• 2761 Citations
  • 21 h-Index
20062019
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Research Output 2006 2019

2019

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

Youens-Clark, K., Bomhoff, M., Ponsero, A. J., Wood-Charlson, E. M., Lynch, J., Choi, I., Hartman, J. H. & Hurwitz, B. L., Aug 1 2019, In : GigaScience. 8, 8

Research output: Contribution to journalComment/debate

Open Access
Microbiota

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

Watts, G. S., Thornton, J. E., Youens-Clark, K., Ponsero, A. J., Slepian, M. J., Menashi, E., Hu, C., Deng, W., Armstrong, D. G., Reed, S., Cranmer, L. D. & Hurwitz, B. L., Jan 1 2019, In : PLoS computational biology. 15, 11, e1006863.

Research output: Contribution to journalArticle

Open Access
Metagenomics
centrifuges
Centrifuges
centrifuge
Classifiers
1 Citation (Scopus)

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

Youens-Clark, K., Bomhoff, M., Ponsero, A. J., Wood-Charlson, E. M., Lynch, J., Choi, I., Hartman, J. H. & Hurwitz, B. L., Jul 1 2019, In : GigaScience. 8, 7

Research output: Contribution to journalArticle

Open Access
Microbiota
Agave
Information Dissemination
Information Storage and Retrieval
Computational Biology
1 Citation (Scopus)

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

Choi, I., Ponsero, A. J., Bomhoff, M., Youens-Clark, K., Hartman, J. H. & Hurwitz, B. L., Feb 1 2019, In : GigaScience. 8, 2

Research output: Contribution to journalArticle

Metagenome
Metagenomics
Biodiversity
Biological Phenomena
Data reduction
22 Citations (Scopus)

Minimum information about an uncultivated virus genome (MIUVIG)

Roux, S., Adriaenssens, E. M., Dutilh, B. E., Koonin, E. V., Kropinski, A. M., Krupovic, M., Kuhn, J. H., Lavigne, R., Brister, J. R., Varsani, A., Amid, C., Aziz, R. K., Bordenstein, S. R., Bork, P., Breitbart, M., Cochrane, G. R., Daly, R. A., Desnues, C., Duhaime, M. B., Emerson, J. B. & 41 others, Enault, F., Fuhrman, J. A., Hingamp, P., Hugenholtz, P., Hurwitz, B. L., Ivanova, N. N., Labonté, J. M., Lee, K. B., Malmstrom, R. R., Martinez-Garcia, M., Mizrachi, I. K., Ogata, H., Páez-Espino, D., Petit, M. A., Putonti, C., Rattei, T., Reyes, A., Rodriguez-Valera, F., Rosario, K., Schriml, L., Schulz, F., Steward, G. F., Sullivan, M., Sunagawa, S., Suttle, C. A., Temperton, B., Tringe, S. G., Thurber, R. V., Webster, N. S., Whiteson, K. L., Wilhelm, S. W., Wommack, K. E., Woyke, T., Wrighton, K. C., Yilmaz, P., Yoshida, T., Young, M. J., Yutin, N., Allen, L. Z., Kyrpides, N. C. & Eloe-Fadrosh, E. A., Jan 1 2019, In : Nature biotechnology. 37, 1, p. 29-37 9 p.

Research output: Contribution to journalArticle

Open Access
Viruses
Genes
Genome
Metagenome
Archaea
2 Citations (Scopus)

The promises and pitfalls of machine learning for detecting viruses in aquatic metagenomes

Ponsero, A. J. & Hurwitz, B. L., Jan 1 2019, In : Frontiers in Microbiology. 10, MAR, 806.

Research output: Contribution to journalReview article

Open Access
Metagenome
Viruses
Ecology
Ecosystem
Machine Learning
2018

Libra: Improved partitioning strategies for massive comparative metagenomics analysis

Choi, I., Bomhoff, M., Ponsero, A. J., Hurwitz, B. L., Youens-Clark, K. & Hartman, J. H., Jun 11 2018, Proceedings of the 9th Workshop on Scientific Cloud Computing, ScienceCloud 2018 - Co-located with HPDC 2018. Association for Computing Machinery, Inc, a2

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Natural sciences computing
Resource allocation
Big data
10 Citations (Scopus)

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

Hurwitz, B. L., Ponsero, A., Thornton, J. & U'Ren, J. M., Jan 15 2018, In : Virus Research. 244, p. 110-115 6 p.

