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MLL translocations specify a distinct gene expression profile that distinguishes a unique leukemia.
Nature genetics Jan, 2002 | Pubmed ID: 11731795
ARACHNE: a whole-genome shotgun assembler.
Genome research Jan, 2002 | Pubmed ID: 11779843
Diffuse large B-cell lymphoma outcome prediction by gene-expression profiling and supervised machine learning.
Nature medicine Jan, 2002 | Pubmed ID: 11786909
Human macrophage activation programs induced by bacterial pathogens.
Proceedings of the National Academy of Sciences of the United States of America Feb, 2002 | Pubmed ID: 11805289
Prediction of central nervous system embryonal tumour outcome based on gene expression.
Nature Jan, 2002 | Pubmed ID: 11807556
On the sequencing of the human genome.
Proceedings of the National Academy of Sciences of the United States of America Mar, 2002 | Pubmed ID: 11880605
The structure of haplotype blocks in the human genome.
Science (New York, N.Y.) Jun, 2002 | Pubmed ID: 12029063
Gene expression correlates of clinical prostate cancer behavior.
Cancer cell Mar, 2002 | Pubmed ID: 12086878
Gene expression signatures define novel oncogenic pathways in T cell acute lymphoblastic leukemia.
Cancer cell Feb, 2002 | Pubmed ID: 12086890
Lymphopenia in the BB rat model of type 1 diabetes is due to a mutation in a novel immune-associated nucleotide (Ian)-related gene.
Genome research Jul, 2002 | Pubmed ID: 12097339
Human genome sequence variation and the influence of gene history, mutation and recombination.
Nature genetics Sep, 2002 | Pubmed ID: 12161752
Abnormal gene expression in cloned mice derived from embryonic stem cell and cumulus cell nuclei.
Proceedings of the National Academy of Sciences of the United States of America Oct, 2002 | Pubmed ID: 12235366
Detecting recent positive selection in the human genome from haplotype structure.
Nature Oct, 2002 | Pubmed ID: 12397357
Detection of regulatory variation in mouse genes.
Nature genetics Nov, 2002 | Pubmed ID: 12410233
Identification of endoglin as a functional marker that defines long-term repopulating hematopoietic stem cells.
Proceedings of the National Academy of Sciences of the United States of America Nov, 2002 | Pubmed ID: 12438646
Using a genome-wide scan and meta-analysis to identify a novel IBD locus and confirm previously identified IBD loci.
Inflammatory bowel diseases Nov, 2002 | Pubmed ID: 12454612
Initial sequencing and comparative analysis of the mouse genome.
Nature Dec, 2002 | Pubmed ID: 12466850
The mosaic structure of variation in the laboratory mouse genome.
Nature Dec, 2002 | Pubmed ID: 12466852
A molecular signature of metastasis in primary solid tumors.
Nature genetics Jan, 2003 | Pubmed ID: 12469122
Meta-analysis of genetic association studies supports a contribution of common variants to susceptibility to common disease.
Nature genetics Feb, 2003 | Pubmed ID: 12524541
Whole-genome sequence assembly for mammalian genomes: Arachne 2.
Genome research Jan, 2003 | Pubmed ID: 12529310
Identification of a gene causing human cytochrome c oxidase deficiency by integrative genomics.
Proceedings of the National Academy of Sciences of the United States of America Jan, 2003 | Pubmed ID: 12529507
More on the sequencing of the human genome.
Proceedings of the National Academy of Sciences of the United States of America Mar, 2003 | Pubmed ID: 12631699
Pathogen discovery from human tissue by sequence-based computational subtraction.
Genomics Mar, 2003 | Pubmed ID: 12659816
The genome sequence of the filamentous fungus Neurospora crassa.
Nature Apr, 2003 | Pubmed ID: 12712197
Sequencing and comparison of yeast species to identify genes and regulatory elements.
Nature May, 2003 | Pubmed ID: 12748633
IBD5 is a general risk factor for inflammatory bowel disease: replication of association with Crohn disease and identification of a novel association with ulcerative colitis.
American journal of human genetics Jul, 2003 | Pubmed ID: 12776251
PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes.
Nature genetics Jul, 2003 | Pubmed ID: 12808457
Phylogenetically and spatially conserved word pairs associated with gene-expression changes in yeasts.
Genome biology , 2003 | Pubmed ID: 12844359
An integrated haplotype map of the human major histocompatibility complex.
American journal of human genetics Sep, 2003 | Pubmed ID: 12920676
Position specific variation in the rate of evolution in transcription factor binding sites.
