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151. NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy

Author

Garth Brown, Donna Maglott, Tatiana Tatusova, and Kim D. Pruitt

Subjects
Sequence profiling tool, GENCODE, Sequence Analysis, RNA, Molecular Sequence Annotation, Genome project, Computational biology, Articles, Genomics, Sequence Analysis, DNA, Biology, Reference Standards, Bioinformatics, Genome, Annotation, Sequence Analysis, Protein, Databases, Genetic, Genetics, RefSeq, Humans, Sequence Analysis, Reference genome
Abstract

The National Center for Biotechnology Information (NCBI) Reference Sequence (RefSeq) database is a collection of genomic, transcript and protein sequence records. These records are selected and curated from public sequence archives and represent a significant reduction in redundancy compared to the volume of data archived by the International Nucleotide Sequence Database Collaboration. The database includes over 16,00 organisms, 2.4 × 0(6) genomic records, 13 × 10(6) proteins and 2 × 10(6) RNA records spanning prokaryotes, eukaryotes and viruses (RefSeq release 49, September 2011). The RefSeq database is maintained by a combined approach of automated analyses, collaboration and manual curation to generate an up-to-date representation of the sequence, its features, names and cross-links to related sources of information. We report here on recent growth, the status of curating the human RefSeq data set, more extensive feature annotation and current policy for eukaryotic genome annotation via the NCBI annotation pipeline. More information about the resource is available online (see http://www.ncbi.nlm.nih.gov/RefSeq/).

Published
2011

152. Entrez Gene: gene-centered information at NCBI

Author

Tatiana Tatusova, Kim D. Pruitt, Donna Maglott, and James Ostell

Subjects
Sequence profiling tool, Internet, National Library of Medicine (U.S.), Sequence analysis, Entrez Gene, HUGO Gene Nomenclature Committee, food and beverages, Computational biology, Articles, Genomics, Biology, Bioinformatics, United States, Entrez, User-Computer Interface, Genes, Databases, Genetic, RefSeq, Genetics, natural sciences, GeneRIF, Reference genome
Abstract

Entrez Gene (www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene) is NCBI's database for gene-specific information. It does not include all known or predicted genes; instead Entrez Gene focuses on the genomes that have been completely sequenced, that have an active research community to contribute gene-specific information, or that are scheduled for intense sequence analysis. The content of Entrez Gene represents the result of curation and automated integration of data from NCBI's Reference Sequence project (RefSeq), from collaborating model organism databases, and from many other databases available from NCBI. Records are assigned unique, stable and tracked integers as identifiers. The content (nomenclature, map location, gene products and their attributes, markers, phenotypes, and links to citations, sequences, variation details, maps, expression, homologs, protein domains and external databases) is updated as new information becomes available. Entrez Gene is a step forward from NCBI's LocusLink, with both a major increase in taxonomic scope and improved access through the many tools associated with NCBI Entrez.

Published
2010
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154. α5β1 integrin antagonists reduce chemotherapy-induced premature senescence and facilitate apoptosis in human glioblastoma cells

Author

Ken Takeda, David Y. Leger, Monique Dontenwill, Marie Stiborová, Sophie Martin, Anne Maglott, Dominique Bonnet, and Eva Martinkova

Subjects
Senescence, Aging, Cancer Research, Programmed cell death, Tumor suppressor gene, Pyridines, medicine.medical_treatment, Blotting, Western, Integrin, Antineoplastic Agents, Apoptosis, Cell Line, Tumor, medicine, Humans, Gene silencing, Spiro Compounds, RNA, Messenger, RNA, Small Interfering, Chemotherapy, Temozolomide, biology, Brain Neoplasms, Reverse Transcriptase Polymerase Chain Reaction, Oncology, Cancer research, biology.protein, Propionates, Tumor Suppressor Protein p53, Glioblastoma, Integrin alpha5beta1, medicine.drug
Abstract

The alpha5beta1 integrin represent a new therapeutic target for glioblastoma, which are malignant brain tumors difficult to cure with conventional therapies. Glioblastoma are known to be highly resistant to chemotherapy. We, therefore, investigated whether blocking alpha5beta1 integrin with specific nonpeptidic antagonists concomitantly with chemotherapy (ellipticine and temozolomide) may impact the response to chemotherapy of human glioblastoma. Here we show that inhibiting alpha5beta1 integrin with 2 selective ligands (SJ749 and K34c) decreases chemotherapy-induced premature senescence and facilitates cell apoptosis in a functional p53 background (U87MG cells). When p53 is mutated and inactive (U373 cells), chemotherapy induces p53-independent cell apoptosis instead of senescence that is not improved by integrin antagonists. Silencing p53 in U87MG cells with siRNA as well as evaluating HCT116 p53+/+ and p53-/- colon carcinoma cell behavior support the hypothesis of an as yet unknown effect of alpha5beta1 integrin antagonists on the control of chemotherapy-induced premature senescence and apoptosis. alpha5beta1 integrin antagonists modulate the p53 signaling induced by chemotherapy. Our results highlight a new role of the alpha5beta1 integrin in the control of glioblastoma aggressiveness and responsiveness to chemotherapy, which may have a crucial impact in the clinical management of patients suffering from brain tumors.

Published
2010
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156. Human immunodeficiency virus type 1, human protein interaction database at NCBI

Author

Donna Maglott, Roger G. Ptak, Kenneth S. Katz, Kim D. Pruitt, William Fu, and Brigitte E. Sanders-Beer

Subjects
MEDLINE, Biology, computer.software_genre, gag Gene Products, Human Immunodeficiency Virus, Protein–protein interaction, Viral Proteins, 03 medical and health sciences, Protein Interaction Mapping, Computer Graphics, Genetics, RefSeq, Humans, HIV vaccine, Databases, Protein, GeneRIF, 030304 developmental biology, Acquired Immunodeficiency Syndrome, 0303 health sciences, Database, Entrez Gene, 030302 biochemistry & molecular biology, Proteins, Articles, 3. Good health, HIV-1, Identification (biology), computer, Reference genome
Abstract

The 'Human Immunodeficiency Virus Type 1 (HIV-1), Human Protein Interaction Database', available through the National Library of Medicine at www.ncbi.nlm.nih.gov/RefSeq/HIVInteractions, was created to catalog all interactions between HIV-1 and human proteins published in the peer-reviewed literature. The database serves the scientific community exploring the discovery of novel HIV vaccine candidates and therapeutic targets. To facilitate this discovery approach, the following information for each HIV-1 human protein interaction is provided and can be retrieved without restriction by web-based downloads and ftp protocols: Reference Sequence (RefSeq) protein accession numbers, Entrez Gene identification numbers, brief descriptions of the interactions, searchable keywords for interactions and PubMed identification numbers (PMIDs) of journal articles describing the interactions. Currently, 2589 unique HIV-1 to human protein interactions and 5135 brief descriptions of the interactions, with a total of 14,312 PMID references to the original articles reporting the interactions, are stored in this growing database. In addition, all protein-protein interactions documented in the database are integrated into Entrez Gene records and listed in the 'HIV-1 protein interactions' section of Entrez Gene reports. The database is also tightly linked to other databases through Entrez Gene, enabling users to search for an abundance of information related to HIV pathogenesis and replication.

Published
2009
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157. Short Communication: Cataloguing the HIV Type 1 Human Protein Interaction Network

Author

Mikhail N. Rozanov, Donna Maglott, Carl W. Dieffenbach, Jonathan E. Dickerson, John W. Pinney, Brigitte E Sanders-Beer, Kenneth S. Katz, Roger G. Ptak, Kim D. Pruitt, David Robertson, and William Fu

Subjects
Regulation of gene expression, Entrez Gene, Immunology, Computational biology, Biology, Bioinformatics, Protein–protein interaction, Entrez, Infectious Diseases, Interaction network, Virology, RefSeq, Identification (biology), Protein kinase A
Abstract

Although many interactions between HIV-1 and human proteins have been reported in the scientific literature, no publicly accessible source for efficiently reviewing this information was available. Therefore, a project was initiated in an attempt to catalogue all published interactions between HIV-1 and human proteins. HIV-related articles in PubMed were used to develop a database containing names, Entrez GeneIDs, and RefSeq protein accession numbers of interacting proteins. Furthermore, brief descriptions of the interactions, PubMed identification numbers of articles describing the interactions, and keywords for searching the interactions were incorporated. Over 100,000 articles were reviewed, resulting in the identification of 1448 human proteins that interact with HIV-1 comprising 2589 unique HIV-1-to-human protein interactions. Preliminary analysis of the extracted data indicates 32% were direct physical interactions (e.g., binding) and 68% were indirect interactions (e.g., upregulation through activation of signaling pathways). Interestingly, 37% of human proteins in the database were found to interact with more than one HIV-1 protein. For example, the signaling protein mitogen-activated protein kinase 1 has a surprising range of interactions with 10 different HIV-1 proteins. Moreover, large numbers of interactions were published for the HIV-1 regulatory protein Tat and envelope proteins: 30% and 33% of total interactions identified, respectively. The database is accessible at http://www.ncbi.nlm.nih.gov/RefSeq/HIVInteractions/ and is cross-linked to other National Center for Biotechnology Information databases and programs via Entrez Gene. This database represents a unique and continuously updated scientific resource for understanding HIV-1 replication and pathogenesis to assist in accelerating the development of effective therapeutic and vaccine interventions.

Published
2008
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158. What everybody should know about the rat genome and its online resources

Author

Howard J. Jacob, Jim Kent, Xosé M. Fernández-Suárez, Ewan Birney, George M. Weinstock, Kim D. Pruitt, Richard A. Gibbs, Kim C. Worley, Donna Maglott, Donna Karolchik, Garth Brown, and Simon N. Twigger

Subjects
Complex disease, Genome browser, Computational biology, Biology, Polymorphism, Single Nucleotide, Genome, Rats, Mutant Strains, Article, Rat Genome Database, Databases, Genetic, Genetics, RefSeq, Animals, Humans, Ensembl, Gene, Whole genome sequencing, Internet, Genetic Diseases, Inborn, Computational Biology, Genetic Variation, Genomics, Sequence Analysis, DNA, Rats, Disease Models, Animal, Haplotypes
Abstract

It has been four years since the original publication of the draft sequence of the rat genome. Five groups are now working together to assemble, annotate and release an updated version of the rat genome. As the prevailing model for physiology, complex disease and pharmacological studies, there is an acute need for the rat's genomic resources to keep pace with the rat's prominence in the laboratory. In this commentary, we describe the current status of the rat genome sequence and the plans for its impending 'upgrade'. We then cover the key online resources providing access to the rat genome, including the new SNP views at Ensembl, the RefSeq and Genes databases at the US National Center for Biotechnology Information, Genome Browser at the University of California Santa Cruz and the disease portals for cardiovascular disease and obesity at the Rat Genome Database.

Published
2008
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159. ClinVar: improving access to variant interpretations and supporting evidence

Author

Landrum, Melissa J, primary, Lee, Jennifer M, additional, Benson, Mark, additional, Brown, Garth R, additional, Chao, Chen, additional, Chitipiralla, Shanmuga, additional, Gu, Baoshan, additional, Hart, Jennifer, additional, Hoffman, Douglas, additional, Jang, Wonhee, additional, Karapetyan, Karen, additional, Katz, Kenneth, additional, Liu, Chunlei, additional, Maddipatla, Zenith, additional, Malheiro, Adriana, additional, McDaniel, Kurt, additional, Ovetsky, Michael, additional, Riley, George, additional, Zhou, George, additional, Holmes, J Bradley, additional, Kattman, Brandi L, additional, and Maglott, Donna R, additional

Published
2017
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161. Database resources of the National Center for Biotechnology Information

Author

Ew, Sayers, Barrett T, Da, Benson, Sh, Bryant, Canese K, Chetvernin V, Dm, Church, DiCuccio M, Edgar R, Federhen S, Feolo M, Ly, Geer, Helmberg W, Kapustin Y, David Landsman, Dj, Lipman, Tl, Madden, Dr, Maglott, Miller V, Mizrachi I, Ostell J, Kd, Pruitt, Gd, Schuler, Sequeira E, St, Sherry, Shumway M, Sirotkin K, Souvorov A, Starchenko G, Ta, Tatusova, Wagner L, Yaschenko E, and Ye J

Subjects
Models, Molecular, Proteomics, PubMed, Genotype, Sequence Homology, Gene Expression, 03 medical and health sciences, 0302 clinical medicine, Databases, Genetic, Genetics, Animals, Humans, natural sciences, 030304 developmental biology, 0303 health sciences, Internet, National Library of Medicine (U.S.), Articles, Genomics, United States, 3. Good health, Protein Structure, Tertiary, Systems Integration, Phenotype, Genes, 030220 oncology & carcinogenesis, Corrigendum, Databases, Nucleic Acid, Sequence Alignment, 030217 neurology & neurosurgery
Abstract

In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data available through NCBI's web site. NCBI resources include Entrez, the Entrez Programming Utilities, My NCBI, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link, Electronic PCR, OrfFinder, Spidey, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genome, Genome Project and related tools, the Trace, Assembly, and Short Read Archives, the Map Viewer, Model Maker, Evidence Viewer, Clusters of Orthologous Groups, Influenza Viral Resources, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus, Entrez Probe, GENSAT, Database of Genotype and Phenotype, Online Mendelian Inheritance in Man, Online Mendelian Inheritance in Animals, the Molecular Modeling Database, the Conserved Domain Database, the Conserved Domain Architecture Retrieval Tool and the PubChem suite of small molecule databases. Augmenting the web applications are custom implementations of the BLAST program optimized to search specialized data sets. These resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.

