All Stories

  1. Single-cell carbon storage dynamics drive conditional fitness in microbes

    Article • April 2026, openRxiv

    Professor Adam P Arkin

  2. The WalRK two-component system in Streptococcus pneumoniae ensures robustness of secondary wall polymer attachment

    Article • March 2026, openRxiv

    Professor Adam P Arkin

  3. Niche exclusion of a lung pathogen in mice with designed probiotic communities

    Article • December 2025, eLife

    Professor Adam P Arkin

  4. Niche exclusion of a lung pathogen in mice with designed probiotic communities

    Article • December 2025, eLife

    Professor Adam P Arkin

  5. Construction of a randomly barcoded insertional mutant library in the filamentous fungus Trichoderma atroviride

    Article • December 2025, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

  6. Phylogeny-agnostic strain-level prediction of phage-host interactions from genomes

    Article • December 2025, Springer Science + Business Media

    Professor Adam P Arkin

  7. Droplet-based Random Barcode Transposon-site Sequencing (Droplet RB-TnSeq) to characterize phage-host interactions

    Article • September 2025, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

  8. Dual transposon sequencing profiles the genetic interaction landscape in bacteria

    Article • Science, September 2025, American Association for the Advancement of Science

    Professor Adam P Arkin

  9. Sediment and groundwater metagenomes from subsurface microbial communities from the Oak Ridge National Laboratory Oak Ridge Reservation, Oak Ridge, Tennessee, USA

    Article • Microbiology Resource Announcements, June 2025, ASM Journals

    Professor Adam P Arkin

  10. Novel origin of replication for environmentally isolated Pantoea strain enables expression of heterologous proteins, pathways and products

    Article • May 2025, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

  11. Modest functional diversity decline and pronounced composition shifts of microbial communities in a mixed waste-contaminated aquifer

    Article • Microbiome, April 2025, Springer Science + Business Media

    Professor Adam P Arkin

  12. Modified PowerMax Soil Kit Protocol for DNA Extraction from Sediment or Water Filters v1

    Article • March 2025, Springer Science + Business Media

    Professor Adam P Arkin

  13. Lactuchelins: New lipopeptide siderophores from Pseudomonas lactucae inhibit Xanthomonas campestris pv.campestris 8004

    Article • February 2025, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

  14. Bridging the gap: pathway programs for inclusion and persistence in microbiology

    Article • Trends in Microbiology, February 2025, Elsevier

    Professor Adam P Arkin

  15. Emergence and disruption of cooperativity in a denitrifying microbial community

    Article • The ISME Journal, January 2025, Oxford University Press (OUP)

    Professor Adam P Arkin

  16. Modest functional diversity decline and pronounced composition shifts of microbial communities in a uranium-contaminated aquifer

    Article • December 2024, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

  17. Improving the annotation of amino acid biosynthesis pathways: GapMind 2024

    Article • October 2024, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

  18. Acetaminophen production in the edible, filamentous cyanobacterium Arthrospira platensis

    Article • Biotechnology and Bioengineering, October 2024, Wiley

    Professor Adam P Arkin

  19. High-throughput protein characterization by complementation using DNA barcoded fragment libraries

    Article • Molecular Systems Biology, October 2024, Springer Science + Business Media

    Professor Adam P Arkin

  20. Metabolic alterations in Crohn’s disease: A Systematic Review

    Article • October 2024, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

  21. Nitrogen accountancy in space agriculture

    Article • npj Microgravity, September 2024, Springer Science + Business Media

    Professor Adam P Arkin

  22. Dual transposon sequencing (Dual Tn-seq) to probe genome-wide genetic interactions

    Article • September 2024, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

  23. Potential applications of microbial genomics in nuclear non-proliferation

    Article • Frontiers in Microbiology, September 2024, Frontiers

    Professor Adam P Arkin

  24. High-throughput genetics enables identification of nutrient utilization and accessory energy metabolism genes in a model methanogen

    Article • mBio, September 2024, ASM Journals

    Professor Adam P Arkin

  25. Barcoded overexpression screens in gut Bacteroidales identify genes with roles in carbon utilization and stress resistance

    Article • Nature Communications, August 2024, Springer Science + Business Media

    Professor Adam P Arkin

  26. Complementation, Selection Assays (Coaux-Seq) v1

    Article • July 2024, ZappyLab, Inc.

    Professor Adam P Arkin

  27. Genomic Fragment Library Generation (Coaux-Seq) v1

    Article • July 2024, ZappyLab, Inc.

    Professor Adam P Arkin

  28. Genomic and environmental controls on Castellaniella biogeography in an anthropogenically disturbed subsurface

    Article • Environmental Microbiome, April 2024, Springer Science + Business Media

    Professor Adam P Arkin

  29. Interactive Tools for Functional Annotation of Bacterial Genomes

    Article • April 2024, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

  30. Contribution of Microorganisms with the Clade II Nitrous Oxide Reductase to Suppression of Surface Emissions of Nitrous Oxide

    Article • Environmental Science & Technology, April 2024, American Chemical Society (ACS)

    Professor Adam P Arkin

  31. A fast comparative genome browser for diverse bacteria and archaea

    Article • PLOS One, April 2024, PLOS

    Professor Adam P Arkin

  32. High-throughput genetics enables identification of nutrient utilization and accessory energy metabolism genes in a model methanogen

    Article • March 2024, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

  33. Assessment of Genome Interpretation,for computational genetic variant interpretation methods

    Article • February 2024, Springer Science + Business Media

    Dr Peter K Rogan, Professor Adam P Arkin

  34. Niche exclusion of a lung pathogen in mice with designed probiotic communities

    Article • February 2024, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

  35. Domains of life sciences in spacefaring: what, where, and how to get involved

    Article • npj Microgravity, January 2024, Springer Science + Business Media

    Professor Adam P Arkin

  36. A bacterial sensor taxonomy across earth ecosystems for machine learning applications

    Article • mSystems, January 2024, ASM Journals

    Professor Adam P Arkin

  37. Environmental stress mediates groundwater microbial community assembly

    Article • Nature Microbiology, January 2024, Springer Science + Business Media

    Professor Jianjun Wang, Professor Adam P Arkin

  38. Fitness factors impacting survival of a subsurface bacterium in contaminated groundwater

    Article • The ISME Journal, January 2024, Oxford University Press (OUP)

