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1. Strong Association of Socioeconomic Status and Genetic Ancestry in Latinos: Implications for Admixture Studies of Type 2 Diabetes

Author

Florez, J. C., Price, A. L., Campbell, D., Riba, L., Parra, M. V., Yu, F., Duque, C., Saxena, R., Gallego, N., Tello-Ruiz, M., Franco, L., Rodríguez-Torres, M., Villegas, A., Bedoya, G., Aguilar-Salinas, C. A., Tusié-Luna, M. T., Ruiz-Linares, A., Reich, D., Gibbon, Sahra, editor, Santos, Ricardo Ventura, editor, and Sans, Mónica, editor

Published
2011
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4. Current status of the multinational Arabidopsis community

Author

Parry, Geraint, Provart, Nicholas J., Brady, Siobhan M., Uzilday, Baris, Adams, K., Araújo, W., Aubourg, S., Baginsky, S., Bakker, E., Bärenfaller, K., Batley, J., Beale, M., Beilstein, M., Belkhadir, Y., Berardini, T., Bergelson, J., Blanco-Herrera, F., Brady, S., Braun, Hans-Peter, Briggs, S., Brownfield, L., Cardarelli, M., Castellanos-Uribe, M., Coruzzi, G., Dassanayake, M., Jaeger, G.D., Dilkes, B., Doherty, C., Ecker, J., Edger, P., Edwards, D., Kasmi, F.E., Eriksson, M., Exposito-Alonso, M., Falter-Braun, P., Fernie, A., Ferro, M., Fiehn, O., Friesner, J., Greenham, K., Guo, Y., Hamann, T., Hancock, A., Hauser, M.-T., Heazlewood, J., Ho, C.-H., Hõrak, H., Huala, E., Hwang, I., Iuchi, S., Jaiswal, P., Jakobson, L., Jiang, Y., Jiao, Y., Jones, A., Kadota, Y., Khurana, J., Kliebenstein, D., Knee, E., Kobayashi, M., Koch, M., Krouk, G., Larson, T., Last, R., Lepiniec, L., Li, S., Lurin, C., Lysak, M., Maere, S., Malinowski, R., Maumus, F., May, S., Mayer, K., Mendoza-Cozatl, D., Mendoza-Poudereux, I., Meyers, B., Micol, J.L., Millar, H., Mock, H.-P., Mukhtar, K., Mukhtar, S., Murcha, M., Nakagami, H., Nakamura, Y., Nicolov, L., Nikolau, B., Nowack, M., Nunes-Nesi, A., Palmgren, M., Parry, G., Patron, N., Peck, S., Pedmale, U., Perrot-Rechenmann, C., Pieruschka, R., Pío-Beltrán, J., Pires, J.C., Provart, N., Rajjou, L., Reiser, L., Reumann, S., Rhee, S., Rigas, S., Rolland, N., Romanowski, A., Santoni, V., Savaldi-Goldstein, S., Schmitz, R., Schulze, W., Seki, M., Shimizu, K.K., Slotkin, K., Small, I., Somers, D., Sozzani, R., Spillane, C., Srinivasan, R., Taylor, N., Tello-Ruiz, M.-K., Thelen, J., Tohge, T., Town, C., Toyoda, T., Uzilday, B., Peer, Y.V.D., Wijk, K., Gillhaussen, P.V., Walley, J., Ware, D., Weckwerth, W., Whitelegge, J., Wienkoop, S., Wright, C., Wrzaczek, M., Yamazaki, M., Yanovsky, M., Žárský, V., Zhong, X., Biological Systems Engineering, Organisms and Environment Research Division, Cardiff School of Biosciences, Cardiff University, University of Toronto, University of California [Davis] (UC Davis), University of California, Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany, Department of Ecology and Evolution [Chicago], University of Chicago, Biochimie et Physiologie Moléculaire des Plantes (BPMP), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Unité de recherche en génomique végétale (URGV), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Rothamsted Research, Biotechnology and Biological Sciences Research Council (BBSRC), University of Arizona, Gregor Mendel Institute (GMI) - Vienna Biocenter (VBC), Austrian Academy of Sciences (OeAW), University of California (UC), Center for Genomics and Systems Biology, Department of Biology [New York], New York University [New York] (NYU), NYU System (NYU)-NYU System (NYU)-New York University [New York] (NYU), NYU System (NYU)-NYU System (NYU), Flanders Institute for Biotechnology, National Center for Atmospheric Research [Boulder] (NCAR), Max Planck Institute of Molecular Plant Physiology (MPI-MP), Max-Planck-Gesellschaft, Laboratoire de Biologie à Grande Échelle (BGE - UMR S1038), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA), Agricultural Sustainability Institute and Department of Neurobiology, Physiology, and Behavior, Norwegian University of Science and Technology (NTNU), University of Melbourne, King Abdullah University of Science and Technology (KAUST), University of Chinese Academy of Sciences [Beijing] (UCAS), The Sainsbury Laboratory [Norwich] (TSL), IBM Research – Tokyo, University Medical Center Groningen [Groningen] (UMCG), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre for Novel Agricultural Products, Department of Biology, University of York [York, UK], Biologie des Semences (LBS), Institut National de la Recherche Agronomique (INRA)-Institut National Agronomique Paris-Grignon (INA P-G), Sichuan University [Chengdu] (SCU), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Department of Plant Systems Biology, Unité de Recherche Génomique Info (URGI), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Nottingham, UK (UON), Institute of Bioinformatics and System Biology (IBIS), Helmholtz Zentrum München = German Research Center for Environmental Health, Saint Mary's University [Halifax], Max Planck Institute for Plant Breeding Research (MPIPZ), National Institute of Genetics (NIG), University of Copenhagen = Københavns Universitet (UCPH), Division of Biology [La Jolla], University of California [San Diego] (UC San Diego), University of California (UC)-University of California (UC), Earlham Institute [Norwich], Forschungszentrum Jülich GmbH | Centre de recherche de Juliers, Helmholtz-Gemeinschaft = Helmholtz Association, University of Missouri [Columbia] (Mizzou), University of Missouri System, Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Department of Plant Biology, Carnegie Institution for Science, Dynamique du protéome et biogenèse du chloroplaste (ChloroGenesis), Physiologie cellulaire et végétale (LPCV), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA), Plateforme de Spectrométrie de Masse Protéomique - Mass Spectrometry Proteomics Platform (MSPP), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Plant Systems Biology, Institute of Physiology and Biotechnology of plants, RIKEN Center for Sustainable Resource Science [Yokohama] (RIKEN CSRS), RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN), Unité de recherche Génétique et amélioration des plantes (GAP), Institut National de la Recherche Agronomique (INRA), Department of Biology, Duke University, Genetics and Biotechnology Lab, Plant & AgriBiosciences Research Centre (PABC), School of Natural Sciences, National University of Ireland [Galway] (NUI Galway), Universidade Federal de São Paulo, RIKEN Plant Science Center and RIKEN Bioinformatics and Systems Engineering Division, Cold Spring Harbor Laboratory (CSHL), University of Vienna [Vienna], University of California [Los Angeles] (UCLA), Department of Plant Molecular Biology, Université de Lausanne = University of Lausanne (UNIL), UKRI-BBSRC grant BB/M004376/1, HHMI Faculty Scholar Fellowship, Turkiye Bilimsel ve Teknolojik Arastirma Kurumu (TUBITAK) 118Z137, UK Research & Innovation (UKRI) Biotechnology and Biological Sciences Research Council (BBSRC) BB/M004376/1, Sainsbury Lab, Norwich Research Park, Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Helmholtz-Zentrum München (HZM), University of Copenhagen = Københavns Universitet (KU), University of California-University of California, Carnegie Institution for Science [Washington], Université de Lausanne (UNIL), Ege Üniversitesi, Organismal and Evolutionary Biology Research Programme, Plant Biology, Viikki Plant Science Centre (ViPS), Receptor-Ligand Signaling Group, University of Zurich, Parry, Geraint, Provart, Nicholas J, and Brady, Siobhan M

