BIOMEX: an interactive workflow for (single cell) omics data interpretation and visualization

An Integrated Gene Expression Landscape Profiling Approach to Identify Lung Tumor Endothelial Cell Heterogeneity and Angiogenic Candidates

(2020) Jermaine Goveia et al.   CANCER CELL

Single-Cell Transcriptome Atlas of Murine Endothelial Cells

(2020) Joanna Kalucka et al.   CELL

The EXPANDER Integrated Platform for Transcriptome Analysis

(2019) Tom Aharon Hait et al.   JOURNAL OF MOLECULAR BIOLOGY

OUP accepted manuscript

(2018)   BRIEFINGS IN BIOINFORMATICS

Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors

(2018) Laleh Haghverdi et al.   NATURE BIOTECHNOLOGY

scmap: projection of single-cell RNA-seq data across data sets

(2018) Vladimir Yu Kiselev et al.   NATURE METHODS

Impairment of Angiogenesis by Fatty Acid Synthase Inhibition Involves mTOR Malonylation

(2018) Ulrike Bruning et al.   Cell Metabolism

Instant Clue: A Software Suite for Interactive Data Visualization and Analysis

(2018) Hendrik Nolte et al.   Scientific Reports

Identification of cell types in a mouse brain single-cell atlas using low sampling coverage

(2018) Aparna Bhaduri et al.   BMC BIOLOGY

Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris

(2018) et al.   NATURE

EndoDB: a database of endothelial cell transcriptomics data

(2018) Shawez Khan et al.   NUCLEIC ACIDS RESEARCH

Integrative Analysis of Microarray Data to Reveal Regulation Patterns in the Pathogenesis of Hepatocellular Carcinoma

(2017) Juan Chen et al.   Gut and Liver

ranger: A Fast Implementation of Random Forests for High Dimensional Data in C++ and R

(2017) Marvin N. Wright et al.   Journal of Statistical Software

Cholangiocarcinoma — evolving concepts and therapeutic strategies

(2017) Sumera Rizvi et al.   Nature Reviews Clinical Oncology

NOREVA: normalization and evaluation of MS-based metabolomics data

(2017) Bo Li et al.   NUCLEIC ACIDS RESEARCH

The Human Cell Atlas

(2017) Aviv Regev et al.   eLife

CEA but not CA19-9 is an independent prognostic factor in patients undergoing resection of cholangiocarcinoma

(2017) Sven H. Loosen et al.   Scientific Reports

Genome, transcriptome and proteome: the rise of omics data and their integration in biomedical sciences

(2016) Claudia Manzoni et al.   BRIEFINGS IN BIOINFORMATICS

The Perseus computational platform for comprehensive analysis of (prote)omics data

(2016) Stefka Tyanova et al.   NATURE METHODS

Principal component analysis: a review and recent developments

(2016) Ian T. Jolliffe et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES

From big data analysis to personalized medicine for all: challenges and opportunities

(2015) Akram Alyass et al.   BMC Medical Genomics

FlowSOM: Using self-organizing maps for visualization and interpretation of cytometry data

(2015) Sofie Van Gassen et al.   CYTOMETRY PART A

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Big Data: Astronomical or Genomical?

(2015) Zachary D. Stephens et al.   PLOS BIOLOGY

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

ArrayExpress update—simplifying data submissions

(2014) Nikolay Kolesnikov et al.   NUCLEIC ACIDS RESEARCH

Fast Principal Component Analysis of Large-Scale Genome-Wide Data

(2014) Gad Abraham et al.   PLoS One

Pathview: an R/Bioconductor package for pathway-based data integration and visualization

(2013) Weijun Luo et al.   BIOINFORMATICS

GSVA: gene set variation analysis for microarray and RNA-Seq data

(2013) Sonja Hänzelmann et al.   BMC BIOINFORMATICS

Computing: A vision for data science

(2013) Chris A. Mattmann   NATURE

The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud

(2013) Katherine Wolstencroft et al.   NUCLEIC ACIDS RESEARCH

XCMS Online: A Web-Based Platform to Process Untargeted Metabolomic Data

(2012) Ralf Tautenhahn et al.   ANALYTICAL CHEMISTRY

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

ROAST: rotation gene set tests for complex microarray experiments

(2010) Di Wu et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

MetaboAnalyst: a web server for metabolomic data analysis and interpretation

(2009) J. Xia et al.   NUCLEIC ACIDS RESEARCH

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY