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Items: 1 to 50 of 103

1.

Integrating host response and unbiased microbe detection for lower respiratory tract infection diagnosis in critically ill adults.

Langelier C, Kalantar KL, Moazed F, Wilson MR, Crawford ED, Deiss T, Belzer A, Bolourchi S, Caldera S, Fung M, Jauregui A, Malcolm K, Lyden A, Khan L, Vessel K, Quan J, Zinter M, Chiu CY, Chow ED, Wilson J, Miller S, Matthay MA, Pollard KS, Christenson S, Calfee CS, DeRisi JL.

Proc Natl Acad Sci U S A. 2018 Nov 27. pii: 201809700. doi: 10.1073/pnas.1809700115. [Epub ahead of print]

2.

Existing Climate Change Will Lead to Pronounced Shifts in the Diversity of Soil Prokaryotes.

Ladau J, Shi Y, Jing X, He JS, Chen L, Lin X, Fierer N, Gilbert JA, Pollard KS, Chu H.

mSystems. 2018 Oct 23;3(5). pii: e00167-18. doi: 10.1128/mSystems.00167-18. eCollection 2018 Sep-Oct.

3.

A most wanted list of conserved microbial protein families with no known domains.

Wyman SK, Avila-Herrera A, Nayfach S, Pollard KS.

PLoS One. 2018 Oct 17;13(10):e0205749. doi: 10.1371/journal.pone.0205749. eCollection 2018.

4.

Phylogeny-corrected identification of microbial gene families relevant to human gut colonization.

Bradley PH, Nayfach S, Pollard KS.

PLoS Comput Biol. 2018 Aug 9;14(8):e1006242. doi: 10.1371/journal.pcbi.1006242. eCollection 2018 Aug.

5.

Developmental Loci Harbor Clusters of Accelerated Regions That Evolved Independently in Ape Lineages.

Kostka D, Holloway AK, Pollard KS.

Mol Biol Evol. 2018 Aug 1;35(8):2034-2045. doi: 10.1093/molbev/msy109.

6.

American Gut: an Open Platform for Citizen Science Microbiome Research.

McDonald D, Hyde E, Debelius JW, Morton JT, Gonzalez A, Ackermann G, Aksenov AA, Behsaz B, Brennan C, Chen Y, DeRight Goldasich L, Dorrestein PC, Dunn RR, Fahimipour AK, Gaffney J, Gilbert JA, Gogul G, Green JL, Hugenholtz P, Humphrey G, Huttenhower C, Jackson MA, Janssen S, Jeste DV, Jiang L, Kelley ST, Knights D, Kosciolek T, Ladau J, Leach J, Marotz C, Meleshko D, Melnik AV, Metcalf JL, Mohimani H, Montassier E, Navas-Molina J, Nguyen TT, Peddada S, Pevzner P, Pollard KS, Rahnavard G, Robbins-Pianka A, Sangwan N, Shorenstein J, Smarr L, Song SJ, Spector T, Swafford AD, Thackray VG, Thompson LR, Tripathi A, Vázquez-Baeza Y, Vrbanac A, Wischmeyer P, Wolfe E, Zhu Q; American Gut Consortium , Knight R.

mSystems. 2018 May 15;3(3). pii: e00031-18. doi: 10.1128/mSystems.00031-18. eCollection 2018 May-Jun.

7.

The Epstein-Barr virus episome maneuvers between nuclear chromatin compartments during reactivation.

Moquin SA, Thomas S, Whalen S, Warburton A, Fernandez SG, McBride AA, Pollard KS, Miranda JJL.

J Virol. 2017 Nov 15. pii: JVI.01413-17. doi: 10.1128/JVI.01413-17. [Epub ahead of print]

8.

A communal catalogue reveals Earth's multiscale microbial diversity.

