E S Lander

Summary

Affiliation: Massachusetts Institute of Technology
Country: USA

Publications

  1. pmc Position specific variation in the rate of evolution in transcription factor binding sites
    Alan M Moses
    Graduate Group in Biophysics, University of California, Berkeley, CA 94720, USA
    BMC Evol Biol 3:19. 2003
  2. ncbi request reprint Characterization of single-nucleotide polymorphisms in coding regions of human genes
    M Cargill
    Whitehead Institute MIT Center for Genome Research, Cambridge, Massachusetts 02139, USA
    Nat Genet 22:231-8. 1999
  3. ncbi request reprint Initial sequencing and analysis of the human genome
    E S Lander
    Whitehead Institute for Biomedical Research, Center for Genome Research, Cambridge, Massachusetts 02142, USA
    Nature 409:860-921. 2001
  4. ncbi request reprint Large-scale discovery and genotyping of single-nucleotide polymorphisms in the mouse
    K Lindblad-Toh
    Whitehead Institute MIT Center for Genome Research, Whitehead Institute for Biomedical Research, Cambridge, MA, USA
    Nat Genet 24:381-6. 2000
  5. ncbi request reprint Linkage disequilibrium in the human genome
    D E Reich
    Whitehead Institute MIT Center for Genome Research, Nine Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 411:199-204. 2001
  6. ncbi request reprint Ploidy regulation of gene expression
    T Galitski
    Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
    Science 285:251-4. 1999
  7. ncbi request reprint Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome
    D G Wang
    Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA 02142, USA
    Science 280:1077-82. 1998
  8. ncbi request reprint Serrate2 is disrupted in the mouse limb-development mutant syndactylism
    A Sidow
    Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
    Nature 389:722-5. 1997
  9. ncbi request reprint The vibrator mutation causes neurodegeneration via reduced expression of PITP alpha: positional complementation cloning and extragenic suppression
    B A Hamilton
    Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
    Neuron 18:711-22. 1997
  10. ncbi request reprint The mouse pudgy mutation disrupts Delta homologue Dll3 and initiation of early somite boundaries
    K Kusumi
    Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
    Nat Genet 19:274-8. 1998

Detail Information

Publications123 found, 100 shown here

  1. pmc Position specific variation in the rate of evolution in transcription factor binding sites
    Alan M Moses
    Graduate Group in Biophysics, University of California, Berkeley, CA 94720, USA
    BMC Evol Biol 3:19. 2003
    ..Comparison of non-coding DNA from related species has shown considerable promise in identifying these functional non-coding sequences, even though relatively little is known about their evolution...
  2. ncbi request reprint Characterization of single-nucleotide polymorphisms in coding regions of human genes
    M Cargill
    Whitehead Institute MIT Center for Genome Research, Cambridge, Massachusetts 02139, USA
    Nat Genet 22:231-8. 1999
    ..The lower allele frequency of missense cSNPs has implications for the compilation of a comprehensive catalogue, as well as for the subsequent application to disease association...
  3. ncbi request reprint Initial sequencing and analysis of the human genome
    E S Lander
    Whitehead Institute for Biomedical Research, Center for Genome Research, Cambridge, Massachusetts 02142, USA
    Nature 409:860-921. 2001
    ..We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence...
  4. ncbi request reprint Large-scale discovery and genotyping of single-nucleotide polymorphisms in the mouse
    K Lindblad-Toh
    Whitehead Institute MIT Center for Genome Research, Whitehead Institute for Biomedical Research, Cambridge, MA, USA
    Nat Genet 24:381-6. 2000
    ..We have also developed a multiplex genotyping procedure by which a genome scan can be performed with only six genotyping reactions per animal...
  5. ncbi request reprint Linkage disequilibrium in the human genome
    D E Reich
    Whitehead Institute MIT Center for Genome Research, Nine Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 411:199-204. 2001
    ..By contrast, LD in a Nigerian population extends markedly less far. The results illuminate human history, suggesting that LD in northern Europeans is shaped by a marked demographic event about 27,000-53,000 years ago...
  6. ncbi request reprint Ploidy regulation of gene expression
    T Galitski
    Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
    Science 285:251-4. 1999
    ..Moreover, ploidy regulation of the FLO11 gene had direct consequences for yeast development...
