All Stories

  1. A method for achieving complete microbial genomes and improving bins from metagenomics data

    Article • PLoS Computational Biology, May 2021, PLOS

    Professor Adam P Arkin

  2. Genomewide and Enzymatic Analysis Reveals Efficient D-Galacturonic Acid Metabolism in the Basidiomycete Yeast Rhodosporidium toruloides

    Article • mSystems, December 2019, ASM Journals

    Professor Adam P Arkin

  3. Genome-wide and enzymatic analysis reveals efficient D-galacturonic acid metabolism in the basidiomycete yeast Rhodosporidium toruloides

    Article • June 2019, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

  4. Multiplexed CRISPR-Cas9 based genome editing of Rhodosporidium toruloides

    Article • February 2019, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

  5. Curated BLAST for Genomes

    Article • January 2019, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

  6. Dual-barcoded shotgun expression library sequencing for high-throughput characterization of functional traits in bacteria

    Article • Nature Communications, January 2019, Springer Science + Business Media

    Professor Adam P Arkin

  7. Genetic dissection of interspecific differences in yeast thermotolerance

    Article • Nature Genetics, October 2018, Springer Science + Business Media

    Professor Adam P Arkin

  8. Evaluation of 244,000 synthetic sequences reveals design principles to optimize translation in Escherichia coli

    Article • Nature Biotechnology, September 2018, Springer Science + Business Media

    Professor Adam P Arkin

  9. Dub-seq: dual-barcoded shotgun expression library sequencing for high-throughput characterization of functional traits

    Article • August 2018, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

  10. KBase: The United States Department of Energy Systems Biology Knowledgebase

    Article • Nature Biotechnology, July 2018, Springer Science + Business Media

    Professor Adam P Arkin, Prof Sergei Maslov

  11. Massive Factorial Design Untangles Coding Sequences Determinants Of Translation Efficacy

    Article • October 2017, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

  12. Massive Phenotypic Measurements Reveal Complex Physiological Consequences Of Differential Translation Efficacies

    Article • October 2017, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

  13. Environmental Selection, Dispersal, and Organism Interactions Shape Community Assembly in High-Throughput Enrichment Culturing

    Article • Applied and Environmental Microbiology, August 2017, ASM Journals

    Professor Adam P Arkin

  14. Programming mRNA decay to modulate synthetic circuit resource allocation

    Article • Nature Communications, April 2017, Nature

    Professor Adam P Arkin

  15. The DOE Systems Biology Knowledgebase (KBase)

    Article • December 2016, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

  16. Programming mRNA decay to modulate synthetic circuit resource allocation

    Article • October 2016, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

  17. QTL-guided metabolic engineering of a complex trait

    Article • October 2016, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

  18. A Comparison of the Costs and Benefits of Bacterial Gene Expression

    Article • PLoS ONE, October 2016, PLOS

    Professor Adam P Arkin

  19. Metabolic engineering of the oleaginous yeast Rhodosporidium toruloides IFO0880 for lipid overproduction during high-density fermentation

    Article • Applied Microbiology and Biotechnology, September 2016, Springer Science + Business Media

    Professor Adam P Arkin

  20. Deep Annotation of Protein Function across Diverse Bacteria from Mutant Phenotypes

    Article • August 2016, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

  21. Novel Metal Cation Resistance Systems from Mutant Fitness Analysis of Denitrifying Pseudomonas stutzeri

    Article • Applied and Environmental Microbiology, July 2016, ASM Journals

    Professor Adam P Arkin

  22. Exometabolomics Assisted Design and Validation of Synthetic Obligate Mutualism

    Article • ACS Synthetic Biology, July 2016, American Chemical Society (ACS)

    Professor Adam P Arkin

  23. Rapid and Efficient One-Step Metabolic Pathway Integration in E. coli

    Article • ACS Synthetic Biology, July 2016, American Chemical Society (ACS)

    Professor Adam P Arkin

  24. Rapid and efficient galactose fermentation by engineered Saccharomyces cerevisiae

    Article • Journal of Biotechnology, July 2016, Elsevier

    Professor Adam P Arkin

  25. A Theoretical Lower Bound for Selection on the Expression Levels of Proteins

    Article • Genome Biology and Evolution, June 2016, Oxford University Press (OUP)

    Professor Adam P Arkin

  26. Measurement and modeling of intrinsic transcription terminators

    Article • Nucleic Acids Research, April 2016, Oxford University Press (OUP)

    Professor Adam P Arkin

  27. Transcriptional bursting explains the noise-versus-mean relationship in mRNA and protein levels

    Article • April 2016, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

  28. Gene Amplification on Demand Accelerates Cellobiose Utilization in Engineered Saccharomyces cerevisiae

    Article • Applied and Environmental Microbiology, April 2016, ASM Journals

    Professor Adam P Arkin

  29. Lateral Gene Transfer in a Heavy Metal-Contaminated-Groundwater Microbial Community

    Article • mBio, April 2016, ASM Journals

    Professor Adam P Arkin

  30. A Comparison of the Costs and Benefits of Bacterial Gene Expression

    Article • February 2016, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

  31. Weakly Deleterious Mutations and Low Rates of Recombination Limit the Impact of Natural Selection on Bacterial Genomes

    Article • mBio, December 2015, ASM Journals

    Professor Adam P Arkin

  32. Grand challenges in space synthetic biology

    Article • Journal of The Royal Society Interface, December 2015, Royal Society Publishing

    Professor Adam P Arkin

  33. Genome-Wide Tuning of Protein Expression Levels to Rapidly Engineer Microbial Traits

    Article • ACS Synthetic Biology, November 2015, American Chemical Society (ACS)

    Professor Adam P Arkin

  34. EngineeringRhodosporidium toruloidesfor increased lipid production

    Article • Biotechnology and Bioengineering, November 2015, Wiley

    Professor Adam P Arkin

  35. Complete Genome Sequences of Four Escherichia coli ST95 Isolates from Bloodstream Infections

    Article • Genome Announcements, November 2015, ASM Journals

    Professor Craig M Stephens, Professor Adam P Arkin

  36. A Slow-Release Substrate Stimulates Groundwater Microbial Communities for Long-Term in Situ Cr(VI) Reduction

    Article • Environmental Science & Technology, November 2015, American Chemical Society (ACS)

