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2. Liver Disease

Author

Shiela Sherlock, G. E. W. Wolstenholme, Shiela Sherlock, G. E. W. Wolstenholme

Published
2009

3. Integrated genomic analyses of ovarian carcinoma

Author

Bell, D., Berchuck, A., Birrer, M., Chien, J., Cramer, D. W., Dao, F., Dhir, R., DiSaia, P., Gabra, H., Glenn, P., Godwin, A. K., Gross, J., Hartmann, L., Huang, M., Huntsman, D. G., Iacocca, M., Imielinski, M., Kalloger, S., Karlan, B. Y., Morrison, C., Mutch, D., Olvera, N., Orsulic, S., Park, K., Petrelli, N., Rabeno, B., Rader, J. S., Sikic, B. I., Smith-McCune, K., Sood, A. K., Bowtell, D., Testa, J. R., Chang, K., Dinh, H. H., Drummond, J. A., Fowler, G., Gunaratne, P., Hawes, A. C., Kovar, C. L., Lewis, L. R., Morgan, M. B., Newsham, I. F., Santibanez, J., Reid, J. G., Trevino, L. R., Wu, Y.-Q., Wang, M., Muzny, D. M., Wheeler, D. A., Gibbs, R. A., Sivachenko, A. Y., Sougnez, C., Wilkinson, J., Bloom, T., Fennell, T., Baldwin, J., Gabriel, S., Lander, E. S., Ding, L., Fulton, R. S., Koboldt, D. C., McLellan, M. D., Wylie, T., Walker, J., O’Laughlin, M., Dooling, D. J., Fulton, L., Abbott, R., Dees, N. D., Zhang, Q., Kandoth, C., Wendl, M., Schierding, W., Shen, D., Harris, C. C., Schmidt, H., Kalicki, J., Delehaunty, K. D., Fronick, C. C., Demeter, R., Cook, L., Wallis, J. W., Lin, L., Magrini, V. J., Hodges, J. S., Eldred, J. M., Smith, S. M., Pohl, C. S., Vandin, F., Raphael, B. J., Weinstock, G. M., Mardis, E. R., Wilson, R. K., Meyerson, M., Winckler, W., Verhaak, R. G. W., Carter, S. L., Mermel, C. H., Nguyen, H., Onofrio, R. C., Hubbard, D., Gupta, S., Crenshaw, A., Ramos, A. H., Protopopov, A., Zhang, Juinhua, Kim, T. M., Perna, I., Xiao, Y., Ren, G., Sathiamoorthy, N., Lee, E., Park, P. J., Kucherlapati, R., Absher, D. M., Waite, L., Sherlock, G., Brooks, J. D., Li, J. Z., Xu, J., Myers, R. M., Laird, P. W., Cope, L., Herman, J. G., Shen, H., Weisenberger, D. J., Noushmehr, H., Pan, F., Triche, T., Jr, Berman, B. P., Van Den Berg, D. J., Buckley, J., Baylin, S. B., Jakkula, L. R., Dorton, S., Marr, H., Choi, Y. G., Wang, V., Wang, N. J., Ngai, J., Conboy, J. G., Feiler, H. S., Socci, N. D., Liang, Y., Lash, A. E., Brennan, C., Viale, A., Meng, S., Shi, Y., Li, L., Turman, Y. J., Zang, D., Helms, E. B., Zhou, X., Wu, J., Topal, M. D., Zhang, Junihua, Wu, C. J., Shukla, S., Sivachenko, A., Jing, R., Liu, Y., Noble, M., Carter, H., Kim, D., Karchin, R., Korkola, J. E., Heiser, L. M., Cho, R. J., Hu, Z., Parvin, B., Cerami, E., Olshen, A., Reva, B., Antipin, Y., Shen, R., Mankoo, P., Sheridan, R., Ciriello, G., Chang, W. K., Bernanke, J. A., Haussler, D., Benz, C. C., Stuart, J. M., Benz, S. C., Sanborn, J. Z., Vaske, C. J., Zhu, J., Szeto, C., Scott, G. K., Yau, C., Wilkerson, M. D., Zhang, N., Akbani, R., Baggerly, K. A., Yung, W. K., Weinstein, J. N., Shelton, T., Grimm, D., Hatfield, M., Morris, S., Yena, P., Rhodes, P., Sherman, M., Paulauskis, J., Millis, S., Kahn, A., Greene, J. M., Sfeir, R., Jensen, M. A., Chen, J., Whitmore, J., Alonso, S., Jordan, J., Chu, A., Zhang, Jinghui, Barker, A., Compton, C., Eley, G., Ferguson, M., Fielding, P., Gerhard, D. S., Myles, R., Schaefer, C., Mills Shaw, K. R., Vaught, J., Vockley, J. B., Good, P. J., Guyer, M. S., Ozenberger, B., Peterson, J., and Thomson, E.

