Evaluation of next generation sequencing platforms for population targeted sequencing studies (2009)
Harismendy, Olivier, Ng, Pauline C, Strausberg, Robert L, Wang, Xiaoyun, Stockwell, Timothy B, Beeson, Karen Y, ...
Abstract Background Next generation sequencing (NGS) platforms are currently being utilized for targeted sequencing of candidate genes or genomic intervals to perform sequence-based association...
The HuRef Browser: a web resource for individual human genomics (2009)
Axelrod, Nelson, Lin, Yuan, Ng, Pauline C., Stockwell, Timothy B., Crabtree, Jonathan, Huang, Jiaqi, ...
The HuRef Genome Browser is a web application for the navigation and analysis of the previously published genome of a human individual, termed HuRef. The browser provides a comparative view between...
The diploid genome sequence of an individual human (2008)
Samuel Levy, Granger Sutton, Pauline C. Ng, Lars Feuk, Aaron L. Halpern, Brian P. Walenz, ...
Presented here is a genome sequence of an individual human. It was produced from;32 million random DNA fragments, sequenced by Sanger dideoxy technology and assembled into 4,528 scaffolds, comprising...
The diploid genome sequence of an individual human (2008)
Samuel Levy, Granger Sutton, Pauline C. Ng, Lars Feuk, Aaron L. Halpern, Brian P. Walenz, ...
Presented here is a genome sequence of an individual human. It was produced from;32 million random DNA fragments, sequenced by Sanger dideoxy technology and assembled into 4,528 scaffolds, comprising...
Advances in Brief A Public Database for Gene Expression in Human Cancers 1 (2007)
Anita Lal, Alex E. Lash, Stephen F. Altschul, Victor Velculescu, Lin Zhang, Roger E. Mclendon, ...
A public database, SAGEmap, was created as a component of the Cancer Genome Anatomy Project to provide a central location for depositing, retrieving, and analyzing human gene expression data. This...
The Diploid Genome Sequence of an Individual Human (2007)
Samuel Levy, Granger Sutton, Pauline C. Ng, Lars Feuk, Aaron L. Halpern, Brian P. Walenz, ...
Presented here is a genome sequence of an individual human. It was produced from ∼32 million random DNA fragments, sequenced by Sanger dideoxy technology and assembled into 4,528 scaffolds,...
Survey Sequencing and Comparative Analysis of the Elephant Shark (Callorhinchus milii) Genome (2007)
Byrappa Venkatesh, Ewen F. Kirkness, Yong-Hwee Loh, Aaron L. Halpern, Alison P. Lee, Justin Johnson, ...
Owing to their phylogenetic position, cartilaginous fishes (sharks, rays, skates, and chimaeras) provide a critical reference for our understanding of vertebrate genome evolution. The relatively...
The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families (2007)
Shibu Yooseph, Granger Sutton, Douglas B. Rusch, Aaron L. Halpern, Shannon J. Williamson, Karin Remington, ...
Metagenomics projects based on shotgun sequencing of populations of micro-organisms yield insight into protein families. We used sequence similarity clustering to explore proteins with a...
Douglas B. Rusch, Aaron L. Halpern, Granger Sutton, Karla B. Heidelberg, Shannon Williamson, Shibu Yooseph, ...
The world's oceans contain a complex mixture of micro-organisms that are for the most part, uncharacterized both genetically and biochemically. We report here a metagenomic study of the marine...
Chanock, Stephen J, Burdett, Laurie, Yeager, Meredith, Llaca, Victor, Langerød, Anita, Presswalla, Shafaq, ...
Abstract Introduction Genomic alterations have been observed in breast carcinomas that affect the capacity of cells to regulate proliferation, signaling, and metastasis. Re-sequence studies have...
The Sorcerer II global ocean sampling expedition: expanding the universe of protein families (2007)
Shibu Yooseph, Granger Sutton, Douglas B. Rusch, Aaron L. Halpern, Shannon J. Williamson, Karin Remington, ...
Metagenomics projects based on shotgun sequencing of populations of micro-organisms yield insight into protein families. We used sequence similarity clustering to explore proteins with a...
Chanock, Stephen J, Burdett, Laurie, Yeager, Meredith, Llaca, Victor, Langerød, Anita, Presswalla, Shafaq, ...