Thompson LR, Sanders JG, McDonald D, Amir A, Ladau J, Locey KJ, Prill RJ, Tripathi A, Gibbons SM, Ackermann G, Navas-Molina JA, Janssen S, Kopylova E, Vázquez-Baeza Y, González A, Morton JT, Mirarab S, Zech Xu Z, Jiang L, Haroon MF, Kanbar J, Zhu Q, Jin Song S, Kosciolek T, Bokulich NA, Lefler J, Brislawn CJ, Humphrey G, Owens SM, Hampton-Marcell J, Berg-Lyons D, McKenzie V, Fierer N, Fuhrman JA, Clauset A, Stevens RL, Shade A, Pollard KS, Goodwin KD, Jansson JK, Gilbert JA, Knight R; Earth Microbiome Project Consortium.

Nature. 2017 Nov 23;551(7681):457-463. doi: 10.1038/nature24621. Epub 2017 Nov 1.

9.

Human evolution: the non-coding revolution.

Franchini LF, Pollard KS.

BMC Biol. 2017 Oct 2;15(1):89. doi: 10.1186/s12915-017-0428-9. Review.

10.

Development of Inflammatory Bowel Disease Is Linked to a Longitudinal Restructuring of the Gut Metagenome in Mice.

Sharpton T, Lyalina S, Luong J, Pham J, Deal EM, Armour C, Gaulke C, Sanjabi S, Pollard KS.

mSystems. 2017 Sep 5;2(5). pii: e00036-17. doi: 10.1128/mSystems.00036-17. eCollection 2017 Sep-Oct.

11.

Topical silver diamine fluoride for dental caries arrest in preschool children: A randomized controlled trial and microbiological analysis of caries associated microbes and resistance gene expression.

Milgrom P, Horst JA, Ludwig S, Rothen M, Chaffee BW, Lyalina S, Pollard KS, DeRisi JL, Mancl L.

J Dent. 2018 Jan;68:72-78. doi: 10.1016/j.jdent.2017.08.015. Epub 2017 Sep 1.

12.

Genomic analyses identify hundreds of variants associated with age at menarche and support a role for puberty timing in cancer risk.

Day FR, Thompson DJ, Helgason H, Chasman DI, Finucane H, Sulem P, Ruth KS, Whalen S, Sarkar AK, Albrecht E, Altmaier E, Amini M, Barbieri CM, Boutin T, Campbell A, Demerath E, Giri A, He C, Hottenga JJ, Karlsson R, Kolcic I, Loh PR, Lunetta KL, Mangino M, Marco B, McMahon G, Medland SE, Nolte IM, Noordam R, Nutile T, Paternoster L, Perjakova N, Porcu E, Rose LM, Schraut KE, Segrè AV, Smith AV, Stolk L, Teumer A, Andrulis IL, Bandinelli S, Beckmann MW, Benitez J, Bergmann S, Bochud M, Boerwinkle E, Bojesen SE, Bolla MK, Brand JS, Brauch H, Brenner H, Broer L, Brüning T, Buring JE, Campbell H, Catamo E, Chanock S, Chenevix-Trench G, Corre T, Couch FJ, Cousminer DL, Cox A, Crisponi L, Czene K, Davey Smith G, de Geus EJCN, de Mutsert R, De Vivo I, Dennis J, Devilee P, Dos-Santos-Silva I, Dunning AM, Eriksson JG, Fasching PA, Fernández-Rhodes L, Ferrucci L, Flesch-Janys D, Franke L, Gabrielson M, Gandin I, Giles GG, Grallert H, Gudbjartsson DF, Guénel P, Hall P, Hallberg E, Hamann U, Harris TB, Hartman CA, Heiss G, Hooning MJ, Hopper JL, Hu F, Hunter DJ, Ikram MA, Im HK, Järvelin MR, Joshi PK, Karasik D, Kellis M, Kutalik Z, LaChance G, Lambrechts D, Langenberg C, Launer LJ, Laven JSE, Lenarduzzi S, Li J, Lind PA, Lindstrom S, Liu Y, Luan J, Mägi R, Mannermaa A, Mbarek H, McCarthy MI, Meisinger C, Meitinger T, Menni C, Metspalu A, Michailidou K, Milani L, Milne RL, Montgomery GW, Mulligan AM, Nalls MA, Navarro P, Nevanlinna H, Nyholt DR, Oldehinkel AJ, O'Mara TA, Padmanabhan S, Palotie A, Pedersen N, Peters A, Peto J, Pharoah PDP, Pouta A, Radice P, Rahman I, Ring SM, Robino A, Rosendaal FR, Rudan I, Rueedi R, Ruggiero D, Sala CF, Schmidt MK, Scott RA, Shah M, Sorice R, Southey MC, Sovio U, Stampfer M, Steri M, Strauch K, Tanaka T, Tikkanen E, Timpson NJ, Traglia M, Truong T, Tyrer JP, Uitterlinden AG, Edwards DRV, Vitart V, Völker U, Vollenweider P, Wang Q, Widen E, van Dijk KW, Willemsen G, Winqvist R, Wolffenbuttel BHR, Zhao JH, Zoledziewska M, Zygmunt M, Alizadeh BZ, Boomsma DI, Ciullo M, Cucca F, Esko T, Franceschini N, Gieger C, Gudnason V, Hayward C, Kraft P, Lawlor DA, Magnusson PKE, Martin NG, Mook-Kanamori DO, Nohr EA, Polasek O, Porteous D, Price AL, Ridker PM, Snieder H, Spector TD, Stöckl D, Toniolo D, Ulivi S, Visser JA, Völzke H, Wareham NJ, Wilson JF; LifeLines Cohort Study; InterAct Consortium; kConFab/AOCS Investigators; Endometrial Cancer Association Consortium; Ovarian Cancer Association Consortium; PRACTICAL consortium, Spurdle AB, Thorsteindottir U, Pollard KS, Easton DF, Tung JY, Chang-Claude J, Hinds D, Murray A, Murabito JM, Stefansson K, Ong KK, Perry JRB.