Published
2007

162. List of Contributors

Author

Haley Abel, Shankar Ajay, Hussam Al-Kateb, Sami S. Amr, Andrew J. Bredemeyer, Fengqi Chang, Elizabeth C. Chastain, Deanna M. Church, Paul Cliften, Catherine E. Cottrell, Andrew Drury, Eric Duncavage, Birgit Funke, Amy S. Gargis, Ian S. Hagemann, Tina M. Hambuch, Madhuri R. Hegde, Michelle Hogue, Vanessa L. Horner, Lisa Kalman, Shamika Ketkar, Roger D. Klein, Shashikant Kulkarni, William A. LaFramboise, Marilyn M. Li, Cindy J. Liu, Geoffrey L. Liu, Ira M. Lubin, Elaine Lyon, Donna R. Maglott, Rong Mao, John Mayfield, Carri-Lyn Mead, Rakesh Nagarajan, Yuri E. Nikiforov, Marina N. Nikiforova, Alex Nord, Brendan D. O’Fallon, John Pfeifer, Colin Pritchard, Erica Ramos, Kris Rickhoff, Kristina A. Roberts, Wendy S. Rubinstein, Stephen J. Salipante, Marc Salit, Jennifer K. Sehn, Benjamin D. Solomon, Stephanie Solomon, David H. Spencer, Bin Zhang, and Justin Zook

Published
2015
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163. Reference Databases for Disease Associations

Author

Donna Maglott, Deanna M. Church, and Wendy S. Rubinstein

Subjects
medicine.medical_specialty, dbSNP, Database, Genome-wide association study, Context (language use), Disease, Biology, computer.software_genre, Data sharing, Variation (linguistics), medicine, Medical genetics, Baseline (configuration management), computer
Abstract

Making sense of the human variation in the context of human disease has many challenges. A medical genetics professional faced with a list of identified variants must be able to evaluate, and reevaluate, whether there are prior reports about any variant, what the current interpretation of that variant might be, and/or if there are predicted consequences. The sources of publicly available information are diverse, so the genetics professional needs to know not only how to find information, but also how large centralized databases and datasets are maintained in case a current interpretation is not highly supported. This chapter provides an overview of how human genetic information is ascertained—both the common variation to provide the baseline of information about variation unlikely to be the primary cause of a disorder, and the rarer variation that may contribute to disease. It summarizes the features of major databases that archive submissions about variation (dbSNP, dbVar), about variation–disease associations (dbGaP), and clinical interpretations of variation (ClinVar). It also summarizes major tools that support access to these data by several paths, e.g., by location on the genome, by gene, and by disease or measured phenotype. The chapter also describes community efforts to encourage data sharing and to develop standards that promote the development of clinical grade databases.

Published
2015
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164. The Small α5β1 Integrin Antagonist, SJ749, Reduces Proliferation and Clonogenicity of Human Astrocytoma Cells

Author

Philippe Rondé, Anne Maglott, Petr Bartik, Guy Fuhrmann, Philippe Klotz, Sedat Cosgun, Kenneth Takeda, Sophie Martin, and Monique Dontenwill

Subjects
Cancer Research, Cell type, animal structures, Pyridines, Angiogenesis, Integrin, Cell Growth Processes, Astrocytoma, Cell morphology, Substrate Specificity, Cell Line, Tumor, Spheroids, Cellular, Cell Adhesion, Humans, Spiro Compounds, Tumor Stem Cell Assay, Dose-Response Relationship, Drug, biology, Brain Neoplasms, Cell growth, In vitro, Cell biology, Fibronectin, Oncology, Cell culture, embryonic structures, Immunology, cardiovascular system, biology.protein, Propionates, Integrin alpha5beta1
Abstract

The potential role of α5β1 integrins in cancer has recently attracted much interest. However, few α5β1-selective antagonists have been developed compared with other integrins. The most specific nonpeptidic α5β1 antagonist described thus far, SJ749, inhibits angiogenesis by affecting adhesion and migration of endothelial cells. We investigated the effects of SJ749 in two human astrocytoma cell lines, A172 and U87, which express different levels of α5β1. SJ749 dose-dependently inhibited adhesion of both cell types on fibronectin. Application of SJ749 to spread cells led to formation of nonadherent spheroids for A172 cells but had no effect on U87 cell morphology. SJ749 also reduced proliferation of A172 cells due to a long lasting G0-G1 arrest, whereas U87 cells were only slightly affected. However, under nonadherent culture conditions (soft agar), SJ749 significantly reduced the number of colonies formed only by U87 cells. As U87 cells express more α5β1 than A172 cells, we specifically examined the effect of SJ749 on A172 cells overexpressing α5. Treatment of α5-A172 cells with SJ749 decreased colony formation similarly to that observed in U87 cells. Therefore, in nonadherent conditions, the effect of SJ749 on tumor cell growth characteristics depends on the level of α5β1 expression. Our study highlights the importance of α5β1 as an anticancer target and shows for the first time that a small nonpeptidic α5β1-specific antagonist affects proliferation of tumor cells. (Cancer Res 2006; 66(12): 6002-7)

Published
2006
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165. Pharmacogenetic Allele Nomenclature

Author

Kalman, L.V., Agúndez, J.A.G., Appell, M.L. (M Lindqvist), Black, J.L. (Jynene), Bell, G.C., Boukouvala, S., Bruckner, C., Bruford, E. (Elspeth), Caudle, K., Coulthard, S.A., Daly, A.K., Del Tredici, A.L., Den Dunnen, J.T., Drozda, K., Everts, R.E. (Robin), Flockhart, D., Freimuth, R.R., Gaedigk, A., Hachad, H., Hartshorne, T., Ingelman-Sundberg, M. (Magnus), Klein, T.E. (T.), Lauschke, V.M., Maglott, D. (Donna), McLeod, H.L. (Howard), McMillin, G.A., Meyer, U.A., Müller, D.J., Nickerson, D.A. (Deborah), Oetting, W.S., Pacanowski, M., Pratt, V.M., Relling, M.V. (Mary), Roberts, A., Flesch-Janys, D. (Dieter), Sangkuhl, K., Schwab, M., Scott, S.A. (S.), Sim, S.C., Thirumaran, R.K., Toji, L.H., Tyndale, R.F., Schaik, R.H.N. (Ron) van, Whirl-Carrillo, M., Yeo, K.T.J., Zanger, U. (Ulrich), Kalman, L.V., Agúndez, J.A.G., Appell, M.L. (M Lindqvist), Black, J.L. (Jynene), Bell, G.C., Boukouvala, S., Bruckner, C., Bruford, E. (Elspeth), Caudle, K., Coulthard, S.A., Daly, A.K., Del Tredici, A.L., Den Dunnen, J.T., Drozda, K., Everts, R.E. (Robin), Flockhart, D., Freimuth, R.R., Gaedigk, A., Hachad, H., Hartshorne, T., Ingelman-Sundberg, M. (Magnus), Klein, T.E. (T.), Lauschke, V.M., Maglott, D. (Donna), McLeod, H.L. (Howard), McMillin, G.A., Meyer, U.A., Müller, D.J., Nickerson, D.A. (Deborah), Oetting, W.S., Pacanowski, M., Pratt, V.M., Relling, M.V. (Mary), Roberts, A., Flesch-Janys, D. (Dieter), Sangkuhl, K., Schwab, M., Scott, S.A. (S.), Sim, S.C., Thirumaran, R.K., Toji, L.H., Tyndale, R.F., Schaik, R.H.N. (Ron) van, Whirl-Carrillo, M., Yeo, K.T.J., and Zanger, U. (Ulrich)

Abstract

This article provides nomenclature recommendations developed by an international workgroup to increase transparency and standardization of pharmacogenetic (PGx) result reporting. Presently, sequence variants identified by PGx tests are described using different nomenclature systems. In addition, PGx analysis may detect different sets of variants for each gene, which can affect interpretation of results. This practice has caused confusion and may thereby impede the adoption of clinical PGx testing. Standardization is critical to move PGx forward.

Published
2016
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166. HGVS Recommendations for the Description of Sequence Variants: 2016 Update

Author

den Dunnen, JT, Dalgleish, R, Maglott, DR, Hart, RK, Greenblatt, MS, McGowan-Jordan, J, Roux, A-F, Smith, T, Antonarakis, SE, Taschner, PEM, den Dunnen, JT, Dalgleish, R, Maglott, DR, Hart, RK, Greenblatt, MS, McGowan-Jordan, J, Roux, A-F, Smith, T, Antonarakis, SE, and Taschner, PEM

Abstract

The consistent and unambiguous description of sequence variants is essential to report and exchange information on the analysis of a genome. In particular, DNA diagnostics critically depends on accurate and standardized description and sharing of the variants detected. The sequence variant nomenclature system proposed in 2000 by the Human Genome Variation Society has been widely adopted and has developed into an internationally accepted standard. The recommendations are currently commissioned through a Sequence Variant Description Working Group (SVD-WG) operating under the auspices of three international organizations: the Human Genome Variation Society (HGVS), the Human Variome Project (HVP), and the Human Genome Organization (HUGO). Requests for modifications and extensions go through the SVD-WG following a standard procedure including a community consultation step. Version numbers are assigned to the nomenclature system to allow users to specify the version used in their variant descriptions. Here, we present the current recommendations, HGVS version 15.11, and briefly summarize the changes that were made since the 2000 publication. Most focus has been on removing inconsistencies and tightening definitions allowing automatic data processing. An extensive version of the recommendations is available online, at http://www.HGVS.org/varnomen.

Published
2016

167. NCBI's genome annotation projects

Author

Maglott, D.R., Agarwala, R., Chen, H-C., Chetvernin, S., Church, D., Ermolaeva, O., Jang, W., Kitts, P., Kans, J., Lipman, D., Ostell, J., Pruitt, K., Resenchuk, S., Schuler, G., Sherry, S., Tatusova, T., and Wheelan, S.

Subjects
Human genetics -- Research, Genetic disorders -- Research, Genetic research -- Information management, Biological sciences
Published
2001

168. Database resources of the National Center for Biotechnology Information

Author

Wheeler, David L., Barrett, Tanya, Benson, Dennis A., Bryant, Stephen H., Canese, Kathi, Church, Deanna M., DiCuccio, Michael, Edgar, Ron, Federhen, Scott, Helmberg, Wolfgang, Kenton, David L., Khovayko, Oleg, Lipman, David J., Madden, Thomas L., Maglott, Donna R., Ostell, James, Pontius, Joan U., Pruitt, Kim D., Schuler, Gregory D., Schriml, Lynn M., Sequeira, Edwin, Sherry, Steven T., Sirotkin, Karl, Starchenko, Grigory, Suzek, Tugba O., Tatusov, Roman, Tatusova, Tatiana A., Wagner, Lukas, and Yaschenko, Eugene

Subjects
Models, Molecular, Databases, Factual, 03 medical and health sciences, 0302 clinical medicine, Databases, Genetic, Protein Interaction Mapping, Genetics, Animals, Humans, natural sciences, Amino Acid Sequence, Conserved Sequence, 030304 developmental biology, 0303 health sciences, National Library of Medicine (U.S.), Gene Expression Profiling, Computational Biology, Articles, Genomics, United States, Protein Structure, Tertiary, 3. Good health, Phenotype, Genes, Sequence Alignment, Software, 030217 neurology & neurosurgery
Abstract

In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data retrieval systems and computational resources for the analysis of data in GenBank and other biological data made available through NCBI's website. NCBI resources include Entrez, Entrez Programming Utilities, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR, OrfFinder, Spidey, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genomes and related tools, the Map Viewer, Model Maker, Evidence Viewer, Clusters of Orthologous Groups (COGs), Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, SAGEmap, Gene Expression Omnibus (GEO), Online Mendelian Inheritance in Man (OMIM), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD) and the Conserved Domain Architecture Retrieval Tool (CDART). Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized datasets. All of the resources can be accessed through the NCBI home page at http://www.ncbi.nlm.nih.gov.

Published
2004
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169. Connecting Sequence and Biology in the Laboratory Mouse

Author

Joel E. Richardson, Lois J. Maltais, Donna Maglott, Richard M. Baldarelli, Martin Ringwald, Benjamin L. King, Deanna M. Church, James A. Kadin, Lynn M. Schriml, Lori E. Corbani, Janan T. Eppig, Jun Adachi, Takeya Kasukawa, Louise M. McKenzie, Kim D. Pruitt, Longlong Yang, Yunxia Zhu, David P. Hill, Sharon Cousins, Deborah J Reed, Masaaki Furuno, Dong Qi, Sridhar Ramachandran, Judith A. Blake, Kenneth S. Frazer, Dirck W. Bradt, and Carol J. Bult

Subjects
DNA, Complementary, ved/biology.organism_classification_rank.species, Context (language use), Computational biology, Mouse Genome Informatics, Biology, Genome, DNA sequencing, Transcriptome, Mice, Databases, Genetic, Computer Graphics, Genetics, Animals, natural sciences, Model organism, Gene, Genetics (clinical), Internet, Base Sequence, ved/biology, Computational Biology, Resources, Genes, Informatics
Abstract

The Mouse Genome Sequencing Consortium and the RIKEN Genome Exploration Research grouphave generated large sets of sequence data representing the mouse genome and transcriptome, respectively. These data provide a valuable foundation for genomic research. The challenges for the informatics community are how to integrate these data with the ever-expanding knowledge about the roles of genes and gene products in biological processes, and how to provide useful views to the scientific community. Public resources, such as the National Center for Biotechnology Information (NCBI; http://www.ncbi.nih.gov), and model organism databases, such as the Mouse Genome Informatics database (MGI; http://www.informatics.jax.org), maintain the primary data and provide connections between sequence and biology. In this paper, we describe how the partnership of MGI and NCBI LocusLink contributes to the integration of sequence and biology, especially in the context of the large-scale genome and transcriptome data now available for the laboratory mouse. In particular, we describe the methods and results of integration of 60,770 FANTOM2 mouse cDNAs with gene records in the databases of MGI and LocusLink.

Published
2003
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170. NCBI Reference Sequence Project: update and current status

Author

Donna Maglott, Kim D. Pruitt, and Tatiana Tatusova

Subjects
Genetics, Whole genome sequencing, Pseudogene, Proteins, Genomics, Articles, Computational biology, Biology, Genome, United States, Rats, Alternative Splicing, Mice, Databases, Genetic, RefSeq, Animals, Humans, RNA, Pseudogenes, Biotechnology, Reference genome
Abstract

The goal of the NCBI Reference Sequence (RefSeq) project is to provide the single best non-redundant and comprehensive collection of naturally occurring biological molecules, representing the central dogma. Nucleotide and protein sequences are explicitly linked on a residue-by-residue basis in this collection. Ideally all molecule types will be available for each well-studied organism, but the initial database collection pragmatically includes only those molecules and organisms that are most readily identified. Thus different amounts of information are available for different organisms at any given time. Furthermore, for some organisms additional intermediate records are provided when the genome sequence is not yet finished. The collection is supplied by NCBI through three distinct pipelines in addition to collaborations with community groups. The collection is curated on an ongoing basis. Additional information about the NCBI RefSeq project is available at http://www.ncbi.nih.gov/RefSeq/.

