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Mutant phenotypes for thousands of bacterial genes of unknown function.

Price MN, Wetmore KM, Waters RJ, Callaghan M, Ray J, Liu H, Kuehl JV, Melnyk RA, Lamson JS, Suh Y, Carlson HK, Esquivel Z, Sadeeshkumar H, Chakraborty R, Zane GM, Rubin BE, Wall JD, Visel A, Bristow J, Blow MJ, Arkin AP, Deutschbauer AM.

Nature. 2018 May;557(7706):503-509. doi: 10.1038/s41586-018-0124-0. Epub 2018 May 16.


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

Paradis CJ, Dixon ER, Lui LM, Arkin AP, Parker JC, Istok JD, Perfect E, McKay LD, Hazen TC.

Ground Water. 2018 Apr 15. doi: 10.1111/gwat.12770. [Epub ahead of print]


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

Christensen GA, Moon J, Veach AM, Mosher JJ, Wymore AM, van Nostrand JD, Zhou J, Hazen TC, Arkin AP, Elias DA.

PLoS One. 2018 Mar 20;13(3):e0194663. doi: 10.1371/journal.pone.0194663. eCollection 2018.


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

Coradetti ST, Pinel D, Geiselman GM, Ito M, Mondo SJ, Reilly MC, Cheng YF, Bauer S, Grigoriev IV, Gladden JM, Simmons BA, Brem RB, Arkin AP, Skerker JM.

Elife. 2018 Mar 9;7. pii: e32110. doi: 10.7554/eLife.32110.


Microbial Functional Gene Diversity Predicts Groundwater Contamination and Ecosystem Functioning.

He Z, Zhang P, Wu L, Rocha AM, Tu Q, Shi Z, Wu B, Qin Y, Wang J, Yan Q, Curtis D, Ning D, Van Nostrand JD, Wu L, Yang Y, Elias DA, Watson DB, Adams MWW, Fields MW, Alm EJ, Hazen TC, Adams PD, Arkin AP, Zhou J.

MBio. 2018 Feb 20;9(1). pii: e02435-17. doi: 10.1128/mBio.02435-17.


Magic Pools: Parallel Assessment of Transposon Delivery Vectors in Bacteria.

Liu H, Price MN, Waters RJ, Ray J, Carlson HK, Lamson JS, Chakraborty R, Arkin AP, Deutschbauer AM.

mSystems. 2018 Jan 16;3(1). pii: e00143-17. doi: 10.1128/mSystems.00143-17. eCollection 2018 Jan-Feb.


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

Price MN, Zane GM, Kuehl JV, Melnyk RA, Wall JD, Deutschbauer AM, Arkin AP.

PLoS Genet. 2018 Jan 11;14(1):e1007147. doi: 10.1371/journal.pgen.1007147. eCollection 2018 Jan.


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

Zhou A, Lau R, Baran R, Ma J, von Netzer F, Shi W, Gorman-Lewis D, Kempher ML, He Z, Qin Y, Shi Z, Zane GM, Wu L, Bowen BP, Northen TR, Hillesland KL, Stahl DA, Wall JD, Arkin AP, Zhou J.

MBio. 2017 Nov 14;8(6). pii: e01780-17. doi: 10.1128/mBio.01780-17.


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

Yaegashi J, Kirby J, Ito M, Sun J, Dutta T, Mirsiaghi M, Sundstrom ER, Rodriguez A, Baidoo E, Tanjore D, Pray T, Sale K, Singh S, Keasling JD, Simmons BA, Singer SW, Magnuson JK, Arkin AP, Skerker JM, Gladden JM.

Biotechnol Biofuels. 2017 Oct 23;10:241. doi: 10.1186/s13068-017-0927-5. eCollection 2017.


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

De León KB, Zane GM, Trotter VV, Krantz GP, Arkin AP, Butland GP, Walian PJ, Fields MW, Wall JD.

MBio. 2017 Oct 17;8(5). pii: e01696-17. doi: 10.1128/mBio.01696-17.


A metabolic pathway for catabolizing levulinic acid in bacteria.

Rand JM, Pisithkul T, Clark RL, Thiede JM, Mehrer CR, Agnew DE, Campbell CE, Markley AL, Price MN, Ray J, Wetmore KM, Suh Y, Arkin AP, Deutschbauer AM, Amador-Noguez D, Pfleger BF.