  7. ncbi request reprint Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome
    D G Wang
    Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA 02142, USA
    Science 280:1077-82. 1998
    ..The results provide a characterization of human diversity at the nucleotide level and demonstrate the feasibility of large-scale identification of human SNPs...
  8. ncbi request reprint Serrate2 is disrupted in the mouse limb-development mutant syndactylism
    A Sidow
    Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
    Nature 389:722-5. 1997
    ..In addition to cloning the sm gene, we have mapped three modifiers of sm, for which we suggest possible candidate genes...
  9. ncbi request reprint The vibrator mutation causes neurodegeneration via reduced expression of PITP alpha: positional complementation cloning and extragenic suppression
    B A Hamilton
    Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
    Neuron 18:711-22. 1997
    ..The vibrator phenotype is suppressed in one intercross. We performed a complete genome scan and mapped a major suppressor locus (Mvb-1) to proximal chromosome 19...
  10. ncbi request reprint The mouse pudgy mutation disrupts Delta homologue Dll3 and initiation of early somite boundaries
    K Kusumi
    Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
    Nat Genet 19:274-8. 1998
    ..Viability analysis also indicates an important role in early development. The results point to a key role for a Notch-signalling pathway in the initiation of patterning of vertebrate paraxial mesoderm...
  11. ncbi request reprint The structure of haplotype blocks in the human genome
    Stacey B Gabriel
    Whitehead MIT Center for Genome Research, Cambridge, MA 02139, USA
    Science 296:2225-9. 2002
    ..Our results provide a foundation for the construction of a haplotype map of the human genome, facilitating comprehensive genetic association studies of human disease...
  12. ncbi request reprint High-resolution haplotype structure in the human genome
    M J Daly
    Whitehead Institute Massachusetts Institute of Technology, Center for Genome Research, Cambridge, Massachusetts, USA
    Nat Genet 29:229-32. 2001
    ..If our observed structure is general (and published data suggest that it may be), it offers a coherent framework for creating a haplotype map of the human genome...
  13. ncbi request reprint The common PPARgamma Pro12Ala polymorphism is associated with decreased risk of type 2 diabetes
    D Altshuler
    Whitehead Institute MIT Center for Genome Research, Cambridge, Massachusetts, USA
    Nat Genet 26:76-80. 2000
    ..Because the risk allele occurs at such high frequency, its modest effect translates into a large population attributable risk-influencing as much as 25% of type 2 diabetes in the general population...
  14. pmc Parametric and nonparametric linkage analysis: a unified multipoint approach
    L Kruglyak
    Whitehead Institute for Biomedical Research, Cambridge
    Am J Hum Genet 58:1347-63. 1996
    ..The package allows efficient multipoint analysis of pedigree data to be performed rapidly in a single user-friendly environment...
  15. ncbi request reprint Chromosomal landscape of nucleosome-dependent gene expression and silencing in yeast
    J J Wyrick
    Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
    Nature 402:418-21. 1999
    ..These results indicate that histones make Sir-independent contributions to telomeric silencing, and that the role of histones located elsewhere in chromosomes is gene specific rather than generally repressive...
  16. ncbi request reprint Positive natural selection in the human lineage
    P C Sabeti
    Broad Institute of MIT and Harvard, Cambridge, MA, USA
    Science 312:1614-20. 2006
    ....
  17. pmc Genomewide search in Canadian families with inflammatory bowel disease reveals two novel susceptibility loci
    J D Rioux
    Whitehead Institute Massachusetts Institute of Technology, Center for Genome Research, Cambridge, MA 02139, USA
    Am J Hum Genet 66:1863-70. 2000
    ..Both of these genomic regions contain numerous genes that are important to the immune and inflammatory systems and that provide good targets for future candidate-gene studies...
  18. ncbi request reprint Molecular classification of cancer: class discovery and class prediction by gene expression monitoring
    T R Golub
    Whitehead Institute Massachusetts Institute of Technology Center for Genome Research, Cambridge, MA 02139, USA
    Science 286:531-7. 1999
    ....
  19. pmc ARACHNE: a whole-genome shotgun assembler
    Serafim Batzoglou
    Laboratory for Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
    Genome Res 12:177-89. 2002
    ..The assembly was rapid: the Drosophila assembly required only 21 hours on a single 667 MHz processor and used 8.4 Gb of memory...
  20. ncbi request reprint Searching for signals of evolutionary selection in 168 genes related to immune function
    Emily C Walsh
    Novartis Institutes for BioMedical Research, 250 Mass Ave, Cambridge, MA 02139, USA
    Hum Genet 119:92-102. 2006
    ....