Published
2003
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171. Gene: a gene-centered information resource at NCBI

Author

Kim D. Pruitt, Terence Murphy, Donna Maglott, Kenneth S. Katz, Igor Tolstoy, Michael Ovetsky, Vichet Hem, Tatiana Tatusova, Garth Brown, Olga Ermolaeva, and Craig Wallin

Subjects
Genetics, Sequence profiling tool, Internet, National Library of Medicine (U.S.), Genetic Variation, Genomics, Computational biology, Biology, Genome, United States, Entrez, Phenotype, Genes, Databases, Genetic, RefSeq, Database Issue, GeneRIF, Gene, Reference genome
Abstract

The National Center for Biotechnology Information's (NCBI) Gene database (www.ncbi.nlm.nih.gov/gene) integrates gene-specific information from multiple data sources. NCBI Reference Sequence (RefSeq) genomes for viruses, prokaryotes and eukaryotes are the primary foundation for Gene records in that they form the critical association between sequence and a tracked gene upon which additional functional and descriptive content is anchored. Additional content is integrated based on the genomic location and RefSeq transcript and protein sequence data. The content of a Gene record represents the integration of curation and automated processing from RefSeq, collaborating model organism databases, consortia such as Gene Ontology, and other databases within NCBI. Records in Gene are assigned unique, tracked integers as identifiers. The content (citations, nomenclature, genomic location, gene products and their attributes, phenotypes, sequences, interactions, variation details, maps, expression, homologs, protein domains and external databases) is available via interactive browsing through NCBI's Entrez system, via NCBI's Entrez programming utilities (E-Utilities and Entrez Direct) and for bulk transfer by FTP.

Published
2014

172. 10th International Symposium on SHR and Molecular Medicine¶May 2 – 4, 2001, Berlin-Buch

Author

D Maglott, Z Wang, J Lu, D Chen, J Ginster, M Shimoyama, J Tonellato, R Nigam, Fredrik Ståhl, P Long, Göran Levan, S Twigger, CF Chen, J Eppig, D Pasko, A Kwitek-Black, H Jacob, and Gerhard Schuler

Subjects
Comparative genomics, Mouse Genome Database, ved/biology, business.industry, Genomic research, ved/biology.organism_classification_rank.species, UniGene, Genomics, Computational biology, Biology, Genome, Biotechnology, Rat Genome Database, Drug Discovery, Molecular Medicine, Model organism, business, Genetics (clinical)
Abstract

The Rat Genome Database (RGD) is a NIH funded project who’s stated mission is “to collect, consolidate, and integrate data generated from ongoing rat genetic and genomic research efforts and make these data widely available to the scientific community.” In a collaboration between the Medical College of Wisconsin, the Jackson Lab, the National Center for Biotechnology and Information and the Genetics Lundberg Laboratory, Gothenburg, Sweden, RGD has been created to meet these stated aims. The primary focus of RGD is to aid Rat researchers in their work studying the rat as a model organism for human disease. To support these studies we have integrated a large amount of rat genetic and genomic resources in RGD and these are constantly being expanded through ongoing literature curation. One of the major features of RGD version 1.1, released in January of this year, is incorporation of QTL data to facilitate physiological genomics studies relating disease with the genome. In addition, a dynamic sequence-based homology tool is in final testing which will enable Rat, Mouse and Human researchers to view mapped genes and sequences and their locations in the other two organisms. We hope to release this tool in the second quarter of 2001. This will facilitate the application of results in one species to experiments in another species. In collaboration with the Mouse Genome Database and NCBI, close links are being created between RGD and MGD, LocusLink and UniGene to increase access to each set of data. To support its other general functions RGD has a variety of tools available for the rat researcher, plus ones that are equally useful to researchers working in other organisms and a sampling of these tools will be presented. Thus RGD is not only a valuable resource for those working with the rat but also for researchers in other model organisms wishing to harness the existing genetic and physiological data available in the rat to complement their own work.

Published
2001
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173. The completion of the Mammalian Gene Collection (MGC)

Author

Temple, Gary, Gerhard, Daniela, Rasooly, S. Rebekah, Feingold, Elise A., Good, Peter J., Robinson, Cristen, Mandich, Allison, Derge, Jeffrey G., Lewis, Jeanne, Shoaf, Debonny, Collins, Francis S., Wonhee Jang, Wagner, Lukas, Shenmen, Carolyn M., Misquitta, Leonie, Schaefer, Carl F., Buetow, Kenneth H., Bonner, Tom I., Yankie, Linda, Ward, Ming, Phan, Lon, Astashyn, Alex, Brown, Garth, Farrell, Catherine, Hart, Jennifer, Landrum, Melissa, Maidak, Bonnie L., Murphy, Michael, Murphy, Terence, Rajput, Bhanu, Riddick, Lillian, Webb, David, Weber, Janet, Wu, Wendy, Pruitt, Kim D., Maglott, Donna, Siepel, Adam, Brejova, Brona, Diekhans, Mark, Harte, Rachel, Baertsch, Robert, Kent, Jim, Haussler, David, Brent, Michael, Langton, Laura, Comstock, Charles L.G., Stevens, Michael, Chaochun Wei, van Baren, Marijke J., Salehi-Ashtiani, Kourosh, Murray, Ryan R., Ghamsari, Lila, Mello, Elizabeth, Chenwei Lin, Pennacchio, Christa, Schreiber, Kirsten, Shapiro, Nicole, Marsh, Amber, Pardes, Elizabeth, Moore, Troy, Lebeau, Anita, Muratet, Mike, Simmons, Blake, Kloske, David, Sieja, Stephanie, Hudson, James, Sethupathy, Praveen, Brownstein, Michael, Bhat, Narayan, Lazar, Joseph, Jacob, Howard, Gruber, Chris E., Smith, Mark R., McPherson, John, Garcia, Angela M., Gunaratne, Preethi H., Jiaqian Wu, Muzny, Donna, Gibbs, Richard A., Young, Alice C., Bouffard, Gerard G., Blakesley, Robert W., Mullikin, Jim, Green, Eric D., Dickson, Mark C., Rodriguez, Alex C., Grimwood, Jane, Schmutz, Jeremy, Myers, Richard M., Hirst, Martin, Zeng, Thomas, Kane Tse, Moksa, Michelle, Deng, Merinda, Ma, Kevin, Mah, Diana, Pang, Johnson, Taylor, Greg, Chuah, Eric, Deng, Athena, Fichter, Keith, Go, Anne, Lee, Stephanie, Jing Wang, Griffith, Malachi, Morin, Ryan, Moore, Richard A., Mayo, Michael, Munro, Sarah, Wagner, Susan, Jones, Steven J.M., Holt, Robert A., Marra, Marco A., Sun Lu, Shuwei Yang, Hartigan, James, Graf, Marcus, Wagner, Ralf, Letovksy, Stanley, Pulido, Jacqueline C., Robison, Keith, Esposito, Dominic, Hartley, James, Wall, Vanessa E., Hopkins, Ralph F., Osamu Ohara, and Wiemann, Stefan

Subjects
DNA synthesis -- Research, Mammals -- Genetic aspects, Nucleotide sequencing -- Evaluation, Genetic transcription -- Research, Health
Published
2009

174. The consensus coding sequence (CCDS) project: identifying a common protein-coding gene set for the human and mouse genomes

Author

Pruitt, Kim D., Harrow, Jennifer, Harte, Rachel A., Wallin, Craig, Diekhans, Mark, Maglott, Donna R., Searle, Steve, Farrell, Catherine M., Loveland, Jane E., Ruef, Barbara J., Hart, Elizabeth, Suner, Marie-Marthe, Landrum, Melissa J., Aken, Bronwen, Ayling, Sarah, Baertsch, Robert, Fernandez-Banet, Julio, Cherry,Joshua L., Curwen, Val, DiCuccio, Michael, Kellis, Manolis, Lee, Jennifer, Lin, Michael F., Schuster, Michael, Shkeda, Andrew, Amid, Clara, Brown, Garth, Dukhanina, Oksana, Frankish, Adam, Hart, Jennifer, Maidak, Bonnie L., Mudge, Jonathan, Murphy, Michael R., Murphy, Terence, Rajan, Jeena, Rajput, Bhanu, Riddick, Lillian D., Snow, Catherine, Steward, Charles, Webb, David, Weber, Janet A., Wilming, Laurens, Wenyu Wu, Birney, Ewan, Haussler, David, Hubbard, Tim, Ostell, James, Durbin, Richard, and Lipman, David

Subjects
Human genome -- Research, Genetic code -- Research, Protein biosynthesis -- Analysis, Mice -- Genetic aspects, Health
Published
2009

175. Introducing RefSeq and LocusLink: curated human genome resources at the NCBI

Author

Hugues Sicotte, Kenneth S. Katz, Donna Maglott, and Kim D. Pruitt

Subjects
Genetics, Internet, Databases, Factual, Genome, Human, GENCODE, Genomics, Computational biology, Biology, Entrez, Data sequences, RefSeq, Humans, Coding region, Human genome
Abstract

RefSeq records are included in the Entrez retrieval system (http://www.ncbi.nlm.nih.gov/entrez/). This allows a third query pathway, namely directly by Entrez nucleotide or protein text queries or indirectly by neighboring strategies. LocusLink and RefSeq data are also provided without restriction for ftp transfer (ftp://ncbi.nlm.nih.gov/refseq). Therefore, the combination of LocusLink and RefSeq resources provides a powerful approach to answering such questions as: •Is my sequence from a known gene? (Try blast and look for a RefSeq result.)•What sequence can I use as a standard for gene A? (Try blast or LocusLink.)•Where can I get more information about gene B? (Start at LocusLink.)•What genes are related to disorder Z? (Start at OMIM or LocusLink.)The goal of LocusLink and RefSeq is to include all known genes and their major products. As of the end of August 1999, ∼10 690 loci have been included, 7500 with at least some sequence data and 5985 reference mRNAs. Expanding the LocusLink and RefSeq datasets is an ongoing effort – LocusIDs are established as additional genes are identified, and RefSeq records are added as new links between genes and sequences with complete coding regions are made. The public sites are refreshed weekly. We welcome collaborations with the scientific community to ensure that these resources are as comprehensive and accurate as possible.

Published
2000
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176. The Genome of the Sea Urchin Strongylocentrotus purpuratus