Nat Genet. 2017 Jun;49(6):834-841. doi: 10.1038/ng.3841. Epub 2017 Apr 24.

13.

Cooperative activation of cardiac transcription through myocardin bridging of paired MEF2 sites.

Anderson CM, Hu J, Thomas R, Gainous TB, Celona B, Sinha T, Dickel DE, Heidt AB, Xu SM, Bruneau BG, Pollard KS, Pennacchio LA, Black BL.

Development. 2017 Apr 1;144(7):1235-1241. doi: 10.1242/dev.138487.

14.

Proteobacteria explain significant functional variability in the human gut microbiome.

Bradley PH, Pollard KS.

Microbiome. 2017 Mar 23;5(1):36. doi: 10.1186/s40168-017-0244-z.

15.

Unboxing cluster heatmaps.

Engle S, Whalen S, Joshi A, Pollard KS.

BMC Bioinformatics. 2017 Feb 15;18(Suppl 2):63. doi: 10.1186/s12859-016-1442-6.

16.

Discovery of Reactive Microbiota-Derived Metabolites that Inhibit Host Proteases.

Guo CJ, Chang FY, Wyche TP, Backus KM, Acker TM, Funabashi M, Taketani M, Donia MS, Nayfach S, Pollard KS, Craik CS, Cravatt BF, Clardy J, Voigt CA, Fischbach MA.

Cell. 2017 Jan 26;168(3):517-526.e18. doi: 10.1016/j.cell.2016.12.021. Epub 2017 Jan 19.

17.

Modulation of a Circulating Uremic Solute via Rational Genetic Manipulation of the Gut Microbiota.

Devlin AS, Marcobal A, Dodd D, Nayfach S, Plummer N, Meyer T, Pollard KS, Sonnenburg JL, Fischbach MA.

Cell Host Microbe. 2016 Dec 14;20(6):709-715. doi: 10.1016/j.chom.2016.10.021. Epub 2016 Dec 1.

18.

An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography.

