Simplified ontologies allowing comparison of developmental mammalian gene expression (2007)
Kruger, Adele, Hofmann, Oliver, Carninci, Piero, Hayashizaki, Yoshihide, Hide, Winston
Abstract Model organisms represent an important resource for understanding the fundamental aspects of mammalian biology. Mapping of biological phenomena between model organisms is complex and if it...
Computational selection and prioritization of candidate genes for Fetal Alcohol Syndrome (2007)
Lombard, Zané, Tiffin, Nicki, Hofmann, Oliver, Bajic, Vladimir B, Hide, Winston, Ramsay, Michèle
Abstract Background Fetal alcohol syndrome (FAS) is a serious global health problem and is observed at high frequencies in certain South African communities. Although in utero alcohol exposure is the...
Rapid evolution of cancer/testis genes on the X chromosome (2007)
Stevenson, Brian J, Iseli, Christian, Panji, Sumir, Zahn-Zabal, Monique, Hide, Winston, Old, Lloyd J, ...
Abstract Background Cancer/testis (CT) genes are normally expressed only in germ cells, but can be activated in the cancer state. This unusual property, together with the finding that many CT...
Mice and Men: Their Promoter Properties (2006)
Vladimir B. Bajic, Sin Lam Tan, Alan Christoffels, Christian Schönbach, Leonard Lipovich, Liang Yang, ...
Using the two largest collections of Mus musculus and Homo sapiens transcription start sites (TSSs) determined based on CAGE tags, ditags, full-length cDNAs, and other transcript data, we describe...
Mice and men: Their promoter properties (2006)
Bajic, Vladimir B., Tan, Sin Lam, Christoffels, Alan, Schonbach, Christian, Lilpovich, Leonard, Yang, Liang, ...
Using the two largest collections of Mus musculus and Homo sapiens transcription start sites ( TSSs) determined based on CAGE tags, ditags, full- length cDNAs, and other transcript data, we describe...
CLU: A new algorithm for EST clustering (2005)
Ptitsyn, Andrey, Hide, Winston
Abstract Background The continuous flow of EST data remains one of the richest sources for discoveries in modern biology. The first step in EST data mining is usually associated with EST clustering,...
Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones (2004)
Tadashi Imanishi, Takeshi Itoh, Yutaka Suzuki, Claire O'Donovan, Satoshi Fukuchi, Kanako O. Koyanagi, ...
An international team has systematically validated and annotated just over 21,000 human genes using full-length cDNA, thereby providing a valuable new resource for the human genetics community.
Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones (2004)
Tadashi Imanishi, Takeshi Itoh, Yutaka Suzuki, Claire O'Donovan, Satoshi Fukuchi, Kanako O. Koyanagi, ...
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...
Transcriptome Analysis of Mouse Stem Cells and Early Embryos (2003)
Alexei A. Sharov, Yulan Piao, Ryo Matoba, Dawood B. Dudekula, Yong Qian, Vincent VanBuren, ...
250,000 EST sequences from oocytes, blastocysts, and embryonic and adult stem cells contribute to the annotation of the mouse genome and suggest genes that contribute to the unique features of these...
Transcriptome Analysis of Mouse Stem Cells and Early Embryos (2003)
Alexei A. Sharov, Yulan Piao, Ryo Matoba, Dawood B. Dudekula, Yong Qian, Vincent VanBuren, ...
Understanding and harnessing cellular potency are fundamental in biology and are also critical to the future therapeutic use of stem cells. Transcriptome analysis of these pluripotent cells is a...
New methods for finding disease-susceptibility genes: impact and potential (2003)
McCarthy, Mark I, Smedley, Damian, Hide, Winston
Abstract Improved techniques for defining disease-gene location and evaluating the biological candidacy of regional transcripts will hasten disease-gene discovery.
Gey Van Pittius, Nico C, Gamieldien, Junaid, Hide, Winston, Brown, Gordon D, Siezen, Roland J, Beyers, Albert D
Abstract Background The genome of Mycobacterium tuberculosis H37Rv has five copies of a cluster of genes known as the ESAT-6 loci. These clusters contain members of the CFP-10 ( lhp ) and ESAT-6 (...
