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Author Details

Sergei Maslov
University of Illinois Urbana-Champaign
1993
73
26
PMIDPaper TitleJournal TitlePublished Year
35950958Transformer Neural Networks for Protein Family and Interaction Prediction Tasks.J Comput Biol2023
37971967FUN-PROSE: A deep learning approach to predict condition-specific gene expression in fungi.PLoS Comput Biol2023
36993761Predicting metabolic response to dietary intervention using deep learning.bioRxiv2023
37380829Functional convergence in slow-growing microbial communities arises from thermodynamic constraints.ISME J2023
36977046Gut Microbiome-Host Metabolome Homeostasis upon Exposure to PFOS and GenX in Male Mice.Toxics2023
34524425A cross-study analysis of drug response prediction in cancer cell lines.Brief Bioinform2022
36574450Fine-scale diversity of microbial communities due to satellite niches in boom and bust environments.PLoS Comput Biol2022
34795267Complementary resource preferences spontaneously emerge in diauxic microbial communities.Nat Commun2021
33593911Structured sequences emerge from random pool when replicated by templated ligation.Proc Natl Acad Sci U S A2021
33637740Ecology-guided prediction of cross-feeding interactions in the human gut microbiome.Nat Commun2021
33833080Time-dependent heterogeneity leads to transient suppression of the COVID-19 epidemic, not herd immunity.Proc Natl Acad Sci U S A2021
34747698Stochastic social behavior coupled to COVID-19 dynamics leads to waves, plateaus, and an endemic state.Elife2021
32358533Hitchhiking, collapse, and contingency in phage infections of migrating bacterial populations.ISME J2020
33378363Emergency ventilator for COVID-19.PLoS One2020
33077929The network structure and eco-evolutionary dynamics of CRISPR-induced immune diversification.Nat Ecol Evol2020
32810127Modeling microbial cross-feeding at intermediate scale portrays community dynamics and species coexistence.PLoS Comput Biol2020
31856158Evidence for a multi-level trophic organization of the human gut microbiome.PLoS Comput Biol2019
31756158Multistability and regime shifts in microbial communities explained by competition for essential nutrients.Elife2019
31690591Regime Shifts in a Phage-Bacterium Ecosystem and Strategies for Its Control.mSystems2019
29756882Diversity, Stability, and Reproducibility in Stochastically Assembled Microbial Ecosystems.Phys Rev Lett2018
30022156Multiple stable states in microbial communities explained by the stable marriage problem.ISME J2018
29979655KBase: The United States Department of Energy Systems Biology Knowledgebase.Nat Biotechnol2018
30577754Predicting tumor cell line response to drug pairs with deep learning.BMC Bioinformatics2018
30292218Onset of natural selection in populations of autocatalytic heteropolymers.J Chem Phys2018
28051127Population cycles and species diversity in dynamic Kill-the-Winner model of microbial ecosystems.Sci Rep2017
28950542Severe population collapses and species extinctions in multihost epidemic dynamics.Phys Rev E2017
28751420Recombination-Driven Genome Evolution and Stability of Bacterial Species.Genetics2017
28605556Family-specific scaling laws in bacterial genomes.Nucleic Acids Res2017
27015116Large-scale atlas of microarray data reveals the distinct expression landscape of different tissues in Arabidopsis.Plant J2016
27982071Pan- and core- network analysis of co-expression genes in a model plant.Sci Rep2016
27760135DREISS: Using State-Space Models to Infer the Dynamics of Gene Expression Driven by External and Internal Regulatory Networks.PLoS Comput Biol2016
27563305Large-Scale Public Transcriptomic Data Mining Reveals a Tight Connection between the Transport of Nitrogen and Other Transport Processes in Arabidopsis.Front Plant Sci2016
25607953Transcriptional responses to sucrose mimic the plant-associated life style of the plant growth promoting endophyte Enterobacter sp. 638.PLoS One2015
26367172Diversity Waves in Collapse-Driven Population Dynamics.PLoS Comput Biol2015
26233165Spontaneous emergence of autocatalytic information-coding polymers.J Chem Phys2015
