Genomes and Genes
Summary: The complete genetic complement contained in the DNA of a set of CHROMOSOMES in a HUMAN. The length of the human genome is about 3 billion base pairs.
Publications250 found, 100 shown here
- Ultrafast and memory-efficient alignment of short DNA sequences to the human genomeBen Langmead
Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, University of Maryland, College Park, MD 20742, USA
Genome Biol 10:R25. 2009..For the human genome, Burrows-Wheeler indexing allows Bowtie to align more than 25 million reads per CPU hour with a memory ..
- A map of human genome variation from population-scale sequencingRichard M Durbin
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
Nature 467:1061-73. 2010The 1000 Genomes Project aims to provide a deep characterization of human genome sequence variation as a foundation for investigating the relationship between genotype and phenotype...
- PLINK: a tool set for whole-genome association and population-based linkage analysesShaun Purcell
Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA
Am J Hum Genet 81:559-75. 2007..Analysis of the patterns of segmental sharing has the potential to map disease loci that contain multiple rare variants in a population-based linkage analysis...
- High-resolution profiling of histone methylations in the human genomeArtem Barski
Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892, USA
Cell 129:823-37. 2007..Z, RNA polymerase II, and the insulator binding protein CTCF across the human genome using the Solexa 1G sequencing technology...
- Mapping short DNA sequencing reads and calling variants using mapping quality scoresHeng Li
The Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom
Genome Res 18:1851-8. 2008..Both read mapping and genotype calling are evaluated on simulated data and real data. MAQ is accurate, efficient, versatile, and user-friendly. It is freely available at http://maq.sourceforge.net...
- Comprehensive mapping of long-range interactions reveals folding principles of the human genomeErez Lieberman-Aiden
Broad Institute of Harvard and Massachusetts Institute of Technology MIT, MA 02139, USA
Science 326:289-93. 2009..We constructed spatial proximity maps of the human genome with Hi-C at a resolution of 1 megabase...
- Origins and functional impact of copy number variation in the human genomeDonald F Conrad
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK
Nature 464:704-12. 2010....
- Accurate whole human genome sequencing using reversible terminator chemistryDavid R Bentley
Illumina Cambridge Ltd Formerly Solexa Ltd, Chesterford Research Park, Little Chesterford, Nr Saffron Walden, Essex CB10 1XL, UK
Nature 456:53-9. 2008..We demonstrate application of this approach to human genome sequencing on flow-sorted X chromosomes and then scale the approach to determine the genome sequence of a male ..
- Principal components analysis corrects for stratification in genome-wide association studiesAlkes L Price
Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
Nat Genet 38:904-9. 2006..Our simple, efficient approach can easily be applied to disease studies with hundreds of thousands of markers...
- Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genomeMichael Weber
Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH 4058 Basel, Switzerland
Nat Genet 39:457-66. 2007..Moreover, we observe that inactive unmethylated CpG island promoters show elevated levels of dimethylation of Lys4 of histone H3, suggesting that this chromatin mark may protect DNA from methylation...
- Combinatorial patterns of histone acetylations and methylations in the human genomeZhibin Wang
Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, US National Institutes of Health, Bethesda, Maryland 20892, USA
Nat Genet 40:897-903. 2008..Our data suggest that these histone modifications may act cooperatively to prepare chromatin for transcriptional activation...
- A census of human cancer genesP Andrew Futreal
Cancer Genome Project, Human Genome Analysis Group and Pfam Group, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton Cambs, CB10 1SA, UK
Nat Rev Cancer 4:177-83. 2004
- Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot projectEwan Birney
Nature 447:799-816. 2007..generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project...
- The human genome browser at UCSCW James Kent
Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Cruz, CA 95064, USA
Genome Res 12:996-1006. 2002..The conceptual and technical framework of the browser, its underlying MYSQL database, and overall use are described. The web site currently serves over 50,000 pages per day to over 3000 different users...
- Comprehensive genomic characterization defines human glioblastoma genes and core pathwaysRoger McLendon
Nature 455:1061-8. 2008..Together, these findings establish the feasibility and power of TCGA, demonstrating that it can rapidly expand knowledge of the molecular basis of cancer...
- The protein kinase complement of the human genomeG Manning
SUGEN Inc, 230 East Grand Avenue, South San Francisco, CA 94080, USA
Science 298:1912-34. 2002We have catalogued the protein kinase complement of the human genome (the "kinome") using public and proprietary genomic, complementary DNA, and expressed sequence tag (EST) sequences...
- Genome-wide mapping of in vivo protein-DNA interactionsDavid S Johnson
Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305 5120, USA
Science 316:1497-502. 2007..NRSF; also known as REST, for repressor element-1 silencing transcription factor) to 1946 locations in the human genome. The data display sharp resolution of binding position [+/-50 base pairs (bp)], which facilitated our finding ..
- The impact of retrotransposons on human genome evolutionRichard Cordaux
CNRS UMR 6556 Ecologie, Evolution, Symbiose, Universite de Poitiers, 40 Avenue du Recteur Pineau, Poitiers, France
Nat Rev Genet 10:691-703. 2009..over the past 80 million years of primate evolution and now account for approximately one-third of the human genome. In this Review, we focus on this major class of elements and discuss the many ways that they affect the human ..
