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20022019

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Article
2019

Reproducible biomedical benchmarking in the cloud: Lessons from crowd-sourced data challenges

Ellrott, K., Buchanan, A., Creason, A., Mason, M., Schaffter, T., Hoff, B., Eddy, J., Chilton, J. M., Yu, T., Stuart, J. M., Saez-Rodriguez, J., Stolovitzky, G., Boutros, P. C. & Guinney, J., Sep 10 2019, In : Genome biology. 20, 1, 195.

Research output: Contribution to journalArticle

Open Access
2 Scopus citations
2018

Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection

ICGC-TCGA DREAM Somatic Mutation Calling Challenge Participants, Nov 6 2018, In : Genome biology. 19, 1, 188.

Research output: Contribution to journalArticle

8 Scopus citations

Germline contamination and leakage in whole genome somatic single nucleotide variant detection

Sendorek, D. H., Caloian, C., Ellrott, K., Bare, J. C., Yamaguchi, T. N., Ewing, A. D., Houlahan, K. E., Norman, T. C., Margolin, A. A., Stuart, J. M. & Boutros, P. C., Jan 31 2018, In : BMC bioinformatics. 19, 1, 28.

Research output: Contribution to journalArticle

1 Scopus citations

Population-level distribution and putative immunogenicity of cancer neoepitopes

Wood, M. A., Paralkar, M., Paralkar, M. P., Nguyen, A., Struck, A. J., Ellrott, K., Margolin, A., Nellore, A. & Thompson, R., Apr 13 2018, In : BMC Cancer. 18, 1, 414.

Research output: Contribution to journalArticle

10 Scopus citations

Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines

MC3 Working Group & The Cancer Genome Atlas Research Network, Mar 28 2018, In : Cell Systems. 6, 3, p. 271-281.e7

Research output: Contribution to journalArticle

93 Scopus citations

Valection: Design optimization for validation and verification studies

Cooper, C. I., Yao, D., Sendorek, D. H., Yamaguchi, T. N., P'ng, C., Houlahan, K. E., Caloian, C., Fraser, M., Ellrott, K., Margolin, A. A., Bristow, R. G., Stuart, J. M. & Boutros, P. C., Sep 25 2018, In : BMC bioinformatics. 19, 1, 339.

Research output: Contribution to journalArticle

2 Scopus citations
2017

A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines

Gonen, M., Weir, B. A., Cowley, G. S., Vazquez, F., Guan, Y., Jaiswal, A., Karasuyama, M., Uzunangelov, V., Wang, T., Tsherniak, A., Howell, S., Marbach, D., Hoff, B., Norman, T. C., Airola, A., Bivol, A., Bunte, K., Carlin, D., Chopra, S., Deran, A. & 25 others, Ellrott, K., Gopalacharyulu, P., Graim, K., Kaski, S., Khan, S. A., Newton, Y., Ng, S., Pahikkala, T., Paull, E., Sokolov, A., Tang, H., Tang, J., Wennerberg, K., Xie, Y., Zhan, X., Zhu, F., Aittokallio, T., Mamitsuka, H., Stuart, J. M., Boehm, J. S., Root, D. E., Xiao, G., Stolovitzky, G., Hahn, W. C. & Margolin, A., 2017, (Accepted/In press) In : Cell Systems.

Research output: Contribution to journalArticle

7 Scopus citations

Prophetic Granger Causality to infer gene regulatory networks

Carlin, D. E., Paull, E. O., Graim, K., Wong, C. K., Bivol, A., Ryabinin, P., Ellrott, K., Sokolov, A. & Stuart, J. M., Dec 1 2017, In : PLoS One. 12, 12, e0170340.

Research output: Contribution to journalArticle

5 Scopus citations

TumorMap: Exploring the molecular similarities of cancer samples in an interactive portal

Newton, Y., Novak, A. M., Swatloski, T., McColl, D. C., Chopra, S., Graim, K., Weinstein, A. S., Baertsch, R., Salama, S. R., Ellrott, K., Chopra, M., Goldstein, T. C., Haussler, D., Morozova, O. & Stuart, J. M., Nov 1 2017, In : Cancer Research. 77, 21, p. e111-e114

Research output: Contribution to journalArticle

16 Scopus citations
2015

Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection

Ewing, A. D., Houlahan, K. E., Hu, Y., Ellrott, K., Caloian, C., Yamaguchi, T. N., Bare, J. C., P'Ng, C., Waggott, D., Sabelnykova, V. Y., Kellen, M. R., Norman, T. C., Haussler, D., Friend, S. H., Stolovitzky, G., Margolin, A. A., Stuart, J. M. & Boutros, P. C., Jun 30 2015, In : Nature Methods. 12, 7, p. 623-630 8 p.