BMC evolutionary biology Aug, 2003 | Pubmed ID: 12946282
Genetic dissection of lymphopenia from autoimmunity by introgression of mutated Ian5 gene onto the F344 rat.
Journal of autoimmunity Dec, 2003 | Pubmed ID: 14624755
Integrated analysis of protein composition, tissue diversity, and gene regulation in mouse mitochondria.
Cell Nov, 2003 | Pubmed ID: 14651853
Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae.
Nature Apr, 2004 | Pubmed ID: 15004568
Genetic dissection of complex traits with chromosome substitution strains of mice.
Science (New York, N.Y.) Apr, 2004 | Pubmed ID: 15031436
Assessing the impact of population stratification on genetic association studies.
Nature genetics Apr, 2004 | Pubmed ID: 15052270
Erralpha and Gabpa/b specify PGC-1alpha-dependent oxidative phosphorylation gene expression that is altered in diabetic muscle.
Proceedings of the National Academy of Sciences of the United States of America Apr, 2004 | Pubmed ID: 15100410
Enhancing linkage analysis of complex disorders: an evaluation of high-density genotyping.
Human molecular genetics Sep, 2004 | Pubmed ID: 15238506
Chromosomes 6 and 13 harbor genes that regulate pubertal timing in mouse chromosome substitution strains.
Endocrinology Oct, 2004 | Pubmed ID: 15284200
Methods in comparative genomics: genome correspondence, gene identification and regulatory motif discovery.
Journal of computational biology : a journal of computational molecular cell biology , 2004 | Pubmed ID: 15285895
Transgenic rescue demonstrates involvement of the Ian5 gene in T cell development in the rat.
Physiological genomics Oct, 2004 | Pubmed ID: 15328390
Transcriptional regulatory code of a eukaryotic genome.
Nature Sep, 2004 | Pubmed ID: 15343339
Eric S. Lander.
Nature reviews. Drug discovery Sep, 2004 | Pubmed ID: 15368656
Mapping quantitative trait loci for anxiety in chromosome substitution strains of mice.
Genetics Feb, 2005 | Pubmed ID: 15371360
Genomewide search and association studies in a Finnish celiac disease population: Identification of a novel locus and replication of the HLA and CTLA4 loci.
American journal of medical genetics. Part A Nov, 2004 | Pubmed ID: 15386476
Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype.
Nature Oct, 2004 | Pubmed ID: 15496914
A complex interaction of imprinted and maternal-effect genes modifies sex determination in Odd Sex (Ods) mice.
Genetics Nov, 2004 | Pubmed ID: 15579706
Genomic maps and comparative analysis of histone modifications in human and mouse.
Cell Jan, 2005 | Pubmed ID: 15680324
Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals.
Nature Mar, 2005 | Pubmed ID: 15735639
A high-resolution linkage-disequilibrium map of the human major histocompatibility complex and first generation of tag single-nucleotide polymorphisms.
American journal of human genetics Apr, 2005 | Pubmed ID: 15747258
An initial strategy for the systematic identification of functional elements in the human genome by low-redundancy comparative sequencing.
Proceedings of the National Academy of Sciences of the United States of America Mar, 2005 | Pubmed ID: 15778292
Assembly of polymorphic genomes: algorithms and application to Ciona savignyi.
Genome research Aug, 2005 | Pubmed ID: 16077012
A high-density screen for linkage in multiple sclerosis.
American journal of human genetics Sep, 2005 | Pubmed ID: 16080120
DNA sequence and analysis of human chromosome 18.
Nature Sep, 2005 | Pubmed ID: 16177791
Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.
Proceedings of the National Academy of Sciences of the United States of America Oct, 2005 | Pubmed ID: 16199517
Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis.
Nucleic acids research , 2005 | Pubmed ID: 16224102
The case for selection at CCR5-Delta32.
PLoS biology Nov, 2005 | Pubmed ID: 16248677
Genome sequence, comparative analysis and haplotype structure of the domestic dog.
Nature Dec, 2005 | Pubmed ID: 16341006
Searching for signals of evolutionary selection in 168 genes related to immune function.
Human genetics Mar, 2006 | Pubmed ID: 16362345
DNA sequence and analysis of human chromosome 8.
Nature Jan, 2006 | Pubmed ID: 16421571
A large family of ancient repeat elements in the human genome is under strong selection.
Proceedings of the National Academy of Sciences of the United States of America Feb, 2006 | Pubmed ID: 16477033
Human chromosome 11 DNA sequence and analysis including novel gene identification.
