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Items: 1 to 50 of 107

1.

Minimal Interspecies Interaction Adjustment (MIIA): Inference of Neighbor-Dependent Interactions in Microbial Communities.

Song HS, Lee JY, Haruta S, Nelson WC, Lee DY, Lindemann SR, Fredrickson JK, Bernstein HC.

Front Microbiol. 2019 Jun 11;10:1264. doi: 10.3389/fmicb.2019.01264. eCollection 2019.

2.

Comparison of sequence-specific oligonucleotide probe vs next generation sequencing for HLA-A, B, C, DRB1, DRB3/B4/B5, DQA1, DQB1, DPA1, and DPB1 typing: Toward single-pass high-resolution HLA typing in support of solid organ and hematopoietic cell transplant programs.

Smith AG, Pereira S, Jaramillo A, Stoll ST, Khan FM, Berka N, Mostafa AA, Pando MJ, Usenko CY, Bettinotti MP, Pyo CW, Nelson WC, Willis A, Askar M, Geraghty DE.

HLA. 2019 Sep;94(3):296-306. doi: 10.1111/tan.13619. Epub 2019 Jul 15.

3.

Eleven Amino Acids of HLA-DRB1 and Fifteen Amino Acids of HLA-DRB3, 4, and 5 Include Potentially Causal Residues Responsible for the Risk of Childhood Type 1 Diabetes.

Zhao LP, Papadopoulos GK, Kwok WW, Xu B, Kong M, Moustakas AK, Bondinas GP, Carlsson A, Elding-Larsson H, Ludvigsson J, Marcus C, Persson M, Samuelsson U, Wang R, Pyo CW, Nelson WC, Geraghty DE, Lernmark Å.

Diabetes. 2019 Aug;68(8):1692-1704. doi: 10.2337/db19-0273. Epub 2019 May 24.

PMID:
31127057
4.

Correction for Christensen et al., "Identification of Novel Protein Lysine Acetyltransferases in Escherichia coli".

Christensen DG, Meyer JG, Baumgartner JT, D'Souza AK, Nelson WC, Payne SH, Kuhn ML, Schilling B, Wolfe AJ.

MBio. 2019 Apr 9;10(2). pii: e00592-19. doi: 10.1128/mBio.00592-19. No abstract available.

5.

Identification of Novel Protein Lysine Acetyltransferases in Escherichia coli.

Christensen DG, Meyer JG, Baumgartner JT, D'Souza AK, Nelson WC, Payne SH, Kuhn ML, Schilling B, Wolfe AJ.

MBio. 2018 Oct 23;9(5). pii: e01905-18. doi: 10.1128/mBio.01905-18. Erratum in: MBio. 2019 Apr 9;10(2):.

6.

Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.

Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C; Genome Standards Consortium, Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T.

Nat Biotechnol. 2018 Jul 6;36(7):660. doi: 10.1038/nbt0718-660a. No abstract available.

PMID:
29979671
7.

Corrigendum: Saliniramus fredricksonii gen. nov., sp. nov., a heterotrophic halophile isolated from Hot Lake, Washington, a member of a novel lineage (Salinarimonadaceae fam. nov.) within the order Rhizobiales, and reclassification of the genus Salinarimonas Liu et al. 2010 into Salinarimonadaceae.

Cole JK, Morton BR, Cardamone HC, Lake HRR, Dohnalkova AC, Kim YM, Kyle JE, Maezato Y, Dana KL, Metz TO, Romine MF, Nelson WC, Lindemann SR.

Int J Syst Evol Microbiol. 2018 Jun;68(6):2116-2123. doi: 10.1099/ijsem.0.002807.

PMID:
29855404
8.

Salinivirga fredricksonii gen. nov., sp. nov., a heterotrophic halophile isolated from a photosynthetic mat, a member of a novel lineage (Salinarimonadaceae fam. nov.) within the order Rhizobiales, and reclassification of the genus Salinarimonas Liu et al. 2010 into Salinarimonadaceae.

Cole JK, Morton BR, Cardamone HC, Lake HRR, Dohnalkova AC, Kim YM, Kyle JE, Maezato Y, Dana KL, Metz TO, Romine MF, Nelson WC, Lindemann SR.

Int J Syst Evol Microbiol. 2018 May;68(5):1591-1598. doi: 10.1099/ijsem.0.002715. Epub 2018 Mar 26.

PMID:
29580321
9.

Publisher Correction: Influences of organic carbon speciation on hyporheic corridor biogeochemistry and microbial ecology.

Stegen JC, Johnson T, Fredrickson JK, Wilkins MJ, Konopka AE, Nelson WC, Arntzen EV, Chrisler WB, Chu RK, Fansler SJ, Graham EB, Kennedy DW, Resch CT, Tfaily M, Zachara J.

Nat Commun. 2018 Mar 7;9(1):1034. doi: 10.1038/s41467-018-03572-7.

10.

Draft Genome Sequence of Cyanobacterium sp. Strain HL-69, Isolated from a Benthic Microbial Mat from a Magnesium Sulfate-Dominated Hypersaline Lake.

Mobberley JM, Romine MF, Cole JK, Maezato Y, Lindemann SR, Nelson WC.

Genome Announc. 2018 Feb 8;6(6). pii: e01583-17. doi: 10.1128/genomeA.01583-17.

11.

Influences of organic carbon speciation on hyporheic corridor biogeochemistry and microbial ecology.

Stegen JC, Johnson T, Fredrickson JK, Wilkins MJ, Konopka AE, Nelson WC, Arntzen EV, Chrisler WB, Chu RK, Fansler SJ, Graham EB, Kennedy DW, Resch CT, Tfaily M, Zachara J.

Nat Commun. 2018 Feb 8;9(1):585. doi: 10.1038/s41467-018-02922-9. Erratum in: Nat Commun. 2018 Mar 7;9(1):1034.

12.

Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.

Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C; Genome Standards Consortium, Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T.

Nat Biotechnol. 2018 Feb 6;36(2):196. doi: 10.1038/nbt0218-196a. No abstract available.

13.

Phenotypic responses to interspecies competition and commensalism in a naturally-derived microbial co-culture.

Khan N, Maezato Y, McClure RS, Brislawn CJ, Mobberley JM, Isern N, Chrisler WB, Markillie LM, Barney BM, Song HS, Nelson WC, Bernstein HC.

Sci Rep. 2018 Jan 10;8(1):297. doi: 10.1038/s41598-017-18630-1.

14.

Geochemical and Microbial Community Attributes in Relation to Hyporheic Zone Geological Facies.

Hou Z, Nelson WC, Stegen JC, Murray CJ, Arntzen E, Crump AR, Kennedy DW, Perkins MC, Scheibe TD, Fredrickson JK, Zachara JM.

Sci Rep. 2017 Sep 20;7(1):12006. doi: 10.1038/s41598-017-12275-w.

15.

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.

Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C; Genome Standards Consortium, Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T.

Nat Biotechnol. 2017 Aug 8;35(8):725-731. doi: 10.1038/nbt.3893. Erratum in: Nat Biotechnol. 2018 Feb 6;36(2):196. Nat Biotechnol. 2018 Jul 6;36(7):660.

16.

Building and validating a prediction model for paediatric type 1 diabetes risk using next generation targeted sequencing of class II HLA genes.

Zhao LP, Carlsson A, Larsson HE, Forsander G, Ivarsson SA, Kockum I, Ludvigsson J, Marcus C, Persson M, Samuelsson U, Örtqvist E, Pyo CW, Bolouri H, Zhao M, Nelson WC, Geraghty DE, Lernmark Å; Better Diabetes Diagnosis (BDD) Study Group.

Diabetes Metab Res Rev. 2017 Nov;33(8). doi: 10.1002/dmrr.2921. Epub 2017 Sep 15. Erratum in: Diabetes Metab Res Rev. 2018 Feb;34(2):.

PMID:
28755385
17.

Predicting Species-Resolved Macronutrient Acquisition during Succession in a Model Phototrophic Biofilm Using an Integrated 'Omics Approach.

Lindemann SR, Mobberley JM, Cole JK, Markillie LM, Taylor RC, Huang E, Chrisler WB, Wiley HS, Lipton MS, Nelson WC, Fredrickson JK, Romine MF.

Front Microbiol. 2017 Jun 13;8:1020. doi: 10.3389/fmicb.2017.01020. eCollection 2017.

18.

Targeted quantification of functional enzyme dynamics in environmental samples for microbially mediated biogeochemical processes.

Li M, Gao Y, Qian WJ, Shi L, Liu Y, Nelson WC, Nicora CD, Resch CT, Thompson C, Yan S, Fredrickson JK, Zachara JM, Liu C.

Environ Microbiol Rep. 2017 Oct;9(5):512-521. doi: 10.1111/1758-2229.12558. Epub 2017 Jul 13.