Published
2011
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5. Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus

Author

de Vries, R.P. Riley, R. Wiebenga, A. Aguilar-Osorio, G. Amillis, S. Uchima, C.A. Anderluh, G. Asadollahi, M. Askin, M. Barry, K. Battaglia, E. Bayram, O. Benocci, T. Braus-Stromeyer, S.A. Caldana, C. Cánovas, D. Cerqueira, G.C. Chen, F. Chen, W. Choi, C. Clum, A. dos Santos, R.A.C. de Lima Damásio, A.R. Diallinas, G. Emri, T. Fekete, E. Flipphi, M. Freyberg, S. Gallo, A. Gournas, C. Habgood, R. Hainaut, M. Harispe, M.L. Henrissat, B. Hildén, K.S. Hope, R. Hossain, A. Karabika, E. Karaffa, L. Karányi, Z. Kraševec, N. Kuo, A. Kusch, H. LaButti, K. Lagendijk, E.L. Lapidus, A. Levasseur, A. Lindquist, E. Lipzen, A. Logrieco, A.F. MacCabe, A. Mäkelä, M.R. Malavazi, I. Melin, P. Meyer, V. Mielnichuk, N. Miskei, M. Molnár, A.P. Mulé, G. Ngan, C.Y. Orejas, M. Orosz, E. Ouedraogo, J.P. Overkamp, K.M. Park, H.-S. Perrone, G. Piumi, F. Punt, P.J. Ram, A.F.J. Ramón, A. Rauscher, S. Record, E. Riaño-Pachón, D.M. Robert, V. Röhrig, J. Ruller, R. Salamov, A. Salih, N.S. Samson, R.A. Sándor, E. Sanguinetti, M. Schütze, T. Sepčić, K. Shelest, E. Sherlock, G. Sophianopoulou, V. Squina, F.M. Sun, H. Susca, A. Todd, R.B. Tsang, A. Unkles, S.E. van de Wiele, N. van Rossen-Uffink, D. de Castro Oliveira, J.V. Vesth, T.C. Visser, J. Yu, J.-H. Zhou, M. Andersen, M.R. Archer, D.B. Baker, S.E. Benoit, I. Brakhage, A.A. Braus, G.H. Fischer, R. Frisvad, J.C. Goldman, G.H. Houbraken, J. Oakley, B. Pócsi, I. Scazzocchio, C. Seiboth, B. vanKuyk, P.A. Wortman, J. Dyer, P.S. Grigoriev, I.V.

Abstract

Background: The fungal genus Aspergillus is of critical importance to humankind. Species include those with industrial applications, important pathogens of humans, animals and crops, a source of potent carcinogenic contaminants of food, and an important genetic model. The genome sequences of eight aspergilli have already been explored to investigate aspects of fungal biology, raising questions about evolution and specialization within this genus. Results: We have generated genome sequences for ten novel, highly diverse Aspergillus species and compared these in detail to sister and more distant genera. Comparative studies of key aspects of fungal biology, including primary and secondary metabolism, stress response, biomass degradation, and signal transduction, revealed both conservation and diversity among the species. Observed genomic differences were validated with experimental studies. This revealed several highlights, such as the potential for sex in asexual species, organic acid production genes being a key feature of black aspergilli, alternative approaches for degrading plant biomass, and indications for the genetic basis of stress response. A genome-wide phylogenetic analysis demonstrated in detail the relationship of the newly genome sequenced species with other aspergilli. Conclusions: Many aspects of biological differences between fungal species cannot be explained by current knowledge obtained from genome sequences. The comparative genomics and experimental study, presented here, allows for the first time a genus-wide view of the biological diversity of the aspergilli and in many, but not all, cases linked genome differences to phenotype. Insights gained could be exploited for biotechnological and medical applications of fungi. © 2017 The Author(s).

