Dr. Max Alekseyev


Contact Info
Research
Teaching
Publications
Resume

Publications


2017

S. Aganezov and M. A. Alekseyev. "CAMSA: a Tool for Comparative Analysis and Merging of Scaffold Assemblies", 2017. (submitted) bioRxiv:10.1101/069153

M. A. Alekseyev, J. M. Grau, and A. Oller-Marcen. "On the congruence 1n + 2n + ... + nn ≡ p (mod n)", 2017. (submitted) arXiv:1602.02407

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 Bioinformatics, 2017. (in press)

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 Bioinformatics, 2017. (in press)

M. A. Alekseyev. "On Enumeration of Dyck--Schröder Paths". Journal of Combinatorial Mathematics and Combinatorial Computing, 2017. (in press) arXiv:1601.06158

R. R. Aidagulov and M. A. Alekseyev. "On p-adic approximation of sums of binomial coefficients". Journal of Mathematical Sciences, 2017. (in press) arXiv:1602.02632

M. A. Alekseyev and G. P. Michon. "Making Walks Count: From Silent Circles to Hamiltonian Cycles". In: The Mathematics of Various Entertaining Subjects (MOVES), Vol. 2, Princeton University Press, 2017. (in press) arXiv:1602.01396

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

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

R. R. Aidagulov and M. A. Alekseyev. "On p-adic approximation of sums of binomial coefficients" (in Russian). Fundamentalnaya i Prikladnaya Matematika 21:1 (2016), 37–48.

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), BMC Bioinformatics 17:Suppl 14 (2016), 3. doi:10.1186/s12859-016-1263-7

M. A. Alekseyev. "Problem 4101". Crux Mathematicorum 42:1 (2016), 28.

M. A. Alekseyev. "Problem 11922". American Mathematical Monthly 123:7 (2016), 722. doi:10.4169/amer.math.monthly.123.7.722

M. A. Alekseyev. "Weighted de Bruijn Graphs for the Menage Problem and Its Generalizations". Proceedings of the 27th International Workshop on Combinatorial Algorithms (IWOCA 2016). Lecture Notes in Computer Science 9843 (2016), 151–162. doi:10.1007/978-3-319-44543-4_12 arXiv:1510.07926

N. Alexeev and M. A. Alekseyev. "Combinatorial Scoring of Phylogenetic Networks". Proceedings of the 22nd International Computing and Combinatorics Conference (COCOON 2016). 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

M. A. Alekseyev. "Computing the Inverses, their Power Sums, and Extrema for Euler's Totient and Other Multiplicative Functions". Journal of Integer Sequences 19:5 (2016), Article 16.5.2. arXiv:1401.6054

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), 150–164. 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". Proceedings of the 14th Asia Pacific Bioinformatics Conference (APBC 2016). BMC Genomics 17:Suppl 1 (2016), 13. doi:10.1186/s12864-015-2306-6

M. A. Alekseyev and T. Berger. "Solving the Tower of Hanoi with Random Moves". In: J. Beineke, J. Rosenhouse (eds.) The Mathematics of Various Entertaining Subjects: Research in Recreational Math, Princeton University Press, 2016, pp. 65–79. ISBN 978-0-691-16403-8 arXiv:1304.3780

2015

N. Alexeev and M. A. Alekseyev. "Estimation of the True Evolutionary Distance under the Fragile Breakage Model". Proceedings of the 5th IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS 2015), 1-1. doi:10.1109/iccabs.2015.7344706

N. Alexeev, A. Pologova, and M. A. Alekseyev. "Generalized Hultman Numbers and the Distribution of Multi-break Distances". Proceedings of the 2nd International Conference on Algorithms for Computational Biology (AlCoB 2015), Lecture Notes in Computer Science 9199 (2015), 3-12. doi:10.1007/978-3-319-21233-3_1