PMID:
28618201
19.

Effect of Water Chemistry and Hydrodynamics on Nitrogen Transformation Activity and Microbial Community Functional Potential in Hyporheic Zone Sediment Columns.

Liu Y, Liu C, Nelson WC, Shi L, Xu F, Liu Y, Yan A, Zhong L, Thompson C, Fredrickson JK, Zachara JM.

Environ Sci Technol. 2017 May 2;51(9):4877-4886. doi: 10.1021/acs.est.6b05018. Epub 2017 Apr 18.

PMID:
28391700
20.

Organismal and spatial partitioning of energy and macronutrient transformations within a hypersaline mat.

Mobberley JM, Lindemann SR, Bernstein HC, Moran JJ, Renslow RS, Babauta J, Hu D, Beyenal H, Nelson WC.

FEMS Microbiol Ecol. 2017 Apr 1;93(4). doi: 10.1093/femsec/fix028.

21.

Underlying mechanisms for syntrophic metabolism of essential enzyme cofactors in microbial communities.

Romine MF, Rodionov DA, Maezato Y, Osterman AL, Nelson WC.

ISME J. 2017 Jun;11(6):1434-1446. doi: 10.1038/ismej.2017.2. Epub 2017 Feb 10.

22.

Maternal and fetal human leukocyte antigen class Ia and II alleles in severe preeclampsia and eclampsia.

Emmery J, Hachmon R, Pyo CW, Nelson WC, Geraghty DE, Andersen AM, Melbye M, Hviid TV.

Genes Immun. 2016 Jun;17(4):251-60. doi: 10.1038/gene.2016.20. Epub 2016 Apr 28.

PMID:
27121092
23.

Groundwater-surface water mixing shifts ecological assembly processes and stimulates organic carbon turnover.

Stegen JC, Fredrickson JK, Wilkins MJ, Konopka AE, Nelson WC, Arntzen EV, Chrisler WB, Chu RK, Danczak RE, Fansler SJ, Kennedy DW, Resch CT, Tfaily M.

Nat Commun. 2016 Apr 7;7:11237. doi: 10.1038/ncomms11237.

24.

Next-Generation Sequencing Reveals That HLA-DRB3, -DRB4, and -DRB5 May Be Associated With Islet Autoantibodies and Risk for Childhood Type 1 Diabetes.

Zhao LP, Alshiekh S, Zhao M, Carlsson A, Larsson HE, Forsander G, Ivarsson SA, Ludvigsson J, Kockum I, Marcus C, Persson M, Samuelsson U, Örtqvist E, Pyo CW, Nelson WC, Geraghty DE, Lernmark Å; Better Diabetes Diagnosis (BDD) Study Group.

Diabetes. 2016 Mar;65(3):710-8. doi: 10.2337/db15-1115. Epub 2016 Jan 6.

25.

Identification and Resolution of Microdiversity through Metagenomic Sequencing of Parallel Consortia.

Nelson WC, Maezato Y, Wu YW, Romine MF, Lindemann SR.

Appl Environ Microbiol. 2015 Oct 23;82(1):255-67. doi: 10.1128/AEM.02274-15. Print 2016 Jan 1.

26.

The reduced genomes of Parcubacteria (OD1) contain signatures of a symbiotic lifestyle.

Nelson WC, Stegen JC.

Front Microbiol. 2015 Jul 21;6:713. doi: 10.3389/fmicb.2015.00713. eCollection 2015.

27.

Simultaneous and selective isolation of multiple subpopulations of rare cells from peripheral blood using ensemble-decision aliquot ranking (eDAR).

Zhao M, Wei B, Nelson WC, Schiro PG, Chiu DT.

Lab Chip. 2015 Aug 21;15(16):3391-6. doi: 10.1039/c5lc00384a.

PMID:
26160592
28.

An integrated genotyping approach for HLA and other complex genetic systems.

Nelson WC, Pyo CW, Vogan D, Wang R, Pyon YS, Hennessey C, Smith A, Pereira S, Ishitani A, Geraghty DE.

Hum Immunol. 2015 Dec;76(12):928-38. doi: 10.1016/j.humimm.2015.05.001. Epub 2015 May 28.

29.

Trichodesmium genome maintains abundant, widespread noncoding DNA in situ, despite oligotrophic lifestyle.