    Professor Terry C Hazen, Professor Adam P Arkin

  37. Comparative metagenomics reveals impact of contaminants on groundwater microbiomes

    Article • Frontiers in Microbiology, October 2015, Frontiers

    Professor Adam P Arkin, Dr Susannah Green Tringe

  38. The essential gene set of a photosynthetic organism

    Article • Proceedings of the National Academy of Sciences, October 2015, Proceedings of the National Academy of Sciences

    Professor Adam P Arkin

  39. Determining Roles of Accessory Genes in Denitrification by Mutant Fitness Analyses

    Article • Applied and Environmental Microbiology, October 2015, ASM Journals

    Professor Adam P Arkin

  40. Complete Genome Sequence of Pelosinus fermentans JBW45, a Member of a Remarkably Competitive Group of Negativicutes in the Firmicutes ...

    Article • Genome Announcements, September 2015, ASM Journals

    Dr Judy D Wall, Professor Adam P Arkin, Laura B Camilleri, Kara De Leon

  41. A Method to Constrain Genome-Scale Models with 13C Labeling Data

    Article • PLoS Computational Biology, September 2015, PLOS

    Professor Adam P Arkin

  42. Molybdenum Availability Is Key to Nitrate Removal in Contaminated Groundwater Environments

    Article • Applied and Environmental Microbiology, May 2015, ASM Journals

    Professor Terry C Hazen, Professor Adam P Arkin

  43. Complete Genome Sequence of Cupriavidus basilensis 4G11, Isolated from the Oak Ridge Field Research Center Site

    Article • Genome Announcements, May 2015, ASM Journals

    Professor Adam P Arkin

  44. Novel Mechanism for Scavenging of Hypochlorite Involving a Periplasmic Methionine-Rich Peptide and Methionine Sulfoxide Reductase

    Article • mBio, May 2015, ASM Journals

    Professor Adam P Arkin

  45. Rapid Quantification of Mutant Fitness in Diverse Bacteria by Sequencing Randomly Bar-Coded Transposons

    Article • mBio, May 2015, ASM Journals

    Professor Adam P Arkin

  46. Natural Bacterial Communities Serve as Quantitative Geochemical Biosensors

    Article • mBio, May 2015, ASM Journals

    Professor Terry C Hazen, Professor Adam P Arkin

  47. Dynamic Succession of Groundwater Functional Microbial Communities in Response to Emulsified Vegetable Oil Amendment during SustainedIn SituU(VI) Reduction

    Article • Applied and Environmental Microbiology, April 2015, ASM Journals

    Professor Adam P Arkin

  48. Rapid selective sweep of pre-existing polymorphisms and slow fixation of new mutations in experimental evolution of Desulfovibrio vulgaris

    Article • The ISME Journal, April 2015, Nature

    Professor Terry C Hazen, Professor Adam P Arkin

  49. Monofluorophosphate Is a Selective Inhibitor of Respiratory Sulfate-Reducing Microorganisms

    Article • Environmental Science & Technology, March 2015, American Chemical Society (ACS)

    Professor Adam P Arkin

  50. Independence of Nitrate and Nitrite Inhibition of Desulfovibrio vulgaris Hildenborough and Use of Nitrite as a Substrate for Growth

    Article • Environmental Science & Technology, January 2015, American Chemical Society (ACS)

    Professor Adam P Arkin

  51. Pattern formation with a compartmental lateral inhibition system

    Article • December 2014, Institute of Electrical & Electronics Engineers (IEEE)

    Professor Adam P Arkin

  52. Mechanisms of direct inhibition of the respiratory sulfate-reduction pathway by (per)chlorate and nitrate

    Article • The ISME Journal, November 2014, Oxford University Press (OUP)

    Professor Adam P Arkin

  53. Towards synthetic biological approaches to resource utilization on space missions

    Article • Journal of The Royal Society Interface, November 2014, Royal Society Publishing

    Professor Adam P Arkin

  54. The genetic basis of energy conservation in the sulfate-reducing bacterium Desulfovibrio alaskensis G20

    Article • Frontiers in Microbiology, October 2014, Frontiers

    Professor Adam P Arkin

  55. Rex (Encoded by DVU_0916) in Desulfovibrio vulgaris Hildenborough Is a Repressor of Sulfate Adenylyl Transferase and Is Regulated by NADH

    Article • Journal of Bacteriology, October 2014, ASM Journals

    Dr Judy D Wall, Dr Pavel Novichkov, Professor Adam P Arkin

  56. Characterization of Wastewater Treatment Plant Microbial Communities and the Effects of Carbon Sources on Diversity in Laboratory Models

    Article • PLoS ONE, August 2014, PLOS

    Professor Adam P Arkin, Professor Terry C Hazen

  57. Selection of chromosomal DNA libraries using a multiplex CRISPR system

    Article • eLife, August 2014, eLife

    Professor Adam P Arkin

  58. Towards an Informative Mutant Phenotype for Every Bacterial Gene

    Article • Journal of Bacteriology, August 2014, ASM Journals

    Professor Adam P Arkin

  59. Conservation of Transcription Start Sites within Genes across a Bacterial Genus

    Article • mBio, July 2014, ASM Journals

    Professor Adam P Arkin

  60. Interactive XCMS Online: Simplifying Advanced Metabolomic Data Processing and Subsequent Statistical Analyses

    Article • Analytical Chemistry, June 2014, American Chemical Society (ACS)

    Professor Adam P Arkin

  61. Metabolomic data streaming for biology-dependent data acquisition

    Article • Nature Biotechnology, June 2014, Springer Science + Business Media

    Professor Adam P Arkin

  62. Functional Genomics with a Comprehensive Library of Transposon Mutants for the Sulfate-Reducing Bacterium Desulfovibrio alaskensis G20

    Article • mBio, May 2014, ASM Journals

    Professor Adam P Arkin

  63. Avoidance of Truncated Proteins from Unintended Ribosome Binding Sites within Heterologous Protein Coding Sequences

    Article • ACS Synthetic Biology, May 2014, American Chemical Society (ACS)

