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Owen R White
 

Owen R White Ph.D.

Academic Title: Professor
Primary Appointment: Epidemiology & Public Health
Additional Title(s): Associate Director, Institute for Genome Sciences
owhite@som.umaryland.edu
Location: Bio Park 2, 6th floor
Phone: (410) 706-6751
Phone: (410) 706-6755
Fax: (410) 706-6756

Personal History:

Owen R. White is the Director of the Bioinformatics department at the Institute for Genome Sciences (IGS) and a Professor of Epidemiology and Public Health at the University of Maryland School of Medicine in Baltimore, Maryland.

The IGS Bioinformatics group annotates (or interprets and analyses) the huge strings of sequencing data from genomic and biomedical researchers at the center. Dr. White and the IGS Bioinformatics department are involved in large-scale annotation, ontology development and data sharing. They are the lead institution for the Human Microbiome Project’s central data repository or the Data Analysis and Coordination Center (known as the HMP DACC).

The HMP was launched by the National Institutes of Health to fuel research into the microbes that live in the various environments of the human body, and to look for correlations between changes in the microbiome and human health. The HMP DACC is the central repository for all HMP data, providing specialized data management and analysis infrastructure to facilitate discoveries about the microbiome.

Research Interests:

Annotation

Dr. White has overseen the annotation of hundreds of genomes sequenced using computer analyses such as pairwise searches, multiple sequence alignments, and numerous other methods in combination with systematic manual evaluation. This administration of analysis has served to generate highly uniform annotation that includes the genomes for Arabidopsis, the mosquito Aedes agypti, parasitic organisms such as Trypanosoma Brucei and Plasmodium falciparum, human ESTs and many Bacterial and Archaeal species. He has also developed automated annotation systems such as TIGRFams, Genome Properties, as well as the Annotation Engine.

Interfaces

One challenge presented by large-scale genome sequencing efforts is effective display of uniform information to the scientific community. Dr. White has been responsible for the development of several web resources such as the Comprehensive Microbial Resource (CMR) which contains annotation of all complete microbial genomes, and Pathema, an NIAID sponsored bioinformatics resource center to support the biodefense community. More recent development is Gemina, a web-based system designed to identify infectious pathogens and their representative genomic sequences through selection of associated epidemiology metadata.

Comparative genomics

In addition to previous works that include the CMR and the TIGRFam dataset Dr. White has participated in development of numerous tools for genome comparison. This includes analysis of plant, fungal, malarial, trypanosomid, Archaeal and Prokaryotic species. His current research includes development of an open source system, Sybil, that is a web-based software package for comparative genomics. Sybil is a comprehensive set of comparative analysis tools of Prokaryotic and Eukaryotic systems. It incorporates many open source components and performs pre-computes of data enabling users to perform variety of comparative analysis methods.

Management, training and support

Prior to coming to the University of Maryland, Dr. White led a staff of 65 people comprised of PhD-level analysts, Software Engineers, Staff Scientists and Bioinformatics Engineers that supplied core services to research faculty. During this time he advanced the use of documenting standard operational procedures, matrix management and employee training practices. His current staff is comprised of 18 people that are similarly engaged in supplying both core services, developing Open Source resources for the community and performing genomic research functions for faculty at IGS. Another critical product of Dr. White's research is to engage other researchers in large-scale interoperation, for annotation, ontology development, and data sharing. The fact that Dr. White was among the 10 most-cited scientists is a direct reflection of his support for several significant efforts.


Publications:

Recent Publications

Wortman, J.R., Fedorova, N., Crabtree, J., Joardar, V., Maiti, R., Haas, B.J., Amedeo, P., Lee, E., Angiuoli, S.V., Jiang, B., Anderson, M.J., Denning, D.W., White, O.R., Nierman, W.C., 2006. Whole genome comparison of the A. fumigatus family. Med Mycol 44 Suppl, 3-7.

Hotopp, J.C., Lin, M., Madupu, R., Crabtree, J., Angiuoli, S.V., Eisen, J., Seshadri, R., Ren, Q., Wu, M., Utterback, T.R., Smith, S., Lewis, M., Khouri, H., Zhang, C., Niu, H., Lin, Q., Ohashi, N., Zhi, N., Nelson, W., Brinkac, L.M., Dodson, R.J., Rosovitz, M.J., Sundaram, J., Daugherty, S.C., Davidsen, T., Durkin, A.S., Gwinn, M., Haft, D.H., Selengut, J.D., Sullivan, S.A., Zafar, N., Zhou, L., Benahmed, F., Forberger, H., Halpin, R., Mulligan, S., Robinson, J., White, O., Rikihisa, Y., Tettelin, H., 2006. Comparative genomics of emerging human ehrlichiosis agents. PLoS genetics 2, e21.