Research output: Contribution to journalReview article

Metagenome
Bacteriophages
Prophages
Bacterial Genomes
Viral Genome
2017
5 Citations (Scopus)

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

Watts, G. S., Youens-Clark, K., Slepian, M. J., Wolk, D., Oshiro, M. M., Metzger, G. S., Dhingra, D., Cranmer, L. D. & Hurwitz, B. L., Dec 1 2017, In : Journal of Applied Microbiology. 123, 6, p. 1584-1596 13 p.

Research output: Contribution to journalArticle

rRNA Genes
Bacteria
Ions
Databases
Metagenomics
3 Citations (Scopus)

Genetic variation for domestication-related traits revealed in a cultivated rice, Nipponbare (Oryza sativa ssp. japonica) × ancestral rice, O. nivara, mapping population

Eizenga, G. C., Sanchez, P. L., Jackson, A. K., Edwards, J. D., Hurwitz, B. L., Wing, R. A. & Kudrna, D. A., Nov 1 2017, In : Molecular Breeding. 37, 11, 135.

Research output: Contribution to journalArticle

Oryza nivara
domestication
Oryza sativa
rice
genetic variation
41 Citations (Scopus)

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, B. L. & Sullivan, M., Jan 1 2017, In : ISME Journal. 11, 1, p. 7-14 8 p.

Research output: Contribution to journalReview article

energy conversion
Ecology
open reading frames
Software
researchers

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

Hurwitz, B. L., Kindler, L., Stoliartchouk, A. & Teytelman, L., 2017, In : F1000Research. 5, 2271.

Research output: Contribution to journalArticle

Innovation
Virology
Network protocols
Metagenomics
Research Personnel
35 Citations (Scopus)

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

Genoscope Technical Team & Tara Oceans Consortium Coordinators, Aug 1 2017, In : Scientific data. 4, 170093.

Research output: Contribution to journalArticle

Plankton
Nucleotides
Ocean
Genomics
data access
2016
19 Citations (Scopus)

Computational prospecting the great viral unknown

Hurwitz, B. L., U'Ren, J. M. & Youens-Clark, K., May 1 2016, In : FEMS Microbiology Letters. 363, 10, fnw077.

Research output: Contribution to journalShort survey

Bacteriophages
Metagenomics
Genes
Metagenome
Bacteria

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

Kindler, L., Stoliartchouk, A., Teytelman, L. & Hurwitz, B. L., 2016, In : F1000Research. 5, 2271.

Research output: Contribution to journalArticle

Innovation
Virology
Network protocols
Metagenomics
Research Personnel
10 Citations (Scopus)

Protocols.io: Virtual Communities for Protocol Development and Discussion

Teytelman, L., Stoliartchouk, A., Kindler, L. & Hurwitz, B. L., Aug 22 2016, In : PLoS Biology. 14, 8, e1002538.

Research output: Contribution to journalArticle

Social Planning
researchers
Research
Research Personnel
methodology
5 Citations (Scopus)

Skin and soft tissue infections

Moffarah, A. S., Al Mohajer, M., Hurwitz, B. L. & Armstrong, D. G., 2016, In : Microbiology spectrum. 4, 4, DMIH2-0014-2015.

Research output: Contribution to journalArticle

Soft Tissue Infections
skin
Skin
Immunocompromised Host
Molecular Diagnostic Techniques
39 Citations (Scopus)

Viral metabolic reprogramming in marine ecosystems

Hurwitz, B. L. & U'Ren, J. M., Jun 1 2016, In : Current Opinion in Microbiology. 31, p. 161-168 8 p.

Research output: Contribution to journalArticle

Ecosystem
Bacteriophages
Genes
Metagenomics
Carbohydrate Metabolism
2015
69 Citations (Scopus)

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

Hurwitz, B. L., Brum, J. R. & Sullivan, M., Feb 22 2015, In : ISME Journal. 9, 2, p. 472-484 13 p.

Research output: Contribution to journalArticle

Pacific Ocean
niche
niches
gene
ocean
3 Citations (Scopus)

Draft genome sequence of the ale-fermenting Saccharomyces cerevisiae strain GSY2239

U'Ren, J. M., Wisecaver, J. H., Paek, A. L., Dunn, B. L. & Hurwitz, B. L., 2015, In : Genome Announcements. 3, 4, e00776-15.

Research output: Contribution to journalArticle

Saccharomyces cerevisiae
Yeasts
Genome
53 Citations (Scopus)

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

Spichler, A., Hurwitz, B. L., Armstrong, D. G. & Lipsky, B. A., Jan 7 2015, In : BMC Medicine. 13, 1, 2.

