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Items: 30

1.

Gut Microbiome-Based Metagenomic Signature for Non-invasive Detection of Advanced Fibrosis in Human Nonalcoholic Fatty Liver Disease.

Loomba R, Seguritan V, Li W, Long T, Klitgord N, Bhatt A, Dulai PS, Caussy C, Bettencourt R, Highlander SK, Jones MB, Sirlin CB, Schnabl B, Brinkac L, Schork N, Chen CH, Brenner DA, Biggs W, Yooseph S, Venter JC, Nelson KE.

Cell Metab. 2017 May 2;25(5):1054-1062.e5. doi: 10.1016/j.cmet.2017.04.001.

2.

Utilization of defined microbial communities enables effective evaluation of meta-genomic assemblies.

Greenwald WW, Klitgord N, Seguritan V, Yooseph S, Venter JC, Garner C, Nelson KE, Li W.

BMC Genomics. 2017 Apr 13;18(1):296. doi: 10.1186/s12864-017-3679-5.

3.

A robust ambient temperature collection and stabilization strategy: Enabling worldwide functional studies of the human microbiome.

Anderson EL, Li W, Klitgord N, Highlander SK, Dayrit M, Seguritan V, Yooseph S, Biggs W, Venter JC, Nelson KE, Jones MB.

Sci Rep. 2016 Aug 25;6:31731. doi: 10.1038/srep31731.

4.

Microbial diversity in individuals and their household contacts following typical antibiotic courses.

Abeles SR, Jones MB, Santiago-Rodriguez TM, Ly M, Klitgord N, Yooseph S, Nelson KE, Pride DT.

Microbiome. 2016 Jul 30;4(1):39. doi: 10.1186/s40168-016-0187-9.

5.

Library preparation methodology can influence genomic and functional predictions in human microbiome research.

Jones MB, Highlander SK, Anderson EL, Li W, Dayrit M, Klitgord N, Fabani MM, Seguritan V, Green J, Pride DT, Yooseph S, Biggs W, Nelson KE, Venter JC.

Proc Natl Acad Sci U S A. 2015 Nov 10;112(45):14024-9. doi: 10.1073/pnas.1519288112. Epub 2015 Oct 28.

6.

Isolation of a significant fraction of non-phototroph diversity from a desert Biological Soil Crust.

Nunes da Rocha U, Cadillo-Quiroz H, Karaoz U, Rajeev L, Klitgord N, Dunn S, Truong V, Buenrostro M, Bowen BP, Garcia-Pichel F, Mukhopadhyay A, Northen TR, Brodie EL.

Front Microbiol. 2015 Apr 14;6:277. doi: 10.3389/fmicb.2015.00277. eCollection 2015.

7.

A rapid molecular approach for chromosomal phasing.

Regan JF, Kamitaki N, Legler T, Cooper S, Klitgord N, Karlin-Neumann G, Wong C, Hodges S, Koehler R, Tzonev S, McCarroll SA.

PLoS One. 2015 Mar 4;10(3):e0118270. doi: 10.1371/journal.pone.0118270. eCollection 2015.

8.

Multiplexed target detection using DNA-binding dye chemistry in droplet digital PCR.

McDermott GP, Do D, Litterst CM, Maar D, Hindson CM, Steenblock ER, Legler TC, Jouvenot Y, Marrs SH, Bemis A, Shah P, Wong J, Wang S, Sally D, Javier L, Dinio T, Han C, Brackbill TP, Hodges SP, Ling Y, Klitgord N, Carman GJ, Berman JR, Koehler RT, Hiddessen AL, Walse P, Bousse L, Tzonev S, Hefner E, Hindson BJ, Cauly TH 3rd, Hamby K, Patel VP, Regan JF, Wyatt PW, Karlin-Neumann GA, Stumbo DP, Lowe AJ.

Anal Chem. 2013 Dec 3;85(23):11619-27. doi: 10.1021/ac403061n. Epub 2013 Nov 19.

PMID:
24180464
9.

The COMBREX project: design, methodology, and initial results.

Anton BP, Chang YC, Brown P, Choi HP, Faller LL, Guleria J, Hu Z, Klitgord N, Levy-Moonshine A, Maksad A, Mazumdar V, McGettrick M, Osmani L, Pokrzywa R, Rachlin J, Swaminathan R, Allen B, Housman G, Monahan C, Rochussen K, Tao K, Bhagwat AS, Brenner SE, Columbus L, de Crécy-Lagard V, Ferguson D, Fomenkov A, Gadda G, Morgan RD, Osterman AL, Rodionov DA, Rodionova IA, Rudd KE, Söll D, Spain J, Xu SY, Bateman A, Blumenthal RM, Bollinger JM, Chang WS, Ferrer M, Friedberg I, Galperin MY, Gobeill J, Haft D, Hunt J, Karp P, Klimke W, Krebs C, Macelis D, Madupu R, Martin MJ, Miller JH, O'Donovan C, Palsson B, Ruch P, Setterdahl A, Sutton G, Tate J, Yakunin A, Tchigvintsev D, Plata G, Hu J, Greiner R, Horn D, Sjölander K, Salzberg SL, Vitkup D, Letovsky S, Segrè D, DeLisi C, Roberts RJ, Steffen M, Kasif S.

