Search filters

List of works by Adam Arkin

"Replica-extraction-transfer" nanostructure-initiator mass spectrometry imaging of acoustically printed bacteria

scientific article

A Comparison of the Costs and Benefits of Bacterial Gene Expression

scientific article

A Comparison of the Costs and Benefits of Bacterial Gene Expression

article

A Defined Medium for Cultivation and Exometabolite Profiling of Soil Bacteria

scientific article published on 25 May 2022

A Highly Expressed High-Molecular-Weight S-Layer Complex of Pelosinus sp. Strain UFO1 Binds Uranium.

scientific article published on 2 December 2016

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

scientific article

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

scientific article published in 2022

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

scientific article published on 2 April 2015

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

scientific article published on 11 June 2016

A bacterial sensor taxonomy across earth ecosystems for machine learning applications

scientific article published on 23 January 2024

A dual receptor crosstalk model of G-protein-coupled signal transduction

scientific article

A genomic catalog of Earth's microbiomes

scientific article published on 09 November 2020

A latent variable model for chemogenomic profiling

scientific article published on 26 May 2005

A mechanical explanation for cytoskeletal rings and helices in bacteria

scientific article

A metabolic pathway for catabolizing levulinic acid in bacteria

scientific article published on 25 September 2017

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

scientific article

A novel method for accurate operon predictions in all sequenced prokaryotes

scientific article

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

scientific article published on 18 September 2020

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

scientific article published in May 2006

A universal TagModule collection for parallel genetic analysis of microorganisms

scientific article

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

scientific article published on May 2014

A versatile platform strain for high-fidelity multiplex genome editing

scientific article published on 01 April 2019

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

scientific article

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

scientific article published on 30 September 2012

An allosteric model for transmembrane signaling in bacterial chemotaxis

scientific article published in October 2004

Analysis of a ferric uptake regulator (Fur) mutant of Desulfovibrio vulgaris Hildenborough

scientific article

Applications of imaging spectroscopy in molecular biology. II. Colony screening based on absorption spectra.

scientific article

Appreciation of the Machinations of the Blind Watchmaker

article published in 2008

Author Correction: A genomic catalog of Earth's microbiomes

correction of a scholarly article

Automated Abstraction Methodology for Genetic Regulatory Networks

Autonomous Mobile Robot Control Based on White Blood Cell Chemotaxis

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

Avoidance of truncated proteins from unintended ribosome binding sites within heterologous protein coding sequences

scientific article published on 8 May 2014

Bayesian multiple-instance motif discovery with BAMBI: inference of recombinase and transcription factor binding sites

scientific article published on 24 September 2011

BglBricks: A flexible standard for biological part assembly

scientific article

Biofilm Interaction Mapping and Analysis (BIMA) of Interspecific Interactions in <i>Pseudomonas</i> Co-culture Biofilms

publication published on 09 December 2021

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

scientific article published in 2021

Biological networks

scientific article

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

scientific article published in 2022

CRISPR-Cas9 Circular Permutants as Programmable Scaffolds for Genome Modification

scientific article published on 01 January 2019

Cell biology. The case for RNA.

scientific article published on November 2010

Cell-wide responses to low-oxygen exposure in Desulfovibrio vulgaris Hildenborough

scientific article

Cellular response of Shewanella oneidensis to strontium stress

scientific article published in January 2006

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

article

Characterization of NaCl tolerance in Desulfovibrio vulgaris Hildenborough through experimental evolution

scientific article published on 11 April 2013

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

scientific article published on 19 October 2020

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

scientific article published on 10 May 2020

Characterization of wastewater treatment plant microbial communities and the effects of carbon sources on diversity in laboratory models

scientific article

Chemogenomic profiling: identifying the functional interactions of small molecules in yeast

scholarly article

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

scientific article

Combinatorial latency reactivation for HIV-1 subtypes and variants

scientific article

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

scientific article

Comparative genomics of the dormancy regulons in mycobacteria

scientific article

Comparative metagenomics reveals impact of contaminants on groundwater microbiomes

scientific article published on 31 October 2015

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

scientific article published on 14 May 2015

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

scientific article

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

scientific article

Complete genome sequence of "Enterobacter lignolyticus" SCF1

scientific article (publication date: 15 October 2011)

