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Items: 1 to 50 of 191

1.

A new family of transcriptional regulators of tungstoenzymes and molybdate/tungstate transport.

Rajeev L, Garber ME, Zane GM, Price MN, Dubchak I, Wall JD, Novichkov PS, Mukhopadhyay A, Kazakov AE.

Environ Microbiol. 2018 Dec 10. doi: 10.1111/1462-2920.14500. [Epub ahead of print]

PMID:
30536693
2.

Whole-Genome Analysis of Introgression Between the Spotted Owl and Barred Owl (Strix occidentalis and Strix varia, Respectively; Aves: Strigidae) in Western North America.

Hanna ZR, Dumbacher JP, Bowie RCK, Henderson JB, Wall JD.

G3 (Bethesda). 2018 Dec 10;8(12):3945-3952. doi: 10.1534/g3.118.200754.

3.

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. 2018 Oct 5. doi: 10.1111/1462-2920.14435. [Epub ahead of print]

PMID:
30289197
4.

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.

5.

A novel whole-cell biosensor of Pseudomonas aeruginosa to monitor the expression of quorum sensing genes.

Zhang C, Parrello D, Brown PJB, Wall JD, Hu Z.

Appl Microbiol Biotechnol. 2018 Jul;102(14):6023-6038. doi: 10.1007/s00253-018-9044-z. Epub 2018 May 5.

PMID:
29730766
6.

Youth Disclosure of Sexual Orientation to Siblings and Extended Family.

Grafsky EL, Hickey K, Nguyen HN, Wall JD.

Fam Relat. 2018 Feb;67(1):147-160. doi: 10.1111/fare.12299. Epub 2018 Jan 4.

PMID:
29568144
7.

Cr(VI) reduction and physiological toxicity are impacted by resource ratio in Desulfovibrio vulgaris.

Franco LC, Steinbeisser S, Zane GM, Wall JD, Fields MW.

Appl Microbiol Biotechnol. 2018 Mar;102(6):2839-2850. doi: 10.1007/s00253-017-8724-4. Epub 2018 Feb 10.

8.

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.

9.

Disentangling Immediate Adaptive Introgression from Selection on Standing Introgressed Variation in Humans.

Jagoda E, Lawson DJ, Wall JD, Lambert D, Muller C, Westaway M, Leavesley M, Capellini TD, Mirazón Lahr M, Gerbault P, Thomas MG, Migliano AB, Willerslev E, Metspalu M, Pagani L.

Mol Biol Evol. 2017 Dec 6. doi: 10.1093/molbev/msx314. [Epub ahead of print]

10.

Carbon Amendments Alter Microbial Community Structure and Net Mercury Methylation Potential in Sediments.

Christensen GA, Somenahally AC, Moberly JG, Miller CM, King AJ, Gilmour CC, Brown SD, Podar M, Brandt CC, Brooks SC, Palumbo AV, Wall JD, Elias DA.

Appl Environ Microbiol. 2018 Jan 17;84(3). pii: e01049-17. doi: 10.1128/AEM.01049-17. Print 2018 Feb 1.

11.

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.

12.

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.

13.

Northern Spotted Owl (Strix occidentalis caurina) Genome: Divergence with the Barred Owl (Strix varia) and Characterization of Light-Associated Genes.

Hanna ZR, Henderson JB, Wall JD, Emerling CA, Fuchs J, Runckel C, Mindell DP, Bowie RCK, DeRisi JL, Dumbacher JP.

Genome Biol Evol. 2017 Oct 1;9(10):2522-2545. doi: 10.1093/gbe/evx158.

14.

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.

15.

Isolation, Characterization and Bioactivities of an Extracellular Polysaccharide Produced from Streptomyces sp. MOE6.

Elnahas MO, Amin MA, Hussein MMD, Shanbhag VC, Ali AE, Wall JD.

Molecules. 2017 Aug 24;22(9). pii: E1396. doi: 10.3390/molecules22091396.

16.

Complete Genome Sequencing of Streptomyces sp. Strain MOE7, Which Produces an Extracellular Polysaccharide with Antioxidant and Antitumor Activities.

Elnahas MO, De León KB, Amin MA, Hussein MMD, Ali AE, Wall JD.