    Professor Adam P Arkin

  64. Indirect and suboptimal control of gene expression is widespread in bacteria

    Article • Molecular Systems Biology, April 2014, EMBO

    Professor Adam P Arkin

  65. Dissecting a complex chemical stress: chemogenomic profiling of plant hydrolysates

    Article • Molecular Systems Biology, April 2014, EMBO

    Professor Adam P Arkin

  66. Genetic basis for nitrate resistance in Desulfovibrio strains

    Article • Frontiers in Microbiology, April 2014, Frontiers

    Professor Adam P Arkin

  67. A versatile framework for microbial engineering using synthetic non-coding RNAs

    Article • Nature Reviews Microbiology, April 2014, Springer Science + Business Media

    Professor Adam P Arkin

  68. The energy‐conserving electron transfer system used by Desulfovibrio alaskensis strain G20 during pyruvate fermentation involves reduction of endogenously formed fumarate and cytoplasmic and membrane‐bound complexes,...

    Article • Environmental Microbiology, March 2014, Wiley

    Professor Adam P Arkin

  69. Stochasticity, succession, and environmental perturbations in a fluidic ecosystem

    Article • Proceedings of the National Academy of Sciences, February 2014, Proceedings of the National Academy of Sciences

    Professor Terry C Hazen, Professor Adam P Arkin

  70. Transcript level and sequence determinants of protein abundance and noise in Escherichia coli

    Article • Nucleic Acids Research, February 2014, Oxford University Press (OUP)

    Professor Adam P Arkin

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

    Article • Bioinformatics, January 2014, Oxford University Press (OUP)

    Professor Adam P Arkin

  72. Fermentation of hydrolysate detoxified by pervaporation through block copolymer membranes

    Article • Green Chemistry, January 2014, Royal Society of Chemistry

    Professor Adam P Arkin

  73. Hexavalent Chromium Reduction under Fermentative Conditions with Lactate Stimulated Native Microbial Communities

    Article • PLoS ONE, December 2013, PLOS

    Professor Terry C Hazen, Professor Adam P Arkin

  74. Synthetic biology

    Article • Current Opinion in Chemical Biology, December 2013, Elsevier

    Professor Adam P Arkin

  75. A wise consistency: engineering biology for conformity, reliability, predictability

    Article • Current Opinion in Chemical Biology, December 2013, Elsevier

    Professor Adam P Arkin

  76. Changes in microbial dynamics during long-term decomposition in tropical forests

    Article • Soil Biology and Biochemistry, November 2013, Elsevier

    Professor Terry C Hazen, Professor Adam P Arkin

  77. “Replica-Extraction-Transfer” Nanostructure-Initiator Mass Spectrometry Imaging of Acoustically Printed Bacteria

    Article • Analytical Chemistry, October 2013, American Chemical Society (ACS)

    Professor Adam P Arkin

  78. Control of methionine metabolism by the SahR transcriptional regulator in Proteobacteria

    Article • Environmental Microbiology, October 2013, Wiley

    Professor Adam P Arkin, Dr Pavel Novichkov

  79. Flexibility of Syntrophic Enzyme Systems in Desulfovibrio Species Ensures Their Adaptation Capability to Environmental Changes

    Article • Journal of Bacteriology, August 2013, ASM Journals

    Professor Adam P Arkin

  80. StressChip as a High-Throughput Tool for Assessing Microbial Community Responses to Environmental Stresses

    Article • Environmental Science & Technology, August 2013, American Chemical Society (ACS)

    Professor Terry C Hazen, Professor Adam P Arkin

  81. Composability of regulatory sequences controlling transcription and translation in Escherichia coli

    Article • Proceedings of the National Academy of Sciences, August 2013, Proceedings of the National Academy of Sciences

    Professor Adam P Arkin

  82. New Family of Tungstate-Responsive Transcriptional Regulators in Sulfate-Reducing Bacteria

    Article • Journal of Bacteriology, August 2013, ASM Journals

    Dr Pavel Novichkov, Professor Adam P Arkin

  83. Genetic Selection for Context-Dependent Stochastic Phenotypes: Sp1 and TATA Mutations Increase Phenotypic Noise in HIV-1 Gene Expression

    Article • PLoS Computational Biology, July 2013, PLOS

    Professor Adam P Arkin

  84. Effects of Genetic Variation on the E. coli Host-Circuit Interface

    Article • Cell Reports, July 2013, Elsevier

    Professor Adam P Arkin

  85. Characterization of NaCl tolerance in Desulfovibrio vulgaris Hildenborough through experimental evolution

    Article • The ISME Journal, April 2013, Oxford University Press (OUP)

    Professor Terry C Hazen, Professor Adam P Arkin

  86. RegTransBase – a database of regulatory sequences and interactions based on literature: a resource for investigating transcriptional regulation in prokaryotes

    Article • BMC Genomics, April 2013, Springer Science + Business Media

    Professor Adam P Arkin, Dr Pavel Novichkov

  87. Measurement and modeling of intrinsic transcription terminators

    Article • Nucleic Acids Research, March 2013, Oxford University Press (OUP)

    Professor Adam P Arkin

  88. Precise and reliable gene expression via standard transcription and translation initiation elements

    Article • Nature Chemical Biology, March 2013, Springer Science + Business Media

    Professor Adam P Arkin

  89. Quantitative estimation of activity and quality for collections of functional genetic elements

    Article • Nature Chemical Biology, March 2013, Springer Science + Business Media

    Professor Adam P Arkin

  90. Modular Design of a Synthetic Payload Delivery Device

    Article • ACS Synthetic Biology, March 2013, American Chemical Society (ACS)

    Professor Adam P Arkin

  91. Rational and Evolutionary Engineering Approaches Uncover a Small Set of Genetic Changes Efficient for Rapid Xylose Fermentation in Saccharomyces cerevisiae