Published
2017

6. Literature-based gene curation and proposed genetic nomenclature for Cryptococcus

Author

Inglis, DO, Skrzypek, MS, Liaw, E, Moktali, V, Sherlock, G, and Stajich, JE

Abstract

Cryptococcus, a major cause of disseminated infections in immunocompromised patients, kills over 600,000 people per year worldwide. Genes involved in the virulence of the meningitis-causing fungus are being characterized at an increasing rate, and to date, at least 648 Cryptococcus gene names have been published. However, these data are scattered throughout the literature and are challenging to find. Furthermore, conflicts in locus identification exist, so that named genes have been subsequently published under new names or names associated with one locus have been used for another locus. To avoid these conflicts and to provide a central source of Cryptococcus gene information, we have collected all published Cryptococcus gene names from the scientific literature and associated them with standard Cryptococcus locus identifiers and have incorporated them into FungiDB (www.fungidb.org). FungiDB is a panfungal genome database that collects gene information and functional data and provides search tools for 61 species of fungi and oomycetes. We applied these published names to a manually curated ortholog set of all Cryptococcus species currently in FungiDB, including Cryptococcus neoformans var. neoformans strains JEC21 and B-3501A, C. neoformans var. grubii strain H99, and Cryptococcus gattii strains R265 and WM276, and have written brief descriptions of their functions. We also compiled a protocol for gene naming that summarizes guidelines proposed by members of the Cryptococcus research community. The centralization of genomic and literature-based information for Cryptococcus at FungiDB will help researchers communicate about genes of interest, such as those related to virulence, and will further facilitate research on the pathogen. © 2014, American Society for Microbiology. All Rights Reserved.

Published
2014
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7. Integrated genomic analyses of ovarian carcinoma

