Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 1 to 50 of 258

1.

Structural basis for AcrVA4 inhibition of specific CRISPR-Cas12a.

Knott GJ, Cress BF, Liu JJ, Thornton BW, Lew RJ, Al-Shayeb B, Rosenberg DJ, Hammel M, Adler BA, Lobba MJ, Xu M, Arkin AP, Fellmann C, Doudna JA.

Elife. 2019 Aug 9;8. pii: e49110. doi: 10.7554/eLife.49110. [Epub ahead of print]

2.

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

Zelaya AJ, Parker AE, Bailey KL, Zhang P, Van Nostrand J, Ning D, Elias DA, Zhou J, Hazen TC, Arkin AP, Fields MW.

Water Res. 2019 Jul 26;164:114917. doi: 10.1016/j.watres.2019.114917. [Epub ahead of print]

PMID:
31387058
3.

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

Thorgersen MP, Ge X, Poole FL 2nd, Price MN, Arkin AP, Adams MWW.

Appl Environ Microbiol. 2019 Aug 14;85(17). pii: e00896-19. doi: 10.1128/AEM.00896-19. Print 2019 Sep 1.

PMID:
31253673
4.

Massively Parallel Fitness Profiling Reveals Multiple Novel Enzymes in Pseudomonas putida Lysine Metabolism.

Thompson MG, Blake-Hedges JM, Cruz-Morales P, Barajas JF, Curran SC, Eiben CB, Harris NC, Benites VT, Gin JW, Sharpless WA, Twigg FF, Skyrud W, Krishna RN, Pereira JH, Baidoo EEK, Petzold CJ, Adams PD, Arkin AP, Deutschbauer AM, Keasling JD.

MBio. 2019 May 7;10(3). pii: e02577-18. doi: 10.1128/mBio.02577-18.

5.

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

Savitskaya J, Protzko RJ, Li FZ, Arkin AP, Dueber JE.

Sci Rep. 2019 Apr 9;9(1):5815. doi: 10.1038/s41598-019-41759-0.

6.

Curated BLAST for Genomes.

Price MN, Arkin AP.

mSystems. 2019 Mar 26;4(2). pii: e00072-19. doi: 10.1128/mSystems.00072-19. eCollection 2019 Mar-Apr.

7.

Correction: 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. 2019 Apr 3;15(4):e1008106. doi: 10.1371/journal.pgen.1008106. eCollection 2019 Apr.

8.

Multiplexed CRISPR-Cas9-Based Genome Editing of Rhodosporidium toruloides.

Otoupal PB, Ito M, Arkin AP, Magnuson JK, Gladden JM, Skerker JM.

mSphere. 2019 Mar 20;4(2). pii: e00099-19. doi: 10.1128/mSphere.00099-19.

9.

A versatile platform strain for high-fidelity multiplex genome editing.

Egbert RG, Rishi HS, Adler BA, McCormick DM, Toro E, Gill RT, Arkin AP.

Nucleic Acids Res. 2019 Apr 8;47(6):3244-3256. doi: 10.1093/nar/gkz085.

10.

Oxidative Pathways of Deoxyribose and Deoxyribonate Catabolism.

Price MN, Ray J, Iavarone AT, Carlson HK, Ryan EM, Malmstrom RR, Arkin AP, Deutschbauer AM.

mSystems. 2019 Feb 5;4(1). pii: e00297-18. doi: 10.1128/mSystems.00297-18. eCollection 2019 Jan-Feb.

11.

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

Mutalik VK, Novichkov PS, Price MN, Owens TK, Callaghan M, Carim S, Deutschbauer AM, Arkin AP.

Nat Commun. 2019 Jan 18;10(1):308. doi: 10.1038/s41467-018-08177-8.

12.

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

Sanchez MR, Payen C, Cheong F, Hovde BT, Bissonnette S, Arkin AP, Skerker JM, Brem RB, Caudy AA, Dunham MJ.

Genome Res. 2019 Mar;29(3):396-406. doi: 10.1101/gr.232330.117. Epub 2019 Jan 11.

PMID:
30635343
13.

CRISPR-Cas9 Circular Permutants as Programmable Scaffolds for Genome Modification.

Oakes BL, Fellmann C, Rishi H, Taylor KL, Ren SM, Nadler DC, Yokoo R, Arkin AP, Doudna JA, Savage DF.

Cell. 2019 Jan 10;176(1-2):254-267.e16. doi: 10.1016/j.cell.2018.11.052.

PMID:
30633905
14.

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

Carlson HK, Price MN, Callaghan M, Aaring A, Chakraborty R, Liu H, Kuehl JV, Arkin AP, Deutschbauer AM.

ISME J. 2019 Apr;13(4):937-949. doi: 10.1038/s41396-018-0328-1. Epub 2018 Dec 6.

PMID:
30523276
15.

Designing Spatially Distributed Gene Regulatory Networks To Elicit Contrasting Patterns.

