Recursive Ensemble Mutagenesis: A Combinatorial Optimization Technique for Protein Engineering. - D. C. Youvan; Adam P. Arkin; M. M. Yang (PPSN, 1992)

Motifs and modules in cellular signal processing. - Sergey Plyasunov; Adam P. Arkin (ICASSP, 2002)

Motifs and Modules in Cellular Signal Processing: Applications to Microbial Stress Response Pathways. - Adam P. Arkin (CSB, 2003)

The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. - Michael Hucka; Andrew Finney; Herbert M. Sauro; H. Bolouri; John C. Doyle 001; Hiroaki Kitano; Adam P. Arkin; Benjamin J. Bornstein; Dennis Bray; Athel Cornish-Bowden; Autumn A. Cuellar; Serge Dronov; et al. (Bioinform., 2003)

Autonomous Mobile Robot Control Based on White Blood Cell Chemotaxis. - Matthew D. Onsum; Adam P. Arkin (CMSB, 2004)

Robust design of biological experiments. - Patrick Flaherty; Michael I. Jordan; Adam P. Arkin (NIPS, 2005)

A latent variable model for chemogenomic profiling. - Patrick Flaherty; Guri Giaever; Jochen Kumm; Michael I. Jordan; Adam P. Arkin (Bioinform., 2005)

Dissimilatory Metabolism of Nitrogen Oxides in Bacteria: Comparative Reconstruction of Transcriptional Networks. - Dmitry A. Rodionov; Inna Dubchak; Adam P. Arkin; Eric J. Alm; Mikhail S. Gelfand (PLoS Comput. Biol., 2005)

OpWise: Operons aid the identification of differentially expressed genes in bacterial microarray experiments. - Morgan N. Price; Adam P. Arkin; Eric J. Alm (BMC Bioinform., 2006)

Averaging Methods for Stochastic Dynamics of Complex Reaction Networks: Description of Multiscale Couplings. - Sergey Plyasunov; Adam P. Arkin (Multiscale Model. Simul., 2006)

The Evolution of Two-Component Systems in Bacteria Reveals Different Strategies for Niche Adaptation. - Eric J. Alm; Katherine H. Huang; Adam P. Arkin (PLoS Comput. Biol., 2006)

Automated Abstraction Methodology for Genetic Regulatory Networks. - Hiroyuki Kuwahara; Chris J. Myers; Michael S. Samoilov; Nathan A. Barker; Adam P. Arkin (Trans. Comp. Sys. Biology, 2006)

Efficient stochastic sensitivity analysis of discrete event systems. - Sergey Plyasunov; Adam P. Arkin (J. Comput. Phys., 2007)

RegTransBase - a database of regulatory sequences and interactions in a wide range of prokaryotic genomes. - Alexei E. Kazakov; Michael J. Cipriano; Pavel S. Novichkov; Simon Minovitsky; Dmitry V. Vinogradov; Adam P. Arkin; Andrey A. Mironov; Mikhail S. Gelfand; Inna Dubchak (Nucleic Acids Res., 2007)

Orthologous Transcription Factors in Bacteria Have Different Functions and Regulate Different Genes. - Morgan N. Price; Paramvir S. Dehal; Adam P. Arkin (PLoS Comput. Biol., 2007)

A Dual Receptor Crosstalk Model of G-Protein-Coupled Signal Transduction. - Patrick Flaherty; Mala L. Radhakrishnan; Tuan Dinh; Robert A. Rebres; Tamara I. Roach; Michael I. Jordan; Adam P. Arkin (PLoS Comput. Biol., 2008)

Appreciation of the Machinations of the Blind Watchmaker. - Adam P. Arkin; John Doyle 001 (IEEE Trans. Autom. Control., 2008)

Stochastic Models of Biological Processes. - Steven S. Andrews; Tuan Dinh; Adam P. Arkin (Encyclopedia of Complexity and Systems Science, 2009)

Inference of binding sites with a Bayesian multiple-instance motif discovery method. - Guido H. Jajamovich; Michael S. Samoilov; Xiaodong Wang 001; Adam P. Arkin (Allerton, 2010)

MicrobesOnline: an integrated portal for comparative and functional genomics. - Paramvir S. Dehal; Marcin P. Joachimiak; Morgan N. Price; John T. Bates; Jason K. Baumohl; Dylan Chivian; Greg D. Friedland; Katherine H. Huang; Keith Keller; Pavel S. Novichkov; Inna Dubchak; Eric J. Alm; et al. (Nucleic Acids Res., 2010)

RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes. - Pavel S. Novichkov; Olga N. Laikova; Elena S. Novichkova; Mikhail S. Gelfand; Adam P. Arkin; Inna Dubchak; Dmitry A. Rodionov (Nucleic Acids Res., 2010)

RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach. - Pavel S. Novichkov; Dmitry A. Rodionov; Elena D. Stavrovskaya; Elena S. Novichkova; Alexei E. Kazakov; Mikhail S. Gelfand; Adam P. Arkin; Andrey A. Mironov; Inna Dubchak (Nucleic Acids Res., 2010)

Detailed Simulations of Cell Biology with Smoldyn 2.1. - Steven S. Andrews; Nathan J. Addy; Roger Brent; Adam P. Arkin (PLoS Comput. Biol., 2010)

Computational Models of HIV-1 Resistance to Gene Therapy Elucidate Therapy Design Principles. - Sharon Aviran; Priya S. Shah; David V. Schaffer; Adam P. Arkin (PLoS Comput. Biol., 2010)

