Max Alekseyev, Ph.D. - Publications

Affiliations: 
Computer Science and Engineering University of California, San Diego, La Jolla, CA 
Area:
Bioinformatics, proteomics, mass spectrometry

33 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
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  0.96
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  0.96
2015 Rozanov D, Cheltsov A, Sergienko E, Vasile S, Golubkov V, Aleshin AE, Levin T, Traer E, Hann B, Freimuth J, Alexeev N, Alekseyev MA, Budko SP, Bächinger HP, Spellman P. TRAIL-Based High Throughput Screening Reveals a Link between TRAIL-Mediated Apoptosis and Glutathione Reductase, a Key Component of Oxidative Stress Response. Plos One. 10: e0129566. PMID 26075913 DOI: 10.1371/Journal.Pone.0129566  0.96
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  0.96
2015 Alekseyev MA, Basova MG, Zolotykh NYU. On the minimal teaching sets of two-dimensional threshold functions Siam Journal On Discrete Mathematics. 29: 157-165. DOI: 10.1137/140978090  0.96
2015 Alexeev N, Alekseyev MA. Estimation of the true evolutionary distance under the fragile breakage model 2015 Ieee 5th International Conference On Computational Advances in Bio and Medical Sciences, Iccabs 2015. DOI: 10.1109/ICCABS.2015.7344706  0.96
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  0.96
2015 Jiang S, Alekseyev MA. Implicit transpositions in shortest DCJ scenarios Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 9199: 13-24. DOI: 10.1007/978-3-319-21233-3_2  0.96
2015 Alexeev N, Pologova A, Alekseyev MA. Generalized hultman numbers and the distribution of multi-break distances Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 9199: 3-12. DOI: 10.1007/978-3-319-21233-3_1  0.96
2015 Alexeev N, Aidagulov R, Alekseyev MA. A computational method for the rate estimation of evolutionary transpositions Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 9043: 471-480.  0.96
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  0.96
2014 Alekseyev MA, Tengely S. On integral points on biquadratic curves and near-multiples of squares in lucas sequences Journal of Integer Sequences. 17.  0.96
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  0.96
2013 Nikolenko SI, Korobeynikov AI, Alekseyev MA. BayesHammer: Bayesian clustering for error correction in single-cell sequencing. Bmc Genomics. 14: S7. PMID 23368723 DOI: 10.1186/1471-2164-14-S1-S7  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
2010 Alekseyev MA. On the number of two-dimensional threshold functions Siam Journal On Discrete Mathematics. 24: 1617-1631. DOI: 10.1137/090750184  0.96
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  0.96
2009 Alekseyev MA, Pevzner PA. Breakpoint graphs and ancestral genome reconstructions. Genome Research. 19: 943-57. PMID 19218533 DOI: 10.1101/Gr.082784.108  0.96
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  0.96
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  0.96
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  0.96
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  0.96
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  0.96
2007 Alekseyev MA, Pevzner PA. Whole genome duplications and contracted breakpoint graphs Siam Journal On Computing. 36: 1748-1763. DOI: 10.1137/05064727X  0.96
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.  0.96
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.  0.96
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  0.96
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