Tei M, Perkins ML, Hsia J, Arcak M, Arkin AP.

ACS Synth Biol. 2019 Jan 18;8(1):119-126. doi: 10.1021/acssynbio.8b00377. Epub 2018 Dec 24.

16.

Genetic dissection of interspecific differences in yeast thermotolerance.

Weiss CV, Roop JI, Hackley RK, Chuong JN, Grigoriev IV, Arkin AP, Skerker JM, Brem RB.

Nat Genet. 2018 Nov;50(11):1501-1504. doi: 10.1038/s41588-018-0243-4. Epub 2018 Oct 8.

17.

Iron- and aluminium-induced depletion of molybdenum in acidic environments impedes the nitrogen cycle.

Ge X, Vaccaro BJ, Thorgersen MP, Poole FL 2nd, Majumder EL, Zane GM, De León KB, Lancaster WA, Moon JW, Paradis CJ, von Netzer F, Stahl DA, Adams PD, Arkin AP, Wall JD, Hazen TC, Adams MWW.

Environ Microbiol. 2019 Jan;21(1):152-163. doi: 10.1111/1462-2920.14435. Epub 2018 Nov 21.

PMID:
30289197
18.

Impact of hydrologic boundaries on microbial planktonic and biofilm communities in shallow terrestrial subsurface environments.

Smith HJ, Zelaya AJ, De León KB, Chakraborty R, Elias DA, Hazen TC, Arkin AP, Cunningham AB, Fields MW.

FEMS Microbiol Ecol. 2018 Dec 1;94(12). doi: 10.1093/femsec/fiy191. Review.

19.

Engineering Kluyveromyces marxianus as a Robust Synthetic Biology Platform Host.

Cernak P, Estrela R, Poddar S, Skerker JM, Cheng YF, Carlson AK, Chen B, Glynn VM, Furlan M, Ryan OW, Donnelly MK, Arkin AP, Taylor JW, Cate JHD.

MBio. 2018 Sep 25;9(5). pii: e01410-18. doi: 10.1128/mBio.01410-18.

20.

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

Cambray G, Guimaraes JC, Arkin AP.

Nat Biotechnol. 2018 Nov;36(10):1005-1015. doi: 10.1038/nbt.4238. Epub 2018 Sep 24.

PMID:
30247489
21.

KBase: The United States Department of Energy Systems Biology Knowledgebase.

Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL, Maslov S, Dehal P, Ware D, Perez F, Canon S, Sneddon MW, Henderson ML, Riehl WJ, Murphy-Olson D, Chan SY, Kamimura RT, Kumari S, Drake MM, Brettin TS, Glass EM, Chivian D, Gunter D, Weston DJ, Allen BH, Baumohl J, Best AA, Bowen B, Brenner SE, Bun CC, Chandonia JM, Chia JM, Colasanti R, Conrad N, Davis JJ, Davison BH, DeJongh M, Devoid S, Dietrich E, Dubchak I, Edirisinghe JN, Fang G, Faria JP, Frybarger PM, Gerlach W, Gerstein M, Greiner A, Gurtowski J, Haun HL, He F, Jain R, Joachimiak MP, Keegan KP, Kondo S, Kumar V, Land ML, Meyer F, Mills M, Novichkov PS, Oh T, Olsen GJ, Olson R, Parrello B, Pasternak S, Pearson E, Poon SS, Price GA, Ramakrishnan S, Ranjan P, Ronald PC, Schatz MC, Seaver SMD, Shukla M, Sutormin RA, Syed MH, Thomason J, Tintle NL, Wang D, Xia F, Yoo H, Yoo S, Yu D.

Nat Biotechnol. 2018 Jul 6;36(7):566-569. doi: 10.1038/nbt.4163. No abstract available.

22.

Deciphering microbial interactions in synthetic human gut microbiome communities.

Venturelli OS, Carr AC, Fisher G, Hsu RH, Lau R, Bowen BP, Hromada S, Northen T, Arkin AP.

Mol Syst Biol. 2018 Jun 21;14(6):e8157. doi: 10.15252/msb.20178157.

23.

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.

24.

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. 2019 Mar;57(2):292-302. doi: 10.1111/gwat.12770. Epub 2018 Apr 30.

PMID:
29656383
25.

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.

26.

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.

27.

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.

28.

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.

29.

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. Erratum in: PLoS Genet. 2019 Apr 3;15(4):e1008106.

30.

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.

31.

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.

32.

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.

33.

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.

34.

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.

35.

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.

36.

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.

37.

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.

38.

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.

39.

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.

40.

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.

41.

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.

42.

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.

PMID:
28300407
43.

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.

PMID:
28216106
44.

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.

45.

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.

46.

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.

PMID:
28053156
47.

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.

48.

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.

49.

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 MWW.

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

50.

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.

Supplemental Content

Loading ...
Support Center