    Professor Adam P Arkin

  39. Interactive tools for functional annotation of bacterial genomes

    Article • Database, January 2024, Oxford University Press (OUP)

    Professor Adam P Arkin

  40. Mixed waste contamination selects for a mobile genetic element population enriched in multiple heavy metal resistance genes

    Article • ISME Communications, January 2024, Oxford University Press (OUP)

    Professor Adam P Arkin

  41. Molecular mechanisms and environmental adaptations of flagellar loss and biofilm growth of Rhodanobacter under environmental stress

    Article • The ISME Journal, January 2024, Oxford University Press (OUP)

    Professor Adam P Arkin

  42. Systematic and scalable genome-wide essentiality mapping to identify nonessential genes in phages

    Article • PLoS Biology, December 2023, PLOS

    Professor Adam P Arkin

  43. Mixed nitrate and metal contamination influences operational speciation of toxic and essential elements

    Article • Environmental Pollution, December 2023, Elsevier

    Professor Adam P Arkin

  44. Mixed Waste Contamination Selects for a Mobile Genetic Element Population Enriched in Multiple Heavy Metal Resistance Genes

    Article • November 2023, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

  45. Evaluating E. coli genome‐scale metabolic model accuracy with high‐throughput mutant fitness data

    Article • Molecular Systems Biology, October 2023, Springer Science + Business Media

    Professor Adam P Arkin

  46. ModelSEED v2: High-throughput genome-scale metabolic model reconstruction with enhanced energy biosynthesis pathway prediction

    Article • October 2023, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

  47. Eliminating genes for a two‐component system increases PHB productivity in Cupriavidus basilensis 4G11 under PHB suppressing, nonstress conditions

    Article • Biotechnology and Bioengineering, August 2023, Wiley

    Professor Adam P Arkin

  48. A fast comparative genome browser for diverse bacteria and archaea

    Article • August 2023, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

  49. Geochemical constraints on bacteriophage infectivity in terrestrial environments

    Article • ISME Communications, August 2023, Oxford University Press (OUP)

    Professor Adam P Arkin

  50. Distinct Depth-Discrete Profiles of Microbial Communities and Geochemical Insights in the Subsurface Critical Zone

    Article • Applied and Environmental Microbiology, June 2023, ASM Journals

    Professor Adam P Arkin

  51. Genome-wide CRISPRi knockdown to map gene essentiality landscape in coliphages λ and P1

    Article • May 2023, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

  52. Microbial biomanufacturing for space-exploration—what to take and when to make

    Article • Nature Communications, April 2023, Springer Science + Business Media

    Professor Adam P Arkin

  53. Engineering osmolysis susceptibility in Cupriavidus necator and Escherichia coli for recovery of intracellular products

    Article • Microbial Cell Factories, April 2023, Springer Science + Business Media

    Professor Adam P Arkin

  54. Geochemical constraints on bacteriophage infectivity in terrestrial environments

    Article • April 2023, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

  55. Large-scale genetic characterization of the model sulfate-reducing bacterium, Desulfovibrio vulgaris Hildenborough

    Article • Frontiers in Microbiology, March 2023, Frontiers

    Professor Adam P Arkin

  56. Many Families of Lids for TonB-dependent Transporters inBacteroides

    Article • March 2023, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

  57. Multicopy suppressor screens reveal convergent evolution of single-gene lysis proteins

    Article • Nature Chemical Biology, February 2023, Springer Science + Business Media

    Professor Adam P Arkin

  58. Quantifying the local adaptive landscape of a nascent bacterial community

    Article • Nature Communications, January 2023, Springer Science + Business Media

    Professor Adam P Arkin

  59. Critical assessment ofE. coligenome-scale metabolic model with high-throughput mutant fitness data

    Article • January 2023, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

  60. Data‐driven flow‐map models for data‐efficient discovery of dynamics and fast uncertainty quantification of biological and biochemical systems

    Article • Biotechnology and Bioengineering, January 2023, Wiley

    Professor Adam P Arkin

  61. Interactive Analysis of Functional Residues in Protein Families

    Article • mSystems, December 2022, ASM Journals

    Professor Adam P Arkin

  62. Publisher Correction: Metagenome-assembled genome extraction and analysis from microbiomes using KBase

    Article • Nature Protocols, November 2022, Springer Science + Business Media

    Professor Adam P Arkin

  63. Metagenome-assembled genome extraction and analysis from microbiomes using KBase

    Article • Nature Protocols, November 2022, Springer Science + Business Media

    Professor Adam P Arkin

  64. Towards Environmental Control of Microbiomes

    Article • November 2022, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

  65. Barcoded overexpression screens in gut Bacteroidales identify genes with new roles in carbon utilization and stress resistance

    Article • October 2022, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

  66. The importance of getting (and giving) credit for data

    Article • PLoS Computational Biology, September 2022, PLOS

    Elisha Wood-Charlson, Zachary Crockett, Professor Adam P Arkin

  67. Eliminating Genes for a Two Component System Increases PHB Productivity in Cupriavidus basilensis 4G11 Under PHB Suppressing, Non-Stress Conditions

    Article • September 2022, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

  68. Ecophysiological and genomic analyses of a representative isolate of highly abundant Bacillus cereus strains in contaminated subsurface sediments

    Article • Environmental Microbiology, September 2022, Wiley

    Professor Adam P Arkin

  69. Deep surveys of transcriptional modules with Massive Associative K-biclustering (MAK)

    Article • August 2022, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

  70. Development of a Markerless Deletion Mutagenesis System in Nitrate-Reducing Bacterium Rhodanobacter denitrificans

    Article • Applied and Environmental Microbiology, July 2022, ASM Journals

    Professor Adam P Arkin

  71. Acetaminophen production in the edible, filamentous cyanobacteriumArthrospira platensis

    Article • July 2022, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

  72. Interactive analysis of functional residues in protein families

    Article • July 2022, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

  73. Space bioprocess engineering on the horizon

    Article • Communications Engineering, June 2022, Springer Science + Business Media

