio Blanca, Robert S. Harris, David Koslicki, Paul Medvedev
2022	J	`jnl`	The limitations of the theoretical analysis of applied algorithms. CoRR Paul Medvedev
2022	J	`jnl`	The minimizer Jaccard estimator is biased and inconsistent. Bioinform. Mahdi Belbasi, Antonio Blanca, Robert S. Harris, David Koslicki, Paul Medvedev
2022	J	`jnl`	Theoretical analysis of edit distance algorithms: an applied perspective. CoRR Paul Medvedev
2022	B	`conf`	Uncovering Hidden Assembly Artifacts: When Unitigs are not Safe and Bidirected Graphs are not Helpful (ABSTRACT). RECOMB Amatur Rahman, Paul Medvedev
2021	J	`jnl`	Disk compression of k-mer sets. Algorithms Mol. Biol. Amatur Rahman, Rayan Chikhi, Paul Medvedev
2021	—	`conf`	GYAN: Accelerating Bioinformatics Tools in Galaxy with GPU-Aware Computation Mapping. IPDPS Workshops 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
2021	J	`jnl`	What do Eulerian and Hamiltonian cycles have to do with genome assembly? PLoS Comput. Biol. Paul Medvedev, Mihai Pop
2020	J	`jnl`	Bipartite graphs of small readability. Theor. Comput. Sci. Rayan Chikhi, Vladan Jovicic, Stefan Kratsch, Paul Medvedev, Martin Milanic, Sofya Raskhodnikova, Nithin Varma
2020	J	`jnl`	De Novo Clustering of Long-Read Transcriptome Data Using a Greedy, Quality Value-Based Algorithm. J. Comput. Biol. Kristoffer Sahlin, Paul Medvedev
2020	C	`conf`	Disk Compression of k-mer Sets. WABI Amatur Rahman, Rayan Chikhi, Paul Medvedev
2020	J	`jnl`	Improved representation of sequence bloom trees. Bioinform. Robert S. Harris, Paul Medvedev
2020	B	`conf`	Representation of k-mer Sets Using Spectrum-Preserving String Sets. RECOMB Amatur Rahman, Paul Medvedev
2020	J	`jnl`	Ten Simple Rules for writing algorithmic bioinformatics conference papers. PLoS Comput. Biol. Paul Medvedev
2019	J	`jnl`	An Optimal ACM Trans. Algorithms Massimo Cairo, Paul Medvedev, Nidia Obscura Acosta, Romeo Rizzi, Alexandru I. Tomescu
2019	J	`jnl`	Data structures to represent sets of k-long DNA sequences. CoRR Rayan Chikhi, Jan Holub, Paul Medvedev
2019	B	`conf`	De Novo Clustering of Long-Read Transcriptome Data Using a Greedy, Quality-Value Based Algorithm. RECOMB Kristoffer Sahlin, Paul Medvedev
2019	J	`jnl`	Modeling biological problems in computer science: a case study in genome assembly. Briefings Bioinform. Paul Medvedev
2019	J	`jnl`	Toward fast and accurate SNP genotyping from whole genome sequencing data for bedside diagnostics. Bioinform. Chen Sun, Paul Medvedev
2018	J	`jnl`	AllSome Sequence Bloom Trees. J. Comput. Biol. Chen Sun, Robert S. Harris, Rayan Chikhi, Paul Medvedev
2018	Misc	`conf`	Bipartite Graphs of Small Readability. COCOON Rayan Chikhi, Vladan Jovicic, Stefan Kratsch, Paul Medvedev, Martin Milanic, Sofya Raskhodnikova, Nithin Varma
2018	J	`jnl`	Bipartite Graphs of Small Readability. CoRR Rayan Chikhi, Vladan Jovicic, Stefan Kratsch, Paul Medvedev, Martin Milanic, Sofya Raskhodnikova, Nithin Varma
2018	—	`conf`	Introduction to HiCOMB 2018. IPDPS Workshops Srinivas Aluru, David A. Bader, Paul Medvedev
2018	Misc	`conf`	Parallel Read Partitioning for Concurrent Assembly of Metagenomic Data. HiPC Vasudevan Rengasamy, Mahmut T. Kandemir, Paul Medvedev, Kamesh Madduri
2018	J	`jnl`	RecoverY: k-mer-based read classification for Y-chromosome-specific sequencing and assembly. Bioinform. Samarth Rangavittal, Robert S. Harris, Monika Cechova, Marta Tomaszkiewicz, Rayan Chikhi, Kateryna D. Makova, Paul Medvedev
2017	B	`conf`	AllSome Sequence Bloom Trees. RECOMB Chen Sun, Robert S. Harris, Rayan Chikhi, Paul Medvedev
2017	J	`jnl`	Modeling Biological Problems in Computer Science: A Case Study in Genome Assembly. CoRR Paul Medvedev
2017	B	`conf`	Optimal Omnitig Listing for Safe and Complete Contig Assembly. CPM Massimo Cairo, Paul Medvedev, Nidia Obscura Acosta, Romeo Rizzi, Alexandru I. Tomescu
2017	—	`conf`	Parallel and Memory-Efficient Preprocessing for Metagenome Assembly. IPDPS Workshops Vasudevan Rengasamy, Paul Medvedev, Kamesh Madduri
2017	J	`jnl`	Safe and Complete Contig Assembly Through Omnitigs. J. Comput. Biol. Alexandru I. Tomescu, Paul Medvedev
2017	J	`jnl`	TwoPaCo: an efficient algorithm to build the compacted de Bruijn graph from many complete genomes. Bioinform. Ilya Minkin, Son K. Pham, Paul Medvedev
2017	J	`jnl`	VarMatch: robust matching of small variant datasets using flexible scoring schemes. Bioinform. Chen Sun, Paul Medvedev