  21. pmc Remodeling of yeast genome expression in response to environmental changes
    H C Causton
    Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, Massachusetts 02142, USA
    Mol Biol Cell 12:323-37. 2001
    ..These results provide a global description of the transcriptional response to environmental change and extend our understanding of the role of activators in effecting this response...
  22. pmc Genome sequence, comparative analysis, and population genetics of the domestic horse
    C M Wade
    Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA
    Science 326:865-7. 2009
    ..Linkage disequilibrium, showing the influences of early domestication of large herds of female horses, is intermediate in length between dog and human, and there is long-range haplotype sharing among breeds...
  23. pmc Genomewide linkage analysis of stature in multiple populations reveals several regions with evidence of linkage to adult height
    J N Hirschhorn
    Whitehead MIT Center for Genome Research, One Kendall Square, Cambridge, MA 02139, USA
    Am J Hum Genet 69:106-16. 2001
    ..These studies suggest that highly heritable complex traits such as stature may be genetically tractable and provide insight into the genetic architecture of complex traits...
  24. doi request reprint A composite of multiple signals distinguishes causal variants in regions of positive selection
    Sharon R Grossman
    Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
    Science 327:883-6. 2010
    ..CMS can not just identify individual loci but implicates precise variants selected by evolution...
  25. ncbi request reprint Detecting recent positive selection in the human genome from haplotype structure
    Pardis C Sabeti
    Whitehead Institute MIT Center for Genome Research, Nine Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 419:832-7. 2002
    ..More generally, the method could be used to scan the entire genome for evidence of recent positive selection...
  26. ncbi request reprint On the allelic spectrum of human disease
    D E Reich
    The Whitehead Institute MIT Center for Genome Research, Nine Cambidge Center, Cambridge, MA 02142, USA
    Trends Genet 17:502-10. 2001
    ..It also has bearing on the Common Disease/Common Variants (CD/CV) hypothesis, predicting that at loci where the total frequency of disease alleles is not too small, disease loci will have relatively simple spectra...
  27. pmc Lower-than-expected linkage disequilibrium between tightly linked markers in humans suggests a role for gene conversion
    K Ardlie
    Center for Genome Research, Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA, USA
    Am J Hum Genet 69:582-9. 2001
    ..This estimate is an order of magnitude higher than most estimates based on nucleotide diversity. The most likely explanation of this discrepancy is that gene conversion increases the apparent rate of recombination between nearby loci...
  28. ncbi request reprint A YAC-based physical map of the mouse genome
    C Nusbaum
    Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
    Nat Genet 22:388-93. 1999
    ..More generally, use of this map in addition to a newly constructed radiation hybrid (RH) map provides a comprehensive framework for mouse genomic studies...
  29. pmc Transcriptional regulatory code of a eukaryotic genome
    Christopher T Harbison
    Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 431:99-104. 2004
    ..We find that environment-specific use of regulatory elements predicts mechanistic models for the function of a large population of yeast's transcriptional regulators...
  30. pmc Effects of p53 mutations on apoptosis in mouse intestinal and human colonic adenomas
    A Fazeli
    Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
    Proc Natl Acad Sci U S A 94:10199-204. 1997
    ....
  31. ncbi request reprint Disruption of the nuclear hormone receptor RORalpha in staggerer mice
    B A Hamilton
    Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
    Nature 379:736-9. 1996
    ..We propose a model based on these results, in which RORalpha interacts with the thyroid hormone signalling pathway to induce Purkinje-cell maturation...
  32. pmc Expression analysis with oligonucleotide microarrays reveals that MYC regulates genes involved in growth, cell cycle, signaling, and adhesion
    H A Coller
    Center for Genome Research, Whitehead Institute for Biomedical Research, Cambridge, MA 02139, USA
    Proc Natl Acad Sci U S A 97:3260-5. 2000
    ..The genes that displayed an expression profile most similar to endogenous Myc in microarray-based expression profiling of myeloid differentiation models were highly enriched for MYC target genes...
  33. pmc Systematic discovery of regulatory motifs in conserved regions of the human genome, including thousands of CTCF insulator sites
    Xiaohui Xie
    Broad Institute of MIT and Harvard, Massachusetts Institute of Technology and Harvard Medical School, Cambridge, MA 02142, USA
    Proc Natl Acad Sci U S A 104:7145-50. 2007
    ..These sites may thus partition the human genome into domains of expression...