Research output: Contribution to journalArticle

120 Scopus citations
2013

Comprehensivemolecular characterization of clear cell renal cell carcinoma

Creighton, C. J., Morgan, M., Gunaratne, P. H., Wheeler, D. A., Gibbs, R. A., Robertson, G., Chu, A., Beroukhim, R., Cibulskis, K., Signoretti, S., Vandin, F., Wu, H. T., Raphael, B. J., Verhaak, R. G. W., Tamboli, P., Torres-Garcia, W., Akbani, R., Weinstein, J. N., Reuter, V., Hsieh, J. J. & 268 others, Brannon, A. R., Hakimi, A. A., Jacobsen, A., Ciriello, G., Reva, B., Ricketts, C. J., Linehan, W. M., Stuart, J. M., Rathmell, W. K., Hui, S., Laird, P. W., Muzny, D., Davis, C., Liu, X., Chang, K., Kakkar, N., Treviño, L. R., Benton, S., Reid, J. G., Morton, D., Doddapaneni, H., Yi, H., Lewis, L., Huyen, D., Kovar, C., Zhu, Y., Santibanez, J., Min, W., Hale, W., Kalra, D., Getz, G., Lawrence, M. S., Sougnez, C., Carter, S. L., Sivachenko, A., Lee, L., Stewart, C., Voet, D., Fisher, S., Gabriel, S. B., Lander, E., Schumacher, S. E., Tabak, B., Saksena, G., Onofrio, R. C., Cherniack, A. D., Gentry, J., Ardlie, K., Meyerson, M., Chun, H. J. E., Mungall, A. J., Sipahimalani, P., Stoll, D., Ally, A., Balasundaram, M., Butterfield, Y. S. N., Carlsen, R., Carter, C., Chuah, E., Coope, R. J. N., Dhalla, N., Gorski, S., Guin, R., Hirst, C., Hirst, M., Holt, R. A., Lebovitz, C., Lee, D., Li, H. I., Mayo, M., Moore, R. A., Pleasance, E., Plettner, P., Schein, J. E., Shafiei, A., Slobodan, J. R., Tam, A., Thiessen, N., Varhol, R. J., Wye, N., Zhao, Y., Birol, I., Jones, S. J. M., Marra, M. A., Auman, J. T., Tan, D., Jones, C. D., Hoadley, K. A., Mieczkowski, P. A., Mose, L. E., Jefferys, S. R., Topal, M. D., Liquori, C., Turman, Y. J., Yan, S., Waring, S., Buda, E., Walsh, J., Wu, J., Bodenheimer, T., Hoyle, A. P., Simons, J. V., Soloway, M. G., Balu, S., Parker, J. S., Hayes, D. N., Perou, C. M., Kucherlapati, R., Park, P., Triche, T., Weisenberger, D. J., Lai, P. H., Bootwalla, M. S., Maglinte, D. T., Mahurkar, S., Berman, B. P., Van Den Berg, D. J., Cope, L., Baylin, S. B., Noble, M. S., DiCara, D., Zhang, H., Cho, J., Heiman, D. I., Gehlenborg, N., Mallard, W., Pei, L., Frazer, S., Stojanov, P., Liu, Y., Zhou, L., Kim, J., Chin, L., Benz, C., Yau, C., Reynolds, S. M., Shmulevich, I., Vegesna, R., Kim, H., Wei, Z., Cogdell, D., Jonasch, E., Ding, Z., Lu, Y., Zhang, N., Unruh, A. K., Casasent, T. D., Wakefield, C., Tsavachidou, D., Mills, G. B., Gao, J., Cerami, E., Gross, B., Aksoy, B. A., Sinha, R., Weinhold, N., Sumer, S. O., Taylor, B. S., Shen, R., Ostrovnaya, I., Berger, M. F., Ladanyi, M., Sander, C., Fei, S. S., Stout, A., Spellman, P. T., Rubin, D. L., Liu, T. T., Sam, N., Paull, E. O., Carlin, D., Goldstein, T., Waltman, P., Ellrott, K., Jing, Z., Haussler, D., Xiao, W., Shelton, C., Gardner, J., Penny, R., Sherman, M., Mallery, D., Morris, S., Paulauskis, J., Burnett, K., Shelton, T., Kaelin, W. G., Choueiri, T., Atkins, M. B., Curley, E., Tickoo, S., Thorne, L., Boice, L., Mei, H., Fisher, J. C., Vocke, C. D., Peterson, J., Worrell, R., Merino, M. J., Schmidt, L. S., Czerniak, B. A., Aldape, K. D., Wood, C. G., Boyd, J., Weaver, J. E., Iacocca, M. V., Petrelli, N., Witkin, G., Brown, J., Czerwinski, C., Huelsenbeck-Dill, L., Rabeno, B., Myers, J., Morrison, C., Bergsten, J., Eckman, J., Harr, J., Smith, C., Tucker, K., Zach, L. A., Bshara, W., Gaudioso, C., Dhir, R., Maranchie, J., Nelson, J., Parwani, A., Potapova, C. O., Fedosenko, K., Cheville, J. C., Thompson, R. H., Mosquera, J. M., Rubin, M. A., Blute, M. L., Pihl, T., Jensen, M., Sfeir, R., Kahn, A., Chu, A., Kothiyal, P., Snyder, E., Pontius, J., Ayala, B., Backus, M., Walton, J., Baboud, J., Berton, D., Nicholls, M., Srinivasan, D., Raman, R., Girshik, S., Kigonya, P., Alonso, S., Sanbhadti, R., Barletta, S., Pot, D., Sheth, M., Demchok, J. A., Davidsen, T., Wang, Z., Yang, L., Tarnuzzer, R. W., Zhang, J., Eley, G., Ferguson, M. L., Mills Shaw, K. R., Guyer, M. S., Ozenberger, B. A. & Sofia, H. J., Aug 28 2013, In : Nature. 499, 7456, p. 43-49 7 p.

Research output: Contribution to journalArticle

1530 Scopus citations

The somatic genomic landscape of glioblastoma

TCGA Research Network, Oct 10 2013, In : Cell. 155, 2, 1 p.

Research output: Contribution to journalArticle

1857 Scopus citations

The UCSC cancer genomics browser: Update 2013

Goldman, M., Craft, B., Swatloski, T., Ellrott, K., Cline, M., Diekhans, M., Ma, S., Wilks, C., Stuart, J., Haussler, D. & Zhu, J., Jan 1 2013, In : Nucleic acids research. 41, D1, p. D949-D954

