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List of works by Adam Arkin

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

scientific article (publication date: 10 March 2010)
Functional profiling of the Saccharomyces cerevisiae genome

scientific article (publication date: 25 July 2002)
The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models

scientific article (publication date: March 2003)
Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression

scientific article (publication date: 28 February 2013)
Control, exploitation and tolerance of intracellular noise

scientific article
Diverse Bacterial Genes Modulate Plant Root Association by Beneficial Bacteria

scientific article published on 15 December 2020
Stochastic Kinetic Analysis of Developmental Pathway Bifurcation in Phage λ-Infected Escherichia coli Cells

scientific article published on August 1, 1998
Stochastic gene expression in a lentiviral positive-feedback loop: HIV-1 Tat fluctuations drive phenotypic diversity

scientific article published in July 2005
Chemogenomic profiling: identifying the functional interactions of small molecules in yeast

scholarly article
MicrobesOnline: an integrated portal for comparative and functional genomics

scientific article
A novel method for accurate operon predictions in all sequenced prokaryotes

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

scientific article published on 10 March 2013
Environmentally controlled invasion of cancer cells by engineered bacteria

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

scientific article
Environmental signal integration by a modular AND gate

scientific article
BglBricks: A flexible standard for biological part assembly

scientific article
Environmental genomics reveals a single-species ecosystem deep within Earth

scientific article
Detailed simulations of cell biology with Smoldyn 2.1

scientific article
Stochasticity, succession, and environmental perturbations in a fluidic ecosystem

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

scientific article
Composability of regulatory sequences controlling transcription and translation in Escherichia coli

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

scientific article
The MicrobesOnline Web site for comparative genomics

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

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

scientific article published on May 31, 2012
Diversity in times of adversity: probabilistic strategies in microbial survival games

scientific article (publication date: May 2005)
Global transcriptome analysis of the heat shock response of Shewanella oneidensis

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

scientific article
Selection of chromosomal DNA libraries using a multiplex CRISPR system

scientific article
Motifs, modules and games in bacteria

scientific article
RNA processing enables predictable programming of gene expression

scientific article published on 16 September 2012
Versatile RNA-sensing transcriptional regulators for engineering genetic networks

scientific article
Overview of the Alliance for Cellular Signaling

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

scientific article
Simulation of prokaryotic genetic circuits

scientific article published in January 1998
KBase: The United States Department of Energy Systems Biology Knowledgebase

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

scientific article published on 3 November 2006
RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach

scientific article
The life-cycle of operons

scientific article published on 23 June 2006
Biological networks

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
Combinatorial latency reactivation for HIV-1 subtypes and variants

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

scientific article published on 12 May 2015
Quantitative estimation of activity and quality for collections of functional genetic elements

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

scientific article published on 7 January 2008
Modeling and automation of sequencing-based characterization of RNA structure

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

scientific article published on June 2005

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