  34. ncbi request reprint Human genome sequence variation and the influence of gene history, mutation and recombination
    David E Reich
    Whitehead Institute MIT Center for Genome Research, One Kendall Square, Cambridge, Massachusetts 02139, USA
    Nat Genet 32:135-42. 2002
    ....
  35. ncbi request reprint Detection of regulatory variation in mouse genes
    Christopher R Cowles
    Whitehead Institute and MIT Center for Genome Research, Nine Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nat Genet 32:432-7. 2002
    ..The results indicate that larger-scale surveys in both mouse and human could identify a substantial number of genes with common regulatory variation...
  36. pmc Identification of endoglin as a functional marker that defines long-term repopulating hematopoietic stem cells
    Chang Zheng Chen
    Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA 02142, USA
    Proc Natl Acad Sci U S A 99:15468-73. 2002
    ..Our overall strategy may be applicable for the identification of markers for other tissue-specific stem cells...
  37. pmc Dissecting direct reprogramming through integrative genomic analysis
    Tarjei S Mikkelsen
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 454:49-55. 2008
    ..We demonstrate that RNA inhibition of transcription factors can facilitate reprogramming, and that treatment with DNA methyltransferase inhibitors can improve the overall efficiency of the reprogramming process...
  38. ncbi request reprint Meta-analysis of genetic association studies supports a contribution of common variants to susceptibility to common disease
    Kirk E Lohmueller
    Whitehead Massachuetts Institute of Technology Center for Genome Research, Cambridge, Massachusetts 02139, USA
    Nat Genet 33:177-82. 2003
    ..We conclude that there are probably many common variants in the human genome with modest but real effects on common disease risk, and that studies using large samples will convincingly identify such variants...
  39. pmc DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage
    Michael C Zody
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Massachusetts 02142, USA
    Nature 440:1045-9. 2006
    ..Examination of the main classes of duplicated segments provides insight into the dynamics underlying expansion of chromosome-specific, low-copy repeats in the human genome...
  40. pmc A large family of ancient repeat elements in the human genome is under strong selection
    Michael Kamal
    Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
    Proc Natl Acad Sci U S A 103:2740-5. 2006
    ..Although the precise function of these elements remains unknown, the evidence suggests that this unusual family may play a cis-regulatory or structural role in mammalian genomes...
  41. pmc Genetic mapping in human disease
    David Altshuler
    Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
    Science 322:881-8. 2008
    ....
  42. ncbi request reprint Mapping of a gene for type 2 diabetes associated with an insulin secretion defect by a genome scan in Finnish families
    M M Mahtani
    Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
    Nat Genet 14:90-4. 1996
    ..We infer the existence of a gene NIDDM2 causing NIDDM associated with low insulin secretion, and suggest that NIDDM2 and MODY3 may represent different alleles of the same gene...
  43. ncbi request reprint Genetic variation in the 5q31 cytokine gene cluster confers susceptibility to Crohn disease
    J D Rioux
    Whitehead Institute/Massachusetts Institute of Technology, Center for Genome Research, Cambridge, Massachusetts, USA
    Nat Genet 29:223-8. 2001
    ..These results have important implications for Crohn disease in particular and LD mapping in general...
  44. ncbi request reprint Sib-pair collection strategies for complex diseases
    M I McCarthy
    Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA
    Genet Epidemiol 15:317-40. 1998
    ..In addition, these findings suggest that a further explanation for failure to replicate positive complex trait linkages lies in differences in ascertainment strategy between data sets...
  45. ncbi request reprint MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations
    E S Lander
    Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142
    Genomics 1:174-81. 1987
    ..MAPMAKER has been applied to the construction of linkage maps in a number of organisms, including the human and several plants, and we outline the mapping strategies that have been used...
  46. ncbi request reprint Association analysis of NOTCH4 loci in schizophrenia using family and population-based controls
    P Sklar
    Department of Psychiatry, Massachusetts General Hospital, Boston, Massachusetts, USA
    Nat Genet 28:126-8. 2001
    ..These data strongly suggest that NOTCH4 is not a significant susceptibility allele for schizophrenia...