Research output: Contribution to journalArticle

109 Scopus citations
2012

Comprehensive genomic characterization of squamous cell lung cancers

Hammerman, P. S., Voet, D., Lawrence, M. S., Voet, D., Jing, R., Cibulskis, K., Sivachenko, A., Stojanov, P., McKenna, A., Lander, E. S., Gabriel, S., Getz, G., Imielinski, M., Helman, E., Hernandez, B., Pho, N. H., Meyerson, M., Chu, A., Hye-Chun, J. E., Mungall, A. J. & 316 others, Pleasance, E., Robertson, A. G., Sipahimalani, P., Stoll, D., Balasundaram, M., Birol, I., Butterfield, Y. S. N., Chuah, E., Coope, R. J. N., Corbett, R., Dhalla, N., Guin, R., He, A., Hirst, C., Hirst, M., Holt, R. A., Lee, D., Li, H. I., Mayo, M., Moore, R. A., Mungall, K., Nip, K. M., Olshen, A., Schein, J. E., Slobodan, J. R., Tam, A., Thiessen, N., Varhol, R., Zeng, T., Zhao, Y., Jones, S. J. M., Marra, M. A., Saksena, G., Cherniack, A. D., Schumacher, S. E., Tabak, B., Carter, S. L., Nguyen, H., Onofrio, R. C., Crenshaw, A., Ardlie, K., Beroukhim, R., Winckler, W., Protopopov, A., Zhang, J., Hadjipanayis, A., Lee, S., Xi, R., Yang, L., Ren, X., Zhang, H., Shukla, S., Chen, P. C., Haseley, P., Lee, E., Chin, L., Park, P. J., Kucherlapati, R., Socci, N. D., Liang, Y., Schultz, N., Borsu, L., Lash, A. E., Viale, A., Sander, C., Ladanyi, M., Auman, J. T., Hoadley, K. A., Wilkerson, M. D., Shi, Y., Liquori, C., Meng, S., Li, L., Turman, Y. J., Topal, M. D., Tan, D., Waring, S., Buda, E., Walsh, J., Jones, C. D., Mieczkowski, P. A., Singh, D., Wu, J., Gulabani, A., Dolina, P., Bodenheimer, T., Hoyle, A. P., Simons, J. V., Soloway, M. G., Stuart, J., Mose, L. E., Jefferys, S. R., Balu, S., O'Connor, B. D., Chiang, D., Liu, J., Chiang, D. Y., Hayes, D. N., Perou, C. M., Cope, L., Weisenberger, D., Danilova, L., Weisenberger, D. J., Maglinte, D. T., Pan, F., Van Den Berg, D. J., Triche, T., Herman, J. G., Baylin, S. B., Laird, P. W., Noble, M., Gehlenborg, N., DiCara, D., Zhang, J., Wu, C. J., Liu, S. Y., Zou, L., Lin, P., Cho, J., Nazaire, M. D., Robinson, J., Thorvaldsdottir, H., Mesirov, J., Sinha, R., Ciriello, G., Cerami, E., Gross, B., Jacobsen, A., Gao, J., Aksoy, B. A., Weinhold, N., Ramirez, R., Taylor, B. S., Antipin, Y., Reva, B., Mo, Q., Seshan, V., Paik, P. K., Akbani, R., Zhang, N., Broom, B. M., Casasent, T., Unruh, A., Wakefield, C., Cason, R. C., Baggerly, K. A., Weinstein, J. N., Haussler, D., Benz, C. C., Stuart, J. M., Zhu, J., Szeto, C., Scott, G. K., Yau, C., Ng, S., Goldstein, T., Waltman, P., Sokolov, A., Collisson, E., Ellrott, K., Collisson, E. A., Zerbino, D., Ma, S., Craft, B., Du, Y., Cabanski, C., Walter, V., Marron, J. S., Liu, Y., Wang, K., Prins, J. F., Creighton, C. J., Zhang, Y., Travis, W. D., Rekhtman, N., Yi, J., Aubry, M. C., Cheney, R., Dacic, S., Flieder, D., Funkhouser, W., Illei, P., Myers, J., Tsao, M. S., Penny, R., Mallery, D., Shelton, T., Hatfield, M., Morris, S., Yena, P., Shelton, C., Sherman, M., Paulauskis, J., Govindan, R., Azodo, I., Beer, D., Bose, R., Byers, L. A., Carbone, D., Chang, L. W., Chun, E., Ding, L., Heymach, J., Ida, C., Johnson, B., Jurisica, I., Kaufman, J., Kosari, F., Kwiatkowski, D., Maher, C. A., Pao, W., Peifer, M., Robertson, G., Rusch, V., Siegfried, J., Sougnez, C., Thomas, R. K., Tomaszek, S., Vaske, C., Wheeler, D., Wigle, D. A., Wilks, C., Zhang, J. J., Jensen, M. A., Sfeir, R., Kahn, A. B., Chu, A. L., Kothiyal, P., Wang, Z., Snyder, E. E., Pontius, J., Pihl, T. D., Backus, M., Walton, J., Baboud, J., Berton, D. L., Nicholls, M. C., Srinivasan, D., Raman, R., Girshik, S., Kigonya, P. A., Alonso, S., Sanbhadti, R. N., Barletta, S. P., Greene, J. M., Pot, D. A., Bandarchi-Chamkhaleh, B., Boyd, J., Weaver, J., Azodo, I. A., Tomaszek, S. C., Yang, P., Brock, M. V., Rogers, K., Rutledge, M., Brown, T., Lee, B., Shin, J., Trusty, D., Dhir, R., Siegfried, J. M., Potapova, O., Fedosenko, K. V., Zakowski, M., Nemirovich-Danchenko, E., Iacocca, M. V., Brown, J., Rabeno, B., Czerwinski, C., Petrelli, N., Fan, Z., Todaro, N., Eckman, J., Rathmell, W. K., Thorne, L. B., Huang, M., Boice, L., Hill, A., Curley, E., Morrison, C., Gaudioso, C., Bartlett, J. M. S., Kodeeswaran, S., Zanke, B., Sekhon, H., David, K., Juhl, H., Le, X. V., Kohl, B., Thorp, R., Tien, N. V., Bang, N. V., Sussman, H., Phu, B. D., Hajek, R., Hung, N. P., Khan, K. Z., Muley, T., Mills Shaw, K. R., Sheth, M., Yang, L., Demchok, J. A., Davidsen, T., Buetow, K., Eley, G., Ferguson, M., Dillon, L. A. L., Schaefer, C., Guyer, M. S., Ozenberger, B. A., Palchik, J. D., Peterson, J., Sofia, H. J., Thomson, E., Johnson, B. E. & Shen, R., Sep 27 2012, In : Nature. 489, 7417, p. 519-525 7 p.