    Professor Adam P Arkin

  74. Systems-informed genome mining for electroautotrophic microbial production

    Article • Bioelectrochemistry, June 2022, Elsevier

    Professor Adam P Arkin

  75. Charting a narrow course for direct electron uptake-facilitated electromicrobial production

    Article • May 2022, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

  76. A Defined Medium for Cultivation and Exometabolite Profiling of Soil Bacteria

    Article • Frontiers in Microbiology, May 2022, Frontiers

    Professor Adam P Arkin

  77. Complete Genome Sequence of Bacillus cereus Strain CPT56D-587-MTF, Isolated from a Nitrate- and Metal-Contaminated Subsurface Environment

    Article • Microbiology Resource Announcements, May 2022, ASM Journals

    Professor Adam P Arkin

  78. Photovoltaics-Driven Power Production Can Support Human Exploration on Mars

    Article • Frontiers in Astronomy and Space Sciences, April 2022, Frontiers

    Professor Adam P Arkin

  79. Filling gaps in bacterial catabolic pathways with computation and high-throughput genetics

    Article • PLoS Genetics, April 2022, PLOS

    Professor Adam P Arkin

  80. EcoFun-MAP: An Ecological Function Oriented Metagenomic Analysis Pipeline

    Article • April 2022, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

  81. A Phage Foundry Framework to Systematically Develop Viral Countermeasures to Combat Antibiotic-Resistant Bacterial Pathogens

    Article • iScience, April 2022, Elsevier

    Professor Adam P Arkin

  82. Genotype to ecotype in niche environments: adaptation of Arthrobacter to carbon availability and environmental conditions

    Article • ISME Communications, March 2022, Oxford University Press (OUP)

    Professor Adam P Arkin

  83. Genomic Features and Pervasive Negative Selection in Rhodanobacter Strains Isolated from Nitrate and Heavy Metal Contaminated Aquifer

    Article • Microbiology Spectrum, February 2022, ASM Journals

    Professor Adam P Arkin

  84. Data-Driven Flow-Map Models for Data-Efficient Discovery of Dynamics and Fast Uncertainty Quantification of Biological and Biochemical Systems

    Article • February 2022, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

  85. Global Analysis of Biomineralization Genes in Magnetospirillum magneticum AMB-1

    Article • mSystems, February 2022, ASM Journals

    Professor Adam P Arkin

  86. Quantifying the Local Adaptive Landscape of a Nascent Bacterial Community

    Article • February 2022, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

  87. Parallel multicopy-suppressor screens reveal convergent evolution of phage-encoded single gene lysis proteins

    Article • January 2022, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

  88. CORAL: A framework for rigorous self-validated data modeling and integrative, reproducible data analysis

    Article • GigaScience, January 2022, Oxford University Press (OUP)

    Professor Adam P Arkin

  89. Space Bioprocess Engineering on the Horizon

    Article • December 2021, MDPI AG

    Professor Adam P Arkin

  90. Biofilm Interaction Mapping and Analysis (BIMA) of Interspecific Interactions in Pseudomonas Co-culture Biofilms

    Article • Frontiers in Microbiology, December 2021, Frontiers

    Professor Adam P Arkin

  91. A KBase case study on genome-wide transcriptomics and plant primary metabolism in response to drought stress in Sorghum.

    Article • Current Plant Biology, December 2021, Elsevier

    Professor Adam P Arkin

  92. The genetic basis of phage susceptibility, cross-resistance and host-range in Salmonella

    Article • Microbiology, December 2021, Society for General Microbiology

    Professor Adam P Arkin

  93. iVirus 2.0: Cyberinfrastructure-supported tools and data to power DNA virus ecology

    Article • ISME Communications, December 2021, Oxford University Press (OUP)

    Professor Adam P Arkin

  94. GapMind for Carbon Sources: Automated annotations of catabolic pathways

    Article • November 2021, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

  95. Bioinformatic Teaching Resources – For Educators, by Educators – Using KBase, a Free, User-Friendly, Open Source Platform

    Article • Frontiers in Education, October 2021, Frontiers

    Professor Adam P Arkin

  96. A Simple, Cost-Effective, and Automation-Friendly Direct PCR Approach for Bacterial Community Analysis

    Article • mSystems, October 2021, ASM Journals

    Professor Adam P Arkin

  97. Deciphering Microbial Metal Toxicity Responses via Random Bar Code Transposon Site Sequencing and Activity-Based Metabolomics

    Article • Applied and Environmental Microbiology, October 2021, ASM Journals

    Professor Adam P Arkin

  98. Evaluating the Cost of Pharmaceutical Purification for a Long-Duration Space Exploration Medical Foundry

    Article • Frontiers in Microbiology, October 2021, Frontiers

    Professor Adam P Arkin

  99. Sustained Ability of a Natural Microbial Community to Remove Nitrate from Groundwater

    Article • Ground Water, September 2021, Wiley

    Professor Adam P Arkin

  100. Mapping the genetic landscape of biomineralization in Magnetospirillum magneticum AMB-1 with RB-Tnseq

    Article • August 2021, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

  101. Production of PHB From CO2-Derived Acetate With Minimal Processing Assessed for Space Biomanufacturing

    Article • Frontiers in Microbiology, July 2021, Frontiers

    Professor Adam P Arkin

  102. Towards a Biomanufactory on Mars

    Article • Frontiers in Astronomy and Space Sciences, July 2021, Frontiers

    Professor Adam P Arkin

  103. Ecogenomics of Groundwater Phages Suggests Niche Differentiation Linked to Specific Environmental Tolerance

    Article • mSystems, June 2021, ASM Journals

    Professor Adam P Arkin

  104. Chromosome assembled and annotated genome sequence of Aspergillus flavus NRRL 3357

    Article • G3 Genes Genomes Genetics, June 2021, Oxford University Press (OUP)