Author

Amro Hamdoun, Virginia Brockton, Huyen Dinh, Qiang Tu, Richard O. Hynes, Maria Ina Arnone, Wratko Hlavina, L. Courtney Smith, Mariano A. Loza, David R. Burgess, Matthew P. Hoffman, Florian Raible, Qiu Autumn Yuan, Geoffrey Okwuonu, Mark Y. Tong, Jennifer Hume, Donna Maglott, Manisha Goel, Olivier Fedrigo, Manuel L. Gonzalez-Garay, Celina E. Juliano, Judith Hernandez, Gary M. Wessel, William F. Marzluff, Audrey J. Majeske, Christian Gache, Louise Duloquin, Xingzhi Song, François Lapraz, Fowler J, Alexandre Souvorov, Jared V. Goldstone, Georgia Panopoulou, Sandra Hines, Kyle M. Judkins, Clay Davis, Christine G. Elsik, Paul Kitts, Mariano Loza-Coll, Greg Wray, Taku Hibino, Eric Röttinger, Allison M. Churcher, Annamaria Locascio, Arcady Mushegian, Masashi Kinukawa, Anna Reade, Katherine M. Buckley, I. R. Gibbons, Bert Gold, Aleksandar Milosavljevic, David Epel, Victor D. Vacquier, Ling Ling Pu, Vincenzo Cavalieri, Erin L. Allgood, Lan Zhang, Lynne V. Nazareth, Constantin N. Flytzanis, Ian Bosdet, Yi-Hsien Su, Zeev Pancer, Matthew L. Rowe, Robert C. Angerer, David R. McClay, William H. Klein, Rachel F. Gray, Julian L. Wong, Shunsuke Yaguchi, Robert Bellé, Aaron J. Mackey, Herath Jayantha Gunaratne, Karl Frederik Bergeron, Bruce P. Brandhorst, Greg Murray, Avis H. Cohen, Stephanie Bell, Kristin Tessmar-Raible, Ian K. Townley, Bertrand Cosson, Thomas D. Glenn, Jongmin Nam, Cynthia A. Bradham, Michael Dean, Joseph Chacko, Anthony J. Robertson, Margherita Branno, Valeria Matranga, K. James Durbin, Esther Miranda, Lili Chen, Eran Elhaik, Robert D. Burke, Rita A. Wright, Paola Oliveri, Sandra L. Lee, Gary W. Moy, Alexander E Primus, Shawn S. McCafferty, Cristina Calestani, David A. Garfield, Erica Sodergren, Karen Wilson, Joel Smith, Marco A. Marra, Cynthia Messier, Julia Morales, Kim D. Pruitt, Rachel Thorn, Rachel Gill, John S. Taylor, Mark E. Hahn, Victor Sapojnikov, Meredith Howard-Ashby, Lynne M. Angerer, Maurice R. Elphick, Kathy R. Foltz, Anne Marie Genevière, Justin T. Reese, Blanca E. Galindo, Kim C. Worley, Andrew Leone, Glen Humphrey, Kevin Berney, Olga Ermolaeva, George Miner, David P. Terwilliger, Elly Suk Hen Chow, Lora Lewis, Dan Graur, C. Titus Brown, Gerard Manning, Kevin J. Peterson, Angela Jolivet, Michele K. Anderson, Francesca Rizzo, Ekaterina Voronina, Thierry Lepage, Giorgio Matassi, Antonio Fernandez-Guerra, Mamoru Nomura, Charles A. Whittaker, James R.R. Whittle, James A. Coffman, George M. Weinstock, Mohammed M. Idris, Ashlan M. Musante, Sebastian D. Fugmann, Katherine D. Walton, Sorin Istrail, Shu-Yu Wu, Cerrissa Hamilton, Jonah Cool, Jacqueline E. Schein, Stacey M. Curry, Athula Wikramanayke, Seth Carbonneau, Blair J. Rossetti, Christopher E. Killian, Melissa J. Landrum, Amanda P. Rawson, Jenifer C. Croce, Ryan C. Range, Rahul Satija, John J. Stegeman, Yufeng Shen, Cavit Agca, Terry Gaasterland, Rocky Cheung, Takae Kiyama, Nikki Adams, Jonathan P. Rast, Robert Piotr Olinski, Andrew Cree, Mark Scally, Shuguang Liang, David A. Parker, Rebecca Thomason, Gretchen E. Hofmann, Michelle M. Roux, Ronghui Xu, Robert A. Obar, Enrique Arboleda, Odile Mulner-Lorillon, Shannon Dugan-Rocha, David J. Bottjer, Gabriele Amore, Manoj P. Samanta, Waraporn Tongprasit, Véronique Duboc, La Ronda Jackson, Fred H. Wilt, Viktor Stolc, Anna T. Neill, Michael Raisch, Pei Yun Lee, Jia L. Song, Margaret Morgan, Brian T. Livingston, Sofia Hussain, Zheng Wei, Bryan J. Cole, Tonya F. Severson, Victor V. Solovyev, Finn Hallböök, Donna M. Muzny, Christine A. Byrum, Albert J. Poustka, Xiuqian Mu, Andrew R. Jackson, Shin Heesun, Euan R. Brown, Nansheng Chen, Patrick Cormier, Ralph Haygood, Pedro Martinez, R. Andrew Cameron, D. Wang, Wendy S. Beane, Eric H. Davidson, Christie Kovar, Hemant Kelkar, Charles A. Ettensohn, Sham V. Nair, Robert L. Morris, Stefan C. Materna, Michael C. Thorndyke, Richard A. Gibbs, Dan O Mellott, Department of Physiology and Biophysics, Stony Brook University [The State University of New York] ( SBU ), Astronomy Unit ( AU ), Queen Mary University of London ( QMUL ), Urban and Industrial Air Quality Group, CSIRO Energy Technology, Commonwealth Scientific and Industrial Research Organisation Energy Technology ( CSIRO Energy Technology ), Commonwealth Scientific and Industrial Research Organisation, Center for Polymer Studies ( CPS ), Boston University [Boston] ( BU ), Physics Department [Boston] ( BU-Physics ), Max Planck Institute for Psycholinguistics, Max-Planck-Institut, Department of Biology [Norton], Wheaton College [Norton], Mathematical Institute [Oxford] ( MI ), University of Oxford [Oxford], Centre for the Analysis of Time Series ( CATS ), London School of Economics and Political Science ( LSE ), Thomas Jefferson National Accelerator Facility ( Jefferson Lab ), Thomas Jefferson National Accelerator Facility, Laboratoire d'Energétique et de Mécanique Théorique Appliquée ( LEMTA ), Université de Lorraine ( UL ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire Evolution, Génomes et Spéciation ( LEGS ), Centre National de la Recherche Scientifique ( CNRS ), Department of Geology, University of Illinois at Urbana-Champaign [Urbana], Department of Electrical and Computer Engineering [Portland] ( ECE ), Portland State University [Portland] ( PSU ), Saint-Gobain Crystals [USA], SAINT-GOBAIN, Institute for Animal Health ( IAH ), Biotechnology and Biological Sciences Research Council, Center for Agricultural Resources Research, Chinese Academy of Sciences [Changchun Branch] ( CAS ), Ipsen Inc. [Milford] ( Ipsen ), IPSEN, Department of Physics [Berkeley], University of California [Berkeley], Institute for Climate and Atmospheric Science [Leeds] ( ICAS ), University of Leeds, Chung-Ang University ( CAU ), Chung-Ang University [Seoul], Antarctic Climate and Ecosystems Cooperative Research Center ( ACE-CRC ), Institute of Aerodynamics and Fluid Mechanics ( AER ), Technische Universität München [München] ( TUM ), Mer et santé ( MS ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Centre National de la Recherche Scientifique ( CNRS ), Imperial College London, Radio and Atmospheric Sciences Division, National Physical Laboratory [Teddington] ( NPL ), International Research Institute for Climate and Society ( IRI ), Earth Institute at Columbia University, Columbia University [New York]-Columbia University [New York], Soils Group, The Macaulay Institute, Department of Haematology, University of Cambridge [UK] ( CAM ), School of Biology and Biochemistry, Queen's University, Leslie Hill Institute for Plant Conservation ( PCU ), University of Cape Town, Institute for Microelectronics and Microsystems/ Istituto per la Microelettronica e Microsistemi ( IMM ), Consiglio Nazionale delle Ricerche ( CNR ), Laboratoire d'acoustique de l'université du Mans ( LAUM ), Le Mans Université ( UM ) -Centre National de la Recherche Scientifique ( CNRS ), Interactive Systems Labs ( ISL ), Carnegie Mellon University [Pittsburgh] ( CMU ), Dalian Institute of Chemical Physics ( DICP ), Architectures, Languages and Compilers to Harness the End of Moore Years ( ALCHEMY ), Laboratoire de Recherche en Informatique ( LRI ), Université Paris-Sud - Paris 11 ( UP11 ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -CentraleSupélec-Centre National de la Recherche Scientifique ( CNRS ) -Université Paris-Sud - Paris 11 ( UP11 ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -CentraleSupélec-Centre National de la Recherche Scientifique ( CNRS ) -Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique ( Inria ), Clean Air Task Force ( CATF ), Clean Air Task Force, Space Physics Laboratory, Indian Space Research Organisation ( ISRO ), Centre d'études et de recherches appliquées à la gestion ( CERAG ), Université Pierre Mendès France - Grenoble 2 ( UPMF ) -Centre National de la Recherche Scientifique ( CNRS ), Department of Microbiology and Immunology, College of Medicine and Health Sciences-Sultan Qaboos University, European Molecular Biology Laboratory [Heidelberg] ( EMBL ), Department of Biostatistics, University of Michigan [Ann Arbor], Department of Radiation Oncology [Michigan] ( Radonc ), Department of Physics and Astronomy [Leicester], University of Leicester, Informatique, Biologie Intégrative et Systèmes Complexes ( IBISC ), Université d'Évry-Val-d'Essonne ( UEVE ) -Centre National de la Recherche Scientifique ( CNRS ), Institut für Meteorologie und Klimaforschung ( IMK ), Karlsruher Institut für Technologie ( KIT ), Physics Department [UNB], University of New Brunswick ( UNB ), Laboratoire Parole et Langage ( LPL ), Centre National de la Recherche Scientifique ( CNRS ) -Aix Marseille Université ( AMU ), Institut des Sciences Chimiques de Rennes ( ISCR ), Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -Ecole Nationale Supérieure de Chimie de Rennes-Institut National des Sciences Appliquées ( INSA ) -Centre National de la Recherche Scientifique ( CNRS ), Biogéosciences [Dijon] ( BGS ), Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique ( CNRS ), Bioprojet, Laboratoire de Matériaux à Porosité Contrôlée ( LMPC ), Université de Haute-Alsace (UHA) Mulhouse - Colmar ( Université de Haute-Alsace (UHA) ) -Ecole Nationale Supérieure de Chimie de Mulhouse-Centre National de la Recherche Scientifique ( CNRS ), School of Information Engineering [USTB] ( SIE ), University of Science and Technology Beijing [Beijing] ( USTB ), Laboratory for Atmospheric and Space Physics [Boulder] ( LASP ), University of Colorado Boulder [Boulder], Department of Applied Mathematics [Sheffield], University of Sheffield [Sheffield], School of Mathematics and Statistics [Sheffield] ( SoMaS ), Laboratoire de Mécanique de Lille - FRE 3723 ( LML ), Université de Lille, Sciences et Technologies-Ecole Centrale de Lille-Centre National de la Recherche Scientifique ( CNRS ), Computer Science Department [UCLA] ( CSD ), University of California at Los Angeles [Los Angeles] ( UCLA ), Développement et évolution ( DE ), Université Paris-Sud - Paris 11 ( UP11 ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de Biologie du Développement de Villefranche sur mer ( LBDV ), Laboratoire Pierre Aigrain ( LPA ), Fédération de recherche du Département de physique de l'Ecole Normale Supérieure - ENS Paris ( FRDPENS ), Centre National de la Recherche Scientifique ( CNRS ) -École normale supérieure - Paris ( ENS Paris ) -Centre National de la Recherche Scientifique ( CNRS ) -École normale supérieure - Paris ( ENS Paris ) -Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Université Paris Diderot - Paris 7 ( UPD7 ) -Centre National de la Recherche Scientifique ( CNRS ), Department of Mathematics and Statistics [Mac Gill], McGill University, Departamento de Botánica [Comahue], Universidad nacional del Comahue, Bioénergétique Cellulaire et Pathologique ( BECP ), Université Joseph Fourier - Grenoble 1 ( UJF ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ), Environnements et Paléoenvironnements OCéaniques ( EPOC ), Observatoire aquitain des sciences de l'univers ( OASU ), Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers ( INSU - CNRS ) -Centre National de la Recherche Scientifique ( CNRS ) -Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers ( INSU - CNRS ) -Centre National de la Recherche Scientifique ( CNRS ) -École pratique des hautes études ( EPHE ) -Centre National de la Recherche Scientifique ( CNRS ), Institut Jacques Monod ( IJM ), Université Paris Diderot - Paris 7 ( UPD7 ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratori Nazionali del Sud ( LNS ), National Institute for Nuclear Physics ( INFN ), Departament de Matemàtiques [Barcelona], Universitat Autònoma de Barcelona [Barcelona] ( UAB ), Max-Planck-Institut für Kohlenforschung (coal research), Institute of Oceanology [CAS] ( IOCAS ), National Chiao Tung University ( NCTU ), Department of Hydrology and Water Resources ( HWR ), University of Arizona, Centre for Educational Technology, Environment Department [York], University of York [York, UK], State Key Laboratory of Nuclear Physics and Technology ( SKL-NPT ), Peking University [Beijing], Department of Physics and Astronomy [Iowa City], University of Iowa [Iowa], NASA Ames Research Center ( ARC ), Department of Materials, Digital Language & Knowledge Contents Research Association ( DICORA ), Hankuk University of Foreign Studies, Department of Physics [Coventry], University of Warwick [Coventry], Space Science and Technology Department [Didcot] ( RAL Space ), STFC Rutherford Appleton Laboratory ( RAL ), Science and Technology Facilities Council ( STFC ) -Science and Technology Facilities Council ( STFC ), Institut de biologie et chimie des protéines [Lyon] ( IBCP ), Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique ( CNRS ), H M Nautical Almanac Office [RAL] ( HMNAO ), Rutherford Appleton Laboratory, United Kingdom Met Office [Exeter], University College of London [London] ( UCL ), Department of Pathology and Laboratory Medicine [UCLA], University of California at Los Angeles [Los Angeles] ( UCLA ) -School of Medicine, School of Earth and Environmental Sciences [Seoul] ( SEES ), Seoul National University [Seoul], Department of Chemistry, Seoul Women's University, MicroMachines Centre ( MMC ), Nanyang Technological University [Singapour], Regroupement Québécois sur les Matériaux de Pointe ( RQMP ), École Polytechnique de Montréal ( EPM ) -Université de Sherbrooke [Sherbrooke]-McGill University-Université de Montréal-Fonds Québécois de Recherche sur la Nature et les Technologies ( FQRNT ), Département de Physique [Montréal], Université de Montréal, School of Earth and Environment [Leeds] ( SEE ), Centre for Ecology and Hydrology ( CEH ), Natural Environment Research Council ( NERC ), Norwegian Institute for Water Research ( NIVA ), Norwegian Institute for Water Research, Stony Brook University [SUNY] (SBU), State University of New York (SUNY)-State University of New York (SUNY), Astronomy Unit [London] (AU), Queen Mary University of London (QMUL), Commonwealth Scientific and Industrial Research Organisation Energy Technology (CSIRO Energy Technology), Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), Department of Biochemistry and Molecular Biology [Houston], The University of Texas Medical School at Houston, Mathematical Institute [Oxford] (MI), University of Oxford, Centre for the Analysis of Time Series (CATS), London School of Economics and Political Science (LSE), Thomas Jefferson National Accelerator Facility (Jefferson Lab), Laboratoire Énergies et Mécanique Théorique et Appliquée (LEMTA ), Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Evolution, Génomes et Spéciation (LEGS), Centre National de la Recherche Scientifique (CNRS), University of Illinois System-University of Illinois System, Department of Electrical and Computer Engineering [Portland] (ECE), Portland State University [Portland] (PSU), Saint-Gobain, Institute for Animal Health (IAH), Biotechnology and Biological Sciences Research Council (BBSRC), Chinese Academy of Sciences [Changchun Branch] (CAS), Ipsen Inc. [Milford] (Ipsen), University of California [Berkeley] (UC Berkeley), University of California (UC)-University of California (UC), Institute for Climate and Atmospheric Science [Leeds] (ICAS), School of Earth and Environment [Leeds] (SEE), University of Leeds-University of Leeds, Chung-Ang University (CAU), Antarctic Climate and Ecosystems Cooperative Research Centre (ACE-CRC), Institute of Aerodynamics and Fluid Mechanics (AER), Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), Mer et santé (MS), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), National Physical Laboratory [Teddington] (NPL), International Research Institute for Climate and Society (IRI), Macaulay Institute, University of Cambridge [UK] (CAM), Queen's University [Kingston, Canada], Leslie Hill Institute for Plant Conservation (PCU), Istituto per la Microelettronica e Microsistemi [Catania] (IMM), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Laboratoire d'Acoustique de l'Université du Mans (LAUM), Le Mans Université (UM)-Centre National de la Recherche Scientifique (CNRS), Interactive Systems Labs (ISL), Carnegie Mellon University [Pittsburgh] (CMU), Dalian Institute of Chemical Physics (DICP), Architectures, Languages and Compilers to Harness the End of Moore Years (ALCHEMY), Laboratoire de Recherche en Informatique (LRI), Université Paris-Sud - Paris 11 (UP11)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Clean Air Task Force (CATF), Indian Space Research Organisation (ISRO), Centre d'études et de recherches appliquées à la gestion (CERAG), Université Pierre Mendès France - Grenoble 2 (UPMF)-Centre National de la Recherche Scientifique (CNRS), Sultan Qaboos University (SQU)-College of Medicine and Health Sciences [Baylor], Baylor University-Baylor University, European Molecular Biology Laboratory [Heidelberg] (EMBL), University of Michigan System-University of Michigan System, Department of Radiation Oncology [Michigan] (Radonc), Informatique, Biologie Intégrative et Systèmes Complexes (IBISC), Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Institute for Meteorology and Climate Research (IMK), Karlsruhe Institute of Technology (KIT), University of New Brunswick (UNB), Laboratoire Parole et Langage (LPL), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut des Sciences Chimiques de Rennes (ISCR), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Biogéosciences [UMR 6282] (BGS), Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Matériaux à Porosité Contrôlée (LMPC), Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS), School of Information Engineering [USTB] (SIE), University of Science and Technology Beijing [Beijing] (USTB), Laboratory for Atmospheric and Space Physics [Boulder] (LASP), University of Colorado [Boulder], School of Mathematics and Statistics [Sheffield] (SoMaS), Laboratoire de Mécanique de Lille - FRE 3723 (LML), Université de Lille, Sciences et Technologies-Centrale Lille-Centre National de la Recherche Scientifique (CNRS), Computer Science Department [UCLA] (CSD), University of California [Los Angeles] (UCLA), Développement et évolution (DE), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biologie du Développement de Villefranche sur mer (LBDV), Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Pierre Aigrain (LPA), Fédération de recherche du Département de physique de l'Ecole Normale Supérieure - ENS Paris (FRDPENS), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Department of Mathematics and Statistics [Montréal], McGill University = Université McGill [Montréal, Canada], Departamento de Botánica [Bariloche], Centro Regional Universitario Bariloche [Bariloche] (CRUB), Universidad Nacional del Comahue [Neuquén] (UNCOMA)-Universidad Nacional del Comahue [Neuquén] (UNCOMA), Bioénergétique Cellulaire et Pathologique (BECP), Université Joseph Fourier - Grenoble 1 (UJF)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Environnements et Paléoenvironnements OCéaniques (EPOC), Observatoire aquitain des sciences de l'univers (OASU), Université Sciences et Technologies - Bordeaux 1 (UB)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Sciences et Technologies - Bordeaux 1 (UB)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Institut Jacques Monod (IJM (UMR_7592)), Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Laboratori Nazionali del Sud (LNS), Istituto Nazionale di Fisica Nucleare (INFN), Departament de Matemàtiques [Barcelona] (UAB), Universitat Autònoma de Barcelona (UAB), Max-Planck-Institut für Kohlenforschung (Coal Research), Max-Planck-Gesellschaft, CAS Institute of Oceanology (IOCAS), Chinese Academy of Sciences [Beijing] (CAS), National Chiao Tung University (NCTU), Department of Hydrology and Water Resources (HWR), State Key Laboratory of Nuclear Physics and Technology (SKL-NPT), University of Iowa [Iowa City], NASA Ames Research Center (ARC), Digital Language & Knowledge Contents Research Association (DICORA), Space Science and Technology Department [Didcot] (RAL Space), STFC Rutherford Appleton Laboratory (RAL), Science and Technology Facilities Council (STFC)-Science and Technology Facilities Council (STFC), Institut de biologie et chimie des protéines [Lyon] (IBCP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), H M Nautical Almanac Office [RAL] (HMNAO), University College of London [London] (UCL), University of California (UC)-University of California (UC)-School of Medicine, School of Earth and Environmental Sciences [Seoul] (SEES), Seoul National University [Seoul] (SNU), MicroMachines Centre (MMC), Regroupement Québécois sur les Matériaux de Pointe (RQMP), École Polytechnique de Montréal (EPM)-Université de Sherbrooke (UdeS)-McGill University = Université McGill [Montréal, Canada]-Université de Montréal (UdeM)-Fonds Québécois de Recherche sur la Nature et les Technologies (FQRNT), Université de Montréal (UdeM), Centre for Ecology and Hydrology (CEH), Natural Environment Research Council (NERC), Norwegian Institute for Water Research (NIVA), SEA URCHIN GENOME SEQUENCING CONSORTIUM, SODERGREN E, WEINSTOCK GM, DAVIDSON EH, CAMERON RA, GIBBS RA, ANGERER RC, ANGERER LM, ARNONE MI, BURGESS DR, BURKE RD, COFFMAN JA, DEAN M, ELPHICK MR, ETTENSOHN CA, FOLTZ KR, HAMDOUN A, HYNES RO, KLEIN WH, MARZLUFF W, MCCLAY DR, MORRIS RL, MUSHEGIAN A, RAST JP, SMITH LC, THORNDYKE MC, VACQUIER VD, WESSEL GM, WRAY G, ZHANG L, ELSIK CG, ERMOLAEVA O, HLAVINA W, HOFMANN G, KITTS P, LANDRUM MJ, MACKEY AJ, MAGLOTT D, PANOPOULOU G, POUSTKA AJ, PRUITT K, SAPOJNIKOV V, SONG X, SOUVOROV A, SOLOVYEV V, WEI Z, WHITTAKER CA, WORLEY K, DURBIN KJ, SHEN Y, FEDRIGO O, GARFIELD D, HAYGOOD R, PRIMUS A, SATIJA R, SEVERSON T, GONZALEZ-GARAY ML, JACKSON AR, MILOSAVLJEVIC A, TONG M, KILLIAN CE, LIVINGSTON BT, WILT FH, ADAMS N, BELLE R, CARBONNEAU S, CHEUNG R, CORMIER P, COSSON B, CROCE J, FERNANDEZ-GUERRA A, GENEVIERE AM, GOEL M, KELKAR H, MORALES J, MULNER-LORILLON O, ROBERTSON AJ, GOLDSTONE JV, COLE B, EPEL D, GOLD B, HAHN ME, HOWARD-ASHBY M, SCALLY M, STEGEMAN JJ, ALLGOOD EL, COOL J, JUDKINS KM, MCCAFFERTY SS, MUSANTE AM, OBAR RA, RAWSON AP, ROSSETTI BJ, GIBBONS IR, HOFFMAN MP, LEONE A, ISTRAIL S, MATERNA SC, SAMANTA MP, STOLC V, TONGPRASIT W, TU Q, BERGERON KF, BRANDHORST BP, WHITTLE J, BERNEY K, BOTTJER DJ, CALESTANI C, PETERSON K, CHOW E, YUAN QA, ELHAIK E, GRAUR D, REESE JT, BOSDET I, HEESUN S, MARRA MA, SCHEIN J, ANDERSON MK, BROCKTON V, BUCKLEY KM, COHEN AH, FUGMANN SD, HIBINO T, LOZA-COLL M, MAJESKE AJ, MESSIER C, NAIR SV, PANCER Z, TERWILLIGER DP, AGCA C, ARBOLEDA E, CHEN N, CHURCHER AM, HALLBOOK F, HUMPHREY GW, IDRIS MM, KIYAMA T, LIANG S, MELLOTT D, MU X, MURRAY G, OLINSKI RP, RAIBLE F, ROWE M, TAYLOR JS, TESSMAR-RAIBLE K, WANG D, WILSON KH, YAGUCHI S, GAASTERLAND T, GALINDO BE, GUNARATNE HJ, JULIANO C, KINUKAWA M, MOY GW, NEILL AT, NOMURA M, RAISCH M, READE A, ROUX MM, SONG JL, SU YH, TOWNLEY IK, VORONINA E, WONG JL, AMORE G, BRANNO M, BROWN ER, CAVALIERI, V, DUBOC V, DULOQUIN L, FLYTZANIS C, GACHE C, LAPRAZ F, LEPAGE T, LOCASCIO A, MART, University of California-University of California, Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC), Consiglio Nazionale delle Ricerche (CNR), Centre National de la Recherche Scientifique (CNRS)-Le Mans Université (UM), Centre National de la Recherche Scientifique (CNRS)-Université Pierre Mendès France - Grenoble 2 (UPMF), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Biogéosciences [UMR 6282] [Dijon] (BGS), Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Ecole Nationale Supérieure de Chimie de Mulhouse-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Diderot - Paris 7 (UPD7)-Fédération de recherche du Département de physique de l'Ecole Normale Supérieure - ENS Paris (FRDPENS), Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE), University of California-University of California-School of Medicine, Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS), Université de Lille, Sciences et Technologies-Centre National de la Recherche Scientifique (CNRS)-Centrale Lille, Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Joseph Fourier - Grenoble 1 (UJF), University of Manchester Institute of Science and Technology (UMIST), Condensed Matter Physics and Materials Science Department, Brookhaven National Laboratory, Brookhaven National Laboratory [Upton, NY] (BNL), UT-Battelle, LLC-Stony Brook University [SUNY] (SBU), State University of New York (SUNY)-State University of New York (SUNY)-U.S. Department of Energy [Washington] (DOE)-UT-Battelle, LLC-Stony Brook University [SUNY] (SBU), State University of New York (SUNY)-State University of New York (SUNY)-U.S. Department of Energy [Washington] (DOE), Baylor College of Medicine (BCM), Baylor University, Laboratoire de Traitement de l'Information Medicale (LaTIM), Université européenne de Bretagne - European University of Brittany (UEB)-Université de Brest (UBO)-Télécom Bretagne-Institut Mines-Télécom [Paris] (IMT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre Hospitalier Régional Universitaire de Brest (CHRU Brest), Laboratoire de Modélisation et Simulation Multi Echelle (MSME), Université Paris-Est Marne-la-Vallée (UPEM)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS), Duke University [Durham], Instituto Andaluz de Geofísica y Prevención de Desastres Sísmicos [Granada] (IAGPDS), Universidad de Granada (UGR), Laboratoire d'Ingénierie des Matériaux de Bretagne (LIMATB), Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-Université de Brest (UBO), University of New South Wales [Sydney] (UNSW), Celera Genomics (CRA), Celera Genomics, Paléobiodiversité et paléoenvironnements, Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Università degli Studi di Roma Tor Vergata [Roma], Unité de recherches forestières (BORDX PIERR UR ), Institut National de la Recherche Agronomique (INRA), Deptartment of Neuroscience, Uppsala University, State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology (NIGPAS-CAS), Chinese Academy of Sciences [Nanjing Branch]-Chinese Academy of Sciences [Nanjing Branch], Institut Méditerranéen d'Ecologie et de Paléoécologie (IMEP), Université Paul Cézanne - Aix-Marseille 3-Université de Provence - Aix-Marseille 1-Avignon Université (AU)-Centre National de la Recherche Scientifique (CNRS), Key Laboratory of Ocean Circulation and Waves, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China, Université Paris Diderot - Paris 7 (UPD7), Department of Physical and Environmental Sciences [Toronto], University of Toronto at Scarborough, inconnu temporaire UPEMLV, Inconnu, Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Department of Atmospheric Sciences [Seattle], University of Washington [Seattle], National Institute of Advanced Industrial Science and Technology (AIST), Department of Pharmacy, Università degli studi di Genova = University of Genoa (UniGe), Interdisciplinary Arts and Sciences Department, St. Vincent's Hospital, Sydney, Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Department of Electrical Engineering (DEE-POSTECH), Pohang University of Science and Technology (POSTECH), Centre Suisse d'Electronique et de Microtechnique SA [Neuchatel] (CSEM), Centre Suisse d'Electronique et Microtechnique SA (CSEM), Human Genome Sequencing Center [Houston] (HGSC), Brookhaven National Laboratory, Meteorological Service of Canada, 4905 Dufferin Street, Université européenne de Bretagne - European University of Brittany (UEB)-Télécom Bretagne-Centre Hospitalier Régional Universitaire de Brest (CHRU Brest)-Université de Brest (UBO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Mines-Télécom [Paris] (IMT), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Université Paris-Est Marne-la-Vallée (UPEM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Unité de Recherches Forestières, Department of Physical and Environmental Sciences, University of Toronto [Scarborough, Canada], National Institute for Nuclear Physics (INFN), University of Genoa (UNIGE), Institut de Recherche pour le Développement (IRD)-Institut Universitaire Européen de la Mer (IUEM), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Universidad de Granada = University of Granada (UGR), Laboratoire d'Energétique et de Mécanique Théorique Appliquée (LEMTA ), Technische Universität München [München] (TUM), Queen's University [Kingston], Centre National de la Recherche Scientifique (CNRS)-Université Pierre Mendès France - Grenoble 2 (UPMF)-Université Grenoble Alpes (UGA), Institut für Meteorologie und Klimaforschung (IMK), Karlsruher Institut für Technologie (KIT), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU), Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Rennes-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES), Centre National de la Recherche Scientifique (CNRS)-Université de Lille, Sciences et Technologies-Ecole Centrale de Lille-Université de Lille, Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE)-Centre National de la Recherche Scientifique (CNRS), Universitat Autònoma de Barcelona [Barcelona] (UAB), École Polytechnique de Montréal (EPM)-Université de Sherbrooke [Sherbrooke]-Université de Montréal [Montréal]-McGill University-Fonds Québécois de Recherche sur la Nature et les Technologies (FQRNT), Université de Montréal [Montréal], U.S. Department of Energy [Washington] (DOE)-UT-Battelle, LLC-Stony Brook University [SUNY] (SBU), Université de Bretagne Sud (UBS)-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-Université de Brest (UBO)-Université de Brest (UBO), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC), Université Paul Cézanne - Aix-Marseille 3-Centre National de la Recherche Scientifique (CNRS)-Avignon Université (AU)-Université de Provence - Aix-Marseille 1, Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université de Lille, Sciences et Technologies-Ecole Centrale de Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS), École normale supérieure - Paris (ENS Paris), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Male, MESH: Signal Transduction, MESH: Sequence Analysis, DNA, MESH : Transcription Factors, MESH : Calcification, Physiologic, Genome, MESH : Proteins, 0302 clinical medicine, MESH : Embryonic Development, MESH: Gene Expression Regulation, Developmental, Innate, MESH: Embryonic Development, Developmental, Nervous System Physiological Phenomena, MESH: Animals, MESH: Proteins, [SDV.BDD]Life Sciences [q-bio]/Development Biology, Complement Activation, ComputingMilieux_MISCELLANEOUS, MESH: Evolution, Molecular, MESH : Strongylocentrotus purpuratus, Genetics, 0303 health sciences, MESH: Nervous System Physiological Phenomena, Multidisciplinary, biology, Medicine (all), MESH: Immunologic Factors, Gene Expression Regulation, Developmental, Genome project, MESH: Transcription Factors, MESH : Immunity, Innate, MESH : Complement Activation, MESH: Genes, Bacterial artificial chromosome (BAC)DeuterostomesStrongylocentrotus purpuratusVertebrate innovations, Echinoderm, MESH : Nervous System Physiological Phenomena, embryonic structures, MESH: Cell Adhesion Molecules, MESH : Genes, MESH: Immunity, Innate, Sequence Analysis, Signal Transduction, MESH: Computational Biology, Genome evolution, MESH: Complement Activation, Sequence analysis, Evolution, MESH: Strongylocentrotus purpuratus, MESH : Male, Embryonic Development, MESH : Immunologic Factors, Article, MESH: Calcification, Physiologic, Calcification, MESH : Cell Adhesion Molecules, Evolution, Molecular, 03 medical and health sciences, Calcification, Physiologic, Animals, Immunologic Factors, MESH: Genome, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, MESH : Evolution, Molecular, Physiologic, Gene, Strongylocentrotus purpuratus, [ SDV.BBM ] Life Sciences [q-bio]/Biochemistry, Molecular Biology, 030304 developmental biology, MESH : Signal Transduction, Bacterial artificial chromosome, Immunity, Molecular, Computational Biology, Proteins, Cell Adhesion Molecules, Genes, Immunity, Innate, Transcription Factors, Sequence Analysis, DNA, DNA, biology.organism_classification, MESH: Male, Gene Expression Regulation, MESH : Animals, MESH : Gene Expression Regulation, Developmental, MESH : Genome, 030217 neurology & neurosurgery, MESH : Computational Biology, MESH : Sequence Analysis, DNA
Abstract

