Splicing and Junction Mapping

LR-Split-seq – mapping and modeling the genomic basis of differential RNA isoform expression at single-cell resolution

Alternative RNA isoforms are defined by promoter choice, alternative splicing, and polyA site select...
AS-Quant – Detection and Visualization of Alternative Splicing Events with RNA-seq Data

A simplistic understanding of the central dogma falls short in correlating the number of genes in th...
FUNGI – Fusion Gene Integration Toolset

Fusion genes are both useful cancer biomarkers and important drug targets. Finding relevant fusion g...
2passtools: two-pass alignment using machine-learning-filtered splice junctions increases the accuracy of intron detection in long-read RNA sequencing

Transcription of eukaryotic genomes involves complex alternative processing of RNAs. Sequencing of f...
McSplicer – a probabilistic model for estimating splice site usage from RNA-seq data

Alternative splicing removes intronic sequences from transcripts in alternative ways to produce diff...

LR-Split-seq – mapping and modeling the genomic basis of differential RNA isoform expression at single-cell resolution

April 28, 2021 Leave a comment 1,571 Views

Alternative RNA isoforms are defined by promoter choice, alternative splicing, and polyA site selection. Although differential isoform expression is known to play a large regulatory role in eukaryotes, it has proved challenging to study with standard short-read RNA-seq because of ...

AS-Quant – Detection and Visualization of Alternative Splicing Events with RNA-seq Data

April 26, 2021 Leave a comment 1,506 Views

A simplistic understanding of the central dogma falls short in correlating the number of genes in the genome to the number of proteins in the proteome.

FUNGI – Fusion Gene Integration Toolset

March 31, 2021 Leave a comment 990 Views

Fusion genes are both useful cancer biomarkers and important drug targets. Finding relevant fusion genes is challenging due to genomic instability resulting in a high number of passenger events...

2passtools: two-pass alignment using machine-learning-filtered splice junctions increases the accuracy of intron detection in long-read RNA sequencing

March 2, 2021 Leave a comment 1,087 Views

Transcription of eukaryotic genomes involves complex alternative processing of RNAs. Sequencing of full-length RNAs using long reads reveals the...

McSplicer – a probabilistic model for estimating splice site usage from RNA-seq data

February 2, 2021 Leave a comment 1,196 Views

Alternative splicing removes intronic sequences from transcripts in alternative ways to produce different forms (isoforms) of mature mRNA. The composition of expressed transcripts and their alternative forms give specific functionalities to cells in a particular...

Arriba – accurate and efficient detection of gene fusions from RNA sequencing data

January 15, 2021 Leave a comment 1,821 Views

The identification of gene fusions from RNA sequencing data is a routine task in cancer research and precision oncology. However, despite the...

MetaTX -new model solves problem of isoform ambiguity

November 4, 2020 Leave a comment 1,362 Views

A new statistical model from Xi’an Jiaotong-Liverpool University aims to solve the problem of isoform ambiguity related to RNA modifications. The paper, published on 2 November in the leading...

DIGGER: exploring the functional role of alternative splicing in protein interactions

October 29, 2020 Leave a comment 1,649 Views

Alternative splicing plays a major role in regulating the functional repertoire of the proteome. However, isoform-specific effects to protein-protein interactions (PPIs) are usually overlooked, making it impossible to judge the functional role of individual exons on a systems biology level. ...

VALERIE – visualising alternative splicing events from single-cell RNA sequencing experiments

September 10, 2020 Leave a comment 1,755 Views

University of Oxford researchers present VALERIE (Visualising alternative splicing events from single-cell ribonucleic acid-sequencing experiments), an R package for visualising alternative splicing events at single-cell resolution. To explore any given specified genomic region, corresponding to an alternative splicing event, VALERIE ...

MINTIE – identifying novel structural and splice variants in transcriptomes using RNA-seq data

July 21, 2020 Leave a comment 1,800 Views

Genomic rearrangements can modify gene function by altering transcript sequences, and have been shown to be drivers in both cancer and rare...

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RNA-Seq Blog Transcriptome Research & Industry News

Splicing and Junction Mapping

LR-Split-seq – mapping and modeling the genomic basis of differential RNA isoform expression at single-cell resolution

AS-Quant – Detection and Visualization of Alternative Splicing Events with RNA-seq Data

FUNGI – Fusion Gene Integration Toolset

2passtools: two-pass alignment using machine-learning-filtered splice junctions increases the accuracy of intron detection in long-read RNA sequencing

McSplicer – a probabilistic model for estimating splice site usage from RNA-seq data

LR-Split-seq – mapping and modeling the genomic basis of differential RNA isoform expression at single-cell resolution

AS-Quant – Detection and Visualization of Alternative Splicing Events with RNA-seq Data

FUNGI – Fusion Gene Integration Toolset

2passtools: two-pass alignment using machine-learning-filtered splice junctions increases the accuracy of intron detection in long-read RNA sequencing

McSplicer – a probabilistic model for estimating splice site usage from RNA-seq data

Arriba – accurate and efficient detection of gene fusions from RNA sequencing data

MetaTX -new model solves problem of isoform ambiguity

DIGGER: exploring the functional role of alternative splicing in protein interactions

VALERIE – visualising alternative splicing events from single-cell RNA sequencing experiments

MINTIE – identifying novel structural and splice variants in transcriptomes using RNA-seq data

Direct RNA sequencing reveals SARS-CoV-2 m6A sites

Single-cell RNA sequencing identifies of early-stage lung cancer biomarkers from circulating blood

scRNA-seq – Introduction to single cell RNA-seq data analysis

m6A-seq2 – multiplexed profiling facilitates robust m6A quantification at site, gene and sample resolution

Scientists use m6A RNA sequencing to gain new understanding of how brain cells talk

RNA sequencing data for FFPE tumor blocks can be used for robust estimation of tumor mutation burden in individual biosamples

Positions for Postdoc/Research Staff/PhD student interested in single-cell transcriptomics at the Stony Brook University