PLoS Biol. 2013;11(8):e1001638. doi: 10.1371/journal.pbio.1001638. Epub 2013 Aug 27. No abstract available.

10.

The ability of flux balance analysis to predict evolution of central metabolism scales with the initial distance to the optimum.

Harcombe WR, Delaney NF, Leiby N, Klitgord N, Marx CJ.

PLoS Comput Biol. 2013;9(6):e1003091. doi: 10.1371/journal.pcbi.1003091. Epub 2013 Jun 20.

11.

Dynamic cyanobacterial response to hydration and dehydration in a desert biological soil crust.

Rajeev L, da Rocha UN, Klitgord N, Luning EG, Fortney J, Axen SD, Shih PM, Bouskill NJ, Bowen BP, Kerfeld CA, Garcia-Pichel F, Brodie EL, Northen TR, Mukhopadhyay A.

ISME J. 2013 Nov;7(11):2178-91. doi: 10.1038/ismej.2013.83. Epub 2013 Jun 6.

12.

Deep sequencing of the oral microbiome reveals signatures of periodontal disease.

Liu B, Faller LL, Klitgord N, Mazumdar V, Ghodsi M, Sommer DD, Gibbons TR, Treangen TJ, Chang YC, Li S, Stine OC, Hasturk H, Kasif S, Segrè D, Pop M, Amar S.

PLoS One. 2012;7(6):e37919. doi: 10.1371/journal.pone.0037919. Epub 2012 Jun 4.

13.

Detection of transcriptional triggers in the dynamics of microbial growth: application to the respiratorily versatile bacterium Shewanella oneidensis.

Beg QK, Zampieri M, Klitgord N, Collins SB, Altafini C, Serres MH, Segrè D.

Nucleic Acids Res. 2012 Aug;40(15):7132-49. doi: 10.1093/nar/gks467. Epub 2012 May 25.

14.

Host-pathogen interactome mapping for HTLV-1 and -2 retroviruses.

Simonis N, Rual JF, Lemmens I, Boxus M, Hirozane-Kishikawa T, Gatot JS, Dricot A, Hao T, Vertommen D, Legros S, Daakour S, Klitgord N, Martin M, Willaert JF, Dequiedt F, Navratil V, Cusick ME, Burny A, Van Lint C, Hill DE, Tavernier J, Kettmann R, Vidal M, Twizere JC.

Retrovirology. 2012 Mar 29;9:26. doi: 10.1186/1742-4690-9-26.

15.

Ecosystems biology of microbial metabolism.

Klitgord N, Segrè D.

Curr Opin Biotechnol. 2011 Aug;22(4):541-6. doi: 10.1016/j.copbio.2011.04.018. Epub 2011 May 16. Review.

PMID:
21592777
16.

Environments that induce synthetic microbial ecosystems.

Klitgord N, Segrè D.

PLoS Comput Biol. 2010 Nov 18;6(11):e1001002. doi: 10.1371/journal.pcbi.1001002.

17.

COMBREX: a project to accelerate the functional annotation of prokaryotic genomes.

Roberts RJ, Chang YC, Hu Z, Rachlin JN, Anton BP, Pokrzywa RM, Choi HP, Faller LL, Guleria J, Housman G, Klitgord N, Mazumdar V, McGettrick MG, Osmani L, Swaminathan R, Tao KR, Letovsky S, Vitkup D, Segrè D, Salzberg SL, Delisi C, Steffen M, Kasif S.

Nucleic Acids Res. 2011 Jan;39(Database issue):D11-4. doi: 10.1093/nar/gkq1168. Epub 2010 Nov 21.

18.

A genome-wide gene function prediction resource for Drosophila melanogaster.

Yan H, Venkatesan K, Beaver JE, Klitgord N, Yildirim MA, Hao T, Hill DE, Cusick ME, Perrimon N, Roth FP, Vidal M.

PLoS One. 2010 Aug 12;5(8):e12139. doi: 10.1371/journal.pone.0012139.

19.

Co-evolution of metabolism and protein sequences.

Schütte M, Klitgord N, Segrè D, Ebenhöh O.

Genome Inform. 2010 Jan;22:156-66.

20.
21.

Edgetic perturbation models of human inherited disorders.

Zhong Q, Simonis N, Li QR, Charloteaux B, Heuze F, Klitgord N, Tam S, Yu H, Venkatesan K, Mou D, Swearingen V, Yildirim MA, Yan H, Dricot A, Szeto D, Lin C, Hao T, Fan C, Milstein S, Dupuy D, Brasseur R, Hill DE, Cusick ME, Vidal M.