Tettelin, H., Masignani, V., Cieslewicz, M.J., Donati, C., Medini, D., Ward, N.L., Angiuoli, S.V., Crabtree, J., Jones, A.L., Durkin, A.S., Deboy, R.T., Davidsen, T.M., Mora, M., Scarselli, M., Margarit y Ros, I., Peterson, J.D., Hauser, C.R., Sundaram, J.P., Nelson, W.C., Madupu, R., Brinkac, L.M., Dodson, R.J., Rosovitz, M.J., Sullivan, S.A., Daugherty, S.C., Haft, D.H., Selengut, J., Gwinn, M.L., Zhou, L., Zafar, N., Khouri, H., Radune, D., Dimitrov, G., Watkins, K., O'Connor, K.J., Smith, S., Utterback, T.R., White, O., Rubens, C.E., Grandi, G., Madoff, L.C., Kasper, D.L., Telford, J.L., Wessels, M.R., Rappuoli, R., Fraser, C.M., 2005. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome". Proceedings of the National Academy of Sciences of the United States of America 102, 13950-13955.

Nierman, W.C., Pain, A., Anderson, M.J., Wortman, J.R., Kim, H.S., Arroyo, J., Berriman, M., Abe, K., Archer, D.B., Bermejo, C., Bennett, J., Bowyer, P., Chen, D., Collins, M., Coulsen, R., Davies, R., Dyer, P.S., Farman, M., Fedorova, N., Fedorova, N., Feldblyum, T.V., Fischer, R., Fosker, N., Fraser, A., Garcia, J.L., Garcia, M.J., Goble, A., Goldman, G.H., Gomi, K., Griffith-Jones, S., Gwilliam, R., Haas, B., Haas, H., Harris, D., Horiuchi, H., Huang, J., Humphray, S., Jimenez, J., Keller, N., Khouri, H., Kitamoto, K., Kobayashi, T., Konzack, S., Kulkarni, R., Kumagai, T., Lafon, A., Latge, J.P., Li, W., Lord, A., Lu, C., Majoros, W.H., May, G.S., Miller, B.L., Mohamoud, Y., Molina, M., Monod, M., Mouyna, I., Mulligan, S., Murphy, L., O'Neil, S., Paulsen, I., Penalva, M.A., Pertea, M., Price, C., Pritchard, B.L., Quail, M.A., Rabbinowitsch, E., Rawlins, N., Rajandream, M.A., Reichard, U., Renauld, H., Robson, G.D., Rodriguez de Cordoba, S., Rodriguez-Pena, J.M., Ronning, C.M., Rutter, S., Salzberg, S.L., Sanchez, M., Sanchez-Ferrero, J.C., Saunders, D., Seeger, K., Squares, R., Squares, S., Takeuchi, M., Tekaia, F., Turner, G., Vazquez de Aldana, C.R., Weidman, J., White, O., Woodward, J., Yu, J.H., Fraser, C., Galagan, J.E., Asai, K., Machida, M., Hall, N., Barrell, B., Denning, D.W., 2005. Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus. Nature 438, 1151-1156.

Joardar, V., Lindeberg, M., Jackson, R.W., Selengut, J., Dodson, R., Brinkac, L.M., Daugherty, S.C., Deboy, R., Durkin, A.S., Giglio, M.G., Madupu, R., Nelson, W.C., Rosovitz, M.J., Sullivan, S., Crabtree, J., Creasy, T., Davidsen, T., Haft, D.H., Zafar, N., Zhou, L., Halpin, R., Holley, T., Khouri, H., Feldblyum, T., White, O., Fraser, C.M., Chatterjee, A.K., Cartinhour, S., Schneider, D.J., Mansfield, J., Collmer, A., Buell, C.R., 2005. Whole-genome sequence analysis of Pseudomonas syringae pv. phaseolicola 1448A reveals divergence among pathovars in genes involved in virulence and transposition. Journal of bacteriology 187, 6488-6498.