Nayfach S, Rodriguez-Mueller B, Garud N, Pollard KS.

Genome Res. 2016 Nov;26(11):1612-1625. Epub 2016 Oct 18.

19.

Toward Accurate and Quantitative Comparative Metagenomics.

Nayfach S, Pollard KS.

Cell. 2016 Aug 25;166(5):1103-1116. doi: 10.1016/j.cell.2016.08.007. Review.

20.

Urban greenness influences airborne bacterial community composition.

Mhuireach G, Johnson BR, Altrichter AE, Ladau J, Meadow JF, Pollard KS, Green JL.

Sci Total Environ. 2016 Nov 15;571:680-7. doi: 10.1016/j.scitotenv.2016.07.037. Epub 2016 Jul 11.

21.

Toward a Predictive Understanding of Earth's Microbiomes to Address 21st Century Challenges.

Blaser MJ, Cardon ZG, Cho MK, Dangl JL, Donohue TJ, Green JL, Knight R, Maxon ME, Northen TR, Pollard KS, Brodie EL.

MBio. 2016 May 13;7(3). pii: e00714-16. doi: 10.1128/mBio.00714-16.

22.

Features that define the best ChIP-seq peak calling algorithms.

Thomas R, Thomas S, Holloway AK, Pollard KS.

Brief Bioinform. 2017 May 1;18(3):441-450. doi: 10.1093/bib/bbw035.

23.

Enhancer-promoter interactions are encoded by complex genomic signatures on looping chromatin.

Whalen S, Truty RM, Pollard KS.

Nat Genet. 2016 May;48(5):488-96. doi: 10.1038/ng.3539. Epub 2016 Apr 4.

24.

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.

25.

Bat Accelerated Regions Identify a Bat Forelimb Specific Enhancer in the HoxD Locus.

Booker BM, Friedrich T, Mason MK, VanderMeer JE, Zhao J, Eckalbar WL, Logan M, Illing N, Pollard KS, Ahituv N.

PLoS Genet. 2016 Mar 28;12(3):e1005738. doi: 10.1371/journal.pgen.1005738. eCollection 2016 Mar.

26.

Complex Interdependence Regulates Heterotypic Transcription Factor Distribution and Coordinates Cardiogenesis.

Luna-Zurita L, Stirnimann CU, Glatt S, Kaynak BL, Thomas S, Baudin F, Samee MA, He D, Small EM, Mileikovsky M, Nagy A, Holloway AK, Pollard KS, Müller CW, Bruneau BG.

Cell. 2016 Feb 25;164(5):999-1014. doi: 10.1016/j.cell.2016.01.004. Epub 2016 Feb 11.

27.

Joint mouse-human phenome-wide association to test gene function and disease risk.

Wang X, Pandey AK, Mulligan MK, Williams EG, Mozhui K, Li Z, Jovaisaite V, Quarles LD, Xiao Z, Huang J, Capra JA, Chen Z, Taylor WL, Bastarache L, Niu X, Pollard KS, Ciobanu DC, Reznik AO, Tishkov AV, Zhulin IB, Peng J, Nelson SF, Denny JC, Auwerx J, Lu L, Williams RW.

Nat Commun. 2016 Feb 2;7:10464. doi: 10.1038/ncomms10464.

28.

Accelerated Evolution of Enhancer Hotspots in the Mammal Ancestor.

Holloway AK, Bruneau BG, Sukonnik T, Rubenstein JL, Pollard KS.

Mol Biol Evol. 2016 Apr;33(4):1008-18. doi: 10.1093/molbev/msv344. Epub 2015 Dec 29.

29.
30.

Automated and Accurate Estimation of Gene Family Abundance from Shotgun Metagenomes.

Nayfach S, Bradley PH, Wyman SK, Laurent TJ, Williams A, Eisen JA, Pollard KS, Sharpton TJ.

PLoS Comput Biol. 2015 Nov 13;11(11):e1004573. doi: 10.1371/journal.pcbi.1004573. eCollection 2015 Nov.