Nature Mar, 2006 | Pubmed ID: 16554811
A lentiviral RNAi library for human and mouse genes applied to an arrayed viral high-content screen.
Cell Mar, 2006 | Pubmed ID: 16564017
Analysis of the DNA sequence and duplication history of human chromosome 15.
Nature Mar, 2006 | Pubmed ID: 16572171
Reactive oxygen species have a causal role in multiple forms of insulin resistance.
Nature Apr, 2006 | Pubmed ID: 16612386
DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage.
Nature Apr, 2006 | Pubmed ID: 16625196
Identification and classification of conserved RNA secondary structures in the human genome.
PLoS computational biology Apr, 2006 | Pubmed ID: 16628248
A bivalent chromatin structure marks key developmental genes in embryonic stem cells.
Cell Apr, 2006 | Pubmed ID: 16630819
Genetic evidence for complex speciation of humans and chimpanzees.
Nature Jun, 2006 | Pubmed ID: 16710306
A family of conserved noncoding elements derived from an ancient transposable element.
Proceedings of the National Academy of Sciences of the United States of America Aug, 2006 | Pubmed ID: 16864796
Genome-scale loss-of-function screening with a lentiviral RNAi library.
Nature methods Sep, 2006 | Pubmed ID: 16929317
The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease.
Science (New York, N.Y.) Sep, 2006 | Pubmed ID: 17008526
A second fatty acid amide hydrolase with variable distribution among placental mammals.
The Journal of biological chemistry Dec, 2006 | Pubmed ID: 17015445
Deuterostome phylogeny reveals monophyletic chordates and the new phylum Xenoturbellida.
Nature Nov, 2006 | Pubmed ID: 17051155
Chromosome substitution strains: a new way to study genetically complex traits.
Methods in molecular medicine , 2006 | Pubmed ID: 17071995
A genome-wide map of diversity in Plasmodium falciparum.
Nature genetics Jan, 2007 | Pubmed ID: 17159979
A second major histocompatibility complex susceptibility locus for multiple sclerosis.
Annals of neurology Mar, 2007 | Pubmed ID: 17252545
The mammalian epigenome.
Cell Feb, 2007 | Pubmed ID: 17320505
Sleep-related epilepsy in the A/J mouse.
Sleep Feb, 2007 | Pubmed ID: 17326542
Systematic discovery of regulatory motifs in conserved regions of the human genome, including thousands of CTCF insulator sites.
Proceedings of the National Academy of Sciences of the United States of America Apr, 2007 | Pubmed ID: 17442748
Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences.
Nature May, 2007 | Pubmed ID: 17495919
Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome.
Genome research Jun, 2007 | Pubmed ID: 17567995
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.
Nature Jun, 2007 | Pubmed ID: 17571346
Integrative genomic approaches identify IKBKE as a breast cancer oncogene.
Cell Jun, 2007 | Pubmed ID: 17574021
Genome-wide maps of chromatin state in pluripotent and lineage-committed cells.
Nature Aug, 2007 | Pubmed ID: 17603471
Risk alleles for multiple sclerosis identified by a genomewide study.
The New England journal of medicine Aug, 2007 | Pubmed ID: 17660530
Comment on "The consensus coding sequences of human breast and colorectal cancers".
Science (New York, N.Y.) Sep, 2007 | Pubmed ID: 17872428
Efficient mapping of mendelian traits in dogs through genome-wide association.
Nature genetics Nov, 2007 | Pubmed ID: 17906626
Genome-wide detection and characterization of positive selection in human populations.
Nature Oct, 2007 | Pubmed ID: 17943131
Characterizing the cancer genome in lung adenocarcinoma.
Nature Dec, 2007 | Pubmed ID: 17982442
28-way vertebrate alignment and conservation track in the UCSC Genome Browser.
Genome research Dec, 2007 | Pubmed ID: 17984227
Distinguishing protein-coding and noncoding genes in the human genome.
Proceedings of the National Academy of Sciences of the United States of America Dec, 2007 | Pubmed ID: 18040051
Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma.
Proceedings of the National Academy of Sciences of the United States of America Dec, 2007 | Pubmed ID: 18077431
Quality scores and SNP detection in sequencing-by-synthesis systems.
Genome research May, 2008 | Pubmed ID: 18212088
ALLPATHS: de novo assembly of whole-genome shotgun microreads.
Genome research May, 2008 | Pubmed ID: 18340039
Loss of E-cadherin promotes metastasis via multiple downstream transcriptional pathways.
Cancer research May, 2008 | Pubmed ID: 18483246
Dissecting direct reprogramming through integrative genomic analysis.
