ExpressVis: a biologist-oriented interactive web server for exploring multi-omics data

eVITTA: a web-based visualization and inference toolbox for transcriptome analysis

(2021) Xuanjin Cheng et al.   NUCLEIC ACIDS RESEARCH

OmicsAnalyst: a comprehensive web-based platform for visual analytics of multi-omics data

(2021) Guangyan Zhou et al.   NUCLEIC ACIDS RESEARCH

Database resources of the national center for biotechnology information

(2021) Eric W Sayers et al.   NUCLEIC ACIDS RESEARCH

The reactome pathway knowledgebase 2022

(2021) Marc Gillespie et al.   NUCLEIC ACIDS RESEARCH

piNET: a versatile web platform for downstream analysis and visualization of proteomics data

(2020) Behrouz Shamsaei et al.   NUCLEIC ACIDS RESEARCH

Proteomic analysis revealed common, unique and systemic signatures in gender-dependent hepatocarcinogenesis

(2020) Huiling Li et al.   Biology of Sex Differences

UniProt: the universal protein knowledgebase in 2021

(2020) et al.   NUCLEIC ACIDS RESEARCH

Proteomics identifies new therapeutic targets of early-stage hepatocellular carcinoma

(2019) Ying Jiang et al.   NATURE

Integrated Proteogenomic Characterization of HBV-Related Hepatocellular Carcinoma

(2019) Qiang Gao et al.   CELL

PANDA-view: an easy-to-use tool for statistical analysis and visualization of quantitative proteomics data

(2018) Cheng Chang et al.   BIOINFORMATICS

Visualizing omics and clinical data: Which challenges for dealing with their variety?

(2018) Fleur Mougin et al.   METHODS

KeggExp: a web server for visual integration of KEGG pathways and expression profile data

(2018) Xian Liu et al.   BIOINFORMATICS

PANDA: A comprehensive and flexible tool for quantitative proteomics data analysis

(2018) Cheng Chang et al.   BIOINFORMATICS

iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data

(2018) Steven Xijin Ge et al.   BMC BIOINFORMATICS

PPIExp: A Web-Based Platform for Integration and Visualization of Protein–Protein Interaction Data and Spatiotemporal Proteomics Data

(2018) Xian Liu et al.   JOURNAL OF PROTEOME RESEARCH

KEGG: new perspectives on genomes, pathways, diseases and drugs

(2016) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

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

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

fastcluster: Fast Hierarchical, Agglomerative Clustering Routines forRandPython

(2015) Daniel Müllner   Journal of Statistical Software

NCBI GEO: archive for functional genomics data sets—update

(2012) Tanya Barrett et al.   NUCLEIC ACIDS RESEARCH

Visualizing biological data—now and in the future

(2010) Seán I O'Donoghue et al.   NATURE METHODS

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

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS