Research Papers

2017

  • P. Avdeyev, S. Jiang, and M. A. Alekseyev. “Implicit Transpositions in DCJ Scenarios”. Front. Genet. 8 (2017), 212. doi:10.3389/fgene.2017.00212
  • S. Aganezov and M. A. Alekseyev. “CAMSA: a Tool for Comparative Analysis and Merging of Scaffold Assemblies”. BMC Bioinformatics 18:Suppl 15 (2017), 496. doi:10.1186/s12859-017-1919-y bioRxiv:10.1101/069153
  • N. Alexeev and M. A. Alekseyev. “Estimation of the True Evolutionary Distance under the Fragile Breakage Model”. BMC Genomics 18:Suppl 4 (2017), 356. doi:10.1186/s12864-017-3733-3 arXiv:1510.08002
  • S. Aganezov and M. A. Alekseyev. “Orientation of Ordered Scaffolds”. Proceedings of the 15th Annual RECOMB Satellite Workshop on Comparative Genomics (RECOMB-CG 2017). Lecture Notes in Computer Science 10562 (2017), 179–196. doi:10.1007/978-3-319-67979-2_10
  • P. Avdeyev, N. Alexeev, Y. Rong, and M. A. Alekseyev. “A Unified ILP Framework for Genome Median, Halving, and Aliquoting Problems under DCJ”. Proceedings of the 15th Annual RECOMB Satellite Workshop on Comparative Genomics (RECOMB-CG 2017). Lecture Notes in Computer Science 10562 (2017), 156–178. doi:10.1007/978-3-319-67979-2_9
  • N. Alexeev, A. Pologova, and M. A. Alekseyev. “Generalized Hultman Numbers and Cycle Structures of Breakpoint Graphs”. Journal of Computational Biology 24:2 (2017), 93–105. doi:10.1089/cmb.2016.0190 arXiv:1503.05285

2016

  • N. Alexeev, P. Avdeyev, and M. A. Alekseyev. “Comparative Genomics Meets Topology: a Novel View on Genome Median and Halving Problems”. Proceedings of the 14th Annual RECOMB Satellite Workshop on Comparative Genomics (RECOMB-CG 2016), Montreal, Canada. BMC Bioinformatics 17:Suppl 14 (2016), 3. doi:10.1186/s12859-016-1263-7
  • N. Alexeev and M. A. Alekseyev. “Combinatorial Scoring of Phylogenetic Networks”. Proceedings the 22nd International Computing and Combinatorics Conference (COCOON 2016), Ho Chi Minh, Vietnam. Lecture Notes in Computer Science 9797 (2016), 560–572. doi:10.1007/978-3-319-42634-1_45 arXiv:1602.02841
  • S. Aganezov and M. A. Alekseyev. “Multi-genome Scaffold Co-Assembly Based on the Analysis of Gene Orders and Genomic Repeats”. Proceedings of the 12th International Symposium on Bioinformatics Research and Applications (ISBRA 2016), Lecture Notes in Computer Science 9683 (2016), 237–249. doi:10.1007/978-3-319-38782-6_20
  • P. Avdeyev, S. Jiang, S. Aganezov, F. Hu, and M. A. Alekseyev. “Reconstruction of ancestral genomes in presence of gene gain and loss”. Journal of Computational Biology 23:3 (2016), pp. 1–15. doi:10.1089/cmb.2015.0160   bioRxiv:10.1101/040196
  • Y.-C. Liu, S.-D. Hsu, C.-H. Chou, W.-Y. Huang, Y.-H. Chen, C.-Y. Liu, G.-J. Lyu, S.-Z. Huang, S. Aganezov, M. A. Alekseyev, C.-D. Hsiao, and H.-D. Huang. “Transcriptome sequencing based annotation and homologous evidence based scaffolding of Anguilla japonica draft genome”. BMC Genomics 17:Suppl 1 (2016), 13. doi:10.1186/s12864-015-2306-6

2015

  • N. Alexeev, A. Pologova, and M. A. Alekseyev. “Generalized Hultman Numbers and the Distribution of Multi-break Distances”, Lecture Notes in Computer Science 9199 (2015), pp. 3-12. doi:10.1007/978-3-319-21233-3_1 arXiv:1503.05285
  • S. Jiang and M. A. Alekseyev. “Implicit Transpositions in Shortest DCJ Scenarios”, Lecture Notes in Computer Science 9199 (2015), pp. 13-24. doi:10.1007/978-3-319-21233-3_2
  • D. Rozanov, A. Cheltsov, E. Sergienko, S. Vasile, V. Golubkov, A. E. Aleshin, T. Levin, E. Traer, B. Hann, J. Freimuth, N. Alexeev, M. A. Alekseyev, S. P. Budko, H. P. Bächinger, and P. Spellman. “TRAIL-Based High Throughput Screening Reveals a Link between TRAIL-Mediated Apoptosis and Glutathione Reductase, a Key Component of Oxidative Stress Response”, PLoS ONE 10:6 (2015), e0129566. doi:10.1371/journal.pone.0129566
  • S. Aganezov, N. Sitdykova, AGC Consortium, and M. A. Alekseyev. “Scaffold assembly based on genome rearrangement analysis”, Computational Biology and Chemistry 57 (2015), pp. 46-53. doi:10.1016/j.compbiolchem.2015.02.005
  • N. Alexeev, R. Aidagulov, and M. A. Alekseyev. “A Computational Method for the Rate Estimation of Evolutionary Transpositions”, Lecture Notes in Computer Science9043 (2015), pp. 471-480. doi:10.1007/978-3-319-16483-0_46   arXiv:1501.07546
  • D. E. Neafsey, R. M. Waterhouse, M. R. Abai, S. S. Aganezov, M. A. Alekseyev et al. “Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes”, Science 347:6217 (2015), 1258522. doi:10.1126/science.1258522

< 2015

  • S. Jiang and M. A. Alekseyev. “Linearization of Median Genomes under DCJ”. Lecture Notes in Computer Science 8701 (2014), pp. 97-106. doi:10.1007/978-3-662-44753-6_8
  • S. Aganezov and M. A. Alekseyev. “On pairwise distances and median score of three genomes under DCJ”. BMC Bioinformatics 13:Suppl 19 (2012), pp. S1. doi:10.1186/1471-2105-13-S19-S1 arXiv:1208.0133
  • S. Jiang and M. A. Alekseyev. “Weighted genomic distance can hardly impose a bound on the proportion of transpositions”. Lecture Notes in Computer Science 6577 (2011), pp. 124-133. doi:10.1007/978-3-642-20036-6_13 arXiv:1012.2422

 

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