Adam P. Arkin

46 papers A* 1A 1C 1Misc 1Journal 36Unranked 5
YearRankTypeTitle / Venue / Authors
2024 J jnl
Interactive tools for functional annotation of bacterial genomes.
Database J. Biol. Databases Curation
Morgan N. Price, Adam P. Arkin
2022 J jnl
Ten simple rules for getting and giving credit for data.
PLoS Comput. Biol.
Elisha M. Wood-Charlson, Zachary Crockett, Chris Erdmann, Adam P. Arkin, Carly B. Robinson
2021 J jnl
A method for achieving complete microbial genomes and improving bins from metagenomics data.
PLoS Comput. Biol.
Lauren M. Lui, Torben N. Nielsen, Adam P. Arkin
2021 J jnl
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.
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
2021 J jnl
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.
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
2018 J jnl
Mutant phenotypes for thousands of bacterial genes of unknown function.
Nat.
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
2017 J jnl
Erratum to: The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism.
BMC Bioinform.
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
2017 J jnl
The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism.
BMC Bioinform.
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
2015 J jnl
A Method to Constrain Genome-Scale Models with
PLoS Comput. Biol.
Héctor García Martín, Vinay Satish Kumar, Daniel Weaver, Amit Ghosh, Victor Chubukov, Aindrila Mukhopadhyay, Adam P. Arkin, Jay D. Keasling
2014 J jnl
D-Tailor: automated analysis and design of DNA sequences.
Bioinform.
Joao C. Guimaraes, Miguel Rocha, Adam P. Arkin, Guillaume Cambray
2014 J jnl
Pattern Formation with a Compartmental Lateral Inhibition System.
CoRR
Ana Sofia Rufino Ferreira, Justin Hsia, Murat Arcak, Michel M. Maharbiz, Adam P. Arkin
2014 — conf
Pattern formation with a compartmental lateral inhibition system.
CDC
Ana Sofia Rufino Ferreira, Justin Hsia, Murat Arcak, Michel M. Maharbiz, Adam P. Arkin
2013 J jnl
Genetic Selection for Context-Dependent Stochastic Phenotypes: Sp1 and TATA Mutations Increase Phenotypic Noise in HIV-1 Gene Expression.
PLoS Comput. Biol.
Kathryn Miller-Jensen, Ron Skupsky, Priya S. Shah, Adam P. Arkin, David V. Schaffer
2013 J jnl
Inference of gene regulatory networks from genome-wide knockout fitness data.
Bioinform.
Liming Wang, Xiaodong Wang, Adam P. Arkin, Michael S. Samoilov
2013 J jnl
Metallochaperones Regulate Intracellular Copper Levels.
PLoS Comput. Biol.
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
2013 J jnl
metaMicrobesOnline: phylogenomic analysis of microbial communities.
Nucleic Acids Res.
Dylan Chivian, Paramvir S. Dehal, Keith Keller, Adam P. Arkin
2012 J jnl
RegPrecise web services interface: programmatic access to the transcriptional regulatory interactions in bacteria reconstructed by comparative genomics.
Nucleic Acids Res.
Pavel S. Novichkov, Thomas S. Brettin, Elena S. Novichkova, Paramvir S. Dehal, Adam P. Arkin, Inna Dubchak, Dmitry A. Rodionov
2011 J jnl
GLAMM: Genome-Linked Application for Metabolic Maps.
Nucleic Acids Res.
John T. Bates, Dylan Chivian, Adam P. Arkin
2011 A* conf
Joint DAC/IWBDA special session design and synthesis of biological circuits.
DAC
Douglas Densmore, Mark Horowitz, Smita Krishnaswamy, Xiling Shen, Adam P. Arkin, Erik Winfree, Chris Voigt
2011 C conf
Modeling sporulation decisions in Bacillus subtilis as optimal evolutionary decision-making.
ACC
Michael Morimoto, Adam P. Arkin, Kameshwar Poolla
2011 J jnl
WIST: toolkit for rapid, customized LIMS development.
Bioinform.
Y. Wayne Huang, Adam P. Arkin, John-Marc Chandonia
2010 J jnl
Computational Models of HIV-1 Resistance to Gene Therapy Elucidate Therapy Design Principles.
PLoS Comput. Biol.
Sharon Aviran, Priya S. Shah, David V. Schaffer, Adam P. Arkin
2010 J jnl
Detailed Simulations of Cell Biology with Smoldyn 2.1.
PLoS Comput. Biol.
