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2. Integrative annotation of 21,037 human genes validated by full-length cDNA clones

Author

Imanishi, Tadashi, Itoh, Takeshi, Suzuki, Yutaka, O'Donovan, Claire, Fukuchi, Satoshi, Koyanagi Kanako, O., Barrero Roberto, A., Tamura, Takuro, Yamaguchi-Kabata, Yumi, Tanino, Motohiko, Yura, Kei, Miyazaki, Satoru, Ikeo, Kazuho, Homma, Keiichi, Kasprzyk, Arek, Nishikawa, Tetsuo, Hirakawa, Mika, Thierry-Mieg, Jean, Thierry-Mieg, Danielle, Ashurst, Jennifer, Jia, Libin, Nakao, Mitsuteru, Thomas, Michael, A., Mulder, Nicola, Karavidopoulou, Youla, Jin, Lihua, Kim, Sangsoo, Yasuda, Tomohiro, Lenhard, Boris, Eveno, Eric, Suzuki, Yoshiyuki, Takeda, Jun-Ichi, Gough, Craig, Hilton, Phillip, Fujii, Yasuyuki, Sakai, Hiroaki, Tanaka, Susumu, Amid, Clara, Bellgard, Matthew, de Fatima Bonaldo, Maria, Bono, Hidemasa, Bromberg Susan, K., Brookes Anthony, J., Bruford, Elspeth, Carninci, Piero, Chelala, Claude, Couillault, Christine, de Souza Sandro, J., Debily, Marie-Anne, Devignes, Marie-Dominique, Dubchak, Inna, Endo, Toshinori, Estreicher, Anne, Eyras, Eduardo, Fukami-Kobayashi, Kaoru, Gopinath Gopal, R., Graudens, Esther, Hahn, Yoonsoo, Han, Ze-Guang, Han, Michael, Hanada, Kousuke, Hanaoka, Hideki, Harada, Erimi, Hashimoto, Katsuyuki, Yamasaki, Chisato, Hinz, Ursula, Hirai, Momoki, Hishiki, Teruyoshi, Hopkinson, Ian, Imbeaud, Sandrine, Inoko, Hidetoshi, Kanapin, Alexander, Kaneko, Yayoi, Kasukawa, Takeya, Kelso, Janet, Kersey, Paul, Kikuno, Reiko, Kimura, Kouichi, Korn, Bernhard, Kuryshev, Vladimir, Makalowska, Izabela, Makino, Takashi, Mano, Shuhei, Mariage-Samson, Regine, Mashima, Jun, Matsuda, Hideo, Mewes, Hans-Werner, Minoshima, Shinsei, Nagai, Keiichi, Nagasaki, Hideki, Nagata, Naoki, Nigam, Rajni, Ogasawara, Osamu, Ohara, Osamu, Ohtsubo, Masafumi, Okada, Norihiro, Okido, Toshihisa, Oota, Satoshi, Ota, Motonori, Ota, Toshio, Otsuki, Tetsuji, Piatier-Tonneau, Dominique, Poustka, Annemarie, Ren, Shuang-Xi, Saitou, Naruya, Sakai, Katsunaga, Sakamoto, Shigetaka, Sakate, Ryuichi, Schupp, Ingo, Servant, Florence, Sherry, Stephen, Shiba, Rie, Sugano, Sumio, Knowledge representation, reasonning (ORPAILLEUR), INRIA Lorraine, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique de Lorraine (INPL)-Université Nancy 2-Université Henri Poincaré - Nancy 1 (UHP)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique de Lorraine (INPL)-Université Nancy 2-Université Henri Poincaré - Nancy 1 (UHP), Genexpress, Centre National de la Recherche Scientifique (CNRS), The University of Tokyo (UTokyo), and Institut National de Recherche en Informatique et en Automatique (Inria)-Université Henri Poincaré - Nancy 1 (UHP)-Université Nancy 2-Institut National Polytechnique de Lorraine (INPL)-Centre National de la Recherche Scientifique (CNRS)-Université Henri Poincaré - Nancy 1 (UHP)-Université Nancy 2-Institut National Polytechnique de Lorraine (INPL)-Centre National de la Recherche Scientifique (CNRS)

