Identification and validation of differentially expressed transcripts by RNA-sequencing of formalin-fixed, paraffin-embedded (FFPE) lung tissue from patients with Idiopathic Pulmonary Fibrosis

Integrated Genomics Reveals Convergent Transcriptomic Networks Underlying Chronic Obstructive Pulmonary Disease and Idiopathic Pulmonary Fibrosis

(2016) Rebecca L. Kusko et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

A Novel Genomic Signature with Translational Significance for Human Idiopathic Pulmonary Fibrosis

(2015) Yasmina Bauer et al.   AMERICAN JOURNAL OF RESPIRATORY CELL AND MOLECULAR BIOLOGY

Integrative phenotyping framework (iPF): integrative clustering of multiple omics data identifies novel lung disease subphenotypes

(2015) SungHwan Kim et al.   BMC GENOMICS

Transcriptional phenotyping of fibrotic lung disease: a new gold standard?

(2015) Toby M Maher   Lancet Respiratory Medicine

Classification of usual interstitial pneumonia in patients with interstitial lung disease: assessment of a machine learning approach using high-dimensional transcriptional data

(2015) Su Yeon Kim et al.   Lancet Respiratory Medicine

Molecular biomarkers in idiopathic pulmonary fibrosis

(2014) Brett Ley et al.   AMERICAN JOURNAL OF PHYSIOLOGY-LUNG CELLULAR AND MOLECULAR PHYSIOLOGY

Comparison of RNA-Seq by poly (A) capture, ribosomal RNA depletion, and DNA microarray for expression profiling

(2014) Wei Zhao et al.   BMC GENOMICS

Whole-Transcriptome profiling of formalin-fixed, paraffin-embedded renal cell carcinoma by RNA-seq

(2014) Ping Li et al.   BMC GENOMICS

Next-generation RNA Sequencing of Archival Formalin-fixed Paraffin-embedded Urothelial Bladder Cancer

(2014) Yu Liu et al.   EUROPEAN UROLOGY

Next-Generation Sequencing of RNA and DNA Isolated from Paired Fresh-Frozen and Formalin-Fixed Paraffin-Embedded Samples of Human Cancer and Normal Tissue

(2014) Jakob Hedegaard et al.   PLoS One

Idiopathic Pulmonary Fibrosis: From Epithelial Injury to Biomarkers - Insights from the Bench Side

(2014) Keren Borensztajn et al.   RESPIRATION

Heterogeneous gene expression signatures correspond to distinct lung pathologies and biomarkers of disease severity in idiopathic pulmonary fibrosis

(2014) Daryle J DePianto et al.   THORAX

Usual interstitial pneumonia-patternfibrosis in surgical lung biopsies. Clinical, radiological and histopathological clues to aetiology

(2013) Maxwell Smith et al.   JOURNAL OF CLINICAL PATHOLOGY

The current position of surgical lung biopsy in the diagnosis of idiopathic pulmonary fibrosis

(2013) Riitta Kaarteenaho   RESPIRATORY RESEARCH

Expression of cilium-associated genes defines novel molecular subtypes of idiopathic pulmonary fibrosis

(2013) Ivana V Yang et al.   THORAX

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Personalized medicine: applying ‘omics’ to lung fibrosis

(2012) Jose D Herazo-Maya et al.   Biomarkers in Medicine

Report on emerging technologies for translational bioinformatics: a symposium on gene expression profiling for archival tissues

(2012) Levi Waldron et al.   BMC CANCER

Biomarkers in idiopathic pulmonary fibrosis

(2012) Yingze Zhang et al.   CURRENT OPINION IN PULMONARY MEDICINE

Divergence of tight and adherens junction factors in alveolar epithelium in pulmonary fibrosis

(2012) Elisa Lappi-Blanco et al.   HUMAN PATHOLOGY

High-throughput RNA sequencing of a formalin-fixed, paraffin-embedded autopsy lung tissue sample from the 1918 influenza pandemic

(2012) Yong-Li Xiao et al.   JOURNAL OF PATHOLOGY

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Whole Transcriptome RNA-Seq Analysis of Breast Cancer Recurrence Risk Using Formalin-Fixed Paraffin-Embedded Tumor Tissue

(2012) Dominick Sinicropi et al.   PLoS One

An Official ATS/ERS/JRS/ALAT Statement: Idiopathic Pulmonary Fibrosis: Evidence-based Guidelines for Diagnosis and Management

(2011) Ganesh Raghu et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

mRNA transcript quantification in archival samples using multiplexed, color-coded probes

(2011) Patricia P Reis et al.   BMC BIOTECHNOLOGY

Evolving Genomic Approaches to Idiopathic Pulmonary Fibrosis: Moving Beyond Genes

(2011) Daniel J. Kass et al.   CTS-Clinical and Translational Science

Idiopathic pulmonary fibrosis

(2011) Talmadge E King et al.   LANCET

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Gene Expression Profiles of Acute Exacerbations of Idiopathic Pulmonary Fibrosis

(2009) Kazuhisa Konishi et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

WNT5A Is a Regulator of Fibroblast Proliferation and Resistance to Apoptosis

(2009) Louis J. Vuga et al.   AMERICAN JOURNAL OF RESPIRATORY CELL AND MOLECULAR BIOLOGY

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

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

Molecular Phenotypes Distinguish Patients with Relatively Stable from Progressive Idiopathic Pulmonary Fibrosis (IPF)

(2009) Kathy Boon et al.   PLoS One

RNA expression analysis from formalin fixed paraffin embedded tissues

(2008) Susan M. Farragher et al.   HISTOCHEMISTRY AND CELL BIOLOGY

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Functional Wnt Signaling Is Increased in Idiopathic Pulmonary Fibrosis

(2008) Melanie Königshoff et al.   PLoS One

Idiopathic Pulmonary Fibrosis: Aberrant Recapitulation of Developmental Programs?

(2008) Moisés Selman et al.   PLOS MEDICINE

MMP1 and MMP7 as Potential Peripheral Blood Biomarkers in Idiopathic Pulmonary Fibrosis

(2008) Ivan O Rosas et al.   PLOS MEDICINE

Oxidative Stress, Plasminogen Activator Inhibitor 1, and Lung Fibrosis

(2007) Rui-Ming Liu   ANTIOXIDANTS & REDOX SIGNALING