22 Result(s)
within
Noam Shoresh
English
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Article
Long-range phasing of dynamic, tissue-specific and allele-specific regulatory elements
Epigenomic maps identify gene regulatory elements by their chromatin state. However, prevailing short-read sequencing methods cannot effectively distinguish alleles, evaluate the interdependence of elements in...
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Open AccessAuthor Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes
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Open AccessDetecting sample swaps in diverse NGS data types using linkage disequilibrium
As the number of genomics datasets grows rapidly, sample mislabeling has become a high stakes issue. We present CrosscheckFingerprints (Crosscheck), a tool for quantifying sample-relatedness and detecting inco...
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Open AccessExpanded encyclopaedias of DNA elements in the human and mouse genomes
The human and mouse genomes contain instructions that specify RNAs and proteins and govern the timing, magnitude, and cellular context of their production. To better delineate these elements, phase III of the ...
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Open AccessHybridization-based capture of pathogen mRNA enables paired host-pathogen transcriptional analysis
Dual transcriptional profiling of host and bacteria during infection is challenging due to the low abundance of bacterial mRNA. We report Pathogen Hybrid Capture (PatH-Cap), a method to enrich for bacterial mR...
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Simultaneous detection of genotype and phenotype enables rapid and accurate antibiotic susceptibility determination
Multidrug resistant organisms are a serious threat to human health1,2. Fast, accurate antibiotic susceptibility testing (AST) is a critical need in addressing escalating antibiotic resistance, since delays in ide...
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Publisher Correction: Enhancer signatures stratify and predict outcomes of non-functional pancreatic neuroendocrine tumors
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Enhancer signatures stratify and predict outcomes of non-functional pancreatic neuroendocrine tumors
Most pancreatic neuroendocrine tumors (PNETs) do not produce excess hormones and are therefore considered ‘non-functional’1–3. As clinical behaviors vary widely and distant metastases are eventually lethal2,4, bi...
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Open AccessRapid identification and phylogenetic classification of diverse bacterial pathogens in a multiplexed hybridization assay targeting ribosomal RNA
Rapid bacterial identification remains a critical challenge in infectious disease diagnostics. We developed a novel molecular approach to detect and identify a wide diversity of bacterial pathogens in a single...
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Heritability enrichment of specifically expressed genes identifies disease-relevant tissues and cell types
We introduce an approach to identify disease-relevant tissues and cell types by analyzing gene expression data together with genome-wide association study (GWAS) summary statistics. Our approach uses stratifie...
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Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state
Chromatin state is analyzed for the first time in single cells, revealing new cell subpopulations.
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Polyploidy can drive rapid adaptation in yeast
In vitro evolution experiments on haploid, diploid, and tetraploid yeast strains show that adaptation is faster in tetraploids, providing direct quantitative evidence that in some environments polyploidy can acce...
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Open AccessIntegrative analysis of 111 reference human epigenomes
The reference human genome sequence set the stage for studies of genetic variation and its association with human disease, but epigenomic studies lack a similar reference. To address this need, the NIH Roadmap...
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Genetic and epigenetic fine map** of causal autoimmune disease variants
Genome-wide association studies have identified loci underlying human diseases, but the causal nucleotide changes and mechanisms remain largely unknown. Here we developed a fine-map** algorithm to identify c...
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Optimization of lag time underlies antibiotic tolerance in evolved bacterial populations
Repeated exposure of the bacterium Escherichia coli to clinically relevant concentrations of ampicillin results in the evolution of tolerance—the ability to survive until the antibiotic concentration diminishes—t...
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Open AccessComparative analysis of metazoan chromatin organization
A large collection of new modENCODE and ENCODE genome-wide chromatin data sets from cell lines and developmental stages in worm, fly and human are analysed; this reveals many conserved features of chromatin or...
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Data exploration
Enhancement of pattern discovery through graphical representation of data.
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Map** and analysis of chromatin state dynamics in nine human cell types
Chromatin profiling has emerged as a powerful means of genome annotation and detection of regulatory activity. The approach is especially well suited to the characterization of non-coding portions of the genom...
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Chromatin profiling by directly sequencing small quantities of immunoprecipitated DNA
Single-molecule sequencing of poly(A)-tailed chromatin immunoprecipitated DNA proves equal in sensitivity and accuracy to amplification-based sequencing technologies and allows analysis of samples sizes as sma...
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Open AccessAnalytical Results for Individual and Group Selection of Any Intensity
The idea of evolutionary game theory is to relate the payoff of a game to reproductive success (= fitness). An underlying assumption in most models is that fitness is a linear function of the payoff. For stoch...