    Article • PLoS ONE, February 2013, PLOS

    Professor Adam P Arkin

  92. Modeling coagulation activation in trauma patients

    Article • Journal of Critical Care, February 2013, Elsevier

    Professor Adam P Arkin

  93. Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression

    Article • Cell, February 2013, Elsevier

    Professor Adam P Arkin

  94. Metallochaperones Regulate Intracellular Copper Levels

    Article • PLoS Computational Biology, January 2013, PLOS

    Professor Adam P Arkin

  95. From Biological Parts to Circuit Design

    Article • January 2013, Elsevier

    Professor Adam P Arkin

  96. Correction: Global analysis of host response to induction of a latent bacteriophage

    Article • BMC Microbiology, January 2013, Springer Science + Business Media

    Professor Adam P Arkin

  97. RegPrecise 3.0 – A resource for genome-scale exploration of transcriptional regulation in bacteria

    Article • BMC Genomics, January 2013, Springer Science + Business Media

    Professor Adam P Arkin, Dr Pavel Novichkov

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

    Article • Bioinformatics, December 2012, Oxford University Press (OUP)

    Professor Adam P Arkin

  99. Variation among Desulfovibrio Species in Electron Transfer Systems Used for Syntrophic Growth

    Article • Journal of Bacteriology, December 2012, ASM Journals

    Professor Adam P Arkin

  100. metaMicrobesOnline: phylogenomic analysis of microbial communities

    Article • Nucleic Acids Research, November 2012, Oxford University Press (OUP)

    Professor Adam P Arkin

  101. Metabolic Footprinting of Mutant Libraries to Map Metabolite Utilization to Genotype

    Article • ACS Chemical Biology, October 2012, American Chemical Society (ACS)

    Professor Adam P Arkin

  102. Sequestration-based bistability enables tuning of the switching boundaries and design of a latch

    Article • Molecular Systems Biology, October 2012, EMBO

    Professor Adam P Arkin

  103. Transcription Factor Family-Based Reconstruction of Singleton Regulons and Study of the Crp/Fnr, ArsR, and GntR Families in Desulfovibrionales Genomes

    Article • Journal of Bacteriology, October 2012, ASM Journals

    Dr Pavel Novichkov, Professor Adam P Arkin

  104. Engineering robust control of two-component system phosphotransfer using modular scaffolds

    Article • Proceedings of the National Academy of Sciences, October 2012, Proceedings of the National Academy of Sciences

    Professor Adam P Arkin

  105. An adaptor from translational to transcriptional control enables predictable assembly of complex regulation

    Article • Nature Chemical Biology, September 2012, Springer Science + Business Media

    Professor Adam P Arkin

  106. RNA processing enables predictable programming of gene expression

    Article • Nature Biotechnology, September 2012, Springer Science + Business Media

    Professor Adam P Arkin

  107. Draft Genome Sequence of Pelosinus fermentans JBW45, Isolated during In Situ Stimulation for Cr(VI) Reduction

    Article • Journal of Bacteriology, September 2012, ASM Journals

    Professor Adam P Arkin, Laura B Camilleri, Kara De Leon

  108. Draft Genome Sequences for Two Metal-Reducing Pelosinus fermentans Strains Isolated from a Cr(VI)-Contaminated Site and for Type Strain R7

    Article • Journal of Bacteriology, August 2012, ASM Journals

    Professor Adam P Arkin

  109. Deletion of the Desulfovibrio vulgaris Carbon Monoxide Sensor Invokes Global Changes in Transcription

    Article • Journal of Bacteriology, August 2012, ASM Journals

    Professor Adam P Arkin

  110. Functional responses of methanogenic archaea to syntrophic growth

    Article • The ISME Journal, June 2012, Oxford University Press (OUP)

    Professor Adam P Arkin

  111. Manipulation of the carbon storage regulator system for metabolite remodeling and biofuel production in Escherichia coli

    Article • Microbial Cell Factories, June 2012, Springer Science + Business Media

    Professor Adam P Arkin

  112. Contextualizing context for synthetic biology – identifying causes of failure of synthetic biological systems

    Article • Biotechnology Journal, May 2012, Wiley

    Professor Adam P Arkin

  113. Transcriptomic and proteomic analyses of Desulfovibrio vulgaris biofilms: Carbon and energy flow contribute to the distinct biofilm growth state

    Article • BMC Genomics, April 2012, Springer Science + Business Media

    Professor Adam P Arkin

  114. Rationally designed families of orthogonal RNA regulators of translation

    Article • Nature Chemical Biology, March 2012, Springer Science + Business Media

    Professor Adam P Arkin

  115. Engineering naturally occurring trans-acting non-coding RNAs to sense molecular signals

    Article • Nucleic Acids Research, March 2012, Oxford University Press (OUP)

    Professor Adam P Arkin

  116. Preface

    Article • January 2012, Elsevier

    Professor Adam P Arkin

  117. Chromatin accessibility at the HIV LTR promoter sets a threshold for NF-κB mediated viral gene expression

    Article • Integrative Biology, January 2012, Oxford University Press (OUP)

    Professor Adam P Arkin

  118. Functional Characterization of Crp/Fnr-Type Global Transcriptional Regulators in Desulfovibrio vulgaris Hildenborough

    Article • Applied and Environmental Microbiology, December 2011, ASM Journals

    Professor Terry C Hazen, Professor Adam P Arkin

  119. Evidence-Based Annotation of Gene Function in Shewanella oneidensis MR-1 Using Genome-Wide Fitness Profiling across 121 Conditions

    Article • PLoS Genetics, November 2011, PLOS

    Professor Adam P Arkin

  120. Systematic mapping of two component response regulators to gene targets in a model sulfate reducing bacterium

    Article • Genome Biology, October 2011, Springer Science + Business Media

    Professor Adam P Arkin

  121. Toward rational design of bacterial genomes

    Article • Current Opinion in Microbiology, October 2011, Elsevier

    Professor Adam P Arkin

  122. Varying virulence: epigenetic control of expression noise and disease processes

    Article • Trends in Biotechnology, October 2011, Elsevier

    Professor Adam P Arkin

  123. Complete genome sequence of “Enterobacter lignolyticus” SCF1

    Article • Standards in Genomic Sciences, September 2011, Springer Science + Business Media

    Professor Terry C Hazen, Professor Adam P Arkin, Dr Nikos C Kyrpides

  124. Towards a Rigorous Network of Protein-Protein Interactions of the Model Sulfate Reducer Desulfovibrio vulgaris Hildenborough