Genome Announc. 2017 Jun 1;5(22). pii: e00442-17. doi: 10.1128/genomeA.00442-17.

17.

Inferring Human Demographic Histories of Non-African Populations from Patterns of Allele Sharing.

Wall JD.

Am J Hum Genet. 2017 May 4;100(5):766-772. doi: 10.1016/j.ajhg.2017.04.002.

18.

Systems biology guided by XCMS Online metabolomics.

Huan T, Forsberg EM, Rinehart D, Johnson CH, Ivanisevic J, Benton HP, Fang M, Aisporna A, Hilmers B, Poole FL, Thorgersen MP, Adams MWW, Krantz G, Fields MW, Robbins PD, Niedernhofer LJ, Ideker T, Majumder EL, Wall JD, Rattray NJW, Goodacre R, Lairson LL, Siuzdak G.

Nat Methods. 2017 Apr 27;14(5):461-462. doi: 10.1038/nmeth.4260. No abstract available.

19.

Mechanism for microbial population collapse in a fluctuating resource environment.

Turkarslan S, Raman AV, Thompson AW, Arens CE, Gillespie MA, von Netzer F, Hillesland KL, Stolyar S, López García de Lomana A, Reiss DJ, Gorman-Lewis D, Zane GM, Ranish JA, Wall JD, Stahl DA, Baliga NS.

Mol Syst Biol. 2017 Mar 20;13(3):919. doi: 10.15252/msb.20167058.

20.

The direct role of selenocysteine in [NiFeSe] hydrogenase maturation and catalysis.

Marques MC, Tapia C, Gutiérrez-Sanz O, Ramos AR, Keller KL, Wall JD, De Lacey AL, Matias PM, Pereira IAC.

Nat Chem Biol. 2017 May;13(5):544-550. doi: 10.1038/nchembio.2335. Epub 2017 Mar 20.

PMID:
28319099
21.

Archaic admixture in human history.

Wall JD, Yoshihara Caldeira Brandt D.

Curr Opin Genet Dev. 2016 Dec;41:93-97. doi: 10.1016/j.gde.2016.07.002. Epub 2016 Sep 20. Review.

PMID:
27662059
22.

A genomic history of Aboriginal Australia.

Malaspinas AS, Westaway MC, Muller C, Sousa VC, Lao O, Alves I, Bergström A, Athanasiadis G, Cheng JY, Crawford JE, Heupink TH, Macholdt E, Peischl S, Rasmussen S, Schiffels S, Subramanian S, Wright JL, Albrechtsen A, Barbieri C, Dupanloup I, Eriksson A, Margaryan A, Moltke I, Pugach I, Korneliussen TS, Levkivskyi IP, Moreno-Mayar JV, Ni S, Racimo F, Sikora M, Xue Y, Aghakhanian FA, Brucato N, Brunak S, Campos PF, Clark W, Ellingvåg S, Fourmile G, Gerbault P, Injie D, Koki G, Leavesley M, Logan B, Lynch A, Matisoo-Smith EA, McAllister PJ, Mentzer AJ, Metspalu M, Migliano AB, Murgha L, Phipps ME, Pomat W, Reynolds D, Ricaut FX, Siba P, Thomas MG, Wales T, Wall CM, Oppenheimer SJ, Tyler-Smith C, Durbin R, Dortch J, Manica A, Schierup MH, Foley RA, Lahr MM, Bowern C, Wall JD, Mailund T, Stoneking M, Nielsen R, Sandhu MS, Excoffier L, Lambert DM, Willerslev E.

Nature. 2016 Oct 13;538(7624):207-214. doi: 10.1038/nature18299. Epub 2016 Sep 21.

PMID:
27654914
23.

Genomic analyses inform on migration events during the peopling of Eurasia.