  47. ncbi request reprint Family-based association study of 76 candidate genes in bipolar disorder: BDNF is a potential risk locus. Brain-derived neutrophic factor
    P Sklar
    Department of Psychiatry, Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
    Mol Psychiatry 7:579-93. 2002
    ..5 kb 3'. Therefore, this study of 76 candidate genes has identified BDNF as a potential risk allele that will require additional study to confirm...
  48. ncbi request reprint Analysis of the DNA sequence and duplication history of human chromosome 15
    Michael C Zody
    Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, Massachusetts 02141, USA
    Nature 440:671-5. 2006
    ..Finally, we demonstrate that some remaining gaps in the genome sequence are probably due to structural polymorphisms between haplotypes; this may explain a significant fraction of the gaps remaining in the human genome...
  49. ncbi request reprint Genetic evidence for complex speciation of humans and chimpanzees
    Nick Patterson
    Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
    Nature 441:1103-8. 2006
    ..These unexpected features would be explained if the human and chimpanzee lineages initially diverged, then later exchanged genes before separating permanently...
  50. pmc Assisted assembly: how to improve a de novo genome assembly by using related species
    Sante Gnerre
    Broad Institute of Harvard and MIT, Cambridge Center, Cambridge, Massachusetts 02142, USA
    Genome Biol 10:R88. 2009
    ..We show that the information provided by aligning the whole-genome shotgun reads of the target against a reference genome can be used to substantially improve the quality of the resulting assembly...
  51. ncbi request reprint The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease
    Justin Lamb
    Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
    Science 313:1929-35. 2006
    ..These results indicate the feasibility of the approach and suggest the value of a large-scale community Connectivity Map project...
  52. ncbi request reprint DNA sequence and analysis of human chromosome 8
    Chad Nusbaum
    Broad Institute of MIT and Harvard, 320 Charles St, Cambridge, Massachusetts 02141, USA
    Nature 439:331-5. 2006
    ..The data from chromosome 8 should allow a better understanding of both normal and disease biology and genome evolution...
  53. ncbi request reprint Genome sequence, comparative analysis and haplotype structure of the domestic dog
    Kerstin Lindblad-Toh
    Broad Institute of Harvard and MIT, 320 Charles Street, Cambridge, Massachusetts 02141, USA
    Nature 438:803-19. 2005
    ..The current SNP map now makes it possible for genome-wide association studies to identify genes responsible for diseases and traits, with important consequences for human and companion animal health...
  54. pmc The case for selection at CCR5-Delta32
    Pardis C Sabeti
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
    PLoS Biol 3:e378. 2005
    ..More broadly, the results have general implications for the design of future studies to detect the signs of positive selection in the human genome...
  55. pmc Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs
    Mitchell Guttman
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
    Nat Biotechnol 28:503-10. 2010
    ..Our results open the way to direct experimental manipulation of thousands of noncoding RNAs and demonstrate the power of ab initio reconstruction to render a comprehensive picture of mammalian transcriptomes...
  56. ncbi request reprint DNA sequence and analysis of human chromosome 18
    Chad Nusbaum
    Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, Massachusetts 02141, USA
    Nature 437:551-5. 2005
    ..This has important implications for the nature and roles of non-protein-coding sequence elements...
  57. pmc Genome-wide detection and characterization of positive selection in human populations
    Pardis C Sabeti
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA
    Nature 449:913-8. 2007
    ....
  58. pmc A family of conserved noncoding elements derived from an ancient transposable element
    Xiaohui Xie
    Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
    Proc Natl Acad Sci U S A 103:11659-64. 2006
    ..In addition, we identify 95 additional CNE families that likely predate the mammalian radiation. The results highlight both the creative role of transposons and the importance of CNE families...
  59. ncbi request reprint Efficient mapping of mendelian traits in dogs through genome-wide association
    Elinor K Karlsson
    Broad Institute of Harvard and Massachusetts Institute of Technology MIT, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nat Genet 39:1321-8. 2007
    ....
  60. pmc Distinguishing protein-coding and noncoding genes in the human genome
    Michele Clamp
    Broad Institute of Massachusetts Institute of Technology and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
    Proc Natl Acad Sci U S A 104:19428-33. 2007
    ..It also provides a principled methodology for evaluating future proposed additions to the human gene catalog. Finally, the results indicate that there has been relatively little true innovation in mammalian protein-coding genes...
