Adam P. Arkin

Publication Activity (10 Years)

Years Active: 1992-2022
Publications (10 Years): 8

Top Topics

Lateral Inhibition

Gene Expression

Gene Regulatory Networks

Top Venues

PLoS Comput. Biol.

Nucleic Acids Res.

Publications

Elisha M. Wood-Charlson, Zachary Crockett, Chris Erdmann, Adam P. Arkin, Carly B. Robinson
Ten simple rules for getting and giving credit for data. PLoS Comput. Biol. 18 (9) (2022)
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, Jeffrey Kimbrel, Patrik D'haeseleer, Sean R. McCorkle, Jay R. Bolton, Erik Pearson, Shane Canon, Elisha M. Wood-Charlson, Robert W. Cottingham, Adam P. Arkin, Christopher S. Henry
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). Nucleic Acids Res. 49 (Database-Issue) (2021)
Lauren M. Lui, Torben N. Nielsen, Adam P. Arkin
A method for achieving complete microbial genomes and improving bins from metagenomics data. PLoS Comput. Biol. 17 (5) (2021)
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, Jeffrey A. Kimbrel, Patrik D'haeseleer, Sean R. McCorkle, Jay R. Bolton, Erik Pearson, Shane Canon, Elisha M. Wood-Charlson, Robert W. Cottingham, Adam P. Arkin, Christopher S. Henry
The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes. Nucleic Acids Res. 49 (Database-Issue) (2021)
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, Harini Sadeeshkumar, Romy Chakraborty, Grant M. Zane, Benjamin E. Rubin, Judy D. Wall, Axel Visel, James Bristow, Matthew J. Blow, Adam P. Arkin, Adam M. Deutschbauer
Mutant phenotypes for thousands of bacterial genes of unknown function. Nat. 557 (7706) (2018)
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
The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism. BMC Bioinform. 18 (1) (2017)
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
Erratum to: The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism. BMC Bioinform. 18 (1) (2017)
Héctor García Martín, Vinay Satish Kumar, Daniel Weaver, Amit Ghosh, Victor Chubukov, Aindrila Mukhopadhyay, Adam P. Arkin, Jay D. Keasling
C Labeling Data. PLoS Comput. Biol. 11 (9) (2015)
Ana Sofia Rufino Ferreira, Justin Hsia, Murat Arcak, Michel M. Maharbiz, Adam P. Arkin
Pattern formation with a compartmental lateral inhibition system. CDC (2014)
Ana Sofia Rufino Ferreira, Justin Hsia, Murat Arcak, Michel M. Maharbiz, Adam P. Arkin
Pattern Formation with a Compartmental Lateral Inhibition System. CoRR (2014)
Joao C. Guimaraes, Miguel Rocha, Adam P. Arkin, Guillaume Cambray
D-Tailor: automated analysis and design of DNA sequences. Bioinform. 30 (8) (2014)
Kathryn Miller-Jensen, Ron Skupsky, Priya S. Shah, Adam P. Arkin, David V. Schaffer
Genetic Selection for Context-Dependent Stochastic Phenotypes: Sp1 and TATA Mutations Increase Phenotypic Noise in HIV-1 Gene Expression. PLoS Comput. Biol. 9 (7) (2013)
Dylan Chivian, Paramvir S. Dehal, Keith Keller, Adam P. Arkin
metaMicrobesOnline: phylogenomic analysis of microbial communities. Nucleic Acids Res. 41 (Database-Issue) (2013)
Liming Wang, Xiaodong Wang, Adam P. Arkin, Michael S. Samoilov
Inference of gene regulatory networks from genome-wide knockout fitness data. Bioinform. 29 (3) (2013)
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
Metallochaperones Regulate Intracellular Copper Levels. PLoS Comput. Biol. 9 (1) (2013)
Pavel S. Novichkov, Thomas S. Brettin, Elena S. Novichkova, Paramvir S. Dehal, Adam P. Arkin, Inna Dubchak, Dmitry A. Rodionov
RegPrecise web services interface: programmatic access to the transcriptional regulatory interactions in bacteria reconstructed by comparative genomics. Nucleic Acids Res. 40 (Web-Server-Issue) (2012)
Michael Morimoto, Adam P. Arkin, Kameshwar Poolla
Modeling sporulation decisions in Bacillus subtilis as optimal evolutionary decision-making. ACC (2011)
Douglas Densmore, Mark Horowitz, Smita Krishnaswamy, Xiling Shen, Adam P. Arkin, Erik Winfree, Chris Voigt
Joint DAC/IWBDA special session design and synthesis of biological circuits. DAC (2011)
Y. Wayne Huang, Adam P. Arkin, John-Marc Chandonia
WIST: toolkit for rapid, customized LIMS development. Bioinform. 27 (3) (2011)
John T. Bates, Dylan Chivian, Adam P. Arkin
GLAMM: Genome-Linked Application for Metabolic Maps. Nucleic Acids Res. 39 (Web-Server-Issue) (2011)
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
RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach. Nucleic Acids Res. 38 (Web-Server-Issue) (2010)