INTRODUCTION: Genomic alterations have been observed in breast carcinomas that affect the capacity of cells to regulate proliferation, signaling, and metastasis. Re-sequence studies have investigated...
Grigoriadis, Anita, Mackay, Alan, Reis-Filho, Jorge S, Steele, Dawn, Iseli, Christian, Stevenson, Brian J, ...
Abstract Introduction Diverse microarray and sequencing technologies have been widely used to characterise the molecular changes in malignant epithelial cells in breast cancers. Such gene expression...
The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families (2006)
Yooseph, Shibu, Sutton, Granger, Rusch, Douglas B., Halpern, Aaron L., Williamson, Shannon J., Remington, Karin, ...
Tumor microenvironments, the immune system and cancer survival (2005)
Abstract The study of cancer immunology has recently been reinvigorated by the application of new research tools and technologies, as well as by refined bioinformatics methods for interpretation of...
An atlas of human gene expression from massively parallel signature sequencing (MPSS) (2005)
Jongeneel, C. Victor, Delorenzi, Mauro, Iseli, Christian, Zhou, Daixing, Haudenschild, Christian D., Khrebtukova, Irina, ...
We have used massively parallel signature sequencing (MPSS) to sample the transcriptomes of 32 normal human tissues to an unprecedented depth, thus documenting the patterns of expression of almost...
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...
Human, Mouse, and Rat Genome Large-Scale Rearrangements: Stability Versus Speciation (2004)
Zhao, Shaying, Shetty, Jyoti, Hou, Lihua, Delcher, Arthur, Zhu, Baoli, Osoegawa, Kazutoyo, ...
Using paired-end sequences from bacterial artificial chromosomes, we have constructed high-resolution synteny and rearrangement breakpoint maps among human, mouse, and rat genomes. Among the >300...
Human, Mouse, and Rat Genome Large-Scale Rearrangements: Stability Versus Speciation (2004)
Zhao, Shaying, Shetty, Jyoti, Hou, Lihua, Delcher, Arthur, Zhu, Baoli, Osoegawa, Kazutoyo, ...
Using paired-end sequences from bacterial artificial chromosomes, we have constructed high-resolution synteny and rearrangement breakpoint maps among human, mouse, and rat genomes. Among the >300...
Long-Range Heterogeneity at the 3' Ends of Human mRNAs (2002)
Iseli, Christian, Stevenson, Brian J., De Souza, Sandro J., Samaia, Helena B., Camargo, Anamaria A., Buetow, Kenneth H., ...
Long-Range Heterogeneity at the 3' Ends of Human mRNAs (2002)
Iseli, Christian, Stevenson, Brian J., De Souza, Sandro J., Samaia, Helena B., Camargo, Anamaria A., Buetow, Kenneth H., ...
Genome and genetic resources from the Cancer Genome Anatomy Project (2001)
Riggins, Gregory J., Strausberg, Robert L.
The Cancer Genome Anatomy Project (CGAP) is a collaborative network of cancer researchers with a common goal: to decipher the genetic changes that occur during cancer formation and progression. The...
SAGEmap: A Public Gene Expression Resource (2000)
Lash, Alex E., Tolstoshev, Carolyn M., Wagner, Lukas, Schuler, Gregory D., Strausberg, Robert L., Riggins, Gregory J., ...
Nucleotide sequence of gene for phenylalanine ammonia-lyase from Rhodotorula rubra (1988)
Filpula, David, Vaslet, Charles A., Levy, Allison, Sykes, Audrey, Strausberg, Robert L.
An anatomy of normal and malignant gene expression
Boon, Kathy, Osório, Elisson C., Greenhut, Susan F., Schaefer, Carl F., Shoemaker, Jennifer, Polyak, Kornelia, ...
A gene's expression pattern provides clues to its role in normal physiology and disease. To provide quantitative expression levels on a genome-wide scale, the Cancer Genome Anatomy Project (CGAP)...
Jongeneel, C. Victor, Iseli, Christian, Stevenson, Brian J., Riggins, Gregory J., Lal, Anita, Mackay, Alan, ...
Whereas information is rapidly accumulating about the structure and position of genes encoded in the human genome, less is known about the complexity and relative abundance of their expression in...