    Professor Adam P Arkin

  105. Evaluating the cost of pharmaceutical purification for a long-duration space exploration medical foundry

    Article • June 2021, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

  106. Sustained ability of a natural microbial community to remove nitrate from groundwater

    Article • May 2021, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

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

    Article • PLoS Computational Biology, May 2021, PLOS

    Professor Adam P Arkin

  108. Author Correction: A genomic catalog of Earth’s microbiomes

    Article • Nature Biotechnology, April 2021, Springer Science + Business Media

    Dr Susannah Green Tringe, Gerard Muyzer, PhD David Paez-Espino, Professor Adam P Arkin, Dr Nikos C Kyrpides

  109. Mechanism Across Scales: A Holistic Modeling Framework Integrating Laboratory and Field Studies for Microbial Ecology

    Article • Frontiers in Microbiology, March 2021, Frontiers

    Professor Adam P Arkin

  110. Deletion Mutants, Archived Transposon Library, and Tagged Protein Constructs of the Model Sulfate-Reducing Bacterium Desulfovibrio vulgaris Hildenborough

    Article • Microbiology Resource Announcements, March 2021, ASM Journals

    Professor Adam P Arkin

  111. Molecular pharming to support human life on the moon, mars, and beyond

    Article • Critical Reviews in Biotechnology, March 2021, Taylor & Francis

    Professor Adam P Arkin

  112. A simple, cost-effective and automation-friendly direct PCR approach for bacterial community analysis

    Article • March 2021, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

  113. Functional genetics of human gut commensal Bacteroides thetaiotaomicron reveals metabolic requirements for growth across environments

    Article • Cell Reports, March 2021, Elsevier

    Professor Adam P Arkin

  114. Systematic discovery of pseudomonad genetic factors involved in sensitivity to tailocins

    Article • The ISME Journal, March 2021, Oxford University Press (OUP)

    Professor Adam P Arkin

  115. Four families of folate-independent methionine synthases

    Article • PLoS Genetics, February 2021, PLOS

    Professor Adam P Arkin

  116. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression

    Article • Cell, February 2021, Elsevier

    Professor Adam P Arkin

  117. Large-scale Genetic Characterization of a Model Sulfate-Reducing Bacterium

    Article • January 2021, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

  118. Diverse Bacterial Genes Modulate Plant Root Association by Beneficial Bacteria

    Article • mBio, December 2020, ASM Journals

    Professor Adam P Arkin

  119. Systems-informed genome mining for electroautotrophic microbial production

    Article • December 2020, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

  120. Publisher Correction: A genomic catalog of Earth’s microbiomes

    Article • Nature Biotechnology, November 2020, Springer Science + Business Media

    Dr Nikos C Kyrpides, Dr Susannah Green Tringe, PhD David Paez-Espino, Professor Adam P Arkin

  121. The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes

    Article • Nucleic Acids Research, November 2020, Oxford University Press (OUP)

    Professor Adam P Arkin

  122. A genomic catalog of Earth’s microbiomes

    Article • Nature Biotechnology, November 2020, Springer Science + Business Media

    Dr Nikos C Kyrpides, Dr Susannah Green Tringe, Gerard Muyzer, PhD David Paez-Espino, Professor Adam P Arkin

  123. Draft Genome Sequence of Bacillus sp. Strain EB106-08-02-XG196, Isolated from High-Nitrate-Contaminated Sediment

    Article • Microbiology Resource Announcements, October 2020, ASM Journals

    Professor Adam P Arkin

  124. Characterization of a Metal-Resistant Bacillus Strain With a High Molybdate Affinity ModA From Contaminated Sediments at the Oak Ridge Reservation

    Article • Frontiers in Microbiology, October 2020, Frontiers

    Professor Adam P Arkin

  125. High-throughput mapping of the phage resistance landscape in E. coli

    Article • PLoS Biology, October 2020, PLOS

    Professor Adam P Arkin

  126. In-field bioreactors demonstrate dynamic shifts in microbial communities in response to geochemical perturbations

    Article • PLOS One, September 2020, PLOS

    Dr Dwayne A Elias, Professor Adam P Arkin

  127. The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes

    Article • Nucleic Acids Research, September 2020, Oxford University Press (OUP)

    Professor Adam P Arkin

  128. A quantitative framework reveals ecological drivers of grassland microbial community assembly in response to warming

    Article • Nature Communications, September 2020, Springer Science + Business Media

    Professor Adam P Arkin

  129. Characterization of subsurface media from locations up- and down-gradient of a uranium-contaminated aquifer

    Article • Chemosphere, September 2020, Elsevier

    Professor Adam P Arkin

  130. Effects of Genetic and Physiological Divergence on the Evolution of a Sulfate-Reducing Bacterium under Conditions of Elevated Temperature

    Article • mBio, August 2020, ASM Journals

    Professor Adam P Arkin

  131. Ecogenomics of groundwater viruses suggests niche differentiation linked to specific environmental tolerance

    Article • July 2020, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

  132. Redefining fundamental concepts of transcription initiation in bacteria

    Article • Nature Reviews Genetics, July 2020, Springer Science + Business Media

    Professor Adam P Arkin

  133. GapMind: Automated Annotation of Amino Acid Biosynthesis

    Article • mSystems, June 2020, ASM Journals

    Professor Adam P Arkin

  134. Systematic Discovery of Pseudomonad Genetic Factors Involved in Sensitivity to Tailocins

    Article • May 2020, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

  135. Selective carbon sources influence the end products of microbial nitrate respiration

    Article • The ISME Journal, May 2020, Oxford University Press (OUP)

    Professor Adam P Arkin

  136. The Genetic Basis of phage susceptibility, cross-resistance and host-range in Salmonella

    Article • April 2020, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

  137. Four Families of Folate-independent Methionine Synthases

    Article • April 2020, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

  138. Small and mighty: adaptation of superphylum Patescibacteria to groundwater environment drives their genome simplicity