Complete genome sequence of Pseudomonas stutzeri strain RCH2 isolated from a Hexavalent Chromium [Cr(VI)] contaminated site

scientific article published on 08 February 2017

Complex systems: from chemistry to systems biology

scholarly article

Complexity in bacterial cell-cell communication: quorum signal integration and subpopulation signaling in the Bacillus subtilis phosphorelay

scientific article

Composability of regulatory sequences controlling transcription and translation in Escherichia coli

scientific article

Computational models of HIV-1 resistance to gene therapy elucidate therapy design principles

scientific article

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

Conservation of transcription start sites within genes across a bacterial genus

scientific article

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

scientific article published on May 31, 2012

Contribution of mobile genetic elements toDesulfovibrio vulgarisgenome plasticity

scientific article published on 01 September 2009

Control motifs for intracellular regulatory networks.

scientific article

Control of methionine metabolism by the SahR transcriptional regulator in Proteobacteria

scientific article

Control of stochastic gene expression by host factors at the HIV promoter

scientific article

Control, exploitation and tolerance of intracellular noise

scientific article

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

article

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

scientific article published on 6 August 2013

Correction: The Life-Cycle of Operons.

scientific article published on 28 July 2006

Curated BLAST for Genomes

Curated BLAST for Genomes

scientific article published on 26 March 2019

D-Tailor: automated analysis and design of DNA sequences

scientific article

Data Standards for the Genomes to Life Program

Data and Databases

Deciphering microbial interactions in synthetic human gut microbiome communities.

scientific article

Deep Annotation of Protein Function across Diverse Bacteria from Mutant Phenotypes

article

Deletion of the Desulfovibrio vulgaris carbon monoxide sensor invokes global changes in transcription

scientific article

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

Design and construction of a double inversion recombination switch for heritable sequential genetic memory

scientific article

Design and diversity in bacterial chemotaxis: a comparative study in Escherichia coli and Bacillus subtilis

scientific article

Detailed simulations of cell biology with Smoldyn 2.1

scientific article

Determination of causal connectivities of species in reaction networks

scientific article

Determining Roles of Accessory Genes in Denitrification by Mutant Fitness Analyses

scientific article published on 9 October 2015

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

Development of a low bias method for characterizing viral populations using next generation sequencing technology

scientific article (publication date: 22 October 2010)

Deviant effects in molecular reaction pathways

scientific article published in October 2006

Digital Imaging Spectroscopy

Dissecting a complex chemical stress: chemogenomic profiling of plant hydrolysates

scientific article

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

Dissimilatory metabolism of nitrogen oxides in bacteria: comparative reconstruction of transcriptional networks

scientific article

Diverse Bacterial Genes Modulate Plant Root Association by Beneficial Bacteria

scientific article published on 15 December 2020

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

scientific article (publication date: May 2005)

Draft Genome Sequence for Desulfovibrio africanus Strain PCS.

scientific article published on March 2013

Draft Genome Sequences of Two Janthinobacteriumlividum Strains, Isolated from Pristine Groundwater Collected from the Oak Ridge Field Research Center

scientific article published on 29 June 2017

Draft genome sequence of Pelosinus fermentans JBW45, isolated during in situ stimulation for Cr(VI) reduction

scientific article

Draft genome sequences for two metal-reducing Pelosinus fermentans strains isolated from a Cr(VI)-contaminated site and for type strain R7

scientific article

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

scientific article published in Nature Communications

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

Dynamic Succession of Groundwater Functional Microbial Communities in Response to Emulsified Vegetable Oil Amendment during Sustained In Situ U(VI) Reduction.

scientific article published on 10 April 2015

Dynamic Succession of Groundwater Sulfate-Reducing Communities during Prolonged Reduction of Uranium in a Contaminated Aquifer.

scientific article

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

scientific article published on 29 June 2021

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

scientific article published on 18 August 2020

Effects of genetic variation on the E. coli host-circuit interface

scientific article published on 18 July 2013

Efficient stochastic sensitivity analysis of discrete event systems

article

Energetic consequences of nitrite stress in Desulfovibrio vulgaris Hildenborough, inferred from global transcriptional analysis

scientific article

Engineering Kluyveromyces marxianus as a Robust Synthetic Biology Platform Host

scholarly article by Paul Cernak et al published 25 September 2018 in mBio

Engineering Rhodosporidium toruloides for increased lipid production

scientific article published on 19 October 2015

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

scientific article

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

scientific article

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

scientific article published on 04 August 2017

Environmental genomics reveals a single-species ecosystem deep within Earth

scientific article

Environmental signal integration by a modular AND gate

scientific article

Environmentally controlled invasion of cancer cells by engineered bacteria

scientific article

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

scientific article published on 18 April 2017

Erratum: Control, exploitation and tolerance of intracellular noise

scientific article published in Nature

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

scientific article published in 2021

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

scholarly article by Guillaume Cambray et al published 24 September 2018 in Nature Biotechnology