HIV Promoter Integration Site Primarily Modulates Transcriptional Burst Size Rather Than Frequency. - Ron Skupsky; John C. Burnett; Jonathan E. Foley; David V. Schaffer; Adam P. Arkin (PLoS Comput. Biol., 2010)

Modeling sporulation decisions in Bacillus subtilis as optimal evolutionary decision-making. - Michael Morimoto; Adam P. Arkin; Kameshwar Poolla (ACC, 2011)

Joint DAC/IWBDA special session design and synthesis of biological circuits. - Douglas Densmore; Mark Horowitz; Smita Krishnaswamy; Xiling Shen; Adam P. Arkin; Erik Winfree; Chris Voigt (DAC, 2011)

WIST: toolkit for rapid, customized LIMS development. - Y. Wayne Huang; Adam P. Arkin; John-Marc Chandonia (Bioinform., 2011)

GLAMM: Genome-Linked Application for Metabolic Maps. - John T. Bates; Dylan Chivian; Adam P. Arkin (Nucleic Acids Res., 2011)

RegPrecise web services interface: programmatic access to the transcriptional regulatory interactions in bacteria reconstructed by comparative genomics. - Pavel S. Novichkov; Thomas S. Brettin; Elena S. Novichkova; Paramvir S. Dehal; Adam P. Arkin; Inna Dubchak; Dmitry A. Rodionov (Nucleic Acids Res., 2012)

Inference of gene regulatory networks from genome-wide knockout fitness data. - Liming Wang 004; Xiaodong Wang 001; Adam P. Arkin; Michael S. Samoilov (Bioinform., 2013)

metaMicrobesOnline: phylogenomic analysis of microbial communities. - Dylan Chivian; Paramvir S. Dehal; Keith Keller; Adam P. Arkin (Nucleic Acids Res., 2013)

Genetic Selection for Context-Dependent Stochastic Phenotypes: Sp1 and TATA Mutations Increase Phenotypic Noise in HIV-1 Gene Expression. - Kathryn Miller-Jensen; Ron Skupsky; Priya S. Shah; Adam P. Arkin; David V. Schaffer (PLoS Comput. Biol., 2013)

Metallochaperones Regulate Intracellular Copper Levels. - Wyming Lee Pang; Amardeep Kaur; Alexander V. Ratushny; Aleksandar Cvetkovic; Sunil Kumar; Min Pan; Adam P. Arkin; John D. Aitchison; Michael W. W. Adams; Nitin S. Baliga (PLoS Comput. Biol., 2013)

Pattern formation with a compartmental lateral inhibition system. - Ana Sofia Rufino Ferreira; Justin Hsia; Murat Arcak; Michel M. Maharbiz; Adam P. Arkin (CDC, 2014)

D-Tailor: automated analysis and design of DNA sequences. - Joao C. Guimaraes; Miguel Rocha 001; Adam P. Arkin; Guillaume Cambray (Bioinform., 2014)

A Method to Constrain Genome-Scale Models with 13C Labeling Data. - Héctor García Martín; Vinay Satish Kumar; Daniel Weaver; Amit Ghosh; Victor Chubukov; Aindrila Mukhopadhyay; Adam P. Arkin; Jay D. Keasling (PLoS Comput. Biol., 2015)

The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism. - Garrett W. Birkel; Amit Ghosh; Vinay Satish Kumar; Daniel Weaver; David Ando; Tyler W. H. Backman; Adam P. Arkin; Jay D. Keasling; Héctor García Martín (BMC Bioinform., 2017)

Erratum to: The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism. - Garrett W. Birkel; Amit Ghosh; Vinay Satish Kumar; Daniel Weaver; David Ando; Tyler W. H. Backman; Adam P. Arkin; Jay D. Keasling; Héctor García Martín (BMC Bioinform., 2017)

Mutant phenotypes for thousands of bacterial genes of unknown function. - Morgan N. Price; Kelly M. Wetmore; R. Jordan Waters; Mark Callaghan; Jayashree Ray; Hualan Liu; Jennifer V. Kuehl; Ryan A. Melnyk; Jacob S. Lamson; Yumi Suh; Hans K. Carlson; Zuelma Esquivel; et al. (Nat., 2018)

The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes. - Samuel M. D. Seaver; Filipe Liu; Qizhi Zhang; James G. Jeffryes; José P. Faria; Janaka N. Edirisinghe; Michael B. Mundy; Nicholas Chia; Elad Noor; Moritz Emanuel Beber; Aaron A. Best; Matthew DeJongh; et al. (Nucleic Acids Res., 2021)

The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes (Corrigendum). - Samuel M. D. Seaver; Filipe Liu; Qizhi Zhang; James G. Jeffryes; José P. Faria; Janaka N. Edirisinghe; Michael B. Mundy; Nicholas Chia; Elad Noor; Moritz Emanuel Beber; Aaron A. Best; Matthew DeJongh; et al. (Nucleic Acids Res., 2021)

A method for achieving complete microbial genomes and improving bins from metagenomics data. - Lauren M. Lui; Torben N. Nielsen; Adam P. Arkin (PLoS Comput. Biol., 2021)

Ten simple rules for getting and giving credit for data. - Elisha M. Wood-Charlson; Zachary Crockett; Chris Erdmann; Adam P. Arkin; Carly B. Robinson (PLoS Comput. Biol., 2022)

Interactive tools for functional annotation of bacterial genomes. - Morgan N. Price; Adam P. Arkin (Database J. Biol. Databases Curation, 2024)