Applied Bioinf Core

@oxpeter presented a great update on Jupyter Notebooks after attending @JupyterCon, see github.com/abcdbug/dbug for the notes!

Check out our new website! abc.med.cornell.edu

"1 million reads provide good accuracy for the abundance of highly-expressed genes" sciencedirect.com/science/articl…

A comparison of extraction kits for the isolation of total RNA from small tissue samples ncbi.nlm.nih.gov/pmc/articles/P…

Assessing the effects of low-input RNA-seq youtu.be/bB7Xw_S4nqk

Effect of RNA integrity on uniquely mapped reads in RNA-Seq biomedcentral.com/1756-0500/7/753 #bmcresearchnotes

subSeq: Determining appropriate sequencing depth through efficient read subsampling bioinformatics.oxfordjournals.org/content/early/…

RNA-seq Analysis Reveals Contamination of Multiple Nasopharyngeal Carcinoma Cell Lines with HeLa Cell Genomes jvi.asm.org/content/88/18/…

An RNA-seq Transcriptome and Splicing Database of Glia, Neurons, and Vascular Cells of the Cerebral Cortex jneurosci.org/content/34/36/…

Best Paper award at Usenix Security'14 conf: framework for privacy in pharmacogenomic analyses usenix.org/system/files/c… via @jgiannopoulou

The final #GDS policy sets expectations for investigators to broadly & sensibly share research data. 1.usa.gov/1q5iH3h #datasharing

Omics Pipe: A Computational Framework for Reproducible Multi-Omics Data Analysis biorxiv.org/content/early/…

Correlation coefficient is insufficient at assessing equality in replicates jbiolres.com/content/21/1/3 #journalofbiologicalresearch-thessaloniki

Correction of gene expression data: performance-dependency on inter-replicate and inter-treatment biases sciencedirect.com/science/articl…

Detecting and correcting systematic variation in large-scale RNA sequencing data go.nature.com/5vYYFa

Multi-platform assessment of transcriptome profiling using RNA-seq in the ABRF next-gen. sequencing study go.nature.com/vwEy8m

A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the SEQC go.nature.com/gJjAlY

Reagent contamination can critically impact sequence-based microbiome analyses biorxiv.org/content/early/…

Influence of RNA extraction methods and library selection schemes on RNA-seq data biomedcentral.com/1471-2164/15/6… #bmcgenomics

#PLOSONE: A Comparative Study of Techniques for Differential Expression Analysis on RNA-Seq Data dx.plos.org/10.1371/journa…