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Haynes, Matthew R
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Haynes, Matthew R

Graduate Student
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Positions

  • 2014 - Test Prep Tutor, Varsity Tutors

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  • Doctoral Dissertation
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Publications

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  • academic article

    • Panschin, I., Huang, S., Meier-Kolthoff, J. P., Tindall, B. J., Rohde, M., Verbarg, S., Lapidus, A., Han, J., Trong, S., Haynes, M., Reddy, T. B. K., Huntemann, M., et al. Comparing polysaccharide decomposition between the type strains Gramella echinicola KMM 6050(T) (DSM 19838(T)) and Gramella portivictoriae UST040801-001(T) (DSM 23547(T)), and emended description of Gramella echinicola Nedashkovskaya et al. 2005 emend. Shahina et al. 2014 and Gramella portivictoriae Lau et al. 2005 Standards in Genomic Sciences  2016 11  DOI:10.1186/s40793-016-0163-9  PMID:27274783  PMCID:PMC4891872
    • Sakamoto, M., Lapidus, A. L., Han, J., Trong, S., Haynes, M., Reddy, T. B. K., Mikhailova, N., Huntemann, M., Pati, A., Ivanova, N. N., Pukall, R., Markowitz, V. M., et al. High quality draft genome sequence of Bacteroides barnesiae type strain BL2(T) (DSM 18169(T)) from chicken caecum Standards in Genomic Sciences  2015 10  DOI:10.1186/s40793-015-0045-6  PMID:26380636  PMCID:PMC4572637
    • Hahnke, R. L., Stackebrandt, E., Meier-Kolthoff, J. P., Tindall, B. J., Huang, S., Rohde, M., Lapidus, A., Han, J., Trong, S., Haynes, M., Reddy, T. B. K., Huntemann, M., et al. High quality draft genome sequence of Flavobacterium rivuli type strain WB 3.3-2(T) (DSM 21788(T)), a valuable source of polysaccharide decomposing enzymes Standards in Genomic Sciences  2015 10  DOI:10.1186/s40793-015-0032-y  PMID:26380634  PMCID:PMC4572689
    • Sanchez, S. E., Cuevas, D. A., Rostron, J. E., Liang, T. Y., Pivaroff, C. G., Haynes, M. R., Nulton, J., Felts, B., Bailey, B. A., Salamon, P., Edwards, R. A., Burgin, A. B., et al. Phage phenomics: physiological approaches to characterize novel viral proteins Journal of Visualized Experiments : JoVE  2015  DOI:10.3791/52854  PMID:26132888  PMCID:PMC4544906
    • Laviad, S., Lapidus, A., Han, J., Haynes, M., Reddy, T. B. K., Huntemann, M., Pati, A., Ivanova, N. N., Mavromatis, K., Lang, E., Rohde, M., Markowitz, V., et al. High quality draft genome sequence of Brachymonas chironomi AIMA4(T) (DSM 19884(T)) isolated from a Chironomus sp. egg mass Standards in Genomic Sciences  2015 10  DOI:10.1186/s40793-015-0010-4  PMID:26203340  PMCID:PMC4511610
    • McLlroy, S. J., Lapidus, A., Thomsen, T. R., Han, J., Haynes, M., Lobos, E., Huntemann, M., Pati, A., Ivanova, N. N., Markowitz, V., Verbarg, S., Woyke, T., et al. High quality draft genome sequence of Meganema perideroedes str. Gr1(T) and a proposal for its reclassification to the family Meganemaceae fam. nov Standards in Genomic Sciences  2015 10  DOI:10.1186/s40793-015-0013-1  PMID:26203335  PMCID:PMC4511698
    • Gao, X. Y., Zhi, X. Y., Li, H. W., Zhou, Y., Lapidus, A., Han, J., Haynes, M., Lobos, E., Huntemann, M., Pati, A., Ivanova, N. N., Mavromatis, K., et al. Draft genome sequence of Halomonas lutea strain YIM 91125(T) (DSM 23508(T)) isolated from the alkaline Lake Ebinur in Northwest China Standards in Genomic Sciences  2015 10  DOI:10.1186/1944-3277-10-1  PMID:25678942  PMCID:PMC4315136
    • Lim, Y. W., Haynes, M., Furlan, M., Robertson, C. E., Harris, J. K., Rohwer, F. Purifying the impure: sequencing metagenomes and metatranscriptomes from complex animal-associated samples Journal of Visualized Experiments : JoVE  2014  DOI:10.3791/52117  PMID:25549184  PMCID:PMC4354477