    Article • PLoS ONE, June 2011, PLOS

    Professor Terry C Hazen, Professor Adam P Arkin

  125. Joint DAC/IWBDA special session design and synthesis of biological circuits

    Article • June 2011, ACM (Association for Computing Machinery)

    Professor Adam P Arkin

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

    Article • June 2011, Institute of Electrical & Electronics Engineers (IEEE)

    Professor Adam P Arkin

  127. How sulphate-reducing microorganisms cope with stress: lessons from systems biology

    Article • Nature Reviews Microbiology, May 2011, Springer Science + Business Media

    Professor Terry C Hazen, Professor Adam P Arkin

  128. Design and Construction of a Double Inversion Recombination Switch for Heritable Sequential Genetic Memory

    Article • April 2011, Taylor & Francis

    Professor Adam P Arkin

  129. The hunt for the biological transistor

    Article • IEEE Spectrum, March 2011, Institute of Electrical & Electronics Engineers (IEEE)

    Professor Adam P Arkin

  130. Network News: Innovations in 21st Century Systems Biology

    Article • Cell, March 2011, Elsevier

    Professor Adam P Arkin

  131. Regulation of transcription by unnatural amino acids

    Article • Nature Biotechnology, January 2011, Springer Science + Business Media

    Professor Adam P Arkin

  132. Microfluidic fluorescence in situ hybridization and flow cytometry (μFlowFISH)

    Article • Lab on a Chip, January 2011, Royal Society of Chemistry

    Professor Terry C Hazen, Professor Adam P Arkin

  133. Simulated niche partitioning by bacteria

    Article • January 2011, Springer Science + Business Media

    Professor Adam P Arkin

  134. Meta-analysis of global metabolomics and proteomics data to link alterations with phenotype

    Article • Spectroscopy An International Journal, January 2011, Hindawi Publishing Corporation

    Professor Adam P Arkin

  135. Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus

    Article • BMC Genomics, January 2011, Springer Science + Business Media

    Professor Adam P Arkin, Dr Pavel Novichkov

  136. Development of a Low Bias Method for Characterizing Viral Populations Using Next Generation Sequencing Technology

    Article • PLoS ONE, October 2010, PLOS

    Professor Adam P Arkin

  137. HIV Promoter Integration Site Primarily Modulates Transcriptional Burst Size Rather Than Frequency

    Article • PLoS Computational Biology, September 2010, PLOS

    Professor Adam P Arkin

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

    Article • September 2010, Institute of Electrical & Electronics Engineers (IEEE)

    Professor Adam P Arkin

  139. Computational Models of HIV-1 Resistance to Gene Therapy Elucidate Therapy Design Principles

    Article • PLoS Computational Biology, August 2010, PLOS

    Professor Adam P Arkin

  140. Conservation of Modules but not Phenotype in Bacterial Response to Environmental Stress

    Article • May 2010, Office of Scientific and Technical Information (OSTI)

    Professor Terry C Hazen, Professor Adam P Arkin

  141. Revisiting Modes of energy generation in sulfate reducing bacteria

    Article • May 2010, Office of Scientific and Technical Information (OSTI)

    Professor Terry C Hazen, Professor Adam P Arkin

  142. Development of a Model, Metal-reducing Microbial Community for a System Biology Level Assessment of Desulfovibrio vulgaris as part of a Community

    Article • May 2010, Office of Scientific and Technical Information (OSTI)

    Professor Terry C Hazen, Professor Adam P Arkin

  143. Genetic Adaptation to Salt Stress in Experimental Evolution of Desulfovibrio vulgaris Hildenborough

    Article • May 2010, Office of Scientific and Technical Information (OSTI)

    Professor Terry C Hazen, Professor Adam P Arkin

  144. Identification of Small RNAs in Desulfovibrio vulgaris Hildenborough

    Article • May 2010, Office of Scientific and Technical Information (OSTI)

    Professor Adam P Arkin

  145. Hydrogen peroxide‐induced oxidative stress responses in Desulfovibrio vulgaris Hildenborough

    Article • Environmental Microbiology, May 2010, Wiley

    Professor Terry C Hazen, Professor Adam P Arkin

  146. Impact of elevated nitrate on sulfate-reducing bacteria: a comparative Study of Desulfovibrio vulgaris

    Article • The ISME Journal, May 2010, Oxford University Press (OUP)

    Professor Terry C Hazen, Professor Adam P Arkin

  147. Microbial Community Dynamics of Lactate Enriched Hanford Groundwaters

    Article • May 2010, Office of Scientific and Technical Information (OSTI)

    Professor Terry C Hazen, Professor Adam P Arkin

  148. Detailed Simulations of Cell Biology with Smoldyn 2.1

    Article • PLoS Computational Biology, March 2010, PLOS

    Professor Adam P Arkin

  149. FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

    Article • PLoS ONE, March 2010, PLOS

    Professor Adam P Arkin

  150. BglBricks: A flexible standard for biological part assembly

    Article • Journal of Biological Engineering, January 2010, Springer Science + Business Media

    Professor Adam P Arkin

  151. Contribution of mobile genetic elements to Desulfovibrio vulgaris genome plasticity

    Article • Environmental Microbiology, September 2009, Wiley

    Professor Terry C Hazen, Professor Adam P Arkin

  152. Invariability of central metabolic flux distribution in Shewanella oneidensis MR‐1 under environmental or genetic perturbations

    Article • Biotechnology Progress, September 2009, Wiley

    Professor Adam P Arkin

  153. Novel insights into iron metabolism by integrating deletome and transcriptome analysis in an iron deficiency model of the yeast Saccharomyces cerevisiae