We report the sequence and analysis of the 814-megabase genome of the sea urchin Strongylocentrotus purpuratus , a model for developmental and systems biology. The sequencing strategy combined whole-genome shotgun and bacterial artificial chromosome (BAC) sequences. This use of BAC clones, aided by a pooling strategy, overcame difficulties associated with high heterozygosity of the genome. The genome encodes about 23,300 genes, including many previously thought to be vertebrate innovations or known only outside the deuterostomes. This echinoderm genome provides an evolutionary outgroup for the chordates and yields insights into the evolution of deuterostomes.

Published
2006
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178. Landscape scanning of cancer gene panels: A report from the NIH Genetic Testing Registry (GTR).

Author

Rubinstein, Wendy S., primary, Malheiro, Adriana J., additional, Kattman, Brandi L., additional, Gu, Baoshan, additional, Hem, Vichet, additional, Katz, Kenneth S., additional, Ovetsky, Michael, additional, Song, Guangfeng, additional, Villamarin-Salomon, Ricardo, additional, Wallin, Craig, additional, Maglott, Donna R., additional, and Lee, Jennifer M., additional

Published
2016
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179. Using ClinVar as a Resource to Support Variant Interpretation

Author

Harrison, Steven M., primary, Riggs, Erin R., additional, Maglott, Donna R., additional, Lee, Jennifer M., additional, Azzariti, Danielle R., additional, Niehaus, Annie, additional, Ramos, Erin M., additional, Martin, Christa L., additional, Landrum, Melissa J., additional, and Rehm, Heidi L., additional

Published
2016
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180. ClinGen--the Clinical Genome Resource.

Author

Rehm, H.L., Berg, J.S., Brooks, L.D., Bustamante, C.D., Evans, J.P., Landrum, M.J., Ledbetter, D.H., Maglott, D.R., Martin, C.L., Nussbaum, R.L., Plon, S.E., Ramos, E.M., Sherry, S.T., Watson, M.S., Loeys, B.L., et al., Rehm, H.L., Berg, J.S., Brooks, L.D., Bustamante, C.D., Evans, J.P., Landrum, M.J., Ledbetter, D.H., Maglott, D.R., Martin, C.L., Nussbaum, R.L., Plon, S.E., Ramos, E.M., Sherry, S.T., Watson, M.S., Loeys, B.L., and et al.

Abstract

Contains fulltext : 156881.pdf (publisher's version ) (Open Access)

Published
2015

181. Mitochondrial Disease Sequence Data Resource (MSeqDR): A global grass-roots consortium to facilitate deposition, curation, annotation, and integrated analysis of genomic data for the mitochondrial disease clinical and research communities

Author

Falk, M.J. (Marni J.), Shen, L. (Lishuang), Gonzalez, M. (Michael), Leipzig, J. (Jeremy), Lott, M.T. (Marie T.), Stassen, A.P.M. (Alphons P.M.), Diroma, M.A. (Maria Angela), Navarro-Gomez, D. (Daniel), Yeske, P. (Philip), Bai, R. (Renkui), Boles, R.G. (Richard G.), Brilhante, V. (Virginia), Ralph, D. (David), DaRe, J.T. (Jeana T.), Shelton, R. (Robert), Terry, S.F. (Sharon), Zhang, Z. (Zhe), Copeland, W.C. (William C.), Oven, M. (Mannis) van, Prokisch, H. (Holger), Wallace, D.C., Attimonelli, M. (Marcella), Krotoski, D. (Danuta), Zuchner, S. (Stephan), Gai, X. (Xiaowu), Bale, S. (Sherri), Bedoyan, J. (Jirair), Behar, D.M. (Doron), Bonnen, P. (Penelope), Brooks, L. (Lisa), Calabrese, C. (Claudia), Calvo, S. (Sarah), Chinnery, P.F. (Patrick), Christodoulou, J. (John), Church, D. (Deanna), Clima, R. (Rosanna), Cohen, B.H. (Bruce H.), Cotton, R.G.H. (Richard), Coo, I.F.M. (René) de, Derbenevoa, O. (Olga), Dunnen, J.T. (Johan) den, Dimmock, D. (David), Enns, G. (Gregory), Gasparre, G. (Giuseppe), Goldstein, A. (Amy), Gonzalez, I. (Iris), Gwinn, K. (Katrina), Hahn, S. (Sihoun), Haas, R.H. (Richard H.), Hakonarson, H. (Hakon), Hirano, M. (Michio), Kerr, D. (Douglas), Li, D. (Dong), Lvova, M. (Maria), Macrae, F. (Finley), Maglott, D. (Donna), McCormick, E. (Elizabeth), Mitchell, G. (Grant), Mootha, V.K. (Vamsi K.), Okazaki, Y. (Yasushi), Pujol, A. (Aurora), Parisi, M. (Melissa), Perin, J.C. (Juan Carlos), Pierce, E.A. (Eric A.), Procaccio, V. (Vincent), Rahman, S. (Shamima), Reddi, H. (Honey), Rehm, H. (Heidi), Riggs, E. (Erin), Rodenburg, R.J.T. (Richard), Rubinstein, Y. (Yaffa), Saneto, R. (Russell), Santorsola, M. (Mariangela), Scharfe, C. (Curt), Sheldon, C. (Claire), Shoubridge, E.A. (Eric), Simone, D. (Domenico), Smeets, B. (Bert), Smeitink, J.A.M. (Jan), Stanley, C. (Christine), Suomalainen, A. (Anu), Tarnopolsky, M.A. (Mark), Thiffault, I. (Isabelle), Thorburn, D.R. (David R.), Hove, J.V. (Johan Van), Wolfe, L. (Lynne), Wong, L.-J. (Lee-Jun), Falk, M.J. (Marni J.), Shen, L. (Lishuang), Gonzalez, M. (Michael), Leipzig, J. (Jeremy), Lott, M.T. (Marie T.), Stassen, A.P.M. (Alphons P.M.), Diroma, M.A. (Maria Angela), Navarro-Gomez, D. (Daniel), Yeske, P. (Philip), Bai, R. (Renkui), Boles, R.G. (Richard G.), Brilhante, V. (Virginia), Ralph, D. (David), DaRe, J.T. (Jeana T.), Shelton, R. (Robert), Terry, S.F. (Sharon), Zhang, Z. (Zhe), Copeland, W.C. (William C.), Oven, M. (Mannis) van, Prokisch, H. (Holger), Wallace, D.C., Attimonelli, M. (Marcella), Krotoski, D. (Danuta), Zuchner, S. (Stephan), Gai, X. (Xiaowu), Bale, S. (Sherri), Bedoyan, J. (Jirair), Behar, D.M. (Doron), Bonnen, P. (Penelope), Brooks, L. (Lisa), Calabrese, C. (Claudia), Calvo, S. (Sarah), Chinnery, P.F. (Patrick), Christodoulou, J. (John), Church, D. (Deanna), Clima, R. (Rosanna), Cohen, B.H. (Bruce H.), Cotton, R.G.H. (Richard), Coo, I.F.M. (René) de, Derbenevoa, O. (Olga), Dunnen, J.T. (Johan) den, Dimmock, D. (David), Enns, G. (Gregory), Gasparre, G. (Giuseppe), Goldstein, A. (Amy), Gonzalez, I. (Iris), Gwinn, K. (Katrina), Hahn, S. (Sihoun), Haas, R.H. (Richard H.), Hakonarson, H. (Hakon), Hirano, M. (Michio), Kerr, D. (Douglas), Li, D. (Dong), Lvova, M. (Maria), Macrae, F. (Finley), Maglott, D. (Donna), McCormick, E. (Elizabeth), Mitchell, G. (Grant), Mootha, V.K. (Vamsi K.), Okazaki, Y. (Yasushi), Pujol, A. (Aurora), Parisi, M. (Melissa), Perin, J.C. (Juan Carlos), Pierce, E.A. (Eric A.), Procaccio, V. (Vincent), Rahman, S. (Shamima), Reddi, H. (Honey), Rehm, H. (Heidi), Riggs, E. (Erin), Rodenburg, R.J.T. (Richard), Rubinstein, Y. (Yaffa), Saneto, R. (Russell), Santorsola, M. (Mariangela), Scharfe, C. (Curt), Sheldon, C. (Claire), Shoubridge, E.A. (Eric), Simone, D. (Domenico), Smeets, B. (Bert), Smeitink, J.A.M. (Jan), Stanley, C. (Christine), Suomalainen, A. (Anu), Tarnopolsky, M.A. (Mark), Thiffault, I. (Isabelle), Thorburn, D.R. (David R.), Hove, J.V. (Johan Van), Wolfe, L. (Lynne), and Wong, L.-J. (Lee-Jun)

Abstract

Success rates for genomic analyses of highly heterogeneous disorders can be greatly improved if a large cohort of patient data is assembled to enhance collective capabilities for accurate sequence variant annotation, analysis, and interpretation. Indeed, molecular diagnostics requires the establishment of robust data resources to enable data sharing that informs accurate understanding of genes, variants, and phenotypes. The "Mitochondrial Disease Sequence Data Resource (MSeqDR) Consortium" is a grass-roots effort facilitated by the United Mitochondrial Disease Foundation to identify and prioritize specific genomic data analysis needs of the global mitochondrial disease clinical and research community. A central Web portal (. https://mseqdr.org) facilitates the coherent compilation, organization, annotation, and analysis of sequence data from both nuclear and mitochondrial genomes of individuals and families with suspected mitochondrial disease. This Web portal provides users with a flexible and expandable suite of resources to enable variant-, gene-, and exome-level sequence analysis in a secure, Web-based, and user-friendly fashion. Users can also elect to share data with other MSeqDR Consortium members, or even the general public, either by custom annotation tracks or through the use of a convenient distributed annotation system (DAS) mechanism. A range of data visualization and analysis tools are provided to facilitate user interrogation and understanding of genomic, and ultimately phenotypic, data of relevance to mitochondrial biology and disease. Currently available tools for nuclear and mitochondrial gene analyses include an MSeqDR GBrowse instance that hosts optimized mitochondrial disease and mitochondrial DNA (mtDNA) specific annotation tracks, as well as an MSeqDR locus-specific database (LSDB) that curates variant data on more than 1300 genes that have been implicated in mitochondrial disease and/or encode mitochondria-localized proteins. MSeqDR is integr

Published
2015
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182. The Human Proteinase-activated Receptor-3 (PAR-3) Gene

Author

William C. Nierman, Lisa D. Cupit, Jean Ann Wainer, Wadie F. Bahou, Donna R. Maglott, Keith A. Moskowitz, and Valentina A. Schmidt

Subjects
Regulation of gene expression, Exon, Thrombin receptor, Gene cluster, Cell Biology, Biology, Vascular endothelial growth inhibitor, Receptor, Cell activation, Molecular Biology, Biochemistry, Molecular biology, Gene
Abstract

Proteolytically activated receptors (PARs) represent an emerging subset of seven transmembrane G protein-coupled receptors that mediate cell activation events by receptor cleavage at distinct scissile bonds located within receptor amino termini. Differential genomic blotting using a yeast artificial chromosome known to contain the PAR-1 and PAR-2 genes identified the PAR-3 gene within a PAR gene cluster spanning ∼100 kilobases at 5q13. The PAR-3 gene is relatively small (∼12 kilobases); and, like the PAR-1 and PAR-2 genes, it displays a two-exon structure, with the majority of the coding sequence and the proteolytic cleavage site contained within the larger second exon. Sequence analysis of the 5′-flanking region demonstrates that the promoter is TATA-less, similar to that seen with PAR-1, with the identification of nucleic acid motifs potentially involved in transcriptional gene regulation, including AP-1, GATA, and octameric sequences. PAR-3 transcripts were apparent in human vascular endothelial cells, although at considerably lower levels than those of PAR-1 and not significantly modulated by the endothelial cell stimulus tumor necrosis factor-α. Likewise, although PAR-3 mRNA was evident in human platelets, receptor cell surface expression was modest (∼10%) compared with that of PAR-1. Thus, although PAR-3 is postulated to represent a second thrombin receptor, its modest endothelial cell and platelet expression suggest that PAR-3 activation by α-thrombin is less relevant for physiological responses in these mature cells. Rather, given its disparately greater expression in megakaryocytes (and megakaryocyte-like human erythroleukemia cells), a regulatory role in cellular development (by protease activation) could be postulated.

Published
1998
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183. Probing structural elements in RNA using engineered disulfide cross- links

Author

Emily J. Maglott and Gary D. Glick

Subjects
Models, Molecular, Hot Temperature, Magnetic Resonance Spectroscopy, Stereochemistry, RNase P, Molecular Sequence Data, Saccharomyces cerevisiae, Biology, Nucleic Acid Denaturation, RNA, Transfer, Phe, Genetics, Disulfides, Nucleic acid structure, chemistry.chemical_classification, Base Sequence, Molecular Structure, Fungal genetics, Ribonuclease T1, RNA, RNA, Fungal, Amino acid, Cross-Linking Reagents, Biochemistry, chemistry, Transfer RNA, Nucleic Acid Conformation, Research Article
Abstract

Three analogs of unmodified yeast tRNAPhe, each possessing a single disulfide cross-link, have been designed and synthesized. One cross-link is between G1 and C72 in the amino acid acceptor stem, a second cross-link is in the central D region of yeast tRNAPhe between C11 and C25 and the third cross-link bridges U16 and C60 at the D loop/T loop interface. Air oxidation to form the cross-links is quantitative and analysis of the cross-linked products by native and denaturing PAGE, RNase T1 mapping, Pb(II) cleavage, UV cross-linking and thermal denaturation demonstrates that the disulfide bridges do not alter folding of the modified tRNAs relative to the parent sequence. The finding that cross-link formation between thiol-derivatized residues correlates with the position of these groups in the crystal structure of native yeast tRNAPhe and that the modifications do not significantly perturb native structure suggests that this methodology should be applicable to the study of RNA structure, conformational dynamics and folding pathways.

