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Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophila genome.
Genome biology , 2002 | Pubmed ID: 12537575
DNA sequence and analysis of human chromosome 18.
Nature Sep, 2005 | Pubmed ID: 16177791
Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis.
Nucleic acids research , 2005 | Pubmed ID: 16224102
Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis.
Nature Nov, 2006 | Pubmed ID: 17080091
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
The genome of the model beetle and pest Tribolium castaneum.
Nature Apr, 2008 | Pubmed ID: 18362917
Genome-scale DNA methylation maps of pluripotent and differentiated cells.
Nature Aug, 2008 | Pubmed ID: 18600261
The maternal-effect, selfish genetic element Medea is associated with a composite Tc1 transposon.
Proceedings of the National Academy of Sciences of the United States of America Jul, 2008 | Pubmed ID: 18621706
Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing.
Nature biotechnology Feb, 2009 | Pubmed ID: 19182786
Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing.
Proceedings of the National Academy of Sciences of the United States of America Mar, 2009 | Pubmed ID: 19208812
High-throughput bisulfite sequencing in mammalian genomes.
Methods (San Diego, Calif.) Jul, 2009 | Pubmed ID: 19442738
ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads.
Genome biology , 2009 | Pubmed ID: 19796385
Comprehensive mapping of long-range interactions reveals folding principles of the human genome.
Science (New York, N.Y.) Oct, 2009 | Pubmed ID: 19815776
Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts.
Genome biology , 2009 | Pubmed ID: 19835606
ZBED6, a novel transcription factor derived from a domesticated DNA transposon regulates IGF2 expression and muscle growth.
PLoS biology Dec, 2009 | Pubmed ID: 20016685
Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution.
Nature methods Feb, 2010 | Pubmed ID: 20062050
Integrative analysis of the melanoma transcriptome.
Genome research Apr, 2010 | Pubmed ID: 20179022
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
Targeted exon sequencing by in-solution hybrid selection.
Current protocols in human genetics / editorial board, Jonathan L. Haines ... [et al.] Jul, 2010 | Pubmed ID: 20582916
Comprehensive comparative analysis of strand-specific RNA sequencing methods.
Nature methods Sep, 2010 | Pubmed ID: 20711195
Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species.
Genome biology , 2010 | Pubmed ID: 20796282
Quantitative comparison of genome-wide DNA methylation mapping technologies.
Nature biotechnology Oct, 2010 | Pubmed ID: 20852634
Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications.
Nature biotechnology Oct, 2010 | Pubmed ID: 20852635
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
Reprogramming factor expression initiates widespread targeted chromatin remodeling.
Cell stem cell Jan, 2011 | Pubmed ID: 21211784
Reference Maps of human ES and iPS cell variation enable high-throughput characterization of pluripotent cell lines.
Cell Feb, 2011 | Pubmed ID: 21295703
Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries.
Genome biology , 2011 | Pubmed ID: 21338519
Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling.
Nature protocols Apr, 2011 | Pubmed ID: 21412275
Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells.
Nature biotechnology May, 2011 | Pubmed ID: 21516085
Full-length transcriptome assembly from RNA-Seq data without a reference genome.
Nature biotechnology Jul, 2011 | Pubmed ID: 21572440
Hybrid selection for sequencing pathogen genomes from clinical samples.
Genome biology , 2011 | Pubmed ID: 21835008
Genomic distribution and inter-sample variation of non-CpG methylation across human cell types.
PLoS genetics Dec, 2011 | Pubmed ID: 22174693
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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