Detection of condition-specific marker genes from RNA-seq data with MGFR

DrImpute: imputing dropout events in single cell RNA sequencing data

(2018) Wuming Gong et al.   BMC BIOINFORMATICS

Precrec: fast and accurate precision–recall and ROC curve calculations in R

(2016) Takaya Saito et al.   BIOINFORMATICS

Tissue Specificity of Human Disease Module

(2016) Maksim Kitsak et al.   Scientific Reports

PPIXpress: construction of condition-specific protein interaction networks based on transcript expression

(2015) Thorsten Will et al.   BIOINFORMATICS

Expression of pre-selected TMEMs with predicted ER localization as potential classifiers of ccRCC tumors

(2015) Tomasz Wrzesiński et al.   BMC CANCER

MGFM: a novel tool for detection of tissue and cell specific marker genes from microarray gene expression data

(2015) Khadija El Amrani et al.   BMC GENOMICS

Relationship between gene expression and lung function in Idiopathic Interstitial Pneumonias

(2015) Mark P. Steele et al.   BMC GENOMICS

HBP21, a chaperone of heat shock protein 70, functions as a tumor suppressor in hepatocellular carcinoma

(2015) Lingxi Jiang et al.   CARCINOGENESIS

The Transcriptome and DNA Methylome Landscapes of Human Primordial Germ Cells

(2015) Fan Guo et al.   CELL

Defining the three cell lineages of the human blastocyst by single-cell RNA-seq

(2015) Paul Blakeley et al.   DEVELOPMENT

AGXT2L1 is down-regulated in heptocellular carcinoma and associated with abnormal lipogenesis

(2015) Qianshan Ding et al.   JOURNAL OF CLINICAL PATHOLOGY

The Reactome pathway Knowledgebase

(2015) Antonio Fabregat et al.   NUCLEIC ACIDS RESEARCH

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells

(2015) Erik Arner et al.   SCIENCE

Epigenetically silenced long noncoding-SRHC promotes proliferation of hepatocellular carcinoma

(2014) Hao Zheng et al.   JOURNAL OF CANCER RESEARCH AND CLINICAL ONCOLOGY

A promoter-level mammalian expression atlas

(2014)   NATURE

TIPE1 induces apoptosis by negatively regulating Rac1 activation in hepatocellular carcinoma cells

(2014) Z Zhang et al.   ONCOGENE

Comparison of RNA-Seq and Microarray in Transcriptome Profiling of Activated T Cells

(2014) Shanrong Zhao et al.   PLoS One

Copy Number Loss of the Interferon Gene Cluster in Melanomas Is Linked to Reduced T Cell Infiltrate and Poor Patient Prognosis

(2014) Peter S. Linsley et al.   PLoS One

Analysis of the Human Tissue-specific Expression by Genome-wide Integration of Transcriptomics and Antibody-based Proteomics

(2013) Linn Fagerberg et al.   MOLECULAR & CELLULAR PROTEOMICS

Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells

(2013) Liying Yan et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

CellFinder: a cell data repository

(2013) Harald Stachelscheid et al.   NUCLEIC ACIDS RESEARCH

A model based criterion for gene expression calls using RNA-seq data

(2013) Günter P. Wagner et al.   THEORY IN BIOSCIENCES

PaGeFinder: quantitative identification of spatiotemporal pattern genes

(2012) J.-B. Pan et al.   BIOINFORMATICS

Building Muscle: Molecular Regulation of Myogenesis

(2012) C. F. Bentzinger et al.   Cold Spring Harbor Perspectives in Biology

RNA sequencing reveals two major classes of gene expression levels in metazoan cells

(2011) D. Hebenstreit et al.   Molecular Systems Biology

SpeCond: a method to detect condition-specific gene expression

(2011) Florence MG Cavalli et al.   GENOME BIOLOGY

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

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

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

TiGER: a database for tissue-specific gene expression and regulation

(2008) Xiong Liu et al.   BMC BIOINFORMATICS