Nature Jul, 2008 | Pubmed ID: 18509334
Genome-scale DNA methylation maps of pluripotent and differentiated cells.
Nature Aug, 2008 | Pubmed ID: 18600261
Somatic mutations affect key pathways in lung adenocarcinoma.
Nature Oct, 2008 | Pubmed ID: 18948947
Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains.
PLoS genetics Oct, 2008 | Pubmed ID: 18974828
Genetic mapping in human disease.
Science (New York, N.Y.) Nov, 2008 | Pubmed ID: 18988837
Sequencing the nuclear genome of the extinct woolly mammoth.
Nature Nov, 2008 | Pubmed ID: 19020620
High-resolution mapping of copy-number alterations with massively parallel sequencing.
Nature methods Jan, 2009 | Pubmed ID: 19043412
Genetic architecture of complex traits: large phenotypic effects and pervasive epistasis.
Proceedings of the National Academy of Sciences of the United States of America Dec, 2008 | Pubmed ID: 19066216
Genome-wide SNP genotyping highlights the role of natural selection in Plasmodium falciparum population divergence.
Genome biology , 2008 | Pubmed ID: 19077304
Sensitive, specific polymorphism discovery in bacteria using massively parallel sequencing.
Nature methods Jan, 2009 | Pubmed ID: 19079253
Highly parallel identification of essential genes in cancer cells.
Proceedings of the National Academy of Sciences of the United States of America Dec, 2008 | Pubmed ID: 19091943
Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals.
Nature Mar, 2009 | Pubmed ID: 19182780
Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing.
Nature biotechnology Feb, 2009 | Pubmed ID: 19182786
Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression.
Proceedings of the National Academy of Sciences of the United States of America Jul, 2009 | Pubmed ID: 19571010
AKT-independent signaling downstream of oncogenic PIK3CA mutations in human cancer.
Cancer cell Jul, 2009 | Pubmed ID: 19573809
Identification of selective inhibitors of cancer stem cells by high-throughput screening.
Cell Aug, 2009 | Pubmed ID: 19682730
Assisted assembly: how to improve a de novo genome assembly by using related species.
Genome biology , 2009 | Pubmed ID: 19712469
Comprehensive mapping of long-range interactions reveals folding principles of the human genome.
Science (New York, N.Y.) Oct, 2009 | Pubmed ID: 19815776
Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1.
Nature Nov, 2009 | Pubmed ID: 19847166
ZBED6, a novel transcription factor derived from a domesticated DNA transposon regulates IGF2 expression and muscle growth.
PLoS biology Dec, 2009 | Pubmed ID: 20016685
A composite of multiple signals distinguishes causal variants in regions of positive selection.
Science (New York, N.Y.) Feb, 2010 | Pubmed ID: 20056855
Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution.
Nature methods Feb, 2010 | Pubmed ID: 20062050
CK1epsilon is required for breast cancers dependent on beta-catenin activity.
PloS one , 2010 | Pubmed ID: 20126544
Genetic resistance to diet-induced obesity in chromosome substitution strains of mice.
Mammalian genome : official journal of the International Mammalian Genome Society Apr, 2010 | Pubmed ID: 20127486
The landscape of somatic copy-number alteration across human cancers.
Nature Feb, 2010 | Pubmed ID: 20164920
Integrative analysis of the melanoma transcriptome.
Genome research Apr, 2010 | Pubmed ID: 20179022
International network of cancer genome projects.
Nature Apr, 2010 | Pubmed ID: 20393554
Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs.
Nature biotechnology May, 2010 | Pubmed ID: 20436462
A draft sequence of the Neandertal genome.
Science (New York, N.Y.) May, 2010 | Pubmed ID: 20448178
Wilms tumor chromatin profiles highlight stem cell properties and a renal developmental network.
Cell stem cell Jun, 2010 | Pubmed ID: 20569696
Subtype-specific genomic alterations define new targets for soft-tissue sarcoma therapy.
Nature genetics Aug, 2010 | Pubmed ID: 20601955
A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response.
Cell Aug, 2010 | Pubmed ID: 20673990
Core epithelial-to-mesenchymal transition interactome gene-expression signature is associated with claudin-low and metaplastic breast cancer subtypes.
Proceedings of the National Academy of Sciences of the United States of America Aug, 2010 | Pubmed ID: 20713713
Comparative epigenomic analysis of murine and human adipogenesis.
Cell Oct, 2010 | Pubmed ID: 20887899
Prepare and inspire.