Subjects
human transcriptome, annotation, [INFO.INFO-OH]Computer Science [cs]/Other [cs.OH], full-length cdna, transcriptome humain, cdna complet
Abstract

publication en ligne. Article dans revue scientifique avec comité de lecture. nationale.; National audience; The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this area is still limited. Several lines of investigation have been used to elucidate the structure and function of the genes in the human genome. Even so, gene prediction remains a difficult task, as the varieties of transcripts of a gene may vary to a great extent. We thus performed an exhaustive integrative characterization of 41,118 full-length cDNAs that capture the gene transcripts as complete functional cassettes, providing an unequivocal report of structural and functional diversity at the gene level. Our international collaboration has validated 21,037 human gene candidates by analysis of high-quality full-length cDNA clones through curation using unified criteria. This led to the identification of 5,155 new gene candidates. It also manifested the most reliable way to control the quality of the cDNA clones. We have developed a human gene database, called the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/). It provides the following: integrative annotation of human genes, description of gene structures, details of novel alternative splicing isoforms, non-protein-coding RNAs, functional domains, subcellular localizations, metabolic pathways, predictions of protein three-dimensional structure, mapping of known single nucleotide polymorphisms (SNPs), identification of polymorphic microsatellite repeats within human genes, and comparative results with mouse full-length cDNAs. The H-InvDB analysis has shown that up to 4% of the human genome sequence (National Center for Biotechnology Information build 34 assembly) may contain misassembled or missing regions. We found that 6.5% of the human gene candidates (1,377 loci) did not have a good protein-coding open reading frame, of which 296 loci are strong candidates for non-protein-coding RNA genes. In addition, among 72,027 uniquely mapped SNPs and insertions/deletions localized within human genes, 13,215 nonsynonymous SNPs, 315 nonsense SNPs, and 452 indels occurred in coding regions. Together with 25 polymorphic microsatellite repeats present in coding regions, they may alter protein structure, causing phenotypic effects or resulting in disease. The H-InvDB platform represents a substantial contribution to resources needed for the exploration of human biology and pathology.