- High-resolution mapping and characterization of open chromatin across the genomeAlan P Boyle
Institute for Genome Sciences and Policy, Duke University, Durham, NC 27708, USA
Cell 132:311-22. 2008..In addition, and unexpectedly, our analyses have uncovered detailed features of nucleosome structure...
- Mutational evolution in a lobular breast tumour profiled at single nucleotide resolutionSohrab P Shah
Molecular Oncology, BC Cancer Agency, 675 West 10th Avenue, Vancouver V5Z 1L3, Canada
Nature 461:809-13. 2009..Taken together, our data show that single nucleotide mutational heterogeneity can be a property of low or intermediate grade primary breast cancers and that significant evolution can occur with disease progression...
- Widespread changes in protein synthesis induced by microRNAsMatthias Selbach
Max Delbruck Center for Molecular Medicine, Robert Rossle Str 10, D 13125 Berlin, Germany
Nature 455:58-63. 2008..Finally, our data suggest that a miRNA can, by direct or indirect effects, tune protein synthesis from thousands of genes...
- Global variation in copy number in the human genomeRichard Redon
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
Nature 444:444-54. 2006..We have constructed a first-generation CNV map of the human genome through the study of 270 individuals from four populations with ancestry in Europe, Africa or Asia (the HapMap ..
- Personalized copy number and segmental duplication maps using next-generation sequencingCan Alkan
Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
Nat Genet 41:1061-7. 2009..2 x 10(-16)). Our method can distinguish between different copies of highly identical genes, providing a more accurate assessment of gene content and insight into functional constraint without the limitations of array-based technology...
- Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's diseaseJeffrey C Barrett
Bioinformatics and Statistical Genetics, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
Nat Genet 40:955-62. 2008..The expanded molecular understanding of the basis of this disease offers promise for informed therapeutic development...
- Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genesBeate Neumann
MitoCheck Project Group, European Molecular Biology Laboratory EMBL, Meyerhofstrasse 1, D 69117 Heidelberg, Germany
Nature 464:721-7. 2010Despite our rapidly growing knowledge about the human genome, we do not know all of the genes required for some of the most basic functions of life...
- A new multipoint method for genome-wide association studies by imputation of genotypesJonathan Marchini
Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK
Nat Genet 39:906-13. 2007..A notable future use of our method will be to boost power by combining data from genome-wide scans that use different SNP sets...
- High-resolution mapping of expression-QTLs yields insight into human gene regulationJean Baptiste Veyrieras
Department of Human Genetics, The University of Chicago, Chicago, IL, USA
PLoS Genet 4:e1000214. 2008..Our results suggest an important role for mRNA stability in determining steady-state mRNA levels, and highlight the potential of eQTL mapping as a high-resolution tool for studying the determinants of gene regulation...
- The consensus coding sequences of human breast and colorectal cancersTobias Sjoblom
Ludwig Center and Howard Hughes Medical Institute, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21231, USA
Science 314:268-74. 2006The elucidation of the human genome sequence has made it possible to identify genetic alterations in cancers in unprecedented detail...
- Human microRNA genes are frequently located at fragile sites and genomic regions involved in cancersGeorge Adrian Calin
Department of Microbiology and Immunology, Division of Clinical Pharmacology, Biostatistics Section, Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
Proc Natl Acad Sci U S A 101:2999-3004. 2004..These data provide a catalog of miR genes that may have roles in cancer and argue that the full complement of miRs in a genome may be extensively involved in cancers...
- Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genomeNathaniel D Heintzman
Ludwig Institute for Cancer Research, University of California San Diego UCSD School of Medicine, 9500 Gilman Drive, La Jolla, California 92093 0653 USA
Nat Genet 39:311-8. 2007..We determined the chromatin modification states in high resolution along 30 Mb of the human genome and found that active promoters are marked by trimethylation of Lys4 of histone H3 (H3K4), whereas enhancers ..
- Annotating the human genome with Disease OntologyJohn D Osborne
Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
BMC Genomics 10:S6. 2009The human genome has been extensively annotated with Gene Ontology for biological functions, but minimally computationally annotated for diseases.
- Patterns of somatic mutation in human cancer genomesChristopher Greenman
Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
Nature 446:153-8. 2007Cancers arise owing to mutations in a subset of genes that confer growth advantage. The availability of the human genome sequence led us to propose that systematic resequencing of cancer genomes for mutations would lead to the discovery ..
- Signals of recent positive selection in a worldwide sample of human populationsJoseph K Pickrell
Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA
Genome Res 19:826-37. 2009..we present an analysis of recent selection in a global sample of 53 populations, using genotype data from the Human Genome Diversity-CEPH Panel...
- GENCODE: producing a reference annotation for ENCODEJennifer Harrow
Wellcome Trust Sanger Institute, Wellcome Trust Campus, Hinxton, Cambridge CB10 1SA, UK
Genome Biol 7:S4.1-9. 2006..This was achieved by a combination of initial manual annotation by the HAVANA team, experimental validation by the GENCODE consortium and a refinement of the annotation based on these experimental results...