31.

MICROBIOME. A unified initiative to harness Earth's microbiomes.

Alivisatos AP, Blaser MJ, Brodie EL, Chun M, Dangl JL, Donohue TJ, Dorrestein PC, Gilbert JA, Green JL, Jansson JK, Knight R, Maxon ME, McFall-Ngai MJ, Miller JF, Pollard KS, Ruby EG, Taha SA; Unified Microbiome Initiative Consortium.

Science. 2015 Oct 30;350(6260):507-8. doi: 10.1126/science.aac8480. Epub 2015 Oct 28. No abstract available.

32.

Genomic approaches to studying human-specific developmental traits.

Franchini LF, Pollard KS.

Development. 2015 Sep 15;142(18):3100-12. doi: 10.1242/dev.120048. Review.

33.

Disruptions in a cluster of computationally identified enhancers near FOXC1 and GMDS may influence brain development.

Haliburton GD, McKinsey GL, Pollard KS.

Neurogenetics. 2016 Jan;17(1):1-9. doi: 10.1007/s10048-015-0458-9. Epub 2015 Sep 17.

34.

Can a few non-coding mutations make a human brain?

Franchini LF, Pollard KS.

Bioessays. 2015 Oct;37(10):1054-61. doi: 10.1002/bies.201500049. Epub 2015 Aug 25.

35.
36.

MetaQuery: a web server for rapid annotation and quantitative analysis of specific genes in the human gut microbiome.

Nayfach S, Fischbach MA, Pollard KS.

Bioinformatics. 2015 Oct 15;31(20):3368-70. doi: 10.1093/bioinformatics/btv382. Epub 2015 Jun 22.

37.

Marked seasonal variation in the wild mouse gut microbiota.

Maurice CF, Knowles SC, Ladau J, Pollard KS, Fenton A, Pedersen AB, Turnbaugh PJ.

ISME J. 2015 Nov;9(11):2423-34. doi: 10.1038/ismej.2015.53. Epub 2015 May 29.

38.

Signatures of accelerated somatic evolution in gene promoters in multiple cancer types.

Smith KS, Yadav VK, Pedersen BS, Shaknovich R, Geraci MW, Pollard KS, De S.

Nucleic Acids Res. 2015 Jun 23;43(11):5307-17. doi: 10.1093/nar/gkv419. Epub 2015 May 1.

39.

Continental-scale distributions of dust-associated bacteria and fungi.

Barberán A, Ladau J, Leff JW, Pollard KS, Menninger HL, Dunn RR, Fierer N.

Proc Natl Acad Sci U S A. 2015 May 5;112(18):5756-61. doi: 10.1073/pnas.1420815112. Epub 2015 Apr 20.

40.

Evolution of lysine acetylation in the RNA polymerase II C-terminal domain.

Simonti CN, Pollard KS, Schröder S, He D, Bruneau BG, Ott M, Capra JA.

BMC Evol Biol. 2015 Mar 10;15:35. doi: 10.1186/s12862-015-0327-z.

41.
42.

Human disease modeling reveals integrated transcriptional and epigenetic mechanisms of NOTCH1 haploinsufficiency.

Theodoris CV, Li M, White MP, Liu L, He D, Pollard KS, Bruneau BG, Srivastava D.

Cell. 2015 Mar 12;160(6):1072-86. doi: 10.1016/j.cell.2015.02.035.

43.

Genomic and network patterns of schizophrenia genetic variation in human evolutionary accelerated regions.

Xu K, Schadt EE, Pollard KS, Roussos P, Dudley JT.

Mol Biol Evol. 2015 May;32(5):1148-60. doi: 10.1093/molbev/msv031. Epub 2015 Feb 12.

44.

Gibbon genome and the fast karyotype evolution of small apes.

