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Items: 29

1.

Identification and quantitation of clinically relevant microbes in patient samples: Comparison of three k-mer based classifiers for speed, accuracy, and sensitivity.

Watts GS, Thornton JE Jr, Youens-Clark K, Ponsero AJ, Slepian MJ, Menashi E, Hu C, Deng W, Armstrong DG, Reed S, Cranmer LD, Hurwitz BL.

PLoS Comput Biol. 2019 Nov 22;15(11):e1006863. doi: 10.1371/journal.pcbi.1006863. eCollection 2019 Nov.

2.

Erratum to: iMicrobe: Tools and data-driven discovery platform for the microbiome sciences.

Youens-Clark K, Bomhoff M, Ponsero AJ, Wood-Charlson EM, Lynch J, Choi I, Hartman JH, Hurwitz BL.

Gigascience. 2019 Aug 1;8(8). pii: giz097. doi: 10.1093/gigascience/giz097. No abstract available.

3.

iMicrobe: Tools and data-dreaiven discovery platform for the microbiome sciences.

Youens-Clark K, Bomhoff M, Ponsero AJ, Wood-Charlson EM, Lynch J, Choi I, Hartman JH, Hurwitz BL.

Gigascience. 2019 Jul 1;8(7). pii: giz083. doi: 10.1093/gigascience/giz083. Erratum in: Gigascience. 2019 Aug 1;8(8):.

4.

The Promises and Pitfalls of Machine Learning for Detecting Viruses in Aquatic Metagenomes.

Ponsero AJ, Hurwitz BL.

Front Microbiol. 2019 Apr 16;10:806. doi: 10.3389/fmicb.2019.00806. eCollection 2019.

5.

Libra: scalable k-mer-based tool for massive all-vs-all metagenome comparisons.

Choi I, Ponsero AJ, Bomhoff M, Youens-Clark K, Hartman JH, Hurwitz BL.

Gigascience. 2019 Feb 1;8(2). doi: 10.1093/gigascience/giy165.

6.

Minimum Information about an Uncultivated Virus Genome (MIUViG).

Roux S, Adriaenssens EM, Dutilh BE, Koonin EV, Kropinski AM, Krupovic M, Kuhn JH, Lavigne R, Brister JR, Varsani A, Amid C, Aziz RK, Bordenstein SR, Bork P, Breitbart M, Cochrane GR, Daly RA, Desnues C, Duhaime MB, Emerson JB, Enault F, Fuhrman JA, Hingamp P, Hugenholtz P, Hurwitz BL, Ivanova NN, Labonté JM, Lee KB, Malmstrom RR, Martinez-Garcia M, Mizrachi IK, Ogata H, Páez-Espino D, Petit MA, Putonti C, Rattei T, Reyes A, Rodriguez-Valera F, Rosario K, Schriml L, Schulz F, Steward GF, Sullivan MB, Sunagawa S, Suttle CA, Temperton B, Tringe SG, Thurber RV, Webster NS, Whiteson KL, Wilhelm SW, Wommack KE, Woyke T, Wrighton KC, Yilmaz P, Yoshida T, Young MJ, Yutin N, Allen LZ, Kyrpides NC, Eloe-Fadrosh EA.

Nat Biotechnol. 2019 Jan;37(1):29-37. doi: 10.1038/nbt.4306. Epub 2018 Dec 17.

7.

Phage hunters: Computational strategies for finding phages in large-scale 'omics datasets.

Hurwitz BL, Ponsero A, Thornton J Jr, U'Ren JM.

Virus Res. 2018 Jan 15;244:110-115. doi: 10.1016/j.virusres.2017.10.019. Epub 2017 Nov 1. Review.

PMID:
29100906
8.

Functional Changes in the Gut Microbiome Contribute to Transforming Growth Factor β-Deficient Colon Cancer.

Daniel SG, Ball CL, Besselsen DG, Doetschman T, Hurwitz BL.

mSystems. 2017 Sep 26;2(5). pii: e00065-17. doi: 10.1128/mSystems.00065-17. eCollection 2017 Sep-Oct.

9.

16S rRNA gene sequencing on a benchtop sequencer: accuracy for identification of clinically important bacteria.

Watts GS, Youens-Clark K, Slepian MJ, Wolk DM, Oshiro MM, Metzger GS, Dhingra D, Cranmer LD, Hurwitz BL.

J Appl Microbiol. 2017 Dec;123(6):1584-1596. doi: 10.1111/jam.13590. Epub 2017 Nov 7.

10.

Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition.

Alberti A, Poulain J, Engelen S, Labadie K, Romac S, Ferrera I, Albini G, Aury JM, Belser C, Bertrand A, Cruaud C, Da Silva C, Dossat C, Gavory F, Gas S, Guy J, Haquelle M, Jacoby E, Jaillon O, Lemainque A, Pelletier E, Samson G, Wessner M; Genoscope Technical Team, Acinas SG, Royo-Llonch M, Cornejo-Castillo FM, Logares R, Fernández-Gómez B, Bowler C, Cochrane G, Amid C, Hoopen PT, De Vargas C, Grimsley N, Desgranges E, Kandels-Lewis S, Ogata H, Poulton N, Sieracki ME, Stepanauskas R, Sullivan MB, Brum JR, Duhaime MB, Poulos BT, Hurwitz BL; Tara Oceans Consortium Coordinators, Pesant S, Karsenti E, Wincker P.

Sci Data. 2017 Aug 1;4:170093. doi: 10.1038/sdata.2017.93.

11.

Method-centered digital communities on protocols.io for fast-paced scientific innovation.

Kindler L, Stoliartchouk A, Teytelman L, Hurwitz BL.

Version 2. F1000Res. 2016 Sep 8 [revised 2017 Jan 1];5:2271. doi: 10.12688/f1000research.9453.2. eCollection 2016.