- Bayesian inference of epistatic interactions in case-control studiesYu Zhang
Department of Statistics, The Pennsylvania State University, Thomas Building 422A, University Park, Pennsylvania 16802, USA
Nat Genet 39:1167-73. 2007Epistatic interactions among multiple genetic variants in the human genome may be important in determining individual susceptibility to common diseases...
- Recurring mutations found by sequencing an acute myeloid leukemia genomeElaine R Mardis
Department of Genetics, Washington University, St Louis, MO 63110, USA
N Engl J Med 361:1058-66. 2009..The full complement of DNA mutations that are responsible for the pathogenesis of acute myeloid leukemia (AML) is not yet known...
- The fundamental role of epigenetic events in cancerPeter A Jones
USC Norris Comprehensive Cancer Center, Department of Urology, Keck School of Medicine, University of Southern California, 1441 Eastlake Avenue, MS 8302L, Los Angeles, California 90089 9181, USA
Nat Rev Genet 3:415-28. 2002..In this review, we discuss these epigenetic events and the molecular alterations that might cause them and/or underlie altered gene expression in cancer...
- Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liverAlayne L Brunner
Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
Genome Res 19:1044-56. 2009..Taken together, our results indicate that hESC differentiation has a unique DNA methylation signature that may not be indicative of in vivo differentiation...
- The impact of recombination on nucleotide substitutions in the human genomeLaurent Duret
Laboratoire de Biometrie et Biologie Evolutive, Universite de Lyon, Universite Lyon 1, CNRS, UMR 5558, Villeurbanne, France
PLoS Genet 4:e1000071. 2008..We show that the predictions of this model fit very well with the observed substitution patterns in the human genome. This model notably explains the positive correlation between substitution rate and recombination rate...
- An evolutionary view of human recombinationGraham Coop
Department of Human Genetics, University of Chicago, 920 East 58th Street, Chicago, Illinois 60637, USA
Nat Rev Genet 8:23-34. 2007....
- Mapping the genetic architecture of gene expression in human liverEric E Schadt
Rosetta Inpharmatics, Seattle, Washington, United States of America
PLoS Biol 6:e107. 2008..We also identify SORT1 and CELSR2 as candidate susceptibility genes for a locus recently associated with coronary artery disease and plasma low-density lipoprotein cholesterol levels in the process...
- A small-cell lung cancer genome with complex signatures of tobacco exposureErin D Pleasance
Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
Nature 463:184-90. 2010..These findings illustrate the potential for next-generation sequencing to provide unprecedented insights into mutational processes, cellular repair pathways and gene networks associated with cancer...
- The structure of haplotype blocks in the human genomeStacey B Gabriel
Whitehead/MIT Center for Genome Research, Cambridge, MA 02139, USA
Science 296:2225-9. 2002..Projects, we characterized haplotype patterns across 51 autosomal regions (spanning 13 megabases of the human genome) in samples from Africa, Europe, and Asia...
- Mobile interspersed repeats are major structural variants in the human genomeCheng Ran Lisa Huang
Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
Cell 141:1171-82. 2010Characterizing structural variants in the human genome is of great importance, but a genome wide analysis to detect interspersed repeats has not been done...
- Genomewide rapid association using mixed model and regression: a fast and simple method for genomewide pedigree-based quantitative trait loci association analysisYurii S Aulchenko
Department of Epidemiology and Biostatistics, Erasmus MC, 3000 CA Rotterdam, The Netherlands
Genetics 177:577-85. 2007..However, there is little or no difference in empirical power of MG and the proposed method. In any scenario, GRAMMAR is much faster than MG and enables rapid analysis of hundreds of thousands of markers...
- HIV-1 integration in the human genome favors active genes and local hotspotsAstrid R W Schroder
Infectious Disease Laboratory, The Salk Institute, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
Cell 110:521-9. 2002..Here we describe mapping of 524 sites of HIV cDNA integration on the human genome sequence. Genes were found to be strongly favored as integration acceptor sites...
- Discovery and annotation of functional chromatin signatures in the human genomeGary Hon
Bioinformatics Program, University of California at San Diego, La Jolla, California, United States of America
PLoS Comput Biol 5:e1000566. 2009..To identify novel chromatin signatures in the human genome, we apply a de novo pattern-finding algorithm to genome-wide maps of histone modifications...
- MBD-isolated Genome Sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genomeDavid Serre
Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic Foundation, 9500 Euclid Ave, mail code NE50, Cleveland, OH 44195, USA
Nucleic Acids Res 38:391-9. 2010..This technique is highly specific and sensitive and can be applied to any biological settings to identify differentially methylated regions at the genomic scale...
- Towards a comprehensive structural variation map of an individual human genomeAndy W Pang
Department of Molecular Genetics, University of Toronto, 1 King s College Circle, Toronto, Ontario M5S 1A8, Canada
Genome Biol 11:R52. 2010..It is still unclear to what extent a typical genome differs from the reference assembly, and the analysis of the genomes sequenced to date have shown varying results for copy number variation (CNV) and inversions...
