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15 results on '"Rovira, H."'

1. Comprehensive molecular characterization of gastric adenocarcinoma

Author

Bass, AJ, Thorsson, V, Shmulevich, I, Reynolds, SM, Miller, M, Bernard, B, Hinoue, T, Laird, PW, Curtis, C, Shen, H, Weisenberger, DJ, Schultz, N, Shen, R, Weinhold, N, Keiser, DP, Bowlby, R, Sipahimalani, P, Cherniack, AD, Getz, G, Liu, Y, Noble, MS, Pedamallu, C, Sougnez, C, Taylor-Weiner, A, Akbani, R, Lee, J-S, Liu, W, Mills, GB, Yang, D, Zhang, W, Pantazi, A, Parfenov, M, Gulley, M, Piazuelo, MB, Schneider, BG, Kim, J, Boussioutas, A, Sheth, M, Demchok, JA, Rabkin, CS, Willis, JE, Ng, S, Garman, K, Beer, DG, Pennathur, A, Raphael, BJ, Wu, H-T, Odze, R, Kim, HK, Bowen, J, Leraas, KM, Lichtenberg, TM, Weaver, L, McLellan, M, Wiznerowicz, M, Sakai, R, Lawrence, MS, Cibulskis, K, Lichtenstein, L, Fisher, S, Gabriel, SB, Lander, ES, Ding, L, Niu, B, Ally, A, Balasundaram, M, Birol, I, Brooks, D, Butterfield, YSN, Carlsen, R, Chu, A, Chu, J, Chuah, E, Chun, H-JE, Clarke, A, Dhalla, N, Guin, R, Holt, RA, Jones, SJM, Kasaian, K, Lee, D, Li, HA, Lim, E, Ma, Y, Marra, MA, Mayo, M, Moore, RA, Mungall, AJ, Mungall, KL, Nip, KM, Robertson, AG, Schein, JE, Tam, A, Thiessen, N, Beroukhim, R, Carter, SL, Cho, J, DiCara, D, Frazer, S, Gehlenborg, N, Heiman, DI, Jung, J, Lin, P, Meyerson, M, Ojesina, AI, Pedamallu, CS, Saksena, G, Schumacher, SE, Stojanov, P, Tabak, B, Voet, D, Rosenberg, M, Zack, TI, Zhang, H, Zou, L, Protopopov, A, Santoso, N, Lee, S, Zhang, J, Mahadeshwar, HS, Tang, J, Ren, X, Seth, S, Yang, L, Xu, AW, Song, X, Xi, R, Bristow, CA, Hadjipanayis, A, Seidman, J, Chin, L, Park, PJ, Kucherlapati, R, Ling, S, Rao, A, Weinstein, JN, Kim, S-B, Lu, Y, Mills, G, Bootwalla, MS, Lai, PH, Triche, T, Van Den Berg, DJ, Baylin, SB, Herman, JG, Murray, BA, Askoy, BA, Ciriello, G, Dresdner, G, Gao, J, Gross, B, Jacobsen, A, Lee, W, Ramirez, R, Sander, C, Senbabaoglu, Y, Sinha, R, Sumer, SO, Sun, Y, Iype, L, Kramer, RW, Kreisberg, R, Rovira, H, Tasman, N, Haussler, D, Stuart, JM, Verhaak, RGW, Leiserson, MDM, Taylor, BS, Black, AD, Carney, JA, Gastier-Foster, JM, Helsel, C, McAllister, C, Ramirez, NC, Tabler, TR, Wise, L, Zmuda, E, Penny, R, Crain, D, Gardner, J, Lau, K, Curely, E, Mallery, D, Morris, S, Paulauskis, J, Shelton, T, Shelton, C, Sherman, M, Benz, C, Lee, J-H, Fedosenko, K, Manikhas, G, Voronina, O, Belyaev, D, Dolzhansky, O, Rathmell, WK, Brzezinski, J, Ibbs, M, Korski, K, Kycler, W, Lazniak, R, Leporowska, E, Mackiewicz, A, Murawa, D, Murawa, P, Spychala, A, Suchorska, WM, Tatka, H, Teresiak, M, Abdel-Misih, R, Bennett, J, Brown, J, Iacocca, M, Rabeno, B, Kwon, S-Y, Kemkes, A, Curley, E, Alexopoulou, I, Engel, J, Bartlett, J, Albert, M, Park, D-Y, Dhir, R, Luketich, J, Landreneau, R, Janjigian, YY, Kelsen, DP, Cho, E, Ladanyi, M, Tang, L, McCall, SJ, Park, YS, Cheong, J-H, Ajani, J, Camargo, MC, Alonso, S, Ayala, B, Jensen, MA, Pihl, T, Raman, R, Walton, J, Wan, Y, Eley, G, Shaw, KRM, Tarnuzzer, R, Wang, Z, Zenklusen, JC, Davidsen, T, Hutter, CM, Sofia, HJ, Burton, R, Chudamani, S, Liu, J, Bass, AJ, Thorsson, V, Shmulevich, I, Reynolds, SM, Miller, M, Bernard, B, Hinoue, T, Laird, PW, Curtis, C, Shen, H, Weisenberger, DJ, Schultz, N, Shen, R, Weinhold, N, Keiser, DP, Bowlby, R, Sipahimalani, P, Cherniack, AD, Getz, G, Liu, Y, Noble, MS, Pedamallu, C, Sougnez, C, Taylor-Weiner, A, Akbani, R, Lee, J-S, Liu, W, Mills, GB, Yang, D, Zhang, W, Pantazi, A, Parfenov, M, Gulley, M, Piazuelo, MB, Schneider, BG, Kim, J, Boussioutas, A, Sheth, M, Demchok, JA, Rabkin, CS, Willis, JE, Ng, S, Garman, K, Beer, DG, Pennathur, A, Raphael, BJ, Wu, H-T, Odze, R, Kim, HK, Bowen, J, Leraas, KM, Lichtenberg, TM, Weaver, L, McLellan, M, Wiznerowicz, M, Sakai, R, Lawrence, MS, Cibulskis, K, Lichtenstein, L, Fisher, S, Gabriel, SB, Lander, ES, Ding, L, Niu, B, Ally, A, Balasundaram, M, Birol, I, Brooks, D, Butterfield, YSN, Carlsen, R, Chu, A, Chu, J, Chuah, E, Chun, H-JE, Clarke, A, Dhalla, N, Guin, R, Holt, RA, Jones, SJM, Kasaian, K, Lee, D, Li, HA, Lim, E, Ma, Y, Marra, MA, Mayo, M, Moore, RA, Mungall, AJ, Mungall, KL, Nip, KM, Robertson, AG, Schein, JE, Tam, A, Thiessen, N, Beroukhim, R, Carter, SL, Cho, J, DiCara, D, Frazer, S, Gehlenborg, N, Heiman, DI, Jung, J, Lin, P, Meyerson, M, Ojesina, AI, Pedamallu, CS, Saksena, G, Schumacher, SE, Stojanov, P, Tabak, B, Voet, D, Rosenberg, M, Zack, TI, Zhang, H, Zou, L, Protopopov, A, Santoso, N, Lee, S, Zhang, J, Mahadeshwar, HS, Tang, J, Ren, X, Seth, S, Yang, L, Xu, AW, Song, X, Xi, R, Bristow, CA, Hadjipanayis, A, Seidman, J, Chin, L, Park, PJ, Kucherlapati, R, Ling, S, Rao, A, Weinstein, JN, Kim, S-B, Lu, Y, Mills, G, Bootwalla, MS, Lai, PH, Triche, T, Van Den Berg, DJ, Baylin, SB, Herman, JG, Murray, BA, Askoy, BA, Ciriello, G, Dresdner, G, Gao, J, Gross, B, Jacobsen, A, Lee, W, Ramirez, R, Sander, C, Senbabaoglu, Y, Sinha, R, Sumer, SO, Sun, Y, Iype, L, Kramer, RW, Kreisberg, R, Rovira, H, Tasman, N, Haussler, D, Stuart, JM, Verhaak, RGW, Leiserson, MDM, Taylor, BS, Black, AD, Carney, JA, Gastier-Foster, JM, Helsel, C, McAllister, C, Ramirez, NC, Tabler, TR, Wise, L, Zmuda, E, Penny, R, Crain, D, Gardner, J, Lau, K, Curely, E, Mallery, D, Morris, S, Paulauskis, J, Shelton, T, Shelton, C, Sherman, M, Benz, C, Lee, J-H, Fedosenko, K, Manikhas, G, Voronina, O, Belyaev, D, Dolzhansky, O, Rathmell, WK, Brzezinski, J, Ibbs, M, Korski, K, Kycler, W, Lazniak, R, Leporowska, E, Mackiewicz, A, Murawa, D, Murawa, P, Spychala, A, Suchorska, WM, Tatka, H, Teresiak, M, Abdel-Misih, R, Bennett, J, Brown, J, Iacocca, M, Rabeno, B, Kwon, S-Y, Kemkes, A, Curley, E, Alexopoulou, I, Engel, J, Bartlett, J, Albert, M, Park, D-Y, Dhir, R, Luketich, J, Landreneau, R, Janjigian, YY, Kelsen, DP, Cho, E, Ladanyi, M, Tang, L, McCall, SJ, Park, YS, Cheong, J-H, Ajani, J, Camargo, MC, Alonso, S, Ayala, B, Jensen, MA, Pihl, T, Raman, R, Walton, J, Wan, Y, Eley, G, Shaw, KRM, Tarnuzzer, R, Wang, Z, Zenklusen, JC, Davidsen, T, Hutter, CM, Sofia, HJ, Burton, R, Chudamani, S, and Liu, J