2016	J	`jnl`	Compacting de Bruijn graphs from sequencing data quickly and in low memory. Bioinform. Rayan Chikhi, Antoine Limasset, Paul Medvedev
2016	J	`jnl`	On the readability of overlap digraphs. Discret. Appl. Math. Rayan Chikhi, Paul Medvedev, Martin Milanic, Sofya Raskhodnikova
2016	B	`conf`	Safe and Complete Contig Assembly Via Omnitigs. RECOMB Alexandru I. Tomescu, Paul Medvedev
2016	J	`jnl`	Safe and complete contig assembly via omnitigs. CoRR Alexandru I. Tomescu, Paul Medvedev
2016	B	`conf`	The Second Decade of the International Conference on Research in Computational Molecular Biology (RECOMB). RECOMB Farhad Hormozdiari, Fereydoun Hormozdiari, Carl Kingsford, Paul Medvedev, Fabio Vandin
2016	J	`jnl`	TwoPaCo: An efficient algorithm to build the compacted de Bruijn graph from many complete genomes. CoRR Ilya Minkin, Son K. Pham, Paul Medvedev
2015	B	`conf`	On the Readability of Overlap Digraphs. CPM Rayan Chikhi, Paul Medvedev, Martin Milanic, Sofya Raskhodnikova
2015	J	`jnl`	On the Representation of De Bruijn Graphs. J. Comput. Biol. Rayan Chikhi, Antoine Limasset, Shaun Jackman, Jared T. Simpson, Paul Medvedev
2015	J	`jnl`	On the readability of overlap digraphs. CoRR Rayan Chikhi, Paul Medvedev, Martin Milanic, Sofya Raskhodnikova
2014	J	`jnl`	Informed and automated Bioinform. Rayan Chikhi, Paul Medvedev
2014	B	`conf`	On the Representation of de Bruijn Graphs. RECOMB Rayan Chikhi, Antoine Limasset, Shaun Jackman, Jared T. Simpson, Paul Medvedev
2014	J	`jnl`	On the representation of de Bruijn graphs. CoRR Rayan Chikhi, Antoine Limasset, Shaun Jackman, Jared T. Simpson, Paul Medvedev
2013	J	`jnl`	Using state machines to model the Ion Torrent sequencing process and to improve read error rates. Bioinform. David Golan, Paul Medvedev
2012	J	`jnl`	Complexity of independent set reconfigurability problems. Theor. Comput. Sci. Marcin Kaminski, Paul Medvedev, Martin Milanic
2011	J	`jnl`	Error correction of high-throughput sequencing datasets with non-uniform coverage. Bioinform. Paul Medvedev, Eric Scott, Boyko Kakaradov, Pavel A. Pevzner
2011	—	`—`	Genome Graphs. Paul Medvedev
2011	B	`conf`	Paired de Bruijn Graphs: A Novel Approach for Incorporating Mate Pair Information into Genome Assemblers. RECOMB Paul Medvedev, Son K. Pham, Mark Chaisson, Glenn Tesler, Pavel A. Pevzner
2011	J	`jnl`	Paired de Bruijn Graphs: A Novel Approach for Incorporating Mate Pair Information into Genome Assemblers. J. Comput. Biol. Paul Medvedev, Son K. Pham, Mark Chaisson, Glenn Tesler, Pavel A. Pevzner
2011	J	`jnl`	Shortest paths between shortest paths. Theor. Comput. Sci. Marcin Kaminski, Paul Medvedev, Martin Milanic
2011	J	`jnl`	The plane-width of graphs. J. Graph Theory Marcin Kaminski, Paul Medvedev, Martin Milanic
2010	J	`jnl`	Rearrangement Models and Single-Cut Operations. J. Comput. Biol. Anne Bergeron, Paul Medvedev, Jens Stoye
2010	C	`conf`	Shortest Paths between Shortest Paths and Independent Sets. IWOCA Marcin Kaminski, Paul Medvedev, Martin Milanic
2010	J	`jnl`	Shortest paths between shortest paths and independent sets CoRR Marcin Kaminski, Paul Medvedev, Martin Milanic
2009	J	`jnl`	A report on the 2009 SIG on short read sequencing and algorithms (Short-SIG). Bioinform. Michael Brudno, Paul Medvedev, Jens Stoye, Francisco M. de la Vega
2009	J	`jnl`	Maximum Likelihood Genome Assembly. J. Comput. Biol. Paul Medvedev, Michael Brudno
2009	J	`jnl`	On the Plane-Width of Graphs. Electron. Notes Discret. Math. Marcin Kaminski, Paul Medvedev, Martin Milanic
2009	—	`conf`	Rearrangement Models and Single-Cut Operations. RECOMB-CG Paul Medvedev, Jens Stoye
2008	B	`conf`	Ab Initio Whole Genome Shotgun Assembly with Mated Short Reads. RECOMB Paul Medvedev, Michael Brudno
2008	J	`jnl`	The Plane-Width of Graphs CoRR Marcin Kaminski, Paul Medvedev, Martin Milanic
2008	J	`jnl`	The relative worst order ratio applied to seat reservation. ACM Trans. Algorithms Joan Boyar, Paul Medvedev
2007	C	`conf`	Computability of Models for Sequence Assembly. WABI Paul Medvedev, Konstantinos Georgiou, Gene Myers, Michael Brudno
2004	—	`conf`	The Relative Worst Order Ratio Applied to Seat Reservation. SWAT Joan Boyar, Paul Medvedev
2001	A*	`conf`	A Self-Coordinating Approach to Distributed Fair Queueing in Ad Hoc Wireless Networks. INFOCOM Haiyun Luo, Paul Medvedev, Jerry Cheng, Songwu Lu