Research output: Contribution to journalArticle

2106 Scopus citations

Comprehensive molecular characterization of human colon and rectal cancer

Muzny, D. M., Bainbridge, M. N., Chang, K., Dinh, H. H., Drummond, J. A., Fowler, G., Kovar, C. L., Lewis, L. R., Morgan, M. B., Newsham, I. F., Reid, J. G., Santibanez, J., Shinbrot, E., Trevino, L. R., Wu, Y. Q., Wang, M., Gunaratne, P., Donehower, L. A., Creighton, C. J., Wheeler, D. A. & 293 others, Gibbs, R. A., Lawrence, M. S., Voet, D., Jing, R., Cibulskis, K., Sivachenko, A., Stojanov, P., McKenna, A., Lander, E. S., Gabriel, S., Ding, L., Fulton, R. S., Koboldt, D. C., Wylie, T., Walker, J., Dooling, D. J., Fulton, L., Delehaunty, K. D., Fronick, C. C., Demeter, R., Mardis, E. R., Wilson, R. K., Chu, A., Chun, H. J. E., Mungall, A. J., Pleasance, E., Gordon Robertson, A., Stoll, D., Balasundaram, M., Birol, I., Butterfield, Y. S. N., Chuah, E., Coope, R. J. N., Dhalla, N., Guin, R., Hirst, C., Hirst, M., Holt, R. A., Lee, D., Li, H. I., Mayo, M., Moore, R. A., Schein, J. E., Slobodan, J. R., Tam, A., Thiessen, N., Varhol, R., Zeng, T., Zhao, Y., Jones, S. J. M., Marra, M. A., Bass, A. J., Ramos, A. H., Saksena, G., Cherniack, A. D., Schumacher, S. E., Tabak, B., Carter, S. L., Pho, N. H., Nguyen, H., Onofrio, R. C., Crenshaw, A., Ardlie, K., Beroukhim, R., Winckler, W., Meyerson, M., Protopopov, A., Hadjipanayis, A., Lee, E., Xi, R., Yang, L., Ren, X., Sathiamoorthy, N., Chen, P. C., Haseley, P., Xiao, Y., Lee, S., Seidman, J., Chin, L., Park, P. J., Kucherlapati, R., Todd Auman, J., Hoadley, K. A., Du, Y., Wilkerson, M. D., Shi, Y., Liquori, C., Meng, S., Li, L., Turman, Y. J., Topal, M. D., Tan, D., Waring, S., Buda, E., Walsh, J., Jones, C. D., Mieczkowski, P. A., Singh, D., Wu, J., Gulabani, A., Dolina, P., Bodenheimer, T., Hoyle, A. P., Simons, J. V., Soloway, M., Mose, L. E., Jefferys, S. R., Balu, S., O'Connor, B. D., Prins, J. F., Chiang, D. Y., Neil Hayes, D., Perou, C. M., Hinoue, T., Weisenberger, D. J., Maglinte, D. T., Pan, F., Berman, B. P., Van Den Berg, D. J., Shen, H., Triche, T., Baylin, S. B., Laird, P. W., Getz, G., Noble, M., Voat, D., Gehlenborg, N., Dicara, D., Zhang, J., Zhang, H., Wu, C. J., Liu, S. Y., Shukla, S., Zhou, L., Lin, P., Park, R. W., Nazaire, M. D., Robinson, J., Thorvaldsdottir, H., Mesirov, J., Thorsson, V., Reynolds, S. M., Bernard, B., Kreisberg, R., Lin, J., Iype, L., Bressler, R., Erkkilä, T., Gundapuneni, M., Liu, Y., Norberg, A., Robinson, T., Yang, D., Zhang, W., Shmulevich, I., De Ronde, J. J., Schultz, N., Cerami, E., Ciriello, G., Goldberg, A. P., Gross, B., Jacobsen, A., Gao, J., Kaczkowski, B., Sinha, R., Arman Aksoy, B., Antipin, Y., Reva, B., Shen, R., Taylor, B. S., Ladanyi, M., Sander, C., Akbani, R., Zhang, N., Broom, B. M., Casasent, T., Unruh, A., Wakefield, C., Hamilton, S. R., Craig Cason, R., Baggerly, K. A., Weinstein, J. N., Haussler, D., Benz, C. C., Stuart, J. M., Benz, S. C., Zachary Sanborn, J., Vaske, C. J., Zhu, J., Szeto, C., Scott, G. K., Yau, C., Ng, S., Goldstein, T., Ellrott, K., Collisson, E., Cozen, A. E., Zerbino, D., Wilks, C., Craft, B., Spellman, P., Penny, R., Shelton, T., Hatfield, M., Morris, S., Yena, P., Shelton, C., Sherman, M., Paulauskis, J., Gastier-Foster, J. M., Bowen, J., Ramirez, N. C., Black, A., Pyatt, R., Wise, L., White, P., Bertagnolli, M., Brown, J., Chan, T. A., Chu, G. C., Czerwinski, C., Denstman, F., Dhir, R., Dörner, A., Fuchs, C. S., Guillem, J. G., Iacocca, M., Juhl, H., Kaufman, A., Iii, B. K., Van Le, X., Mariano, M. C., Medina, E. N., Meyers, M., Nash, G. M., Paty, P. B., Petrelli, N., Rabeno, B., Richards, W. G., Solit, D., Swanson, P., Temple, L., Tepper, J. E., Thorp, R., Vakiani, E., Weiser, M. R., Willis, J. E., Witkin, G., Zeng, Z., Zinner, M. J., Zornig, C., Jensen, M. A., Sfeir, R., Kahn, A. B., Chu, A. L., Kothiyal, P., Wang, Z., Snyder, E. E., Pontius, J., Pihl, T. D., Ayala, B., Backus, M., Walton, J., Whitmore, J., Baboud, J., Berton, D. L., Nicholls, M. C., Srinivasan, D., Raman, R., Girshik, S., Kigonya, P. A., Alonso, S., Sanbhadti, R. N., Barletta, S. P., Greene, J. M., Pot, D. A., Shaw, K. R. M., Dillon, L. A. L., Buetow, K., Davidsen, T., Demchok, J. A., Eley, G., Ferguson, M., Fielding, P., Schaefer, C., Sheth, M., Yang, L., Guyer, M. S., Ozenberger, B. A., Palchik, J. D., Peterson, J., Sofia, H. J. & Thomson., E., Jul 19 2012, In : Nature. 487, 7407, p. 330-337 8 p.

