Ponsero A.J., Bomhoff M., Blumberg K., Youens-Clark K., Herz N.M., Wood-Charlson E.M., Delong E.F., Hurwitz, B.L.. 2020. Planet Microbe: a platform for marine microbiology to discover and analyze interconnected ‘omics and environmental data. Nucleic Acids Research.

Schriml, L.M., Chuvochina, M., Davies, N., Eloe-Fadrosh, E.A., Finn, R.D., Hugenholtz, P., Hunter, C.I., Hurwitz, B.L., Kyrpides, N.C., Meyer, F. and Mizrachi, I.K., 2020. COVID-19 pandemic reveals the peril of ignoring metadata standards. Scientific Data, 7(1), pp.1-4.

Watts, G.S. and Hurwitz, B.L., 2020. Metagenomic Next-Generation Sequencing in Clinical Microbiology. Clinical Microbiology Newsletter, 42(7), pp.53-59.

Watts, G.S., Thornton Jr, J.E., Youens-Clark, K., Ponsero, A.J., Slepian, M.J., Menashi, E., Hu, C., Deng, W., Armstrong, D.G., Reed, S. and Cranmer, L.D., Hurwitz, B.L. 2019. Identification and quantitation of clinically relevant microbes in patient samples: Comparison of three k-mer based classifiers for speed, accuracy, and sensitivity. PLoS computational biology, 15(11), p.e1006863.

Youens-Clark,K., Bomhoff, M; Ponsero, A.; Wood-Charlson, E.; Lynch, J.; Choi, I., Hartman, J.H., Hurwitz, B.L., 2019. iMicrobe: Tools and data-driven discovery platform for the microbiome sciences. GigaScience. In Press.

Ponsero, A. and Hurwitz B.L. 2019 The promises and pitfalls of machine learning for detecting viruses in aquatic metagenomes. Frontiers in Microbiology, 10, 806

Thornton, J. E., Watts, G. S., Youens-Clark, K., Cranmer, L. D., & Hurwitz, B. L. 2019. Speed, accuracy, sensitivity and quality control choices for detecting clinically relevant microbes in whole blood from patients. BioRxiv, 549477.

Choi I, Ponsero, A., Ken Youens-Clark, Matt Bomhoff, George S. Watts, Hartman J, Hurwitz B.L. 2019. Libra: robust biological inferences of global datasets using scalable k-mer based all-vs-all metagenome comparisons. GigaScience.

Roux, S., Adriaenssens, E., Dutilh, B. et al. 2019. Minimum Information about an Uncultivated Virus Genome (MIUViG). Nat Biotechnol 37, 29–37. https://doi.org/10.1038/nbt.4306

Choi I, Ponsero, A., Matthew Bomhoff, Ken Youens-Clark, Matt Bomhoff, Hurwitz B.L., Hartman J, 2018. Libra – improved partitioning strategies for Massive Comparative Metagenomic Analysis. Proceedings of ScienceCloud ‘18.

Hurwitz, B.L., Ponsero, A., Thornton Jr, J. and U’Ren, J.M., 2018. Phage hunters: Computational strategies for finding phages in large-scale ‘omics datasets. Virus research, 244, pp.110-115.

Daniel, S.G., Ball, C.L., Besselsen, D.G., Doetschman, T., Hurwitz, B.L., “Functional changes in the gut microbiome contribute to TGFβ-deficient colon cancer“. MSystems. (2017).

Watts, G., Youens-Clark, K., Slepian, M., Wolk, D., Oshiro, M., Metzger, G., Dhingra, D., Cranmer, L., Hurwitz, B.L., “Accuracy and sensitivity for identification of clinically important bacteria utilizing 16S rRNA gene sequencing on a benchtop sequencer”. Applied Microbiology. In Press. (2017).

Tara Oceans Consortium, “Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition“. Scientific Data. (2017).