Published
1998
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184. The human thrombin receptor and proteinase activated receptor‐2 genes are tightly linked on chromosome 5q13

Author

Donna R. Maglott, Tamara V. Feldblyum, Valentina A. Schmidt, William C. Nierman, and Wadie F. Bahou

Subjects
Genetics, Yeast artificial chromosome, Genetic Linkage, Chromosome Mapping, Receptors, Cell Surface, Hematology, Biology, Blotting, Southern, Gene mapping, Cricetinae, Thrombin receptor, Gene duplication, Animals, Chromosomes, Human, Pair 5, Humans, Receptor, PAR-2, Receptors, Thrombin, Radiation hybrid mapping, Cloning, Molecular, Cell activation, Receptor, Gene
Abstract

The thrombin receptor (TR) and proteinase activated receptor-2 (PAR-2) may represent the prototypes of an emerging family of cell-surface receptors that effect cell activation events mediated by serine proteases generated during inflammatory, fibrinolytic or haemostatic-regulated pathways. To further characterize the molecular genetics of these receptors, we have refined the genetic and physical mapping of both PAR-2 and TR. Utilization of two distinct radiation hybrid mapping panels with different levels of resolution demonstrated that both genes are tightly linked to the microsatellite markers D5S424, D5S1977, D5S2529 and D5S2596 (in order of decreasing LOD scores, from 13.7 for D5S424 to 7.7 for D5S2596). Physical mapping using yeast artificial chromosomes (YACs) and inversion field gel electrophoresis demonstrated that they are maximally separate by 90 kb. If the association of TR and PAR-2 genes resulted from a relatively recent gene duplication event from a common ancestral gene, these observations provide a general framework for the identification of gene transcripts representing alternative proteolytically activated receptors which may be clustered within this region of the human genome. These observations are especially relevant given recent evidence that murine and human platelets express alternative signalling mechanisms or receptors for thrombin.

Published
1997
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186. ClinVar: public archive of relationships among sequence variation and human phenotype

Author

George R. Riley, Donna Maglott, Wonhee Jang, Melissa J. Landrum, Wendy S. Rubinstein, Deanna M. Church, and Jennifer M. Lee

Subjects
Genetics, Internet, dbSNP, computer.internet_protocol, Genome, Human, Genetic Variation, Genomics, Computational biology, Biology, Annotation, Phenotype, VI. Genomic variation, diseases and drugs, Genetic variation, Databases, Genetic, Humans, Human genome, natural sciences, Sequence variation, Human phenotype, computer, XML
Abstract

ClinVar (http://www.ncbi.nlm.nih.gov/clinvar/) provides a freely available archive of reports of relationships among medically important variants and phenotypes. ClinVar accessions submissions reporting human variation, interpretations of the relationship of that variation to human health and the evidence supporting each interpretation. The database is tightly coupled with dbSNP and dbVar, which maintain information about the location of variation on human assemblies. ClinVar is also based on the phenotypic descriptions maintained in MedGen (http://www.ncbi.nlm.nih.gov/medgen). Each ClinVar record represents the submitter, the variation and the phenotype, i.e. the unit that is assigned an accession of the format SCV000000000.0. The submitter can update the submission at any time, in which case a new version is assigned. To facilitate evaluation of the medical importance of each variant, ClinVar aggregates submissions with the same variation/phenotype combination, adds value from other NCBI databases, assigns a distinct accession of the format RCV000000000.0 and reports if there are conflicting clinical interpretations. Data in ClinVar are available in multiple formats, including html, download as XML, VCF or tab-delimited subsets. Data from ClinVar are provided as annotation tracks on genomic RefSeqs and are used in tools such as Variation Reporter (http://www.ncbi.nlm.nih.gov/variation/tools/reporter), which reports what is known about variation based on user-supplied locations.

Published
2013

187. Phenotype–Genotype Integrator (PheGenI): synthesizing genome-wide association study (GWAS) data with existing genomic resources

Author

Erin M. Ramos, Douglas W. Hoffman, Heather Junkins, Lon Phan, Donna Maglott, Mike Feolo, Lucia A. Hindorff, and Stephen T. Sherry

Subjects
Genetics, Internet, Genotype, Genome, Human, Short Report, Computational Biology, Genomics, Single-nucleotide polymorphism, Genome-wide association study, Computational biology, Tag SNP, Biology, Genome, Polymorphism, Single Nucleotide, Phenotype, Expression quantitative trait loci, Databases, Genetic, Humans, Human genome, Genetics (clinical), Software, Genetic association, Genome-Wide Association Study
Abstract

Rapidly accumulating data from genome-wide association studies (GWASs) and other large-scale studies are most useful when synthesized with existing databases. To address this opportunity, we developed the Phenotype–Genotype Integrator (PheGenI), a user-friendly web interface that integrates various National Center for Biotechnology Information (NCBI) genomic databases with association data from the National Human Genome Research Institute GWAS Catalog and supports downloads of search results. Here, we describe the rationale for and development of this resource. Integrating over 66 000 association records with extensive single nucleotide polymorphism (SNP), gene, and expression quantitative trait loci data already available from the NCBI, PheGenI enables deeper investigation and interrogation of SNPs associated with a wide range of traits, facilitating the examination of the relationships between genetic variation and human diseases.

Published
2013

189. The Transcription/<scp>DNA</scp>Repair Factor<scp>TFIIH</scp>

Author

Laura Radu, Arnaud Poterszman, and Anne Maglott-Roth

Subjects
Transcription Factor TFIIH, Xeroderma pigmentosum, medicine, Transcription factor II H, biology.protein, Helicase, Biology, Cyclin-dependent kinase 7, medicine.disease, RNA polymerase II holoenzyme, Molecular biology, Transcription factor II A, Nucleotide excision repair
Abstract

Transcription factor IIH (TFIIH) is a eukaryotic multicomponent macromolecular assembly composed of 10 subunits including two deoxyribonucleic acid (DNA)-dependent helicase activities of opposite polarities and a kinase. Mutations in the helicases xeroderma pigmentosum group D protein (XPD) and xeroderma pigmentosum group B protein (XPB) as well as in the p8/TTD-A subunit of human TFIIH are associated with three dramatic genetic disorders: xeroderma pigmentosum (XP), Cockayne syndrome (CS) and trichothiodystrophy (TTD). Initially recognised as a basal factor responsible for transcription initiation of protein coding genes and transition from initiation to elongation, TFIIH also plays a critical role in nucleotide excision repair via its DNA-opening helicase activity at the site of a lesion. A subcomplex, harbouring its kinase activity, phosphorylates the carboxy-terminal domain (CTD) of ribonucleic acid (RNA) polymerase II as well as a number of transcription regulators including nuclear hormone receptors. Key Concepts: TFIIH is a prime example of multienzyme multitasking macromolecular assembly. Recent data suggest that several components are found in nonTFIIH complexes and that the function of TFIIH is regulated by its subunit composition. The human transcription/DNA repair factor TFIIH is a multi-subunit complex composed two functional and structural entities: core-TFIIH consists of XPB, p62, p52, p44, p34 and p8, whereas the CDK-activating kinase (CAK) subcomplex contains cyclin-dependent kinase 7 (CDK7), cyclin H and MAT1. XPD bridges the core-TFIIH to the CDK activating kinase (CAK) complex, which also exists as a free complex with a distinct function. Although identified as a basal factor responsible for transcription initiation, TFIIH also plays a critical role in nucleotide excision repair and is implicated in the control of cell cycle progression. Key insights into TFIIH result from investigations centred on the analysis of mutations identified in XP, CS and TTD patients. Most mutations identified in patients reside within the noncatalytic regions of the helicases and do not affect the enzymatic activity of TFIIH per se but rather disturb the interactions of the catalytic subunits with their regulatory partners, impairing transcription and DNA repair. Keywords: transcription; DNA repair; helicase; xeroderma pigmentosum; trichothiodystrophy

Published
2013
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190. ARCH domain of XPD, an anchoring platform for CAK that conditions TFIIH DNA repair and transcription activities

Author

Izarn Iltis, Anne Maglott-Roth, Christophe Giraudon, Cathy Braun, Jean-Marc Egly, Wassim Abdulrahman, Laura Radu, Arnaud Poterszman, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and Peney, Maité

Subjects
Iron-Sulfur Proteins, Models, Molecular, Chromatin Immunoprecipitation, DNA Repair, Transcription, Genetic, [SDV.BBM.BS] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], DNA repair, Cell Line, 03 medical and health sciences, 0302 clinical medicine, Discoidin Domain Receptor 1, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, Humans, Trichothiodystrophy Syndromes, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, RNA polymerase II holoenzyme, Xeroderma Pigmentosum Group D Protein, 030304 developmental biology, Genetics, 0303 health sciences, Multidisciplinary, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], biology, General transcription factor, Reverse Transcriptase Polymerase Chain Reaction, Receptor Protein-Tyrosine Kinases, Helicase, Transcription Factor TFIIH, PNAS Plus, Mutation, biology.protein, Transcription factor II H, 030217 neurology & neurosurgery, Transcription factor II A, Nucleotide excision repair
Abstract

International audience; The xeroderma pigmentosum group D (XPD) helicase is a subunit of transcription/DNA repair factor, transcription factor II H (TFIIH) that catalyzes the unwinding of a damaged DNA duplex during nucleotide excision repair. Apart from two canonical helicase domains, XPD is composed of a 4Fe-S cluster domain involved in DNA damage recognition and a module of uncharacterized function termed the “ARCH domain.” By investigating the consequences of a mutation found in a patient with trichothiodystrophy, we show that the ARCH domain is critical for the recruitment of the cyclin-dependent kinase (CDK)-activating kinase (CAK) complex. Indeed, this mutation not only affects the interaction with the MAT1 CAK subunit, thereby decreasing the in vitro basal transcription activity of TFIIH itself and impeding the efficient recruitment of the transcription machinery on the promoter of an activated gene, but also impairs the DNA unwinding activity of XPD and the nucleotide excision repair activity of TFIIH. We further demonstrate the role of CAK in downregulating the XPD helicase activity within TFIIH. Taken together, our results identify the ARCH domain of XPD as a platform for the recruitment of CAK and as a potential molecular switch that might control TFIIH composition and play a key role in the conversion of TFIIH from a factor active in transcription to a factor involved in DNA repair.

Published
2013
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191. Getting Ready for the Human Phenome Project: The 2012 Forum of the Human Variome Project

Author

Eric Y. Zhao, Paul N. Schofield, Andreas Zankl, Carol Hamilton, Jacqueline A. L. MacArthur, Marta Girdea, John C. Carey, Sandra C. Doelken, Tudor Groza, Marc S. Greenblatt, Damian Smedley, Donna Maglott, Beverly Searle, Richard G.H. Cotton, Cynthia L. Smith, Ada Hamosh, Heidi L. Rehm, William S. Oetting, Tim Beck, Berit Kerner, Peter N. Robinson, Inge Bernstein, and Barend Mons

Subjects
Disease gene, databases, phenotype, Interoperability, database interoperability, Genetic variants, Human Variome Project, Disease, Biology, Ontology (information science), Phenome, Bioinformatics, Data science, Article, Human genetics, Genetics, Genetics (clinical), meeting report
Abstract

A forum of the Human Variome Project (HVP) was held as a satellite to the 2012 Annual Meeting of the American Society of Human Genetics in San Francisco, California. The theme of this meeting was “Getting Ready for the Human Phenome Project.” Understanding the genetic contribution to both rare single-gene “Mendelian” disorders and more complex common diseases will require integration of research efforts among many fields and better defined phenotypes. The HVP is dedicated to bringing together researchers and research populations throughout the world to provide the resources to investigate the impact of genetic variation on disease. To this end, there needs to be a greater sharing of phenotype and genotype data. For this to occur, many databases that currently exist will need to become interoperable to allow for the combining of cohorts with similar phenotypes to increase statistical power for studies attempting to identify novel disease genes or causative genetic variants. Improved systems and tools that enhance the collection of phenotype data from clinicians are urgently needed. This meeting begins the HVP’s effort toward this important goal.

Published
2013
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192. Connecting sequence and biology in the laboratory mouse

Author

Baldarelli, Richard M., Hill, David P., Blake, Judith A., Adachi, Jun, Furuno, Masaaki, Bradt, Dirck, Corbani, Lori E., Cousins, Sharon, Frazer, Kenneth S., Qi, Dong, Yang, Longlong, Ramachandran, Sridhar, Reed, Deborah, Zhu, Yunxia, Kasukawa, Takeya, Ringwald, Martin, King, Benjamin L., Maltais, Lois J., McKenzie, Louise M., Schriml, Lynn M., Maglott, Donna, Church, Deanna M., Pruitt, Kim, Eppig, Janan T., Richardson, Joel E., Kadin, Jim A., and Bult, Carol J.

Subjects
Genomes -- Research, Genetic research -- Analysis, Genetic research -- Methods, Nucleotide sequence -- Genetic aspects, Genetic transcription -- Physiological aspects, Methodology -- Analysis, Health
Abstract

The authors describe the development of the catalog of mouse genes to compose genomic. transcript and protein sequences. They report that the main focus of their study has been the RIKEN full-length enriched cDNA clone set.