Research output: Contribution to journalArticle

4055 Scopus citations

Comprehensive molecular portraits of human breast tumours

Koboldt, D. C., Fulton, R. S., McLellan, M. D., Schmidt, H., Kalicki-Veizer, J., McMichael, J. F., Fulton, L. L., Dooling, D. J., Ding, L., Mardis, E. R., Wilson, R. K., Ally, A., Balasundaram, M., Butterfield, Y. S. N., Carlsen, R., Carter, C., Chu, A., Chuah, E., Chun, H. J. E., Coope, R. J. N. & 323 others, Dhalla, N., Guin, R., Hirst, C., Hirst, M., Holt, R. A., Lee, D., Li, H. I., Mayo, M., Moore, R. A., Mungall, A. J., Pleasance, E., Robertson, A. G., Schein, J. E., Shafiei, A., Sipahimalani, P., Slobodan, J. R., Stoll, D., Tam, A., Thiessen, N., Varhol, R. J., Wye, N., Zeng, T., Zhao, Y., Birol, I., Jones, S. J. M., Marra, M. A., Cherniack, A. D., Saksena, G., Onofrio, R. C., Pho, N. H., Carter, S. L., Schumacher, S. E., Tabak, B., Hernandez, B., Gentry, J., Nguyen, H., Crenshaw, A., Ardlie, K., Beroukhim, R., Winckler, W., Getz, G., Gabriel, S. B., Meyerson, M., Chin, L., Kucherlapati, R., Hoadley, K. A., Auman, J. T., Fan, C., Turman, Y. J., Shi, Y., Li, L., Topal, M. D., He, X., Chao, H. H., Prat, A., Silva, G. O., Iglesia, M. D., Zhao, W., Usary, J., Berg, J. S., Adams, M., Booker, J., Wu, J., Gulabani, A., Bodenheimer, T., Hoyle, A. P., Simons, J. V., Soloway, M. G., Mose, L. E., Jefferys, S. R., Balu, S., Parker, J. S., Hayes, D. N., Perou, C. M., Malik, S., Mahurkar, S., Shen, H., Weisenberger, D. J., Triche, T., Lai, P. H., Bootwalla, M. S., Maglinte, D. T., Berman, B. P., Van Den Berg, D. J., Baylin, S. B., Laird, P. W., Creighton, C. J., Donehower, L. A., Noble, M., Voet, D., Gehlenborg, N., Di Cara, D., Zhang, J., Zhang, H., Wu, C. J., Yingchun Liu, S., Lawrence, M. S., Zou, L., Sivachenko, A., Lin, P., Stojanov, P., Jing, R., Cho, J., Sinha, R., Park, R. W., Nazaire, M. D., Robinson, J., Thorvaldsdottir, H., Mesirov, J., Park, P. J., Reynolds, S., Kreisberg, R. B., Bernard, B., Bressler, R., Erkkila, T., Lin, J., Thorsson, V., Zhang, W., Shmulevich, I., Ciriello, G., Weinhold, N., Schultz, N., Gao, J., Cerami, E., Gross, B., Jacobsen, A., Sinha, R., Aksoy, B. A., Antipin, Y., Reva, B., Shen, R., Taylor, B. S., Ladanyi, M., Sander, C., Anur, P., Spellman, P. T., Lu, Y., Liu, W., Verhaak, R. R. G., Mills, G. B., Akbani, R., Zhang, N., Broom, B. M., Casasent, T. D., Wakefield, C., Unruh, A. K., Baggerly, K., Coombes, K., Weinstein, J. N., Haussler, D., Benz, C. C., Stuart, J. M., Benz, S. C., Zhu, J., Szeto, C. C., Scott, G. K., Yau, C., Paull, E. O., Carlin, D., Wong, C., Sokolov, A., Thusberg, J., Mooney, S., Ng, S., Goldstein, T. C., Ellrott, K., Grifford, M., Wilks, C., Ma, S., Craft, B., Yan, C., Hu, Y., Meerzaman, D., Gastier-Foster, J. M., Bowen, J., Ramirez, N. C., Black, A. D., Pyatt, R. E., White, P., Zmuda, E. J., Frick, J., Lichtenberg, T. M., Brookens, R., George, M. M., Gerken, M. A., Harper, H. A., Leraas, K. M., Wise, L. J., Tabler, T. R., McAllister, C., Barr, T., Hart-Kothari, M., Tarvin, K., Saller, C., Sandusky, G., Mitchell, C., Iacocca, M. V., Brown, J., Rabeno, B., Czerwinski, C., Petrelli, N., Dolzhansky, O., Abramov, M., Voronina, O., Potapova, O., Marks, J. R., Suchorska, W. M., Murawa, D., Kycler, W., Ibbs, M., Korski, K., Spychała, A., Murawa, P., Brzeziński, J. J., Perz, H., Łaźniak, R., Teresiak, M., Tatka, H., Leporowska, E., Bogusz-Czerniewicz, M., Malicki, J., Mackiewicz, A., Wiznerowicz, M., Van Le, X., Kohl, B., Viet Tien, N., Thorp, R., Van Bang, N., Sussman, H., Phu, B. D., Hajek, R., Hung, N. P., Phuong, T. V. T., Thang, H. Q., Khan, K. Z., Penny, R., Mallery, D., Curley, E., Shelton, C., Yena, P., Ingle, J. N., Couch, F. J., Lingle, W. L., King, T. A., Gonzalez-Angulo, A. M., Dyer, M. D., Liu, S., Meng, X., Patangan, M., Waldman, F., Stöppler, H., Rathmell, W. K., Thorne, L., Huang, M., Boice, L., Hill, A., Morrison, C., Gaudioso, C., Bshara, W., Daily, K., Egea, S. C., Pegram, M. D., Gomez-Fernandez, C., Dhir, R., Bhargava, R., Brufsky, A., Shriver, C. D., Hooke, J. A., Campbell, J. L., Mural, R. J., Hu, H., Somiari, S., Larson, C., Deyarmin, B., Kvecher, L., Kovatich, A. J., Ellis, M. J., Stricker, T., White, K., Olopade, O., Luo, C., Chen, Y., Bose, R., Chang, L. W., Beck, A. H., Pihl, T., Jensen, M., Sfeir, R., Kahn, A., Chu, A., Kothiyal, P., Wang, Z., Snyder, E., Pontius, J., Ayala, B., Backus, M., Walton, J., Baboud, J., Berton, D., Nicholls, M., Srinivasan, D., Raman, R., Girshik, S., Kigonya, P., Alonso, S., Sanbhadti, R., Barletta, S., Pot, D., Sheth, M., Demchok, J. A., Shaw, K. R. M., Yang, L., Eley, G., Ferguson, M. L., Tarnuzzer, R. W., Zhang, J., Dillon, L. A. L., Buetow, K., Fielding, P., Ozenberger, B. A., Guyer, M. S., Sofia, H. J. & Palchik, J. D., Oct 4 2012, In : Nature. 490, 7418, p. 61-70 10 p.

Research output: Contribution to journalArticle

5615 Scopus citations
2011

TOPSAN: A dynamic web database for structural genomics

Ellrott, K., Zmasek, C. M., Weekes, D., Krishna, S. S., Bakolitsa, C., Godzik, A. & Wooley, J., Jan 1 2011, In : Nucleic acids research. 39, SUPPL. 1, p. D494-D496

Research output: Contribution to journalArticle

16 Scopus citations
2010

A conserved fold for fimbrial components revealed by the crystal structure of a putative fimbrial assembly protein (BT1062) from Bacteroides thetaiotaomicron at 2.2 Å resolution

Xu, Q., Abdubek, P., Astakhova, T., Axelrod, H. L., Bakolitsa, C., Cai, X., Carlton, D., Chen, C., Chiu, H. J., Chiu, M., Clayton, T., Das, D., Deller, M. C., Duan, L., Ellrott, K., Farr, C. L., Feuerhelm, J., Grant, J. C., Grzechnik, A., Han, G. W. & 31 others, Jaroszewski, L., Jin, K. K., Klock, H. E., Knuth, M. W., Kozbial, P., Krishna, S. S., Kumar, A., Marciano, D., McMullan, D., Miller, M. D., Morse, A. T., Nigoghossian, E., Nopakun, A., Okach, L., Puckett, C., Reyes, R., Sefcovic, N., Tien, H. J., Trame, C. B., Van Den Bedem, H., Weekes, D., Wooten, T., Yeh, A., Zhou, J., Hodgson, K. O., Wooley, J., Elsliger, M. A., Deacon, A. M., Godzik, A., Lesley, S. A. & Wilson, I. A., Oct 1 2010, In : Acta Crystallographica Section F: Structural Biology and Crystallization Communications. 66, 10, p. 1281-1286 6 p.