Author

Bell, D, Berchuck, A, Birrer, M, Chien, J, Cramer, DW, Dao, F, Dhir, R, DiSaia, P, Gabra, H, Glenn, P, Godwin, AK, Triche, T, Berman, BP, Van den Berg, DJ, Buckley, J, Baylin, SB, Zhang, J, Spellman, PT, Purdom, E, Iacocca, M, Shelton, T, Voet, D, Neuvial, P, Bengtsson, H, Jakkula, LR, Durinck, S, Han, J, Dorton, S, Marr, H, Zhang, H, Choi, YG, Wang, V, Wilkinson, J, Nguyen, H, Wang, NJ, Imielinski, M, Ngai, J, Conboy, JG, Parvin, B, Feiler, HS, Speed, TP, Gray, JW, Wu, CJ, Bloom, T, Levine, DA, Li, L, Socci, ND, Liang, Y, Taylor, BS, Kalloger, S, Schultz, N, Borsu, L, Lash, AE, Brennan, C, Ardlie, K, Viale, A, Shukla, S, Grimm, D, Sander, C, Ladanyi, M, Hoadley, KA, Meng, S, Du, Y, Karlan, BY, Shi, Y, Fennell, T, Cibulskis, K, Lawrence, MS, Meyerson, M, Hatfield, M, Mills, GB, Sivachenko, A, Jing, R, Park, RW, Liu, Y, Park, PJ, Ramos, AH, Noble, M, Chin, L, Carter, H, Kim, D, Morris, S, Winckler, W, Karchin, R, Morrison, C, Baldwin, J, Korkola, JE, Yena, P, Heiser, LM, Getz, G, Cho, RJ, Hu, Z, Gabriel, S, Mutch, D, Cerami, E, Rhodes, P, Olshen, A, Verhaak, RGW, Lander, ES, Reva, B, Antipin, Y, Shen, R, Olvera, N, Mankoo, P, Sheridan, R, Ciriello, G, Sherman, M, Chang, WK, Bernanke, JA, Hayes, DN, Carter, SL, Haussler, D, Orsulic, S, Benz, CC, Paulauskis, J, Stuart, JM, Zhang, N, Benz, SC, Sanborn, JZ, Vaske, CJ, Mermel, CH, Zhu, J, Szeto, C, Scott, GK, Yau, C, Rabeno, B, Ding, L, Park, K, Balu, S, Perou, CM, Saksena, G, Wilkerson, MD, Millis, S, Kahn, A, Turman, YJ, Fulton, RS, Onofrio, RC, Greene, JM, Sfeir, R, Jensen, MA, Chen, J, Whitmore, J, Alonso, S, Jordan, J, Chu, A, Rader, JS, Koboldt, DC, Zang, D, Gross, J, Barker, A, Compton, C, Eley, G, Ferguson, M, Fielding, P, Gerhard, DS, Myles, R, McLellan, MD, Schaefer, C, Helms, EB, Shaw, KRM, Sikic, BI, Vaught, J, Vockley, JB, Good, PJ, Guyer, MS, Ozenberger, B, Wylie, T, Peterson, J, Thomson, E, Smith-McCune, K, Sood, AK, Bowtell, D, Hubbard, D, Penny, R, Testa, JR, Chang, K, Walker, J, Dinh, HH, Drummond, JA, Fowler, G, Zhou, X, Gunaratne, P, Hawes, AC, Kovar, CL, Lewis, LR, Gupta, S, Morgan, MB, O'Laughlin, M, Newsham, IF, Santibanez, J, Reid, JG, Trevino, LR, Wu, J, Wu, Y-Q, Wang, M, Muzny, DM, Wheeler, DA, Gibbs, RA, Crenshaw, A, Sivachenko, AY, Topal, MD, Sougnez, C, Dooling, DJ, Fulton, L, Akbani, R, Abbott, R, Dees, ND, Zhang, Q, Kandoth, C, Wendl, M, Schierding, W, Shen, D, Harris, CC, Baggerly, KA, Schmidt, H, Wilson, RK, Kalicki, J, Delehaunty, KD, Fronick, CC, Demeter, R, Cook, L, Wallis, JW, Lin, L, Magrini, VJ, Yung, WK, Hodges, JS, Protopopov, A, Eldred, JM, Smith, SM, Pohl, CS, Vandin, F, Raphael, BJ, Weinstock, GM, Mardis, R, Kim, TM, Hartmann, L, Perna, I, Xiao, Y, Ren, G, Sathiamoorthy, N, Petrelli, N, Lee, E, Kucherlapati, R, Absher, DM, Huang, M, Waite, L, Sherlock, G, Brooks, JD, Li, JZ, Weinstein, JN, Xu, J, Myers, RM, Laird, PW, Cope, L, Herman, JG, Shen, H, Huntsman, DG, Weisenberger, DJ, Noushmehr, H, Pan, F, Massachusetts Institute of Technology. Department of Biology, Lander, Eric S., and Meyerson, Matthew L.

Subjects
endocrine system diseases, Serous carcinoma, Messenger, Gene Dosage, Cancer Genome Atlas Research Network, GYNECOLOGIC-ONCOLOGY-GROUP, GRADE SEROUS CARCINOMA, 0302 clinical medicine, Ovarian carcinoma, Aged, Carcinoma, DNA Methylation, Female, Gene Expression Profiling, Gene Expression Regulation, Neoplastic, Humans, MicroRNAs, Middle Aged, Mutation, Ovarian Neoplasms, RNA, Messenger, Genomics, Multidisciplinary, Genetics, HYBRID SELECTION, 0303 health sciences, female genital diseases and pregnancy complications, 3. Good health, Multidisciplinary Sciences, Serous fluid, BRCA MUTATION CARRIERS, 030220 oncology & carcinogenesis, DNA methylation, PARP inhibitor, Science & Technology - Other Topics, General Science & Technology, Biology, Article, 03 medical and health sciences, CLEAR-CELL CARCINOMA, MD Multidisciplinary, microRNA, HIGH-THROUGHPUT ANNOTATION, medicine, DRIVER MUTATIONS, Gene, 030304 developmental biology, Neoplastic, Science & Technology, MUTANT-CELLS, SOMATIC MUTATIONS, medicine.disease, CANCER STATISTICS, Gene Expression Regulation, Cancer research, RNA, Ovarian cancer
Abstract