- Six new loci associated with blood low-density lipoprotein cholesterol, high-density lipoprotein cholesterol or triglycerides in humansSekar Kathiresan
Cardiology Division, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
Nat Genet 40:189-97. 2008..Understanding the molecular, cellular and clinical consequences of the newly identified loci may inform therapy and clinical care...
- A fine-scale map of recombination rates and hotspots across the human genomeSimon Myers
Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK
Science 310:321-4. 2005..We present a high-resolution genetic map of the human genome, based on statistical analyses of genetic variation data, and identify more than 25,000 recombination hotspots, ..
- High-resolution mapping and analysis of copy number variations in the human genome: a data resource for clinical and research applicationsTamim H Shaikh
Division of Genetics, The Children s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
Genome Res 19:1682-90. 2009..Together, this analysis and annotation provides a useful resource to assist with the assessment of CNVs in the contexts of human variation, disease susceptibility, and clinical molecular diagnostics...
- Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVsJoshua M Korn
Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
Nat Genet 40:1253-60. 2008..The Birdsuite software is applied here to data from the Affymetrix SNP 6.0 array. Additionally, we describe a method, implemented in PLINK, to utilize these combined SNP and CNV genotypes for association testing with a phenotype...
- Genetics of gene expression and its effect on diseaseValur Emilsson
deCODE Genetics, 101 Reykjavik, Iceland
Nature 452:423-8. 2008..A core network module in humans and mice was identified that is enriched for genes involved in the inflammatory and immune response and has been found to be causally associated to obesity-related traits...
- Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencingPeter J Campbell
Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
Nat Genet 40:722-9. 2008..By investigating read pairs that did not align correctly with respect to each other on the reference human genome, we characterized 306 germline structural variants and 103 somatic rearrangements to the base-pair level of ..
- Integrating multiple evidence sources to predict transcription factor binding in the human genomeJason Ernst
Machine Learning Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA
Genome Res 20:526-36. 2010..When combined with motif information our method outperforms previous methods for predicting locations of true binding...
- ChromaSig: a probabilistic approach to finding common chromatin signatures in the human genomeGary Hon
Bioinformatics Program, University of California San Diego, La Jolla, California, United States of America
PLoS Comput Biol 4:e1000201. 2008..Applying this algorithm to nine chromatin marks across a 1% sampling of the human genome in HeLa cells, we recover eight clusters of distinct chromatin signatures, five of which correspond to known ..
- Single-molecule sequencing of an individual human genomeDmitry Pushkarev
Department of Bioengineering, Stanford University and Howard Hughes Medical Institute, Stanford, California, USA
Nat Biotechnol 27:847-50. 2009..Here we report the use of single-molecule methods to sequence an individual human genome. We aligned billions of 24- to 70-bp reads (32 bp average) to approximately 90% of the National Center for ..
- A human genome structural variation sequencing resource reveals insights into mutational mechanismsJeffrey M Kidd
Department of Genome Sciences, University of Washington School of Medicine, Seattle, 98195, USA
Cell 143:837-47. 2010Understanding the prevailing mutational mechanisms responsible for human genome structural variation requires uniformity in the discovery of allelic variants and precision in terms of breakpoint delineation...
- Whole-genome analysis of histone H3 lysine 4 and lysine 27 methylation in human embryonic stem cellsGuangjin Pan
Genome Center of Wisconsin, University of Wisconsin Madison, 425 Henry Mall, Madison, WI 53706 1580, USA
Cell Stem Cell 1:299-312. 2007..Our results demonstrate that H3K27me3 modifications change during early differentiation, both relieving existing repressive domains and imparting new ones, and that colocalization with H3K4me3 is not restricted to pluripotent cells...
- Genes mirror geography within EuropeJohn Novembre
Department of Ecology and Evolutionary Biology, Interdepartmental Program in Bioinformatics, University of California Los Angeles, Los Angeles, California 90095, USA
Nature 456:98-101. 2008..variation in a sample of 3,000 European individuals genotyped at over half a million variable DNA sites in the human genome. Despite low average levels of genetic differentiation among Europeans, we find a close correspondence between ..
- Discovery and characterization of chromatin states for systematic annotation of the human genomeJason Ernst
MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, Massachusetts, USA
Nat Biotechnol 28:817-25. 2010A plethora of epigenetic modifications have been described in the human genome and shown to play diverse roles in gene regulation, cellular differentiation and the onset of disease...
- A genomewide admixture mapping panel for Hispanic/Latino populationsXianyun Mao
Department of Anthropology, The Pennsylvania State University, University Park, PA 16801, USA
Am J Hum Genet 80:1171-8. 2007..This genomewide AM panel will make it possible to apply AM approaches in many admixed populations throughout the Americas...
- Selection of genes and single nucleotide polymorphisms for fine mapping starting from a broad linkage regionAn Windelinckx
Research Center for Exercise and Health, Department of Biomedical Kinesiology, Faculty of Kinesiology and Rehabilitation Sciences, Katholieke Universiteit Leuven, Leuven, Belgium
Twin Res Hum Genet 10:871-85. 2007..This resulted in the selection of 331 polymorphisms located in 112 different candidate genes out of an initial set of 23,300 SNPs...