    Article • BMC Genomics, March 2009, Springer Science + Business Media

    Professor Corey Nislow, Professor Adam P Arkin

  154. Control of Stochastic Gene Expression by Host Factors at the HIV Promoter

    Article • PLoS Pathogens, January 2009, PLOS

    Professor Adam P Arkin

  155. Shape, Size, and Robustness: Feasible Regions in the Parameter Space of Biochemical Networks

    Article • PLoS Computational Biology, January 2009, PLOS

    Professor Adam P Arkin

  156. Stochastic Models of Biological Processes

    Article • January 2009, Springer Science + Business Media

    Professor Adam P Arkin

  157. Evolution, ecology and the engineered organism: lessons for synthetic biology

    Article • Genome Biology, January 2009, Springer Science + Business Media

    Professor Adam P Arkin

  158. Snapshot of iron response in Shewanella oneidensis by gene network reconstruction

    Article • BMC Genomics, January 2009, Springer Science + Business Media

    Professor Adam P Arkin

  159. Toward scalable parts families for predictable design of biological circuits

    Article • Current Opinion in Microbiology, December 2008, Elsevier

    Professor Adam P Arkin

  160. Metabolic flux analysis of Shewanella spp. reveals evolutionary robustness in central carbon metabolism

    Article • Biotechnology and Bioengineering, November 2008, Wiley

    Professor Adam P Arkin

  161. FastBLAST: Homology Relationships for Millions of Proteins

    Article • PLoS ONE, October 2008, PLOS

    Professor Adam P Arkin

  162. A Dual Receptor Crosstalk Model of G-Protein-Coupled Signal Transduction

    Article • PLoS Computational Biology, September 2008, PLOS

    Professor Adam P Arkin

  163. Design and Construction of a Double Inversion Recombination Switch for Heritable Sequential Genetic Memory

    Article • PLoS ONE, July 2008, PLOS

    Professor Adam P Arkin

  164. Setting the standard in synthetic biology

    Article • Nature Biotechnology, July 2008, Springer Science + Business Media

    Professor Adam P Arkin

  165. Memory in Microbes: Quantifying History-Dependent Behavior in a Bacterium

    Article • PLoS ONE, February 2008, PLOS

    Professor Adam P Arkin

  166. Horizontal gene transfer and the evolution of transcriptional regulation in Escherichia coli

    Article • Genome Biology, January 2008, Springer Science + Business Media

    Professor Adam P Arkin

  167. Appreciation of the Machinations of the Blind Watchmaker

    Article • IEEE Transactions on Automatic Control, January 2008, Institute of Electrical & Electronics Engineers (IEEE)

    Professor Adam P Arkin

  168. Genetics and Genomics of Sulfate Respiration in Desulfovibrio

    Article • January 2008, Springer Science + Business Media

    Professor Adam P Arkin

  169. Processing Single-Cell Single-Molecule Genomic Information: New Methods for New Data

    Article • November 2007, Institute of Electrical & Electronics Engineers (IEEE)

    Professor Adam P Arkin

  170. Identification of Genes Involved in the Toxic Response of Saccharomyces cerevisiae against Iron and Copper Overload by Parallel Analysis of Deletion Mutants

    Article • Toxicological Sciences, October 2007, Oxford University Press (OUP)

    Professor Adam P Arkin

  171. Response of Desulfovibrio vulgaris to Alkaline Stress

    Article • Journal of Bacteriology, October 2007, ASM Journals

    Professor Adam P Arkin

  172. Orthologous Transcription Factors in Bacteria Have Different Functions and Regulate Different Genes

    Article • PLoS Computational Biology, September 2007, PLOS

    Professor Adam P Arkin

  173. A Mechanical Explanation for Cytoskeletal Rings and Helices in Bacteria

    Article • Biophysical Journal, September 2007, Elsevier

    Professor Adam P Arkin

  174. Global analysis of host response to induction of a latent bacteriophage

    Article • BMC Microbiology, August 2007, Springer Science + Business Media

    Professor Adam P Arkin

  175. Environmental signal integration by a modular AND gate

    Article • Molecular Systems Biology, August 2007, EMBO

    Professor Adam P Arkin

  176. Identification of Genes Involved in the Toxic Response of Saccharomyces cerevisiae against Iron and Copper Overload by Parallel Analysis of Deletion Mutants

    Article • Toxicological Sciences, August 2007, Oxford University Press (OUP)

    Professor Adam P Arkin

  177. Analysis of a Ferric Uptake Regulator (Fur) Mutant of Desulfovibrio vulgaris Hildenborough

    Article • Applied and Environmental Microbiology, July 2007, ASM Journals

    Professor Terry C Hazen, Professor Adam P Arkin

  178. Systems Biology: A Switch for Sex

    Article • Current Biology, June 2007, Elsevier

    Professor Adam P Arkin

  179. Cell-Wide Responses to Low-Oxygen Exposure in Desulfovibrio vulgaris Hildenborough

    Article • Journal of Bacteriology, June 2007, ASM Journals

    Professor Adam P Arkin

  180. Efficient stochastic sensitivity analysis of discrete event systems

    Article • Journal of Computational Physics, February 2007, Elsevier

    Professor Adam P Arkin

  181. RegTransBase--a database of regulatory sequences and interactions in a wide range of prokaryotic genomes

    Article • Nucleic Acids Research, January 2007, Oxford University Press (OUP)

    Professor Adam P Arkin

  182. Systems Biology

    Article • January 2007, Springer Science + Business Media

    Professor Adam P Arkin

  183. From Fluctuations to Phenotypes: The Physiology of Noise

    Article • Science s STKE, December 2006, American Association for the Advancement of Science

    Professor Adam P Arkin

  184. Deviant effects in molecular reaction pathways

    Article • Nature Biotechnology, October 2006, Springer Science + Business Media

    Professor Adam P Arkin

  185. Morphology matters in immune cell chemotaxis: membrane asymmetry affects amplification

    Article • Physical Biology, September 2006, Institute of Physics Publishing

    Professor Adam P Arkin

  186. Simulating cell biology

    Article • Current Biology, July 2006, Elsevier

    Professor Adam P Arkin

  187. The Life-Cycle of Operons

    Article • PLoS Genetics, June 2006, PLOS

    Professor Adam P Arkin

  188. Genomics for environmental microbiology

    Article • Current Opinion in Biotechnology, June 2006, Elsevier

    Professor Adam P Arkin

  189. Salt Stress in Desulfovibrio vulgaris Hildenborough: an Integrated Genomics Approach

    Article • Journal of Bacteriology, June 2006, ASM Journals

    Professor Adam P Arkin

  190. Energetic Consequences of Nitrite Stress in Desulfovibrio vulgaris Hildenborough, Inferred from Global Transcriptional Analysis