Eizenga, G.C, Sanchez, P.L., Hurwitz, B.L., Edwards, J.D., Jackson, A.K., Wing, R., Kudrna, D., “Genetic Variation for Domestication Related Traits Revealed in a Cultivated Rice, Nipponbare (Oryza sativa ssp. japonica) x Ancestral Rice, O. nivara, Mapping Population”. Molecular Breeding. In Press. (2017)

Kindler, L., Stoliartchouk, A., Teytelman, T. and Hurwitz, B.L., “VERVENet: The Viral Ecology Research and Virtual Exchange Network”, F1000 (2017).

Hurwitz, B.L., U,Ren, J.M., and Youens-Clark, K., “Computational Prospecting the Great Viral Unknown“. FEMS Microbiology Letters. (2016).

Hurwitz, B.L. and U,Ren, J.M., “Viral Metabolic Reprogramming in Marine Ecosystems“, Current Opinion in Microbiology, (2016).

Teytelman, T., Stoliartchouk, A., Kindler, L. and Hurwitz, B.L., “protocols.io: virtual communities for protocol development and discussion“. Plos Biology (2016)

Bolduc, B., Youens-Clark, K., Roux, S., Hurwitz, B.L., and Sullivan, M.B. “iVirus: facilitating new insights in viral ecology with software and community datasets imbedded in a cyberinfrastructure”. ISME (2016).

AS Moffarah, M Al Mohajer, Hurwitz, B.L., DG Armstrong. Skin and Soft Tissue Infections”, Microbiology spectrum (2016).

Brum, J., Hurwitz, B.L., Schofield, O., Ducklow, H., Sullivan, M.B., “Seasonal Time Bombs: Dominant temperate viruses affect Southern Ocean microbial dynamics“. ISME. (2015).

U’Ren, J., Wisecaver, J., Paek, A., Dunn, B., Hurwitz, B.L. “Draft genome sequence of the ale-fermenting Saccharomyces cerevisiae strain GSY2239“. Genome Announcements. (2015).

Roux, S., Enault, F., Hurwitz, B.L., Sullivan, M.B., “Virsorter: mining viral signal from microbial genomic data“. PeerJ. (2015).

Armstrong, D. G., Hurwitz, B.L., Lipsky, B.A. “Set Phages to Stun: Reducing the Virulence of S. aureus in Diabetic Foot Ulcers.” Diabetes. (2015).

Armstrong, D. G., Lew, E. J., Hurwitz, B.L., & Wild, T. The Quest for Tissue Repair’s Holy Grail: The Promise of Wound Diagnostics or Just another Fishing Expedition?. Wound Medicine. (2015)

Spichler, A., Hurwitz, B.L., Armstrong, D.G., & Lipsky, B.A. Microbiology of Diabetic Foot Infections: From Louis Pasteur to Crime Scene Investigation. BMC medicine 13.1:2 (2015).

Hurwitz, B. L., Brum, J. R. & Sullivan, M. B. Depth-stratified functional and taxonomic niche specialization in the core and flexible Pacific Ocean Virome. ISME J. (2015).

Hurwitz, B. L., Westveld, A. H., Brum, J. R. & Sullivan, M. B. Modeling ecological drivers in marine viral communities using comparative metagenomics and network analyses. PNAS 111, 10714–10719 (2014).

Rankin, T. M., Giovinco, N. A., Cucher D. J., Watts G., Hurwitz, B., Armstrong D. A.Three-dimensional printing surgical instruments: are we there yet? J. Surg. Res. 189, 193–197 (2014).

Hurwitz, B. L., Hallam, S. J. & Sullivan, M. B. Metabolic reprogramming by viruses in the sunlit and dark ocean. Genome Biol. 14, R123 (2013).

Hurwitz, B. L. & Sullivan, M. B. The Pacific Ocean Virome (POV): a marine viral metagenomic dataset and associated protein clusters for quantitative viral ecology. PLoS One 8, e57355 (2013).

Hurwitz, B. L., Deng, L., Poulos, B. T. & Sullivan, M. B. Evaluation of methods to concentrate and purify ocean virus communities through comparative, replicated metagenomics. Environ. Microbiol. (2013).

