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Max Alekseyev, Ph.D. - Publications

Affiliations: 
Computer Science and Engineering University of California, San Diego, La Jolla, CA 
Area:
Bioinformatics, proteomics, mass spectrometry
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35 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Zamyatin A, Avdeyev P, Liang J, Sharma A, Chen C, Lukyanchikova V, Alexeev N, Tu Z, Alekseyev MA, Sharakhov IV. Chromosome-level genome assemblies of the malaria vectors Anopheles coluzzii and Anopheles arabiensis. Gigascience. 10. PMID 33718948 DOI: 10.1093/gigascience/giab017  0.319
2020 Avdeyev P, Alexeev N, Rong Y, Alekseyev MA. A Unified ILP Framework for Core Ancestral Genome Reconstruction Problems. Bioinformatics (Oxford, England). PMID 32058559 DOI: 10.1093/bioinformatics/btaa100  0.504
2020 Waterhouse RM, Aganezov S, Anselmetti Y, Lee J, Ruzzante L, Reijnders MJMF, Feron R, Bérard S, George P, Hahn MW, Howell PI, Kamali M, Koren S, Lawson D, Maslen G, ... ... Alekseyev MA, et al. Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies. Bmc Biology. 18: 1. PMID 31898513 DOI: 10.1186/S12915-019-0728-3  0.457
2019 Avdeyev P, Jiang S, Alekseyev MA. Linearization of Median Genomes Under the Double-Cut-and-Join-Indel Model. Evolutionary Bioinformatics Online. 15: 1176934318820534. PMID 31217687 DOI: 10.1177/1176934318820534  0.433
2017 Avdeyev P, Jiang S, Alekseyev MA. Implicit Transpositions in DCJ Scenarios. Frontiers in Genetics. 8: 212. PMID 29312438 DOI: 10.3389/fgene.2017.00212  0.505
2017 Aganezov SS, Alekseyev MA. CAMSA: a tool for comparative analysis and merging of scaffold assemblies. Bmc Bioinformatics. 18: 496. PMID 29244014 DOI: 10.1186/s12859-017-1919-y  0.49
2017 Alexeev N, Pologova A, Alekseyev MA. Generalized Hultman Numbers and Cycle Structures of Breakpoint Graphs. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. PMID 28045556 DOI: 10.1089/cmb.2016.0190  0.48
2016 Alexeev N, Avdeyev P, Alekseyev MA. Comparative genomics meets topology: a novel view on genome median and halving problems. Bmc Bioinformatics. 17: 418. PMID 28185564 DOI: 10.1186/s12859-016-1263-7  0.458
2016 Avdeyev P, Jiang S, Aganezov S, Hu F, Alekseyev MA. Reconstruction of Ancestral Genomes in Presence of Gene Gain and Loss. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. PMID 26885568 DOI: 10.1089/cmb.2015.0160  0.516
2016 Liu YC, Hsu SD, Chou CH, Huang WY, Chen YH, Liu CY, Lyu GJ, Huang SZ, Aganezov S, Alekseyev MA, Hsiao CD, Huang HD. Transcriptome sequencing based annotation and homologous evidence based scaffolding of Anguilla japonica draft genome. Bmc Genomics. 17: 13. PMID 26818233 DOI: 10.1186/s12864-015-2306-6  0.422
2016 Liu YC, Hsu SD, Chou CH, Huang WY, Chen YH, Liu CY, Lyu GJ, Huang SZ, Aganezov S, Alekseyev MA, Hsiao CD, Huang HD. Transcriptome sequencing based annotation and homologous evidence based scaffolding of Anguilla japonica draft genome Bmc Genomics. 17. DOI: 10.1186/s12864-015-2306-6  0.422
2015 Aganezov S, Sitdykova N, Alekseyev MA. Scaffold assembly based on genome rearrangement analysis. Computational Biology and Chemistry. 57: 46-53. PMID 25819137 DOI: 10.1016/j.compbiolchem.2015.02.005  0.467
2015 Neafsey DE, Waterhouse RM, Abai MR, Aganezov SS, Alekseyev MA, Allen JE, Amon J, Arcà B, Arensburger P, Artemov G, Assour LA, Basseri H, Berlin A, Birren BW, Blandin SA, et al. Mosquito genomics. Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes. Science (New York, N.Y.). 347: 1258522. PMID 25554792 DOI: 10.1126/Science.1258522  0.405
2015 Aganezov S, Sitdykova N, Alekseyev MA, Neafsey DE, Christophides GK, Collins FH, Emrich SJ, Fontaine MC, Gelbart W, Hahn MW, Howell PI, Kafatos FC, Lawson D, Muskavitch MAT, Waterhouse R, et al. Scaffold assembly based on genome rearrangement analysis Computational Biology and Chemistry. 57: 46-53. DOI: 10.1016/j.compbiolchem.2015.02.005  0.467
2014 Jiang S, Alekseyev MA. Linearization of median genomes under DCJ Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 8701: 97-106. DOI: 10.1007/978-3-662-44753-6-8  0.434