Evidence-based annotation of gene function in Shewanella oneidensis MR-1 using genome-wide fitness profiling across 121 conditions

scientific article

Evidence-based annotation of transcripts and proteins in the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough

scientific article

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

scientific article

Exometabolomics Assisted Design and Validation of Synthetic Obligate Mutualism

scientific article published on 17 February 2016

Experimental Evidence for Turing Structures

article

Expression profiling of hypothetical genes in Desulfovibrio vulgaris leads to improved functional annotation

scientific article published on 17 March 2009

Fast, cheap and somewhat in control

scientific article published on January 2006

FastBLAST: homology relationships for millions of proteins

scientific article

FastTree 2--approximately maximum-likelihood trees for large alignments

scientific article (publication date: 10 March 2010)

Fermentation of hydrolysate detoxified by pervaporation through block copolymer membranes

Fifteen minutes of fim: control of type 1 pili expression in E. coli

scientific article

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

scientific article

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

scientific article published on 13 April 2022

Flexibility of syntrophic enzyme systems in Desulfovibrio species ensures their adaptation capability to environmental changes

scientific article published on 23 August 2013

From Biological Parts to Circuit Design

scholarly article published 2013

From fluctuations to phenotypes: the physiology of noise

scientific article published on 19 December 2006

Functional characterization of Crp/Fnr-type global transcriptional regulators in Desulfovibrio vulgaris Hildenborough

scientific article published on 9 December 2011

Functional genomics of lipid metabolism in the oleaginous yeast Rhodosporidium toruloides.

scientific article published on 9 March 2018

Functional genomics with a comprehensive library of transposon mutants for the sulfate-reducing bacterium Desulfovibrio alaskensis G20.

scientific article

Functional profiling of the Saccharomyces cerevisiae genome

scientific article (publication date: 25 July 2002)

Functional responses of methanogenic archaea to syntrophic growth

scientific article

GLAMM: Genome-Linked Application for Metabolic Maps

scientific article

GapMind: Automated Annotation of Amino Acid Biosynthesis

scientific article published on 23 June 2020

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

scientific article published on 15 April 2016

Genetic "code": representations and dynamical models of genetic components and networks

scientific article

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

Genetic basis for nitrate resistance in Desulfovibrio strains

scientific article

Genetic dissection of interspecific differences in yeast thermotolerance

Genetic interaction mapping with microfluidic-based single cell sequencing

scientific article

Genetic selection for context-dependent stochastic phenotypes: Sp1 and TATA mutations increase phenotypic noise in HIV-1 gene expression

scientific article

Genetics and Genomics of Sulfate Respiration in Desulfovibrio

article

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

scientific article published on 19 October 2015

Genome-wide requirements for resistance to functionally distinct DNA-damaging agents

scientific article

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

scientific article published on 17 December 2019

Genomics for environmental microbiology

scientific article

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

scientific article published in 2022

Global analysis of host response to induction of a latent bacteriophage

scientific article

Global transcriptional, physiological, and metabolite analyses of the responses of Desulfovibrio vulgaris hildenborough to salt adaptation

scientific article

Global transcriptome analysis of the heat shock response of Shewanella oneidensis

scientific article

Grand challenges in space synthetic biology

scientific article

HIV promoter integration site primarily modulates transcriptional burst size rather than frequency

scientific article

Hexavalent chromium reduction under fermentative conditions with lactate stimulated native microbial communities

scientific article

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

scientific article published on 26 July 2019

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

scientific article

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

scientific article published on 13 October 2020

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

scientific article published on 7 January 2008

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

scientific article

Hydrogen peroxide-induced oxidative stress responses in Desulfovibrio vulgaris Hildenborough

scientific article published in October 2010

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

article

Identification of Small RNAs in Desulfovibrio vulgaris Hildenborough

Identification of genes involved in the toxic response of Saccharomyces cerevisiae against iron and copper overload by parallel analysis of deletion mutants

scientific article

Impact of elevated nitrate on sulfate-reducing bacteria: a comparative study of Desulfovibrio vulgaris