    Article • Applied and Environmental Microbiology, June 2006, ASM Journals

    Professor Terry C Hazen, Professor Adam P Arkin

  191. The Histidine Operon Is Ancient

    Article • Journal of Molecular Evolution, April 2006, Springer Science + Business Media

    Professor Adam P Arkin

  192. A tightly regulated inducible expression system utilizing the fim inversion recombination switch

    Article • Biotechnology and Bioengineering, March 2006, Wiley

    Professor Adam P Arkin

  193. Model Discrimination Using Data Collaboration

    Article • The Journal of Physical Chemistry A, March 2006, American Chemical Society (ACS)

    Professor Adam P Arkin

  194. Global Analysis of Heat Shock Response in Desulfovibrio vulgaris Hildenborough

    Article • Journal of Bacteriology, March 2006, ASM Journals

    Professor Adam P Arkin

  195. Transcriptome Profiling of Shewanella oneidensis Gene Expression following Exposure to Acidic and Alkaline pH

    Article • Journal of Bacteriology, February 2006, ASM Journals

    Professor Adam P Arkin

  196. Correction: The Life-Cycle of Operons

    Article • PLoS Genetics, January 2006, PLOS

    Professor Adam P Arkin

  197. Automated Abstraction Methodology for Genetic Regulatory Networks

    Article • January 2006, Springer Science + Business Media

    Professor Adam P Arkin

  198. Environmentally Controlled Invasion of Cancer Cells by Engineered Bacteria

    Article • Journal of Molecular Biology, January 2006, Elsevier

    Professor Adam P Arkin

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

    Article • Multiscale Modeling and Simulation, January 2006, Society for Industrial & Applied Mathematics (SIAM)

    Professor Adam P Arkin

  200. The Evolution of Two-Component Systems in Bacteria Reveals Different Strategies for Niche Adaptation

    Article • PLoS Computational Biology, January 2006, PLOS

    Professor Adam P Arkin

  201. Cellular Response of Shewanella oneidensis to Strontium Stress

    Article • Applied and Environmental Microbiology, January 2006, ASM Journals

    Professor Adam P Arkin

  202. Article • Genome Biology, January 2006, Springer Science + Business Media

    Professor Adam P Arkin

  203. Dissimilatory Metabolism of Nitrogen Oxides in Bacteria: Comparative Reconstruction of Transcriptional Networks

    Article • PLoS Computational Biology, October 2005, PLOS

    Professor Adam P Arkin

  204. Genome-Wide Requirements for Resistance to Functionally Distinct DNA-Damaging Agents

    Article • PLoS Genetics, August 2005, PLOS

    Professor Corey Nislow, Professor Adam P Arkin

  205. Numerical computation of diffusion on a surface

    Article • Proceedings of the National Academy of Sciences, August 2005, Proceedings of the National Academy of Sciences

    Professor Adam P Arkin

  206. Phosphatase localization in bacterial chemotaxis: divergent mechanisms, convergent principles

    Article • Physical Biology, July 2005, Institute of Physics Publishing

    Professor Adam P Arkin

  207. Stochastic Gene Expression in a Lentiviral Positive-Feedback Loop: HIV-1 Tat Fluctuations Drive Phenotypic Diversity

    Article • Cell, July 2005, Elsevier

    Professor Adam P Arkin

  208. The MicrobesOnline Web site for comparative genomics

    Article • Genome Research, June 2005, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

  209. Interruptions in gene expression drive highly expressed operons to the leading strand of DNA replication

    Article • Nucleic Acids Research, June 2005, Oxford University Press (OUP)

    Professor Adam P Arkin

  210. A latent variable model for chemogenomic profiling

    Article • Bioinformatics, May 2005, Oxford University Press (OUP)

    Professor Adam P Arkin

  211. Operon formation is driven by co-regulation and not by horizontal gene transfer

    Article • Genome Research, May 2005, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

  212. Diversity in times of adversity: probabilistic strategies in microbial survival games

    Article • Journal of Theoretical Biology, May 2005, Elsevier

    Professor Adam P Arkin

  213. A microbial modified prisoner's dilemma game: how frequency-dependent selection can lead to random phase variation

    Article • Journal of Theoretical Biology, May 2005, Elsevier

    Professor Adam P Arkin

  214. Transcriptome Analysis of Shewanella oneidensis MR-1 in Response to Elevated Salt Conditions

    Article • Journal of Bacteriology, April 2005, ASM Journals

    Professor Adam P Arkin

  215. A novel method for accurate operon predictions in all sequenced prokaryotes

    Article • Nucleic Acids Research, February 2005, Oxford University Press (OUP)

    Professor Adam P Arkin

  216. Stochastic amplification and signaling in enzymatic futile cycles through noise-induced bistability with oscillations

    Article • Proceedings of the National Academy of Sciences, February 2005, Proceedings of the National Academy of Sciences

    Professor Adam P Arkin

  217. Dissimilatory Metabolism of Nitrogen Oxides in Bacteria: Comparative Reconstruction of Transcriptional Networks

    Article • PLoS Computational Biology, January 2005, PLOS

    Professor Adam P Arkin

  218. Autonomous Mobile Robot Control Based on White Blood Cell Chemotaxis

    Article • January 2005, Springer Science + Business Media

    Professor Adam P Arkin

  219. Global Transcriptome Analysis of the Heat Shock Response of Shewanella oneidensis

    Article • Journal of Bacteriology, November 2004, ASM Journals

    Professor Adam P Arkin

  220. An Allosteric Model for Transmembrane Signaling in Bacterial Chemotaxis

    Article • Journal of Molecular Biology, October 2004, Elsevier

    Professor Adam P Arkin

  221. The old switcheroo: new tricks revealed in ‘Phage Lambda Revisited’

    Article • Current Biology, July 2004, Elsevier

    Professor Adam P Arkin

  222. Response experiments for nonlinear systems with application to reaction kinetics and genetics

    Article • Proceedings of the National Academy of Sciences, April 2004, Proceedings of the National Academy of Sciences