Subjects
0106 biological sciences, Arabidopsis thaliana, [SDV]Life Sciences [q-bio], White Paper, Genetics and Molecular Biology (miscellaneous), Plant Science, Biochemistry, 01 natural sciences, Dewey Decimal Classification::500 | Naturwissenschaften::580 | Pflanzen (Botanik), Research community, Arabidopsis, 1110 Plant Science, 0303 health sciences, Ecology, biology, 1184 Genetics, developmental biology, physiology, ddc:580, Multinational corporation, MAP, 590 Animals (Zoology), Life Sciences & Biomedicine, Arabidopsis research community, Evolution, Steering committee, Multinational Arabidopsis Steering Committee, Library science, 1301 Biochemistry, Genetics and Molecular Biology (miscellaneous), Biochemistry, Genetics and Molecular Biology (miscellaneous), Business and Economics, 10127 Institute of Evolutionary Biology and Environmental Studies, 03 medical and health sciences, Behavior and Systematics, Political science, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, MASC, roadmap, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, [SDV.GEN]Life Sciences [q-bio]/Genetics, Plant Sciences, Botany, 15. Life on land, 11831 Plant biology, biology.organism_classification, White Papers, collaboration, 1105 Ecology, Evolution, Behavior and Systematics, QK1-989, Arabidopsis Thaliana, Collaboration, Research Network, Roadmap, 570 Life sciences, 1182 Biochemistry, cell and molecular biology, 2303 Ecology, 010606 plant biology & botany
Abstract

The multinational Arabidopsis research community is highly collaborative and over the past thirty years these activities have been documented by the Multinational Arabidopsis Steering Committee (MASC). Here, we (a) highlight recent research advances made with the reference plantArabidopsis thaliana; (b) provide summaries from recent reports submitted by MASC subcommittees, projects and resources associated with MASC and from MASC country representatives; and (c) initiate a call for ideas and foci for the "fourth decadal roadmap," which will advise and coordinate the global activities of the Arabidopsis research community., UKRI-BBSRC grant [BB/M004376/1]; HHMI Faculty Scholar Fellowship; Scientific and Technological Research Council of TurkeyTurkiye Bilimsel ve Teknolojik Arastirma Kurumu (TUBITAK) [118Z137], UKRI-BBSRC grant, Grant/Award Number: BB/M004376/1; HHMI Faculty Scholar Fellowship; the Scientific and Technological Research Council of Turkey, Grant/Award Number: 118Z137

Published
2020
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6. Ship manoeuvring in waves: a literature review

Author

Tello Ruiz, M., Candries, M., Vantorre, M., Delefortrie, G., Peeters, P., and Mostaert, F.

Subjects
Ship maneuvering, Literature reviews, Seakeeping
Abstract

Manoeuvring in calm water and wave induced motion in open water have been major concerns over the past years. Although the importance of such theories, developed to improve the safety at sea, their analysis is constrained because of the assumptions and considerations employed. While the ship performs manoeuvres in open sea or sheltered areas, she is subjected to a large number of phenomena thus impairing the overall performance and increasing the probability of hazards and capsizes. Therefore, the conventional analysis of manoeuvring, based only on the horizontal motions, cannot be applied if a more realistic study of the ship dynamics is intended, thus it is necessary to incorporate the vertical motions. In this scope some light has been shed in the recent years to address these problems and the present work aims to present a literature review of the most promising methods up to date and the discussion of the relevant phenomena involved.

Published
2012

7. Strong Association of Socioeconomic Status and Genetic Ancestry in Latinos

Author

Florez, J. C., primary, Tello-Ruiz, M., primary, Franco, L., primary, Rodríguez-Torres, M., primary, Villegas, A., primary, Bedoya, G., primary, Aguilar-Salinas, C. A., primary, Tusié-Luna, M. T., primary, Ruiz-Linares, A., primary, Price, A. L., primary, Campbell, D., primary, Riba, L., primary, Parra, M. V., primary, Yu, F., primary, Duque, C., primary, Saxena, R., primary, Gallego, N., primary, and Reich, D., primary

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8. SorghumBase: a web-based portal for sorghum genetic information and community advancement.