scientific article published on 6 May 2010

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

scientific article published on 15 April 2018

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

scientific article published on 28 September 2020

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

scientific article published on 01 January 2015

Indirect and suboptimal control of gene expression is widespread in bacteria

scientific article published on 16 April 2013

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

scholarly article published September 2010

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

scientific article

Interactive XCMS Online: simplifying advanced metabolomic data processing and subsequent statistical analyses

scientific article

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

scientific article

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

scientific article

Iron- and Aluminum-Induced Depletion of Molybdenum in Acidic Environments Impedes the Nitrogen Cycle

scientific article published on 21 November 2018

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

scientific article published on 09 April 2019

KBase: The United States Department of Energy Systems Biology Knowledgebase

article

Key Metabolites and Mechanistic Changes for Salt Tolerance in an Experimentally Evolved Sulfate-Reducing Bacterium, Desulfovibrio vulgaris.

scientific article published on 14 November 2017

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

scientific article

Magic Pools: Parallel Assessment of Transposon Delivery Vectors in Bacteria

scientific article

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

scientific article

Massive Factorial Design Untangles Coding Sequences Determinants Of Translation Efficacy

Massive Phenotypic Measurements Reveal Complex Physiological Consequences Of Differential Translation Efficacies

article published in 2017

Massively Parallel Fitness Profiling Reveals Multiple Novel Enzymes in Lysine Metabolism

scientific article published on 07 May 2019

Measurement and modeling of intrinsic transcription terminators

scientific article published on 19 March 2013

Measurement and modeling of intrinsic transcription terminators

scientific article published on 29 April 2016

Mechanisms of Chromium and Uranium Toxicity in Pseudomonas stutzeri RCH2 Grown under Anaerobic Nitrate-Reducing Conditions

scientific article published on 10 August 2017

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

scientific article published on 18 November 2014

Memory in microbes: quantifying history-dependent behavior in a bacterium

scientific article

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

MetaMicrobesOnline: phylogenomic analysis of microbial communities

scientific article

Metabolic engineering of a haploid strain derived from a triploid industrial yeast for producing cellulosic ethanol

scientific article published on 16 February 2017

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

scientific article published on 27 September 2016

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

scientific article published in March 2009

Metabolic footprinting of mutant libraries to map metabolite utilization to genotype

scientific article

Metabolomic data streaming for biology-dependent data acquisition

scientific article

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

scientific article published on 25 February 2013

Metallochaperones regulate intracellular copper levels

scientific article

MicrobesOnline: an integrated portal for comparative and functional genomics

scientific article

Microbial Community Dynamics of Lactate Enriched Hanford Groundwaters

Microbial Functional Gene Diversity Predicts Groundwater Contamination and Ecosystem Functioning.

scientific article published on 20 February 2018

Microbial community succession during lactate amendment and electron acceptor limitation reveals a predominance of metal-reducing Pelosinus spp

scientific article published on 20 January 2012

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

scientific article

Model discrimination using data collaboration

scientific article

Modeling and Network Organization

Modeling and automation of sequencing-based characterization of RNA structure

scientific article

Modeling coagulation activation in trauma patients

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

Modular design of a synthetic payload delivery device

scientific article published on 6 March 2013

Modularity of stress response evolution

scholarly article

Molybdenum Availability Is Key to Nitrate Removal in Contaminated Groundwater Environments

scientific article published on 15 May 2015

Monofluorophosphate is a selective inhibitor of respiratory sulfate-reducing microorganisms

scientific article published on 4 March 2015

Morphology matters in immune cell chemotaxis: membrane asymmetry affects amplification

scientific article published on 25 September 2006

Motifs and modules in cellular signal processing

scholarly article published May 2002

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

scholarly article

Motifs, modules and games in bacteria

scientific article

Multiplexed CRISPR-Cas9 based genome editing of Rhodosporidium toruloides

Multiplexed CRISPR-Cas9-Based Genome Editing of

scientific article published on 20 March 2019

Multiplexed RNA structure characterization with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq)

scientific article

Mutant phenotypes for thousands of bacterial genes of unknown function

scientific article published in Nature

Mutual information analysis reveals coevolving residues in Tat that compensate for two distinct functions in HIV-1 gene expression

scientific article published on 17 January 2012

Natural bacterial communities serve as quantitative geochemical biosensors

scientific article published on 12 May 2015

Network news: innovations in 21st century systems biology

scientific article published in March 2011

New family of tungstate-responsive transcriptional regulators in sulfate-reducing bacteria

scientific article

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

scientific article published on 14 August 2019

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

scientific article

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

scientific article

Novel mechanism for scavenging of hypochlorite involving a periplasmic methionine-rich Peptide and methionine sulfoxide reductase