2013 Nurk S, Bankevich A, Antipov D, Gurevich AA, Korobeynikov A, Lapidus A, Prjibelski AD, Pyshkin A, Sirotkin A, Sirotkin Y, Stepanauskas R, Clingenpeel SR, Woyke T, McLean JS, Lasken R, ... ... Alekseyev MA, et al. Assembling single-cell genomes and mini-metagenomes from chimeric MDA products. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 20: 714-37. PMID 24093227 DOI: 10.1089/Cmb.2013.0084  0.586
2013 Pham SK, Antipov D, Sirotkin A, Tesler G, Pevzner PA, Alekseyev MA. Pathset graphs: a novel approach for comprehensive utilization of paired reads in genome assembly. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 20: 359-71. PMID 22803627 DOI: 10.1089/Cmb.2012.0098  0.592
2013 Nurk S, Bankevich A, Antipov D, Gurevich A, Korobeynikov A, Lapidus A, Prjibelsky A, Pyshkin A, Sirotkin A, Sirotkin Y, Stepanauskas R, McLean J, Lasken R, Clingenpeel SR, Woyke T, ... ... Alekseyev MA, et al. Assembling genomes and mini-metagenomes from highly chimeric reads Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 7821: 158-170. DOI: 10.1007/978-3-642-37195-0_13  0.625
2012 Aganezov S, Alekseyev MA. On pairwise distances and median score of three genomes under DCJ. Bmc Bioinformatics. 13: S1. PMID 23282410 DOI: 10.1186/1471-2105-13-S19-S1  0.483
2012 Luo H, Arndt W, Zhang Y, Shi G, Alekseyev MA, Tang J, Hughes AL, Friedman R. Phylogenetic analysis of genome rearrangements among five mammalian orders. Molecular Phylogenetics and Evolution. 65: 871-82. PMID 22929217 DOI: 10.1016/J.Ympev.2012.08.008  0.433
2012 Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 19: 455-77. PMID 22506599 DOI: 10.1089/Cmb.2012.0021  0.594
2011 Jiang S, Alekseyev MA. Weighted genomic distance can hardly impose a bound on the proportion of transpositions Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 6577: 124-133. DOI: 10.1007/978-3-642-20036-6_13  0.382
2010 Alekseyev MA, Pevzner PA. Comparative genomics reveals birth and death of fragile regions in mammalian evolution. Genome Biology. 11: R117. PMID 21118492 DOI: 10.1186/Gb-2010-11-11-R117  0.569
2010 Alekseyev MA, Peng Q, Pevzner PA, Tesler G. Decoding the Genomic Architecture of Mammalian and Plant Genomes: Synteny Blocks and Large-scale Duplications Communications in Information and Systems. 10: 1-22. DOI: 10.4310/Cis.2010.V10.N1.A1  0.648
2010 Alekseyev MA, Pevzner PA. Limited lifespan of fragile regions in mammalian evolution Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 6398: 198-215. DOI: 10.1007/978-3-642-16181-0_17  0.418
2009 Alekseyev MA, Pevzner PA. Breakpoint graphs and ancestral genome reconstructions. Genome Research. 19: 943-57. PMID 19218533 DOI: 10.1101/Gr.082784.108  0.65
2009 Peng Q, Alekseyev MA, Tesler G, Pevzner PA. Decoding synteny blocks and large-scale duplications in mammalian and plant genomes Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 5724: 220-232. DOI: 10.1007/978-3-642-04241-6_19  0.611
2008 Alekseyev MA. Multi-break rearrangements and breakpoint re-uses: from circular to linear genomes. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 15: 1117-31. PMID 18788907 DOI: 10.1089/cmb.2008.0080  0.487
2008 Alekseyev MA, Pevzner PA. Multi-break rearrangements and chromosomal evolution Theoretical Computer Science. 395: 193-202. DOI: 10.1016/J.Tcs.2008.01.013  0.581
2007 Alekseyev MA, Pevzner PA. Are there rearrangement hotspots in the human genome? Plos Computational Biology. 3: e209. PMID 17997591 DOI: 10.1371/Journal.Pcbi.0030209  0.61
2007 Alekseyev MA, Pevzner PA. Colored de Bruijn graphs and the genome halving problem. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 4: 98-107. PMID 17277417 DOI: 10.1109/Tcbb.2007.1002  0.618
2007 Alekseyev MA, Pevzner PA. Whole genome duplications and contracted breakpoint graphs Siam Journal On Computing. 36: 1748-1763. DOI: 10.1137/05064727X  0.655
2007 Alekseyev MA. Multi-break rearrangements: From circular to linear genomes Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 4751: 1-15.  0.448
2004 Alekseyev MA, Pevzner PA. Genome halving problem revisited Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 3328: 1-15.  0.6
2002 Heber S, Alekseyev M, Sze SH, Tang H, Pevzner PA. Splicing graphs and EST assembly problem. Bioinformatics (Oxford, England). 18: S181-8. PMID 12169546  0.614
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