Pagani L, Lawson DJ, Jagoda E, Mörseburg A, Eriksson A, Mitt M, Clemente F, Hudjashov G, DeGiorgio M, Saag L, Wall JD, Cardona A, Mägi R, Wilson Sayres MA, Kaewert S, Inchley C, Scheib CL, Järve M, Karmin M, Jacobs GS, Antao T, Iliescu FM, Kushniarevich A, Ayub Q, Tyler-Smith C, Xue Y, Yunusbayev B, Tambets K, Mallick CB, Saag L, Pocheshkhova E, Andriadze G, Muller C, Westaway MC, Lambert DM, Zoraqi G, Turdikulova S, Dalimova D, Sabitov Z, Sultana GNN, Lachance J, Tishkoff S, Momynaliev K, Isakova J, Damba LD, Gubina M, Nymadawa P, Evseeva I, Atramentova L, Utevska O, Ricaut FX, Brucato N, Sudoyo H, Letellier T, Cox MP, Barashkov NA, Skaro V, Mulahasanovic L, Primorac D, Sahakyan H, Mormina M, Eichstaedt CA, Lichman DV, Abdullah S, Chaubey G, Wee JTS, Mihailov E, Karunas A, Litvinov S, Khusainova R, Ekomasova N, Akhmetova V, Khidiyatova I, Marjanović D, Yepiskoposyan L, Behar DM, Balanovska E, Metspalu A, Derenko M, Malyarchuk B, Voevoda M, Fedorova SA, Osipova LP, Lahr MM, Gerbault P, Leavesley M, Migliano AB, Petraglia M, Balanovsky O, Khusnutdinova EK, Metspalu E, Thomas MG, Manica A, Nielsen R, Villems R, Willerslev E, Kivisild T, Metspalu M.

Nature. 2016 Oct 13;538(7624):238-242. doi: 10.1038/nature19792. Epub 2016 Sep 21.

24.

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.

25.

Development and Validation of Broad-Range Qualitative and Clade-Specific Quantitative Molecular Probes for Assessing Mercury Methylation in the Environment.

Christensen GA, Wymore AM, King AJ, Podar M, Hurt RA Jr, Santillan EU, Soren A, Brandt CC, Brown SD, Palumbo AV, Wall JD, Gilmour CC, Elias DA.

Appl Environ Microbiol. 2016 Sep 16;82(19):6068-78. doi: 10.1128/AEM.01271-16. Print 2016 Oct 1.

26.

Electron transfer pathways of formate-driven H2 production in Desulfovibrio.

Martins M, Mourato C, Morais-Silva FO, Rodrigues-Pousada C, Voordouw G, Wall JD, Pereira IA.

Appl Microbiol Biotechnol. 2016 Sep;100(18):8135-46. doi: 10.1007/s00253-016-7649-7. Epub 2016 Jun 7.

PMID:
27270746
27.

Detecting Recombination Hotspots from Patterns of Linkage Disequilibrium.

Wall JD, Stevison LS.

G3 (Bethesda). 2016 Aug 9;6(8):2265-71. doi: 10.1534/g3.116.029587.

28.

Corrigendum: Model-based analyses of whole-genome data reveal a complex evolutionary history involving archaic introgression in Central African Pygmies.

Hsieh P, Woerner AE, Wall JD, Lachance J, Tishkoff SA, Gutenkunst RN, Hammer MF.

Genome Res. 2016 May;26(5):717.1. doi: 10.1101/gr.206524.116. No abstract available.

29.

A hybrid approach for de novo human genome sequence assembly and phasing.

Mostovoy Y, Levy-Sakin M, Lam J, Lam ET, Hastie AR, Marks P, Lee J, Chu C, Lin C, Džakula Ž, Cao H, Schlebusch SA, Giorda K, Schnall-Levin M, Wall JD, Kwok PY.

Nat Methods. 2016 Jul;13(7):587-90. doi: 10.1038/nmeth.3865. Epub 2016 May 9.

30.

Genomewide ancestry and divergence patterns from low-coverage sequencing data reveal a complex history of admixture in wild baboons.

Wall JD, Schlebusch SA, Alberts SC, Cox LA, Snyder-Mackler N, Nevonen KA, Carbone L, Tung J.

Mol Ecol. 2016 Jul;25(14):3469-83. doi: 10.1111/mec.13684. Epub 2016 Jun 15.

31.

Efficient Genome-Wide Sequencing and Low-Coverage Pedigree Analysis from Noninvasively Collected Samples.