  61. ncbi request reprint Comment on "The consensus coding sequences of human breast and colorectal cancers"
    Gad Getz
    Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
    Science 317:1500. 2007
    ..When these concerns are addressed, few genes with significantly elevated mutation rates remain. Although the biological methodology in Sjöblom et al. is sound, more samples are needed to achieve sufficient power...
  62. pmc Quality scores and SNP detection in sequencing-by-synthesis systems
    William Brockman
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA
    Genome Res 18:763-70. 2008
    ..We demonstrate good specificity in single reads, and excellent specificity (no false positives in 215 kb of genome) in high-coverage data...
  63. ncbi request reprint Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences
    Tarjei S Mikkelsen
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 447:167-77. 2007
    ..A substantial proportion of these eutherian-specific CNEs arose from sequence inserted by transposable elements, pointing to transposons as a major creative force in the evolution of mammalian gene regulation...
  64. pmc Genome-scale DNA methylation maps of pluripotent and differentiated cells
    Alexander Meissner
    Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 454:766-70. 2008
    ..More generally, the results establish reduced representation bisulphite sequencing as a powerful technology for epigenetic profiling of cell populations relevant to developmental biology, cancer and regenerative medicine...
  65. pmc Genome-wide SNP genotyping highlights the role of natural selection in Plasmodium falciparum population divergence
    Daniel E Neafsey
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
    Genome Biol 9:R171. 2008
    ..To that end, we have developed a high throughput single nucleotide polymorphism (SNP) genotyping platform for P. falciparum...
  66. pmc Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals
    Mitchell Guttman
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 458:223-7. 2009
    ..Together, these results define a unique collection of functional lincRNAs that are highly conserved and implicated in diverse biological processes...
  67. pmc Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing
    Andreas Gnirke
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nat Biotechnol 27:182-9. 2009
    ..One lane of Illumina sequence was sufficient to call high-confidence genotypes for 89% of the targeted exon space...
  68. ncbi request reprint Genome-scale loss-of-function screening with a lentiviral RNAi library
    David E Root
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
    Nat Methods 3:715-9. 2006
    ..Initial screening efforts have demonstrated that these libraries and methods are practical and powerful tools for high-throughput lentivirus RNAi screens...
  69. pmc Assembly of polymorphic genomes: algorithms and application to Ciona savignyi
    Jade P Vinson
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141 2023, USA
    Genome Res 15:1127-35. 2005
    ..Our method represented loci in a single copy more reliably and achieved greater contiguity than a conventional whole-genome assembly method...
  70. pmc Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals
    Xiaohui Xie
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA
    Nature 434:338-45. 2005
    ..The overall results provide a systematic view of gene regulation in the human, which will be refined as additional mammalian genomes become available...
  71. pmc An integrated haplotype map of the human major histocompatibility complex
    Emily C Walsh
    Center for Genome Research, Whitehead Institute for Biomedical Research, Cambridge, MA 02139, USA
    Am J Hum Genet 73:580-90. 2003
    ..Furthermore, these data show that multi-SNP haplotypes will likely be a valuable means for refining association signals in this region...
  72. pmc Whole-genome sequence assembly for mammalian genomes: Arachne 2
    David B Jaffe
    Whitehead Institute MIT Center for Genome Research, Cambridge, Massachusetts 02141, USA
    Genome Res 13:91-6. 2003
    ..The outcome of this mouse assembly and its analysis are described in (Mouse Genome Sequencing Consortium 2002)...
  73. ncbi request reprint The genome sequence of the filamentous fungus Neurospora crassa
    James E Galagan
    Whitehead Institute Center for Genome Research, 320 Charles Street, Cambridge, Massachusetts 02141, USA
    Nature 422:859-68. 2003
    ..Genome analysis suggests that RIP has had a profound impact on genome evolution, greatly slowing the creation of new genes through genomic duplication and resulting in a genome with an unusually low proportion of closely related genes...
  74. ncbi request reprint Sequencing and comparison of yeast species to identify genes and regulatory elements
    Manolis Kellis
    Whitehead MIT Center for Genome Research, Nine Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 423:241-54. 2003
    ..We inferred a putative function for most of these motifs, and provided insights into their combinatorial interactions. The results have implications for genome analysis of diverse organisms, including the human...
  75. ncbi request reprint Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae
    Manolis Kellis
    The Broad Institute, Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02138, USA
    Nature 428:617-24. 2004
    ..Strikingly, 95% of cases of accelerated evolution involve only one member of a gene pair, providing strong support for a specific model of evolution, and allowing us to distinguish ancestral and derived functions...
