Visualization of omics data for systems biology
High-throughput studies of biological systems are rapidly accumulating a wealth of'omics'-
scale data. Visualization is a key aspect of both the analysis and understanding of these …
scale data. Visualization is a key aspect of both the analysis and understanding of these …
RNA-Seq technology and its application in fish transcriptomics
X Qian, Y Ba, Q Zhuang, G Zhong - Omics: a journal of integrative …, 2014 - liebertpub.com
High-throughput sequencing technologies, also known as next-generation sequencing
(NGS) technologies, have revolutionized the way that genomic research is advancing. In …
(NGS) technologies, have revolutionized the way that genomic research is advancing. In …
The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data
Next-generation DNA sequencing (NGS) projects, such as the 1000 Genomes Project, are
already revolutionizing our understanding of genetic variation among individuals. However …
already revolutionizing our understanding of genetic variation among individuals. However …
NGS QC Toolkit: a toolkit for quality control of next generation sequencing data
Next generation sequencing (NGS) technologies provide a high-throughput means to
generate large amount of sequence data. However, quality control (QC) of sequence data …
generate large amount of sequence data. However, quality control (QC) of sequence data …
Software for computing and annotating genomic ranges
M Lawrence, W Huber, H Pagès… - PLoS computational …, 2013 - journals.plos.org
We describe Bioconductor infrastructure for representing and computing on annotated
genomic ranges and integrating genomic data with the statistical computing features of R …
genomic ranges and integrating genomic data with the statistical computing features of R …
MULTI-seq: sample multiplexing for single-cell RNA sequencing using lipid-tagged indices
Sample multiplexing facilitates scRNA-seq by reducing costs and identifying artifacts such
as cell doublets. However, universal and scalable sample barcoding strategies have not …
as cell doublets. However, universal and scalable sample barcoding strategies have not …
Comprehensive genomic analysis of malignant pleural mesothelioma identifies recurrent mutations, gene fusions and splicing alterations
R Bueno, EW Stawiski, LD Goldstein, S Durinck… - Nature …, 2016 - nature.com
Abstract We analyzed transcriptomes (n= 211), whole exomes (n= 99) and targeted exomes
(n= 103) from 216 malignant pleural mesothelioma (MPM) tumors. Using RNA-seq data, we …
(n= 103) from 216 malignant pleural mesothelioma (MPM) tumors. Using RNA-seq data, we …
Count-based differential expression analysis of RNA sequencing data using R and Bioconductor
RNA sequencing (RNA-seq) has been rapidly adopted for the profiling of transcriptomes in
many areas of biology, including studies into gene regulation, development and disease. Of …
many areas of biology, including studies into gene regulation, development and disease. Of …
Genome-wide CRISPR screens in primary human T cells reveal key regulators of immune function
Human T cells are central effectors of immunity and cancer immunotherapy. CRISPR-based
functional studies in T cells could prioritize novel targets for drug development and improve …
functional studies in T cells could prioritize novel targets for drug development and improve …
Comprehensive genomic analysis identifies SOX2 as a frequently amplified gene in small-cell lung cancer
Small-cell lung cancer (SCLC) is an exceptionally aggressive disease with poor prognosis.
Here, we obtained exome, transcriptome and copy-number alteration data from …
Here, we obtained exome, transcriptome and copy-number alteration data from …