Research output: Contribution to journalArticle

Diabetic Foot
Crime
Microbiology
Infection
Wounds and Injuries
75 Citations (Scopus)

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

Brum, J. R., Hurwitz, B. L., Schofield, O., Ducklow, H. W. & Sullivan, M., Aug 21 2015, (Accepted/In press) In : ISME Journal.

Research output: Contribution to journalArticle

Oceans and Seas
virus
oceans
Viruses
viruses

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

Armstrong, D. G., Hurwitz, B. L. & Lipsky, B. A., Aug 1 2015, In : Diabetes. 64, 8, p. 2701-2703 3 p.

Research output: Contribution to journalArticle

Staphylococcal Infections
Diabetic Foot
Bacteriophages
Virulence
Staphylococcus aureus
3 Citations (Scopus)

The quest for tissue repair's holy grail: The promise of wound diagnostics or just another fishing expedition?

Armstrong, D. G., Lew, E. J., Hurwitz, B. L. & Wild, T., Apr 1 2015, In : Wound Medicine. 8, p. 1-5 5 p.

Research output: Contribution to journalArticle

Expeditions
Empiricism
Wounds and Injuries
Perfusion
Genome
175 Citations (Scopus)

VirSorter: Mining viral signal from microbial genomic data

Roux, S., Enault, F., Hurwitz, B. L. & Sullivan, M., 2015, In : PeerJ. 2015, 5, e985.

Research output: Contribution to journalArticle

Prophages
Genes
genomics
Metagenomics
Genome
2014
63 Citations (Scopus)
Metagenomics
Oxygen
Marine Biology
Metagenome
Pacific Ocean
107 Citations (Scopus)

Three-dimensional printing surgical instruments: Are we there yet?

Rankin, T. M., Giovinco, N. A., Cucher, D. J., Watts, G. S., Hurwitz, B. L. & Armstrong, D. G., Jun 15 2014, In : Journal of Surgical Research. 189, 2, p. 193-197 5 p.

Research output: Contribution to journalArticle

Surgical Instruments
Operating Rooms
Costs and Cost Analysis
Tissue Scaffolds
Polymerase Chain Reaction
2013
78 Citations (Scopus)

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

Hurwitz, B. L., Deng, L., Poulos, B. T. & Sullivan, M., May 2013, In : Environmental Microbiology. 15, 5, p. 1428-1440 13 p.

Research output: Contribution to journalArticle

Metagenome
Metagenomics
deoxyribonucleases
Deoxyribonucleases
Oceans and Seas
79 Citations (Scopus)

Metabolic reprogramming by viruses in the sunlit and dark ocean

Hurwitz, B. L., Hallam, S. J. & Sullivan, M., Nov 7 2013, In : Genome Biology. 14, 11, R123.

Research output: Contribution to journalArticle

Oceans and Seas
virus
oceans
Pacific Ocean
Viruses
185 Citations (Scopus)
Pacific Ocean
Metagenomics
Ecology
Metagenome
Surface waters
2010
52 Citations (Scopus)

Dynamics of genome evolution in facultative symbionts of aphids

Degnan, P. H., Leonardo, T. E., Cass, B. N., Hurwitz, B. L., Stern, D., Gibbs, R. A., Richards, S. & Moran, N. A., Aug 2010, In : Environmental Microbiology. 12, 8, p. 2060-2069 10 p.

Research output: Contribution to journalArticle

Aphids
symbiont
aphid
symbionts
Aphidoidea
647 Citations (Scopus)