- Efficacy assessment of SNP sets for genome-wide disease association studiesAndreas Wollstein
Cologne Center for Genomics, Cologne, Germany
Nucleic Acids Res 35:e113. 2007..At 50% relative efficacy, the commercial marker sets cover between 19 and 68% of the human genome, depending upon the population under study...
- QuantiSNP: an Objective Bayes Hidden-Markov Model to detect and accurately map copy number variation using SNP genotyping dataStefano Colella
Genomics Laboratory, Wellcome Trust Centre for Human Genetics, Oxford, UK
Nucleic Acids Res 35:2013-25. 2007Array-based technologies have been used to detect chromosomal copy number changes (aneuploidies) in the human genome. Recent studies identified numerous copy number variants (CNV) and some are common polymorphisms that may contribute to ..
- Information capture using SNPs from HapMap and whole-genome chips differs in a sample of inflammatory and cardiovascular gene-centric regions from genome-wide estimatesChris Wallace
Clinical Pharmacology and The Genome Centre, William Harvey Research Institute, Bart s and The London School of Medicine and Dentistry, London EC1M 6BQ, United Kingdom
Genome Res 17:1596-602. 2007....
- A fast boosting-based screening method for large-scale association study in complex traits with genetic heterogeneityLu Yong Wang
Integrated Data Syst Dept, Siemens Corp Res Inc, Princeton, NJ 08540, USA
Conf Proc IEEE Eng Med Biol Soc 1:5771-4. 2006..It provides a relatively fast and fairly good tool for screening and limiting the candidate SNPs for further more complex computational modeling task...
- Coverage and characteristics of the Affymetrix GeneChip Human Mapping 100K SNP setDan L Nicolae
Department of Statistics, The University of Chicago, Chicago, Illinois, USA
PLoS Genet 2:e67. 2006....
- Ancestral genomes reconstruction: an integrated, multi-disciplinary approach is neededMariano Rocchi
Department of Genetics and Microbiology, University of Bari, Bari 70126, Italy
Genome Res 16:1441-4. 2006
- Genome-wide association analysis in sarcoidosis and Crohn's disease unravels a common susceptibility locus on 10p12.2Andre Franke
Institute for Clinical Molecular Biology, Christian Albrechts University, Kiel, Germany
Gastroenterology 135:1207-15. 2008..Crohn's disease (CD) and sarcoidosis (SA) are chronic inflammatory barrier diseases that share several clinical and immunological features, including the occurrence of granulomas...
- What can genome-wide association studies tell us about the genetics of common disease?Mark M Iles
Section of Epidemiology and Biostatistics, Leeds Institute of Molecular Medicine, University of Leeds, Leeds, United Kingdom
PLoS Genet 4:e33. 2008..Thus, although the truth of the common disease / common variant hypothesis remains undecided, recent successes suggest that there are many more common genetic disease-associated variants, requiring larger studies to be identified...
- Druggability of human disease genesMeena Kishore Sakharkar
Nanyang Centre for Supercomputing and Visualization, School of Mechanical and Aerospace Engineering MAE, Nanyang Technological University, Singapore
Int J Biochem Cell Biol 39:1156-64. 2007..to provide an accurate description of gene functions to a set of 1737 highly curated disease genes in the human genome. This analysis is the first attempt on in silico identification of druggable domains within disease genes...
- Replication of genome-wide association signals in UK samples reveals risk loci for type 2 diabetesEleftheria Zeggini
Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, OX3 7LJ, UK
Science 316:1336-41. 2007..The regions identified underscore the importance of pathways influencing pancreatic beta cell development and function in the etiology of type 2 diabetes...
- Are linkage analysis and the collection of family data dead? Prospects for family studies in the age of genome-wide associationFrancoise Clerget-Darpoux
Hum Hered 64:91-6. 2007
- MAX-rank: a simple and robust genome-wide scan for case-control association studiesQizhai Li
Biostatistics Branch, National Cancer Institute, Bethesda, MD 20892, USA
Hum Genet 123:617-23. 2008..Thus, we recommend to use MAX-rank for genome-wide scans. After the top-ranked SNPs are identified, their P-values based on MAX can be calculated and compared with the significance level...
- QuickSNP: an automated web server for selection of tagSNPsDeepak Grover
Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
Nucleic Acids Res 35:W115-20. 2007..The server is freely available and can be accessed at the URL http://bioinformoodics.jhmi.edu/quickSNP.pl...
- The complete genome of an individual by massively parallel DNA sequencingDavid A Wheeler
Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
Nature 452:872-6. 2008..However, the formidable size of the diploid human genome, approximately 6 gigabases, has prevented the routine application of sequencing methods to deciphering complete ..
- Evidence for large inversion polymorphisms in the human genome from HapMap dataVikas Bansal
Department of Computer Science and Engineering, University of California San Diego, La Jolla, California 92093 0004, USA
Genome Res 17:219-30. 2007Knowledge about structural variation in the human genome has grown tremendously in the past few years. However, inversions represent a class of structural variation that remains difficult to detect...