Walworth N, Pfreundt U, Nelson WC, Mincer T, Heidelberg JF, Fu F, Waterbury JB, Glavina del Rio T, Goodwin L, Kyrpides NC, Land ML, Woyke T, Hutchins DA, Hess WR, Webb EA.

Proc Natl Acad Sci U S A. 2015 Apr 7;112(14):4251-6. doi: 10.1073/pnas.1422332112. Epub 2015 Mar 23.

30.

Genome Sequence of the Thermophilic Cyanobacterium Thermosynechococcus sp. Strain NK55a.

Stolyar S, Liu Z, Thiel V, Tomsho LP, Pinel N, Nelson WC, Lindemann SR, Romine MF, Haruta S, Schuster SC, Bryant DA, Fredrickson JK.

Genome Announc. 2014 Jan 30;2(1). pii: e01060-13. doi: 10.1128/genomeA.01060-13.

31.

New generation of ensemble-decision aliquot ranking based on simplified microfluidic components for large-capacity trapping of circulating tumor cells.

Zhao M, Nelson WC, Wei B, Schiro PG, Hakimi BM, Johnson ES, Anand RK, Gyurkey GS, White LM, Whiting SH, Coveler AL, Chiu DT.

Anal Chem. 2013 Oct 15;85(20):9671-7. doi: 10.1021/ac401985r. Epub 2013 Oct 2.

32.

Characterization of eukaryotic microbial diversity in hypersaline Lake Tyrrell, Australia.

Heidelberg KB, Nelson WC, Holm JB, Eisenkolb N, Andrade K, Emerson JB.

Front Microbiol. 2013 May 13;4:115. doi: 10.3389/fmicb.2013.00115. eCollection 2013.

33.

Microbial secondary succession in soil microcosms of a desert oasis in the Cuatro Cienegas Basin, Mexico.

López-Lozano NE, Heidelberg KB, Nelson WC, García-Oliva F, Eguiarte LE, Souza V.

PeerJ. 2013 Mar 5;1:e47. doi: 10.7717/peerj.47. Print 2013.

34.

Novel miniature transposable elements in thermophilic Synechococcus strains and their impact on an environmental population.

Nelson WC, Bhaya D, Heidelberg JF.

J Bacteriol. 2012 Jul;194(14):3636-42. doi: 10.1128/JB.00333-12. Epub 2012 May 4.

35.

Comparative analysis of eukaryotic marine microbial assemblages from 18S rRNA gene and gene transcript clone libraries by using different methods of extraction.

Koid A, Nelson WC, Mraz A, Heidelberg KB.

Appl Environ Microbiol. 2012 Jun;78(11):3958-65. doi: 10.1128/AEM.06941-11. Epub 2012 Mar 23.

36.

Prospects for the study of evolution in the deep biosphere.

Biddle JF, Sylvan JB, Brazelton WJ, Tully BJ, Edwards KJ, Moyer CL, Heidelberg JF, Nelson WC.

Front Microbiol. 2012 Jan 24;2:285. doi: 10.3389/fmicb.2011.00285. eCollection 2011.

37.

Metagenomic analysis of a complex marine planktonic thaumarchaeal community from the Gulf of Maine.

Tully BJ, Nelson WC, Heidelberg JF.

Environ Microbiol. 2012 Jan;14(1):254-67. doi: 10.1111/j.1462-2920.2011.02628.x. Epub 2011 Nov 3.

PMID:
22050608
38.

Mariprofundus ferrooxydans PV-1 the first genome of a marine Fe(II) oxidizing Zetaproteobacterium.

Singer E, Emerson D, Webb EA, Barco RA, Kuenen JG, Nelson WC, Chan CS, Comolli LR, Ferriera S, Johnson J, Heidelberg JF, Edwards KJ.

PLoS One. 2011;6(9):e25386. doi: 10.1371/journal.pone.0025386. Epub 2011 Sep 23.

39.

Dynamic contact angles and hysteresis under electrowetting-on-dielectric.

Nelson WC, Sen P, Kim CJ.

Langmuir. 2011 Aug 16;27(16):10319-26. doi: 10.1021/la2018083. Epub 2011 Jul 13.

40.

Analysis of insertion sequences in thermophilic cyanobacteria: exploring the mechanisms of establishing, maintaining, and withstanding high insertion sequence abundance.

Nelson WC, Wollerman L, Bhaya D, Heidelberg JF.

Appl Environ Microbiol. 2011 Aug;77(15):5458-66. doi: 10.1128/AEM.05090-11. Epub 2011 Jun 10.

41.