    Article • Microbiome, April 2020, Springer Science + Business Media

    Professor Adam P Arkin

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

    Article • March 2020, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

  140. Systematic genome-wide querying of coding and non-coding functional elements inE. coliusing CRISPRi

    Article • March 2020, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

  141. A quantitative framework reveals the ecological drivers of grassland soil microbial community assembly in response to warming

    Article • February 2020, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

  142. High-throughput mapping of the phage resistance landscape inE. coli

    Article • February 2020, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

  143. 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

  144. Selective carbon sources influence the end-products of microbial nitrate respiration

    Article • November 2019, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

  145. High spatiotemporal variability of bacterial diversity over short time scales with unique hydrochemical associations within a shallow aquifer

    Article • Water Research, November 2019, Elsevier

    Professor Adam P Arkin

  146. Nitrate-Utilizing Microorganisms Resistant to Multiple Metals from the Heavily Contaminated Oak Ridge Reservation

    Article • Applied and Environmental Microbiology, September 2019, ASM Journals

    Professor Adam P Arkin

  147. GapMind: Automated annotation of amino acid biosynthesis

    Article • August 2019, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

  148. Structural basis for AcrVA4 inhibition of specific CRISPR-Cas12a

    Article • eLife, August 2019, eLife

    Professor Adam P Arkin

  149. Massively Parallel Fitness Profiling Reveals Multiple Novel Enzymes in Pseudomonas putida Lysine Metabolism

    Article • mBio, June 2019, ASM Journals

    Professor Adam P Arkin

  150. 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

  151. Older Blood Is Associated With Increased Mortality and Adverse Events in Massively Transfused Trauma Patients: Secondary Analysis of the PROPPR Trial

    Article • Annals of Emergency Medicine, June 2019, Elsevier

    Professor Adam P Arkin

  152. Curated BLAST for Genomes

    Article • mSystems, April 2019, ASM Journals

    Professor Adam P Arkin

  153. Multiplexed CRISPR-Cas9-Based Genome Editing of Rhodosporidium toruloides

    Article • mSphere, April 2019, ASM Journals

    Professor Adam P Arkin

  154. Iterative screening methodology enables isolation of strains with improved properties for a FACS-based screen and increased L-DOPA production

    Article • Scientific Reports, April 2019, Springer Science + Business Media

    Professor Adam P Arkin

  155. Correction: Filling gaps in bacterial amino acid biosynthesis pathways with high-throughput genetics

    Article • PLoS Genetics, April 2019, PLOS

    Professor Adam P Arkin

  156. Earlier time to hemostasis is associated with decreased mortality and rate of complications: Results from the Pragmatic Randomized Optimal Platelet and Plasma Ratio trial

    Article • Journal of Trauma and Acute Care Surgery, March 2019, Wolters Kluwer Health

    Professor Adam P Arkin

  157. TEG Lysis Shutdown Represents Coagulopathy in Bleeding Trauma Patients: Analysis of the PROPPR Cohort

    Article • Shock, March 2019, Wolters Kluwer Health

    Professor Adam P Arkin

  158. Oxidative Pathways of Deoxyribose and Deoxyribonate Catabolism

    Article • mSystems, February 2019, ASM Journals

    Professor Adam P Arkin

  159. A versatile platform strain for high-fidelity multiplex genome editing

    Article • Nucleic Acids Research, February 2019, Oxford University Press (OUP)

    Professor Adam P Arkin

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

    Article • February 2019, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

  161. Curated BLAST for Genomes

    Article • January 2019, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

  162. 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

  163. Transposon insertional mutagenesis in Saccharomyces uvarum reveals trans -acting effects influencing species-dependent essential genes

    Article • Genome Research, January 2019, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

  164. CRISPR-Cas9 Circular Permutants as Programmable Scaffolds for Genome Modification

    Article • Cell, January 2019, Elsevier

    Professor Adam P Arkin

  165. Principles of synthetic biology: a MOOC for an emerging field

    Article • Synthetic Biology, January 2019, Oxford University Press (OUP)

    Professor Adam P Arkin

  166. Designing Spatially Distributed Gene Regulatory Networks To Elicit Contrasting Patterns

    Article • ACS Synthetic Biology, December 2018, American Chemical Society (ACS)

    Professor Adam P Arkin

  167. The selective pressures on the microbial community in a metal-contaminated aquifer

    Article • The ISME Journal, December 2018, Oxford University Press (OUP)

    Professor Adam P Arkin

  168. Iron‐ and aluminium‐induced depletion of molybdenum in acidic environments impedes the nitrogen cycle

    Article • Environmental Microbiology, November 2018, Wiley

    Professor Adam P Arkin

  169. Massively parallel fitness profiling reveals multiple novel enzymes inPseudomonas putidalysine metabolism

    Article • October 2018, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

  170. Genetic dissection of interspecific differences in yeast thermotolerance

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

    Professor Adam P Arkin

  171. Impact of hydrologic boundaries on microbial planktonic and biofilm communities in shallow terrestrial subsurface environments

    Article • FEMS Microbiology Ecology, September 2018, Oxford University Press (OUP)

    Professor Adam P Arkin

  172. EngineeringKluyveromyces marxianusas a Robust Synthetic Biology Platform Host

    Article • mBio, September 2018, ASM Journals

    Professor Adam P Arkin

  173. 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

  174. Risk Factors for the Development of Acute Respiratory Distress Syndrome Following Hemorrhage

    Article • Shock, September 2018, Wolters Kluwer Health

    Professor Adam P Arkin

  175. 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

  176. 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

  177. Kluyveromyces marxianus as a robust synthetic biology platform host

    Article • June 2018, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

  178. Mutant phenotypes for thousands of bacterial genes of unknown function

    Article • Nature, May 2018, Springer Science + Business Media

    Professor Adam P Arkin

  179. Improved Method for Estimating Reaction Rates During Push-Pull Tests

    Article • Ground Water, April 2018, Wiley

    Professor Adam P Arkin

  180. Deciphering microbial interactions in synthetic human gut microbiome communities

    Article • December 2017, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

  181. Transposon insertional mutagenesis in Saccharomyces uvarum reveals trans-acting effects influencing species-dependent essential genes