Ron Skupsky, John C. Burnett, Jonathan E. Foley, David V. Schaffer, Adam P. Arkin
HIV Promoter Integration Site Primarily Modulates Transcriptional Burst Size Rather Than Frequency. PLoS Comput. Biol. 6 (9) (2010)
Guido H. Jajamovich, Michael S. Samoilov, Xiaodong Wang, Adam P. Arkin
Inference of binding sites with a Bayesian multiple-instance motif discovery method. Allerton (2010)
Sharon Aviran, Priya S. Shah, David V. Schaffer, Adam P. Arkin
Computational Models of HIV-1 Resistance to Gene Therapy Elucidate Therapy Design Principles. PLoS Comput. Biol. 6 (8) (2010)
Pavel S. Novichkov, Olga N. Laikova, Elena S. Novichkova, Mikhail S. Gelfand, Adam P. Arkin, Inna Dubchak, Dmitry A. Rodionov
RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes. Nucleic Acids Res. 38 (Database-Issue) (2010)
Steven S. Andrews, Nathan J. Addy, Roger Brent, Adam P. Arkin
Detailed Simulations of Cell Biology with Smoldyn 2.1. PLoS Comput. Biol. 6 (3) (2010)
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, Adam P. Arkin
MicrobesOnline: an integrated portal for comparative and functional genomics. Nucleic Acids Res. 38 (Database-Issue) (2010)
Patrick Flaherty, Mala L. Radhakrishnan, Tuan Dinh, Robert A. Rebres, Tamara I. Roach, Michael I. Jordan, Adam P. Arkin
A Dual Receptor Crosstalk Model of G-Protein-Coupled Signal Transduction. PLoS Comput. Biol. 4 (9) (2008)
Adam P. Arkin, John Doyle
Appreciation of the Machinations of the Blind Watchmaker. IEEE Trans. Autom. Control. 53 (2008)
Morgan N. Price, Paramvir S. Dehal, Adam P. Arkin
Orthologous Transcription Factors in Bacteria Have Different Functions and Regulate Different Genes. PLoS Comput. Biol. 3 (9) (2007)
Sergey Plyasunov, Adam P. Arkin
Efficient stochastic sensitivity analysis of discrete event systems. J. Comput. Phys. 221 (2) (2007)
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
RegTransBase - a database of regulatory sequences and interactions in a wide range of prokaryotic genomes. Nucleic Acids Res. 35 (Database-Issue) (2007)
Eric J. Alm, Katherine H. Huang, Adam P. Arkin
The Evolution of Two-Component Systems in Bacteria Reveals Different Strategies for Niche Adaptation. PLoS Comput. Biol. 2 (11) (2006)
Morgan N. Price, Adam P. Arkin, Eric J. Alm
OpWise: Operons aid the identification of differentially expressed genes in bacterial microarray experiments. BMC Bioinform. 7 (2006)
Sergey Plyasunov, Adam P. Arkin
Averaging Methods for Stochastic Dynamics of Complex Reaction Networks: Description of Multiscale Couplings. Multiscale Model. Simul. 5 (2) (2006)
Hiroyuki Kuwahara, Chris J. Myers, Michael S. Samoilov, Nathan A. Barker, Adam P. Arkin
Automated Abstraction Methodology for Genetic Regulatory Networks. Trans. Comp. Sys. Biology 6 (2006)
Dmitry A. Rodionov, Inna Dubchak, Adam P. Arkin, Eric J. Alm, Mikhail S. Gelfand
Dissimilatory Metabolism of Nitrogen Oxides in Bacteria: Comparative Reconstruction of Transcriptional Networks. PLoS Comput. Biol. 1 (5) (2005)
Patrick Flaherty, Guri Giaever, Jochen Kumm, Michael I. Jordan, Adam P. Arkin
A latent variable model for chemogenomic profiling. Bioinform. 21 (15) (2005)
Patrick Flaherty, Michael I. Jordan, Adam P. Arkin
Robust design of biological experiments. NIPS (2005)
Matthew D. Onsum, Adam P. Arkin
Autonomous Mobile Robot Control Based on White Blood Cell Chemotaxis. CMSB (2004)
Michael Hucka, Andrew Finney, Herbert M. Sauro, H. Bolouri, John C. Doyle, Hiroaki Kitano, Adam P. Arkin, Benjamin J. Bornstein, D. Bray, Athel Cornish-Bowden, Autumn A. Cuellar, Serge Dronov, Ernst Dieter Gilles, Martin Ginkel, Victoria Gor, Igor Goryanin, W. J. Hedley, T. Charles Hodgman, Jan-Hendrik S. Hofmeyr, Peter J. Hunter, Nick S. Juty, J. L. Kasberger, Andreas Kremling, Ursula Kummer, Nicolas Le Novère, Leslie M. Loew, D. Lucio, Pedro Mendes, E. Minch, Eric Mjolsness, Yoichi Nakayama, M. R. Nelson, Poul M. F. Nielsen, T. Sakurada, James C. Schaff, Bruce E. Shapiro, Thomas Simon Shimizu, Hugh D. Spence, Jörg Stelling, Koichi Takahashi, Masaru Tomita, J. Wagner, J. Wang
The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinform. 19 (4) (2003)
Adam P. Arkin
Motifs and Modules in Cellular Signal Processing: Applications to Microbial Stress Response Pathways. CSB (2003)
Sergey Plyasunov, Adam P. Arkin
Motifs and modules in cellular signal processing. ICASSP (2002)
D. C. Youvan, Adam P. Arkin, M. M. Yang
Recursive Ensemble Mutagenesis: A Combinatorial Optimization Technique for Protein Engineering. PPSN (1992)