Published
2004

3. Integrative annotation of 21,037 human genes validated by full-length cDNA clones

Author

Richard Roberts, Imanishi, Tadashi, Itoh, Takeshi, Suzuki, Yutaka, O'Donovan, Claire, Fukuchi, Satoshi, Koyanagi, Kanako O, Barrero, Roberto A, Tamura, Takuro, Yamaguchi-Kabata, Yumi, Tanino, Motohiko, Yura, Kei, Miyazaki, Satoru, Ikeo, Kazuho, Homma, Keiichi, Kasprzyk, Arek, Nishikawa, Tetsuo, Hirakawa, Mika, Thierry-Mieg, Jean, Thierry-Mieg, Danielle, Ashurst, Jennifer, Jia, Libin, Nakao, Mitsuteru, Thomas, Michael A, Mulder, Nicola, Karavidopoulou, Youla, Jin, Lihua, Kim, Sangsoo, Yasuda, Tomohiro, Lenhard, Boris, Eveno, Eric, Suzuki, Yoshiyuki, Yamasaki, Chisato, Takeda, Jun-ichi, Gough, Craig, Hilton, Phillip, Fujii, Yasuyuki, Sakai, Hiroaki, Tanaka, Susumu, Amid, Clara, Bellgard, Matthew, Bonaldo, Maria de Fatima, Bono, Hidemasa, Bromberg, Susan K, Brookes, Anthony J, Bruford, Elspeth, Carninci, Piero, Chelala, Claude, Couillault, Christine, Souza, Sandro J. de, Debily, Marie-Anne, Devignes, Marie-Dominique, Dubchak, Inna, Endo, Toshinori, Estreicher, Anne, Eyras, Eduardo, Fukami-Kobayashi, Kaoru, R. Gopinath, Gopal, Graudens, Esther, Hahn, Yoonsoo, Han, Michael, Han, Ze-Guang, Hanada, Kousuke, Hanaoka, Hideki, Harada, Erimi, Hashimoto, Katsuyuki, Hinz, Ursula, Hirai, Momoki, Hishiki, Teruyoshi, Hopkinson, Ian, Imbeaud, Sandrine, Inoko, Hidetoshi, Kanapin, Alexander, Kaneko, Yayoi, Kasukawa, Takeya, Kelso, Janet, Kersey, Paul, Kikuno, Reiko, Kimura, Kouichi, Korn, Bernhard, Kuryshev, Vladimir, Makalowska, Izabela, Makino, Takashi, Mano, Shuhei, Mariage-Samson, Regine, Mashima, Jun, Matsuda, Hideo, Mewes, Hans-Werner, Minoshima, Shinsei, Nagai, Keiichi, Nagasaki, Hideki, Nagata, Naoki, Nigam, Rajni, Ogasawara, Osamu, Ohara, Osamu, Ohtsubo, Masafumi, Okada, Norihiro, Okido, Toshihisa, Oota, Satoshi, Ota, Motonori, Ota, Toshio, Otsuki, Tetsuji, Piatier-Tonneau, Dominique, Poustka, Annemarie, Ren, Shuang-Xi, Saitou, Naruya, Sakai, Katsunaga, Sakamoto, Shigetaka, Sakate, Ryuichi, Schupp, Ingo, Servant, Florence, Sherry, Stephen, Shiba, Rie, Shimizu, Nobuyoshi, Shimoyama, Mary, Simpson, Andrew J, Soares, Bento, Steward, Charles, Suwa, Makiko, Suzuki, Mami, Takahashi, Aiko, Tamiya, Gen, Tanaka, Hiroshi, Taylor, Todd, Terwilliger, Joseph D, Unneberg, Per, Veeramachaneni, Vamsi, Watanabe, Shinya, Wilming, Laurens, Yasuda, Norikazu, Yoo, Hyang-Sook, Stodolsky, Marvin, Makalowski, Wojciech, Go, Mitiko, Nakai, Kenta, Takagi, Toshihisa, Kanehisa, Minoru, Sakaki, Yoshiyuki, Quackenbush, John, Okazaki, Yasushi, Hayashizaki, Yoshihide, Hide, Winston, Chakraborty, Ranajit, Nishikawa, Ken, Sugawara, Hideaki, Tateno, Yoshio, Chen, Zhu, Oishi, Michio, Tonellato, Peter, Apweiler, Rolf, Okubo, Kousaku, Wagner, Lukas, Wiemann, Stefan, Strausberg, Robert