    • Grasis, J. A., Lachnit, T., Anton-Erxleben, F., Lim, Y. W., Schmieder, R., Fraune, S., Franzenburg, S., Insua, S., Machado, G., Haynes, M., Little, M., Kimble, R., et al. Species-specific viromes in the ancestral holobiont Hydra PLoS One  2014 9  DOI:10.1371/journal.pone.0109952  PMID:25343582  PMCID:PMC4208763
    • Kelly, L. W., Williams, G. J., Barott, K. L., Carlson, C. A., Dinsdale, E. A., Edwards, R. A., Haas, A. F., Haynes, M., Lim, Y. W., McDole, T., Nelson, C. E., Sala, E., et al. Local genomic adaptation of coral reef-associated microbiomes to gradients of natural variability and anthropogenic stressors Proceedings of the National Academy of Sciences of the United States of America  2014 111:10227-10232  DOI:10.1073/pnas.1403319111  PMID:24982156  PMCID:PMC4104888
    • Lim, Y. W., Evangelista III, J. S., Schmieder, R., Bailey, B., Haynes, M., Furlan, M., Maughan, H., Edwards, R., Rohwer, F., Conrad, D. Clinical insights from metagenomic analysis of sputum samples from patients with cystic fibrosis Journal of Clinical Microbiology  2014 52:425-437  DOI:10.1128/jcm.02204-13  PMID:24478471  PMCID:PMC3911355
    • Zhou, Y., Li, R., Gao, X. Y., Lapidus, A., Han, J., Haynes, M., Lobos, E., Huntemann, M., Pati, A., Ivanova, N. N., Rohde, M., Mavromatis, K., et al. High quality draft genome sequence of the slightly halophilic bacterium Halomonas zhanjiangensis type strain JSM 078169(T) (DSM 21076(T)) from a sea urchin in southern China Standards in Genomic Sciences  2014 9:1020-1030  DOI:10.4056/sigs.5449586  PMID:25197480  PMCID:PMC4148996
    • Lim, Y. W., Schmieder, R., Haynes, M., Furlan, M., Matthews, T. D., Whiteson, K., Poole, S. J., Hayes, C. S., Low, D. A., Maughan, H., Edwards, R., Conrad, D., et al. Mechanistic model of Rothia mucilaginosa adaptation toward persistence in the CF lung, based on a genome reconstructed from metagenomic data PLoS One  2013 8  DOI:10.1371/journal.pone.0064285  PMID:23737977  PMCID:PMC3667864
    • Mokili, J. L., Dutilh, B. E., Lim, Y. W., Schneider, B. S., Taylor, T., Haynes, M. R., Metzgar, D., Myers, C. A., Blair, P. J., Nosrat, B., Wolfe, N. D., Rohwer, F. Identification of a novel human papillomavirus by metagenomic analysis of samples from patients with febrile respiratory illness PLoS One  2013 8  DOI:10.1371/journal.pone.0058404  PMID:23554892  PMCID:PMC3600855
    • Lim, Y. W., Schmieder, R., Haynes, M., Willner, D., Furlan, M., Youle, M., Abbott, K., Edwards, R., Evangelista, J., Conrad, D., Rohwer, F. Metagenomics and metatranscriptomics: windows on CF-associated viral and microbial communities Journal of Cystic Fibrosis  2013 12:154-164  DOI:10.1016/j.jcf.2012.07.009  PMID:22951208  PMCID:PMC3534838
    • Conrad, D., Haynes, M., Salamon, P., Rainey, P. B., Youle, M., Rohwer, F. Cystic fibrosis therapy: a community ecology perspective American Journal of Respiratory Cell and Molecular Biology  2013 48:150-156  DOI:10.1165/rcmb.2012-0059PS  PMID:23103995  PMCID:PMC3604065
    • Pride, D. T., Salzman, J., Haynes, M., Rohwer, F., Davis-Long, C., White III, R. A., Loomer, P., Armitage, G. C., Relman, D. A. Evidence of a robust resident bacteriophage population revealed through analysis of the human salivary virome ISME Journal  2012 6:915-926  DOI:10.1038/ismej.2011.169  PMID:22158393  PMCID:PMC3329113
    • Willner, D., Haynes, M. R., Furlan, M., Hanson, N., Kirby, B., Lim, Y. W., Rainey, P. B., Schmieder, R., Youle, M., Conrad, D., Rohwer, F. Case studies of the spatial heterogeneity of DNA viruses in the cystic fibrosis lung American Journal of Respiratory Cell and Molecular Biology  2012 46:127-131  DOI:10.1165/rcmb.2011-0253OC  PMID:21980056  PMCID:PMC3361360
    • Willner, D., Haynes, M. R., Furlan, M., Schmieder, R., Lim, Y. W., Rainey, P. B., Rohwer, F., Conrad, D. Spatial distribution of microbial communities in the cystic fibrosis lung ISME Journal  2012 6:471-474  DOI:10.1038/ismej.2011.104  PMID:21796216  PMCID:PMC3260497