Genome sequence of the pea aphid Acyrthosiphon pisum

Richards, S., Gibbs, R. A., Gerardo, N. M., Moran, N., Nakabachi, A., Stern, D., Tagu, D., Wilson, A. C. C., Muzny, D., Kovar, C., Cree, A., Chacko, J., Chandrabose, M. N., Dao, M. D., Dinh, H. H., Gabisi, R. A., Hines, S., Hume, J., Jhangian, S. N., Joshi, V. & 200 others, Lewis, L. R., Liu, Y. S., Lopez, J., Morgan, M. B., Nguyen, N. B., Okwuonu, G. O., Ruiz, S. J., Santibanez, J., Wright, R. A., Fowler, G. R., Hitchens, M. E., Lozado, R. J., Moen, C., Steffen, D., Warren, J. T., Zhang, J., Nazareth, L. V., Chavez, D., Davis, C., Lee, S. L., Patel, B. M., Pu, L. L., Bell, S. N., Johnson, A. J., Vattathil, S., Williams, R. L., Shigenobu, S., Dang, P. M., Morioka, M., Fukatsu, T., Kudo, T., Miyagishima, S. Y., Jiang, H., Worley, K. C., Legeai, F., Gauthier, J. P., Collin, O., Zhang, L., Chen, H. C., Ermolaeva, O., Hlavina, W., Kapustin, Y., Kiryutin, B., Kitts, P., Maglott, D., Murphy, T., Pruitt, K., Sapojnikov, V., Souvorov, A., Thibaud-Nissen, F., Câmara, F., Guigó, R., Stanke, M., Solovyev, V., Kosarev, P., Gilbert, D., Gabaldón, T., Huerta-Cepas, J., Marcet-Houben, M., Pignatelli, M., Moya, A., Rispe, C., Ollivier, M., Quesneville, H., Permal, E., Llorens, C., Futami, R., Hedges, D., Robertson, H. M., Alioto, T., Mariotti, M., Nikoh, N., McCutcheon, J. P., Burke, G., Kamins, A., Latorre, A., Ashton, P., Calevro, F., Charles, H., Colella, S., Douglas, A. E., Jander, G., Jones, D. H., Febvay, G., Kamphuis, L. G., Kushlan, P. F., Macdonald, S., Ramsey, J., Schwartz, J., Seah, S., Thomas, G., Vellozo, A., Cass, B., Degnan, P., Hurwitz, B. L., Leonardo, T., Koga, R., Altincicek, B., Anselme, C., Atamian, H., Barribeau, S. M., De Vos, M., Duncan, E. J., Evans, J., Ghanim, M., Heddi, A., Kaloshian, I., Vincent-Monegat, C., Parker, B. J., Pérez-Brocal, V., Rahbé, Y., Spragg, C. J., Tamames, J., Tamarit, D., Tamborindeguy, C., Vilcinskas, A., Bickel, R. D., Brisson, J. A., Butts, T., Chang, C. C., Christiaens, O., Davis, G. K., Duncan, E., Ferrier, D., Iga, M., Janssen, R., Lu, H. L., McGregor, A., Miura, T., Smagghe, G., Smith, J., Van Der Zee, M., Velarde, R., Wilson, M., Dearden, P., Edwards, O. R., Gordon, K., Hilgarth, R. S., Rider, S. D., Srinivasan, D., Walsh, T. K., Ishikawa, A., Jaubert-Possamai, S., Fenton, B., Huang, W., Rizk, G., Lavenier, D., Nicolas, J., Smadja, C., Zhou, J. J., Vieira, F. G., He, X. L., Liu, R., Rozas, J., Field, L. M., Campbell, P., Carolan, J. C., Fitzroy, C. I. J., Reardon, K. T., Reeck, G. R., Singh, K., Wilkinson, T. L., Huybrechts, J., Abdel-Latief, M., Robichon, A., Veenstra, J. A., Hauser, F., Cazzamali, G., Schneider, M., Williamson, M., Stafflinger, E., Hansen, K. K., Grimmelikhuijzen, C. J. P., Price, D. R. G., Caillaud, M., Van Fleet, E., Ren, Q., Gatehouse, J. A., Brault, V., Monsion, B., Diaz, J., Hunnicutt, L., Ju, H. J., Pechuan, X., Aguilar, J., Cortés, T., Ortiz-Rivas, B., Martínez-Torres, D., Dombrovsky, A., Dale, R. P., Davies, T. G. E., Williamson, M. S., Jones, A., Sattelle, D., Williamson, S., Wolstenholme, A., Cottret, L., Sagot, M. F., Heckel, D. G. & Hunter, W., Feb 2010, In : PLoS Biology. 8, 2, e1000313.

Research output: Contribution to journalArticle

Aphids
Acyrthosiphon pisum
Peas
Genes
Genome
8 Citations (Scopus)

Phylogenomic analysis of BAC-end sequence libraries in Oryza (Poaceae)

Cranston, K. A., Hurwitz, B. L., Sanderson, M., Ware, D., Wing, R. A. & Stein, L., Jul 2010, In : Systematic Botany. 35, 3, p. 512-523 12 p.

Research output: Contribution to journalArticle

Bacterial Artificial Chromosomes
bacterial artificial chromosomes
DNA libraries
Oryza
Poaceae
145 Citations (Scopus)

Rapid genomic characterization of the genus Vitis

Myles, S., Chia, J. M., Hurwitz, B. L., Simon, C., Zhong, G. Y., Buckler, E. & Ware, D., Jan 13 2010, In : PLoS One. 5, 1, e8219.