S. Jiang and M. A. Alekseyev. "Implicit Transpositions in Shortest DCJ Scenarios". Proceedings of the 2nd International Conference on Algorithms for Computational Biology (AlCoB 2015), Lecture Notes in Computer Science 9199 (2015), 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". Proceedings of the 13th Asia-Pacific Bioinformatics Conference (APBC 2015). Computational Biology and Chemistry 57 (2015), 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". Proceedings of the 3rd International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO 2015), Lecture Notes in Computer Science 9043 (2015), 471-480. doi:10.1007/978-3-319-16483-0_46 arXiv:1501.07546

M. A. Alekseyev, M. Basova, and N. Yu. Zolotykh. "On the minimal teaching sets of two-dimensional threshold functions". SIAM Journal on Discrete Mathematics 29:1 (2015), 157-165. doi:10.1137/140978090

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

2014

S. Jiang and M. A. Alekseyev. "Linearization of Median Genomes under DCJ". Proceedings of the 14th Workshop on Algorithms in Bioinformatics (WABI 2014), Lecture Notes in Computer Science 8701 (2014), 97-106. doi:10.1007/978-3-662-44753-6_8

M. A. Alekseyev and Sz. Tengely. "On Integral Points on Biquadratic Curves and Near-Multiples of Squares in Lucas Sequences". Journal of Integer Sequences 17:6 (2014), Article 14.6.6. arXiv:1306.0883

2013

S. Nurk, A. Bankevich, D. Antipov, A. A. Gurevich, A. Korobeynikov, A. Lapidus, A. D. Prjibelsky, A. Pyshkin, A. Sirotkin, Y. Sirotkin, R. Stepanauskas, J. S. McLean, R. Lasken, S. R. Clingenpeel, T. Woyke, G. Tesler, M. A. Alekseyev, and P. A. Pevzner. "Assembling Single-Cell Genomes and Mini-Metagenomes From Chimeric MDA Products". Journal of Computational Biology 20:10 (2013), 714-737. doi:10.1089/cmb.2013.0084

S. K. Pham, D. Antipov, A. Sirotkin, G. Tesler, P. A. Pevzner, and M. A. Alekseyev. "Pathset Graphs: A Novel Approach for Comprehensive Utilization of Paired Reads in Genome Assembly". Journal of Computational Biology 20:4 (2013), 359-371. doi:10.1089/cmb.2012.0098

S. Nurk, A. Bankevich, D. Antipov, A. Gurevich, A. Korobeynikov, A. Lapidus, A. Prjibelsky, A. Pyshkin, A. Sirotkin, Y. Sirotkin, R. Stepanauskas, J. McLean, R. Lasken, S. R. Clingenpeel, T. Woyke, G. Tesler, M. A. Alekseyev, and P. A. Pevzner. "Assembling Genomes and Mini-metagenomes from Highly Chimeric Reads". Proceedings of the 17th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2013), Lecture Notes in Computer Science 7821 (2013), 158–170. doi:10.1007/978-3-642-37195-0_13

S. I. Nikolenko, A. Korobeynikov, and M. A. Alekseyev. "BayesHammer: Bayesian clustering for error correction in single-cell sequencing". Proceedings of the 11th Asia Pacific Bioinformatics Conference (APBC 2013), BMC Genomics 14:Suppl 1 (2013), S7. doi:10.1186/1471-2164-14-S1-S7 arXiv:1211.2756

M. A. Alekseyev. "Problem 3883". Crux Mathematicorum 39:9 (2013), 413. ("Solution 3883", CRUX 40:9 (2015), 398.)

2012

M. A. Alekseyev. "Problem 3766". Crux Mathematicorum 38:7 (2012), 285. ("Solution 3766". CRUX 39:7 (2013), 333-334.)

D. G. Fon-Der-Flaass and M. A. Alekseyev. "Problem 11666". American Mathematical Monthly, 119:8 (2012), 699-700. doi:10.4169/amer.math.monthly.119.08.699 ("Solution 11666". AMM 121:10 (2014), 947-948.)