  76. pmc Erralpha and Gabpa/b specify PGC-1alpha-dependent oxidative phosphorylation gene expression that is altered in diabetic muscle
    Vamsi K Mootha
    The Eli and Edythe L Broad Institute, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139 1561, USA
    Proc Natl Acad Sci U S A 101:6570-5. 2004
    ....
  77. ncbi request reprint Methods in comparative genomics: genome correspondence, gene identification and regulatory motif discovery
    Manolis Kellis
    Whitehead Institute Center for Genome Research, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
    J Comput Biol 11:319-55. 2004
    ..Our methods are validated by the extensive experimental knowledge in yeast and will be invaluable in the study of complex genomes like that of the human...
  78. ncbi request reprint Genomewide search and association studies in a Finnish celiac disease population: Identification of a novel locus and replication of the HLA and CTLA4 loci
    John D Rioux
    Broad Institute Massachusetts Institute of Technology, One Kendall Square, Bldg 300, Cambridge, MA 02139 1561, USA
    Am J Med Genet A 130:345-50. 2004
    ..We also performed targeted typing and analyses that replicated the associations of the HLA and CTLA4 loci...
  79. ncbi request reprint Dissecting the regulatory circuitry of a eukaryotic genome
    F C Holstege
    Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
    Cell 95:717-28. 1998
    ....
  80. pmc Chemosensitivity prediction by transcriptional profiling
    J E Staunton
    Whitehead/Massachusetts Institute of Technology Center for Genome Research, Cambridge, MA 02139, USA
    Proc Natl Acad Sci U S A 98:10787-92. 2001
    ..05) on an independent test set, whereas only 12 of the 232 would be expected to do so by chance. These results suggest that at least for a subset of compounds genomic approaches to chemosensitivity prediction are feasible...
  81. ncbi request reprint Genetic dissection of autoimmune type I diabetes in the BB rat
    H J Jacob
    Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142
    Nat Genet 2:56-60. 1992
    ....
  82. pmc Integrative analysis of the melanoma transcriptome
    Michael F Berger
    The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
    Genome Res 20:413-27. 2010
    ..Taken together, these results may indicate new avenues for target discovery in melanoma, while also providing a template for large-scale transcriptome studies across many tumor types...
  83. pmc ALLPATHS: de novo assembly of whole-genome shotgun microreads
    Jonathan Butler
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA
    Genome Res 18:810-20. 2008
    ..We describe a general method for genome assembly that can be applied to all types of DNA sequence data, not only short read data, but also conventional sequence reads...
  84. pmc Genome-wide maps of chromatin state in pluripotent and lineage-committed cells
    Tarjei S Mikkelsen
    Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
    Nature 448:553-60. 2007
    ..This study provides a framework for the application of comprehensive chromatin profiling towards characterization of diverse mammalian cell populations...
  85. pmc Highly parallel identification of essential genes in cancer cells
    Biao Luo
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
    Proc Natl Acad Sci U S A 105:20380-5. 2008
    ....
  86. ncbi request reprint The mosaic structure of variation in the laboratory mouse genome
    Claire M Wade
    Whitehead Institute for Biomedical Research and Whitehead MIT Center for Genome Research, 9 Cambridge Center, Cambridge, Massachusetts 02139, USA
    Nature 420:574-8. 2002
    ..These observations have important implications for the design and interpretation of positional cloning experiments...
  87. ncbi request reprint PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes
    Vamsi K Mootha
    Whitehead Institute MIT Center for Genome Research, Cambridge, Massachusetts, USA
    Nat Genet 34:267-73. 2003
    ..Our results associate this gene set with clinically important variation in human metabolism and illustrate the value of pathway relationships in the analysis of genomic profiling experiments...
  88. ncbi request reprint Genetic dissection of complex traits with chromosome substitution strains of mice
    Jonathan B Singer
    Broad Institute, Cambridge, MA 02142, USA
    Science 304:445-8. 2004
    ..These results demonstrate that CSSs greatly facilitate the detection and identification of genes that control the wide diversity of naturally occurring phenotypic variation in the A/J and C57BL/6J inbred strains...
  89. pmc Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression
    Ahmad M Khalil
    The Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142, USA
    Proc Natl Acad Sci U S A 106:11667-72. 2009
    ..We propose a model in which some lincRNAs guide chromatin-modifying complexes to specific genomic loci to regulate gene expression...
