Richard Humbert
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Explore the profile of Richard Humbert including associated specialties, affiliations and a list of published articles.
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17
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9062
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Recent Articles
1.
Vierstra J, Rynes E, Sandstrom R, Zhang M, Canfield T, Hansen R, et al.
Science
. 2014 Nov;
346(6212):1007-12.
PMID: 25411453
To study the evolutionary dynamics of regulatory DNA, we mapped >1.3 million deoxyribonuclease I-hypersensitive sites (DHSs) in 45 mouse cell and tissue types, and systematically compared these with human DHS...
2.
Yue F, Cheng Y, Breschi A, Vierstra J, Wu W, Ryba T, et al.
Nature
. 2014 Nov;
515(7527):355-64.
PMID: 25409824
The laboratory mouse shares the majority of its protein-coding genes with humans, making it the premier model organism in biomedical research, yet the two mammals differ in significant ways. To...
3.
Stergachis A, Neph S, Reynolds A, Humbert R, Miller B, Paige S, et al.
Cell
. 2013 Aug;
154(4):888-903.
PMID: 23953118
Cellular-state information between generations of developing cells may be propagated via regulatory regions. We report consistent patterns of gain and loss of DNase I-hypersensitive sites (DHSs) as cells progress from...
4.
Maurano M, Humbert R, Rynes E, Thurman R, Haugen E, Wang H, et al.
Science
. 2012 Sep;
337(6099):1190-5.
PMID: 22955828
Genome-wide association studies have identified many noncoding variants associated with common diseases and traits. We show that these variants are concentrated in regulatory DNA marked by deoxyribonuclease I (DNase I)...
5.
Neph S, Vierstra J, Stergachis A, Reynolds A, Haugen E, Vernot B, et al.
Nature
. 2012 Sep;
489(7414):83-90.
PMID: 22955618
Regulatory factor binding to genomic DNA protects the underlying sequence from cleavage by DNase I, leaving nucleotide-resolution footprints. Using genomic DNase I footprinting across 41 diverse cell and tissue types,...
6.
Thurman R, Rynes E, Humbert R, Vierstra J, Maurano M, Haugen E, et al.
Nature
. 2012 Sep;
489(7414):75-82.
PMID: 22955617
DNase I hypersensitive sites (DHSs) are markers of regulatory DNA and have underpinned the discovery of all classes of cis-regulatory elements including enhancers, promoters, insulators, silencers and locus control regions....
7.
Neph S, Kuehn M, Reynolds A, Haugen E, Thurman R, Johnson A, et al.
Bioinformatics
. 2012 May;
28(14):1919-20.
PMID: 22576172
Unlabelled: The large and growing number of genome-wide datasets highlights the need for high-performance feature analysis and data comparison methods, in addition to efficient data storage and retrieval techniques. We...
8.
Liu M, Li C, Stamatoyannopoulos G, Dorschner M, Humbert R, Stamatoyannopoulos J, et al.
Hum Gene Ther
. 2011 Oct;
23(2):231-7.
PMID: 21981728
Concerns surrounding the oncogenic potential of recombinant gammaretroviral vectors has spurred a great deal of interest in vector integration site (VIS) preferences. Although gammaretroviral vectors exhibit a modest preference for...
9.
Mann T, Humbert R, Dorschner M, Stamatoyannopoulos J, Noble W
Nucleic Acids Res
. 2009 Jun;
37(13):e95.
PMID: 19528077
We developed a primer design method, Pythia, in which state of the art DNA binding affinity computations are directly integrated into the primer design process. We use chemical reaction equilibrium...
10.
Attanasio C, Reymond A, Humbert R, Lyle R, Kuehn M, Neph S, et al.
Genome Biol
. 2008 Dec;
9(12):R168.
PMID: 19055709
Background: Conserved non-coding sequences in the human genome are approximately tenfold more abundant than known genes, and have been hypothesized to mark the locations of cis-regulatory elements. However, the global...