    • Willner, D., Furlan, M., Schmieder, R., Grasis, J. A., Pride, D. T., Relman, D. A., Angly, F. E., McDole, T., Mariella Jr., R. P., Rohwer, F., Haynes, M. Metagenomic detection of phage-encoded platelet-binding factors in the human oral cavity Proceedings of the National Academy of Sciences of the United States of America  2011 108:4547-4553  DOI:10.1073/pnas.1000089107  PMID:20547834  PMCID:PMC3063595
    • Reyes, A., Haynes, M., Hanson, N., Angly, F. E., Heath, A. C., Rohwer, F., Gordon, J. I. Viruses in the faecal microbiota of monozygotic twins and their mothers Nature  2010 466:334-338  DOI:10.1038/nature09199  PMID:20631792  PMCID:PMC2919852
    • Rodriguez-Brito, B., Li, L., Wegley, L., Furlan, M., Angly, F., Breitbart, M., Buchanan, J., Desnues, C., Dinsdale, E., Edwards, R., Felts, B., Haynes, M., et al. Viral and microbial community dynamics in four aquatic environments ISME Journal  2010 4:739-751  DOI:10.1038/ismej.2010.1  PMID:20147985
    • He, S., Kunin, V., Haynes, M., Martin, H. G., Ivanova, N., Rohwer, F., Hugenholtz, P., McMahon, K. D. Metatranscriptomic array analysis of Candidatus Accumulibacter phosphatis-enriched enhanced biological phosphorus removal sludge Environmental Microbiology  2010 12:1205-1217  DOI:10.1111/j.1462-2920.2010.02163.x  PMID:20148930
    • Angly, F. E., Willner, D., Prieto-Davo, A., Edwards, R. A., Schmieder, R., Vega-Thurber, R., Antonopoulos, D. A., Barott, K., Cottrell, M. T., Desnues, C., Dinsdale, E. A., Furlan, M., et al. The GAAS metagenomic tool and its estimations of viral and microbial average genome size in four major biomes PLoS Computational Biology  2009 5  DOI:10.1371/journal.pcbi.1000593  PMID:20011103  PMCID:PMC2781106
    • Willner, D., Furlan, M., Haynes, M., Schmieder, R., Angly, F. E., Silva, J., Tammadoni, S., Nosrat, B., Conrad, D., Rohwer, F. Metagenomic analysis of respiratory tract DNA viral communities in cystic fibrosis and non-cystic fibrosis individuals PLoS One  2009 4  DOI:10.1371/journal.pone.0007370  PMID:19816605  PMCID:PMC2756586
    • Sharon, I., Alperovitch, A., Rohwer, F., Haynes, M., Glaser, F., Atamna-Ismaeel, N., Pinter, R. Y., Partensky, F., Koonin, E. V., Wolf, Y. I., Nelson, N., Beja, O. Photosystem I gene cassettes are present in marine virus genomes Nature  2009 461:258-262  DOI:10.1038/nature08284  PMID:19710652
    • Thurber, R. V., Haynes, M., Breitbart, M., Wegley, L., Rohwer, F. Laboratory procedures to generate viral metagenomes Nature Protocols  2009 4:470-483  DOI:10.1038/nprot.2009.10  PMID:19300441
    • Breitbart, M., Hoare, A., Nitti, A., Siefert, J., Haynes, M., Dinsdale, E., Edwards, R., Souza, V., Rohwer, F., Hollander, D. Metagenomic and stable isotopic analyses of modern freshwater microbialites in Cuatro Cienegas, Mexico Environmental Microbiology  2009 11:16-34  DOI:10.1111/j.1462-2920.2008.01725.x  PMID:18764874
    • Thurber, R. L. V., Barott, K. L., Hall, D., Liu, H., Rodriguez-Mueller, B., Desnues, C., Edwards, R. A., Haynes, M., Angly, F. E., Wegley, L., Rohwer, F. L. Metagenomic analysis indicates that stressors induce production of herpes-like viruses in the coral Porites compressa Proceedings of the National Academy of Sciences of the United States of America  2008 105:18413-18418  DOI:10.1073/pnas.0808985105  PMID:19017800  PMCID:PMC2584576
    • McDaniel, L., Breitbart, M., Mobberley, J., Long, A., Haynes, M., Rohwer, F., Paul, J. H. Metagenomic analysis of lysogeny in Tampa Bay: implications for prophage gene expression PLoS One  2008 3  DOI:10.1371/journal.pone.0003263  PMID:18810270  PMCID:PMC2533394
    • Breitbart, M., Haynes, M., Kelley, S., Angly, F., Edwards, R. A., Felts, B., Mahaffy, J. M., Mueller, J., Nulton, J., Rayhawk, S., Rodriguez-Brito, B., Salamon, P., et al. Viral diversity and dynamics in an infant gut Research in Microbiology  2008 159:367-373  DOI:10.1016/j.resmic.2008.04.006  PMID:18541415