Research output: Contribution to journalArticle

5 Scopus citations

Bacterial Pleckstrin Homology Domains: A Prokaryotic Origin for the PH Domain

Xu, Q., Bateman, A., Finn, R. D., Abdubek, P., Astakhova, T., Axelrod, H. L., Bakolitsa, C., Carlton, D., Chen, C., Chiu, H. J., Chiu, M., Clayton, T., Das, D., Deller, M. C., Duan, L., Ellrott, K., Ernst, D., Farr, C. L., Feuerhelm, J., Grant, J. C. & 32 others, Grzechnik, A., Han, G. W., Jaroszewski, L., Jin, K. K., Klock, H. E., Knuth, M. W., Kozbial, P., Krishna, S. S., Kumar, A., Marciano, D., McMullan, D., Miller, M. D., Morse, A. T., Nigoghossian, E., Nopakun, A., Okach, L., Puckett, C., Reyes, R., Rife, C. L., Sefcovic, N., Tien, H. J., Trame, C. B., van den Bedem, H., Weekes, D., Wooten, T., Hodgson, K. O., Wooley, J., Elsliger, M. A., Deacon, A. M., Godzik, A., Lesley, S. A. & Wilson, I. A., Feb 12 2010, In : Journal of molecular biology. 396, 1, p. 31-46 16 p.

Research output: Contribution to journalArticle

19 Scopus citations

Expansion of the protein repertoire in newly explored environments: Human gut microbiome specific protein families

Ellrott, K., Jaroszewski, L., Li, W., Wooley, J. C. & Godzik, A., Jun 1 2010, In : PLoS computational biology. 6, 6, p. 1-11 11 p.

Research output: Contribution to journalArticle

46 Scopus citations

Structure of a membrane-attack complex/perforin (MACPF) family protein from the human gut symbiont Bacteroides thetaiotaomicron

Xu, Q., Abdubek, P., Astakhova, T., Axelrod, H. L., Bakolitsa, C., Cai, X., Carlton, D., Chen, C., Chiu, H. J., Clayton, T., Das, D., Deller, M. C., Duan, L., Ellrott, K., Farr, C. L., Feuerhelm, J., Grant, J. C., Grzechnik, A., Han, G. W., Jaroszewski, L. & 29 others, Jin, K. K., Klock, H. E., Knuth, M. W., Kozbial, P., Krishna, S. S., Kumar, A., Lam, W. W., Marciano, D., Miller, M. D., Morse, A. T., Nigoghossian, E., Nopakun, A., Okach, L., Puckett, C., Reyes, R., Tien, H. J., Trame, C. B., Van Den Bedem, H., Weekes, D., Wooten, T., Yeh, A., Zhou, J., Hodgson, K. O., Wooley, J., Elsliger, M. A., Deacon, A. M., Godzik, A., Lesley, S. A. & Wilson, I. A., Oct 1 2010, In : Acta Crystallographica Section F: Structural Biology and Crystallization Communications. 66, 10, p. 1297-1305 9 p.

Research output: Contribution to journalArticle

22 Scopus citations

Structure of Bacteroides thetaiotaomicron BT2081 at 2.05 Å resolution: The first structural representative of a new protein family that may play a role in carbohydrate metabolism

Yeh, A. P., Abdubek, P., Astakhova, T., Axelrod, H. L., Bakolitsa, C., Cai, X., Carlton, D., Chen, C., Chiu, H. J., Chiu, M., Clayton, T., Das, D., Deller, M. C., Duan, L., Ellrott, K., Farr, C. L., Feuerhelm, J., Grant, J. C., Grzechnik, A., Han, G. W. & 30 others, Jaroszewski, L., Jin, K. K., Klock, H. E., Knuth, M. W., Kozbial, P., Krishna, S. S., Kumar, A., Lam, W. W., Marciano, D., McMullan, D., Miller, M. D., Morse, A. T., Nigoghossian, E., Nopakun, A., Okach, L., Puckett, C., Reyes, R., Tien, H. J., Trame, C. B., Van Den Bedem, H., Weekes, D., Wooten, T., Xu, Q., Hodgson, K. O., Wooley, J., Elsliger, M. A., Deacon, A. M., Godzik, A., Lesley, S. A. & Wilson, I. A., Oct 1 2010, In : Acta Crystallographica Section F: Structural Biology and Crystallization Communications. 66, 10, p. 1287-1296 10 p.

Research output: Contribution to journalArticle

1 Scopus citations

Structure of BT-3984, a member of the SusD/RagB family of nutrient-binding molecules

Bakolitsa, C., Xu, Q., Rife, C. L., Abdubek, P., Astakhova, T., Axelrod, H. L., Carlton, D., Chen, C., Chiu, H. J., Clayton, T., Das, D., Deller, M. C., Duan, L., Ellrott, K., Farr, C. L., Feuerhelm, J., Grant, J. C., Grzechnik, A., Han, G. W., Jaroszewski, L. & 27 others, Jin, K. K., Klock, H. E., Knuth, M. W., Kozbial, P., Krishna, S. S., Kumar, A., Lam, W. W., Marciano, D., McMullan, D., Miller, M. D., Morse, A. T., Nigoghossian, E., Nopakun, A., Okach, L., Puckett, C., Reyes, R., Tien, H. J., Trame, C. B., Van Den Bedem, H., Weekes, D., Hodgson, K. O., Wooley, J., Elsliger, M. A., Deacon, A. M., Godzik, A., Lesley, S. A. & Wilson, I. A., Oct 1 2010, In : Acta Crystallographica Section F: Structural Biology and Crystallization Communications. 66, 10, p. 1274-1280 7 p.