A catalogue of molecular aberrations that cause ovarian cancer is critical for developing and deploying therapies that will improve patients’ lives. The Cancer Genome Atlas project has analysed messenger RNA expression, microRNA expression, promoter methylation and DNA copy number in 489 high-grade serous ovarian adenocarcinomas and the DNA sequences of exons from coding genes in 316 of these tumours. Here we report that high-grade serous ovarian cancer is characterized by TP53 mutations in almost all tumours (96%); low prevalence but statistically recurrent somatic mutations in nine further genes including NF1, BRCA1, BRCA2, RB1 and CDK12; 113 significant focal DNA copy number aberrations; and promoter methylation events involving 168 genes. Analyses delineated four ovarian cancer transcriptional subtypes, three microRNA subtypes, four promoter methylation subtypes and a transcriptional signature associated with survival duration, and shed new light on the impact that tumours with BRCA1/2 (BRCA1 or BRCA2) and CCNE1 aberrations have on survival. Pathway analyses suggested that homologous recombination is defective in about half of the tumours analysed, and that NOTCH and FOXM1 signalling are involved in serous ovarian cancer pathophysiology., National Institutes of Health (U.S.) (Grant U54HG003067), National Institutes of Health (U.S.) (Grant U54HG003273), National Institutes of Health (U.S.) (Grant U54HG003079), National Institutes of Health (U.S.) (Grant U24CA126543), National Institutes of Health (U.S.) (Grant U24CA126544), National Institutes of Health (U.S.) (Grant U24CA126546), National Institutes of Health (U.S.) (Grant U24CA126551), National Institutes of Health (U.S.) (Grant U24CA126554), National Institutes of Health (U.S.) (Grant U24CA126561), National Institutes of Health (U.S.) (Grant U24CA126563), National Institutes of Health (U.S.) (Grant U24CA143882), National Institutes of Health (U.S.) (Grant U24CA143731), National Institutes of Health (U.S.) (Grant U24CA143835), National Institutes of Health (U.S.) (Grant U24CA143845), National Institutes of Health (U.S.) (Grant U24CA143858), National Institutes of Health (U.S.) (Grant U24CA144025), National Institutes of Health (U.S.) (Grant U24CA143866), National Institutes of Health (U.S.) (Grant U24CA143867), National Institutes of Health (U.S.) (Grant U24CA143848), National Institutes of Health (U.S.) (Grant U24CA143843), National Institutes of Health (U.S.) (Grant R21CA135877)

Published
2010

8. Minimum information specification for in situ hybridization and immunohistochemistry experiments

Author

Deutsch, E.W., Ball, C.A., Berman, J.J., Bova, G.S., Brazma, A., Bumgarner, R.E., Campbell, D., Causton, H.C., Christiansen, J.H., Daian, F., Dauga, D., Davidson, D.R., Gimenez, G., Goo, Y.A., Grimmond, S., Henrich, T., Herrmann, B.G., Johnson, M.H., Korb, M., Mills, J.C., Oudes, A.J., Parkinson, H.E., Pascal, L.E., Pollet, N., Quackenbush, J., Ramialison, M., Ringwald, M., Salgado, David, Sansone, S.A., Sherlock, G., Stoeckert, C.J., Swedlow, J., Taylor, R.C., Walashek, L., Warford, A., Wilkinson, D.G., Zhou, Y., Zon, L.I., Liu, A.Y., True, L.D., Institut de Biologie du Développement de Marseille (IBDM), and Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SDV.BC]Life Sciences [q-bio]/Cellular Biology
Published
2008

9. PortEco: a resource for exploring bacterial biology through high-throughput data and analysis tools

Author

Hu, J.C., primary, Sherlock, G., additional, Siegele, D.A., additional, Aleksander, S.A., additional, Ball, C.A., additional, Demeter, J., additional, Gouni, S., additional, Holland, T.A., additional, Karp, P.D., additional, Lewis, J.E., additional, Liles, N.M., additional, McIntosh, B.K., additional, Mi, H., additional, Muruganujan, A., additional, Wymore, F., additional, and Thomas, P.D., additional

Published
2014
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10. Curation accuracy of model organism databases

Author

Keseler, I. M., primary, Skrzypek, M., additional, Weerasinghe, D., additional, Chen, A. Y., additional, Fulcher, C., additional, Li, G.-W., additional, Lemmer, K. C., additional, Mladinich, K. M., additional, Chow, E. D., additional, Sherlock, G., additional, and Karp, P. D., additional