L, Isogai, Takao, Auffray, Charles, Nomura, Nobuo, Gojobori, Takashi, Sugano, Sumio, Richard Roberts, Imanishi, Tadashi, Itoh, Takeshi, Suzuki, Yutaka, O'Donovan, Claire, Fukuchi, Satoshi, Koyanagi, Kanako O, Barrero, Roberto A, Tamura, Takuro, Yamaguchi-Kabata, Yumi, Tanino, Motohiko, Yura, Kei, Miyazaki, Satoru, Ikeo, Kazuho, Homma, Keiichi, Kasprzyk, Arek, Nishikawa, Tetsuo, Hirakawa, Mika, Thierry-Mieg, Jean, Thierry-Mieg, Danielle, Ashurst, Jennifer, Jia, Libin, Nakao, Mitsuteru, Thomas, Michael A, Mulder, Nicola, Karavidopoulou, Youla, Jin, Lihua, Kim, Sangsoo, Yasuda, Tomohiro, Lenhard, Boris, Eveno, Eric, Suzuki, Yoshiyuki, Yamasaki, Chisato, Takeda, Jun-ichi, Gough, Craig, Hilton, Phillip, Fujii, Yasuyuki, Sakai, Hiroaki, Tanaka, Susumu, Amid, Clara, Bellgard, Matthew, Bonaldo, Maria de Fatima, Bono, Hidemasa, Bromberg, Susan K, Brookes, Anthony J, Bruford, Elspeth, Carninci, Piero, Chelala, Claude, Couillault, Christine, Souza, Sandro J. de, Debily, Marie-Anne, Devignes, Marie-Dominique, Dubchak, Inna, Endo, Toshinori, Estreicher, Anne, Eyras, Eduardo, Fukami-Kobayashi, Kaoru, R. Gopinath, Gopal, Graudens, Esther, Hahn, Yoonsoo, Han, Michael, Han, Ze-Guang, Hanada, Kousuke, Hanaoka, Hideki, Harada, Erimi, Hashimoto, Katsuyuki, Hinz, Ursula, Hirai, Momoki, Hishiki, Teruyoshi, Hopkinson, Ian, Imbeaud, Sandrine, Inoko, Hidetoshi, Kanapin, Alexander, Kaneko, Yayoi, Kasukawa, Takeya, Kelso, Janet, Kersey, Paul, Kikuno, Reiko, Kimura, Kouichi, Korn, Bernhard, Kuryshev, Vladimir, Makalowska, Izabela, Makino, Takashi, Mano, Shuhei, Mariage-Samson, Regine, Mashima, Jun, Matsuda, Hideo, Mewes, Hans-Werner, Minoshima, Shinsei, Nagai, Keiichi, Nagasaki, Hideki, Nagata, Naoki, Nigam, Rajni, Ogasawara, Osamu, Ohara, Osamu, Ohtsubo, Masafumi, Okada, Norihiro, Okido, Toshihisa, Oota, Satoshi, Ota, Motonori, Ota, Toshio, Otsuki, Tetsuji, Piatier-Tonneau, Dominique, Poustka, Annemarie, Ren, Shuang-Xi, Saitou, Naruya, Sakai, Katsunaga, Sakamoto, Shigetaka, Sakate, Ryuichi, Schupp, Ingo, Servant, Florence, Sherry, Stephen, Shiba, Rie, Shimizu, Nobuyoshi, Shimoyama, Mary, Simpson, Andrew J, Soares, Bento, Steward, Charles, Suwa, Makiko, Suzuki, Mami, Takahashi, Aiko, Tamiya, Gen, Tanaka, Hiroshi, Taylor, Todd, Terwilliger, Joseph D, Unneberg, Per, Veeramachaneni, Vamsi, Watanabe, Shinya, Wilming, Laurens, Yasuda, Norikazu, Yoo, Hyang-Sook, Stodolsky, Marvin, Makalowski, Wojciech, Go, Mitiko, Nakai, Kenta, Takagi, Toshihisa, Kanehisa, Minoru, Sakaki, Yoshiyuki, Quackenbush, John, Okazaki, Yasushi, Hayashizaki, Yoshihide, Hide, Winston, Chakraborty, Ranajit, Nishikawa, Ken, Sugawara, Hideaki, Tateno, Yoshio, Chen, Zhu, Oishi, Michio, Tonellato, Peter, Apweiler, Rolf, Okubo, Kousaku, Wagner, Lukas, Wiemann, Stefan, Strausberg, Robert L, Isogai, Takao, Auffray, Charles, Nomura, Nobuo, Gojobori, Takashi, and Sugano, Sumio