H. Luo, W. Arndt, Y. Zhang, G. Shi, M. A. Alekseyev, J. Tang, A. L. Hughes, and R. Friedman. "Phylogenetic Analysis of Genome Rearrangements among Five Mammalian Orders". Molecular Phylogenetics and Evolution 65:3 (2012), 871–882. doi:10.1016/j.ympev.2012.08.008

S. Aganezov and M. A. Alekseyev. "On pairwise distances and median score of three genomes under DCJ". Proceedings of the 10th Annual RECOMB Satellite Workshop on Comparative Genomics (RECOMB-CG 2012), BMC Bioinformatics 13:Suppl 19 (2012), S1. doi:10.1186/1471-2105-13-S19-S1 arXiv:1208.0133

A. Bankevich, S. Nurk, D. Antipov, A. Gurevich, M. Dvorkin, A. Kulikov, V. Lesin, S. Nikolenko, S. Pham, A. Prjibelski, A. Pyshkin, A. Sirotkin, N. Vyahhi, G. Tesler, M. Alekseyev, and P. Pevzner. "SPAdes: a New Genome Assembly Algorithm and its Applications to Single-Cell Sequencing". Journal of Computational Biology 19:5 (2012), 455-477. doi:10.1089/cmb.2012.0021

S. K. Pham, D. Antipov, A. Sirotkin, G. Tesler, P. A. Pevzner, and M. A. Alekseyev. "Pathset Graphs: A Novel Approach for Comprehensive Utilization of Paired Reads in Genome Assembly". Proceedings of the 16th Annual Conference on Research in Computational Molecular Biology (RECOMB 2012), Lecture Notes in Computer Science 7262 (2012), 200-212. doi:10.1007/978-3-642-29627-7_21

2011

M. A. Alekseyev and F. Ruskey. "Problem 11544". American Mathematical Monthly, 118:1 (2011), 84. doi:10.4169/amer.math.monthly.118.01.084

S. Jiang and M. A. Alekseyev. "Weighted genomic distance can hardly impose a bound on the proportion of transpositions". Proceedings of the 15th Annual Conference on Research in Computational Molecular Biology (RECOMB 2011), Lecture Notes in Computer Science 6577 (2011), 124-133. doi:10.1007/978-3-642-20036-6_13 arXiv:1012.2422

M. A. Alekseyev. "On the intersections of Fibonacci, Pell, and Lucas numbers". INTEGERS 11:3 (2011), 239-259. doi:10.1515/INTEG.2011.021 arXiv:1002.1679

M. A. Alekseyev and P. A. Pevzner. "Limited Lifespan of Fragile Regions in Mammalian Evolution". Lecture Notes in Computer Science 6398 (2011), 198-215. doi:10.1007/978-3-642-16181-0_17

2010

M. A. Alekseyev. "On the number of two-dimensional threshold functions". SIAM Journal on Discrete Mathematics 24:4 (2010), 1617-1631. doi:10.1137/090750184 arXiv:0602511

M. A. Alekseyev and P. A. Pevzner. "Comparative Genomics Reveals Birth and Death of Fragile Regions in Mammalian Evolution". Genome Biology 11:11 (2010), R117. doi:10.1186/gb-2010-11-11-r117

Q. Peng, M. Alekseyev, G. Tesler, and P. Pevzner. "Decoding the Genomic Architecture of Mammalian and Plant Genomes: Synteny Blocks and Large-Scale Duplications". Communications in Information and Systems 10:1 (2010), 1-22. doi:10.4310/CIS.2010.v10.n1.a1

2009

Q. Peng, M. Alekseyev, G. Tesler, and P. Pevzner. "Decoding Synteny Blocks and Large-Scale Duplications in Mammalian and Plant Genomes". Lecture Notes in Computer Science 5724 (2009), 220-232. doi:10.1007/978-3-642-04241-6_19

M. A. Alekseyev. "Gene Duplications and Genome Rearrangements". VDM Verlag Dr. Müller, 2009. ISBN: 978-3-639-13615-9

M. A. Alekseyev and P. A. Pevzner. "Breakpoint Graphs and Ancestral Genome Reconstructions". Genome Research 19:5 (2009), 943-957. doi:10.1101/gr.082784.108