scientific article published on 12 May 2015

Numerical computation of diffusion on a surface

scientific article

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

scientific article

OpWise: operons aid the identification of differentially expressed genes in bacterial microarray experiments

scientific article

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

scientific article published on June 2005

Optimizing nucleotide mixtures to encode specific subsets of amino acids for semi-random mutagenesis

scientific article published in March 1992

Orthogonal control of expression mean and variance by epigenetic features at different genomic loci

scientific article published on 5 May 2015

Orthologous transcription factors in bacteria have different functions and regulate different genes

scientific article

Overview of the Alliance for Cellular Signaling

scientific article

Oxidative Pathways of Deoxyribose and Deoxyribonate Catabolism

scientific article published on 01 January 2019

PaperBLAST: Text Mining Papers for Information about Homologs

scientific article

Pattern formation with a compartmental lateral inhibition system

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

scientific article

Photovoltaics-Driven Power Production Can Support Human Exploration on Mars

scientific article published on 27 April 2022

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

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

scientific article published on 10 March 2013

Preface

Principles of synthetic biology: a MOOC for an emerging field

scientific article published on 10 May 2019

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

Programming mRNA decay to modulate synthetic circuit resource allocation

scientific article

Programming mRNA decay to modulate synthetic circuit resource allocation

Publisher Correction: A genomic catalog of Earth's microbiomes

scientific article published on 18 November 2020

QTL-guided metabolic engineering of a complex trait

Quantitative Trait Loci (QTL)-Guided Metabolic Engineering of a Complex Trait

scientific article published on 12 December 2016

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

scientific article

RNA processing enables predictable programming of gene expression

scientific article published on 16 September 2012

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

scientific article

Rapid and efficient galactose fermentation by engineered Saccharomyces cerevisiae

scientific article published on 29 April 2016

Rapid quantification of mutant fitness in diverse bacteria by sequencing randomly bar-coded transposons

scientific article published on 12 May 2015

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

scientific article

Rational and evolutionary engineering approaches uncover a small set of genetic changes efficient for rapid xylose fermentation in Saccharomyces cerevisiae

scientific article

Rationally designed families of orthogonal RNA regulators of translation

scientific article published on 25 March 2012

Reconstruction of regulatory and metabolic pathways in metal-reducing delta-proteobacteria

scientific article

Redefining fundamental concepts of transcription initiation in bacteria

scientific article published on 14 July 2020

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

scientific article

RegPrecise web services interface: programmatic access to the transcriptional regulatory interactions in bacteria reconstructed by comparative genomics

scientific article (publication date: July 2012)

RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes

scientific article

RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach

scientific article

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

scientific article

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

scientific article

Regulation of transcription by unnatural amino acids

scientific article published on 16 January 2011

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

scientific article (publication date: 28 February 2013)

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

scientific article

Response of Desulfovibrio vulgaris to alkaline stress

scientific article

Revisiting Modes of energy generation in sulfate reducing bacteria

Rex (encoded by DVU_0916) in Desulfovibrio vulgaris Hildenborough is a repressor of sulfate adenylyl transferase and is regulated by NADH

scientific article

Rhodosporidium toruloides: a new platform organism for conversion of lignocellulose into terpene biofuels and bioproducts

scientific article

Robust design of biological experiments ⬇️

scientific article published in January 2006

Salt stress in Desulfovibrio vulgaris Hildenborough: an integrated genomics approach

scientific article

Selection of chromosomal DNA libraries using a multiplex CRISPR system

scientific article

Selective carbon sources influence the end products of microbial nitrate respiration

scientific article published on 05 May 2020

Sequencing of multiple clostridial genomes related to biomass conversion and biofuel production

scientific article

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

scientific article

Setting the standard in synthetic biology

scientific article published in July 2008

Signal Processing by Simple Chemical Systems

article

Signal processing by biochemical reaction networks

scholarly article

Simulated niche partitioning by bacteria

scholarly article published 2011

Simulating cell biology.