Research output: Contribution to journalArticle

Vitis
Crops
linkage disequilibrium
Genes
Linkage Disequilibrium
34 Citations (Scopus)

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

Hurwitz, B. L., Kudrna, D. A., Yu, Y., Sebastian, A., Zuccolo, A., Jackson, S. A., Ware, D., Wing, R. A. & Stein, L., Sep 2010, In : Plant Journal. 63, 6, p. 990-1003 14 p.

Research output: Contribution to journalArticle

Oryza
Oryza sativa
rice
genome
Oryza nivara
2009
503 Citations (Scopus)

A first-generation haplotype map of maize

Gore, M. A., Chia, J. M., Elshire, R. J., Sun, Q., Ersoz, E. S., Hurwitz, B. L., Peiffer, J. A., McMullen, M. D., Grills, G. S., Ross-Ibarra, J., Ware, D. H. & Buckler, E. S., Nov 20 2009, In : Science. 326, 5956, p. 1115-1117 3 p.

Research output: Contribution to journalArticle

Haplotypes
Zea mays
Genetic Recombination
Hybrid Vigor
Genome-Wide Association Study
75 Citations (Scopus)

Species trees from highly incongruent gene trees in rice

Cranston, K. A., Hurwitz, B. L., Ware, D., Stein, L. & Wing, R. A., Oct 2009, In : Systematic Biology. 58, 5, p. 489-500 12 p.

Research output: Contribution to journalArticle

rice
gene
Genes
genes
bioinformatics
2008
70 Citations (Scopus)

Construction, alignment and analysis of twelve framework physical maps that represent the ten genome types of the genus Oryza

Kim, H. R., Hurwitz, B. L., Yu, Y., Collura, K., Gill, N., SanMiguel, P., Mullikin, J. C., Maher, C., Nelson, W., Wissotski, M., Braidotti, M., Kudrna, D. A., Goicoechea, J. L., Stein, L., Ware, D., Jackson, S. A., Soderlund, C. & Wing, R. A., Feb 28 2008, In : Genome Biology. 9, 2, R45.

Research output: Contribution to journalArticle

physical chromosome mapping
Oryza
genome
Genome
Bacterial Artificial Chromosomes
123 Citations (Scopus)

Gramene: A growing plant comparative genomics resource

Liang, C., Jaiswal, P., Hebbard, C., Avraham, S., Buckler, E. S., Casstevens, T., Hurwitz, B. L., Mccouch, S., Ni, J., Pujar, A., Ravenscroft, D., Ren, L., Spooner, W., Tecle, I., Thomason, J., Tung, C. W., Wei, X., Yap, I., Youens-Clark, K., Ware, D. & 1 others, Stein, L., Jan 2008, In : Nucleic Acids Research. 36, SUPPL. 1

Research output: Contribution to journalArticle

Genomics
Zea mays
Quantitative Trait Loci
Triticum
Genome
2007
8 Citations (Scopus)

The oryza map alignment project (OMAP): A new resource for comparative genome studies within oryza

Wing, R. A., Kim, H., Goicoechea, J. L., Yu, Y., Kudrna, D. A., Zuccolo, A., Ammiraju, J. S. S., Luo, M., Nelson, W., Ma, J., Sanmiguel, P., Hurwitz, B. L., Ware, D., Brar, D., Mackill, D., Soderlund, C., Stein, L. & Jackson, S., 2007, Rice Functional Genomics: Challenges, Progress and Prospects. Springer New York, p. 395-409 15 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Oryza
Genes
Genome
genome
rice
2006
13 Citations (Scopus)

Integration of hybridization-based markers (overgos) into physical maps for comparative and evolutionary explorations in the genus Oryza and in Sorghum

Hass-Jacobus, B. L., Futrell-Griggs, M., Abernathy, B., Westerman, R., Goicoechea, J. L., Stein, J., Klein, P., Hurwitz, B. L., Zhou, B., Rakhshan, F., Sanyal, A., Gill, N., Lin, J. Y., Walling, J. G., Luo, M. Z., Ammiraju, J. S. S., Kudrna, D. A., Kim, H. R., Ware, D., Wing, R. A. & 2 others, San Miguel, P. & Jackson, S. A., Aug 8 2006, In : BMC Genomics. 7, 199.

Research output: Contribution to journalArticle

Sorghum
Chromosomes
Genome
Oryza
Dermatoglyphics