    Article • November 2017, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

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

    Article • October 2017, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

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

    Article • October 2017, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

  184. Oxidative pathways of deoxyribose and deoxyribonate catabolism

    Article • October 2017, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

  185. Filling Gaps in Bacterial Amino Acid Biosynthesis Pathways with High-throughput Genetics

    Article • September 2017, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

  186. 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

  187. Draft Genome Sequences of Two Janthinobacterium lividum Strains, Isolated from Pristine Groundwater Collected from the Oak Ridge Field Research Center

    Article • Genome Announcements, June 2017, ASM Journals

    Professor Adam P Arkin

  188. PaperBLAST: Text-mining papers for information about homologs

    Article • May 2017, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

  189. Programming mRNA decay to modulate synthetic circuit resource allocation

    Article • Nature Communications, April 2017, Nature

    Professor Adam P Arkin

  190. Erratum to: The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism

    Article • BMC Bioinformatics, April 2017, Springer Science + Business Media

    Professor Adam P Arkin

  191. The DOE Systems Biology Knowledgebase (KBase)

    Article • December 2016, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

  192. Validating Regulatory Predictions from Diverse Bacteria with Mutant Fitness Data

    Article • December 2016, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

  193. Programming mRNA decay to modulate synthetic circuit resource allocation

    Article • October 2016, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

  194. QTL-guided metabolic engineering of a complex trait

    Article • October 2016, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

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

    Article • PLOS One, October 2016, PLOS

    Professor Adam P Arkin

  196. 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

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

    Article • August 2016, openRxiv

    Professor Adam P Arkin

  198. 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

  199. Exometabolomics Assisted Design and Validation of Synthetic Obligate Mutualism

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

    Professor Adam P Arkin

  200. 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

  201. Rapid and efficient galactose fermentation by engineered Saccharomyces cerevisiae

    Article • Journal of Biotechnology, July 2016, Elsevier

    Professor Adam P Arkin

  202. 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

  203. Measurement and modeling of intrinsic transcription terminators

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

    Professor Adam P Arkin

  204. 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

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

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

    Professor Adam P Arkin

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

    Article • mBio, April 2016, ASM Journals

    Professor Adam P Arkin

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

    Article • February 2016, Cold Spring Harbor Laboratory Press

    Professor Adam P Arkin

  208. 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

  209. Grand challenges in space synthetic biology

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

    Professor Adam P Arkin

  210. 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

  211. EngineeringRhodosporidium toruloidesfor increased lipid production

    Article • Biotechnology and Bioengineering, November 2015, Wiley

    Professor Adam P Arkin

  212. 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

  213. 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

  214. Comparative metagenomics reveals impact of contaminants on groundwater microbiomes

    Article • Frontiers in Microbiology, October 2015, Frontiers

    Professor Adam P Arkin, Dr Susannah Green Tringe

  215. 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

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

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

    Professor Adam P Arkin

  217. 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

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

    Article • PLoS Computational Biology, September 2015, PLOS

    Professor Adam P Arkin

  219. 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

  220. 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

  221. 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

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

    Article • mBio, May 2015, ASM Journals

    Professor Adam P Arkin

  223. Natural Bacterial Communities Serve as Quantitative Geochemical Biosensors

    Article • mBio, May 2015, ASM Journals

    Professor Terry C Hazen, Professor Adam P Arkin

  224. 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

  225. 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

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

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

    Professor Adam P Arkin

  227. High-Quality Draft Genome Sequence of Desulfovibrio carbinoliphilus FW-101-2B, an Organic Acid-Oxidizing Sulfate-Reducing Bacterium Isolated from Uranium(VI)-Contaminated Groundwater

    Article • Genome Announcements, March 2015, ASM Journals

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

  228. 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

  229. Pattern formation with a compartmental lateral inhibition system

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

    Professor Adam P Arkin

  230. 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

  231. 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

  232. 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

  233. 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

  234. 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

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

    Article • eLife, August 2014, eLife

    Professor Adam P Arkin

  236. Towards an Informative Mutant Phenotype for Every Bacterial Gene

    Article • Journal of Bacteriology, August 2014, ASM Journals

    Professor Adam P Arkin

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

    Article • mBio, July 2014, ASM Journals

    Professor Adam P Arkin

  238. 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

  239. Metabolomic data streaming for biology-dependent data acquisition

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

    Professor Adam P Arkin

  240. 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

  241. 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

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

    Article • Molecular Systems Biology, April 2014, EMBO

    Professor Adam P Arkin

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

    Article • Molecular Systems Biology, April 2014, EMBO

    Professor Adam P Arkin

  244. Genetic basis for nitrate resistance in Desulfovibrio strains

    Article • Frontiers in Microbiology, April 2014, Frontiers

    Professor Adam P Arkin

  245. 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

  246. 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

  247. 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, Kai Xue

  248. 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

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

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

    Professor Adam P Arkin

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

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

    Professor Adam P Arkin

  251. 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

  252. Synthetic biology

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

    Professor Adam P Arkin

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

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

    Professor Adam P Arkin

  254. 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

  255. “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

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

    Article • Environmental Microbiology, October 2013, Wiley

    Professor Adam P Arkin, Dr Pavel Novichkov

  257. 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

  258. 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

  259. 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

  260. 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

  261. 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

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

    Article • Cell Reports, July 2013, Elsevier

    Professor Adam P Arkin

  263. Draft Genome Sequence for Desulfovibrio africanus Strain PCS

    Article • Genome Announcements, April 2013, ASM Journals

    Professor Adam P Arkin

  264. 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

  265. 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

  266. Measurement and modeling of intrinsic transcription terminators

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

    Professor Adam P Arkin

  267. 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

  268. 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

  269. Modular Design of a Synthetic Payload Delivery Device

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

    Professor Adam P Arkin

  270. 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

  271. Metagenomes of tropical soil-derived anaerobic switchgrass-adapted consortia with and without iron

    Article • Standards in Genomic Sciences, February 2013, Springer Science + Business Media