26153419Recombinant transfer in the basic genome of Escherichia coli.Proc Natl Acad Sci U S A2015
26035282Well-temperate phage: optimal bet-hedging against local environmental collapses.Sci Rep2015
23530195Universal distribution of component frequencies in biological and technological systems.Proc Natl Acad Sci U S A2013
23592969Evolutionary capacitance and control of protein stability in protein-protein interaction networks.PLoS Comput Biol2013
21937509Joint scaling laws in functional and evolutionary categories in prokaryotic genomes.Nucleic Acids Res2012
21368118Topology of protein interaction network shapes protein abundances and strengths of their functional and nonspecific interactions.Proc Natl Acad Sci U S A2011
21625566A toolbox model of evolution of metabolic pathways on networks of arbitrary topology.PLoS Comput Biol2011
19482938Toolbox model of evolution of prokaryotic metabolic networks and their regulation.Proc Natl Acad Sci U S A2009
19765592Understanding the differences between genome sequences of Escherichia coli B strains REL606 and BL21(DE3) and comparison of the E. coli B and K-12 genomes.J Mol Biol2009
18682700Constraints imposed by non-functional protein-protein interactions on gene expression and proteome size.Mol Syst Biol2008
19437675Fluctuations in mass-action equilibrium of protein binding networks.Phys Rev Lett2008
18842147Detection of the dominant direction of information flow and feedback links in densely interconnected regulatory networks.BMC Bioinformatics2008
18971452Promise and pitfalls of extending Google's PageRank algorithm to citation networks.J Neurosci2008
17367202UV-induced mutagenesis in Escherichia coli SOS response: a quantitative model.PLoS Comput Biol2007
19461979Prediction of protein-protein interactions on the basis of evolutionary conservation of protein functions.Evol Bioinform Online2007
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Collaborators

Fei He
Institute of Genetics and Developmental Biology, Chinese Academy of Sciences
Co-authored papers 5
Mark Gerstein
Yale University
Co-authored papers 3
Maulik Shukla
University of Chicago
Co-authored papers 3
Rick Stevens
Argonne National Laboratory
Co-authored papers 3
Daifeng Wang
University of Wisconsin-Madison
Co-authored papers 3
Fangfang Xia
University of Chicago
Co-authored papers 3
Thomas Brettin
University of Chicago
Co-authored papers 3
Koon-Kiu Yan
Co-authored papers 3
Shinjae Yoo
Brookhaven National Laboratory
Co-authored papers 2
James H Doroshow
National Cancer Institute, National Institutes of Health
Co-authored papers 2
Hyunseung Yoo
Translational Research Center, Inha University Hospital
Co-authored papers 2
Doreen Ware
USDA ARS NAA Robert W. Holley Center for Agriculture and Health
Co-authored papers 2
Eugene I Shakhnovich
Harvard University
Co-authored papers 2
Yvonne A Evrard
Frederick National Laboratory for Cancer Research, Inc.
Co-authored papers 2
Sunita Kumari
Manav Rachna International Institute of Research and Studies
Co-authored papers 2
F W Studier
Brookhaven National Laboratory
Co-authored papers 2
Vivek Kumar
Co-authored papers 1
Anna Ritz
Reed College
Co-authored papers 1
Tae Yun Oh
Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine
Co-authored papers 1
Gavin A Price
E.O. Lawrence Berkeley National Laboratory
Co-authored papers 1
Adam P Arkin
Lawrence Berkeley National Laboratory
Co-authored papers 1
Benjamin H Allen
Oak Ridge National Laboratory
Co-authored papers 1
Marissa Mills
Oak Ridge National Laboratory
Co-authored papers 1
Folker Meyer
Institute for Artificial Intelligence, University of Duisburg-Essen
Co-authored papers 1
Dantong Yu
New Jersey Institute of Technology
Co-authored papers 1
Stephen A Boppart
Beckman Institute for Advanced Science and Technology.
Co-authored papers 1
Steven E Brenner
University of California berkeley
Co-authored papers 1
Christopher Bun
Argonne National Laboratory
Co-authored papers 1
Neal Conrad
University of Chicago
Co-authored papers 1
Ala Trusina
Niels Bohr Institute, University of Copenhagen
Co-authored papers 1
Release 1.2