Haft, D.H., Selengut, J.D., Brinkac, L.M., Zafar, N., White, O., 2005. Genome Properties: a system for the investigation of prokaryotic genetic content for microbiology, genome annotation and comparative genomics. Bioinformatics (Oxford, England) 21, 293-306.

Haas, B.J., Wortman, J.R., Ronning, C.M., Hannick, L.I., Smith, R.K., Jr., Maiti, R., Chan, A.P., Yu, C., Farzad, M., Wu, D., White, O., Town, C.D., 2005. Complete reannotation of the Arabidopsis genome: methods, tools, protocols and the final release. BMC biology 3, 7.

Gardner, M.J., Bishop, R., Shah, T., de Villiers, E.P., Carlton, J.M., Hall, N., Ren, Q., Paulsen, I.T., Pain, A., Berriman, M., Wilson, R.J., Sato, S., Ralph, S.A., Mann, D.J., Xiong, Z., Shallom, S.J., Weidman, J., Jiang, L., Lynn, J., Weaver, B., Shoaibi, A., Domingo, A.R., Wasawo, D., Crabtree, J., Wortman, J.R., Haas, B., Angiuoli, S.V., Creasy, T.H., Lu, C., Suh, B., Silva, J.C., Utterback, T.R., Feldblyum, T.V., Pertea, M., Allen, J., Nierman, W.C., Taracha, E.L., Salzberg, S.L., White, O.R., Fitzhugh, H.A., Morzaria, S., Venter, J.C., Fraser, C.M., Nene, V., 2005. Genome sequence of Theileria parva, a bovine pathogen that transforms lymphocytes. Science 309, 134-137.

El-Sayed, N.M., Myler, P.J., Blandin, G., Berriman, M., Crabtree, J., Aggarwal, G., Caler, E., Renauld, H., Worthey, E.A., Hertz-Fowler, C., Ghedin, E., Peacock, C., Bartholomeu, D.C., Haas, B.J., Tran, A.N., Wortman, J.R., Alsmark, U.C., Angiuoli, S., Anupama, A., Badger, J., Bringaud, F., Cadag, E., Carlton, J.M., Cerqueira, G.C., Creasy, T., Delcher, A.L., Djikeng, A., Embley, T.M., Hauser, C., Ivens, A.C., Kummerfeld, S.K., Pereira-Leal, J.B., Nilsson, D., Peterson, J., Salzberg, S.L., Shallom, J., Silva, J.C., Sundaram, J., Westenberger, S., White, O., Melville, S.E., Donelson, J.E., Andersson, B., Stuart, K.D., Hall, N., 2005a. Comparative genomics of trypanosomatid parasitic protozoa. Science 309, 404-409.

El-Sayed, N.M., Myler, P.J., Bartholomeu, D.C., Nilsson, D., Aggarwal, G., Tran, A.N., Ghedin, E., Worthey, E.A., Delcher, A.L., Blandin, G., Westenberger, S.J., Caler, E., Cerqueira, G.C., Branche, C., Haas, B., Anupama, A., Arner, E., Aslund, L., Attipoe, P., Bontempi, E., Bringaud, F., Burton, P., Cadag, E., Campbell, D.A., Carrington, M., Crabtree, J., Darban, H., da Silveira, J.F., de Jong, P., Edwards, K., Englund, P.T., Fazelina, G., Feldblyum, T., Ferella, M., Frasch, A.C., Gull, K., Horn, D., Hou, L., Huang, Y., Kindlund, E., Klingbeil, M., Kluge, S., Koo, H., Lacerda, D., Levin, M.J., Lorenzi, H., Louie, T., Machado, C.R., McCulloch, R., McKenna, A., Mizuno, Y., Mottram, J.C., Nelson, S., Ochaya, S., Osoegawa, K., Pai, G., Parsons, M., Pentony, M., Pettersson, U., Pop, M., Ramirez, J.L., Rinta, J., Robertson, L., Salzberg, S.L., Sanchez,
D.O., Seyler, A., Sharma, R., Shetty, J., Simpson, A.J., Sisk, E., Tammi, M.T., Tarleton, R., Teixeira, S., Van Aken, S., Vogt, C., Ward, P.N., Wickstead, B., Wortman, J., White, O., Fraser, C.M., Stuart, K.D., Andersson, B., 2005b. The genome sequence of Trypanosoma cruzi, etiologic agent of Chagas disease. Science 309, 409-415.