Abstract

The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this area is still limited. Several lines of investigation have been used to elucidate the structure and function of the genes in the human genome. Even so, gene prediction remains a difficult task, as the varieties of transcripts of a gene may vary to a great extent. We thus performed an exhaustive integrative characterization of 41,118 full-length cDNAs that capture the gene transcripts as complete functional cassettes, providing an unequivocal report of structural and functional diversity at the gene level. Our international collaboration has validated 21,037 human gene candidates by analysis of high-quality full-length cDNA clones through curation using unified criteria. This led to the identification of 5,155 new gene candidates. It also manifested the most reliable way to control the quality of the cDNA clones. We have developed a human gene database, called the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/). It provides the following: integrative annotation of human genes, description of gene structures, details of novel alternative splicing isoforms, non-protein-coding RNAs, functional domains, subcellular localizations, metabolic pathways, predictions of protein three-dimensional structure, mapping of known single nucleotide polymorphisms (SNPs), identification of polymorphic microsatellite repeats within human genes, and comparative results with mouse full-length cDNAs. The H-InvDB analysis has shown that up to 4% of the human genome sequence (National Center for Biotechnology Information build 34 assembly) may contain misassembled or missing regions. We found that 6.5% of the human gene candidates (1,377 loci) did not have a good protein-coding open reading frame, of which 296 loci are strong candidates for non-protein-coding RNA genes. In addition

Published
2004

6. ISOLATION AND PARTIAL CHARACTERIZATION OF NITRATE ASSIMILATION MUTANTS OF DUNALIELLA TERTIOLECTA (CHLOROPHYCEAE).

Author

Latorella, A. Henry, Bromberg, Susan K., Lieber, Kent, and Robinson, James

Subjects
*GREEN algae, *DUNALIELLA, *NITRATES, *CHLORATES
Abstract

Fifteen nitrate assimilation-deficient mutants of the euryhaline green algae, Dunaliella tertiolecta Butcher were selected by their chlorate resistance. Ten mutants, unable to grow on either NO[SUB3][SUP-1] but able to grow on NO[SUB2][SUP-1], had no detectable nitrate reductase activity. Five mutants, unable to grow on either NO[SUB3][SUP-1]or NO[SUB2][SUP-1], had depressed levels of both nitrate reductase. A method for assaying methyl viologen-nitrate reductase in the presence of nitrite reductase is described. [ABSTRACT FROM AUTHOR]

Published
1981
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10. Exploring phenotypic data at the rat genome database.

Author

Twigger SN, S Smith J, Zuniga-Meyer A, and Bromberg SK

Subjects
Animals, Computer Graphics, Rats, Chromosome Mapping methods, Database Management Systems, Databases, Genetic, Information Storage and Retrieval methods, Phenotype, User-Computer Interface
Abstract

The laboratory rat, Rattus norvegicus, is an important model of human health and disease, and experimental findings in the rat have direct relevance to human-based research. The Rat Genome Database (RGD, http://rgd.mcw.edu) is a model-organism database that provides access to wide variety of curated rat data such as genes and their homologs, quantitative trait loci, phenotypes, comparative mapping, and genome analysis. We present an overview of the database followed by specific examples that can be used to gain experience in employing RGD to explore the wealth of functional data available for the rat. We show how to make associations with the genome and use comparative tools to link the rat with human and mouse in order to integrate results from these three species of critical biomedical importance.

Published
2006
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11. Integrative annotation of 21,037 human genes validated by full-length cDNA clones.