Carbone L, Harris RA, Gnerre S, Veeramah KR, Lorente-Galdos B, Huddleston J, Meyer TJ, Herrero J, Roos C, Aken B, Anaclerio F, Archidiacono N, Baker C, Barrell D, Batzer MA, Beal K, Blancher A, Bohrson CL, Brameier M, Campbell MS, Capozzi O, Casola C, Chiatante G, Cree A, Damert A, de Jong PJ, Dumas L, Fernandez-Callejo M, Flicek P, Fuchs NV, Gut I, Gut M, Hahn MW, Hernandez-Rodriguez J, Hillier LW, Hubley R, Ianc B, Izsvák Z, Jablonski NG, Johnstone LM, Karimpour-Fard A, Konkel MK, Kostka D, Lazar NH, Lee SL, Lewis LR, Liu Y, Locke DP, Mallick S, Mendez FL, Muffato M, Nazareth LV, Nevonen KA, O'Bleness M, Ochis C, Odom DT, Pollard KS, Quilez J, Reich D, Rocchi M, Schumann GG, Searle S, Sikela JM, Skollar G, Smit A, Sonmez K, ten Hallers B, Terhune E, Thomas GW, Ullmer B, Ventura M, Walker JA, Wall JD, Walter L, Ward MC, Wheelan SJ, Whelan CW, White S, Wilhelm LJ, Woerner AE, Yandell M, Zhu B, Hammer MF, Marques-Bonet T, Eichler EE, Fulton L, Fronick C, Muzny DM, Warren WC, Worley KC, Rogers J, Wilson RK, Gibbs RA.

Nature. 2014 Sep 11;513(7517):195-201. doi: 10.1038/nature13679.

45.

Genome-wide distribution of Auts2 binding localizes with active neurodevelopmental genes.

Oksenberg N, Haliburton GD, Eckalbar WL, Oren I, Nishizaki S, Murphy K, Pollard KS, Birnbaum RY, Ahituv N.

Transl Psychiatry. 2014 Sep 2;4:e431. doi: 10.1038/tp.2014.78.

46.

Exploring the genesis and functions of Human Accelerated Regions sheds light on their role in human evolution.

Hubisz MJ, Pollard KS.

Curr Opin Genet Dev. 2014 Dec;29:15-21. doi: 10.1016/j.gde.2014.07.005. Epub 2014 Aug 23. Review.

47.

Profile hidden Markov models for the detection of viruses within metagenomic sequence data.

Skewes-Cox P, Sharpton TJ, Pollard KS, DeRisi JL.

PLoS One. 2014 Aug 20;9(8):e105067. doi: 10.1371/journal.pone.0105067. eCollection 2014.

48.

Integrating diverse datasets improves developmental enhancer prediction.

Erwin GD, Oksenberg N, Truty RM, Kostka D, Murphy KK, Ahituv N, Pollard KS, Capra JA.

PLoS Comput Biol. 2014 Jun 26;10(6):e1003677. doi: 10.1371/journal.pcbi.1003677. eCollection 2014 Jun.

49.

Liquefaction of semen generates and later degrades a conserved semenogelin peptide that enhances HIV infection.

Roan NR, Liu H, Usmani SM, Neidleman J, Müller JA, Avila-Herrera A, Gawanbacht A, Zirafi O, Chu S, Dong M, Kumar ST, Smith JF, Pollard KS, Fändrich M, Kirchhoff F, Münch J, Witkowska HE, Greene WC.

J Virol. 2014 Jul;88(13):7221-34. doi: 10.1128/JVI.00269-14. Epub 2014 Apr 16.

50.

Exome capture from saliva produces high quality genomic and metagenomic data.

Kidd JM, Sharpton TJ, Bobo D, Norman PJ, Martin AR, Carpenter ML, Sikora M, Gignoux CR, Nemat-Gorgani N, Adams A, Guadalupe M, Guo X, Feng Q, Li Y, Liu X, Parham P, Hoal EG, Feldman MW, Pollard KS, Wall JD, Bustamante CD, Henn BM.

BMC Genomics. 2014 Apr 4;15:262. doi: 10.1186/1471-2164-15-262.

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