Hurwitz, B. L. et al. Rice structural variation: a comparative analysis of structural variation between rice and three of its closest relatives in the genus Oryza. Plant J. 63, 990–1003 (2010).

Degnan P. H., Leonardo T. E., Cass B. N., Hurwitz B., Stern D., Gibbs R. A., Richards S., Moran N. A. Dynamics of genome evolution in facultative symbionts of aphids. Environ. Microbiol. 12, 2060–2069 (2010).

Cranston K. A., Hurwitz, B., Sanderson, M. J., Ware, D., Wing, R. A., and Stein L. Phylogenomic Analysis of BAC-end Sequence Libraries in Oryza (Poaceae). Syst. Bot. 35, 512–523 (2010).

Richards, S. et al. Genome Sequence of the Pea Aphid Acyrthosiphon pisum. PLoS Biol. 8, (2010).

Myles S., Chia J. M., Hurwitz B., Simon C., Zhong G. Y., Buckler E., and Ware D. Rapid Genomic Characterization of the Genus Vitis. PLoS One 5, (2010).

Youens-Clark K, Buckler E, Casstevens T, Chen C, Declerck G, Derwent P, Dharmawardhana P, Jaiswal P, Kersey P, Karthikeyan AS, Lu J, McCouch SR, Ren L, Spooner W, Stein JC, Thomason J, Wei S, Ware D. Gramene database in 2010: updates and extensions. Nucleic Acids Res. 2010 Nov 13. PMID: 21076153.

Cranston, K. A., Hurwitz, B., Ware, D., Stein, L. & Wing, R. A. Species Trees from Highly Incongruent Gene Trees in Rice. Syst. Biol. 58, 489–500 (2009).

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., and Buckler E. S. A First-Generation Haplotype Map of Maize. Science 326, 1115–1117 (2009).

Gore, M. A., Wright, M. H., Ersoz, E. S., Bouffard, P., Szekeres, E. S., Jarvie, T. P., Hurwitz B. L., Narechania, A., Harkins, T. T., Grills, G. S., Ware, D. H., and Buckler, E. S. Large-Scale Discovery of Gene-Enriched SNPs. Plant Genome 2, 121–133 (2009).

Youens-Clark K, Faga B, Yap I, Stein L, Ware D. CMap 1.01: A comparative mapping application for the Internet. Bioinformatics. 2009 Nov 15;25(22):3040-2. doi: 10.1093/bioinformatics/btp458. Epub 2009 Jul 30. PMID: 19648141.

Liang, C., Jaiswal, P., Hebbard, C., Avraham, S., Buckler, E. S., Casstevens, T., Hurwitz, B., 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., and Stein L. Gramene: a growing plant comparative genomics resource. Nucleic Acids Res. 36, D947–D953 (2008).

Kim, H., Hurwitz, B., Yu, Y., Collura, K., Gill, N., SanMiguel, P., Mullikin, J. C., Maher, C., Nelson, W., Wissotski, M., Braidotti, M., Kudrna, D., Goicoechea, J. L., Stein, L., Ware, D., Jackson, S. A., Soderlund, C., and Wing, R. A. Construction, alignment and analysis of twelve framework physical maps that represent the ten genome types of the genus Oryza. Genome Biol. 9, (2008).

Hass-Jacobus, B. L., Futrell-Griggs, M., Abernathy, B., Westerman, R., Goicoechea, J. L., Stein, J., Klein, P., Hurwitz, B., Zhou, B., Rakhshan, F., Sanyal, A., Gill, N., Lin, J. Y., Walling, J. G., Luo, M. Z., Ammiraju, J. S., Kudrna, D., Kim, H. R., Ware, D., Wing, R. A., San Miguel, P., and Jackson S. A. Integration of hybridization-based markers (overgos) into physical maps for comparative and evolutionary explorations in the genus Oryza and in Sorghum. BMC Genomics 7, (2006).