scientific article published in July 2006

Simulation of prokaryotic genetic circuits

scientific article published in January 1998

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

scientific article published on 06 April 2020

Snapshot of iron response in Shewanella oneidensis by gene network reconstruction

scientific article

Statistical Construction of Chemical Reaction Mechanisms from Measured Time-Series

article

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

Stochastic Kinetic Analysis of Developmental Pathway Bifurcation in Phage λ-Infected Escherichia coli Cells ⬇️

scientific article published on August 1, 1998

Stochastic Models of Biological Processes

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

scientific article

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

article

Stochastic gene expression in a lentiviral positive-feedback loop: HIV-1 Tat fluctuations drive phenotypic diversity

scientific article published in July 2005

Stochasticity, succession, and environmental perturbations in a fluidic ecosystem

scientific article

StressChip as a high-throughput tool for assessing microbial community responses to environmental stresses

scientific article

Structural basis for AcrVA4 inhibition of specific CRISPR-Cas12a

scientific article published on 09 August 2019

Synthetic biology

scholarly article by Adam Arkin & Martin Fussenegger published December 2013 in Current Opinion in Chemical Biology

System-Wide Adaptations of Desulfovibrio alaskensis G20 to Phosphate-Limited Conditions

scientific article

Systematic discovery of pseudomonad genetic factors involved in sensitivity to tailocins

scientific article published on 01 March 2021

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

scientific article published on 12 October 2011

Systems biology: a switch for sex.

scientific article

Targeted clinical control of trauma patient coagulation through a thrombin dynamics model

scientific article

Temporal Dynamics of In-Field Bioreactor Populations Reflect the Groundwater System and Respond Predictably to Perturbation.

scientific article published on 23 January 2017

Ten simple rules for getting and giving credit for data

scientific article published on 29 September 2022

The Bacillus subtilis sin operon: an evolvable network motif

scientific article

The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism

scientific article

The MicrobesOnline Web site for comparative genomics

scientific article

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

scientific article published on 28 September 2020

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

scientific article published on 12 November 2020

The electron transfer system of syntrophically grown Desulfovibrio vulgaris

scientific article published on 06 July 2009

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, Hdr-Flox and Rnf.

scientific article published on 5 March 2014

The essential gene set of a photosynthetic organism

scientific article

The evolution of genetic regulatory systems in bacteria

scientific article published on March 2004

The evolution of two-component systems in bacteria reveals different strategies for niche adaptation

scientific article published on 3 November 2006

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

scientific article

The histidine operon is ancient

scientific article published on 11 April 2006

The hunt for the biological transistor

article

The life-cycle of operons

scientific article

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

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

scientific article published on 06 December 2018

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

scientific article (publication date: March 2003)

Theoretical design of a gene therapy to prevent AIDS but not human immunodeficiency virus type 1 infection

scientific article

Toward rational design of bacterial genomes

scientific article published on August 22, 2011

Toward scalable parts families for predictable design of biological circuits

scientific article

Towards Engineering Biological Systems in a Broader Context

scientific article

Towards a Biomanufactory on Mars

scientific article published on 19 July 2021

Towards a rigorous network of protein-protein interactions of the model sulfate reducer Desulfovibrio vulgaris Hildenborough

scientific article

Towards an informative mutant phenotype for every bacterial gene

scientific article

Towards synthetic biological approaches to resource utilization on space missions

scientific article

Tracing determinants of dual substrate specificity in glycoside hydrolase family 5.

scientific article

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

scientific article published on 07 February 2014

Transcription factor family-based reconstruction of singleton regulons and study of the Crp/Fnr, ArsR, and GntR families in Desulfovibrionales genomes

scientific article published on 19 October 2012

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

article published in 2016

Transcriptome analysis of Shewanella oneidensis MR-1 in response to elevated salt conditions

scientific article

Transcriptome profiling of Shewanella oneidensis gene expression following exposure to acidic and alkaline pH.

scientific article

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

scientific article

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

scientific article published on 11 January 2019

Unintended Laboratory-Driven Evolution Reveals Genetic Requirements for Biofilm Formation by Desulfovibrio vulgaris Hildenborough.

scientific article published on 17 October 2017

Use of in-field bioreactors demonstrate groundwater filtration influences planktonic bacterial community assembly, but not biofilm composition

scientific article published on 20 March 2018

Validating regulatory predictions from diverse bacteria with mutant fitness data

scientific article

Variation among Desulfovibrio species in electron transfer systems used for syntrophic growth

scientific article published on 21 December 2012

Varying virulence: epigenetic control of expression noise and disease processes

scientific article published on 21 June 2011

Versatile RNA-sensing transcriptional regulators for engineering genetic networks

scientific article

WIST: toolkit for rapid, customized LIMS development ⬇️

scientific article published on January 21, 2011

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

scientific article

Paulina is supported by:

About Paulina

Help