| 2024 | ISIT | A Family of Permutationally Invariant Quantum Codes. | Arda Aydin, Max A. Alekseyev, Alexander Barg |
| 2024 | IWOCA | On Computing Sets of Integers with Maximum Number of Pairs Summing to Powers of 2. | Max A. Alekseyev |
| 2017 | RECOMB | Orientation of Ordered Scaffolds. | Sergey Aganezov Jr., Max A. Alekseyev |
| 2017 | RECOMB | A Unified ILP Framework for Genome Median, Halving, and Aliquoting Problems Under DCJ. | Pavel Avdeyev, Nikita Alexeev, Yongwu Rong, Max A. Alekseyev |
| 2016 | COCOON | Combinatorial Scoring of Phylogenetic Networks. | Nikita Alexeev, Max A. Alekseyev |
| 2016 | IWOCA | Weighted de Bruijn Graphs for the Menage Problem and Its Generalizations. | Max A. Alekseyev |
| 2014 | WABI | Linearization of Median Genomes under DCJ. | Shuai Jiang, Max A. Alekseyev |
| 2013 | RECOMB | Assembling Genomes and Mini-metagenomes from Highly Chimeric Reads. | Sergey Nurk, Anton Bankevich, Dmitry Antipov, Alexey A. Gurevich, Anton I. Korobeynikov, Alla L. Lapidus, Andrey D. Prjibelsky, Alex Pyshkin, Alexander Sirotkin, Yakov Sirotkin, Ramunas Stepanauskas, Jeffrey S. McLean, Roger Lasken, Scott R. Clingenpeel, Tanja Woyke, Glenn Tesler, Max A. Alekseyev, Pavel A. Pevzner |
| 2012 | RECOMB | Pathset Graphs: A Novel Approach for Comprehensive Utilization of Paired Reads in Genome Assembly. | Son K. Pham, Dmitry Antipov, Alexander Sirotkin, Glenn Tesler, Pavel A. Pevzner, Max A. Alekseyev |
| 2011 | RECOMB | Weighted Genomic Distance Can Hardly Impose a Bound on the Proportion of Transpositions. | Shuai Jiang, Max A. Alekseyev |
| 2010 | RECOMB | Limited Lifespan of Fragile Regions in Mammalian Evolution. | Max A. Alekseyev, Pavel A. Pevzner |
| 2009 | WABI | Decoding Synteny Blocks and Large-Scale Duplications in Mammalian and Plant Genomes. | Qian Peng, Max A. Alekseyev, Glenn Tesler, Pavel A. Pevzner |
| 2007 | RECOMB | Multi-break Rearrangements: From Circular to Linear Genomes. | Max A. Alekseyev |
| 2007 | SODA | Whole genome duplications, multi-break rearrangements, and genome halving problem. | Max A. Alekseyev, Pavel A. Pevzner |
| 2002 | ISMB | Splicing graphs and EST assembly problem. | Steffen Heber, Max A. Alekseyev, Sing-Hoi Sze, Haixu Tang, Pavel A. Pevzner |