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Article
Open AccessmirTarRnaSeq: An R/Bioconductor Statistical Package for miRNA-mRNA Target Identification and Interaction Analysis
We introduce mirTarRnaSeq, an R/Bioconductor package for quantitative assessment of miRNA-mRNA relationships within sample cohorts. mirTarRnaSeq is a statistical package to explore predicted or pre-hypothesized m...
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Article
Open AccessChallenges and emerging directions in single-cell analysis
Single-cell analysis is a rapidly evolving approach to characterize genome-scale molecular information at the individual cell level. Development of single-cell technologies and computational methods has enable...
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Article
Open AccessA multi-omic analysis of human naïve CD4+ T cells
Cellular function and diversity are orchestrated by complex interactions of fundamental biomolecules including DNA, RNA and proteins. Technological advances in genomics, epigenomics, transcriptomics and proteo...
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Article
Open AccessIVT-seq reveals extreme bias in RNA sequencing
RNA-seq is a powerful technique for identifying and quantifying transcription and splicing events, both known and novel. However, given its recent development and the proliferation of library construction meth...
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Article
Retraction Note: Functional dissection of lysine deacetylases reveals that HDAC1 and p300 regulate AMPK
In response to a concern raised by a reader about inconsistencies in our Letter between the results from the primary microarray screen and cell growth validation studies (Supplementary Table 2), we reviewed th...
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Article
Reversible switching between epigenetic states in honeybee behavioral subcastes
This paper reports that there are substantial differences in DNA methylation patterns between nurses and forager caste phenotypes in honeybees, and that reverting foragers back to nurses reestablishes methylat...
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Article
Functional dissection of lysine deacetylases reveals that HDAC1 and p300 regulate AMPK
Genetic interaction profiles of human lysine deacetylases are generated by RNA interference knockdown to reveal the involvement of deacetylases in many critical biological processes, including metabolism, the ...
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Article
Open AccessEffective detection of rare variants in pooled DNA samples using Cross-pool tailcurve analysis
Sequencing targeted DNA regions in large samples is necessary to discover the full spectrum of rare variants. We report an effective Illumina sequencing strategy utilizing pooled samples with novel quality (Sr...
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Article
Effective detection of rare variants in pooled DNA samples using cross-pool tail-curve analysis
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Article
Effective detection of rare variants in pooled DNA samples using cross-pool tail-curve analysis
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Article
Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts
Andrew Feinberg and colleagues show that differential methylation of CpG island shores distinguish human induced pluripotent stem cells from the fibroblasts from which they were derived. These differentially m...
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Protocol
Statistical Analysis of Fitness Data Determined by TAG Hybridization on Microarrays
TAG, or bar-code, microarrays allow measurement of the oligonucleotide sequences (TAGs) that mark each strain of deletion mutants in the Saccharomyces cerevisiae yeast knockout (YKO) collection. Comparison of gen...
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Chapter
Empirical Bayes Analysis of a Microarray Experiment
Microarrays are an example of the powerful high-throughput genomics tools that revolutionized the measurement of biological systems. This technology measures the quantity of nucleic acid molecules present in a...
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Protocol
Analysis of Genetic Interactions on a Genome-Wide Scale in Budding Yeast: Diploid-Based Synthetic Lethality Analysis by Microarray
Comprehensive collections of open reading frame (ORF) deletion mutant strains exist for the budding yeast Saccharomyces cerevisiae. With great prescience, these strains were designed with short molecular bar code...
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Article
Top-down standards will not serve systems biology
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Article
Open AccessBioconductor: open software development for computational biology and bioinformatics
The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. The goals of the project include: fostering collaborative developme...
