Structural exon database, SEDB, mapping exon boundaries on multiple protein structures. - Chesley M. Leslin; Alexej Abyzov; Valentin A. Ilyin (Bioinform., 2004)

Friend, an integrated analytical front-end application for bioinformatics. - Alexej Abyzov; Mounir Errami; Chesley M. Leslin; Valentin A. Ilyin (Bioinform., 2005)

Active Site Prediction for Comparative Model Structures with Thematics. - Ihsan A. Shehadi; Alexej Abyzov; Alper Uzun; Ying Wei; Leonel F. Murga; Valentin A. Ilyin; Mary Jo Ondrechen (J. Bioinform. Comput. Biol., 2005)

TOPOFIT-DB, a database of protein structural alignments based on the TOPOFIT method. - Chesley M. Leslin; Alexej Abyzov; Valentin A. Ilyin (Nucleic Acids Res., 2007)

Structure SNP (StSNP): a web server for mapping and modeling nsSNPs on protein structures with linkage to metabolic pathways. - Alper Uzun; Chesley M. Leslin; Alexej Abyzov; Valentin A. Ilyin (Nucleic Acids Res., 2007)

An AP Endonuclease 1-DNA Polymerase β Complex: Theoretical Prediction of Interacting Surfaces. - Alexej Abyzov; Alper Uzun; Phyllis R. Strauss; Valentin A. Ilyin (PLoS Comput. Biol., 2008)

Analysis of Combinatorial Regulation: Scaling of Partnerships between Regulators with the Number of Governed Targets. - Nitin Bhardwaj; Matthew B. Carson; Alexej Abyzov; Koon-Kiu Yan; Hui Lu 004; Mark B. Gerstein (PLoS Comput. Biol., 2010)

AGE: defining breakpoints of genomic structural variants at single-nucleotide resolution, through optimal alignments with gap excision. - Alexej Abyzov; Mark Gerstein (Bioinform., 2011)

MetaSV: an accurate and integrative structural-variant caller for next generation sequencing. - Marghoob Mohiyuddin; John C. Mu; Jian Li; Narges Bani Asadi; Mark B. Gerstein; Alexej Abyzov; Wing H. Wong; Hugo Y. K. Lam (Bioinform., 2015)

VarSim: a high-fidelity simulation and validation framework for high-throughput genome sequencing with cancer applications. - John C. Mu; Marghoob Mohiyuddin; Jian Li; Narges Bani Asadi; Mark B. Gerstein; Alexej Abyzov; Wing H. Wong; Hugo Y. K. Lam (Bioinform., 2015)

Landscape and variation of novel retroduplications in 26 human populations. - Yan Zhang 032; Shantao Li; Alexej Abyzov; Mark B. Gerstein (PLoS Comput. Biol., 2017)

SCELLECTOR: ranking amplification bias in single cells using shallow sequencing. - Vivekananda Sarangi; Alexandre Jourdon; Taejeong Bae; Arijit Panda; Flora Vaccarino; Alexej Abyzov (BMC Bioinform., 2020)

LongAGE: defining breakpoints of genomic structural variants through optimal and memory efficient alignments of long reads. - Quang Tran 002; Alexej Abyzov (Bioinform., 2021)

OpBerg: Discovering Causal Sentences Using Optimal Alignments. - Justin Wood; Nicholas J. Matiasz; Alcino J. Silva; William Hsu; Alexej Abyzov; Wei Wang 010 (DaWaK, 2022)

All2: A tool for selecting mosaic mutations from comprehensive multi-cell comparisons. - Vivekananda Sarangi; Yeongjun Jang; Milovan Suvakov; Taejeong Bae; Liana Fasching; Shobana Sekar; Livia Tomasini; Jessica Mariani; Flora Vaccarino; Alexej Abyzov (PLoS Comput. Biol., 2022)

Correction: All2: A tool for selecting mosaic mutations from comprehensive multi-cell comparisons. - Vivekananda Sarangi; Yeongjun Jang; Milovan Suvakov; Taejeong Bae; Liana Fasching; Shobana Sekar; Livia Tomasini; Jessica Mariani; Flora Vaccarino; Alexej Abyzov (PLoS Comput. Biol., 2022)