Nat Microbiol. 2017 Dec;2(12):1624-1634. doi: 10.1038/s41564-017-0028-z. Epub 2017 Sep 25.


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

Thorgersen MP, Lancaster WA, Ge X, Zane GM, Wetmore KM, Vaccaro BJ, Poole FL 2nd, Younkin AD, Deutschbauer AM, Arkin AP, Wall JD, Adams MWW.

Front Microbiol. 2017 Aug 10;8:1529. doi: 10.3389/fmicb.2017.01529. eCollection 2017.


PaperBLAST: Text Mining Papers for Information about Homologs.

Price MN, Arkin AP.

mSystems. 2017 Aug 15;2(4). pii: e00039-17. doi: 10.1128/mSystems.00039-17. eCollection 2017 Jul-Aug.


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

Justice NB, Sczesnak A, Hazen TC, Arkin AP.

Appl Environ Microbiol. 2017 Sep 29;83(20). pii: e01253-17. doi: 10.1128/AEM.01253-17. Print 2017 Oct 15.


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

Wu X, Deutschbauer AM, Kazakov AE, Wetmore KM, Cwick BA, Walker RM, Novichkov PS, Arkin AP, Chakraborty R.

Genome Announc. 2017 Jun 29;5(26). pii: e00582-17. doi: 10.1128/genomeA.00582-17.


Validating regulatory predictions from diverse bacteria with mutant fitness data.

Sagawa S, Price MN, Deutschbauer AM, Arkin AP.

PLoS One. 2017 May 24;12(5):e0178258. doi: 10.1371/journal.pone.0178258. eCollection 2017.


Programming mRNA decay to modulate synthetic circuit resource allocation.

Venturelli OS, Tei M, Bauer S, Chan LJG, Petzold CJ, Arkin AP.

Nat Commun. 2017 Apr 26;8:15128. doi: 10.1038/ncomms15128.


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

Birkel GW, Ghosh A, Kumar VS, Weaver D, Ando D, Backman TWH, Arkin AP, Keasling JD, Martín HG.

BMC Bioinformatics. 2017 Apr 18;18(1):219. doi: 10.1186/s12859-017-1631-y. No abstract available.


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

Birkel GW, Ghosh A, Kumar VS, Weaver D, Ando D, Backman TWH, Arkin AP, Keasling JD, Martín HG.

BMC Bioinformatics. 2017 Apr 5;18(1):205. doi: 10.1186/s12859-017-1615-y. Erratum in: BMC Bioinformatics. 2017 Apr 18;18(1):219.


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

Zhang P, He Z, Van Nostrand JD, Qin Y, Deng Y, Wu L, Tu Q, Wang J, Schadt CW, W Fields M, Hazen TC, Arkin AP, Stahl DA, Zhou J.

Environ Sci Technol. 2017 Apr 4;51(7):3609-3620. doi: 10.1021/acs.est.6b02980. Epub 2017 Mar 16.


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

Kim SR, Skerker JM, Kong II, Kim H, Maurer MJ, Zhang GC, Peng D, Wei N, Arkin AP, Jin YS.

Metab Eng. 2017 Mar;40:176-185. doi: 10.1016/j.ymben.2017.02.006. Epub 2017 Feb 16.


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

Chakraborty R, Woo H, Dehal P, Walker R, Zemla M, Auer M, Goodwin LA, Kazakov A, Novichkov P, Arkin AP, Hazen TC.

Stand Genomic Sci. 2017 Feb 8;12:23. doi: 10.1186/s40793-017-0233-7. eCollection 2017.


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

King AJ, Preheim SP, Bailey KL, Robeson MS 2nd, Roy Chowdhury T, Crable BR, Hurt RA Jr, Mehlhorn T, Lowe KA, Phelps TJ, Palumbo AV, Brandt CC, Brown SD, Podar M, Zhang P, Lancaster WA, Poole F, Watson DB, W Fields M, Chandonia JM, Alm EJ, Zhou J, Adams MW, Hazen TC, Arkin AP, Elias DA.

Environ Sci Technol. 2017 Mar 7;51(5):2879-2889. doi: 10.1021/acs.est.6b04751. Epub 2017 Feb 10.


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

Menezes AA, Vilardi RF, Arkin AP, Cohen MJ.

