Automatic pathway building in biological association networks. - Anton Yuryev; Zufar Mulyukov; Ekaterina Kotelnikova; Sergei Maslov; Sergei Egorov; Alexander Nikitin; Nikolai Daraselia; Ilya Mazo (BMC Bioinform., 2006)

Ranking Scientific Publications Using a Simple Model of Network Traffic - Dylan Walker; Huafeng Xie; Koon-Kiu Yan; Sergei Maslov (CoRR, 2006)

Finding scientific gems with Google's PageRank algorithm. - P. Chen; H. Xie; Sergei Maslov; Sidney Redner (J. Informetrics, 2007)

UV-Induced Mutagenesis in Escherichia coli SOS Response: A Quantitative Model. - Sandeep Krishna; Sergei Maslov; Kim Sneppen (PLoS Comput. Biol., 2007)

Topological and Dynamical Properties of Protein Interaction Networks. - Sergei Maslov (Protein-protein Interactions and Networks, 2008)

Detection of the dominant direction of information flow and feedback links in densely interconnected regulatory networks. - Iaroslav Ispolatov; Sergei Maslov (BMC Bioinform., 2008)

A Toolbox Model of Evolution of Metabolic Pathways on Networks of Arbitrary Topology. - Tin Yau Pang; Sergei Maslov (PLoS Comput. Biol., 2011)

Comparative network analysis of gene co-expression networks reveals the conserved and species-specific functions of cell-wall related genes between Arabidopsis and Poplar. - Daifeng Wang; Eric Pan; Gang Fang; Sunita Kumari; Fei He; Doreen Ware; Sergei Maslov; Mark Gerstein (BCB, 2013)

Evolutionary Capacitance and Control of Protein Stability in Protein-Protein Interaction Networks. - Purushottam D. Dixit; Sergei Maslov (PLoS Comput. Biol., 2013)

Universal distribution of component frequencies in biological and technological systems. - Tin Yau Pang; Sergei Maslov (Proc. Natl. Acad. Sci. USA, 2013)

Diversity Waves in Collapse-Driven Population Dynamics. - Sergei Maslov; Kim Sneppen (PLoS Comput. Biol., 2015)

DREISS: Using State-Space Models to Infer the Dynamics of Gene Expression Driven by External and Internal Regulatory Networks. - Daifeng Wang; Fei He; Sergei Maslov; Mark Gerstein (PLoS Comput. Biol., 2016)

Microbial community structure predicted by the stable marriage problem. - Akshit Goyal; Veronika Dubinkina; Sergei Maslov (CoRR, 2017)

Predicting tumor cell line response to drug pairs with deep learning. - Fangfang Xia; Maulik Shukla; Thomas S. Brettin; Cristina Garcia-Cardona; Judith D. Cohn; Jonathan E. Allen; Sergei Maslov; Susan L. Holbeck; James H. Doroshow; Yvonne A. Evrard; Eric A. Stahlberg; Rick L. Stevens (BMC Bioinform., 2018)

Multistability and regime shifts in microbial communities explained by competition for essential nutrients. - Veronika Dubinkina; Yulia Fridman; Parth Pratim Pandey; Sergei Maslov (CoRR, 2019)

Evidence for a multi-level trophic organization of the human gut microbiome. - Tong Wang 033; Akshit Goyal; Veronika Dubinkina; Sergei Maslov (PLoS Comput. Biol., 2019)

Transforming the Language of Life: Transformer Neural Networks for Protein Prediction Tasks. - Ananthan Nambiar; Maeve Heflin; Simon Liu; Sergei Maslov; Mark Hopkins; Anna M. Ritz (BCB, 2020)

Modeling microbial cross-feeding at intermediate scale portrays community dynamics and species coexistence. - Chen Liao; Tong Wang 033; Sergei Maslov; João B. Xavier (PLoS Comput. Biol., 2020)

A cross-study analysis of drug response prediction in cancer cell lines. - Fangfang Xia; Jonathan E. Allen; Prasanna Balaprakash; Thomas S. Brettin; Cristina Garcia-Cardona; Austin Clyde; Judith D. Cohn; James H. Doroshow; Xiaotian Duan; Veronika Dubinkina; Yvonne A. Evrard; Ya Ju Fan; et al. (Briefings Bioinform., 2022)

Fine-scale diversity of microbial communities due to satellite niches in boom and bust environments. - Yulia Fridman; Zihan Wang; Sergei Maslov; Akshit Goyal (PLoS Comput. Biol., 2022)

Semi-Quantitative Group Testing for Efficient and Accurate qPCR Screening of Pathogens with a Wide Range of Loads. - Anantham Nambiar; Chao Pan 003; Vishal Rana; Mahdi Cheraghchi; João Ribeiro 002; Sergei Maslov; Olgica Milenkovic (CoRR, 2023)

Transformer Neural Networks for Protein Family and Interaction Prediction Tasks. - Ananthan Nambiar; Simon Liu; Maeve Heflin; John Malcolm Forsyth; Sergei Maslov; Mark Hopkins; Anna M. Ritz (J. Comput. Biol., 2023)

Predicting metabolomic profiles from microbial composition through neural ordinary differential equations. - Tong Wang 033; Xu-Wen Wang; Kathleen A. Lee-Sarwar; Augusto A. Litonjua; Scott T. Weiss; Yizhou Sun; Sergei Maslov; Yang-Yu Liu (Nat. Mac. Intell., 2023)

FUN-PROSE: A deep learning approach to predict condition-specific gene expression in fungi. - Ananthan Nambiar; Veronika Dubinkina; Simon Liu; Sergei Maslov (PLoS Comput. Biol., 2023)

Semi-quantitative group testing for efficient and accurate qPCR screening of pathogens with a wide range of loads. - Ananthan Nambiar; Chao Pan 003; Vishal Rana; Mahdi Cheraghchi; João Ribeiro 002; Sergei Maslov; Olgica Milenkovic (BMC Bioinform., 2024)

Evolutionary chemical learning in dimerization networks. - Alexei V. Tkachenko; Bortolo Matteo Mognetti; Sergei Maslov (CoRR, 2025)