recent 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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., 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
- 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
- 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., 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
- 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
- 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
- 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., 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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., 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
- 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
- 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
- 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
- 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
- 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
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Haynes, M. R., Heine, A., Wilson, I. A.
Catalytic antibody structures: An early assessment
Israel Journal of Chemistry
1996
36:133-142
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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
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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
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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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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