- Fine mapping of disease genes using tagging SNPsArvid Sjölander
Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
Ann Hum Genet 71:815-27. 2007..The issues we explore are important not only to these types of studies, but also to studies that select tSNPs based on (external) HapMap phase II data, and those that use genome-wide markers...
- Applicability of DNA pools on 500 K SNP microarrays for cost-effective initial screens in genomewide association studiesSophia J Docherty
Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, DeCrispigny Park, London, UK
BMC Genomics 8:214. 2007..We demonstrate that this approach can be effectively applied to the truly genomewide Affymetrix GeneChip Mapping 500 K Array...
- Probabilistic whole-genome alignments reveal high indel rates in the human and mouse genomesGerton Lunter
MRC Functional Genetics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, United Kingdom
Bioinformatics 23:i289-96. 2007..Here, I describe a novel and accurate method for estimating neutral indel rates between divergent pairs of genomes...
- A genome-wide association study identifies six susceptibility loci for chronic lymphocytic leukemiaMaria Chiara Di Bernardo
Section of Cancer Genetics, Institute of Cancer Research, Sutton, Surrey, UK
Nat Genet 40:1204-10. 2008..32 (rs11083846, PRKD2; P = 3.96 x 10(-9)). These data provide the first evidence for the existence of common, low-penetrance susceptibility to a hematological malignancy and new insights into disease causation in CLL...
- Microarray-based DNA methylation profiling: technology and applicationsAxel Schumacher
The Krembil Family Epigenetics Laboratory, Centre for Addiction and Mental Health, 250 College Street, Toronto, ON, Canada M5T 1R8
Nucleic Acids Res 34:528-42. 2006..The principles developed in this work will help to make epigenetic profiling of the entire human genome a routine procedure.
- A genome screen of a large bipolar affective disorder pedigree supports evidence for a susceptibility locus on chromosome 13qR F Badenhop
Garvan Institute of Medical Research, Sydney, 2010 Australia
Mol Psychiatry 6:396-403. 2001..The region on chromosome 13q14-32 has previously been implicated in other bipolar and schizophrenia cohorts. Our results provide further support for the existence of a susceptibility locus on chromosome 13q14...
- Analysis of segmental duplications and genome assembly in the mouseJeffrey A Bailey
Department of Genetics, Center for Computational Genomics, Case Western Reserve University School of Medicine and University Hospitals of Cleveland, Cleveland, Ohio 4410, USA
Genome Res 14:789-801. 2004Limited comparative studies suggest that the human genome is particularly enriched for recent segmental duplications...
- Comparative genomic analysis identifies an ADP-ribosylation factor-like gene as the cause of Bardet-Biedl syndrome (BBS3)Annie P Chiang
Department of Computer and Electrical Engineering, University of Iowa, Iowa City, IA 52242, USA
Am J Hum Genet 75:475-84. 2004..These data illustrate the power of comparative genomic analysis for the study of human disease and identifies a novel BBS gene...
- Population history and natural selection shape patterns of genetic variation in 132 genesJoshua M Akey
Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
PLoS Biol 2:e286. 2004Identifying regions of the human genome that have been targets of natural selection will provide important insights into human evolutionary history and may facilitate the identification of complex disease genes...
- Continued colonization of the human genome by mitochondrial DNAMiria Ricchetti
Unité de Génétique Moléculaire des Levures UFR 927 Univ P et M Curie and URA 2171 CNRS, Department of Structure and Dynamics of Genomes, Institut Pasteur, Paris, France
PLoS Biol 2:E273. 2004..Thus, we measured the fixation rate of NUMTs in the human genome. Six such NUMTs show insertion polymorphism and provide a useful set of DNA markers for human population ..
- A high-resolution comparative map of canine Chromosome 5q14.3-q33 constructed utilizing the 1.5x canine genome sequenceKenine E Comstock
Clinical and Human Biology Divisions, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave, D4-100, P.O. Box 19024, Seattle, Washington 98109-1024, USA
Mamm Genome 15:544-51. 2004..The corresponding region of the human genome is particularly gene rich, containing genes involved in development, metabolism, and cancer that are likely to ..
- A genome annotation-driven approach to cloning the human ORFeomeJohn E Collins
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
Genome Biol 5:R84. 2004..We obtained clones representing 70% of genes on human chromosome 22, whereas searching available cDNA clone collections found at best 48% from a single collection and 60% for all collections combined...
- Exhaustive allelic transmission disequilibrium tests as a new approach to genome-wide association studiesShin Lin
McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Broadway Research Building, Suite 475, 733 N. Broadway, Baltimore, Maryland 21205, USA
Nat Genet 36:1181-8. 2004..These results show that the theoretical benefits of genome-wide association studies are at last realizable...
- Allelic association patterns for a dense SNP mapB S Weir
Program in Statistical Genetics, Department of Statistics, North Carolina State University, Raleigh, North Carolina 27695 7566, USA
Genet Epidemiol 27:442-50. 2004..A useful preliminary investigation of datasets of this type is provided by counting the numbers of distinct multi-locus genotypes in windows of a few markers...