Introduction Single Nucleotide Polymorphisms (SNPs) in virtual expressed gene fragment alignments represent a potentially significant resource for both the detection of non-coding and coding,...
A Statistical Model for Prokaryotic Promoter Prediction (1998)
Introduction A simple, fast and sensitive model for identifying and predicting sequences which have non-random statistical properties and therefore biologically active, such as promoters has been...
Junaid Gamieldien, Winston Hide
Introduction Positive selection is very important for the evolution of a new or improved protein function, as it increases the probability that an advantageous mutation becomes established in a...
A Statistical Model for Prokaryotic Promoter Prediction (1998)
Introduction A simple, fast and sensitive model for identifying and predicting sequences which have non-random statistical properties and therefore biologically active, such as promoters has been...
Junaid Gamieldien, Winston Hide
Introduction Positive selection is very important for the evolution of a new or improved protein function, as it increases the probability that an advantageous mutation becomes established in a...
Introduction Single Nucleotide Polymorphisms (SNPs) in virtual expressed gene fragment alignments represent a potentially significant resource for both the detection of non-coding and coding,...
STACK: Sequence Tag Alignment and Consensus Knowledgebase
Christoffels, Alan, Gelder, Antoine Van, Greyling, Gary, Miller, Robert, Hide, Tania, Hide, Winston
STACK is a tool for detection and visualisation of expressed transcript variation in the context of developmental and pathological states. The datasystem organises and reconstructs human transcripts...
The ESAT-6 gene cluster of Mycobacterium tuberculosis and other high G+C Gram-positive bacteria
Gey Van Pittius, Nico C, Gamieldien, Junaid, Hide, Winston, Brown, Gordon D, Siezen, Roland J, Beyers, Albert D
Assembly, Verification, and Initial Annotation of the NIA Mouse 7.4K cDNA Clone Set
VanBuren, Vincent, Piao, Yulan, Dudekula, Dawood B., Qian, Yong, Carter, Mark G., Martin, Patrick R., ...
A set of 7407 cDNA clones (NIA mouse 7.4K) was assembled from >20 cDNA libraries constructed mainly from early mouse embryos, including several stem cell libraries. The clone set was assembled from...
Brentani, Helena, Caballero, Otávia L., Camargo, Anamaria A., Da Silva, Aline M., Da Silva, Wilson Araújo, Neto, Emmanuel Dias, ...
Whereas genome sequencing defines the genetic potential of an organism, transcript sequencing defines the utilization of this potential and links the genome with most areas of biology. To exploit the...
Transcriptome Analysis of Mouse Stem Cells and Early Embryos
Sharov, Alexei A, Piao, Yulan, Matoba, Ryo, Dudekula, Dawood B, Qian, Yong, VanBuren, Vincent, ...
Understanding and harnessing cellular potency are fundamental in biology and are also critical to the future therapeutic use of stem cells. Transcriptome analysis of these pluripotent cells is a...
Alternative Gene Form Discovery and Candidate Gene Selection from Gene Indexing Projects
Burke, John, Wang, Hui, Hide, Winston, Davison, Daniel B.
Several efforts are under way to partition single-read expressed sequence tag (EST), as well as full-length transcript data, into large-scale gene indices, where transcripts are in common index...
d2_cluster: A Validated Method for Clustering EST and Full-Length cDNA Sequences
Burke, John, Davison, Dan, Hide, Winston
Several efforts are under way to condense single-read expressed sequence tags (ESTs) and full-length transcript data on a large scale by means of clustering or assembly. One goal of these projects is...
New methods for finding disease-susceptibility genes: impact and potential
McCarthy, Mark I, Smedley, Damian, Hide, Winston
Improved techniques for defining disease-gene location and evaluating the biological candidacy of regional transcripts will hasten disease-gene discovery.
Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones
Imanishi, Tadashi, Itoh, Takeshi, Suzuki, Yutaka, O'Donovan, Claire, Fukuchi, Satoshi, Koyanagi, Kanako O, ...
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...
eVOC: A Controlled Vocabulary for Unifying Gene Expression Data
Kelso, Janet, Visagie, Johann, Theiler, Gregory, Christoffels, Alan, Bardien, Soraya, Smedley, Damian, ...
Expression data contribute significantly to the biological value of the sequenced human genome,providing extensive information about gene structure and the pattern of gene expression. ESTs,together...
Tanino, Motohiko, Debily, Marie-Anne, Tamura, Takuro, Hishiki, Teruyoshi, Ogasawara, Osamu, Murakawa, Katsuji, ...
The Human Anatomic Gene Expression Library (H-ANGEL) is a resource for information concerning the anatomical distribution and expression of human gene transcripts. The tool contains protein...
Mehrle, Alexander, Rosenfelder, Heiko, Schupp, Ingo, Del Val, Coral, Arlt, Dorit, Hahne, Florian, ...
LIFEdb () integrates data from large-scale functional genomics assays and manual cDNA annotation with bioinformatics gene expression and protein analysis. New features of LIFEdb include (i) an...
Mice and Men: Their Promoter Properties
Bajic, Vladimir B, Tan, Sin Lam, Christoffels, Alan, Schönbach, Christian, Lipovich, Leonard, Yang, Liang, ...
Using the two largest collections of Mus musculus and Homo sapiens transcription start sites (TSSs) determined based on CAGE tags, ditags, full-length cDNAs, and other transcript data, we describe...
Tiffin, Nicki, Adie, Euan, Turner, Frances, Brunner, Han G., Van Driel, Marc A., Oti, Martin, ...
Genome-wide experimental methods to identify disease genes, such as linkage analysis and association studies, generate increasingly large candidate gene sets for which comprehensive empirical...
STACK: Sequence Tag Alignment and Consensus Knowledgebase
Christoffels, Alan, Gelder, Antoine Van, Greyling, Gary, Miller, Robert, Hide, Tania, Hide, Winston
STACK is a tool for detection and visualisation of expressed transcript variation in the context of developmental and pathological states. The datasystem organises and reconstructs human transcripts...
The ESAT-6 gene cluster of Mycobacterium tuberculosis and other high G+C Gram-positive bacteria
Gey Van Pittius, Nico C, Gamieldien, Junaid, Hide, Winston, Brown, Gordon D, Siezen, Roland J, Beyers, Albert D
Assembly, Verification, and Initial Annotation of the NIA Mouse 7.4K cDNA Clone Set
VanBuren, Vincent, Piao, Yulan, Dudekula, Dawood B., Qian, Yong, Carter, Mark G., Martin, Patrick R., ...
A set of 7407 cDNA clones (NIA mouse 7.4K) was assembled from >20 cDNA libraries constructed mainly from early mouse embryos, including several stem cell libraries. The clone set was assembled from...
Brentani, Helena, Caballero, Otávia L., Camargo, Anamaria A., Da Silva, Aline M., Da Silva, Wilson Araújo, Neto, Emmanuel Dias, ...
Whereas genome sequencing defines the genetic potential of an organism, transcript sequencing defines the utilization of this potential and links the genome with most areas of biology. To exploit the...
Transcriptome Analysis of Mouse Stem Cells and Early Embryos
Sharov, Alexei A, Piao, Yulan, Matoba, Ryo, Dudekula, Dawood B, Qian, Yong, VanBuren, Vincent, ...
Understanding and harnessing cellular potency are fundamental in biology and are also critical to the future therapeutic use of stem cells. Transcriptome analysis of these pluripotent cells is a...
Alternative Gene Form Discovery and Candidate Gene Selection from Gene Indexing Projects
Burke, John, Wang, Hui, Hide, Winston, Davison, Daniel B.
