Read Until: Real time selective sequencing using Oxford Nanopore MinION

AGBT 2016 is happening now and it has been two years since we heard about the first MinION experiment at AGBT 2014. It has been two years since Oxford Nanopore selected participants for its MinION early access program. And  Oxford Nanopore has come a long way since the last two years. Two very interesting papers […]

Cataloging Splice Junctions in all Human RNA-seq data from Sequence Read Archive

One of the biggest sources of complexity in transcriptomes come from ubiquitous splicing. Our knowledge about the prevalence of alternative splicing has greatly increased from our ability to directly sequence the transcritome by using RNA-seq technology. Granted that to fully characterize the isoforms resulting from splicing, one needs long-read transcriptome sequencing. However, the abundance of […]

RECOMB 2016 List of Accepted Papers Available

RECOMB 2016, 20th Annual International Conference on Research in Computational Molecular Biology, has recently announced the list of accepted papers. This year, RECOMB will be held in Santa Monica, California April 17-21, 2016. RECOMB 2016 has accepted 35 papers from a variety of computational biology topics. The accepted papers will be presented as talks at […]

Paper Summary: Systematic bias and batch effects in single-cell RNA-Seq data

Single Cell RNA-seq technology has gained a lot of traction in the last few years, as it can help address a variety of interesting biological problems, ranging from studying development to cancer heterogeneity.  Since the first paper demonstrating the feasibility of single cell transcriptomics with, the number of cells one could assay is also increasing […]

Paper Summary: Fast and accurate single-cell RNA-seq analysis using equivalence class counts

One of the most common applications of single-cell RNA-seq data is to use it to characterize the heterogeneity of  cell populations and identify new cell types or sub-populations.  Typically one uses single-cell RNA-sequencing (RNA-seq) data, quantify gene expression on all cells and use the common gene-expression profile among the cells to characterize the cell-to-cell heterogeneity by […]