Adam P. Arkin

According to our database1, Adam P. Arkin authored at least 37 papers between 1992 and 2017.

Collaborative distances:
  • Dijkstra number2 of four.
  • Erdős number3 of four.



In proceedings 
PhD thesis 





Erratum to: The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism.
BMC Bioinformatics, 2017

The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism.
BMC Bioinformatics, 2017

A Method to Constrain Genome-Scale Models with 13C Labeling Data.
PLoS Computational Biology, 2015

D-Tailor: automated analysis and design of DNA sequences.
Bioinformatics, 2014

Pattern formation with a compartmental lateral inhibition system.
Proceedings of the 53rd IEEE Conference on Decision and Control, 2014

Metallochaperones Regulate Intracellular Copper Levels.
PLoS Computational Biology, 2013

Genetic Selection for Context-Dependent Stochastic Phenotypes: Sp1 and TATA Mutations Increase Phenotypic Noise in HIV-1 Gene Expression.
PLoS Computational Biology, 2013

metaMicrobesOnline: phylogenomic analysis of microbial communities.
Nucleic Acids Research, 2013

Inference of gene regulatory networks from genome-wide knockout fitness data.
Bioinformatics, 2013

RegPrecise web services interface: programmatic access to the transcriptional regulatory interactions in bacteria reconstructed by comparative genomics.
Nucleic Acids Research, 2012

GLAMM: Genome-Linked Application for Metabolic Maps.
Nucleic Acids Research, 2011

WIST: toolkit for rapid, customized LIMS development.
Bioinformatics, 2011

Joint DAC/IWBDA special session design and synthesis of biological circuits.
Proceedings of the 48th Design Automation Conference, 2011

HIV Promoter Integration Site Primarily Modulates Transcriptional Burst Size Rather Than Frequency.
PLoS Computational Biology, 2010

Computational Models of HIV-1 Resistance to Gene Therapy Elucidate Therapy Design Principles.
PLoS Computational Biology, 2010

Detailed Simulations of Cell Biology with Smoldyn 2.1.
PLoS Computational Biology, 2010

RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach.
Nucleic Acids Research, 2010

RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes.
Nucleic Acids Research, 2010

MicrobesOnline: an integrated portal for comparative and functional genomics.
Nucleic Acids Research, 2010

Stochastic Models of Biological Processes.
Proceedings of the Encyclopedia of Complexity and Systems Science, 2009

Appreciation of the Machinations of the Blind Watchmaker.
IEEE Trans. Automat. Contr., 2008

A Dual Receptor Crosstalk Model of G-Protein-Coupled Signal Transduction.
PLoS Computational Biology, 2008

Orthologous Transcription Factors in Bacteria Have Different Functions and Regulate Different Genes.
PLoS Computational Biology, 2007

RegTransBase - a database of regulatory sequences and interactions in a wide range of prokaryotic genomes.
Nucleic Acids Research, 2007

Efficient stochastic sensitivity analysis of discrete event systems.
J. Comput. Phys., 2007

Automated Abstraction Methodology for Genetic Regulatory Networks.
, 2006

The Evolution of Two-Component Systems in Bacteria Reveals Different Strategies for Niche Adaptation.
PLoS Computational Biology, 2006

Averaging Methods for Stochastic Dynamics of Complex Reaction Networks: Description of Multiscale Couplings.
Multiscale Modeling & Simulation, 2006

OpWise: Operons aid the identification of differentially expressed genes in bacterial microarray experiments.
BMC Bioinformatics, 2006

Dissimilatory Metabolism of Nitrogen Oxides in Bacteria: Comparative Reconstruction of Transcriptional Networks.
PLoS Computational Biology, 2005

A latent variable model for chemogenomic profiling.
Bioinformatics, 2005

Robust design of biological experiments.
Proceedings of the Advances in Neural Information Processing Systems 18 [Neural Information Processing Systems, 2005

Autonomous Mobile Robot Control Based on White Blood Cell Chemotaxis.
Proceedings of the Computational Methods in Systems Biology, International Conference, 2004

The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models.
Bioinformatics, 2003

Motifs and Modules in Cellular Signal Processing: Applications to Microbial Stress Response Pathways.
Proceedings of the 2nd IEEE Computer Society Bioinformatics Conference, 2003

Motifs and modules in cellular signal processing.
Proceedings of the IEEE International Conference on Acoustics, 2002

Recursive Ensemble Mutagenesis: A Combinatorial Optimization Technique for Protein Engineering.
Proceedings of the Parallel Problem Solving from Nature 2, 1992