Published
2014
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11. Evolution of pathogenicity and sexual reproduction in eight Candida genomes

Author

Butler, G, Rasmussen, MD, Lin, MF, Santos, MAS, Sakthikumar, S, Munro, CA, Rheinbay, E, Grabherr, M, Forche, A, Reedy, JL, Agrafioti, I, Arnaud, MB, Bates, S, Brown, AJP, Brunke, S, Costanzo, MC, Fitzpatrick, DA, de Groot, PWJ, Harris, D, Hoyer, LL, Hube, B, Klis, FM, Kodira, C, Lennard, N, Logue, ME, Martin, R, Neiman, AM, Nikolaou, E, Quail, MA, Quinn, J, Santos, MC, Schmitzberger, FF, Sherlock, G, Shah, P, Silverstein, KAT, Skrzypek, MS, Soll, D, Staggs, R, Stansfield, I, Stumpf, MPH, Sudbery, PE, Srikantha, T, Zeng, Q, Berman, J, Berriman, M, Heitman, J, Gow, NAR, Lorenz, MC, Birren, BW, Kellis, M, Cuomo, CA, Butler, G, Rasmussen, MD, Lin, MF, Santos, MAS, Sakthikumar, S, Munro, CA, Rheinbay, E, Grabherr, M, Forche, A, Reedy, JL, Agrafioti, I, Arnaud, MB, Bates, S, Brown, AJP, Brunke, S, Costanzo, MC, Fitzpatrick, DA, de Groot, PWJ, Harris, D, Hoyer, LL, Hube, B, Klis, FM, Kodira, C, Lennard, N, Logue, ME, Martin, R, Neiman, AM, Nikolaou, E, Quail, MA, Quinn, J, Santos, MC, Schmitzberger, FF, Sherlock, G, Shah, P, Silverstein, KAT, Skrzypek, MS, Soll, D, Staggs, R, Stansfield, I, Stumpf, MPH, Sudbery, PE, Srikantha, T, Zeng, Q, Berman, J, Berriman, M, Heitman, J, Gow, NAR, Lorenz, MC, Birren, BW, Kellis, M, and Cuomo, CA

Abstract

Candida species are the most common cause of opportunistic fungal infection worldwide. Here we report the genome sequences of six Candida species and compare these and related pathogens and non-pathogens. There are significant expansions of cell wall, secreted and transporter gene families in pathogenic species, suggesting adaptations associated with virulence. Large genomic tracts are homozygous in three diploid species, possibly resulting from recent recombination events. Surprisingly, key components of the mating and meiosis pathways are missing from several species. These include major differences at the mating-type loci (MTL); Lodderomyces elongisporus lacks MTL, and components of the a1/2 cell identity determinant were lost in other species, raising questions about how mating and cell types are controlled. Analysis of the CUG leucine-to-serine genetic-code change reveals that 99% of ancestral CUG codons were erased and new ones arose elsewhere. Lastly, we revise the Candida albicans gene catalogue, identifying many new genes.

Published
2009

12. The Aspergillus Genome Database (AspGD): recent developments in comprehensive multispecies curation, comparative genomics and community resources

Author

Arnaud, M. B., primary, Cerqueira, G. C., additional, Inglis, D. O., additional, Skrzypek, M. S., additional, Binkley, J., additional, Chibucos, M. C., additional, Crabtree, J., additional, Howarth, C., additional, Orvis, J., additional, Shah, P., additional, Wymore, F., additional, Binkley, G., additional, Miyasato, S. R., additional, Simison, M., additional, Sherlock, G., additional, and Wortman, J. R., additional

Published
2011
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13. The Candida genome database incorporates multiple Candida species: multispecies search and analysis tools with curated gene and protein information for Candida albicans and Candida glabrata

Author

Inglis, D. O., primary, Arnaud, M. B., additional, Binkley, J., additional, Shah, P., additional, Skrzypek, M. S., additional, Wymore, F., additional, Binkley, G., additional, Miyasato, S. R., additional, Simison, M., additional, and Sherlock, G., additional

Published
2011
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15. TB database: an integrated platform for tuberculosis research