12.

Seasonal time bombs: dominant temperate viruses affect Southern Ocean microbial dynamics.

Brum JR, Hurwitz BL, Schofield O, Ducklow HW, Sullivan MB.

ISME J. 2017 Feb;11(2):588. doi: 10.1038/ismej.2016.126. No abstract available.

13.

Skin and Soft Tissue Infections.

Moffarah AS, Al Mohajer M, Hurwitz BL, Armstrong DG.

Microbiol Spectr. 2016 Aug;4(4). doi: 10.1128/microbiolspec.DMIH2-0014-2015. Review.

PMID:
27726817
14.

Protocols.io: Virtual Communities for Protocol Development and Discussion.

Teytelman L, Stoliartchouk A, Kindler L, Hurwitz BL.

PLoS Biol. 2016 Aug 22;14(8):e1002538. doi: 10.1371/journal.pbio.1002538. eCollection 2016 Aug.

15.

iVirus: facilitating new insights in viral ecology with software and community data sets imbedded in a cyberinfrastructure.

Bolduc B, Youens-Clark K, Roux S, Hurwitz BL, Sullivan MB.

ISME J. 2017 Jan;11(1):7-14. doi: 10.1038/ismej.2016.89. Epub 2016 Jul 15.

16.

Viral metabolic reprogramming in marine ecosystems.

Hurwitz BL, U'Ren JM.

Curr Opin Microbiol. 2016 Jun;31:161-168. doi: 10.1016/j.mib.2016.04.002. Epub 2016 Apr 16. Review.

PMID:
27088500
17.

Computational prospecting the great viral unknown.

Hurwitz BL, U'Ren JM, Youens-Clark K.

FEMS Microbiol Lett. 2016 May;363(10). pii: fnw077. doi: 10.1093/femsle/fnw077. Epub 2016 Mar 29. Review.

PMID:
27030726
18.

Seasonal time bombs: dominant temperate viruses affect Southern Ocean microbial dynamics.

Brum JR, Hurwitz BL, Schofield O, Ducklow HW, Sullivan MB.

ISME J. 2016 Feb;10(2):437-49. doi: 10.1038/ismej.2015.125. Epub 2015 Aug 21. Erratum in: ISME J. 2017 Feb;11(2):588.

19.

Set Phages to Stun: Reducing the Virulence of Staphylococcus aureus in Diabetic Foot Ulcers.

Armstrong DG, Hurwitz BL, Lipsky BA.

Diabetes. 2015 Aug;64(8):2701-3. doi: 10.2337/db15-0543. No abstract available.

20.

Draft Genome Sequence of the Ale-Fermenting Saccharomyces cerevisiae Strain GSY2239.

U'Ren JM, Wisecaver JH, Paek AL, Dunn BL, Hurwitz BL.

Genome Announc. 2015 Jul 23;3(4). pii: e00776-15. doi: 10.1128/genomeA.00776-15.

21.

VirSorter: mining viral signal from microbial genomic data.

Roux S, Enault F, Hurwitz BL, Sullivan MB.

PeerJ. 2015 May 28;3:e985. doi: 10.7717/peerj.985. eCollection 2015.

22.

Microbiology of diabetic foot infections: from Louis Pasteur to 'crime scene investigation'.

Spichler A, Hurwitz BL, Armstrong DG, Lipsky BA.

BMC Med. 2015 Jan 7;13:2. doi: 10.1186/s12916-014-0232-0. Review.

23.

Depth-stratified functional and taxonomic niche specialization in the 'core' and 'flexible' Pacific Ocean Virome.

Hurwitz BL, Brum JR, Sullivan MB.

ISME J. 2015 Feb;9(2):472-84. doi: 10.1038/ismej.2014.143. Epub 2014 Aug 5.

24.

Modeling ecological drivers in marine viral communities using comparative metagenomics and network analyses.

Hurwitz BL, Westveld AH, Brum JR, Sullivan MB.

Proc Natl Acad Sci U S A. 2014 Jul 22;111(29):10714-9. doi: 10.1073/pnas.1319778111. Epub 2014 Jul 7.

25.

Metabolic reprogramming by viruses in the sunlit and dark ocean.

Hurwitz BL, Hallam SJ, Sullivan MB.

Genome Biol. 2013 Nov 7;14(11):R123. doi: 10.1186/gb-2013-14-11-r123.

26.

The Pacific Ocean virome (POV): a marine viral metagenomic dataset and associated protein clusters for quantitative viral ecology.

Hurwitz BL, Sullivan MB.

PLoS One. 2013;8(2):e57355. doi: 10.1371/journal.pone.0057355. Epub 2013 Feb 28.

27.

Evaluation of methods to concentrate and purify ocean virus communities through comparative, replicated metagenomics.

Hurwitz BL, Deng L, Poulos BT, Sullivan MB.

Environ Microbiol. 2013 May;15(5):1428-40. doi: 10.1111/j.1462-2920.2012.02836.x. Epub 2012 Jul 30.

28.

Rice structural variation: a comparative analysis of structural variation between rice and three of its closest relatives in the genus Oryza.

Hurwitz BL, Kudrna D, Yu Y, Sebastian A, Zuccolo A, Jackson SA, Ware D, Wing RA, Stein L.

Plant J. 2010 Sep;63(6):990-1003. doi: 10.1111/j.1365-313X.2010.04293.x.

29.

A first-generation haplotype map of maize.

Gore MA, Chia JM, Elshire RJ, Sun Q, Ersoz ES, Hurwitz BL, Peiffer JA, McMullen MD, Grills GS, Ross-Ibarra J, Ware DH, Buckler ES.

Science. 2009 Nov 20;326(5956):1115-7. doi: 10.1126/science.1177837.

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