2008

M. A. Alekseyev. "Multi-Break Rearrangements and Breakpoint Re-uses: from Circular to Linear Genomes". Journal of Computational Biology 15:8 (2008), 1117-1131. doi:10.1089/cmb.2008.0080

M. A. Alekseyev and P. A. Pevzner. "Multi-Break Rearrangements and Chromosomal Evolution". Theoretical Computer Science 395:2-3 (2008), 193-202. doi:10.1016/j.tcs.2008.01.013

2007

M. A. Alekseyev and P. A. Pevzner. "Are There Rearrangement Hotspots in the Human Genome?". PLoS Computational Biology 3:11 (2007), e209. doi:10.1371/journal.pcbi.0030209

M. A. Alekseyev. "Multi-Break Rearrangements: from Circular to Linear Genomes". Lecture Notes in Computer Science 4751 (2007), 1-15. doi:10.1007/978-3-540-74960-8_1

M. A. Alekseyev and P. A. Pevzner. "Whole Genome Duplications and Contracted Breakpoint Graphs". SIAM Journal on Computing 36:6 (2007), 1748-1763. doi:10.1137/05064727X

M. A. Alekseyev and P. A. Pevzner. "Colored de Bruijn Graphs and the Genome Halving Problem". IEEE/ACM Transactions on Computational Biology and Bioinformatics 4 (2007), 98-107. doi:10.1109/TCBB.2007.1002

M. A. Alekseyev and P. A. Pevzner. "Whole Genome Duplications, Multi-Break Rearrangements, and Genome Halving Theorem". Proceedings of the 18th Annual ACM-SIAM Symposium on Discrete Algorithms (SODA 2007), 665-679.

M. Alekseyev and E. Deutsch. "Problem 11281". American Mathematical Monthly 114:3 (2007), 259. (Solution 11281, AMM 116:5 (2009), 465)

< 2007

M. A. Alekseyev and P. A. Pevzner. "Genome Halving Problem Revisited". Lecture Notes in Computer Science 3328 (2005), 1-15. doi:10.1007/978-3-540-30538-5_1

M. Alekseyev, D. Barsky, A. Vorobey, G. Merzon, Yu. Prokopchuk, D. Fon-der-Flaass. "On a problem in sequential decoding" (in Russian). Proceedings of the XV International Workshop "Synthesis and Complexity of Controlling Systems", Novosibirsk, Russia, 2004.

S. Heber, M. Alekseyev, S.-H. Sze, H. Tang, and P. A. Pevzner. "Splicing Graphs and EST Assembly Problem". Bioinformatics 18:Suppl 1 (2002), S181-S188. doi:10.1093/bioinformatics/18.suppl_1.S181

M. A. Alekseev, L. Yu. Glebskii, and E. I. Gordon. "On Approximation of Groups, Group Actions, and Hopf Algebras". Journal of Mathematical Sciences 107:5 (2001), 4305-4332. doi:10.1023/A:1012485910692

M. Alekseyev. "Josephus Problem" (in Russian). The Empire of Mathematics 2 (2001), 22-28.

M. A. Alekseyev. "On matrices with pairwise distinct rows and columns" (in Russian). Vestn. Nizhegorod. Univ. N. I. Lobachevskogo, Mat. Model. Optim. Upr. 1 (2001), 284-288.

M. Alekseyev. "On matrices with pairwise distinct rows and columns" (in Russian). Proceeding of the 4th Workshop On Discrete Mathematics And Its Applications, Moscow, Russia, 2000.

M. A. Alekseev, L. Yu. Glebskii, and E. I .Gordon. "On Approximation of Groups, Group Actions, and Hopf Algebras" (in Russian). Zap. Nauchn. Sem. POMI 256 (1999), 224-262.

M. A. Alekseev and E. I. Gordon. "On actions of aproximable groups in the ultraproducts of measurable spaces". Proceedings of the International Conference Dedicated to the 90th Anniversary of L. S. Pontryagin, Moscow, Russia, 1998.