kGEM: An EM-based algorithm for local reconstruction of viral quasispecies. - Alexander Artyomenko; Nicholas Mancuso; Alex Zelikovsky; Pavel Skums; Ion I. Mandoiu (ICCABS, 2013)

Estimation of viral population structure from amplicon-based reads. - Nicholas Mancuso; Alexander Artyomenko; Alex Zelikovsky; Pavel Skums; Ion I. Mandoiu (ICCABS, 2013)

Reconstruction of viral population structure from next-generation sequencing data using multicommodity flows. - Pavel Skums; Nicholas Mancuso; Alexander Artyomenko; Bassam Tork; Ion I. Mandoiu; Yuri Khudyakov; Alex Zelikovsky (BMC Bioinform., 2013)

Reconstruction of influenza a virus variants from PacBio reads. - Alexander Artyomenko; Serghei Mangul; Nicholas C. Wu; Eleazar Eskin; Ren Sun; Alex Zelikovsky (ICCABS, 2014)

Deterministic regression algorithm for transcriptome frequency estimation. - Adrian Caciula; Olga Glebova; Alexander Artyomenko; Serghei Mangul; James Lindsay; Ion I. Mandoiu; Alex Zelikovsky (ICCABS, 2014)

Detection of genetic relatedness between viral samples using EM-based clustering of next-generation sequencing data. - Pavel Skums; Alexander Artyomenko; Olga Glebova; Alex Zelikovsky; David S. Campo; Zoya Dimitrova; Yuri Khudyakov (ICCABS, 2014)

2SNV: Quasispecies reconstruction from PacBio reads. - Alexander Artyomenko; Nicholas C. Wu; Serghei Mangul; Eleazar Eskin; Ren Sun; Alex Zelikovsky (ICCABS, 2015)

Computational framework for next-generation sequencing of heterogeneous viral populations using combinatorial pooling. - Pavel Skums; Alexander Artyomenko; Olga Glebova; Sumathi Ramachandran; Ion I. Mandoiu; David S. Campo; Zoya Dimitrova; Alex Zelikovsky; Yuri Khudyakov (Bioinform., 2015)

Assessment of HCV infection stage as recent or chronic using multi-parameter analysis and machine learning. - Pelin Icer Baykal; Alexander Artyomenko; Sumathi Ramachandran; Yury Khudyakov; Alex Zelikovsky; Pavel Skums (ICCABS, 2017)

Agent-Based in Silico Evolution of HCV Quasispecies. - Alexander Artyomenko; Pelin B. Icer; Pavel Skums; Sumathi Ramachandran; Yury Khudyakov; Alex Zelikovsky (ISBRA, 2017)

Long Single-Molecule Reads Can Resolve the Complexity of the Influenza Virus Composed of Rare, Closely Related Mutant Variants. - Alexander Artyomenko; Nicholas C. Wu; Serghei Mangul; Eleazar Eskin; Ren Sun; Alex Zelikovsky (J. Comput. Biol., 2017)