Abstract

Gastric cancer is a leading cause of cancer deaths, but analysis of its molecular and clinical characteristics has been complicated by histological and aetiological heterogeneity. Here we describe a comprehensive molecular evaluation of 295 primary gastric adenocarcinomas as part of The Cancer Genome Atlas (TCGA) project. We propose a molecular classification dividing gastric cancer into four subtypes: tumours positive for Epstein-Barr virus, which display recurrent PIK3CA mutations, extreme DNA hypermethylation, and amplification of JAK2, CD274 (also known as PD-L1) and PDCD1LG2 (also known as PD-L2); microsatellite unstable tumours, which show elevated mutation rates, including mutations of genes encoding targetable oncogenic signalling proteins; genomically stable tumours, which are enriched for the diffuse histological variant and mutations of RHOA or fusions involving RHO-family GTPase-activating proteins; and tumours with chromosomal instability, which show marked aneuploidy and focal amplification of receptor tyrosine kinases. Identification of these subtypes provides a roadmap for patient stratification and trials of targeted therapies.

Published
2014

2. Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin

Author

Hoadley, K., Yau, C., Wolf, D., Cherniack, A., Tamborero, D., Ng, S., Leiserson, M., Niu, B., McLellan, M., Uzunangelov, V., Zhang, J., Kandoth, C., Akbani, R., Shen, H., Omberg, L., Chu, A., Margolin, A., van't Veer, L., Lopez-Bigas, N., Laird, P., Raphael, B., Ding, L., Robertson, A., Byers, L., Mills, G., Weinstein, J., Van Waes, C., Chen, Z., Collisson, E., Benz, C., Perou, C., Stuart, J., Abbott, R., Abbott, S., Aksoy, B., Aldape, K., Ally, A., Amin, S., Anastassiou, D., Auman, J., Baggerly, K., Balasundaram, M., Balu, S., Baylin, S., Benz, S., Berman, B., Bernard, B., Bhatt, A., Birol, I., Black, A., Bodenheimer, T., Bootwalla, M., Bowen, J., Bressler, R., Bristow, C., Brooks, A., Broom, B., Buda, E., Burton, R., Butterfield, Y., Carlin, D., Carter, S., Casasent, T., Chang, K., Chanock, S., Chin, L., Cho, D., Cho, J., Chuah, E., Chun, H., Cibulskis, K., Ciriello, G., Cleland, J., Cline, M., Craft, B., Creighton, C., Danilova, L., Davidsen, T., Davis, C., Dees, N., Delehaunty, K., Demchok, J., Dhalla, N., DiCara, D., Dinh, H., Dobson, J., Dodda, D., Doddapaneni, H., Donehower, L., Dooling, D., Dresdner, G., Drummond, J., Eakin, A., Edgerton, M., Eldred, J., Eley, G., Ellrott, K., Fan, C., Fei, S., Felau, I., Frazer, S., Freeman, S., Frick, J., Fronick, C., Fulton, L., Fulton, R., Gabriel, S., Gao, J., Gastier-Foster, J., Gehlenborg, N., George, M., Getz, G., Gibbs, R., Goldman, M., Gonzalez-Perez, A., Gross, B., Guin, R., Gunaratne, P., Hadjipanayis, A., Hamilton, M., Hamilton, S., Han, L., Han, Y., Harper, H., Haseley, P., Haussler, D., Hayes, D., Heiman, D., Helman, E., Helsel, C., Herbrich, S., Herman, J., Hinoue, T., Hirst, C., Hirst, M., Holt, R., Hoyle, A., Iype, L., Jacobsen, A., Jeffreys, S., Jensen, M., Jones, C., Jones, S., Ju, Z., Jung, J., Kahles, A., Kahn, A., Kalicki-Veizer, J., Kalra