User profiles for Adam P Arkin
Adam Paul ArkinDepartment of Bioengineering, University of California, Berkeley, Physical Biosciences … Verified email at lbl.gov Cited by 76572 |
Functional profiling of the Saccharomyces cerevisiae genome
Determining the effect of gene deletion is a fundamental approach to understanding gene
function. Conventional genetic screens exhibit biases, and genes contributing to a phenotype …
function. Conventional genetic screens exhibit biases, and genes contributing to a phenotype …
[HTML][HTML] FastTree 2–approximately maximum-likelihood trees for large alignments
Background We recently described FastTree, a tool for inferring phylogenies for alignments
with up to hundreds of thousands of sequences. Here, we describe improvements to …
with up to hundreds of thousands of sequences. Here, we describe improvements to …
FastTree: computing large minimum evolution trees with profiles instead of a distance matrix
Gene families are growing rapidly, but standard methods for inferring phylogenies do not
scale to alignments with over 10,000 sequences. We present FastTree, a method for …
scale to alignments with over 10,000 sequences. We present FastTree, a method for …
The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models
Motivation: Molecular biotechnology now makes it possible to build elaborate systems
models, but the systems biology community needs information standards if models are to be …
models, but the systems biology community needs information standards if models are to be …
[HTML][HTML] Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression
Targeted gene regulation on a genome-wide scale is a powerful strategy for interrogating,
perturbing, and engineering cellular systems. Here, we develop a method for controlling gene …
perturbing, and engineering cellular systems. Here, we develop a method for controlling gene …
[HTML][HTML] A genomic catalog of Earth's microbiomes
The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has
enabled insights into the ecology and evolution of environmental and host-associated …
enabled insights into the ecology and evolution of environmental and host-associated …
Control, exploitation and tolerance of intracellular noise
Noise has many roles in biological function, including generation of errors in DNA
replication leading to mutation and evolution, noise-driven divergence of cell fates, noise-induced …
replication leading to mutation and evolution, noise-driven divergence of cell fates, noise-induced …
[HTML][HTML] KBase: the United States department of energy systems biology knowledgebase
Although similar integrative tools exist (Supplementary Note 2), no other open platform
shares all KBase’s features, which include the following:(i) comprehensive support for data …
shares all KBase’s features, which include the following:(i) comprehensive support for data …
Natural bacterial communities serve as quantitative geochemical biosensors
Biological sensors can be engineered to measure a wide range of environmental conditions.
Here we show that statistical analysis of DNA from natural microbial communities can be …
Here we show that statistical analysis of DNA from natural microbial communities can be …
Stochastic chemical kinetics and the quasi-steady-state assumption: Application to the Gillespie algorithm
Biochemical dynamics are often determined by series of single molecule events such as
gene expression and reactions involving protein concentrations at nanomolar concentrations. …
gene expression and reactions involving protein concentrations at nanomolar concentrations. …