Snyder-Mackler N, Majoros WH, Yuan ML, Shaver AO, Gordon JB, Kopp GH, Schlebusch SA, Wall JD, Alberts SC, Mukherjee S, Zhou X, Tung J.

Genetics. 2016 Jun;203(2):699-714. doi: 10.1534/genetics.116.187492. Epub 2016 Apr 20.

32.

Global Isotope Metabolomics Reveals Adaptive Strategies for Nitrogen Assimilation.

Kurczy ME, Forsberg EM, Thorgersen MP, Poole FL 2nd, Benton HP, Ivanisevic J, Tran ML, Wall JD, Elias DA, Adams MW, Siuzdak G.

ACS Chem Biol. 2016 Jun 17;11(6):1677-85. doi: 10.1021/acschembio.6b00082. Epub 2016 Apr 8.

33.

Transcriptomic and epigenomic characterization of the developing bat wing.

Eckalbar WL, Schlebusch SA, Mason MK, Gill Z, Parker AV, Booker BM, Nishizaki S, Muswamba-Nday C, Terhune E, Nevonen KA, Makki N, Friedrich T, VanderMeer JE, Pollard KS, Carbone L, Wall JD, Illing N, Ahituv N.

Nat Genet. 2016 May;48(5):528-36. doi: 10.1038/ng.3537. Epub 2016 Mar 28.

34.

Model-based analyses of whole-genome data reveal a complex evolutionary history involving archaic introgression in Central African Pygmies.

Hsieh P, Woerner AE, Wall JD, Lachance J, Tishkoff SA, Gutenkunst RN, Hammer MF.

Genome Res. 2016 Mar;26(3):291-300. doi: 10.1101/gr.196634.115. Epub 2016 Feb 17. Erratum in: Genome Res. 2016 May;26(5):717.1.

35.

Whole-genome sequence analyses of Western Central African Pygmy hunter-gatherers reveal a complex demographic history and identify candidate genes under positive natural selection.

Hsieh P, Veeramah KR, Lachance J, Tishkoff SA, Wall JD, Hammer MF, Gutenkunst RN.

Genome Res. 2016 Mar;26(3):279-90. doi: 10.1101/gr.192971.115. Epub 2016 Feb 17.

36.

Bacterial Interactomes: Interacting Protein Partners Share Similar Function and Are Validated in Independent Assays More Frequently Than Previously Reported.

Shatsky M, Allen S, Gold BL, Liu NL, Juba TR, Reveco SA, Elias DA, Prathapam R, He J, Yang W, Szakal ED, Liu H, Singer ME, Geller JT, Lam BR, Saini A, Trotter VV, Hall SC, Fisher SJ, Brenner SE, Chhabra SR, Hazen TC, Wall JD, Witkowska HE, Biggin MD, Chandonia JM, Butland G.

Mol Cell Proteomics. 2016 May;15(5):1539-55. doi: 10.1074/mcp.M115.054692. Epub 2016 Feb 12.

37.

Solids Retention Time Dependent Phototrophic Growth and Population Changes in Chemostat Cultivation Using Wastewater.

Shen Q, Wall JD, Hu Z.

Water Environ Res. 2016 Jan;88(1):5-12. doi: 10.2175/106143014X13975035526103.

PMID:
26803021
38.

The Time Scale of Recombination Rate Evolution in Great Apes.

Stevison LS, Woerner AE, Kidd JM, Kelley JL, Veeramah KR, McManus KF; Great Ape Genome Project, Bustamante CD, Hammer MF, Wall JD.

Mol Biol Evol. 2016 Apr;33(4):928-45. doi: 10.1093/molbev/msv331. Epub 2015 Dec 15.

39.

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.

40.

Regulation of Nitrite Stress Response in Desulfovibrio vulgaris Hildenborough, a Model Sulfate-Reducing Bacterium.

Rajeev L, Chen A, Kazakov AE, Luning EG, Zane GM, Novichkov PS, Wall JD, Mukhopadhyay A.

J Bacteriol. 2015 Nov;197(21):3400-8. doi: 10.1128/JB.00319-15. Epub 2015 Aug 17.

41.

A Post-Genomic View of the Ecophysiology, Catabolism and Biotechnological Relevance of Sulphate-Reducing Prokaryotes.