, D., Kanchi, K., Kane, D., Kim, H., Kim, J., Knijnenburg, T., Koboldt, D., Kovar, C., Kramer, R., Kreisberg, R., Kucherlapati, R., Ladanyi, M., Lander, E., Larson, D., Lawrence, M., Lee, D., Lee, E., Lee, S., Lee, W., Lehmann, K., Leinonen, K., Leraas, K., Lerner, S., Levine, D., Lewis, L., Ley, T., Li, H., Li, J., Li, W., Liang, H., Lichtenberg, T., Lin, J., Lin, L., Lin, P., Liu, W., Liu, Y., Lorenzi, P., Lu, C., Lu, Y., Luquette, L., Ma, S., Magrini, V., Mahadeshwar, H., Mardis, E., Marra, M., Mayo, M., McAllister, C., McGuire, S., McMichael, J., Melott, J., Meng, S., Meyerson, M., Mieczkowski, P., Miller, C., Miller, M., Moore, R., Morgan, M., Morton, D., Mose, L., Mungall, A., Muzny, D., Nguyen, L., Noble, M., Noushmehr, H., O'Laughlin, M., Ojesina, A., Yang, T., Ozenberger, B., Pantazi, A., Parfenov, M., Park, P., Parker, J., Paull, E., Pedamallu, C., Pihl, T., Pohl, C., Pot, D., Protopopov, A., Przytycka, T., Radenbaugh, A., Ramirez, N., Ramirez, R., Ratsch, G., Reid, J., Ren, X., Reva, B., Reynolds, S., Rhie, S., Roach, J., Rovira, H., Ryan, M., Saksena, G., Salama, S., Sander, C., Santoso, N., Schein, J., Schmidt, H., Schultz, N., Schumacher, S., Seidman, J., Senbabaoglu, Y., Seth, S., Sharpe, S., Shen, R., Sheth, M., Shi, Y., Shmulevich, I., Silva, G., Simons, J., Sinha, R., Sipahimalani, P., Smith, S., Sofia, H., Sokolov, A., Soloway, M., Song, X., Sougnez, C., Spellman, P., Staudt, L., Stewart, C., Stojanov, P., Su, X., Sumer, S., Sun, Y., Swatloski, T., Tabak, B., Tam, A., Tan, D., Tang, J., Tarnuzzer, R., Taylor, B., Thiessen, N., Thorsson, V., Triche, T., Van Den Berg, D., Vandin, F., Varhol, Richard, Vaske, C., Veluvolu, U., Verhaak, R., Voet, D., Walker, J., Wallis, J., Waltman, P., Wan, Y., Wang, M., Wang, W., Wang, Z., Waring, S., Weinhold, N., Weisenberger, D., Wendl, M., Wheeler, D., Wilkerson, M., Wilson, R., Wise, L., Wong, A., Wu, C., Wu, H., Wu, J., Wylie, T., Xi, L., Xi, R., Xia, Z., Xu, A., Yang, D., Yang, L., Yang, Y., Yao, J., Yao, R., Ye, K., Yoshihara, K., Yuan, Y., Yung, A., Zack, T., Zeng, D., Zenklusen, J., Zhang, H., Zhang, N., Zhang, Q., Zhang, W., Zhao, W., Zheng, S., Zhu, J., Zmuda, E., Zou, L., Hoadley, K., Yau, C., Wolf, D., Cherniack, A., Tamborero, D., Ng, S., Leiserson, M., Niu, B., McLellan, M., Uzunangelov, V., Zhang, J., Kandoth, C., Akbani, R., Shen, H., Omberg, L., Chu, A., Margolin, A., van't Veer, L., Lopez-Bigas, N., Laird, P., Raphael, B., Ding, L., Robertson, A., Byers, L., Mills, G., Weinstein, J., Van Waes, C., Chen, Z., Collisson, E., Benz, C., Perou, C., Stuart, J., Abbott, R., Abbott, S., Aksoy, B., Aldape, K., Ally, A., Amin, S., Anastassiou, D., Auman, J., Baggerly, K., Balasundaram, M., Balu, S., Baylin, S., Benz, S., Berman, B., Bernard, B., Bhatt, A., Birol, I., Black, A., Bodenheimer, T., Bootwalla, M., Bowen, J., Bressler, R., Bristow, C., Brooks, A., Broom, B., Buda, E., Burton, R., Butterfield, Y., Carlin, D., Carter, S., Casasent, T., Chang, K., Chanock, S., Chin, L., Cho, D., Cho, J., Chuah, E., Chun, H., Cibulskis, K., Ciriello, G., Cleland, J., Cline, M., Craft, B., Creighton, C., Danilova, L., Davidsen, T., Davis, C., Dees, N., Delehaunty, K., Demchok, J., Dhalla, N., DiCara, D., Dinh, H., Dobson, J., Dodda, D., Doddapaneni, H., Donehower, L., Dooling, D., Dresdner, G., Drummond, J., Eakin, A., Edgerton, M., Eldred, J., Eley, G., Ellrott, K., Fan, C., Fei, S., Felau, I., Frazer, S., Freeman, S., Frick, J., Fronick, C., Fulton, L., Fulton, R., Gabriel, S., Gao, J., Gastier-Foster, J., Gehlenborg, N., George, M., Getz, G., Gibbs, R., Goldman, M., Gonzalez-Perez, A., Gross, B., Guin, R., Gunaratne, P., Hadjipanayis, A., Hamilton, M., Hamilton, S., Han, L., Han, Y., Harper, H., Haseley, P., Haussler, D., Hayes, D., Heiman, D., Helman, E., Helsel, C., Herbrich, S., Herman, J., Hinoue, T., Hirst, C., Hirst, M., Holt, R., Hoyle, A., Iype, L., Jacobsen, A., Jeffreys, S., Jensen, M., Jones, C., Jones, S., Ju, Z., Jung, J., Kahles, A., Kahn, A., Kalicki-Veizer, J., Kalra, D., Kanchi, K., Kane, D., Kim, H., Kim, J., Knijnenburg, T., Koboldt, D., Kovar, C., Kramer, R., Kreisberg, R., Kucherlapati, R., Ladanyi, M., Lander, E., Larson, D., Lawrence, M., Lee, D., Lee, E., Lee, S., Lee, W., Lehmann, K., Leinonen, K., Leraas, K., Lerner, S., Levine, D., Lewis, L., Ley, T., Li, H., Li, J., Li, W., Liang, H., Lichtenberg, T., Lin, J., Lin, L., Lin, P., Liu, W., Liu, Y., Lorenzi, P., Lu, C., Lu, Y., Luquette, L., Ma, S., Magrini, V., Mahadeshwar, H., Mardis, E., Marra, M., Mayo, M., McAllister, C., McGuire, S., McMichael, J., Melott, J., Meng, S., Meyerson, M., Mieczkowski, P., Miller, C., Miller, M., Moore, R., Morgan, M., Morton, D., Mose, L., Mungall, A., Muzny, D., Nguyen, L., Noble, M., Noushmehr, H., O'Laughlin, M., Ojesina, A., Yang, T., Ozenberger, B., Pantazi, A., Parfenov, M., Park, P., Parker, J., Paull, E., Pedamallu, C., Pihl, T., Pohl, C., Pot, D., Protopopov, A., Przytycka, T., Radenbaugh, A., Ramirez, N., Ramirez, R., Ratsch, G., Reid, J., Ren, X., Reva, B., Reynolds, S., Rhie, S., Roach, J., Rovira, H., Ryan, M., Saksena, G., Salama, S., Sander, C., Santoso, N., Schein, J., Schmidt, H., Schultz, N., Schumacher, S., Seidman, J., Senbabaoglu, Y., Seth, S., Sharpe, S., Shen, R., Sheth, M., Shi, Y., Shmulevich, I., Silva, G., Simons, J., Sinha, R., Sipahimalani, P., Smith, S., Sofia, H., Sokolov, A., Soloway, M., Song, X., Sougnez, C., Spellman, P., Staudt, L., Stewart, C., Stojanov, P., Su, X., Sumer, S., Sun, Y., Swatloski, T., Tabak, B., Tam, A., Tan, D., Tang, J., Tarnuzzer, R., Taylor, B., Thiessen, N., Thorsson, V., Triche, T., Van Den Berg, D., Vandin, F., Varhol, Richard, Vaske, C., Veluvolu, U., Verhaak, R., Voet, D., Walker, J., Wallis, J., Waltman, P., Wan, Y., Wang, M., Wang, W., Wang, Z., Waring, S., Weinhold, N., Weisenberger, D., Wendl, M., Wheeler, D., Wilkerson, M., Wilson, R., Wise, L., Wong, A., Wu, C., Wu, H., Wu, J., Wylie, T., Xi, L., Xi, R., Xia, Z., Xu, A., Yang, D., Yang, L., Yang, Y., Yao, J., Yao, R., Ye, K., Yoshihara, K., Yuan, Y., Yung, A., Zack, T., Zeng, D., Zenklusen, J., Zhang, H., Zhang, N., Zhang, Q., Zhang, W., Zhao, W., Zheng, S., Zhu, J., Zmuda, E., and Zou, L.