Long-Range Heterogeneity at the 3′ Ends of Human mRNAs
Iseli, Christian, Stevenson, Brian J., De Souza, Sandro J., Samaia, Helena B., Camargo, Anamaria A., Buetow, Kenneth H., ...
The publication of a draft of the human genome and of large collections of transcribed sequences has made it possible to study the complex relationship between the transcriptome and the genome. In...
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...
SAGEmap: A Public Gene Expression Resource
Lash, Alex E., Tolstoshev, Carolyn M., Wagner, Lukas, Schuler, Gregory D., Strausberg, Robert L., Riggins, Gregory J., ...
We have constructed a public gene expression data repository and online data access and analysis, WWW and FTP sites for serial analysis of gene expression (SAGE) data. The WWW and FTP components of...
Identifying Potential Tumor Markers and Antigens by Database Mining and Rapid Expression Screening
Loging, W. Troy, Lal, Anita, Siu, I-Mei, Loney, Tania L., Wikstrand, Carol J., Marra, Marco A., ...
Genes expressed specifically in malignant tissue may have potential as therapeutic targets but have been difficult to locate for most cancers. The information hidden within certain public databases...
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...
Human, Mouse, and Rat Genome Large-Scale Rearrangements: Stability Versus Speciation
Zhao, Shaying, Shetty, Jyoti, Hou, Lihua, Delcher, Arthur, Zhu, Baoli, Osoegawa, Kazutoyo, ...
Using paired-end sequences from bacterial artificial chromosomes, we have constructed high-resolution synteny and rearrangement breakpoint maps among human, mouse, and rat genomes. Among the >300...
Tumor microenvironments, the immune system and cancer survival
Recent microarray analyses of lymphomas suggest that the prognosis of cancer patients is related to an interplay between cancer cells and their microenvironment, including the immune response.
Identification of cancer/testis-antigen genes by massively parallel signature sequencing
Chen, Yao-Tseng, Scanlan, Matthew J., Venditti, Charis A., Chua, Ramon, Theiler, Gregory, Stevenson, Brian J., ...
Massively parallel signature sequencing (MPSS) generates millions of short sequence tags corresponding to transcripts from a single RNA preparation. Most MPSS tags can be unambiguously assigned to...
An atlas of human gene expression from massively parallel signature sequencing (MPSS)
Jongeneel, C. Victor, Delorenzi, Mauro, Iseli, Christian, Zhou, Daixing, Haudenschild, Christian D., Khrebtukova, Irina, ...
We have used massively parallel signature sequencing (MPSS) to sample the transcriptomes of 32 normal human tissues to an unprecedented depth, thus documenting the patterns of expression of almost...
Knutsen, Turid, Gobu, Vasuki, Knaus, Rodger, Padilla-Nash, Hesed, Augustus, Meena, Strausberg, Robert L., ...
To catalogue data on chromosomal aberrations in cancer derived from emerging molecular cytogenetic techniques and to integrate these data with genome maps, we have established two resources, the NCI...
Sequence survey of receptor tyrosine kinases reveals mutations in glioblastomas
Rand, Vikki, Huang, Jiaqi, Stockwell, Tim, Ferriera, Steve, Buzko, Oleksandr, Levy, Samuel, ...
It is now clear that tyrosine kinases represent attractive targets for therapeutic intervention in cancer. Recent advances in DNA sequencing technology now provide the opportunity to survey...
High expression of a cytokeratin-associated protein in many cancers
Egland, Kristi A., Liu, Xiu Fen, Squires, Stephen, Nagata, Satoshi, Man, Yan-Gao, Bera, Tapan K., ...
We have described previously a cDNA library made from membrane-bound polysomal mRNA prepared from breast and prostate cancer cell lines. The library is highly enriched for cDNAs encoding membrane...
The Cancer Genome Anatomy Project: EST Sequencing and the Genetics of Cancer Progression1
Krizman, David B, Wagner, Lukas, Lash, Alex, Strausberg, Robert L, Emmert-Buck, Michael R
As the process of tumor progression proceeds from the normal cellular state to a preneoplastic condition and finally to the fully invasive form, the molecular characteristics of the cell change as...
An anatomy of normal and malignant gene expression
Boon, Kathy, Osório, Elisson C., Greenhut, Susan F., Schaefer, Carl F., Shoemaker, Jennifer, Polyak, Kornelia, ...
