Adam P. Arkin

According to our database, Adam P. Arkin authored at least 45 papers between 1992 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2024

Interactive tools for functional annotation of bacterial genomes.

Morgan N. Price, Adam P. Arkin

Database J. Biol. Databases Curation, January, 2024

2022

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., September, 2022

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

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, 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

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.

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

Nucleic Acids Res., 2021

2018

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, 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

Nat., 2018

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

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

2015

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

2014

D-Tailor: automated analysis and design of DNA sequences.

Joao C. Guimaraes, Miguel Rocha, Adam P. Arkin, Guillaume Cambray

Bioinform., 2014

Pattern formation with a compartmental lateral inhibition system.

Ana Sofia Rufino Ferreira, Justin Hsia, Murat Arcak, Michel M. Maharbiz, Adam P. Arkin

Proceedings of the 53rd IEEE Conference on Decision and Control, 2014

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

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

metaMicrobesOnline: phylogenomic analysis of microbial communities.

Dylan Chivian, Paramvir S. Dehal, Keith Keller, Adam P. Arkin

Nucleic Acids Res., 2013

Inference of gene regulatory networks from genome-wide knockout fitness data.

Liming Wang, Xiaodong Wang, Adam P. Arkin, Michael S. Samoilov

Bioinform., 2013

2012

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

2011

GLAMM: Genome-Linked Application for Metabolic Maps.

John T. Bates, Dylan Chivian, Adam P. Arkin

Nucleic Acids Res., 2011

WIST: toolkit for rapid, customized LIMS development.

Y. Wayne Huang, Adam P. Arkin, John-Marc Chandonia

Bioinform., 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

Proceedings of the 48th Design Automation Conference, 2011

Modeling sporulation decisions in Bacillus subtilis as optimal evolutionary decision-making.

Michael Morimoto, Adam P. Arkin, Kameshwar Poolla

Proceedings of the American Control Conference, 2011

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

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

Detailed Simulations of Cell Biology with Smoldyn 2.1.

Steven S. Andrews, Nathan J. Addy, Roger Brent, Adam P. Arkin

PLoS Comput. Biol., 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

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

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, Adam P. Arkin

Nucleic Acids Res., 2010

Inference of binding sites with a Bayesian multiple-instance motif discovery method.

Guido H. Jajamovich, Michael S. Samoilov, Xiaodong Wang, Adam P. Arkin

Proceedings of the 48th Annual Allerton Conference on Communication, 2010

2009

Stochastic Models of Biological Processes.

Steven S. Andrews, Tuan Dinh, Adam P. Arkin

Proceedings of the Encyclopedia of Complexity and Systems Science, 2009

2008

Appreciation of the Machinations of the Blind Watchmaker.

Adam P. Arkin, John Doyle

IEEE Trans. Autom. Control., 2008

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

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

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

Efficient stochastic sensitivity analysis of discrete event systems.

Sergey Plyasunov, Adam P. Arkin

J. Comput. Phys., 2007

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

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

Averaging Methods for Stochastic Dynamics of Complex Reaction Networks: Description of Multiscale Couplings.

Sergey Plyasunov, Adam P. Arkin

Multiscale Model. Simul., 2006

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

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

A latent variable model for chemogenomic profiling.

Patrick Flaherty, Guri Giaever, Jochen Kumm, Michael I. Jordan, Adam P. Arkin

Bioinform., 2005

Robust design of biological experiments.

Patrick Flaherty, Michael I. Jordan, Adam P. Arkin

Proceedings of the Advances in Neural Information Processing Systems 18 [Neural Information Processing Systems, 2005

2004

Autonomous Mobile Robot Control Based on White Blood Cell Chemotaxis.

Matthew D. Onsum, Adam P. Arkin

Proceedings of the Computational Methods in Systems Biology, International Conference, 2004

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, Hiroaki Kitano, Adam P. Arkin, Benjamin J. Bornstein, Dennis 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

Bioinform., 2003

Motifs and Modules in Cellular Signal Processing: Applications to Microbial Stress Response Pathways.

Adam P. Arkin

Proceedings of the 2nd IEEE Computer Society Bioinformatics Conference, 2003

2002

Motifs and modules in cellular signal processing.

Sergey Plyasunov, Adam P. Arkin

Proceedings of the IEEE International Conference on Acoustics, 2002

1992

Recursive Ensemble Mutagenesis: A Combinatorial Optimization Technique for Protein Engineering.

D. C. Youvan, Adam P. Arkin, M. M. Yang

Proceedings of the Parallel Problem Solving from Nature 2, 1992