Sci Transl Med. 2017 Jan 4;9(371). pii: eaaf5045. doi: 10.1126/scitranslmed.aaf5045.


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

Bosak T, Schubotz F, de Santiago-Torio A, Kuehl JV, Carlson HK, Watson N, Daye M, Summons RE, Arkin AP, Deutschbauer AM.

PLoS One. 2016 Dec 28;11(12):e0168719. doi: 10.1371/journal.pone.0168719. eCollection 2016.


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

Maurer MJ, Sutardja L, Pinel D, Bauer S, Muehlbauer AL, Ames TD, Skerker JM, Arkin AP.

ACS Synth Biol. 2017 Mar 17;6(3):566-581. doi: 10.1021/acssynbio.6b00264. Epub 2016 Dec 28.


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

Thorgersen MP, Lancaster WA, Rajeev L, Ge X, Vaccaro BJ, Poole FL, Arkin AP, Mukhopadhyay A, Adams MW.

Appl Environ Microbiol. 2017 Feb 1;83(4). pii: e03044-16. doi: 10.1128/AEM.03044-16. Print 2017 Feb 15.


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

Price MN, Wetmore KM, Deutschbauer AM, Arkin AP.

PLoS One. 2016 Oct 6;11(10):e0164314. doi: 10.1371/journal.pone.0164314. eCollection 2016.


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

Zhang S, Ito M, Skerker JM, Arkin AP, Rao CV.

Appl Microbiol Biotechnol. 2016 Nov;100(21):9393-9405. Epub 2016 Sep 27.


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

Vaccaro BJ, Lancaster WA, Thorgersen MP, Zane GM, Younkin AD, Kazakov AE, Wetmore KM, Deutschbauer A, Arkin AP, Novichkov PS, Wall JD, Adams MW.

Appl Environ Microbiol. 2016 Sep 16;82(19):6046-56. doi: 10.1128/AEM.01845-16. Print 2016 Oct 1.


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

Price MN, Arkin AP.

Genome Biol Evol. 2016 Jul 2;8(6):1917-28. doi: 10.1093/gbe/evw126.


Rapid and efficient galactose fermentation by engineered Saccharomyces cerevisiae.

Quarterman J, Skerker JM, Feng X, Liu IY, Zhao H, Arkin AP, Jin YS.

J Biotechnol. 2016 Jul 10;229:13-21. doi: 10.1016/j.jbiotec.2016.04.041. Epub 2016 Apr 30.


Measurement and modeling of intrinsic transcription terminators.

Cambray G, Guimaraes JC, Mutalik VK, Lam C, Mai QA, Thimmaiah T, Carothers JM, Arkin AP, Endy D.

Nucleic Acids Res. 2016 Aug 19;44(14):7006. doi: 10.1093/nar/gkw379. Epub 2016 Apr 29. No abstract available.


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

Oh EJ, Skerker JM, Kim SR, Wei N, Turner TL, Maurer MJ, Arkin AP, Jin YS.

Appl Environ Microbiol. 2016 May 31;82(12):3631-3639. doi: 10.1128/AEM.00410-16. Print 2016 Jun 15.


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

Bassalo MC, Garst AD, Halweg-Edwards AL, Grau WC, Domaille DW, Mutalik VK, Arkin AP, Gill RT.

ACS Synth Biol. 2016 Jul 15;5(7):561-8. doi: 10.1021/acssynbio.5b00187. Epub 2016 Apr 22.


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

Hemme CL, Green SJ, Rishishwar L, Prakash O, Pettenato A, Chakraborty R, Deutschbauer AM, Van Nostrand JD, Wu L, He Z, Jordan IK, Hazen TC, Arkin AP, Kostka JE, Zhou J.

MBio. 2016 Apr 5;7(2):e02234-15. doi: 10.1128/mBio.02234-15.


Exometabolomics Assisted Design and Validation of Synthetic Obligate Mutualism.

Kosina SM, Danielewicz MA, Mohammed M, Ray J, Suh Y, Yilmaz S, Singh AK, Arkin AP, Deutschbauer AM, Northen TR.

ACS Synth Biol. 2016 Jul 15;5(7):569-76. doi: 10.1021/acssynbio.5b00236. Epub 2016 Feb 17.


Grand challenges in space synthetic biology.

