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Items: 22

1.

Combinatorial Scoring of Phylogenetic Trees and Networks Based on Homoplasy-Free Characters.

Alexeev N, Alekseyev MA.

J Comput Biol. 2018 Nov;25(11):1203-1219. doi: 10.1089/cmb.2018.0082. Epub 2018 Aug 22.

PMID:
30133318
2.

Implicit Transpositions in DCJ Scenarios.

Avdeyev P, Jiang S, Alekseyev MA.

Front Genet. 2017 Dec 12;8:212. doi: 10.3389/fgene.2017.00212. eCollection 2017.

3.

CAMSA: a tool for comparative analysis and merging of scaffold assemblies.

Aganezov SS, Alekseyev MA.

BMC Bioinformatics. 2017 Dec 6;18(Suppl 15):496. doi: 10.1186/s12859-017-1919-y.

4.

Estimation of the true evolutionary distance under the fragile breakage model.

Alexeev N, Alekseyev MA.

BMC Genomics. 2017 May 24;18(Suppl 4):356. doi: 10.1186/s12864-017-3733-3.

5.

Comparative genomics meets topology: a novel view on genome median and halving problems.

Alexeev N, Avdeyev P, Alekseyev MA.

BMC Bioinformatics. 2016 Nov 11;17(Suppl 14):418. doi: 10.1186/s12859-016-1263-7.

6.

Generalized Hultman Numbers and Cycle Structures of Breakpoint Graphs.

Alexeev N, Pologova A, Alekseyev MA.

J Comput Biol. 2017 Feb;24(2):93-105. doi: 10.1089/cmb.2016.0190. Epub 2017 Jan 3.

PMID:
28045556
7.

Reconstruction of Ancestral Genomes in Presence of Gene Gain and Loss.

Avdeyev P, Jiang S, Aganezov S, Hu F, Alekseyev MA.

J Comput Biol. 2016 Mar;23(3):150-64. doi: 10.1089/cmb.2015.0160. Epub 2016 Feb 17.

PMID:
26885568
8.

Transcriptome sequencing based annotation and homologous evidence based scaffolding of Anguilla japonica draft genome.

Liu YC, Hsu SD, Chou CH, Huang WY, Chen YH, Liu CY, Lyu GJ, Huang SZ, Aganezov S, Alekseyev MA, Hsiao CD, Huang HD.

BMC Genomics. 2016 Jan 11;17 Suppl 1:13. doi: 10.1186/s12864-015-2306-6.

9.

TRAIL-Based High Throughput Screening Reveals a Link between TRAIL-Mediated Apoptosis and Glutathione Reductase, a Key Component of Oxidative Stress Response.

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.

PLoS One. 2015 Jun 15;10(6):e0129566. doi: 10.1371/journal.pone.0129566. eCollection 2015.

10.

Scaffold assembly based on genome rearrangement analysis.

Aganezov S, Sitdykova N; AGC Consortium, Alekseyev MA.

Comput Biol Chem. 2015 Aug;57:46-53. doi: 10.1016/j.compbiolchem.2015.02.005. Epub 2015 Mar 3.

PMID:
25819137
11.

Mosquito genomics. Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes.