Research output: Contribution to journalArticle

6 Scopus citations

Structure of the γ-D-glutamyl-L-diamino acid endopeptidase YkfC from Bacillus cereus in complex with L-Ala-γ-d-Glu: Insights into substrate recognition by NlpC/P60 cysteine peptidases

Xu, Q., Abdubek, P., Astakhova, T., Axelrod, H. L., Bakolitsa, C., Cai, X., Carlton, D., Chen, C., Chiu, H. J., Chiu, M., Clayton, T., Das, D., Deller, M. C., Duan, L., Ellrott, K., Farr, C. L., Feuerhelm, J., Grant, J. C., Grzechnik, A., Han, G. W. & 29 others, Jaroszewski, L., Jin, K. K., Klock, H. E., Knuth, M. W., Kozbial, P., Krishna, S. S., Kumar, A., Lam, W. W., Marciano, D., Miller, M. D., Morse, A. T., Nigoghossian, E., Nopakun, A., Okach, L., Puckett, C., Reyes, R., Tien, H. J., Trame, C. B., Van Den Bedem, H., Weekes, D., Wooten, T., Yeh, A., Hodgson, K. O., Wooley, J., Elsliger, M. A., Deacon, A. M., Godzik, A., Lesley, S. A. & Wilson, I. A., Oct 1 2010, In : Acta Crystallographica Section F: Structural Biology and Crystallization Communications. 66, 10, p. 1354-1364 11 p.

Research output: Contribution to journalArticle

42 Scopus citations

Structures of the first representatives of Pfam family PF06684 (DUF1185) reveal a novel variant of the Bacillus chorismate mutase fold and suggest a role in amino-acid metabolism

Bakolitsa, C., Kumar, A., Jin, K. K., McMullan, D., Krishna, S. S., Miller, M. D., Abdubek, P., Acosta, C., Astakhova, T., Axelrod, H. L., Burra, P., Carlton, D., Chen, C., Chiu, H. J., Clayton, T., Das, D., Deller, M. C., Duan, L., Elias, Y., Ellrott, K. & 37 others, Ernst, D., Farr, C. L., Feuerhelm, J., Grant, J. C., Grzechnik, A., Grzechnik, S. K., Han, G. W., Jaroszewski, L., Johnson, H. A., Klock, H. E., Knuth, M. W., Kozbial, P., Marciano, D., Morse, A. T., Murphy, K. D., Nigoghossian, E., Nopakun, A., Okach, L., Paulsen, J., Puckett, C., Reyes, R., Rife, C. L., Sefcovic, N., Tien, H. J., Trame, C. B., Trout, C. V., Van Den Bedem, H., Weekes, D., White, A., Xu, Q., Hodgson, K. O., Wooley, J., Elsliger, M. A., Deacon, A. M., Godzik, A., Lesley, S. A. & Wilson, I. A., Oct 1 2010, In : Acta Crystallographica Section F: Structural Biology and Crystallization Communications. 66, 10, p. 1182-1189 8 p.

Research output: Contribution to journalArticle

2 Scopus citations

Structures of three members of Pfam PF02663 (FmdE) implicated in microbial methanogenesis reveal a conserved α+Β core domain and an auxiliary C-terminal treble-clef zinc finger

Axelrod, H. L., Das, D., Abdubek, P., Astakhova, T., Bakolitsa, C., Carlton, D., Chen, C., Chiu, H. J., Clayton, T., Deller, M. C., Duan, L., Ellrott, K., Farr, C. L., Feuerhelm, J., Grant, J. C., Grzechnik, A., Han, G. W., Jaroszewski, L., Jin, K. K., Klock, H. E. & 28 others, Knuth, M. W., Kozbial, P., Krishna, S. S., Kumar, A., Lam, W. W., Marciano, D., McMullan, D., Miller, M. D., Morse, A. T., Nigoghossian, E., Nopakun, A., Okach, L., Puckett, C., Reyes, R., Sefcovic, N., Tien, H. J., Trame, C. B., Van Den Bedem, H., Weekes, D., Wooten, T., Xu, Q., Hodgson, K. O., Wooley, J., Elsliger, M. A., Deacon, A. M., Godzik, A., Lesley, S. A. & Wilson, I. A., Oct 1 2010, In : Acta Crystallographica Section F: Structural Biology and Crystallization Communications. 66, 10, p. 1335-1346 12 p.

Research output: Contribution to journalArticle

5 Scopus citations

The crystal structure of a bacterial Sufu-like protein defines a novel group of bacterial proteins that are similar to the N-terminal domain of human Sufu

Das, D., Finn, R. D., Abdubek, P., Astakhova, T., Axelrod, H. L., Bakolitsa, C., Cai, X., Carlton, D., Chen, C., Chiu, H. J., Chiu, M., Clayton, T., Deller, M. C., Duan, L., Ellrott, K., Farr, C. L., Feuerhelm, J., Grant, J. C., Grzechnik, A., Han, G. W. & 31 others, Jaroszewski, L., Jin, K. K., Klock, H. E., Knuth, M. W., Kozbial, P., Sri Krishna, S., Kumar, A., Lam, W. W., Marciano, D., Miller, M. D., Morse, A. T., Nigoghossian, E., Nopakun, A., Okach, L., Puckett, C., Reyes, R., Tien, H. J., Trame, C. B., Van Den Bedem, H., Weekes, D., Wooten, T., Xu, Q., Yeh, A., Zhou, J., Hodgson, K. O., Wooley, J., Elsliger, M. A., Deacon, A. M., Godzik, A., Lesley, S. A. & Wilson, I. A., Nov 1 2010, In : Protein Science. 19, 11, p. 2131-2140 10 p.

Research output: Contribution to journalArticle

4 Scopus citations

The structure of BVU2987 from Bacteroides vulgatus reveals a superfamily of bacterial periplasmic proteins with possible inhibitory function

Das, D., Finn, R. D., Carlton, D., Miller, M. D., Abdubek, P., Astakhova, T., Axelrod, H. L., Bakolitsa, C., Chen, C., Chiu, H. J., Chiu, M., Clayton, T., Deller, M. C., Duan, L., Ellrott, K., Ernst, D., Farr, C. L., Feuerhelm, J., Grant, J. C., Grzechnik, A. & 31 others, Han, G. W., Jaroszewski, L., Jin, K. K., Klock, H. E., Knuth, M. W., Kozbial, P., Krishna, S. S., Kumar, A., Marciano, D., McMullan, D., Morse, A. T., Nigoghossian, E., Nopakun, A., Okach, L., Puckett, C., Reyes, R., Rife, C. L., Sefcovic, N., Tien, H. J., Trame, C. B., Van Den Bedem, H., Weekes, D., Wooten, T., Xu, Q., Hodgson, K. O., Wooley, J., Elsliger, M. A., Deacon, A. M., Godzik, A., Lesley, S. A. & Wilson, I. A., Oct 1 2010, In : Acta Crystallographica Section F: Structural Biology and Crystallization Communications. 66, 10, p. 1265-1273 9 p.