    • Tringe, S. G., Zhang, T., Liu, X., Yu, Y., Lee, W. H., Yap, J., Yao, F., Suan, S. T., Ing, S. K., Haynes, M., Rohwer, F., Wei, C. L., et al. The airborne metagenome in an indoor urban environment PLoS One  2008 3  DOI:10.1371/journal.pone.0001862  PMID:18382653  PMCID:PMC2270337
    • Desnues, C., Rodriguez-Brito, B., Rayhawk, S., Kelley, S., Tran, T., Haynes, M., Liu, H., Furlan, M., Wegley, L., Chau, B., Ruan, Y., Hall, D., et al. Biodiversity and biogeography of phages in modern stromatolites and thrombolites Nature  2008 452:340-343  DOI:10.1038/nature06735  PMID:18311127
    • Dinsdale, E. A., Pantos, O., Smriga, S., Edwards, R. A., Angly, F., Wegley, L., Hatay, M., Hall, D., Brown, E., Haynes, M., Krause, L., Sala, E., et al. Microbial ecology of four coral atolls in the Northern Line Islands PLoS One  2008 3  DOI:10.1371/journal.pone.0001584  PMID:18301735  PMCID:PMC2253183
    • Kunin, V., He, S., Warnecke, F., Peterson, S. B., Martin, H. G., Haynes, M., Ivanova, N., Blackall, L. L., Breitbart, M., Rohwer, F., McMahon, K. D., Hugenholtz, P. A bacterial metapopulation adapts locally to phage predation despite global dispersal Genome Research  2008 18:293-297  DOI:10.1101/gr.6835308  PMID:18077539  PMCID:PMC2203627
    • Dinsdale, E. A., Edwards, R. A., Hall, D., Angly, F., Breitbart, M., Brulc, J. M., Furlan, M., Desnues, C., Haynes, M., Li, L., McDaniel, L., Moran, M. A., et al. Functional metagenomic profiling of nine biomes Nature  2008 452:629-632  DOI:10.1038/nature06810  PMID:18337718
    • Angly, F. E., Felts, B., Breitbart, M., Salamon, P., Edwards, R. A., Carlson, C., Chan, A. M., Haynes, M., Kelley, S., Liu, H., Mahaffy, J. M., Mueller, J. E., et al. The marine viromes of four oceanic regions PLoS Biology  2006 4:2121-2131  DOI:10.1371/journal.pbio.0040368  PMID:17090214  PMCID:PMC1634881
    • Edwards, R. A., Rodriguez-Brito, B., Wegley, L., Haynes, M., Breitbart, M., Peterson, D. M., Saar, M. O., Alexander, S., Alexander Jr., E. C., Rohwer, F. Using pyrosequencing to shed light on deep mine microbial ecology BMC Genomics  2006 7  DOI:10.1186/1471-2164-7-57  PMID:16549033  PMCID:PMC1483832
    • degree-related publication Haynes, M. R., Heine, A., Wilson, I. A. Catalytic antibody structures: An early assessment Israel Journal of Chemistry  1996 36:133-142
    • degree-related publication Haynes, M. R., Lenz, M., Taussig, M. J., Wilson, I. A., Hilvert, D. Sequence similarity and cross-reactivity of a diels-alder catalyst and an anti-progesterone antibody Israel Journal of Chemistry  1996 36:151-159
    • degree-related publication Wilson, I. A., Stanfield, R. L., Arevalo, J. H., Jewell, D. A., Ghiara, J. B., Haynes, M. R., Fremont, D. H., Stura, E. A. Structural basis of immune recognition Protein Engineering  1995 8:113-113
    • degree-related publication Haynes, M. R., Stura, E. A., Hilvert, D., Wilson, I. A. Routes to catalysis - structure of a catalytic antibody and comparison with its natural counterpart Science  1994 263:646-652  DOI:10.1126/science.8303271  PMID:8303271
    • degree-related publication Haynes, M. R., Stura, E. A., Hilvert, D., Wilson, I. A. Crystallization and preliminary structural studies of a chorismate mutase catalytic antibody complexed with a transition-state analog Proteins-Structure Function and Genetics  1994 18:198-200  DOI:10.1002/prot.340180211  PMID:8159668
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Background

education and training

  • Ph.D. in Biology, Scripps Research 1989 - 1995
  • A.B. in Physical Sciences, Harvard University 1981 - 1986

advisee of

  • graduate advising relationship

    • Wilson, Ian, Ph.D.  candidacy, 1990 - 1995
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Contact

full name

  • Matthew R Haynes

geographic location

  • Scripps California 

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