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2020 – today
- 2024
[j39]Tizian Schulz
, Paul Medvedev:
ESKEMAP: exact sketch-based read mapping. Algorithms Mol. Biol. 19(1): 19 (2024)- [j38]Amatur Rahman, Yoann Dufresne, Paul Medvedev:
Compression algorithm for colored de Bruijn graphs. Algorithms Mol. Biol. 19(1): 20 (2024) - [j37]Askar Gafurov, Tomás Vinar, Paul Medvedev, Brona Brejová:
Fast Context-Aware Analysis of Genome Annotation Colocalization. J. Comput. Biol. 31(10): 946-964 (2024) - [c27]Askar Gafurov, Tomás Vinar, Paul Medvedev, Brona Brejová:
Efficient Analysis of Annotation Colocalization Accounting for Genomic Contexts. RECOMB 2024: 38-53 - [c26]Sebastian S. Schmidt, Santeri Toivonen, Paul Medvedev, Alexandru I. Tomescu:
Applying the Safe-And-Complete Framework to Practical Genome Assembly. WABI 2024: 8:1-8:16 - [c25]Md. Hasin Abrar, Paul Medvedev:
PLA-index: A k-mer Index Exploiting Rank Curve Linearity. WABI 2024: 13:1-13:18 - [d1]Md. Hasin Abrar, Paul Medvedev:
pla-index. DROPS Artifacts, 2024
- 2023
- [j36]Paul Medvedev:
Theoretical Analysis of Sequencing Bioinformatics Algorithms and Beyond. Commun. ACM 66(7): 118-125 (2023) - [j35]Paul Medvedev:
Theoretical Analysis of Edit Distance Algorithms. Commun. ACM 66(12): 64-71 (2023) - [c24]Tizian Schulz, Paul Medvedev:
Exact Sketch-Based Read Mapping. WABI 2023: 14:1-14:19 - [c23]Amatur Rahman, Yoann Dufresne, Paul Medvedev:
Compression Algorithm for Colored de Bruijn Graphs. WABI 2023: 17:1-17:14 - 2022
- [j34]Yoann Dufresne, Téo Lemane, Pierre Marijon, Pierre Peterlongo, Amatur Rahman, Marek Kokot, Paul Medvedev, Sebastian Deorowicz, Rayan Chikhi:
The K-mer File Format: a standardized and compact disk representation of sets of k-mers. Bioinform. 38(18): 4423-4425 (2022) - [j33]Mahdi Belbasi, Antonio Blanca, Robert S. Harris, David Koslicki, Paul Medvedev:
The minimizer Jaccard estimator is biased and inconsistent. Bioinform. 38(Supplement_1): i169-i176 (2022) - [j32]Askar Gafurov, Brona Brejová, Paul Medvedev:
Markov chains improve the significance computation of overlapping genome annotations. Bioinform. 38(Supplement_1): i203-i211 (2022) - [j31]Rayan Chikhi, Jan Holub, Paul Medvedev:
Data Structures to Represent a Set of k-long DNA Sequences. ACM Comput. Surv. 54(1): 17:1-17:22 (2022) - [j30]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): 155-168 (2022) - [c22]Amatur Rahman, Paul Medvedev:
Uncovering Hidden Assembly Artifacts: When Unitigs are not Safe and Bidirected Graphs are not Helpful (ABSTRACT). RECOMB 2022: 377-379 - [i11]Paul Medvedev:
Theoretical analysis of edit distance algorithms: an applied perspective. CoRR abs/2204.09535 (2022) - [i10]Paul Medvedev:
The limitations of the theoretical analysis of applied algorithms. CoRR abs/2205.01785 (2022) - 2021
- [j29]Amatur Rahman, Rayan Chikhi, Paul Medvedev:
Disk compression of k-mer sets. Algorithms Mol. Biol. 16(1): 10 (2021) - [j28]Paul Medvedev, Mihai Pop:
What do Eulerian and Hamiltonian cycles have to do with genome assembly? PLoS Comput. Biol. 17(5) (2021) - [c21]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: 194-203 - 2020
- [j27]Robert S. Harris, Paul Medvedev:
Improved representation of sequence bloom trees. Bioinform. 36(3): 721-727 (2020) - [j26]Kristoffer Sahlin, Paul Medvedev:
De Novo Clustering of Long-Read Transcriptome Data Using a Greedy, Quality Value-Based Algorithm. J. Comput. Biol. 27(4): 472-484 (2020) - [j25]Paul Medvedev:
Ten Simple Rules for writing algorithmic bioinformatics conference papers. PLoS Comput. Biol. 16(4) (2020) - [j24]Rayan Chikhi, Vladan Jovicic, Stefan Kratsch, Paul Medvedev, Martin Milanic, Sofya Raskhodnikova, Nithin Varma:
Bipartite graphs of small readability. Theor. Comput. Sci. 806: 402-415 (2020) - [c20]Amatur Rahman, Paul Medvedev:
Representation of k-mer Sets Using Spectrum-Preserving String Sets. RECOMB 2020: 152-168 - [c19]Amatur Rahman, Rayan Chikhi, Paul Medvedev:
Disk Compression of k-mer Sets. WABI 2020: 16:1-16:18
2010 – 2019
- 2019
- [j23]Paul Medvedev:
Modeling biological problems in computer science: a case study in genome assembly. Briefings Bioinform. 20(4): 1376-1383 (2019) - [j22]Chen Sun, Paul Medvedev:
Toward fast and accurate SNP genotyping from whole genome sequencing data for bedside diagnostics. Bioinform. 35(3): 415-420 (2019) - [j21]Massimo Cairo, Paul Medvedev, Nidia Obscura Acosta, Romeo Rizzi, Alexandru I. Tomescu:
An Optimal O(nm) Algorithm for Enumerating All Walks Common to All Closed Edge-covering Walks of a Graph. ACM Trans. Algorithms 15(4): 48:1-48:17 (2019) - [c18]Kristoffer Sahlin, Paul Medvedev:
De Novo Clustering of Long-Read Transcriptome Data Using a Greedy, Quality-Value Based Algorithm. RECOMB 2019: 227-242 - [i9]Rayan Chikhi, Jan Holub, Paul Medvedev:
Data structures to represent sets of k-long DNA sequences. CoRR abs/1903.12312 (2019) - 2018
- [j20]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): 1125-1131 (2018) - [j19]Chen Sun, Robert S. Harris, Rayan Chikhi, Paul Medvedev:
AllSome Sequence Bloom Trees. J. Comput. Biol. 25(5): 467-479 (2018) - [c17]Rayan Chikhi, Vladan Jovicic, Stefan Kratsch, Paul Medvedev, Martin Milanic, Sofya Raskhodnikova, Nithin Varma:
Bipartite Graphs of Small Readability. COCOON 2018: 467-479 - [c16]Vasudevan Rengasamy, Mahmut T. Kandemir, Paul Medvedev, Kamesh Madduri:
Parallel Read Partitioning for Concurrent Assembly of Metagenomic Data. HiPC 2018: 324-333 - [c15]Srinivas Aluru, David A. Bader, Paul Medvedev:
Introduction to HiCOMB 2018. IPDPS Workshops 2018: 226 - [i8]Rayan Chikhi, Vladan Jovicic, Stefan Kratsch, Paul Medvedev, Martin Milanic, Sofya Raskhodnikova, Nithin Varma:
Bipartite Graphs of Small Readability. CoRR abs/1805.04765 (2018) - 2017
- [j18]Chen Sun, Paul Medvedev:
VarMatch: robust matching of small variant datasets using flexible scoring schemes. Bioinform. 33(9): 1301-1308 (2017) - [j17]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): 4024-4032 (2017) - [j16]Alexandru I. Tomescu, Paul Medvedev:
Safe and Complete Contig Assembly Through Omnitigs. J. Comput. Biol. 24(6): 590-602 (2017) - [c14]Massimo Cairo, Paul Medvedev, Nidia Obscura Acosta, Romeo Rizzi, Alexandru I. Tomescu:
Optimal Omnitig Listing for Safe and Complete Contig Assembly. CPM 2017: 29:1-29:12 - [c13]Vasudevan Rengasamy, Paul Medvedev, Kamesh Madduri:
Parallel and Memory-Efficient Preprocessing for Metagenome Assembly. IPDPS Workshops 2017: 283-292 - [c12]Chen Sun, Robert S. Harris, Rayan Chikhi, Paul Medvedev:
AllSome Sequence Bloom Trees. RECOMB 2017: 272-286 - [i7]Paul Medvedev:
Modeling Biological Problems in Computer Science: A Case Study in Genome Assembly. CoRR abs/1706.05429 (2017) - 2016
- [j15]Rayan Chikhi, Antoine Limasset, Paul Medvedev:
Compacting de Bruijn graphs from sequencing data quickly and in low memory. Bioinform. 32(12): 201-208 (2016) - [j14]Rayan Chikhi, Paul Medvedev, Martin Milanic, Sofya Raskhodnikova:
On the readability of overlap digraphs. Discret. Appl. Math. 205: 35-44 (2016) - [c11]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: 3-16 - [c10]Alexandru I. Tomescu, Paul Medvedev:
Safe and Complete Contig Assembly Via Omnitigs. RECOMB 2016: 152-163 - [i6]Alexandru I. Tomescu, Paul Medvedev:
Safe and complete contig assembly via omnitigs. CoRR abs/1601.02932 (2016) - [i5]Ilya Minkin, Son K. Pham, Paul Medvedev:
TwoPaCo: An efficient algorithm to build the compacted de Bruijn graph from many complete genomes. CoRR abs/1602.05856 (2016) - 2015