    Professor Adam P Arkin

  223. The evolution of genetic regulatory systems in bacteria

    Article • Nature Reviews Genetics, March 2004, Springer Science + Business Media

    Professor Adam P Arkin

  224. Design and Diversity in Bacterial Chemotaxis: A Comparative Study in Escherichia coli and Bacillus subtilis

    Article • PLoS Biology, February 2004, PLOS

    Professor Adam P Arkin

  225. Data Standards for the Genomes to Life Program

    Article • January 2004, Office of Scientific and Technical Information (OSTI)

    Professor Adam P Arkin

  226. Theoretical Design of a Gene Therapy To Prevent AIDS but Not Human Immunodeficiency Virus Type 1 Infection

    Article • Journal of Virology, September 2003, ASM Journals

    Professor Adam P Arkin

  227. Motifs, modules and games in bacteria

    Article • Current Opinion in Microbiology, April 2003, Elsevier

    Professor Adam P Arkin

  228. Biological networks

    Article • Current Opinion in Structural Biology, April 2003, Elsevier

    Professor Adam P Arkin

  229. Stochastic chemical kinetics and the quasi-steady-state assumption: Application to the Gillespie algorithm

    Article • The Journal of Chemical Physics, March 2003, American Institute of Physics

    Professor Adam P Arkin

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

    Article • Bioinformatics, March 2003, Oxford University Press (OUP)

    Professor Adam P Arkin

  231. Erratum: Control, exploitation and tolerance of intracellular noise

    Article • Nature, January 2003, Springer Science + Business Media

    Professor Adam P Arkin

  232. Overview of the Alliance for Cellular Signaling

    Article • Nature, December 2002, Springer Science + Business Media

    Professor Adam P Arkin

  233. Control, exploitation and tolerance of intracellular noise

    Article • Nature, November 2002, Springer Science + Business Media

    Professor Adam P Arkin

  234. Signal Processing by Simple Chemical Systems

    Article • The Journal of Physical Chemistry A, October 2002, American Chemical Society (ACS)

    Professor Adam P Arkin

  235. GENETIC“CODE”: Representations and Dynamical Models of Genetic Components and Networks

    Article • Annual Review of Genomics and Human Genetics, September 2002, Annual Reviews

    Professor Adam P Arkin

  236. Functional profiling of the Saccharomyces cerevisiae genome

    Article • Nature, July 2002, Nature

    Professor Adam P Arkin, Professor David J. Garfinkel

  237. Motifs and modules in cellular signal processing

    Article • May 2002, Institute of Electrical & Electronics Engineers (IEEE)

    Professor Adam P Arkin

  238. Fifteen Minutes of fim : Control of Type 1 Pili Expression in E. coli

    Article • OMICS A Journal of Integrative Biology, January 2002, Mary Ann Liebert Inc

    Professor Adam P Arkin

  239. Motifs and modules in cellular signal processing

    Article • January 2002, Institute of Electrical & Electronics Engineers (IEEE)

    Professor Adam P Arkin

  240. Synthetic cell biology

    Article • Current Opinion in Biotechnology, December 2001, Elsevier

    Professor Adam P Arkin

  241. Control Motifs for Intracellular Regulatory Networks*

    Article • Annual Review of Biomedical Engineering, August 2001, Annual Reviews

    Professor Adam P Arkin

  242. On the deduction of chemical reaction pathways from measurements of time series of concentrations

    Article • Chaos An Interdisciplinary Journal of Nonlinear Science, March 2001, American Institute of Physics

    Professor Adam P Arkin

  243. Signal processing by biochemical reaction networks

    Article • May 2000, Cambridge University Press

    Professor Adam P Arkin

  244. Gene regulation: Towards a circuit engineering discipline

    Article • Current Biology, April 2000, Elsevier

    Professor Adam P Arkin

  245. It’s a noisy business! Genetic regulation at the nanomolar scale

    Article • Trends in Genetics, February 1999, Elsevier

    Professor Adam P Arkin

  246. SIMULATION OF PROKARYOTIC GENETIC CIRCUITS

    Article • Annual Review of Biophysics and Biomolecular Structure, June 1998, Annual Reviews

    Professor Adam P Arkin

  247. Steady-State Measurements on the Fructose 6-Phosphate/Fructose 1,6-Bisphosphate Interconversion Cycle

    Article • The Journal of Physical Chemistry B, May 1997, American Chemical Society (ACS)

    Professor Adam P Arkin

  248. Experimental Evidence for Turing Structures

    Article • The Journal of Physical Chemistry B, June 1995, American Chemical Society (ACS)

    Professor Adam P Arkin

  249. Statistical Construction of Chemical Reaction Mechanisms from Measured Time-Series

    Article • The Journal of Physical Chemistry B, January 1995, American Chemical Society (ACS)

    Professor Adam P Arkin

  250. Digital Imaging Spectroscopy

    Article • January 1993, Elsevier

    Professor Adam P Arkin

  251. Optimizing Nucleotide Mixtures to Encode Specific Subsets of Amino Acids for Semi-Random Mutagenesis

    Article • Nature Biotechnology, March 1992, Springer Science + Business Media

    Professor Adam P Arkin

  252. Applications of Imaging Spectroscopy in Molecular Biology II. Colony Screening Based on Absorption Spectra

    Article • Nature Biotechnology, August 1990, Springer Science + Business Media

    Professor Adam P Arkin

  253. Modeling and Network Organization

    Article • Springer Science + Business Media

    Professor Adam P Arkin

  254. Data and Databases

    Article • Springer Science + Business Media

    Professor Adam P Arkin

  255. Adam Arkin at the 2012 DOE JGI Genomics of Energy & Environment Meeting

    Article • SciVee, Inc

    Professor Adam P Arkin

  256. Motifs and modules in cellular signal processing: applications to microbial stress response pathways

    Article • Institute of Electrical & Electronics Engineers (IEEE)

    Professor Adam P Arkin

  257. Playing practical games with bacteria and viruses: exploring the molecular mechanisms behind clever cellular stratagems

    Article • Institute of Electrical & Electronics Engineers (IEEE)

    Professor Adam P Arkin