A gene's expression pattern provides clues to its role in normal physiology and disease. To provide quantitative expression levels on a genome-wide scale, the Cancer Genome Anatomy Project (CGAP)...
Jongeneel, C. Victor, Iseli, Christian, Stevenson, Brian J., Riggins, Gregory J., Lal, Anita, Mackay, Alan, ...
Whereas information is rapidly accumulating about the structure and position of genes encoded in the human genome, less is known about the complexity and relative abundance of their expression in...
Long-Range Heterogeneity at the 3′ Ends of Human mRNAs
Iseli, Christian, Stevenson, Brian J., De Souza, Sandro J., Samaia, Helena B., Camargo, Anamaria A., Buetow, Kenneth H., ...
The publication of a draft of the human genome and of large collections of transcribed sequences has made it possible to study the complex relationship between the transcriptome and the genome. In...
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...
SAGEmap: A Public Gene Expression Resource
Lash, Alex E., Tolstoshev, Carolyn M., Wagner, Lukas, Schuler, Gregory D., Strausberg, Robert L., Riggins, Gregory J., ...
We have constructed a public gene expression data repository and online data access and analysis, WWW and FTP sites for serial analysis of gene expression (SAGE) data. The WWW and FTP components of...
Identifying Potential Tumor Markers and Antigens by Database Mining and Rapid Expression Screening
Loging, W. Troy, Lal, Anita, Siu, I-Mei, Loney, Tania L., Wikstrand, Carol J., Marra, Marco A., ...
Genes expressed specifically in malignant tissue may have potential as therapeutic targets but have been difficult to locate for most cancers. The information hidden within certain public databases...
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...
Human, Mouse, and Rat Genome Large-Scale Rearrangements: Stability Versus Speciation
Zhao, Shaying, Shetty, Jyoti, Hou, Lihua, Delcher, Arthur, Zhu, Baoli, Osoegawa, Kazutoyo, ...
Using paired-end sequences from bacterial artificial chromosomes, we have constructed high-resolution synteny and rearrangement breakpoint maps among human, mouse, and rat genomes. Among the >300...
Tumor microenvironments, the immune system and cancer survival
Recent microarray analyses of lymphomas suggest that the prognosis of cancer patients is related to an interplay between cancer cells and their microenvironment, including the immune response.
Identification of cancer/testis-antigen genes by massively parallel signature sequencing
Chen, Yao-Tseng, Scanlan, Matthew J., Venditti, Charis A., Chua, Ramon, Theiler, Gregory, Stevenson, Brian J., ...
Massively parallel signature sequencing (MPSS) generates millions of short sequence tags corresponding to transcripts from a single RNA preparation. Most MPSS tags can be unambiguously assigned to...
An atlas of human gene expression from massively parallel signature sequencing (MPSS)
Jongeneel, C. Victor, Delorenzi, Mauro, Iseli, Christian, Zhou, Daixing, Haudenschild, Christian D., Khrebtukova, Irina, ...
We have used massively parallel signature sequencing (MPSS) to sample the transcriptomes of 32 normal human tissues to an unprecedented depth, thus documenting the patterns of expression of almost...
Sequence survey of receptor tyrosine kinases reveals mutations in glioblastomas
Rand, Vikki, Huang, Jiaqi, Stockwell, Tim, Ferriera, Steve, Buzko, Oleksandr, Levy, Samuel, ...
It is now clear that tyrosine kinases represent attractive targets for therapeutic intervention in cancer. Recent advances in DNA sequencing technology now provide the opportunity to survey...
High expression of a cytokeratin-associated protein in many cancers
Egland, Kristi A., Liu, Xiu Fen, Squires, Stephen, Nagata, Satoshi, Man, Yan-Gao, Bera, Tapan K., ...
We have described previously a cDNA library made from membrane-bound polysomal mRNA prepared from breast and prostate cancer cell lines. The library is highly enriched for cDNAs encoding membrane...
The Cancer Genome Anatomy Project: EST Sequencing and the Genetics of Cancer Progression1
Krizman, David B, Wagner, Lukas, Lash, Alex, Strausberg, Robert L, Emmert-Buck, Michael R
As the process of tumor progression proceeds from the normal cellular state to a preneoplastic condition and finally to the fully invasive form, the molecular characteristics of the cell change as...
