SILP3: Maximum likelihood approach to scaffolding. - Igor Mandric; James Lindsay; Ion I. Mandoiu; Alex Zelikovsky (ICCABS, 2014)

ScaffMatch: scaffolding algorithm based on maximum weight matching. - Igor Mandric; Alex Zelikovsky (Bioinform., 2015)

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

Fast bootstrapping-based estimation of confidence intervals of expression levels and differential expression from RNA-Seq data. - Igor Mandric; Yvette Temate-Tiagueu; Tatiana Shcheglova; Sahar Al Seesi; Alex Zelikovsky; Ion I. Mandoiu (Bioinform., 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)

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)

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)