A miniature capillary breakup extensional rheometer by electrostatically assisted generation of liquid filaments.

Nelson WC, Kavehpour HP, Kim CJ.

Lab Chip. 2011 Jul 21;11(14):2424-31. doi: 10.1039/c0lc00691b. Epub 2011 Jun 8.

PMID:
21655586
42.

Genomic potential of Marinobacter aquaeolei, a biogeochemical "opportunitroph".

Singer E, Webb EA, Nelson WC, Heidelberg JF, Ivanova N, Pati A, Edwards KJ.

Appl Environ Microbiol. 2011 Apr;77(8):2763-71. doi: 10.1128/AEM.01866-10. Epub 2011 Feb 18.

43.

Incubated protein reduction and digestion on an electrowetting-on-dielectric digital microfluidic chip for MALDI-MS.

Nelson WC, Peng I, Lee GA, Loo JA, Garrell RL, Kim CJ.

Anal Chem. 2010 Dec 1;82(23):9932-7. doi: 10.1021/ac101833b. Epub 2010 Nov 8.

44.

The FibRumBa database: a resource for biologists with interests in gastrointestinal microbial ecology, plant biomass degradation, and anaerobic microbiology.

Morrison M, Daugherty SC, Nelson WC, Davidsen T, Nelson KE; North American Consortium for Fibrolytic Ruminal Bacteria.

Microb Ecol. 2010 Feb;59(2):212-3. doi: 10.1007/s00248-009-9562-4. Epub 2009 Jul 17. No abstract available.

PMID:
19609599
45.

Genome degradation in Brucella ovis corresponds with narrowing of its host range and tissue tropism.

Tsolis RM, Seshadri R, Santos RL, Sangari FJ, Lobo JM, de Jong MF, Ren Q, Myers G, Brinkac LM, Nelson WC, Deboy RT, Angiuoli S, Khouri H, Dimitrov G, Robinson JR, Mulligan S, Walker RL, Elzer PE, Hassan KA, Paulsen IT.

PLoS One. 2009;4(5):e5519. doi: 10.1371/journal.pone.0005519. Epub 2009 May 13.

46.

Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils.

Ward NL, Challacombe JF, Janssen PH, Henrissat B, Coutinho PM, Wu M, Xie G, Haft DH, Sait M, Badger J, Barabote RD, Bradley B, Brettin TS, Brinkac LM, Bruce D, Creasy T, Daugherty SC, Davidsen TM, DeBoy RT, Detter JC, Dodson RJ, Durkin AS, Ganapathy A, Gwinn-Giglio M, Han CS, Khouri H, Kiss H, Kothari SP, Madupu R, Nelson KE, Nelson WC, Paulsen I, Penn K, Ren Q, Rosovitz MJ, Selengut JD, Shrivastava S, Sullivan SA, Tapia R, Thompson LS, Watkins KL, Yang Q, Yu C, Zafar N, Zhou L, Kuske CR.

Appl Environ Microbiol. 2009 Apr;75(7):2046-56. doi: 10.1128/AEM.02294-08. Epub 2009 Feb 5.

47.

Germ warfare in a microbial mat community: CRISPRs provide insights into the co-evolution of host and viral genomes.

Heidelberg JF, Nelson WC, Schoenfeld T, Bhaya D.

PLoS One. 2009;4(1):e4169. doi: 10.1371/journal.pone.0004169. Epub 2009 Jan 9.

48.

Zeta potential and electroosmotic mobility in microfluidic devices fabricated from hydrophobic polymers: 1. The origins of charge.

Tandon V, Bhagavatula SK, Nelson WC, Kirby BJ.

Electrophoresis. 2008 Mar;29(5):1092-101. doi: 10.1002/elps.200700734.

PMID:
18306184
49.

Genomic differences between Fibrobacter succinogenes S85 and Fibrobacter intestinalis DR7, identified by suppression subtractive hybridization.

Qi M, Nelson KE, Daugherty SC, Nelson WC, Hance IR, Morrison M, Forsberg CW.

Appl Environ Microbiol. 2008 Feb;74(4):987-93. Epub 2007 Dec 21.

50.

Candidatus Chloracidobacterium thermophilum: an aerobic phototrophic Acidobacterium.

Bryant DA, Costas AM, Maresca JA, Chew AG, Klatt CG, Bateson MM, Tallon LJ, Hostetler J, Nelson WC, Heidelberg JF, Ward DM.

Science. 2007 Jul 27;317(5837):523-6.

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