Author

Gladman N, Olson A, Wei S, Chougule K, Lu Z, Tello-Ruiz M, Meijs I, Van Buren P, Jiao Y, Wang B, Kumar V, Kumari S, Zhang L, Burke J, Chen J, Burow G, Hayes C, Emendack Y, Xin Z, and Ware D

Subjects
Databases, Genetic, Edible Grain, Genome, Plant genetics, Genomics, Internet, Plant Breeding, Sorghum genetics
Abstract

Main Conclusion: SorghumBase provides a community portal that integrates genetic, genomic, and breeding resources for sorghum germplasm improvement. Public research and development in agriculture rely on proper data and resource sharing within stakeholder communities. For plant breeders, agronomists, molecular biologists, geneticists, and bioinformaticians, centralizing desirable data into a user-friendly hub for crop systems is essential for successful collaborations and breakthroughs in germplasm development. Here, we present the SorghumBase web portal ( https://www.sorghumbase.org ), a resource for the sorghum research community. SorghumBase hosts a wide range of sorghum genomic information in a modular framework, built with open-source software, to provide a sustainable platform. This initial release of SorghumBase includes: (1) five sorghum reference genome assemblies in a pan-genome browser; (2) genetic variant information for natural diversity panels and ethyl methanesulfonate (EMS)-induced mutant populations; (3) search interface and integrated views of various data types; (4) links supporting interconnectivity with other repositories including genebank, QTL, and gene expression databases; and (5) a content management system to support access to community news and training materials. SorghumBase offers sorghum investigators improved data collation and access that will facilitate the growth of a robust research community to support genomics-assisted breeding., (© 2022. This is a U.S. government work and not under copyright protection in the U.S.; foreign copyright protection may apply.)

Published
2022
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9. Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species.

Author

Kersey PJ, Allen JE, Allot A, Barba M, Boddu S, Bolt BJ, Carvalho-Silva D, Christensen M, Davis P, Grabmueller C, Kumar N, Liu Z, Maurel T, Moore B, McDowall MD, Maheswari U, Naamati G, Newman V, Ong CK, Paulini M, Pedro H, Perry E, Russell M, Sparrow H, Tapanari E, Taylor K, Vullo A, Williams G, Zadissia A, Olson A, Stein J, Wei S, Tello-Ruiz M, Ware D, Luciani A, Potter S, Finn RD, Urban M, Hammond-Kosack KE, Bolser DM, De Silva N, Howe KL, Langridge N, Maslen G, Staines DM, and Yates A

Subjects
Amino Acid Sequence, Animals, Base Sequence, Data Mining, Forecasting, Genome, Molecular Sequence Annotation, RNA genetics, User-Computer Interface, Archaea genetics, Bacteria genetics, Databases, Genetic, Databases, Protein, Eukaryota genetics, Genomics
Abstract

Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of programmatic and interactive interfaces to a rich range of data including genome sequence, gene models, transcript sequence, genetic variation, and comparative analysis. This paper provides an update to the previous publications about the resource, with a focus on recent developments and expansions. These include the incorporation of almost 20 000 additional genome sequences and over 35 000 tracks of RNA-Seq data, which have been aligned to genomic sequence and made available for visualization. Other advances since 2015 include the release of the database in Resource Description Framework (RDF) format, a large increase in community-derived curation, a new high-performance protein sequence search, additional cross-references, improved annotation of non-protein-coding genes, and the launch of pre-release and archival sites. Collectively, these changes are part of a continuing response to the increasing quantity of publicly-available genome-scale data, and the consequent need to archive, integrate, annotate and disseminate these using automated, scalable methods., (© The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Published
2018
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10. Ensembl Genomes 2016: more genomes, more complexity.