Rabus R, Venceslau SS, Wöhlbrand L, Voordouw G, Wall JD, Pereira IA.

Adv Microb Physiol. 2015;66:55-321. doi: 10.1016/bs.ampbs.2015.05.002. Epub 2015 Jul 9. Review.

PMID:
26210106
42.

Rapid selective sweep of pre-existing polymorphisms and slow fixation of new mutations in experimental evolution of Desulfovibrio vulgaris.

Zhou A, Hillesland KL, He Z, Schackwitz W, Tu Q, Zane GM, Ma Q, Qu Y, Stahl DA, Wall JD, Hazen TC, Fields MW, Arkin AP, Zhou J.

ISME J. 2015 Nov;9(11):2360-72. doi: 10.1038/ismej.2015.45. Epub 2015 Apr 7.

43.

Examining phylogenetic relationships among gibbon genera using whole genome sequence data using an approximate bayesian computation approach.

Veeramah KR, Woerner AE, Johnstone L, Gut I, Gut M, Marques-Bonet T, Carbone L, Wall JD, Hammer MF.

Genetics. 2015 May;200(1):295-308. doi: 10.1534/genetics.115.174425. Epub 2015 Mar 12.

44.

Site-directed mutagenesis of HgcA and HgcB reveals amino acid residues important for mercury methylation.

Smith SD, Bridou R, Johs A, Parks JM, Elias DA, Hurt RA Jr, Brown SD, Podar M, Wall JD.

Appl Environ Microbiol. 2015 May 1;81(9):3205-17. doi: 10.1128/AEM.00217-15. Epub 2015 Feb 27.

45.

Sulfur isotope fractionation during the evolutionary adaptation of a sulfate-reducing bacterium.

Pellerin A, Anderson-Trocmé L, Whyte LG, Zane GM, Wall JD, Wing BA.

Appl Environ Microbiol. 2015 Apr;81(8):2676-89. doi: 10.1128/AEM.03476-14. Epub 2015 Feb 6.

46.

Biofilm growth mode promotes maximum carrying capacity and community stability during product inhibition syntrophy.

Brileya KA, Camilleri LB, Zane GM, Wall JD, Fields MW.

Front Microbiol. 2014 Dec 15;5:693. doi: 10.3389/fmicb.2014.00693. eCollection 2014.

47.

Independence of nitrate and nitrite inhibition of Desulfovibrio vulgaris Hildenborough and use of nitrite as a substrate for growth.

Korte HL, Saini A, Trotter VV, Butland GP, Arkin AP, Wall JD.

Environ Sci Technol. 2015 Jan 20;49(2):924-31.

PMID:
25534748
48.

Inference of gorilla demographic and selective history from whole-genome sequence data.

McManus KF, Kelley JL, Song S, Veeramah KR, Woerner AE, Stevison LS, Ryder OA, Ape Genome Project G, Kidd JM, Wall JD, Bustamante CD, Hammer MF.

Mol Biol Evol. 2015 Mar;32(3):600-12. doi: 10.1093/molbev/msu394. Epub 2014 Dec 21.

49.

Paleogenomics. Genomic structure in Europeans dating back at least 36,200 years.

Seguin-Orlando A, Korneliussen TS, Sikora M, Malaspinas AS, Manica A, Moltke I, Albrechtsen A, Ko A, Margaryan A, Moiseyev V, Goebel T, Westaway M, Lambert D, Khartanovich V, Wall JD, Nigst PR, Foley RA, Lahr MM, Nielsen R, Orlando L, Willerslev E.

Science. 2014 Nov 28;346(6213):1113-8. doi: 10.1126/science.aaa0114. Epub 2014 Nov 6.

50.

The FlxABCD-HdrABC proteins correspond to a novel NADH dehydrogenase/heterodisulfide reductase widespread in anaerobic bacteria and involved in ethanol metabolism in Desulfovibrio vulgaris Hildenborough.

Ramos AR, Grein F, Oliveira GP, Venceslau SS, Keller KL, Wall JD, Pereira IA.

Environ Microbiol. 2015 Jul;17(7):2288-305. doi: 10.1111/1462-2920.12689. Epub 2015 Jan 27.

PMID:
25367508

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