Abstract

© 2014 Elsevier Inc. Recent genomic analyses of pathologically defined tumor types identify 'within-a-tissue' disease subtypes. However, the extent to which genomic signatures are shared across tissues is still unclear. We performed an integrative analysis using five genome-wide platforms and one proteomic platform on 3,527 specimens from 12 cancer types, revealing a unified classification into 11 major subtypes. Five subtypes were nearly identical to their tissue-oforigin counterparts, but several distinct cancer types were found to converge into common subtypes. Lung squamous, head and neck, and a subset of bladder cancers coalesced into one subtype typified by TP53 alterations, TP63 amplifications, and high expression of immune and proliferation pathway genes. Of note, bladder cancers split into three pancancer subtypes. The multiplatform classification, while correlated with tissue-of-origin, provides independent information for predicting clinical outcomes. All data sets are available for data-mining from a unified resource to support further biological discoveries and insights into novel therapeutic strategies.

Published
2014

5. Fastbreak: a tool for analysis and visualization of structural variations in genomic data.

Author

Bressler R, Lin J, Eakin A, Robinson T, Kreisberg R, Rovira H, Knijnenburg T, Boyle J, and Shmulevich I

Abstract

Genomic studies are now being undertaken on thousands of samples requiring new computational tools that can rapidly analyze data to identify clinically important features. Inferring structural variations in cancer genomes from mate-paired reads is a combinatorially difficult problem. We introduce Fastbreak, a fast and scalable toolkit that enables the analysis and visualization of large amounts of data from projects such as The Cancer Genome Atlas.

Published
2012
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6. Increasing coverage of transcription factor position weight matrices through domain-level homology.

Author

Bernard B, Thorsson V, Rovira H, and Shmulevich I

Subjects
Algorithms, Animals, Computational Biology methods, DNA chemistry, Humans, Models, Statistical, Oligonucleotide Array Sequence Analysis methods, Protein Binding, Reproducibility of Results, Sequence Analysis, DNA, Software, Systems Biology methods, DNA metabolism, Position-Specific Scoring Matrices, Transcription Factors metabolism
Abstract

Transcription factor-DNA interactions, central to cellular regulation and control, are commonly described by position weight matrices (PWMs). These matrices are frequently used to predict transcription factor binding sites in regulatory regions of DNA to complement and guide further experimental investigation. The DNA sequence preferences of transcription factors, encoded in PWMs, are dictated primarily by select residues within the DNA binding domain(s) that interact directly with DNA. Therefore, the DNA binding properties of homologous transcription factors with identical DNA binding domains may be characterized by PWMs derived from different species. Accordingly, we have implemented a fully automated domain-level homology searching method for identical DNA binding sequences.By applying the domain-level homology search to transcription factors with existing PWMs in the JASPAR and TRANSFAC databases, we were able to significantly increase coverage in terms of the total number of PWMs associated with a given species, assign PWMs to transcription factors that did not previously have any associations, and increase the number of represented species with PWMs over an order of magnitude. Additionally, using protein binding microarray (PBM) data, we have validated the domain-level method by demonstrating that transcription factor pairs with matching DNA binding domains exhibit comparable DNA binding specificity predictions to transcription factor pairs with completely identical sequences.The increased coverage achieved herein demonstrates the potential for more thorough species-associated investigation of protein-DNA interactions using existing resources. The PWM scanning results highlight the challenging nature of transcription factors that contain multiple DNA binding domains, as well as the impact of motif discovery on the ability to predict DNA binding properties. The method is additionally suitable for identifying domain-level homology mappings to enable utilization of additional information sources in the study of transcription factors. The domain-level homology search method, resulting PWM mappings, web-based user interface, and web API are publicly available at http://dodoma.systemsbiology.netdodoma.systemsbiology.net.

Published
2012
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7. EPEPT: a web service for enhanced P-value estimation in permutation tests.