- [j13]Rayan Chikhi, Antoine Limasset, Shaun Jackman, Jared T. Simpson, Paul Medvedev:
On the Representation of De Bruijn Graphs. J. Comput. Biol. 22(5): 336-352 (2015) - [c9]Rayan Chikhi, Paul Medvedev, Martin Milanic, Sofya Raskhodnikova:
On the Readability of Overlap Digraphs. CPM 2015: 124-137 - [i4]Rayan Chikhi, Paul Medvedev, Martin Milanic, Sofya Raskhodnikova:
On the readability of overlap digraphs. CoRR abs/1504.04616 (2015) - 2014
- [j12]Rayan Chikhi, Paul Medvedev:
Informed and automated k-mer size selection for genome assembly. Bioinform. 30(1): 31-37 (2014) - [c8]Rayan Chikhi, Antoine Limasset, Shaun Jackman, Jared T. Simpson, Paul Medvedev:
On the Representation of de Bruijn Graphs. RECOMB 2014: 35-55 - [i3]Rayan Chikhi, Antoine Limasset, Shaun Jackman, Jared T. Simpson, Paul Medvedev:
On the representation of de Bruijn graphs. CoRR abs/1401.5383 (2014) - 2013
- [j11]David Golan, Paul Medvedev:
Using state machines to model the Ion Torrent sequencing process and to improve read error rates. Bioinform. 29(13): 344-351 (2013) - 2012
- [j10]Marcin Kaminski, Paul Medvedev, Martin Milanic:
Complexity of independent set reconfigurability problems. Theor. Comput. Sci. 439: 9-15 (2012) - 2011
- [b1]Paul Medvedev:
Genome Graphs. University of Toronto, Canada, 2011 - [j9]Paul Medvedev, Eric Scott, Boyko Kakaradov, Pavel A. Pevzner:
Error correction of high-throughput sequencing datasets with non-uniform coverage. Bioinform. 27(13): 137-141 (2011) - [j8]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): 1625-1634 (2011) - [j7]Marcin Kaminski, Paul Medvedev, Martin Milanic:
The plane-width of graphs. J. Graph Theory 68(3): 229-245 (2011) - [j6]Marcin Kaminski, Paul Medvedev, Martin Milanic:
Shortest paths between shortest paths. Theor. Comput. Sci. 412(39): 5205-5210 (2011) - [c7]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: 238-251 - 2010
- [j5]Anne Bergeron, Paul Medvedev, Jens Stoye:
Rearrangement Models and Single-Cut Operations. J. Comput. Biol. 17(9): 1213-1225 (2010) - [c6]Marcin Kaminski, Paul Medvedev, Martin Milanic:
Shortest Paths between Shortest Paths and Independent Sets. IWOCA 2010: 56-67 - [i2]Marcin Kaminski, Paul Medvedev, Martin Milanic:
Shortest paths between shortest paths and independent sets. CoRR abs/1008.4563 (2010)
2000 – 2009
- 2009
- [j4]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): 2863-2864 (2009) - [j3]Marcin Kaminski, Paul Medvedev, Martin Milanic:
On the Plane-Width of Graphs. Electron. Notes Discret. Math. 34: 633-637 (2009) - [j2]Paul Medvedev, Michael Brudno:
Maximum Likelihood Genome Assembly. J. Comput. Biol. 16(8): 1101-1116 (2009) - [c5]Paul Medvedev, Jens Stoye:
Rearrangement Models and Single-Cut Operations. RECOMB-CG 2009: 84-97 - 2008
- [j1]Joan Boyar, Paul Medvedev:
The relative worst order ratio applied to seat reservation. ACM Trans. Algorithms 4(4): 48:1-48:22 (2008) - [c4]Paul Medvedev, Michael Brudno:
Ab Initio Whole Genome Shotgun Assembly with Mated Short Reads. RECOMB 2008: 50-64 - [i1]Marcin Kaminski, Paul Medvedev, Martin Milanic:
The Plane-Width of Graphs. CoRR abs/0812.4346 (2008) - 2007
- [c3]Paul Medvedev, Konstantinos Georgiou, Gene Myers, Michael Brudno:
Computability of Models for Sequence Assembly. WABI 2007: 289-301 - 2004
- [c2]Joan Boyar, Paul Medvedev:
The Relative Worst Order Ratio Applied to Seat Reservation. SWAT 2004: 90-101 - 2001
- [c1]Haiyun Luo, Paul Medvedev, Jerry Cheng, Songwu Lu:
A Self-Coordinating Approach to Distributed Fair Queueing in Ad Hoc Wireless Networks. INFOCOM 2001: 1370-1379
Coauthor Index
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last updated on 2025-01-21 00:08 CET by the dblp team
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