Mol Syst Biol. 2009;5:321. doi: 10.1038/msb.2009.80. Epub 2009 Nov 3.

22.

Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network.

Simonis N, Rual JF, Carvunis AR, Tasan M, Lemmens I, Hirozane-Kishikawa T, Hao T, Sahalie JM, Venkatesan K, Gebreab F, Cevik S, Klitgord N, Fan C, Braun P, Li N, Ayivi-Guedehoussou N, Dann E, Bertin N, Szeto D, Dricot A, Yildirim MA, Lin C, de Smet AS, Kao HL, Simon C, Smolyar A, Ahn JS, Tewari M, Boxem M, Milstein S, Yu H, Dreze M, Vandenhaute J, Gunsalus KC, Cusick ME, Hill DE, Tavernier J, Roth FP, Vidal M.

Nat Methods. 2009 Jan;6(1):47-54.

23.

An empirical framework for binary interactome mapping.

Venkatesan K, Rual JF, Vazquez A, Stelzl U, Lemmens I, Hirozane-Kishikawa T, Hao T, Zenkner M, Xin X, Goh KI, Yildirim MA, Simonis N, Heinzmann K, Gebreab F, Sahalie JM, Cevik S, Simon C, de Smet AS, Dann E, Smolyar A, Vinayagam A, Yu H, Szeto D, Borick H, Dricot A, Klitgord N, Murray RR, Lin C, Lalowski M, Timm J, Rau K, Boone C, Braun P, Cusick ME, Roth FP, Hill DE, Tavernier J, Wanker EE, Barabási AL, Vidal M.

Nat Methods. 2009 Jan;6(1):83-90. doi: 10.1038/nmeth.1280. Epub 2008 Dec 7.

24.

A protein domain-based interactome network for C. elegans early embryogenesis.

Boxem M, Maliga Z, Klitgord N, Li N, Lemmens I, Mana M, de Lichtervelde L, Mul JD, van de Peut D, Devos M, Simonis N, Yildirim MA, Cokol M, Kao HL, de Smet AS, Wang H, Schlaitz AL, Hao T, Milstein S, Fan C, Tipsword M, Drew K, Galli M, Rhrissorrakrai K, Drechsel D, Koller D, Roth FP, Iakoucheva LM, Dunker AK, Bonneau R, Gunsalus KC, Hill DE, Piano F, Tavernier J, van den Heuvel S, Hyman AA, Vidal M.

Cell. 2008 Aug 8;134(3):534-45. doi: 10.1016/j.cell.2008.07.009. Erratum in: Cell. 2012 Dec 21;151(7):1633.

25.

Revisiting the Saccharomyces cerevisiae predicted ORFeome.

Li QR, Carvunis AR, Yu H, Han JD, Zhong Q, Simonis N, Tam S, Hao T, Klitgord NJ, Dupuy D, Mou D, Wapinski I, Regev A, Hill DE, Cusick ME, Vidal M.

Genome Res. 2008 Aug;18(8):1294-303. doi: 10.1101/gr.076661.108. Epub 2008 May 23.

26.

Novel insights into RNAi off-target effects using C. elegans paralogs.

Rual JF, Klitgord N, Achaz G.

BMC Genomics. 2007 Apr 19;8:106.

27.

Intrinsic disorder is a common feature of hub proteins from four eukaryotic interactomes.

Haynes C, Oldfield CJ, Ji F, Klitgord N, Cusick ME, Radivojac P, Uversky VN, Vidal M, Iakoucheva LM.

PLoS Comput Biol. 2006 Aug 4;2(8):e100. Epub 2006 Jun 23.

28.

Towards a proteome-scale map of the human protein-protein interaction network.

Rual JF, Venkatesan K, Hao T, Hirozane-Kishikawa T, Dricot A, Li N, Berriz GF, Gibbons FD, Dreze M, Ayivi-Guedehoussou N, Klitgord N, Simon C, Boxem M, Milstein S, Rosenberg J, Goldberg DS, Zhang LV, Wong SL, Franklin G, Li S, Albala JS, Lim J, Fraughton C, Llamosas E, Cevik S, Bex C, Lamesch P, Sikorski RS, Vandenhaute J, Zoghbi HY, Smolyar A, Bosak S, Sequerra R, Doucette-Stamm L, Cusick ME, Hill DE, Roth FP, Vidal M.

Nature. 2005 Oct 20;437(7062):1173-8. Epub 2005 Sep 28.

PMID:
16189514
29.

Interactome: gateway into systems biology.

Cusick ME, Klitgord N, Vidal M, Hill DE.

Hum Mol Genet. 2005 Oct 15;14 Spec No. 2:R171-81. Epub 2005 Sep 14. Review.

PMID:
16162640
30.

Adult myogenesis in Drosophila melanogaster can proceed independently of myocyte enhancer factor-2.

Baker PW, Tanaka KK, Klitgord N, Cripps RM.

Genetics. 2005 Aug;170(4):1747-59. Epub 2005 Jun 14.

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