Author

Imanishi T, Itoh T, Suzuki Y, O'Donovan C, Fukuchi S, Koyanagi KO, Barrero RA, Tamura T, Yamaguchi-Kabata Y, Tanino M, Yura K, Miyazaki S, Ikeo K, Homma K, Kasprzyk A, Nishikawa T, Hirakawa M, Thierry-Mieg J, Thierry-Mieg D, Ashurst J, Jia L, Nakao M, Thomas MA, Mulder N, Karavidopoulou Y, Jin L, Kim S, Yasuda T, Lenhard B, Eveno E, Suzuki Y, Yamasaki C, Takeda J, Gough C, Hilton P, Fujii Y, Sakai H, Tanaka S, Amid C, Bellgard M, Bonaldo Mde F, Bono H, Bromberg SK, Brookes AJ, Bruford E, Carninci P, Chelala C, Couillault C, de Souza SJ, Debily MA, Devignes MD, Dubchak I, Endo T, Estreicher A, Eyras E, Fukami-Kobayashi K, Gopinath GR, Graudens E, Hahn Y, Han M, Han ZG, Hanada K, Hanaoka H, Harada E, Hashimoto K, Hinz U, Hirai M, Hishiki T, Hopkinson I, Imbeaud S, Inoko H, Kanapin A, Kaneko Y, Kasukawa T, Kelso J, Kersey P, Kikuno R, Kimura K, Korn B, Kuryshev V, Makalowska I, Makino T, Mano S, Mariage-Samson R, Mashima J, Matsuda H, Mewes HW, Minoshima S, Nagai K, Nagasaki H, Nagata N, Nigam R, Ogasawara O, Ohara O, Ohtsubo M, Okada N, Okido T, Oota S, Ota M, Ota T, Otsuki T, Piatier-Tonneau D, Poustka A, Ren SX, Saitou N, Sakai K, Sakamoto S, Sakate R, Schupp I, Servant F, Sherry S, Shiba R, Shimizu N, Shimoyama M, Simpson AJ, Soares B, Steward C, Suwa M, Suzuki M, Takahashi A, Tamiya G, Tanaka H, Taylor T, Terwilliger JD, Unneberg P, Veeramachaneni V, Watanabe S, Wilming L, Yasuda N, Yoo HS, Stodolsky M, Makalowski W, Go M, Nakai K, Takagi T, Kanehisa M, Sakaki Y, Quackenbush J, Okazaki Y, Hayashizaki Y, Hide W, Chakraborty R, Nishikawa K, Sugawara H, Tateno Y, Chen Z, Oishi M, Tonellato P, Apweiler R, Okubo K, Wagner L, Wiemann S, Strausberg RL, Isogai T, Auffray C, Nomura N, Gojobori T, and Sugano S

Subjects
Alternative Splicing genetics, Genes genetics, Humans, Internet, Microsatellite Repeats genetics, Open Reading Frames genetics, Polymorphism, Genetic, Polymorphism, Single Nucleotide, Protein Structure, Tertiary, Computational Biology methods, DNA, Complementary genetics, Databases, Genetic, Genes physiology, Genome, Human
Abstract

The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this area is still limited. Several lines of investigation have been used to elucidate the structure and function of the genes in the human genome. Even so, gene prediction remains a difficult task, as the varieties of transcripts of a gene may vary to a great extent. We thus performed an exhaustive integrative characterization of 41,118 full-length cDNAs that capture the gene transcripts as complete functional cassettes, providing an unequivocal report of structural and functional diversity at the gene level. Our international collaboration has validated 21,037 human gene candidates by analysis of high-quality full-length cDNA clones through curation using unified criteria. This led to the identification of 5,155 new gene candidates. It also manifested the most reliable way to control the quality of the cDNA clones. We have developed a human gene database, called the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/). It provides the following: integrative annotation of human genes, description of gene structures, details of novel alternative splicing isoforms, non-protein-coding RNAs, functional domains, subcellular localizations, metabolic pathways, predictions of protein three-dimensional structure, mapping of known single nucleotide polymorphisms (SNPs), identification of polymorphic microsatellite repeats within human genes, and comparative results with mouse full-length cDNAs. The H-InvDB analysis has shown that up to 4% of the human genome sequence (National Center for Biotechnology Information build 34 assembly) may contain misassembled or missing regions. We found that 6.5% of the human gene candidates (1,377 loci) did not have a good protein-coding open reading frame, of which 296 loci are strong candidates for non-protein-coding RNA genes. In addition, among 72,027 uniquely mapped SNPs and insertions/deletions localized within human genes, 13,215 nonsynonymous SNPs, 315 nonsense SNPs, and 452 indels occurred in coding regions. Together with 25 polymorphic microsatellite repeats present in coding regions, they may alter protein structure, causing phenotypic effects or resulting in disease. The H-InvDB platform represents a substantial contribution to resources needed for the exploration of human biology and pathology., Competing Interests: The authors have declared that no conflicts of interest exist.

Published
2004
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