Steven S. Andrews, Nathan J. Addy, Roger Brent, Adam P. Arkin
2010 J jnl
HIV Promoter Integration Site Primarily Modulates Transcriptional Burst Size Rather Than Frequency.
PLoS Comput. Biol.
Ron Skupsky, John C. Burnett, Jonathan E. Foley, David V. Schaffer, Adam P. Arkin
2010 — conf
Inference of binding sites with a Bayesian multiple-instance motif discovery method.
Allerton
Guido H. Jajamovich, Michael S. Samoilov, Xiaodong Wang, Adam P. Arkin
2010 J jnl
MicrobesOnline: an integrated portal for comparative and functional genomics.
Nucleic Acids Res.
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
2010 J jnl
RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes.
Nucleic Acids Res.
Pavel S. Novichkov, Olga N. Laikova, Elena S. Novichkova, Mikhail S. Gelfand, Adam P. Arkin, Inna Dubchak, Dmitry A. Rodionov
2010 J jnl
RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach.
Nucleic Acids Res.
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
2009 — ch.
Stochastic Models of Biological Processes.
Encyclopedia of Complexity and Systems Science
Steven S. Andrews, Tuan Dinh, Adam P. Arkin
2008 J jnl
A Dual Receptor Crosstalk Model of G-Protein-Coupled Signal Transduction.
PLoS Comput. Biol.
Patrick Flaherty, Mala L. Radhakrishnan, Tuan Dinh, Robert A. Rebres, Tamara I. Roach, Michael I. Jordan, Adam P. Arkin
2008 J jnl
Appreciation of the Machinations of the Blind Watchmaker.
IEEE Trans. Autom. Control.
Adam P. Arkin, John Doyle
2007 J jnl
Efficient stochastic sensitivity analysis of discrete event systems.
J. Comput. Phys.
Sergey Plyasunov, Adam P. Arkin
2007 J jnl
Orthologous Transcription Factors in Bacteria Have Different Functions and Regulate Different Genes.
PLoS Comput. Biol.
Morgan N. Price, Paramvir S. Dehal, Adam P. Arkin
2007 J jnl
RegTransBase - a database of regulatory sequences and interactions in a wide range of prokaryotic genomes.
Nucleic Acids Res.
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
2006 J jnl
Automated Abstraction Methodology for Genetic Regulatory Networks.
Trans. Comp. Sys. Biology
Hiroyuki Kuwahara, Chris J. Myers, Michael S. Samoilov, Nathan A. Barker, Adam P. Arkin
2006 J jnl
Averaging Methods for Stochastic Dynamics of Complex Reaction Networks: Description of Multiscale Couplings.
Multiscale Model. Simul.
Sergey Plyasunov, Adam P. Arkin
2006 J jnl
OpWise: Operons aid the identification of differentially expressed genes in bacterial microarray experiments.
BMC Bioinform.
Morgan N. Price, Adam P. Arkin, Eric J. Alm
2006 J jnl
The Evolution of Two-Component Systems in Bacteria Reveals Different Strategies for Niche Adaptation.
PLoS Comput. Biol.
Eric J. Alm, Katherine H. Huang, Adam P. Arkin
2005 J jnl
A latent variable model for chemogenomic profiling.
Bioinform.
Patrick Flaherty, Guri Giaever, Jochen Kumm, Michael I. Jordan, Adam P. Arkin
2005 J jnl
Dissimilatory Metabolism of Nitrogen Oxides in Bacteria: Comparative Reconstruction of Transcriptional Networks.
PLoS Comput. Biol.
Dmitry A. Rodionov, Inna Dubchak, Adam P. Arkin, Eric J. Alm, Mikhail S. Gelfand
2005 — conf
Robust design of biological experiments.
NIPS
Patrick Flaherty, Michael I. Jordan, Adam P. Arkin
2004 — conf
Autonomous Mobile Robot Control Based on White Blood Cell Chemotaxis.
CMSB
Matthew D. Onsum, Adam P. Arkin
2003 — conf
Motifs and Modules in Cellular Signal Processing: Applications to Microbial Stress Response Pathways.
CSB
Adam P. Arkin
2003 J jnl
The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models.
Bioinform.
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
2002 Misc conf
Motifs and modules in cellular signal processing.
ICASSP
Sergey Plyasunov, Adam P. Arkin
1992 A conf
Recursive Ensemble Mutagenesis: A Combinatorial Optimization Technique for Protein Engineering.
PPSN
D. C. Youvan, Adam P. Arkin, M. M. Yang