  90. pmc Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles
    Aravind Subramanian
    Broad Institute of Massachusetts Institute of Technology and Harvard, 320 Charles Street, Cambridge, MA 02141, USA
    Proc Natl Acad Sci U S A 102:15545-50. 2005
    ..The GSEA method is embodied in a freely available software package, together with an initial database of 1,325 biologically defined gene sets...
  91. ncbi request reprint A lentiviral RNAi library for human and mouse genes applied to an arrayed viral high-content screen
    Jason Moffat
    Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
    Cell 124:1283-98. 2006
    ..This work provides a widely applicable resource for loss-of-function screens, as well as a roadmap for its application to biological discovery...
  92. ncbi request reprint The plasticity of dendritic cell responses to pathogens and their components
    Q Huang
    Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
    Science 294:870-5. 2001
    ..These results reveal that dendritic cells sense diverse pathogens and elicit tailored pathogen-specific immune responses...
  93. ncbi request reprint A radiation hybrid map of mouse genes
    T J Hudson
    Center for Genome Research, Whitehead Institute Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
    Nat Genet 29:201-5. 2001
    ..It includes 3,658 genes homologous to the human genome sequence and provides a framework for overlaying the human genome sequence to the mouse and for sequencing the mouse genome...
  94. ncbi request reprint Positional cloning of the nude locus: genetic, physical, and transcription maps of the region and mutations in the mouse and rat
    J A Segre
    Whitehead Institute for Biomedical Research, Cambridge Massachusetts 02142, USA
    Genomics 28:549-59. 1995
    ..Nature 372: 103-107, 1994). We report as well the mutations in the rat rnu allele and the complete coding sequence of the rat whn mRNA...
  95. ncbi request reprint Lgn1, a gene that determines susceptibility to Legionella pneumophila, maps to mouse chromosome 13
    W F Dietrich
    Whitehead Institute MIT Genome Center, Cambridge, Massachusetts 02139, USA
    Genomics 26:443-50. 1995
    ..In the absence of any regional candidates for Lgn1, this map position will facilitate positional cloning attempts directed at this gene...
  96. pmc Effectors of a developmental mitogen-activated protein kinase cascade revealed by expression signatures of signaling mutants
    H D Madhani
    Whitehead Massachusetts Institute of Technology, Center for Genome Research, Department of Biology, Cambridge, MA 02142, USA
    Proc Natl Acad Sci U S A 96:12530-5. 1999
    ..Thus, the Kss1 MAPK cascade programs development by coordinately modulating a cell adhesion factor, a secreted host-destroying activity, and a specialized subunit of the Cdc28 cyclin-dependent kinase...
  97. ncbi request reprint Chromosome substitution strains: a new way to study genetically complex traits
    Annie E Hill
    Whitehead Institute for Biomedical Research, Cambridge, MA, USA
    Methods Mol Med 128:153-72. 2006
    ..Several published studies demonstrate the considerable utility of these strains and new applications for CSSs continue to be discovered...
  98. pmc Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis
    Alexander Meissner
    Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Nine Cambridge Center, Cambridge, MA 02142, USA
    Nucleic Acids Res 33:5868-77. 2005
    ..Near-complete bisulfite conversion and largely unbiased representation of RRBS libraries suggest that random shotgun bisulfite sequencing can be scaled to a genome-wide approach...
  99. pmc Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma
    Rameen Beroukhim
    Broad Institute, Massachusetts Institute of Technology and Harvard University, 7 Cambridge Center, Cambridge, MA 02142, USA
    Proc Natl Acad Sci U S A 104:20007-12. 2007
    ..Our results support the feasibility and utility of systematic characterization of the cancer genome...
  100. pmc Deletion of cytosolic phospholipase A(2) suppresses Apc(Min)-induced tumorigenesis
    K H Hong
    Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
    Proc Natl Acad Sci U S A 98:3935-9. 2001
    ..The tumorigenic effect of sPLA(2) mutations is likely to be through a completely different pathway...
  101. doi request reprint SNP genotyping defines complex gene-flow boundaries among African malaria vector mosquitoes
    D E Neafsey
    Broad Institute, Cambridge, MA 02142, USA
    Science 330:514-7. 2010
    ..Complex genomic differentiation among speciating vector mosquito populations implies that tools for genome-wide monitoring of population structure will prove useful for the advancement of malaria eradication...