Research output: Contribution to journalArticle

7 Scopus citations

The structure of KPN03535 (gi|152972051), a novel putative lipoprotein from Klebsiella pneumoniae, reveals an OB-fold

Das, D., Kozbial, P., Han, G. W., Carlton, D., Jaroszewski, L., Abdubek, P., Astakhova, T., Axelrod, H. L., Bakolitsa, C., Chen, C., Chiu, H. J., Chiu, M., Clayton, T., Deller, M. C., Duan, L., Ellrott, K., Elsliger, M. A., Ernst, D., Farr, C. L., Feuerhelm, J. & 33 others, Grzechnik, A., Grant, J. C., Jin, K. K., Johnson, H. A., Klock, H. E., Knuth, M. W., Krishna, S. S., Kumar, A., Marciano, D., McMullan, D., Miller, M. D., Morse, A. T., Nigoghossian, E., Nopakun, A., Okach, L., Oommachen, S., Paulsen, J., Puckett, C., Reyes, R., Rife, C. L., Sefcovic, N., Tien, H. J., Trame, C. B., Van Den Bedem, H., Weekes, D., Wooten, T., Xu, Q., Hodgson, K. O., Wooley, J., Deacon, A. M., Godzik, A., Lesley, S. A. & Wilson, I. A., Oct 1 2010, In : Acta Crystallographica Section F: Structural Biology and Crystallization Communications. 66, 10, p. 1254-1260 7 p.

Research output: Contribution to journalArticle

2 Scopus citations

The structure of the first representative of Pfam family PF09836 reveals a two-domain organization and suggests involvement in transcriptional regulation

Das, D., Grishin, N. V., Kumar, A., Carlton, D., Bakolitsa, C., Miller, M. D., Abdubek, P., Astakhova, T., Axelrod, H. L., Burra, P., Chen, C., Chiu, H. J., Chiu, M., Clayton, T., Deller, M. C., Duan, L., Ellrott, K., Ernst, D., Farr, C. L., Feuerhelm, J. & 36 others, Grzechnik, A., Grzechnik, S. K., Grant, J. C., Han, G. W., Jaroszewski, L., Jin, K. K., Johnson, H. A., Klock, H. E., Knuth, M. W., Kozbial, P., Krishna, S. S., Marciano, D., McMullan, D., Morse, A. T., Nigoghossian, E., Nopakun, A., Okach, L., Oommachen, S., Paulsen, J., Puckett, C., Reyes, R., Rife, C. L., Sefcovic, N., Tien, H. J., Trame, C. B., Van Den Bedem, H., Weekes, D., Wooten, T., Xu, Q., Hodgson, K. O., Wooley, J., Elsliger, M. A., Deacon, A. M., Godzik, A., Lesley, S. A. & Wilson, I. A., Oct 1 2010, In : Acta Crystallographica Section F: Structural Biology and Crystallization Communications. 66, 10, p. 1174-1181 8 p.

Research output: Contribution to journalArticle

4 Scopus citations
2009

Structural and functional characterizations of SsgB, a conserved activator of developmental cell division in morphologically complex actinomycetes

Xu, Q., Traag, B. A., Willemse, J., McMullan, D., Miller, M. D., Elsliger, M. A., Abdubek, P., Astakhova, T., Axelrod, H. L., Bakolitsa, C., Carlton, D., Chen, C., Chiu, H. J., Chruszcz, M., Clayton, T., Das, D., Deller, M. C., Duan, L., Ellrott, K., Ernst, D. & 38 others, Farr, C. L., Feuerhelm, J., Grant, J. C., Grzechnik, A., Grzechnik, S. K., Ha, G. W., Jaroszewski, L., Jin, K. K., Klock, H. E., Knuth, M. W., Kozbial, P., Krishna, S. S., Kumar, A., Marciano, D., Minor, W., Mommaas, A. M., Morse, A. T., Nigoghossian, E., Nopakun, A., Okach, L., Oommachen, S., Paulsen, J., Puckett, C., Reyes, R., Rife, C. L., Sefcovic, N., Tien, H. J., Trame, C. B., van den Bedem, H., Wang, S., Weekes, D., Hodgson, K. O., Wooley, J., Deacon, A. M., Godzik, A., Lesley, S. A., Wilson, I. A. & van Wezel, G. P., Sep 11 2009, In : Journal of Biological Chemistry. 284, 37, p. 25268-25279 12 p.

Research output: Contribution to journalArticle

15 Scopus citations
2008

Improving the performance of protein threading using insertion/deletion frequency arrays

Ellrott, K., Guo, J. T., Olman, V. & Xu, Y., Jun 1 2008, In : Journal of Bioinformatics and Computational Biology. 6, 3, p. 585-602 18 p.

Research output: Contribution to journalArticle

1 Scopus citations
2007
9 Scopus citations
2006
2 Scopus citations
2004

PROSPECT-PSPP: An automatic computational pipeline for protein structure prediction

Guo, J. T., Ellrott, K., Chung, W. J., Xu, D., Passovets, S. & Xu, Y., Jul 1 2004, In : Nucleic acids research. 32, WEB SERVER ISS., p. W522-W525

Research output: Contribution to journalArticle

14 Scopus citations
2003

A computational pipeline for protein structure prediction and analysis at genome scale

Shah, M., Passovets, S., Kim, D., Ellrott, K., Wang, L., Vokler, I., LoCascio, P., Xu, D. & Xu, Y., Oct 12 2003, In : Bioinformatics. 19, 15, p. 1985-1996 12 p.

Research output: Contribution to journalArticle

15 Scopus citations

PROSPECT II: Protein structure prediction program for genome-scale applications

Kim, D., Xu, D., Guo, J. T., Ellrott, K. & Xu, Y., Sep 1 2003, In : Protein Engineering. 16, 9, p. 641-650 10 p.

Research output: Contribution to journalArticle

80 Scopus citations
2002

Identifying transcription factor binding sites through Markov chain optimization

Ellrott, K., Yang, C., Sladek, F. M. & Jiang, T., Jan 1 2002, In : Bioinformatics. 18, SUPPL. 2, p. S100-S109

Research output: Contribution to journalArticle

Open Access
69 Scopus citations

Restriction enzyme recognition sequence search program

Ellrott, K. P., Kasarjian, J. K. A., Jiang, T. & Ryu, J., Dec 1 2002, In : BioTechniques. 33, 6, p. 1322-1326 5 p.

Research output: Contribution to journalArticle

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