Published
2003

193. Integration of Transcript and Genetic Maps of Chromosome 16 at Near-1-Mb Resolution: Demonstration of a 'Hot Spot' for Recombination at 16p12

Author

D.F. CALLEN, S.A. LANE, H. KOZMAN, G. KREMMIDIOTIS, S.A. WHITMORE, M. LOWENSTEIN, N.A. DOGGETT, N. KENMOCHI, D.C. PAGE, D.R. MAGLOTT, W.C. NIERMAN, K. MURAKAWA, R. BERRY, J.M. SIKELA, R. HOULGATTE, C. AUFFRAY, and G.R. SUTHERLAND

Subjects
Genetic Markers, Databases, Factual, Transcription, Genetic, Molecular Sequence Data, Hybrid Cells, Biology, Polymerase Chain Reaction, Genetic recombination, Cell Fusion, Mice, Chromosome 16, Gene mapping, Human Genome Project, Genetics, Animals, Humans, Gene, DNA Primers, Recombination, Genetic, Base Sequence, Gene map, Breakpoint, Chromosome Mapping, Genetic marker, Chromosome Deletion, Chromosome 22, Chromosomes, Human, Pair 16
Abstract

A single mapping resource, a mouse/human somatic cell panel with average distance between breakpoints of 1.2 Mb and a potential resolution of 1 Mb, has been utilized to integrate the genetic map and a transcript map of human chromosome 16. This map includes 141 genetic markers and 200 genes and transcripts. The localization of four genes (CHEL3, TK2, TRG1, and MMP9) reported to map to chromosome 16 could not be confirmed, and for three of these localizations to other human chromosomes are reported. A correlation between genetic and physical distance over a region estimated to be 23 Mb on the short arm of chromosome 16 identified an interval demonstrating a greatly increased rate of recombination where, in females, 1 cM is equivalent to a physical distance of 100 kb.

Published
1995
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194. Landscape scanning of cancer gene panels: A report from the NIH Genetic Testing Registry (GTR)

Author

Malheiro Aj, Brandi L. Kattman, Kenneth S. Katz, Vichet Hem, Guangfeng Song, Craig Wallin, Wendy S. Rubinstein, Baoshan Gu, Michael Ovetsky, Jennifer M. Lee, Donna Maglott, and Ricardo Villamarin-Salomon

Subjects
Oncology, Cancer Research, medicine.medical_specialty, medicine.diagnostic_test, business.industry, Bioinformatics, 03 medical and health sciences, 0302 clinical medicine, 030220 oncology & carcinogenesis, Internal medicine, Medicine, Cancer gene, business, 030217 neurology & neurosurgery, Medical literature, Genetic testing
Abstract

e13120Background: Genetic testing of tumors and germlines has proliferated in oncology, as gauged by ASCO’s meeting topics and the medical literature. A quantitative appraisal of orderable genetic ...

Published
2016
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195. Integrin α5β1 plays a critical role in resistance to temozolomide by interfering with the p53 pathway in high-grade glioma

Author

Jacqueline Lehmann-Che, Pascal Chastagner, Hana Janouskova, Catherine Bossert, Sophie Martin, Jan Teisinger, Dominique Guenot, Eric Guérin, Anne Maglott, David Y. Leger, Sophie Pinel, Fanny Noulet, François Plénat, Julien Godet, Monique Dontenwill, Natacha Entz-Werle, Laboratoire de Biophotonique et Pharmacologie - UMR 7213 (LBP), Centre National de la Recherche Scientifique (CNRS)-Réseau nanophotonique et optique, Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA)), Développement et physiopathologie de l'intestin et du pancréas, Institut National de la Santé et de la Recherche Médicale (INSERM), Centre de Recherche en Automatique de Nancy (CRAN), Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Signalisation, Génomique et Recherche Translationnelle en Oncologie (SIGRETO), Université Henri Poincaré - Nancy 1 (UHP), Pathologie et virologie moléculaire (PVM (UMR_7151)), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Diderot - Paris 7 (UPD7), and Université Paris Diderot - Paris 7 (UPD7)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Cancer Research, medicine.medical_treatment, MESH: Piperazines, MESH: Antineoplastic Agents, Alkylating, Piperazines, law.invention, Mice, 0302 clinical medicine, law, Gene expression, Cytotoxic T cell, MESH: Animals, MESH: Tumor Suppressor Protein p53, MESH: Treatment Outcome, 0303 health sciences, Brain Neoplasms, MESH: Glioblastoma, Imidazoles, MESH: Drug Resistance, Neoplasm, 3. Good health, Dacarbazine, Treatment Outcome, Oncology, 030220 oncology & carcinogenesis, MESH: Brain Neoplasms, MESH: Imidazoles, medicine.drug, Integrin alpha5beta1, MESH: Cell Line, Tumor, Integrin, [SDV.CAN]Life Sciences [q-bio]/Cancer, Biology, MESH: Dacarbazine, 03 medical and health sciences, Glioma, Cell Line, Tumor, medicine, Temozolomide, Animals, Humans, Antineoplastic Agents, Alkylating, MESH: Mice, 030304 developmental biology, Chemotherapy, MESH: Humans, MESH: Integrin alpha5beta1, Activator (genetics), medicine.disease, Drug Resistance, Neoplasm, biology.protein, Cancer research, Suppressor, Tumor Suppressor Protein p53, Glioblastoma
Abstract

Integrins play a role in the resistance of advanced cancers to radiotherapy and chemotherapy. In this study, we show that high expression of the α5 integrin subunit compromises temozolomide-induced tumor suppressor p53 activity in human glioblastoma cells. We found that depletion of the α5 integrin subunit increased p53 activity and temozolomide sensitivity. However, when cells were treated with the p53 activator nutlin-3a, the protective effect of α5 integrin on p53 activation and cell survival was lost. In a functional p53 background, nutlin-3a downregulated the α5 integrin subunit, thereby increasing the cytotoxic effect of temozolomide. Clinically, α5β1 integrin expression was associated with a more aggressive phenotype in brain tumors, and high α5 integrin gene expression was associated with decreased survival of patients with high-grade glioma. Taken together, our findings indicate that negative cross-talk between α5β1 integrin and p53 supports glioma resistance to temozolomide, providing preclinical proof-of-concept that α5β1 integrin represents a therapeutic target for high-grade brain tumors. Direct activation of p53 may remain a therapeutic option in the subset of patients with high-grade gliomas that express both functional p53 and a high level of α5β1 integrin. Cancer Res; 72(14); 3463–70. ©2012 AACR.

Published
2012
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196. Integrin α5β1 plays a critical role in resistance to temozolomide by interfering with the p53 pathway in high grade glioma

Author

Janouskova, H., Maglott, A., Leger, D.Y., Bossert, C., Noulet, F., Guérin, Emilie, Guenot, D., Pinel, S., Chastagner, P., Plenat, F., Entz-Werle, N., Lehmann-Che, J., Godet, J., Martin, S., Teisinger, J., Dontenwill, M., Laboratoire de Biophotonique et Pharmacologie - UMR 7213 (LBP), Centre National de la Recherche Scientifique (CNRS)-Réseau nanophotonique et optique, Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA)), and Barthel, Ingrid

Subjects
[SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, [SDV.BC] Life Sciences [q-bio]/Cellular Biology, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2012

197. Chromosome assignment of human brain expressed sequence tags (ESTs) by analyzing fluorescently labeled PCR products from hybrid cell panels

Author

Donna R. Maglott, W.C. Nierman, C. Jones, Huda Y. Zoghbi, A. S. Durkin, and Christine A. Kozak

Subjects
DNA, Complementary, Molecular Sequence Data, Gene Expression, Hybrid Cells, Biology, Polymerase Chain Reaction, Genome, Mice, Gene mapping, Cricetinae, Complementary DNA, Gene expression, Genetics, medicine, Animals, Humans, Molecular Biology, Genetics (clinical), Fluorescent Dyes, Expressed sequence tag, Base Sequence, Brain, Chromosome Mapping, Chromosome, DNA, Human brain, medicine.anatomical_structure, Genetic marker, Microtubule-Associated Proteins, Information Systems
Abstract

Sixty-three human brain cDNA sequences were newly assigned to individual human chromosomes. Ten of these were subregionally localized, and one was also mapped in the mouse genome. Four previously reported assignments were refined. PCR primers were designed from expressed sequence tags (ESTs) and tested for specific amplification from human genomic DNA. DNA was then amplified, often in multiplexed PCR reactions, using DNA from somatic cell hybrid mapping panels as templates. The amplification products were identified using an automated fluorescence detection system. Chromosomal assignments were made by discordancy analysis. Thirteen newly localized cDNAs exhibited homology to previously reported sequences. EST01471 was shown to correspond to human microtubule-associated protein 1B (MAP1B), confirming the previous mapping of this gene to human chromosome 5. Other genes tentatively assigned to chromosomes based on these results were a component of the signal peptide receptor of the endoplasmic reticulum (EST00745) and a cyclic AMP-regulated phosphoprotein (EST01041) on chromosome 1, a protein phosphatase 2A 55-kDa regulatory subunit (EST01650) on chromosome 4, an NAD(P) transhydrogenase (EST01744) on chromosome 5, ribosomal proteins LI a or Lib (EST01627) and L18a (EST01583), a brain transcription factor (BF-1, EST00795) on chromosome 14, a milk fat globule membrane-related protein (EST01678) on chromosome 15, a putative peptide initiation factor (EST00675) on chromosome 17, thiosulfate sulfurtransferase (TST) on chromosome 22, and moesin (MSN) (EST00896) and a human equivalent of rat spot 14 (S14) (EST00887) on Xp11→cen and Xpter→p21.3, respectively.

Published
1994
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198. Database resources of the National Center for Biotechnology Information

Author

E. W. Sayers, T. Barrett, D. A. Benson, E. Bolton, S. H. Bryant, K. Canese, V. Chetvernin, D. M. Church, M. DiCuccio, S. Federhen, M. Feolo, I. M. Fingerman, L. Y. Geer, W. Helmberg, Y. Kapustin, S. Krasnov, D. Landsman, D. J. Lipman, Z. Lu, T. L. Madden, T. Madej, D. R. Maglott, A. Marchler-Bauer, V. Miller, I. Karsch-Mizrachi, J. Ostell, A. Panchenko, L. Phan, K. D. Pruitt, G. D. Schuler, E. Sequeira, S. T. Sherry, M. Shumway, K. Sirotkin, D. Slotta, A. Souvorov, G. Starchenko, T. A. Tatusova, L. Wagner, Y. Wang, W. J. Wilbur, E. Yaschenko, and J. Ye

Subjects
Models, Molecular, 0303 health sciences, Internet, PubMed, National Library of Medicine (U.S.), Sequence Analysis, RNA, Gene Expression, Genomics, Sequence Analysis, DNA, Articles, United States, 3. Good health, Small Molecule Libraries, 03 medical and health sciences, 0302 clinical medicine, Databases as Topic, Sequence Analysis, Protein, 030220 oncology & carcinogenesis, Databases, Genetic, Genetics, natural sciences, Periodicals as Topic, Databases, Protein, Sequence Alignment, 030304 developmental biology
Abstract

In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI Website. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central (PMC), Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Primer-BLAST, COBALT, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, dbVar, Epigenomics, Genome and related tools, the Map Viewer, Model Maker, Evidence Viewer, Trace Archive, Sequence Read Archive, BioProject, BioSample, Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus (GEO), Probe, Online Mendelian Inheritance in Animals (OMIA), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART), Biosystems, Protein Clusters and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.

Published
2011

199. Pyridylthiourea-grafted polyethylenimine offers an effective assistance to siRNA-mediated gene silencing in vitro and in vivo

Author

Benoît Frisch, Eric Guérin, Gaëlle Creusat, Anne Maglott, Monique Dontenwill, Guy Zuber, Bénédicte Pons, and Jean-Sébastien Thomann

Subjects
Male, Small interfering RNA, Erythrocytes, Endosome, Cell Survival, Pharmaceutical Science, Mice, Nude, Chemical synthesis, Hemolysis, chemistry.chemical_compound, Mice, In vivo, Cell Line, Tumor, Neoplasms, Gene silencing, Animals, Humans, Polyethyleneimine, Gene Silencing, RNA, Small Interfering, Polyethylenimine, Sheep, Chemistry, Thiourea, Molecular biology, In vitro, Nucleic acid, Biophysics, Hydrophobic and Hydrophilic Interactions, Neoplasm Transplantation
Abstract

Success of synthetic interfering nucleic acids (siRNAs)-based therapy relies almost exclusively on effective, safe and preferably nanometric delivery systems which can be easily prepared, even at high concentrations. We prepared by chemical synthesis various self-assembling polymers to entrap siRNAs into stable polyplexes outside cells but with a disassembly potential upon sensing endosomal acidity. Our results revealed that pyridylthiourea-grafted polyethylenimine (πPEΙ) followed the above-mentioned principles. It led to above 90% siRNA-mediated gene silencing in vitro on U87 cells at 10 nM siRNA concentration and did not have a hemolytic activity. Assembly of siRNA/πPEΙ at high concentration was then studied and 4.5% glucose solution, pH 6.0, yielded stable colloidal solutions with sizes slightly below 100 nm for several hours. A single injection of these concentrated siRNA polyplexes into luciferase-expressing human glioblastoma tumors, which were subcutaneously xenografted into nude mice, led to a significant 30% siRNA-mediated luciferase gene silencing 4 days post-injection. Our results altogether substantiate the potential of self-assembling cationic polymers with a pH-sensitive disassembly switch for siRNA delivery in vitro and also in vivo experiments.

Published
2011

200. Is nutlin-3A a new therapeutic option for a subset of high grade glioma expressing a wild type P53 and high α5β1 integrin?

Author

Janouskova, Hana, Maglott, Anne, Leger, David Y, Bossert, Catherine, Noulet, Fanny, Guérin, Eric, Guenot, Dominique, Pinel, Sophie, Chastagner, Pascal, Plénat, François, Entz-Werlé, Natacha, Godet, Julien, Martin, Sophie, Dotenwill, Monique, Maquin, Didier, Laboratoire de Biophotonique et Pharmacologie - UMR 7213 (LBP), Centre National de la Recherche Scientifique (CNRS)-Réseau nanophotonique et optique, Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA))-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Université de Haute-Alsace (UHA) Mulhouse - Colmar (Université de Haute-Alsace (UHA)), Développement et physiopathologie de l'intestin et du pancréas, Institut National de la Santé et de la Recherche Médicale (INSERM), Signalisation, Génomique et Recherche Translationnelle en Oncologie (SIGRETO), and Université Henri Poincaré - Nancy 1 (UHP)

Subjects
[SDV.CAN] Life Sciences [q-bio]/Cancer, [SDV.CAN]Life Sciences [q-bio]/Cancer
Abstract

published in Oncologie 13(9)S4; National audience

Published
2011

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