-
Protocol
Comparative Methods for Demystifying Spatial Transcriptomics
Spatial Transcriptomics (ST), coined as the term for parallel RNA-Seq on cell populations ordered spatially on a histological tissue section, has recently become increasingly popular, especially in experiments...
-
Article
Open AccessAnalysis of ovarian transcriptomes reveals thousands of novel genes in the insect vector Rhodnius prolixus
Rhodnius prolixus is a Triatominae insect species and a primary vector of Chagas disease. The genome of R. prolixus has been recently sequenced and partially assembled, but few transcriptome analyses have been pe...
-
Article
Open AccessLandscape of the spliced leader trans-splicing mechanism in Schistosoma mansoni
Spliced leader dependent trans-splicing (SLTS) has been described as an important RNA regulatory process that occurs in different organisms, including the trematode Schistosoma mansoni. We identified more than se...
-
Article
Open AccessThe effects of death and post-mortem cold ischemia on human tissue transcriptomes
Post-mortem tissues samples are a key resource for investigating patterns of gene expression. However, the processes triggered by death and the post-mortem interval (PMI) can significantly alter physiologicall...
-
Protocol
Comparative Genomics in Homo sapiens
Genomes can be compared at different levels of divergence, either between species or within species. Within species genomes can be compared between different subpopulations, such as human subpopulations from d...
-
Protocol
Comparative Genomics in Drosophila
Since the pioneering studies of Thomas Hunt Morgan and coworkers at the dawn of the twentieth century, Drosophila melanogaster and its sister species have tremendously contributed to unveil the rules underlying a...
-
Article
Open AccessSequence variation between 462 human individuals fine-tunes functional sites of RNA processing
Recent advances in the cost-efficiency of sequencing technologies enabled the combined DNA- and RNA-sequencing of human individuals at the population-scale, making genome-wide investigations of the inter-indiv...
-
Protocol
Analysis of Alternative Splicing Events in Custom Gene Datasets by AStalavista
Alternative splicing (AS) is a eukaryotic principle to derive more than one RNA product from transcribed genes by removing distinct subsets of introns from a premature polymer. We know today that this process ...
-
Article
Correction: Corrigendum: Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories
Nat. Biotechnol. 31, 1015–1022 (2013); doi:10.1038/nbt.2702; published online 15 September 2013; corrected after print 8 November 2013 In the version of this article initially published, in the list of members...
-
Article
Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories
RNA sequencing of 465 human lymphoblastoid cell lines across seven European laboratories shows the feasibility of transcriptome sequencing for population-wide and cross-biobank studies.
-
Article
Transcriptome and genome sequencing uncovers functional variation in humans
Genome sequencing projects are discovering millions of genetic variants in humans, and interpretation of their functional effects is essential for understanding the genetic basis of variation in human traits. ...
-
Article
Open AccessThe Genotype-Tissue Expression (GTEx) project
Genome-wide association studies have identified thousands of loci for common diseases, but, for the majority of these, the mechanisms underlying disease susceptibility remain unknown. Most associated variants ...
-
Article
The GEM mapper: fast, accurate and versatile alignment by filtration
A sequence read mapper for versatile searching of genome space that returns all matches with precision and speed.
-
Article
Open AccessLandscape of transcription in human cells
Eukaryotic cells make many types of primary and processed RNAs that are found either in specific subcellular compartments or throughout the cells. A complete catalogue of these RNAs is not yet available and th...
-
Article
Nucleosome positioning as a determinant of exon recognition
Chromatin influences transcription, but its effects on downstream processing have been less clear. Analyses of published high-throughput data examining nucleosomal positions in T cell and C. elegans genomes now i...
-
Chapter and Conference Paper
Exact Transcriptome Reconstruction from Short Sequence Reads
In this paper we address the problem of characterizing the RNA complement of a given cell type, that is, the set of RNA species and their relative copy number, from a large set of short sequence reads which ha...
-
Chapter and Conference Paper
Bubbles: Alternative Splicing Events of Arbitrary Dimension in Splicing Graphs
Eukaryotic splicing structures are known to involve a high degree of alternative forms derived from a premature transcript by alternative splicing (AS). With the advent of new sequencing technologies, evidence...
-
Article
Open AccessBased Upon Repeat Pattern (BURP): an algorithm to characterize the long-term evolution of Staphylococcus aureus populations based on spa polymorphisms
For ty** of Staphylococcus aureus, DNA sequencing of the repeat region of the protein A (spa) gene is a well established discriminatory method for outbreak investigations. Recently, it was hypothesized that thi...
-
Chapter and Conference Paper
Alignment of Tandem Repeats with Excision, Duplication, Substitution and Indels (EDSI)
Traditional sequence comparison by alignment applies a mutation model comprising two events, substitutions and indels (insertions or deletions) of single positions (SI). However, modern genetic analysis knows a...
-
Article
Open AccessRIDOM: Comprehensive and public sequence database for identification of Mycobacteriumspecies
Molecular identification of Mycobacterium species has two primary advantages when compared to phenotypic identification: rapid turn-around time and improved accuracy. The information content of the 5' end of the ...