Author

Kersey PJ, Allen JE, Armean I, Boddu S, Bolt BJ, Carvalho-Silva D, Christensen M, Davis P, Falin LJ, Grabmueller C, Humphrey J, Kerhornou A, Khobova J, Aranganathan NK, Langridge N, Lowy E, McDowall MD, Maheswari U, Nuhn M, Ong CK, Overduin B, Paulini M, Pedro H, Perry E, Spudich G, Tapanari E, Walts B, Williams G, Tello-Ruiz M, Stein J, Wei S, Ware D, Bolser DM, Howe KL, Kulesha E, Lawson D, Maslen G, and Staines DM

Subjects
Animals, Diploidy, Eukaryota genetics, Genetic Variation, Genome, Polyploidy, Sequence Alignment, Databases, Genetic, Genome, Bacterial, Genome, Fungal, Genome, Plant, Invertebrates genetics
Abstract

Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of programmatic and interactive interfaces to a rich range of data including reference sequence, gene models, transcriptional data, genetic variation and comparative analysis. This paper provides an update to the previous publications about the resource, with a focus on recent developments. These include the development of new analyses and views to represent polyploid genomes (of which bread wheat is the primary exemplar); and the continued up-scaling of the resource, which now includes over 23 000 bacterial genomes, 400 fungal genomes and 100 protist genomes, in addition to 55 genomes from invertebrate metazoa and 39 genomes from plants. This dramatic increase in the number of included genomes is one part of a broader effort to automate the integration of archival data (genome sequence, but also associated RNA sequence data and variant calls) within the context of reference genomes and make it available through the Ensembl user interfaces., (© The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Published
2016
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11. Linkage disequilibrium mapping of the replicated type 2 diabetes linkage signal on chromosome 1q.

Author

Prokopenko I, Zeggini E, Hanson RL, Mitchell BD, Rayner NW, Akan P, Baier L, Das SK, Elliott KS, Fu M, Frayling TM, Groves CJ, Gwilliam R, Scott LJ, Voight BF, Hattersley AT, Hu C, Morris AD, Ng M, Palmer CN, Tello-Ruiz M, Vaxillaire M, Wang CR, Stein L, Chan J, Jia W, Froguel P, Elbein SC, Deloukas P, Bogardus C, Shuldiner AR, and McCarthy MI

Subjects
Adaptor Proteins, Signal Transducing genetics, Chromosome Mapping, DNA-Binding Proteins genetics, Ethnicity genetics, Gene Frequency, Genetic Variation, Histone-Lysine N-Methyltransferase, Humans, Reference Values, Risk Assessment, Transcription Factors genetics, White People genetics, Chromosomes, Human, Pair 1, Diabetes Mellitus, Type 2 genetics, Linkage Disequilibrium, Polymorphism, Single Nucleotide
Abstract

Objective: Linkage of the chromosome 1q21-25 region to type 2 diabetes has been demonstrated in multiple ethnic groups. We performed common variant fine-mapping across a 23-Mb interval in a multiethnic sample to search for variants responsible for this linkage signal., Research Design and Methods: In all, 5,290 single nucleotide polymorphisms (SNPs) were successfully genotyped in 3,179 type 2 diabetes case and control subjects from eight populations with evidence of 1q linkage. Samples were ascertained using strategies designed to enhance power to detect variants causal for 1q linkage. After imputation, we estimate approximately 80% coverage of common variation across the region (r (2) > 0.8, Europeans). Association signals of interest were evaluated through in silico replication and de novo genotyping in approximately 8,500 case subjects and 12,400 control subjects., Results: Association mapping of the 23-Mb region identified two strong signals, both of which were restricted to the subset of European-descent samples. The first mapped to the NOS1AP (CAPON) gene region (lead SNP: rs7538490, odds ratio 1.38 [95% CI 1.21-1.57], P = 1.4 x 10(-6), in 999 case subjects and 1,190 control subjects); the second mapped within an extensive region of linkage disequilibrium that includes the ASH1L and PKLR genes (lead SNP: rs11264371, odds ratio 1.48 [1.18-1.76], P = 1.0 x 10(-5), under a dominant model). However, there was no evidence for association at either signal on replication, and, across all data (>24,000 subjects), there was no indication that these variants were causally related to type 2 diabetes status., Conclusions: Detailed fine-mapping of the 23-Mb region of replicated linkage has failed to identify common variant signals contributing to the observed signal. Future studies should focus on identification of causal alleles of lower frequency and higher penetrance.