Buell, C.R., Yuan, Q., Ouyang, S., Liu, J., Zhu, W., Wang, A., Maiti, R., Haas, B., Wortman, J., Pertea, M., Jones, K.M., Kim, M., Overton, L., Tsitrin, T., Fadrosh, D., Bera, J., Weaver, B., Jin, S., Johri, S., Reardon, M., Webb, K., Hill, J., Moffat, K., Tallon, L., Van Aken, S., Lewis, M., Utterback, T., Feldblyum, T., Zismann, V., Iobst, S., Hsiao, J., de Vazeille, A.R., Salzberg, S.L., White, O., Fraser, C., Yu, Y., Kim, H., Rambo, T., Currie, J., Collura, K., Kernodle-Thompson, S., Wei, F., Kudrna, K., Ammiraju, J.S., Luo, M., Goicoechea, J.L., Wing, R.A., Henry, D., Oates, R., Palmer, M., Pries, G., Saski, C., Simmons, J., Soderlund, C., Nelson, W., de la Bastide, M., Spiegel, L., Nascimento, L., Huang, E., Preston, R., Zutavern, T., Palmer, L., O'Shaughnessy, A., Dike, S., McCombie, W.R., Minx, P., Cordum, H., Wilson, R., Jin, W., Lee, H.R., Jiang, J., Jackson, S., 2005. Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species. Genome research 15, 1284-1291.

Ayele, M., Haas, B.J., Kumar, N., Wu, H., Xiao, Y., Van Aken, S., Utterback, T.R., Wortman, J.R., White, O.R., Town, C.D., 2005. Whole genome shotgun sequencing of Brassica oleracea and its application to gene discovery and annotation in Arabidopsis. Genome research 15, 487-495.

Nierman, W.C., DeShazer, D., Kim, H.S., Tettelin, H., Nelson, K.E., Feldblyum, T., Ulrich, R.L., Ronning, C.M., Brinkac, L.M., Daugherty, S.C., Davidsen, T.D., Deboy, R.T., Dimitrov, G., Dodson, R.J., Durkin, A.S., Gwinn, M.L., Haft, D.H., Khouri, H., Kolonay, J.F., Madupu, R., Mohammoud, Y., Nelson, W.C., Radune, D., Romero, C.M., Sarria, S., Selengut, J., Shamblin, C., Sullivan, S.A., White, O., Yu, Y., Zafar, N., Zhou, L., Fraser, C.M., 2004. Structural flexibility in the Burkholderia mallei genome. Proceedings of the National Academy of Sciences of the United States of America 101, 14246-14251.

Nelson, K.E., Fouts, D.E., Mongodin, E.F., Ravel, J., DeBoy, R.T., Kolonay, J.F., Rasko, D.A., Angiuoli, S.V., Gill, S.R., Paulsen, I.T., Peterson, J., White, O., Nelson, W.C., Nierman, W., Beanan, M.J., Brinkac, L.M., Daugherty, S.C., Dodson, R.J., Durkin, A.S., Madupu, R., Haft, D.H., Selengut, J., Van Aken, S., Khouri, H., Fedorova, N., Forberger, H., Tran, B., Kathariou, S., Wonderling, L.D., Uhlich, G.A., Bayles, D.O., Luchansky, J.B., Fraser, C.M., 2004. Whole genome comparisons of serotype 4b and 1/2a strains of the food-borne pathogen Listeria  onocytogenes reveal new insights into the core genome components of this species. Nucleic acids research 32, 2386-2395.

Wortman, J.R., Haas, B.J., Hannick, L.I., Smith, R.K., Jr., Maiti, R., Ronning, C.M., Chan, A.P., Yu, C., Ayele, M., Whitelaw, C.A., White, O.R., Town, C.D., 2003. Annotation of the Arabidopsis genome. Plant physiology 132, 461-468.

Read, T.D., Peterson, S.N., Tourasse, N., Baillie, L.W., Paulsen, I.T., Nelson, K.E., Tettelin, H., Fouts, D.E., Eisen, J.A., Gill, S.R., Holtzapple, E.K., Okstad, O.A., Helgason, E., Rilstone, J., Wu, M., Kolonay, J.F., Beanan, M.J., Dodson, R.J., Brinkac, L.M., Gwinn, M., DeBoy, R.T., Madpu, R., Daugherty, S.C., Durkin, A.S., Haft, D.H., Nelson, W.C., Peterson, J.D., Pop, M., Khouri, H.M., Radune, D., Benton, J.L.,  Mahamoud, Y., Jiang, L., Hance, I.R., Weidman, J.F., Berry, K.J., Plaut, R.D., Wolf, A.M., Watkins, K.L., Nierman, W.C., Hazen, A., Cline, R., Redmond, C., Thwaite, J.E., White, O., Salzberg, S.L., Thomason, B., Friedlander, A.M., Koehler, T.M., Hanna, P.C., Kolsto, A.B., Fraser, C.M., 2003a. The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria. Nature 423, 81-86.