Author

Knijnenburg TA, Lin J, Rovira H, Boyle J, and Shmulevich I

Subjects
Humans, Internet, Programming Languages, Regression Analysis, Computational Biology methods, Software
Abstract

Background: In computational biology, permutation tests have become a widely used tool to assess the statistical significance of an event under investigation. However, the common way of computing the P-value, which expresses the statistical significance, requires a very large number of permutations when small (and thus interesting) P-values are to be accurately estimated. This is computationally expensive and often infeasible. Recently, we proposed an alternative estimator, which requires far fewer permutations compared to the standard empirical approach while still reliably estimating small P-values., Results: The proposed P-value estimator has been enriched with additional functionalities and is made available to the general community through a public website and web service, called EPEPT. This means that the EPEPT routines can be accessed not only via a website, but also programmatically using any programming language that can interact with the web. Examples of web service clients in multiple programming languages can be downloaded. Additionally, EPEPT accepts data of various common experiment types used in computational biology. For these experiment types EPEPT first computes the permutation values and then performs the P-value estimation. Finally, the source code of EPEPT can be downloaded., Conclusions: Different types of users, such as biologists, bioinformaticians and software engineers, can use the method in an appropriate and simple way.

Published
2011
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8. SEQADAPT: an adaptable system for the tracking, storage and analysis of high throughput sequencing experiments.

Author

Burdick DB, Cavnor CC, Handcock J, Killcoyne S, Lin J, Marzolf B, Ramsey SA, Rovira H, Bressler R, Shmulevich I, and Boyle J

Subjects
Algorithms, Base Sequence, Database Management Systems, Internet, Sequence Analysis, DNA instrumentation, Computational Biology methods, Sequence Analysis, DNA methods, Software
Abstract

Background: High throughput sequencing has become an increasingly important tool for biological research. However, the existing software systems for managing and processing these data have not provided the flexible infrastructure that research requires., Results: Existing software solutions provide static and well-established algorithms in a restrictive package. However as high throughput sequencing is a rapidly evolving field, such static approaches lack the ability to readily adopt the latest advances and techniques which are often required by researchers. We have used a loosely coupled, service-oriented infrastructure to develop SeqAdapt. This system streamlines data management and allows for rapid integration of novel algorithms. Our approach also allows computational biologists to focus on developing and applying new methods instead of writing boilerplate infrastructure code., Conclusion: The system is based around the Addama service architecture and is available at our website as a demonstration web application, an installable single download and as a collection of individual customizable services.

Published
2010
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9. Complicated bronchiolitis: another use for your bedside ultrasound in the emergency department.

Author

Soto F, Soltero R, and Rovira H

Subjects
Bronchiolitis diagnostic imaging, Diaphragmatic Eventration complications, Diaphragmatic Eventration diagnostic imaging, Diaphragmatic Eventration surgery, Humans, Incidental Findings, Infant, Liver diagnostic imaging, Male, Phrenic Nerve abnormalities, Radiography, Ultrasonography, Bronchiolitis complications, Diaphragmatic Eventration diagnosis, Emergency Service, Hospital, Point-of-Care Systems
Abstract

Diaphragmatic eventration or diaphragmatic herniations are congenital defect that involve abnormal development of the diaphragm and stretching of the muscular fibers leading to protrusion of abdominal organs into the thoracic cavity. Left sided defects will lead to stomach contents into the chest cavity while, right sided defects will have bowel or liver in the thoracic cavity. Infants with Congenital diaphragmatic hernia often present with respiratory distress that can be life-threatening unless treated appropriately. Bedside ultrasound in the Emergency Department, performed by the Emergency Physician can be a very useful tool in diagnosing conditions such as this one. We present a case of diaphragmatic eventration in a two month old male sent to Emergency Department (ED) by his primary care physician due to a severe case of bronchiolitis.

Published
2009

10. Adaptable data management for systems biology investigations.

Author

Boyle J, Rovira H, Cavnor C, Burdick D, Killcoyne S, and Shmulevich I

Subjects
Information Storage and Retrieval, User-Computer Interface, Computational Biology methods, Database Management Systems standards, Systems Biology
Abstract

Background: Within research each experiment is different, the focus changes and the data is generated from a continually evolving barrage of technologies. There is a continual introduction of new techniques whose usage ranges from in-house protocols through to high-throughput instrumentation. To support these requirements data management systems are needed that can be rapidly built and readily adapted for new usage., Results: The adaptable data management system discussed is designed to support the seamless mining and analysis of biological experiment data that is commonly used in systems biology (e.g. ChIP-chip, gene expression, proteomics, imaging, flow cytometry). We use different content graphs to represent different views upon the data. These views are designed for different roles: equipment specific views are used to gather instrumentation information; data processing oriented views are provided to enable the rapid development of analysis applications; and research project specific views are used to organize information for individual research experiments. This management system allows for both the rapid introduction of new types of information and the evolution of the knowledge it represents., Conclusion: Data management is an important aspect of any research enterprise. It is the foundation on which most applications are built, and must be easily extended to serve new functionality for new scientific areas. We have found that adopting a three-tier architecture for data management, built around distributed standardized content repositories, allows us to rapidly develop new applications to support a diverse user community.

