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2020 – today
- 2024
[j35]Morgan N. Price, Adam P. Arkin:
Interactive tools for functional annotation of bacterial genomes. Database J. Biol. Databases Curation 2024 (2024)- 2022
- [j34]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): 1010476 (2022) - 2021
- [j33]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 (Corrigendum). Nucleic Acids Res. 49(Database-Issue): D1555 (2021) - [j32]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): D575-D588 (2021) - [j31]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)
2010 – 2019
- 2018
- [j30]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): 503-509 (2018) - 2017
- [j29]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): 205:1-205:11 (2017) - [j28]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): 219:1-219:2 (2017) - 2015
- [j27]Héctor García Martín, Vinay Satish Kumar, Daniel Weaver, Amit Ghosh, Victor Chubukov, Aindrila Mukhopadhyay, Adam P. Arkin, Jay D. Keasling:
A Method to Constrain Genome-Scale Models with 13C Labeling Data. PLoS Comput. Biol. 11(9) (2015) - 2014
- [j26]Joao C. Guimaraes, Miguel Rocha, Adam P. Arkin, Guillaume Cambray:
D-Tailor: automated analysis and design of DNA sequences. Bioinform. 30(8): 1087-1094 (2014) - [c9]Ana Sofia Rufino Ferreira, Justin Hsia, Murat Arcak, Michel M. Maharbiz, Adam P. Arkin:
Pattern formation with a compartmental lateral inhibition system. CDC 2014: 5413-5418 - [i1]Ana Sofia Rufino Ferreira, Justin Hsia, Murat Arcak, Michel M. Maharbiz, Adam P. Arkin:
Pattern Formation with a Compartmental Lateral Inhibition System. CoRR abs/1407.6426 (2014) - 2013
- [j25]Liming Wang, Xiaodong Wang, Adam P. Arkin, Michael S. Samoilov:
Inference of gene regulatory networks from genome-wide knockout fitness data. Bioinform. 29(3): 338-346 (2013) - [j24]Dylan Chivian, Paramvir S. Dehal, Keith Keller, Adam P. Arkin:
metaMicrobesOnline: phylogenomic analysis of microbial communities. Nucleic Acids Res. 41(Database-Issue): 648-654 (2013) - [j23]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) - [j22]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) - 2012
- [j21]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): 604-608 (2012) - 2011
- [j20]Y. Wayne Huang, Adam P. Arkin, John-Marc Chandonia:
WIST: toolkit for rapid, customized LIMS development. Bioinform. 27(3): 437-438 (2011) - [j19]John T. Bates, Dylan Chivian, Adam P. Arkin:
GLAMM: Genome-Linked Application for Metabolic Maps. Nucleic Acids Res. 39(Web-Server-Issue): 400-405 (2011) - [c8]Michael Morimoto, Adam P. Arkin, Kameshwar Poolla:
Modeling sporulation decisions in Bacillus subtilis as optimal evolutionary decision-making. ACC 2011: 3508-3513 - [c7]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: 114-115 - 2010
- [j18]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): 111-118 (2010) - [j17]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): 396-400 (2010) - [j16]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): 299-307 (2010) - [j15]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) - [j14]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) - [j13]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) - [c6]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: 487-494
2000 – 2009
- 2009
- [r1]Steven S. Andrews, Tuan Dinh, Adam P. Arkin:
Stochastic Models of Biological Processes. Encyclopedia of Complexity and Systems Science 2009: 8730-8749 - 2008
- [j12]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) - [j11]Adam P. Arkin, John Doyle:
Appreciation of the Machinations of the Blind Watchmaker. IEEE Trans. Autom. Control. 53: 8-9 (2008) - 2007
- [j10]Sergey Plyasunov, Adam P. Arkin:
Efficient stochastic sensitivity analysis of discrete event systems. J. Comput. Phys. 221(2): 724-738 (2007) - [j9]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): 407-412 (2007) - [j8]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) - 2006
- [j7]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: 19 (2006) - [j6]Sergey Plyasunov, Adam P. Arkin:
Averaging Methods for Stochastic Dynamics of Complex Reaction Networks: Description of Multiscale Couplings. Multiscale Model. Simul. 5(2): 497-513 (2006) - [j5]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) - [j4]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: 150-175 (2006) - 2005
- [j3]Patrick Flaherty, Guri Giaever, Jochen Kumm, Michael I. Jordan, Adam P. Arkin:
A latent variable model for chemogenomic profiling. Bioinform. 21(15): 3286-3293 (2005) - [j2]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) - [c5]Patrick Flaherty, Michael I. Jordan, Adam P. Arkin:
Robust design of biological experiments. NIPS 2005: 363-370 - 2004
- [c4]Matthew D. Onsum, Adam P. Arkin:
Autonomous Mobile Robot Control Based on White Blood Cell Chemotaxis. CMSB 2004: 9-19 - 2003
- [j1]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:
The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinform. 19(4): 524-531 (2003) - [c3]Adam P. Arkin:
Motifs and Modules in Cellular Signal Processing: Applications to Microbial Stress Response Pathways. CSB 2003: 33 - 2002
- [c2]Sergey Plyasunov, Adam P. Arkin:
Motifs and modules in cellular signal processing. ICASSP 2002: 4032-4035
1990 – 1999
- 1992
- [c1]D. C. Youvan, Adam P. Arkin, M. M. Yang:
Recursive Ensemble Mutagenesis: A Combinatorial Optimization Technique for Protein Engineering. PPSN 1992: 403-412
Coauthor Index
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