Hiplot: a comprehensive and easy-to-use web service for boosting publication-ready biomedical data visualization

Exploration of Coding and Non-coding Variants in Cancer Using GenomePaint

(2021) Xin Zhou et al.   CANCER CELL

UCSCXenaShiny: an R/CRAN package for interactive analysis of UCSC Xena data

(2021) Shixiang Wang et al.   BIOINFORMATICS

Visualizing and interpreting cancer genomics data via the Xena platform

(2020) Mary J. Goldman et al.   NATURE BIOTECHNOLOGY

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update

(2020) Vahid Jalili et al.   NUCLEIC ACIDS RESEARCH

NASQAR: a web-based platform for high-throughput sequencing data analysis and visualization

(2020) Ayman Yousif et al.   BMC BIOINFORMATICS

Next-Generation Analytics for Omics Data

(2020) Jun Li et al.   CANCER CELL

cola: an R/Bioconductor package for consensus partitioning through a general framework

(2020) Zuguang Gu et al.   NUCLEIC ACIDS RESEARCH

Molecular and pharmacological modulators of the tumor immune contexture revealed by deconvolution of RNA-seq data

(2019) Francesca Finotello et al.   Genome Medicine

Comprehensive evaluation of transcriptome-based cell-type quantification methods for immuno-oncology

(2019) Gregor Sturm et al.   BIOINFORMATICS

Pediatric Cancer Variant Pathogenicity Information Exchange (PeCanPIE): a cloud-based platform for curating and classifying germline variants

(2019) Michael N. Edmonson et al.   GENOME RESEARCH

Deep learning in biomedicine

(2018) Michael Wainberg et al.   NATURE BIOTECHNOLOGY

Transcriptional landscape of B cell precursor acute lymphoblastic leukemia based on an international study of 1,223 cases

(2018) Jian-Feng Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nextflow enables reproducible computational workflows

(2017) Paolo Di Tommaso et al.   NATURE BIOTECHNOLOGY

Meta-analytical methods to identify who benefits most from treatments: daft, deluded, or deft approach?

(2017) David J Fisher et al.   BMJ-British Medical Journal

Meta-analytical methods to identify who benefits most from treatments: daft, deluded, or deft approach?

(2017) David J Fisher et al.   BMJ-British Medical Journal

Simultaneous enumeration of cancer and immune cell types from bulk tumor gene expression data

(2017) Julien Racle et al.   eLife

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

Mass-spectrometric exploration of proteome structure and function

(2016) Ruedi Aebersold et al.   NATURE

Exploring genomic alteration in pediatric cancer using ProteinPaint

(2016) Xin Zhou et al.   NATURE GENETICS

Robust enumeration of cell subsets from tissue expression profiles

(2015) Aaron M Newman et al.   NATURE METHODS

The cBio Cancer Genomics Portal: An Open Platform for Exploring Multidimensional Cancer Genomics Data: Figure 1.

(2012) Ethan Cerami et al.   Cancer Discovery

Visualizing genomes: techniques and challenges

(2010) Cydney B Nielsen et al.   NATURE METHODS

Visualization of omics data for systems biology

(2010) Nils Gehlenborg et al.   NATURE METHODS