Published
2009
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12. A genomewide admixture map for Latino populations.

Author

Price AL, Patterson N, Yu F, Cox DR, Waliszewska A, McDonald GJ, Tandon A, Schirmer C, Neubauer J, Bedoya G, Duque C, Villegas A, Bortolini MC, Salzano FM, Gallo C, Mazzotti G, Tello-Ruiz M, Riba L, Aguilar-Salinas CA, Canizales-Quinteros S, Menjivar M, Klitz W, Henderson B, Haiman CA, Winkler C, Tusie-Luna T, Ruiz-Linares A, and Reich D

Subjects
Alleles, Black People, Case-Control Studies, Chromosomes, Human, Computer Simulation, Databases, Genetic, Genetic Markers, Genetic Predisposition to Disease, Genetic Testing, Humans, Indians, North American, Reproducibility of Results, White People, Black or African American, Chromosome Mapping, Genetics, Population, Genome, Human, Hispanic or Latino genetics
Abstract

Admixture mapping is an economical and powerful approach for localizing disease genes in populations of recently mixed ancestry and has proven successful in African Americans. The method holds equal promise for Latinos, who typically inherit a mix of European, Native American, and African ancestry. However, admixture mapping in Latinos has not been practical because of the lack of a map of ancestry-informative markers validated in Native American and other populations. To address this, we screened multiple databases, containing millions of markers, to identify 4,186 markers that were putatively informative for determining the ancestry of chromosomal segments in Latino populations. We experimentally validated each of these markers in at least 232 new Latino, European, Native American, and African samples, and we selected a subset of 1,649 markers to form an admixture map. An advantage of our strategy is that we focused our map on markers distinguishing Native American from other ancestries and restricted it to markers with very similar frequencies in Europeans and Africans, which decreased the number of markers needed and minimized the possibility of false disease associations. We evaluated the effectiveness of our map for localizing disease genes in four Latino populations from both North and South America.

Published
2007
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13. WormBase: a multi-species resource for nematode biology and genomics.

Author

Harris TW, Chen N, Cunningham F, Tello-Ruiz M, Antoshechkin I, Bastiani C, Bieri T, Blasiar D, Bradnam K, Chan J, Chen CK, Chen WJ, Davis P, Kenny E, Kishore R, Lawson D, Lee R, Muller HM, Nakamura C, Ozersky P, Petcherski A, Rogers A, Sabo A, Schwarz EM, Van Auken K, Wang Q, Durbin R, Spieth J, Sternberg PW, and Stein LD

Subjects
Animals, Computational Biology, Information Storage and Retrieval, Internet, User-Computer Interface, Caenorhabditis genetics, Caenorhabditis elegans genetics, Databases, Genetic, Genomics
Abstract

WormBase (http://www.wormbase.org/) is the central data repository for information about Caenorhabditis elegans and related nematodes. As a model organism database, WormBase extends beyond the genomic sequence, integrating experimental results with extensively annotated views of the genome. The WormBase Consortium continues to expand the biological scope and utility of WormBase with the inclusion of large-scale genomic analyses, through active data and literature curation, through new analysis and visualization tools, and through refinement of the user interface. Over the past year, the nearly complete genomic sequence and comparative analyses of the closely related species Caenorhabditis briggsae have been integrated into WormBase, including gene predictions, ortholog assignments and a new synteny viewer to display the relationships between the two species. Extensive site-wide refinement of the user interface now provides quick access to the most frequently accessed resources and a consistent browsing experience across the site. Unified single-page views now provide complete summaries of commonly accessed entries like genes. These advances continue to increase the utility of WormBase for C.elegans researchers, as well as for those researchers exploring problems in functional and comparative genomics in the context of a powerful genetic system.

Published
2004
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