Read, T.D., Myers, G.S., Brunham, R.C., Nelson, W.C., Paulsen, I.T., Heidelberg, J., Holtzapple, E., Khouri, H., Federova, N.B., Carty, H.A., Umayam, L.A., Haft, D.H., Peterson, J., Beanan, M.J., White, O., Salzberg, S.L., Hsia, R.C., McClarty, G., Rank, R.G., Bavoil, P.M., Fraser, C.M., 2003b. Genome sequence of Chlamydophila caviae (Chlamydia psittaci GPIC): examining the role of niche-specific genes in the evolution of the Chlamydiaceae. Nucleic acids research 31, 2134-2147.

Methe, B.A., Nelson, K.E., Eisen, J.A., Paulsen, I.T., Nelson, W., Heidelberg, J.F., Wu, D., Wu, M., Ward, N., Beanan, M.J., Dodson, R.J., Madupu, R., Brinkac, L.M., Daugherty, S.C., DeBoy, R.T., Durkin, A.S., Gwinn, M., Kolonay, J.F., Sullivan, S.A., Haft, D.H., Selengut, J., Davidsen, T.M., Zafar, N., White, O., Tran, B., Romero, C., Forberger, H.A., Weidman, J., Khouri, H., Feldblyum, T.V., Utterback, T.R., Van Aken, S.E., Lovley, D.R., Fraser, C.M., 2003. Genome of Geobacter sulfurreducens: metal reduction in subsurface environments. Science
302, 1967-1969.

Haft, D.H., Selengut, J.D., White, O., 2003. The TIGRFAMs database of protein families. Nucleic acids research 31, 371-373.

Haas, B.J., Delcher, A.L., Mount, S.M., Wortman, J.R., Smith, R.K., Jr., Hannick, L.I., Maiti, R., Ronning, C.M., Rusch, D.B., Town, C.D., Salzberg, S.L., White, O., 2003. Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic acids research 31, 5654-5666.

El-Sayed, N.M., Ghedin, E., Song, J., MacLeod, A., Bringaud, F., Larkin, C., Wanless, D., Peterson, J., Hou, L., Taylor, S., Tweedie, A., Biteau, N., Khalak, H.G., Lin, X., Mason, T., Hannick, L., Caler, E., Blandin, G., Bartholomeu, D., Simpson, A.J., Kaul, S., Zhao, H., Pai, G., Van Aken, S., Utterback, T., Haas, B., Koo, H.L., Umayam, L., Suh, B., Gerrard, C., Leech, V., Qi, R., Zhou, S., Schwartz, D., Feldblyum, T., Salzberg, S., Tait, A., Turner, C.M., Ullu, E., White, O., Melville, S., Adams, M.D., Fraser, C.M., Donelson, J.E., 2003. The sequence and analysis of Trypanosoma brucei chromosome II. Nucleic acids research 31, 4856-4863.

Buell, C.R., Joardar, V., Lindeberg, M., Selengut, J., Paulsen, I.T., Gwinn, M.L., Dodson, R.J., Deboy, R.T., Durkin, A.S., Kolonay, J.F., Madupu, R., Daugherty, S., Brinkac, L., Beanan, M.J., Haft, D.H., Nelson, W.C., Davidsen, T., Zafar, N., Zhou, L., Liu, J., Yuan, Q., Khouri, H., Fedorova, N., Tran, B., Russell, D., Berry, K., Utterback, T., Van Aken, S.E., Feldblyum, T.V., D'Ascenzo, M., Deng, W.L., Ramos, A.R., Alfano, J.R., Cartinhour, S., Chatterjee, A.K., Delaney, T.P., Lazarowitz, S.G., Martin, G.B., Schneider, D.J., Tang, X., Bender, C.L., White, O., Fraser, C.M., Collmer, A., 2003. The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000. Proceedings of the National Academy of Sciences of the United States of America 100, 10181-10186.


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