- Development of an integrated genome informatics, data management and workflow infrastructure: a toolbox for the study of complex disease geneticsOliver S Burren
Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Addenbrooke's Hospital, Cambridge, CB2 2XY, UK
Hum Genomics 1:98-109. 2004..Our system is applicable to any genetic study of complex disease, of either large or small scale...
- Integrative genomics: in silico coupling of rat physiology and complex traits with mouse and human dataSimon N Twigger
Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
Genome Res 14:651-60. 2004..mechanism by which physiological knowledge obtained in model systems such as the rat can be projected onto the human genome to further the research on human disease...
- Similarities and differences in genome-wide expression data of six organismsSven Bergmann
Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
PLoS Biol 2:E9. 2004..Our results demonstrate the potential of combining sequence and expression data for improving functional gene annotation and expanding our understanding of how gene expression and diversity evolved...
- SNP500Cancer: a public resource for sequence validation and assay development for genetic variation in candidate genesBernice R Packer
Intramural Research Support Program, SAIC Frederick, NCI FCRDC, Frederick, MD, USA
Nucleic Acids Res 32:D528-32. 2004..The SNP500Cancer Database is freely accessible via the web page at http://snp500cancer.nci.nih.gov/...
- Genomics. New mapping project splits the communityJennifer Couzin
Science 296:1391-3. 2002
- Evolutionary genetics. Jumbled DNA separates chimps and humansElizabeth Pennisi
Science 298:719-21. 2002
- ParaDB: a tool for paralogy mapping in vertebrate genomesMagalie Leveugle
Laboratoire d Oncologie Moleculaire, Unite 119 INSERM, Marseille, France
Nucleic Acids Res 31:63-7. 2003..In addition, we provide BLAST results for each protein sequence, InParanoid orthologs and 'In-Paralogs' data, previously established paralogy data, and, to compare vertebrates and Drosophila, orthology data...
- Informatics for unveiling hidden genome signaturesTakashi Abe
Division of Evolutionary Genetics, Department of Population Genetics, National Institute of Genetics, The Graduate University for Advanced Studies, Mishima, Shizuoka-ken 411-8540, Japan
Genome Res 13:693-702. 2003..Because the classification power is very high, the SOM is an efficient and fundamental bioinformatic strategy for extracting a wide range of genomic information from a vast amount of sequences...
- Ty3 viruslike particle morphogenesis and host interactionsSuzanne Sandmeyer; Fiscal Year: 2010Retrotransposons comprise almost half of the human genome and substantial fractions of other metazoan genomes. Nonetheless, the mechanisms and localization of retrotransposon assembly are poorly understood...
- A Haplotype Map for Multiple SclerosisStephen L Hauser; Fiscal Year: 2010..result of rapid progress in defining the landscape of genetic organization and cataloging variation across the human genome. This proposal builds on the availability of second generation, high-quality genome-wide association results ..
- True Direct Single Molecule RNA SequencingPATRICE MARIE MILOS; Fiscal Year: 2010..PUBLIC HEALTH RELEVANCE: In 2003, Human Genome Project (HGP) released a working draft of the human genome sequence...
- Genome-scale anaylsis of DNA methylation in CpG Islands with bisulfite sequencingKun Zhang; Fiscal Year: 2009..processes as well as the etiology of many human diseases However, in contrast to rapid advances in human genome sequencing, it is still impractical to characterize the methylation status of every single CpG in the human ..
- Genome-scale anaylsis of DNA methylation in CpG Islands with bisulfite sequencingKun Zhang; Fiscal Year: 2009..processes as well as the etiology of many human diseases However, in contrast to rapid advances in human genome sequencing, it is still impractical to characterize the methylation status of every single CpG in the human ..
- Genome-scale anaylsis of DNA methylation in CpG Islands with bisulfite sequencingKUN contact ZHANG; Fiscal Year: 2010..processes as well as the etiology of many human diseases However, in contrast to rapid advances in human genome sequencing, it is still impractical to characterize the methylation status of every single CpG in the human ..
- Methylation Landscape of the Human GenomeTimothy Bestor; Fiscal Year: 2003The information content of the human genome is expanded by the covalent methylation of cytosine residues, which introduces approximately 3 X 10(7) residues of 5-methylcytosine per haploid genome...
- Chemical Genomics Paradigm for Epigenetic RegulationMing Ming Zhou; Fiscal Year: 2010..in post genomic biomedical research is to translate the information encoded in genes and gene products of the human genome into an understanding of their functions in cellular physiology and patho- physiology, and into new approaches ..
- Chemical Genomics Paradigm for Epigenetic RegulationMing Ming Zhou; Fiscal Year: 2009..in post genomic biomedical research is to translate the information encoded in genes and gene products of the human genome into an understanding of their functions in cellular physiology and patho- physiology, and into new approaches ..
- Generation of an In Vivo Human Genome Transcriptional Enhancer DatasetLen Pennacchio; Fiscal Year: 2009Our ability to identify the majority of exons in the human genome has been dramatically facilitated by the availability of extensive experimental data (EST, cDNA, and protein sequences) thereby providing training sets for the development ..