Several efforts are under way to partition single-read expressed sequence tag (EST), as well as full-length transcript data, into large-scale gene indices, where transcripts are in common index...
d2_cluster: A Validated Method for Clustering EST and Full-Length cDNA Sequences
Burke, John, Davison, Dan, Hide, Winston
Several efforts are under way to condense single-read expressed sequence tags (ESTs) and full-length transcript data on a large scale by means of clustering or assembly. One goal of these projects is...
New methods for finding disease-susceptibility genes: impact and potential
McCarthy, Mark I, Smedley, Damian, Hide, Winston
Improved techniques for defining disease-gene location and evaluating the biological candidacy of regional transcripts will hasten disease-gene discovery.
Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones
Imanishi, Tadashi, Itoh, Takeshi, Suzuki, Yutaka, O'Donovan, Claire, Fukuchi, Satoshi, Koyanagi, Kanako O, ...
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...
eVOC: A Controlled Vocabulary for Unifying Gene Expression Data
Kelso, Janet, Visagie, Johann, Theiler, Gregory, Christoffels, Alan, Bardien, Soraya, Smedley, Damian, ...
Expression data contribute significantly to the biological value of the sequenced human genome,providing extensive information about gene structure and the pattern of gene expression. ESTs,together...
Tanino, Motohiko, Debily, Marie-Anne, Tamura, Takuro, Hishiki, Teruyoshi, Ogasawara, Osamu, Murakawa, Katsuji, ...
The Human Anatomic Gene Expression Library (H-ANGEL) is a resource for information concerning the anatomical distribution and expression of human gene transcripts. The tool contains protein...
Mehrle, Alexander, Rosenfelder, Heiko, Schupp, Ingo, Del Val, Coral, Arlt, Dorit, Hahne, Florian, ...
LIFEdb () integrates data from large-scale functional genomics assays and manual cDNA annotation with bioinformatics gene expression and protein analysis. New features of LIFEdb include (i) an...
Mice and Men: Their Promoter Properties
Bajic, Vladimir B, Tan, Sin Lam, Christoffels, Alan, Schönbach, Christian, Lipovich, Leonard, Yang, Liang, ...
Using the two largest collections of Mus musculus and Homo sapiens transcription start sites (TSSs) determined based on CAGE tags, ditags, full-length cDNAs, and other transcript data, we describe...
Tiffin, Nicki, Adie, Euan, Turner, Frances, Brunner, Han G., Van Driel, Marc A., Oti, Martin, ...
Genome-wide experimental methods to identify disease genes, such as linkage analysis and association studies, generate increasingly large candidate gene sets for which comprehensive empirical...
Rapid evolution of cancer/testis genes on the X chromosome
Stevenson, Brian J, Iseli, Christian, Panji, Sumir, Zahn-Zabal, Monique, Hide, Winston, Old, Lloyd J, ...
Computational selection and prioritization of candidate genes for Fetal Alcohol Syndrome
Lombard, Zané, Tiffin, Nicki, Hofmann, Oliver, Bajic, Vladimir B, Hide, Winston, Ramsay, Michèle
Simplified ontologies allowing comparison of developmental mammalian gene expression
Kruger, Adele, Hofmann, Oliver, Carninci, Piero, Hayashizaki, Yoshihide, Hide, Winston
The Developmental eVOC ontologies presented are simplified orthogonal ontologies describing the temporal and spatial distribution of developmental human and mouse anatomy.
Chopera, Denis R., Woodman, Zenda, Mlisana, Koleka, Mlotshwa, Mandla, Martin, Darren P., Seoighe, Cathal, ...
One of the most important genetic factors known to affect the rate of disease progression in HIV-infected individuals is the genotype at the Class I Human Leukocyte Antigen (HLA) locus, which...
Schwegmann, Anita, Guler, Reto, Cutler, Antony J., Arendse, Berenice, Horsnell, William G. C., Flemming, Alexandra, ...
Activation of macrophages and subsequent “killing” effector functions against infectious pathogens are essential for the establishment of protective immunity. NF-IL6 is a transcription factor...