    Dr Susannah Green Tringe, Professor Adam P Arkin

  272. Modeling coagulation activation in trauma patients

    Article • Journal of Critical Care, February 2013, Elsevier

    Professor Adam P Arkin

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

    Article • Cell, February 2013, Elsevier

    Professor Adam P Arkin

  274. Metallochaperones Regulate Intracellular Copper Levels

    Article • PLoS Computational Biology, January 2013, PLOS

    Professor Adam P Arkin

  275. From Biological Parts to Circuit Design

    Article • January 2013, Elsevier

    Professor Adam P Arkin

  276. 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

  277. 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

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

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

    Professor Adam P Arkin

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

    Article • Journal of Bacteriology, December 2012, ASM Journals

    Professor Adam P Arkin

  280. metaMicrobesOnline: phylogenomic analysis of microbial communities

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

    Professor Adam P Arkin

  281. 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

  282. 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

  283. 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

  284. 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

  285. 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

  286. RNA processing enables predictable programming of gene expression

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

    Professor Adam P Arkin

  287. 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

  288. 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

  289. 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

  290. Functional responses of methanogenic archaea to syntrophic growth

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

    Professor Adam P Arkin

  291. 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

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

    Article • Biotechnology Journal, May 2012, Wiley

    Professor Adam P Arkin

  293. 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

  294. Rationally designed families of orthogonal RNA regulators of translation

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

    Professor Adam P Arkin

  295. 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

  296. Preface

    Article • January 2012, Elsevier

    Professor Adam P Arkin

  297. 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

  298. 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

  299. 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

  300. 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

  301. Toward rational design of bacterial genomes

    Article • Current Opinion in Microbiology, October 2011, Elsevier

    Professor Adam P Arkin

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

    Article • Trends in Biotechnology, October 2011, Elsevier

    Professor Adam P Arkin

  303. 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

  304. 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

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

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

    Professor Adam P Arkin

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

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

    Professor Adam P Arkin

  307. 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

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

    Article • April 2011, Taylor & Francis

    Professor Adam P Arkin

  309. The hunt for the biological transistor

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

    Professor Adam P Arkin

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

    Article • Cell, March 2011, Elsevier

    Professor Adam P Arkin

  311. Regulation of transcription by unnatural amino acids

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

    Professor Adam P Arkin

  312. 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

  313. Simulated niche partitioning by bacteria

    Article • January 2011, Springer Science + Business Media

    Professor Adam P Arkin

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

    Article • Spectroscopy An International Journal, January 2011, Wiley

    Professor Adam P Arkin

  315. 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

  316. 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

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

    Article • PLoS Computational Biology, September 2010, PLOS

    Professor Adam P Arkin

  318. 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

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

    Article • PLoS Computational Biology, August 2010, PLOS

    Professor Adam P Arkin

  320. 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

  321. 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

  322. 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

  323. 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

  324. Identification of Small RNAs in Desulfovibrio vulgaris Hildenborough

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

    Professor Adam P Arkin

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

    Article • Environmental Microbiology, May 2010, Wiley

    Professor Terry C Hazen, Professor Adam P Arkin

  326. 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

  327. 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

  328. Detailed Simulations of Cell Biology with Smoldyn 2.1

    Article • PLoS Computational Biology, March 2010, PLOS

    Professor Adam P Arkin

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

    Article • PLOS One, March 2010, PLOS

    Professor Adam P Arkin

  330. BglBricks: A flexible standard for biological part assembly

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

    Professor Adam P Arkin

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

    Article • Environmental Microbiology, September 2009, Wiley

    Professor Terry C Hazen, Professor Adam P Arkin

  332. 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

  333. 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

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

    Article • PLoS Pathogens, January 2009, PLOS

    Professor Adam P Arkin

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

    Article • PLoS Computational Biology, January 2009, PLOS

    Professor Adam P Arkin

  336. Stochastic Models of Biological Processes

    Article • January 2009, Springer Science + Business Media

    Professor Adam P Arkin

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

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

    Professor Adam P Arkin

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

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

    Professor Adam P Arkin

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

    Article • Current Opinion in Microbiology, December 2008, Elsevier

    Professor Adam P Arkin

  340. Correction

    Article • Biophysical Journal, December 2008, Elsevier

    Professor Adam P Arkin

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

    Article • Biotechnology and Bioengineering, November 2008, Wiley

    Professor Adam P Arkin

  342. FastBLAST: Homology Relationships for Millions of Proteins

    Article • PLOS One, October 2008, PLOS

    Professor Adam P Arkin

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

    Article • PLoS Computational Biology, September 2008, PLOS

    Professor Adam P Arkin

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

    Article • PLOS One, July 2008, PLOS

    Professor Adam P Arkin

  345. Setting the standard in synthetic biology

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

    Professor Adam P Arkin

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

    Article • PLOS One, February 2008, PLOS

    Professor Adam P Arkin

  347. 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

  348. 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

  349. Genetics and Genomics of Sulfate Respiration in Desulfovibrio

    Article • January 2008, Springer Science + Business Media

    Professor Adam P Arkin

  350. 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

  351. 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

  352. Response of Desulfovibrio vulgaris to Alkaline Stress

    Article • Journal of Bacteriology, October 2007, ASM Journals

    Professor Adam P Arkin

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

    Article • PLoS Computational Biology, September 2007, PLOS

    Professor Adam P Arkin

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

    Article • Biophysical Journal, September 2007, Elsevier

    Professor Adam P Arkin

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

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

    Professor Adam P Arkin

  356. Environmental signal integration by a modular AND gate

    Article • Molecular Systems Biology, August 2007, EMBO

    Professor Adam P Arkin