Menezes AA, Montague MG, Cumbers J, Hogan JA, Arkin AP.

J R Soc Interface. 2015 Dec 6;12(113):20150803. doi: 10.1098/rsif.2015.0803. Review.


Comparative metagenomics reveals impact of contaminants on groundwater microbiomes.

Hemme CL, Tu Q, Shi Z, Qin Y, Gao W, Deng Y, Nostrand JD, Wu L, He Z, Chain PS, Tringe SG, Fields MW, Rubin EM, Tiedje JM, Hazen TC, Arkin AP, Zhou J.

Front Microbiol. 2015 Oct 31;6:1205. doi: 10.3389/fmicb.2015.01205. eCollection 2015.


Towards Engineering Biological Systems in a Broader Context.

Venturelli OS, Egbert RG, Arkin AP.

J Mol Biol. 2016 Feb 27;428(5 Pt B):928-44. doi: 10.1016/j.jmb.2015.10.025. Epub 2015 Nov 3. Review.


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

Stephens CM, Skerker JM, Sekhon MS, Arkin AP, Riley LW.

Genome Announc. 2015 Nov 5;3(6). pii: e01241-15. doi: 10.1128/genomeA.01241-15.


The essential gene set of a photosynthetic organism.

Rubin BE, Wetmore KM, Price MN, Diamond S, Shultzaberger RK, Lowe LC, Curtin G, Arkin AP, Deutschbauer A, Golden SS.

Proc Natl Acad Sci U S A. 2015 Dec 1;112(48):E6634-43. doi: 10.1073/pnas.1519220112. Epub 2015 Oct 27.


Engineering Rhodosporidium toruloides for increased lipid production.

Zhang S, Skerker JM, Rutter CD, Maurer MJ, Arkin AP, Rao CV.

Biotechnol Bioeng. 2016 May;113(5):1056-66. doi: 10.1002/bit.25864. Epub 2015 Nov 10.


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

Freed EF, Winkler JD, Weiss SJ, Garst AD, Mutalik VK, Arkin AP, Knight R, Gill RT.

ACS Synth Biol. 2015 Nov 20;4(11):1244-53. doi: 10.1021/acssynbio.5b00133. Epub 2015 Nov 5.


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

Vaccaro BJ, Thorgersen MP, Lancaster WA, Price MN, Wetmore KM, Poole FL 2nd, Deutschbauer A, Arkin AP, Adams MW.

Appl Environ Microbiol. 2015 Oct 9;82(1):51-61. doi: 10.1128/AEM.02602-15. Print 2016 Jan 1.


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

De León KB, Utturkar SM, Camilleri LB, Elias DA, Arkin AP, Fields MW, Brown SD, Wall JD.

Genome Announc. 2015 Sep 24;3(5). pii: e01090-15. doi: 10.1128/genomeA.01090-15.


Molybdenum Availability Is Key to Nitrate Removal in Contaminated Groundwater Environments.

Thorgersen MP, Lancaster WA, Vaccaro BJ, Poole FL, Rocha AM, Mehlhorn T, Pettenato A, Ray J, Waters RJ, Melnyk RA, Chakraborty R, Hazen TC, Deutschbauer AM, Arkin AP, Adams MW.

Appl Environ Microbiol. 2015 Aug;81(15):4976-83. doi: 10.1128/AEM.00917-15. Epub 2015 May 15.


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

Ray J, Waters RJ, Skerker JM, Kuehl JV, Price MN, Huang J, Chakraborty R, Arkin AP, Deutschbauer A.

Genome Announc. 2015 May 14;3(3). pii: e00322-15. doi: 10.1128/genomeA.00322-15.


Natural bacterial communities serve as quantitative geochemical biosensors.

Smith MB, Rocha AM, Smillie CS, Olesen SW, Paradis C, Wu L, Campbell JH, Fortney JL, Mehlhorn TL, Lowe KA, Earles JE, Phillips J, Techtmann SM, Joyner DC, Elias DA, Bailey KL, Hurt RA Jr, Preheim SP, Sanders MC, Yang J, Mueller MA, Brooks S, Watson DB, Zhang P, He Z, Dubinsky EA, Adams PD, Arkin AP, Fields MW, Zhou J, Alm EJ, Hazen TC.

MBio. 2015 May 12;6(3):e00326-15. doi: 10.1128/mBio.00326-15.

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