- Generation of an In Vivo Human Genome Transcriptional Enhancer DatasetLen Pennacchio; Fiscal Year: 2009Our ability to identify the majority of exons in the human genome has been dramatically facilitated by the availability of extensive experimental data (EST, cDNA, and protein sequences) thereby providing training sets for the ..
- Analysis of Redox Modulated Signaling Networks in Response to Ionizing RadiationCristina Furdui; Fiscal Year: 2010..The completion of the human genome project and genetic screenings of several hundreds of human cancers over the last years, have led to the ..
- Analysis of the Human c-myc Gene Replication OriginMichael Leffak; Fiscal Year: 2009..replicator as a replication origin are the same at its endogenous chromosomal site and at ectopic sites in the human genome. In this application, the c-myc replicator will be used as a model mammalian replication origin to study the ..
- The repetitive DNA structure of the human genomePETER WARBURTON; Fiscal Year: 2009The repetitive DNA structure of the human genome The recent completion of the human genome project gives today's scientists the privileged opportunity to provide, for the first and only time, a detailed comprehensive description of ..
- Repetitive DNA structure of the human genomePETER WARBURTON; Fiscal Year: 2007The repetitive DNA structure of the human genome The recent completion of the human genome project gives today's scientists the privileged opportunity to provide, for the first and only time, a detailed comprehensive description of the ..
- Tailor-made variants of site-specific recombinases as tools for genome engineerinYuri Voziyanov; Fiscal Year: 2009..We aim to (1) identify and classify all DNA sequences in human genome that resemble native recombination target for Flp, FRT; (2) evolve Flp variants that can recombine the ..
- Tailor-made variants of site-specific recombinases as tools for genome engineerinYuri Voziyanov; Fiscal Year: 2010..We aim to (1) identify and classify all DNA sequences in human genome that resemble native recombination target for Flp, FRT;(2) evolve Flp variants that can recombine the ..
- Retrotransposon expression within ribosomal gene lociThomas H Eickbush; Fiscal Year: 2011..For example, at least 40% of the human genome is composed of these reverse transcripts...
- Retrotransposon expression within ribosomal gene lociThomas H Eickbush; Fiscal Year: 2010..For example, at least 40% of the human genome is composed of these reverse transcripts...
- Line-1 Retrotransposition in Human Embryonic Stem CellsJohn Moran; Fiscal Year: 2009..The overwhelming majority of L1s can no longer move (i.e., retrotranspose). However, the average human genome contains ~80-100 retrotransposition-competent L1s (RC-L1s) and their mobility, in both germ line and somatic ..
- Line-1 Retrotransposition in Human Embryonic Stem CellsJohn V Moran; Fiscal Year: 2010..The overwhelming majority of L1s can no longer move (i.e., retrotranspose). However, the average human genome contains ~80-100 retrotransposition-competent L1s (RC-L1s) and their mobility, in both germ line and somatic ..
- NEUROBIOLOGY AND GENETICS OF AUTISMM Spence; Fiscal Year: 2004..and ACTH respond and interact differently before and after challenge in some children with AD and (3) the Human Genome Project has provided ahead of schedule a dense map of the human genome including about half of the expressed ..
- Generation of an In Vivo Human Genome Enhancer DatasetLEN ALEXANDER PENNACCHIO; Fiscal Year: 2010..this renewal application is to identify and define the in vivo activities of a sizeable set of enhancers in the human genome to serve as a springboard for broad community access...
- A systematic RNAi-based map of C. elegans embryogenesisFabio Piano; Fiscal Year: 2007One of the next major goals of the Human Genome Project is to identify the function of all the genes it encodes...
- Quantitative Redox BiologyGarry Buettner; Fiscal Year: 2009One of the major accomplishments in biology of the last century has been the sequencing of the human genome. This has brought about a revolution, allowing researchers to gain information on cellular proteins, function, and human health ..
- Quantitative Redox BiologyGarry R Buettner; Fiscal Year: 2010One of the major accomplishments in biology of the last century has been the sequencing of the human genome. This has brought about a revolution, allowing researchers to gain information on cellular proteins, function, and human health ..
- ADDRESSING THE ISSUE OF GAP REGIONS IN GENOME SEQUENCINGJohn SantaLucia; Fiscal Year: 2001DESCRIPTION: (Adapted from the investigator's abstract) The Human Genome Project (HGP) promises to deliver a complete human genome sequence by the year 2005...
- Genome-wide Copy Number Variation and Breast Cancer RiskJirong Long; Fiscal Year: 2009..duplication and/or deletion, termed as copy number variation (CNV), has been shown to frequently occur in the human genome. CNVs account for more nucleotide variation than SNPs and they may be an unrecognized source of breast cancer ..
- Genome-wide Copy Number Variation and Breast Cancer RiskJirong Long; Fiscal Year: 2010..duplication and/or deletion, termed as copy number variation (CNV), has been shown to frequently occur in the human genome. CNVs account for more nucleotide variation than SNPs and they may be an unrecognized source of breast cancer ..