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, Brockman AI, Burkot TR, Burt A, Chan CS, Chauve C, Chiu JC, Christensen M, Costantini C, Davidson VL, Deligianni E, Dottorini T, Dritsou V, Gabriel SB, Guelbeogo WM, Hall AB, Han MV, Hlaing T, Hughes DS, Jenkins AM, Jiang X, Jungreis I, Kakani EG, Kamali M, Kemppainen P, Kennedy RC, Kirmitzoglou IK, Koekemoer LL, Laban N, Langridge N, Lawniczak MK, Lirakis M, Lobo NF, Lowy E, MacCallum RM, Mao C, Maslen G, Mbogo C, McCarthy J, Michel K, Mitchell SN, Moore W, Murphy KA, Naumenko AN, Nolan T, Novoa EM, O'Loughlin S, Oringanje C, Oshaghi MA, Pakpour N, Papathanos PA, Peery AN, Povelones M, Prakash A, Price DP, Rajaraman A, Reimer LJ, Rinker DC, Rokas A, Russell TL, Sagnon N, Sharakhova MV, Shea T, Simão FA, Simard F, Slotman MA, Somboon P, Stegniy V, Struchiner CJ, Thomas GW, Tojo M, Topalis P, Tubio JM, Unger MF, Vontas J, Walton C, Wilding CS, Willis JH, Wu YC, Yan G, Zdobnov EM, Zhou X, Catteruccia F, Christophides GK, Collins FH, Cornman RS, Crisanti A, Donnelly MJ, Emrich SJ, Fontaine MC, Gelbart W, Hahn MW, Hansen IA, Howell PI, Kafatos FC, Kellis M, Lawson D, Louis C, Luckhart S, Muskavitch MA, Ribeiro JM, Riehle MA, Sharakhov IV, Tu Z, Zwiebel LJ, Besansky NJ.

Science. 2015 Jan 2;347(6217):1258522. doi: 10.1126/science.1258522. Epub 2014 Nov 27.

12.

Assembling single-cell genomes and mini-metagenomes from chimeric MDA products.

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, Tesler G, Alekseyev MA, Pevzner PA.

J Comput Biol. 2013 Oct;20(10):714-37. doi: 10.1089/cmb.2013.0084.

13.

BayesHammer: Bayesian clustering for error correction in single-cell sequencing.

Nikolenko SI, Korobeynikov AI, Alekseyev MA.

BMC Genomics. 2013;14 Suppl 1:S7. doi: 10.1186/1471-2164-14-S1-S7. Epub 2013 Jan 21.

14.

On pairwise distances and median score of three genomes under DCJ.

Aganezov S Jr, Alekseyev MA.

BMC Bioinformatics. 2012;13 Suppl 19:S1. doi: 10.1186/1471-2105-13-S19-S1. Epub 2012 Dec 19.

15.

Phylogenetic analysis of genome rearrangements among five mammalian orders.

Luo H, Arndt W, Zhang Y, Shi G, Alekseyev MA, Tang J, Hughes AL, Friedman R.

Mol Phylogenet Evol. 2012 Dec;65(3):871-82. doi: 10.1016/j.ympev.2012.08.008. Epub 2012 Aug 21.

16.

Pathset graphs: a novel approach for comprehensive utilization of paired reads in genome assembly.

Pham SK, Antipov D, Sirotkin A, Tesler G, Pevzner PA, Alekseyev MA.

J Comput Biol. 2013 Apr;20(4):359-71. doi: 10.1089/cmb.2012.0098. Epub 2012 Jul 17.

17.

SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.

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, Pevzner PA.

J Comput Biol. 2012 May;19(5):455-77. doi: 10.1089/cmb.2012.0021. Epub 2012 Apr 16.

18.

Comparative genomics reveals birth and death of fragile regions in mammalian evolution.

Alekseyev MA, Pevzner PA.

Genome Biol. 2010;11(11):R117. doi: 10.1186/gb-2010-11-11-r117. Epub 2010 Nov 30.

19.

Breakpoint graphs and ancestral genome reconstructions.

Alekseyev MA, Pevzner PA.

Genome Res. 2009 May;19(5):943-57. doi: 10.1101/gr.082784.108. Epub 2009 Feb 13.

20.

Multi-break rearrangements and breakpoint re-uses: from circular to linear genomes.

Alekseyev MA.

J Comput Biol. 2008 Oct;15(8):1117-31. doi: 10.1089/cmb.2008.0080.

PMID:
18788907
21.

Are there rearrangement hotspots in the human genome?

Alekseyev MA, Pevzner PA.

PLoS Comput Biol. 2007 Nov;3(11):e209. Epub 2007 Sep 14.

22.

Colored de Bruijn graphs and the genome halving problem.

Alekseyev MA, Pevzner PA.

IEEE/ACM Trans Comput Biol Bioinform. 2007 Jan-Mar;4(1):98-107.

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