Science (New York, N.Y.) Oct, 2010 | Pubmed ID: 20929738
The NIH Roadmap Epigenomics Mapping Consortium.
Nature biotechnology Oct, 2010 | Pubmed ID: 20944595
Large intergenic non-coding RNA-RoR modulates reprogramming of human induced pluripotent stem cells.
Nature genetics Dec, 2010 | Pubmed ID: 21057500
Estrogen expands breast cancer stem-like cells through paracrine FGF/Tbx3 signaling.
Proceedings of the National Academy of Sciences of the United States of America Dec, 2010 | Pubmed ID: 21098263
High-quality draft assemblies of mammalian genomes from massively parallel sequence data.
Proceedings of the National Academy of Sciences of the United States of America Jan, 2011 | Pubmed ID: 21187386
MicroRNA-15a and -16-1 act via MYB to elevate fetal hemoglobin expression in human trisomy 13.
Proceedings of the National Academy of Sciences of the United States of America Jan, 2011 | Pubmed ID: 21205891
Integrative genomics viewer.
Nature biotechnology Jan, 2011 | Pubmed ID: 21221095
Genetic predisposition directs breast cancer phenotype by dictating progenitor cell fate.
Cell stem cell Feb, 2011 | Pubmed ID: 21295272
Initial impact of the sequencing of the human genome.
Nature Feb, 2011 | Pubmed ID: 21307931
The genomic complexity of primary human prostate cancer.
Nature Feb, 2011 | Pubmed ID: 21307934
Genome-sequencing anniversary. The accelerator.
Science (New York, N.Y.) Feb, 2011 | Pubmed ID: 21350161
Initial genome sequencing and analysis of multiple myeloma.
Nature Mar, 2011 | Pubmed ID: 21430775
Identification and functional validation of the novel antimalarial resistance locus PF10_0355 in Plasmodium falciparum.
PLoS genetics Apr, 2011 | Pubmed ID: 21533027
QnAs with Eric S. Lander. Interview by Prashant Nair.
Proceedings of the National Academy of Sciences of the United States of America Jul, 2011 | Pubmed ID: 21606349
Systematic investigation of genetic vulnerabilities across cancer cell lines reveals lineage-specific dependencies in ovarian cancer.
Proceedings of the National Academy of Sciences of the United States of America Jul, 2011 | Pubmed ID: 21746896
The mutational landscape of head and neck squamous cell carcinoma.
Science (New York, N.Y.) Aug, 2011 | Pubmed ID: 21798893
Stochastic state transitions give rise to phenotypic equilibrium in populations of cancer cells.
Cell Aug, 2011 | Pubmed ID: 21854987
lincRNAs act in the circuitry controlling pluripotency and differentiation.
Nature Sep, 2011 | Pubmed ID: 21874018
The genome of the green anole lizard and a comparative analysis with birds and mammals.
Nature Sep, 2011 | Pubmed ID: 21881562
Genomic sequencing of colorectal adenocarcinomas identifies a recurrent VTI1A-TCF7L2 fusion.
Nature genetics Oct, 2011 | Pubmed ID: 21892161
A high-resolution map of human evolutionary constraint using 29 mammals.
Nature Oct, 2011 | Pubmed ID: 21993624
SF3B1 and other novel cancer genes in chronic lymphocytic leukemia.
The New England journal of medicine Dec, 2011 | Pubmed ID: 22150006
Detecting novel associations in large data sets.
Science (New York, N.Y.) Dec, 2011 | Pubmed ID: 22174245
The mystery of missing heritability: Genetic interactions create phantom heritability.
Proceedings of the National Academy of Sciences of the United States of America Jan, 2012 | Pubmed ID: 22223662
Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011.
Proceedings of the National Academy of Sciences of the United States of America Feb, 2012 | Pubmed ID: 22315421
Nynke L. van Berkum*,1,
Erez Lieberman-Aiden*,2,3,4,5,
Louise Williams*,2,
Maxim Imakaev6,
Andreas Gnirke2,
Leonid A. Mirny3,6,
Job Dekker1,
Eric S. Lander2,7,8
1Program in Gene Function and Expression, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School,
2, Broad Institute of Harvard and Massachusetts Institute of Technology,
3Division of Health Sciences and Technology, Massachusetts Institute of Technology,
4Program for Evolutionary Dynamics, Department of Organismic and Evolutionary Biology, Department of Mathematics, Harvard University ,
5Department of Applied Mathematics, Harvard University ,
6Department of Physics, Massachusetts Institute of Technology,
7Department of Systems Biology, Harvard Medical School,
8Department of Biology, Massachusetts Institute of Technology
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