A. Rocha

发表

Molybdenum Availability Is Key to Nitrate Removal in Contaminated Groundwater Environments

Adam P. Arkin, Romy Chakraborty, Terry C. Hazen, 2015, Applied and Environmental Microbiology.

Microbial Functional Gene Diversity Predicts Groundwater Contamination and Ecosystem Functioning

A. Arkin, Jizhong Zhou, P. Adams, 2018, mBio.

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

A. Arkin, Jizhong Zhou, D. Stahl, 2020, Microbiome.

Large Circular Plasmids from Groundwater Plasmidomes Span Multiple Incompatibility Groups and Are Enriched in Multimetal Resistance Genes

J. Chandonia, Yu-Wei Wu, S. Singer, 2019, mBio.

Plasmid DNA analysis of pristine groundwater microbial communities reveal extensive presence of metal resistance genes

Yu-Wei Wu, S. Singer, T. Hazen, 2017, bioRxiv.

Advances in monitoring environmental microbes.

T. Hazen, S. Techtmann, A. Rocha, 2013, Current opinion in biotechnology.

EcoFun-MAP: An Ecological Function Oriented Metagenomic Analysis Pipeline

A. Arkin, Jizhong Zhou, Zhili He, 2022, bioRxiv.

Peculiar citric acid cycle of hydrothermal vent chemolithoautotroph Hydrogenovibrio crunogenus, and insights into carbon metabolism by obligate autotrophs

K. Rosario, L. Mcdaniel, C. Staley, 2017, FEMS microbiology letters.

Detecting Pathway Cross-Talks by Analyzing Conserved Functional Modules across Multiple Phenotype-Expressing Organisms

Nagiza F. Samatova, Ye Jin, Zhengzhang Chen, 2011, 2011 IEEE International Conference on Bioinformatics and Biomedicine.

Natural Bacterial Communities Serve as Quantitative Geochemical Biosensors

Ping Zhang, Eric J Alm, Paul D Adams, 2015, mBio.

In-silico identification of phenotype-biased functional modules

N. Samatova, J. Mihelcic, Kanchana Padmanabhan, 2012, Proteome Science.

Construction of Viable Soil Defined Media Using Quantitative Metabolomics Analysis of Soil Metabolites

R. Chakraborty, T. Northen, T. Hazen, 2017, Front. Microbiol..

Construction of soil defined media using quantitative exometabolomic analysis of soil metabolites

R. Chakraborty, T. Northen, T. Hazen, 2017, bioRxiv.

Lawrence Berkeley National Laboratory Recent Work Title Construction of viable soil defined media using quantitative metabolomics analysis of soil metabolites Permalink

R. Chakraborty, T. Northen, T. Hazen, 2017 .

RiboSyn is a New Method for Measuring Specific Growth Rates of Distinct Microbial Populations in Natural Systems

P. Stroot, S. Dupont, A. M. Rocha, 2007 .

Incorporation of Leucine and Thymidine by Estuarine Phytoplankton: Implications for Bacterial Productivity Estimates

George E. Boneillo, M. Mulholland, A. M. Rocha, 2011 .

Spice: discovery of phenotype-determining component interplays

Nagiza F. Samatova, Zhengzhang Chen, James R. Mihelcic, 2012, BMC Systems Biology.

DENSE: efficient and prior knowledge-driven discovery of phenotype-associated protein functional modules

N. Samatova, A. Choudhary, J. Mihelcic, 2011, BMC Systems Biology.

NIBBS-Search for Fast and Accurate Prediction of Phenotype-Biased Metabolic Systems

Nagiza F. Samatova, James R. Mihelcic, Matthew C. Schmidt, 2012, PLoS Comput. Biol..

In-silico identification of phenotype-biased functional modules

N. Samatova, J. Mihelcic, Kanchana Padmanabhan, 2012, Proteome Science.

Efficient α, β-motif finder for identification of phenotype-related functional modules

Nagiza F. Samatova, Zhengzhang Chen, James R. Mihelcic, 2011, BMC Bioinformatics.

Efficient alpha, beta-motif Finder for Identification of Phenotype-related Functional Modules

Nagiza F. Samatova, Zhengzhang Chen, Matthew C. Schmidt, 2011, BMC Bioinform..