Published
2009
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12. [Evaluation of the efficacy of the combination amoxicillin-clavulanic acid-tobramycin for the prevention of infections after surgery for ORL cancers].

Author

Philip V, Saux MC, Rovira H, Boutin F, and Traissac L

Subjects
Aged, Clinical Protocols, Drug Therapy, Combination, Female, Humans, Male, Middle Aged, Postoperative Complications prevention & control, Amoxicillin therapeutic use, Bacterial Infections prevention & control, Clavulanic Acids therapeutic use, Otorhinolaryngologic Neoplasms surgery, Tobramycin therapeutic use
Abstract

The clinic and economic evaluation of a probabilist antibiotherapy Augmentin/Nebcine administered until the wound healing was studied in 60 patients, operated of upper aerodigestives tracts cancer. The antibiotherapy efficiency was estimated at the end of 6 days in terms of clinic and bacteriologic results. In case of therapeutic failure, the treatment was adapted according to antibiogram results. The association Augmentin/Nebcine was effective in 93% of cases. Antibiotherapy was to be modified for five patients (one for allergy and four for bacteriological unsuccessful). The bacteriologic sample shows the predominance of Gram(-) germs. 83% of them were sensitive to one of these antibiotics in vitro. The daily mean cost of antibiotherapy was about FF 71. The overcost, due to antibiotherapy failures, represented only 1% of the whole cost of the 60 treatments. These results justify the use of a large spectrum antibiotherapy reaching Gram(-) germs.

Published
1992

13. [Our experience with percutaneous endoscopic gastrostomy in pharyngo-laryngeal surgery].

Author

Bertrand B, De Monredon O, Rovira HP, Devars F, and Traissac L

Subjects
Adult, Aged, Deglutition Disorders etiology, Deglutition Disorders therapy, Endoscopy, Enteral Nutrition instrumentation, Head and Neck Neoplasms complications, Humans, Male, Middle Aged, Enteral Nutrition methods, Gastrostomy methods, Head and Neck Neoplasms surgery
Abstract

Percutaneous endoscopic gastrostomy (PEG), is an enteral feeding procedure, easy to tolerate and simple to perform. PEG appears to be an alternative to surgical gastrostomy. Used in ten patients with E.N.T. cancer, we only observe two minor complications. Advisable in a first time for the feeding of patients with palliative treatment, we propose PEG for patients in position to have a long and difficult rehabilitation of swallowing.

Published
1992

14. [Electromyography of the larynx in the diagnosis of spontaneous or post-thyroidectomy laryngeal paralysis].

Author

Traissac L, Gioux M, Rovira HP, Henry C, and Bertrand B

Subjects
Electromyography, Humans, Laryngeal Nerves physiopathology, Thyroidectomy adverse effects, Larynx physiopathology, Vocal Cord Paralysis etiology
Abstract

Electromyographic assessment (EMG) of the larynx is very important for diagnostic and prognostic in cases of unmoving larynx: definition that authors like better than larynx palsie or recurrent nerve palsie because it is impossible to know why the larynx do not move in many cases (15f for 20 cases in the experience of the authors). EMG must be realized on several muscles and not only on the vocal fold muscle. It is necessary to realize several EMG to have a good follow up. If we have the proof that it is a case of definitive recurrent palsie the authors think that it is now, indication of nervous selective anastomosis by micro-surgery.

Published
1991

15. [Evaluation of voice quality. Experimental approach and modeling of the prosthetic voice of laryngectomized patients].

Author

Rovira HP, Cazals Y, and Traissac L

Subjects
Acoustics, Biomechanical Phenomena, Humans, Laryngectomy rehabilitation, Larynx, Artificial, Voice Quality physiology
Abstract

The authors describe their initial results with the parametric assessment of voice quality, which still is mainly subjective. This analysis will be used both in audiology and phonology. A first approach is made on the experimental model of a laryngectomee with a Bordeaux-type phonatory implant. Such patients allow a simpler analysis of voice production both incoustics and with an electromyographic control. The analysis of the data and their statistical validation is based on the use of original computer software.

Published
1991

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