Author

Reddy, T. B. K., primary, Riley, R., additional, Wymore, F., additional, Montgomery, P., additional, DeCaprio, D., additional, Engels, R., additional, Gellesch, M., additional, Hubble, J., additional, Jen, D., additional, Jin, H., additional, Koehrsen, M., additional, Larson, L., additional, Mao, M., additional, Nitzberg, M., additional, Sisk, P., additional, Stolte, C., additional, Weiner, B., additional, White, J., additional, Zachariah, Z. K., additional, Sherlock, G., additional, Galagan, J. E., additional, Ball, C. A., additional, and Schoolnik, G. K., additional

Published
2009
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16. Changes to NIH Grant System May Backfire

Author

Karp, P. D., primary, Sherlock, G., additional, Gerlt, J. A., additional, Sim, I., additional, Paulsen, I., additional, Babbitt, P. C., additional, Laderoute, K., additional, Hunter, L., additional, Sternberg, P., additional, Wooley, J., additional, and Bourne, P. E., additional

Published
2008
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17. The Stanford Tissue Microarray Database

Author

Marinelli, R. J., primary, Montgomery, K., additional, Liu, C. L., additional, Shah, N. H., additional, Prapong, W., additional, Nitzberg, M., additional, Zachariah, Z. K., additional, Sherlock, G. J., additional, Natkunam, Y., additional, West, R. B., additional, van de Rijn, M., additional, Brown, P. O., additional, and Ball, C. A., additional

Published
2007
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18. The Stanford Microarray Database: implementation of new analysis tools and open source release of software

Author

Demeter, J., primary, Beauheim, C., additional, Gollub, J., additional, Hernandez-Boussard, T., additional, Jin, H., additional, Maier, D., additional, Matese, J. C., additional, Nitzberg, M., additional, Wymore, F., additional, Zachariah, Z. K., additional, Brown, P. O., additional, Sherlock, G., additional, and Ball, C. A., additional

Published
2007
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23. Using the Saccharomyces Genome Database (SGD) for analysis of protein similarities and structure

Author

Chervitz, S. A., primary, Hester, E. T., additional, Ball, C. A., additional, Dolinski, K., additional, Dwight, S. S., additional, Harris, M. A., additional, Juvik, G., additional, Malekian, A., additional, Roberts, S., additional, Roe, T., additional, Scafe, C., additional, Schroeder, M., additional, Sherlock, G., additional, Weng, S., additional, Zhu, Y., additional, Cherry, J. M., additional, and Botstein, D., additional

Published
1999
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49. Missing value estimation methods for DNA microarrays.

Author

Troyanskaya, O, Cantor, M, Sherlock, G, Brown, P, Hastie, T, Tibshirani, R, Botstein, D, and Altman, R B

Abstract

Gene expression microarray experiments can generate data sets with multiple missing expression values. Unfortunately, many algorithms for gene expression analysis require a complete matrix of gene array values as input. For example, methods such as hierarchical clustering and K-means clustering are not robust to missing data, and may lose effectiveness even with a few missing values. Methods for imputing missing data are needed, therefore, to minimize the effect of incomplete data sets on analyses, and to increase the range of data sets to which these algorithms can be applied. In this report, we investigate automated methods for estimating missing data.

Published
2001
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50. Integrating functional genomic information into the Saccharomyces genome database.

Author

Ball, C A, Dolinski, K, Dwight, S S, Harris, M A, Issel-Tarver, L, Kasarskis, A, Scafe, C R, Sherlock, G, Binkley, G, Jin, H, Kaloper, M, Orr, S D, Schroeder, M, Weng, S, Zhu, Y, Botstein, D, and Cherry, J M

Abstract

The Saccharomyces Genome Database (SGD) stores and organizes information about the nearly 6200 genes in the yeast genome. The information is organized around the 'locus page' and directs users to the detailed information they seek. SGD is endeavoring to integrate the existing information about yeast genes with the large volume of data generated by functional analyses that are beginning to appear in the literature and on web sites. New features will include searches of systematic analyses and Gene Summary Paragraphs that succinctly review the literature for each gene. In addition to current information, such as gene product and phenotype descriptions, the new locus page will also describe a gene product's cellular process, function and localization using a controlled vocabulary developed in collaboration with two other model organism databases. We describe these developments in SGD through the newly reorganized locus page. The SGD is accessible via the WWW at http://genome-www.stanford.edu/Saccharomyces/

Published
2000
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