  357. 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

  358. 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

  359. Systems Biology: A Switch for Sex

    Article • Current Biology, June 2007, Elsevier

    Professor Adam P Arkin

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

    Article • Journal of Bacteriology, June 2007, ASM Journals

    Professor Adam P Arkin

  361. Efficient stochastic sensitivity analysis of discrete event systems

    Article • Journal of Computational Physics, February 2007, Elsevier

    Professor Adam P Arkin

  362. 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

  363. Systems Biology

    Article • January 2007, Springer Science + Business Media

    Professor Adam P Arkin

  364. 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

  365. Deviant effects in molecular reaction pathways

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

    Professor Adam P Arkin

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

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

    Professor Adam P Arkin

  367. Simulating cell biology

    Article • Current Biology, July 2006, Elsevier

    Professor Adam P Arkin

  368. The Life-Cycle of Operons

    Article • PLoS Genetics, June 2006, PLOS

    Professor Adam P Arkin

  369. Genomics for environmental microbiology

    Article • Current Opinion in Biotechnology, June 2006, Elsevier

    Professor Adam P Arkin

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

    Article • Journal of Bacteriology, June 2006, ASM Journals

    Professor Adam P Arkin

  371. 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

  372. The Histidine Operon Is Ancient

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

    Professor Adam P Arkin

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

    Article • Biotechnology and Bioengineering, March 2006, Wiley

    Professor Adam P Arkin

  374. Model Discrimination Using Data Collaboration

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

    Professor Adam P Arkin

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

    Article • Journal of Bacteriology, March 2006, ASM Journals

    Professor Adam P Arkin

  376. 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

  377. Correction: The Life-Cycle of Operons

    Article • PLoS Genetics, January 2006, PLOS

    Professor Adam P Arkin

  378. Automated Abstraction Methodology for Genetic Regulatory Networks

    Article • January 2006, Springer Science + Business Media

    Professor Adam P Arkin

  379. Environmentally Controlled Invasion of Cancer Cells by Engineered Bacteria

    Article • Journal of Molecular Biology, January 2006, Elsevier

    Professor Adam P Arkin

  380. 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

  381. 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

  382. Cellular Response of Shewanella oneidensis to Strontium Stress

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

    Professor Adam P Arkin

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

    Professor Adam P Arkin

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

    Article • PLoS Computational Biology, October 2005, PLOS

    Professor Adam P Arkin

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

    Article • PLoS Genetics, August 2005, PLOS

    Professor Corey Nislow, Professor Adam P Arkin

  386. 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

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

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

    Professor Adam P Arkin

  388. 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

  389. The MicrobesOnline Web site for comparative genomics

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

    Professor Adam P Arkin

  390. 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

  391. A latent variable model for chemogenomic profiling

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

    Professor Adam P Arkin

  392. 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

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

    Article • Journal of Theoretical Biology, May 2005, Elsevier

    Professor Adam P Arkin

  394. 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

  395. 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

  396. 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

  397. 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

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

    Article • PLoS Computational Biology, January 2005, PLOS

    Professor Adam P Arkin

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

    Article • January 2005, Springer Science + Business Media

    Professor Adam P Arkin

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

    Article • Journal of Bacteriology, November 2004, ASM Journals

    Professor Adam P Arkin

  401. An Allosteric Model for Transmembrane Signaling in Bacterial Chemotaxis

    Article • Journal of Molecular Biology, October 2004, Elsevier

    Professor Adam P Arkin

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

    Article • Current Biology, July 2004, Elsevier

    Professor Adam P Arkin

  403. 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

  404. The evolution of genetic regulatory systems in bacteria

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

    Professor Adam P Arkin

  405. 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

  406. Data Standards for the Genomes to Life Program

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

    Professor Adam P Arkin

  407. 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

  408. Motifs, modules and games in bacteria

    Article • Current Opinion in Microbiology, April 2003, Elsevier

    Professor Adam P Arkin

  409. Biological networks

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

    Professor Adam P Arkin

  410. 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

  411. 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

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

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

    Professor Adam P Arkin

  413. Overview of the Alliance for Cellular Signaling

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

    Professor Adam P Arkin

  414. Control, exploitation and tolerance of intracellular noise

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

    Professor Adam P Arkin

  415. Signal Processing by Simple Chemical Systems

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

    Professor Adam P Arkin

  416. 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

  417. Functional profiling of the Saccharomyces cerevisiae genome

    Article • Nature, July 2002, Nature

    Professor Adam P Arkin, Professor David J. Garfinkel

  418. Motifs and modules in cellular signal processing

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

    Professor Adam P Arkin

  419. 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

  420. Motifs and modules in cellular signal processing

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

    Professor Adam P Arkin

  421. Synthetic cell biology

    Article • Current Opinion in Biotechnology, December 2001, Elsevier

    Professor Adam P Arkin

  422. Control Motifs for Intracellular Regulatory Networks*

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

    Professor Adam P Arkin

  423. 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

  424. Signal processing by biochemical reaction networks

    Article • May 2000, Cambridge University Press

    Professor Adam P Arkin

  425. Gene regulation: Towards a circuit engineering discipline

    Article • Current Biology, April 2000, Elsevier

    Professor Adam P Arkin

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

    Article • Trends in Genetics, February 1999, Elsevier

    Professor Adam P Arkin

  427. SIMULATION OF PROKARYOTIC GENETIC CIRCUITS

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

    Professor Adam P Arkin

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

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

    Professor Adam P Arkin

  429. Experimental Evidence for Turing Structures

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

    Professor Adam P Arkin

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

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

    Professor Adam P Arkin

  431. Digital Imaging Spectroscopy

    Article • January 1993, Elsevier

    Professor Adam P Arkin

  432. 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

  433. 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

  434. Modeling and Network Organization

    Article • Springer Science + Business Media

    Professor Adam P Arkin

  435. Data and Databases

    Article • Springer Science + Business Media

    Professor Adam P Arkin

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

    Article • SciVee, Inc

    Professor Adam P Arkin

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

    Article • Institute of Electrical & Electronics Engineers (IEEE)

    Professor Adam P Arkin

  438. 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