Grigoriadis, Anita, Mackay, Alan, Reis-Filho, Jorge S, Steele, Dawn, Iseli, Christian, Stevenson, Brian J, ...
The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families
Yooseph, Shibu, Sutton, Granger, Rusch, Douglas B, Halpern, Aaron L, Williamson, Shannon J, Remington, Karin, ...
Metagenomics projects based on shotgun sequencing of populations of micro-organisms yield insight into protein families. We used sequence similarity clustering to explore proteins with a...
Rusch, Douglas B, Halpern, Aaron L, Sutton, Granger, Heidelberg, Karla B, Williamson, Shannon, Yooseph, Shibu, ...
The world's oceans contain a complex mixture of micro-organisms that are for the most part, uncharacterized both genetically and biochemically. We report here a metagenomic study of the marine...
Chanock, Stephen J, Burdett, Laurie, Yeager, Meredith, Llaca, Victor, Langerød, Anita, Presswalla, Shafaq, ...
Survey Sequencing and Comparative Analysis of the Elephant Shark (Callorhinchus milii) Genome
Venkatesh, Byrappa, Kirkness, Ewen F, Loh, Yong-Hwee, Halpern, Aaron L, Lee, Alison P, Johnson, Justin, ...
Owing to their phylogenetic position, cartilaginous fishes (sharks, rays, skates, and chimaeras) provide a critical reference for our understanding of vertebrate genome evolution. The relatively...
Molecular Profiling of Clinical Tissue Specimens : Feasibility and Applications
Emmert-Buck, Michael R., Strausberg, Robert L., Krizman, David B., Bonaldo, M. Fatima, Bonner, Robert F., Bostwick, David G., ...
Evaluation of Non-Formalin Tissue Fixation for Molecular Profiling Studies
Gillespie, John W., Best, Carolyn J.M., Bichsel, Verena E., Cole, Kristina A., Greenhut, Susan F., Hewitt, Stephen M., ...
Using a general strategy for evaluating clinical tissue specimens, we found that 70% ethanol fixation and paraffin embedding is a useful method for molecular profiling studies. Human prostate and...
Molecular Profiling of Clinical Tissue Specimens: Feasibility and Applications
Emmert-Buck, Michael R., Strausberg, Robert L., Krizman, David B., Bonaldo, M. Fatima, Bonner, Robert F., Bostwick, David G., ...
The Diploid Genome Sequence of an Individual Human
Levy, Samuel, Sutton, Granger, Ng, Pauline C, Feuk, Lars, Halpern, Aaron L, Walenz, Brian P, ...
Presented here is a genome sequence of an individual human. It was produced from ∼32 million random DNA fragments, sequenced by Sanger dideoxy technology and assembled into 4,528 scaffolds,...
Genetic Variation in an Individual Human Exome
Ng, Pauline C., Levy, Samuel, Huang, Jiaqi, Stockwell, Timothy B., Walenz, Brian P., Li, Kelvin, ...
There is much interest in characterizing the variation in a human individual, because this may elucidate what contributes significantly to a person's phenotype, thereby enabling personalized...
The HuRef Browser: a web resource for individual human genomics
Axelrod, Nelson, Lin, Yuan, Ng, Pauline C., Stockwell, Timothy B., Crabtree, Jonathan, Huang, Jiaqi, ...
The HuRef Genome Browser is a web application for the navigation and analysis of the previously published genome of a human individual, termed HuRef. The browser provides a comparative view between...
Evaluation of next generation sequencing platforms for population targeted sequencing studies
Harismendy, Olivier, Ng, Pauline C, Strausberg, Robert L, Wang, Xiaoyun, Stockwell, Timothy B, Beeson, Karen Y, ...
Human sequence generated from three next-generation sequencing platforms reveals systematic variability in sequence coverage due to local sequence characteristics.
Transcriptome-guided characterization of genomic rearrangements in a breast cancer cell line
Zhao, Qi, Caballero, Otavia L., Levy, Samuel, Stevenson, Brian J., Iseli, Christian, De Souza, Sandro J., ...
We have identified new genomic alterations in the breast cancer cell line HCC1954, using high-throughput transcriptome sequencing. With 120 Mb of cDNA sequences, we were able to identify genomic...