Protein Conformation Motion Modeling Using Sep-CMA-ES. - Maxim Buzdalov 001; Sergey Knyazev; Yuri Porozov (ICMLA, 2014)

Coarse-grained model of protein interaction for bio-inspired nano-communication. - Sergey Knyazev; Sergey Tarakanov; Vladimir Kuznetsov; Yuri Porozov; Yevgeni Koucheryavy; Eugene O. Stepanov (ICUMT, 2014)

Metabolic Analysis of Metatranscriptomic Data from Planktonic Communities. - Igor Mandric; Sergey Knyazev; Cory Padilla; Frank Stewart; Ion I. Mandoiu; Alex Zelikovsky (ISBRA, 2017)

Repeat-aware evaluation of scaffolding tools. - Igor Mandric; Sergey Knyazev; Alex Zelikovsky (Bioinform., 2018)

QUENTIN: reconstruction of disease transmissions from viral quasispecies genomic data. - Pavel Skums; Alex Zelikovsky; Rahul Singh; Walker Gussler; Zoya Dimitrova; Sergey Knyazev; Igor Mandric; Sumathi Ramachandran; David S. Campo; Deeptanshu Jha; Leonid Bunimovich; Elizabeth Costenbader; et al. (Bioinform., 2018)

Benchmarking of computational error-correction methods for next-generation sequencing data. - Keith Mitchell; Jaqueline J. Brito; Igor Mandric; Qiaozhen Wu; Sergey Knyazev; Sei Chang; Lana S. Martin; Aaron Karlsberg; Ekaterina Gerasimov; Russell Littman; Brian L. Hill; Nicholas C. Wu; et al. (BCB, 2020)

Clustering Based Identification of SARS-CoV-2 Subtypes. - Andrew Melnyk; Fatemeh Mohebbi; Sergey Knyazev; Bikram Sahoo; Roya Hosseini; Pavel Skums; Alex Zelikovsky; Murray Patterson (ICCABS, 2020)

Estimating Enzyme Participation in Metabolic Pathways for Microbial Communities from RNA-seq Data. - Filipp Rondel; Akram Sadat Hosseini; Bikram Sahoo; Sergey Knyazev; Igor Mandric; Frank Stewart; Ion I. Mandoiu; Bogdan Pasaniuc; Alex Zelikovsky (ISBRA, 2020)

A Novel Network Representation of SARS-CoV-2 Sequencing Data. - Sergey Knyazev; Daniel Novikov; Mark Grinshpon; Harman Singh; Ram Ayyala; Varuni Sarwal; Roya Hosseini; Pelin Icer Baykal; Pavel Skums; Ellsworth Campbell; Serghei Mangul; Alex Zelikovsky (ISBRA, 2021)

Epidemiological data analysis of viral quasispecies in the next-generation sequencing era. - Sergey Knyazev; Lauren Hughes; Pavel Skums; Alexander Zelikovsky (Briefings Bioinform., 2021)

From Alpha to Zeta: Identifying Variants and Subtypes of SARS-CoV-2 Via Clustering. - Andrew Melnyk; Fatemeh Mohebbi; Sergey Knyazev; Bikram Sahoo; Roya Hosseini; Pavel Skums; Alex Zelikovsky; Murray Patterson (J. Comput. Biol., 2021)

Scalable Reconstruction of SARS-CoV-2 Phylogeny with Recurrent Mutations. - Daniel Novikov; Sergey Knyazev; Mark Grinshpon; Pelin B. Icer; Pavel Skums; Alex Zelikovsky (J. Comput. Biol., 2021)

Pipeline for Analyzing Activity of Metabolic Pathways in Planktonic Communities Using Metatranscriptomic Data. - Filipp Rondel; Roya Hosseini; Bikram Sahoo; Sergey Knyazev; Igor Mandric; Frank Stewart; Ion I. Mandoiu; Bogdan Pasaniuc; Yuri Porozov; Alexander Zelikovsky (J. Comput. Biol., 2021)

MicrobeTrace: Retooling molecular epidemiology for rapid public health response. - Ellsworth M. Campbell; Anthony Boyles; Anupama Shankar; Jay Kim; Sergey Knyazev; Roxana Cintron; William M. Switzer (PLoS Comput. Biol., 2021)

Estimating Enzyme Expression and Metabolic Pathway Activity in Borreliella-Infected and Uninfected Mice. - Filipp Rondel; Hafsa Farooq; Roya Hosseini; Akshay Juyal; Sergey Knyazev; Serghei Mangul; Artem S. Rogovskyy; Alexander Zelikovsky (J. Comput. Biol., 2025)