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Methods to read out naturally occurring or experimentally introduced nucleic acid modifications are emerging as powerful tools to study dynamic cellular processes. The recovery, quantification and...

To find marker genes in single-cell RNA-seq data, many popular methods now follow a common approach to find differentially expressed genes between a small group of highly homogeneous cells and the rest of the data (the outside group), and assume ...

A novel computer algorithm allows researchers to evaluate drugs’ effects and find new targets using models of cancer cell metabolism. Its developers report that rFASTCORMICS builds these models, which...

Integration of single-cell RNA sequencing (scRNA-seq) data from multiple experiments, laboratories and technologies can uncover biological insights, but current methods for scRNA-seq data integration are limited by a requirement for datasets to derive from...

RNA sequencing (RNA-seq) has become the standard means of analyzing gene and transcript expression in high-throughput. While previously sequence alignment was a time demanding step...

Investigators at Rutgers Cancer Institute of New Jersey have developed a computational method that uncovers clinically relevant gene expression patterns in large cohorts of breast cancer patients. This method, which is applicable to the analysis of all cancers...

Single-cell RNA sequencing (scRNA-seq) enables the high-throughput quantification of transcriptional profiles in single cells. In contrast to bulk RNA-seq, additional preprocessing steps such as cell barcode identification or unique molecular identifier (UMI) deconvolution are necessary for preprocessing of data from ...

Dynamic and reversible RNA modifications such as N6-methyladenosine (m6A) can play important roles in regulating messenger RNA (mRNA) splicing, export, stability and translation. Defective mRNA modification through altered expression of the methyltransferase and/or demethylases results in developmental defects and cancer ...

Researchers from Medical University of Innsbruck introduce quanTIseq, a method to quantify the fractions of ten immune cell types from bulk RNA-sequencing data. quanTIseq was extensively validated in blood and tumor samples using simulated, flow...

Quantification of DNA sequence tags from engineered constructs such as plasmids, transposons, or other transgenes underlies many functional genomics measurements. Typically, such measurements rely on PCR followed by next...