A network-based algorithm for the identification of moonlighting noncoding RNAs and its application in sepsis

Exploiting locational and topological overlap model to identify modules in protein interaction networks

(2019) Lixin Cheng et al.   BMC BIOINFORMATICS

LncBook: a curated knowledgebase of human long non-coding RNAs

(2019) Lina Ma et al.   NUCLEIC ACIDS RESEARCH

Analysis of long noncoding RNAs highlights region-specific altered expression patterns and diagnostic roles in Alzheimer’s disease

(2018) Meng Zhou et al.   BRIEFINGS IN BIOINFORMATICS

SMILE: a novel procedure for subcellular module identification with localisation expansion

(2018) Lixin Cheng et al.   IET Systems Biology

Recurrence-associated long non-coding RNA signature for determining the risk of recurrence in patients with colon cancer

(2018) Meng Zhou et al.   Molecular Therapy-Nucleic Acids

Full Characterization of Localization Diversity in the Human Protein Interactome

(2017) Lixin Cheng et al.   JOURNAL OF PROTEOME RESEARCH

A subcellular map of the human proteome

(2017) Peter J. Thul et al.   SCIENCE

Classification of patients with sepsis according to blood genomic endotype: a prospective cohort study

(2017) Brendon P Scicluna et al.   Lancet Respiratory Medicine

Moonlighting proteins in cancer

(2016) Kyung-Won Min et al.   CANCER LETTERS

ICN: a normalization method for gene expression data considering the over-expression of informative genes

(2016) Lixin Cheng et al.   Molecular BioSystems

A long non-coding RNA signature to improve prognosis prediction of gastric cancer

(2016) Xiaoqiang Zhu et al.   Molecular Cancer

A scored human protein–protein interaction network to catalyze genomic interpretation

(2016) Taibo Li et al.   NATURE METHODS

RAID v2.0: an updated resource of RNA-associated interactions across organisms

(2016) Ying Yi et al.   NUCLEIC ACIDS RESEARCH

Metabolic Enzymes Moonlighting in the Nucleus: Metabolic Regulation of Gene Transcription

(2016) Aristeidis E. Boukouris et al.   TRENDS IN BIOCHEMICAL SCIENCES

Linking Long Noncoding RNA Localization and Function

(2016) Ling-Ling Chen   TRENDS IN BIOCHEMICAL SCIENCES

CrossNorm: a novel normalization strategy for microarray data in cancers

(2016) Lixin Cheng et al.   Scientific Reports

Revealing protein–lncRNA interaction

(2015) Fabrizio Ferrè et al.   BRIEFINGS IN BIOINFORMATICS

Identification of lncRNA-associated competing triplets reveals global patterns and prognostic markers for cancer

(2015) Peng Wang et al.   NUCLEIC ACIDS RESEARCH

Tissue-based map of the human proteome

(2015) M. Uhlen et al.   SCIENCE

Mitochondrial Proteins Moonlighting in the Nucleus

(2015) Richard M. Monaghan et al.   TRENDS IN BIOCHEMICAL SCIENCES

Extreme multifunctional proteins identified from a human protein interaction network

(2015) Charles E. Chapple et al.   Nature Communications

Why study moonlighting proteins?

(2015) Constance J. Jeffery   Frontiers in Genetics

Gene duplication and the evolution of moonlighting proteins

(2015) Adriana Espinosa-Cantú et al.   Frontiers in Genetics

Gene co-expression analysis identifies common modules related to prognosis and drug resistance in cancer cell lines

(2014) Wei Liu et al.   INTERNATIONAL JOURNAL OF CANCER

In the right place at the right time: visualizing and understanding mRNA localization

(2014) Adina R. Buxbaum et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Functional module identification in protein interaction networks by interaction patterns

(2013) Yijie Wang et al.   BIOINFORMATICS

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

Integrative genomic analyses reveal clinically relevant long noncoding RNAs in human cancer

(2013) Zhou Du et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Severe Sepsis and Septic Shock

(2013) Derek C. Angus et al.   NEW ENGLAND JOURNAL OF MEDICINE

starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein–RNA interaction networks from large-scale CLIP-Seq data

(2013) Jun-Hao Li et al.   NUCLEIC ACIDS RESEARCH

Identifying functional modules in interaction networks through overlapping Markov clustering

(2012) Y.-K. Shih et al.   BIOINFORMATICS

PCDq: human protein complex database with quality index which summarizes different levels of evidences of protein complexes predicted from H-Invitational protein-protein interactions integrative dataset

(2012) Shingo Kikugawa et al.   BMC Systems Biology

Detecting overlapping protein complexes in protein-protein interaction networks

(2012) Tamás Nepusz et al.   NATURE METHODS

Principal component analysis based methods in bioinformatics studies

(2011) S. Ma et al.   BRIEFINGS IN BIOINFORMATICS

GOSemSim: an R package for measuring semantic similarity among GO terms and gene products

(2010) G. Yu et al.   BIOINFORMATICS

Identification of differential gene pathways with principal component analysis

(2009) Shuangge Ma et al.   BIOINFORMATICS

The Human Protein Atlas-a tool for pathology

(2008) F Pontén et al.   JOURNAL OF PATHOLOGY