RNA-Seq-based toxicogenomic assessment of fresh frozen and formalin-fixed tissues yields similar mechanistic insights

The roles of FOXM1 in pancreatic stem cells and carcinogenesis

(2013) Ming Quan et al.   Molecular Cancer

Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories

(2013) Peter A C 't Hoen et al.   NATURE BIOTECHNOLOGY

Comparative analysis of RNA sequencing methods for degraded or low-input samples

(2013) Xian Adiconis et al.   NATURE METHODS

The Reactome pathway knowledgebase

(2013) David Croft et al.   NUCLEIC ACIDS RESEARCH

RNA-Seq Profiling Reveals Novel Hepatic Gene Expression Pattern in Aflatoxin B1 Treated Rats

(2013) B. Alex Merrick et al.   PLoS One

Gene Expression, Single Nucleotide Variant and Fusion Transcript Discovery in Archival Material from Breast Tumors

(2013) Nadine Norton et al.   PLoS One

Preparation of archival formalin-fixed paraffin-embedded mouse liver samples for use with the Agilent gene expression microarray platform

(2013) A. Francina Jackson et al.   JOURNAL OF PHARMACOLOGICAL AND TOXICOLOGICAL METHODS

Formalin fixation in the ‘-omics’ era: a primer for the surgeon-scientist

(2012) Adam Frankel   ANZ JOURNAL OF SURGERY

Testing an Aflatoxin B1 Gene Signature in Rat Archival Tissues

(2012) B. Alex Merrick et al.   CHEMICAL RESEARCH IN TOXICOLOGY

Fast Computation and Applications of Genome Mappability

(2012) Thomas Derrien et al.   PLoS One

Selective Depletion of rRNA Enables Whole Transcriptome Profiling of Archival Fixed Tissue

(2012) John D. Morlan et al.   PLoS One

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

(2012) Dominick Sinicropi et al.   PLoS One

Liver Hypertrophy

(2012) A. P. Hall et al.   TOXICOLOGIC PATHOLOGY

Identification of novel transcripts in annotated genomes using RNA-Seq

(2011) A. Roberts et al.   BIOINFORMATICS

Clinical relevance of DNA microarray analyses using archival formalin-fixed paraffin-embedded breast cancer specimens

(2011) Al Muktafi Sadi et al.   BMC CANCER

Expression profiling of formalin-fixed paraffin-embedded primary breast tumors using cancer-specific and whole genome gene panels on the DASL®platform

(2011) Monica M Reinholz et al.   BMC Medical Genomics

A methodology for utilization of predictive genomic signatures in FFPE samples

(2011) Jennifer A Freedman et al.   BMC Medical Genomics

Effect of Aflatoxin B1 on Nuclear Receptors PXR, CAR, and AhR and Their Target Cytochromes P450 mRNA Expression in Primary Cultures of Human Hepatocytes

(2011) Imen Ayed-Boussema et al.   INTERNATIONAL JOURNAL OF TOXICOLOGY

Genome-wide Gene Expression Profiling of Formalin-fixed Paraffin-Embedded Breast Cancer Core Biopsies Using Microarrays

(2011) Jan Budczies et al.   JOURNAL OF HISTOCHEMISTRY & CYTOCHEMISTRY

An RNA-Seq Strategy to Detect the Complete Coding and Non-Coding Transcriptome Including Full-Length Imprinted Macro ncRNAs

(2011) Ru Huang et al.   PLoS One

Analyses and interpretation of whole-genome gene expression from formalin-fixed paraffin-embedded tissue: an illustration with breast cancer tissues

(2010) Muhammad G Kibriya et al.   BMC GENOMICS

A Novel Role for the Dioxin Receptor in Fatty Acid Metabolism and Hepatic Steatosis

(2010) Jung Hoon Lee et al.   GASTROENTEROLOGY

Quantitative Expression Profiling in Formalin-Fixed Paraffin-Embedded Samples by Affymetrix Microarrays

(2010) Diana Abdueva et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

3′-End Sequencing for Expression Quantification (3SEQ) from Archival Tumor Samples

(2010) Andrew H. Beck et al.   PLoS One

Ontology-Based Meta-Analysis of Global Collections of High-Throughput Public Data

(2010) Ilya Kupershmidt et al.   PLoS One

Hepatic Enzyme Induction

(2010) Robert R. Maronpot et al.   TOXICOLOGIC PATHOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Microarray analysis of RNA extracted from formalin-fixed, paraffin-embedded and matched fresh-frozen ovarian adenocarcinomas

(2009) Grazyna Fedorowicz et al.   BMC Medical Genomics

Identification of methods for use of formalin-fixed, paraffin-embedded tissue samples in RNA expression profiling

(2009) Lisa Roberts et al.   GENOMICS

Analysis of gene expression in stage I serous tumors identifies critical pathways altered in ovarian cancer

(2009) Jeremy Chien et al.   GYNECOLOGIC ONCOLOGY

The Japanese toxicogenomics project: Application of toxicogenomics

(2009) Takeki Uehara et al.   MOLECULAR NUTRITION & FOOD RESEARCH

Whole-Genome Gene Expression Profiling of Formalin-Fixed, Paraffin-Embedded Tissue Samples

(2009) Craig April et al.   PLoS One

Predicting the hepatocarcinogenic potential of alkenylbenzene flavoring agents using toxicogenomics and machine learning

(2009) Scott S. Auerbach et al.   TOXICOLOGY AND APPLIED PHARMACOLOGY

Acquisition of biologically relevant gene expression data by Affymetrix microarray analysis of archival formalin-fixed paraffin-embedded tumours

(2008) K M Linton et al.   BRITISH JOURNAL OF CANCER

TEAD1 and c-Cbl are novel prostate basal cell markers that correlate with poor clinical outcome in prostate cancer

(2008) J F Knight et al.   BRITISH JOURNAL OF CANCER

RNA expression analysis from formalin fixed paraffin embedded tissues

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

A novel approach for reliable microarray analysis of microdissected tumor cells from formalin-fixed and paraffin-embedded colorectal cancer resection specimens

(2008) Silke Lassmann et al.   JOURNAL OF MOLECULAR MEDICINE-JMM

Quantitative expression profiling of highly degraded RNA from formalin-fixed, paraffin-embedded breast tumor biopsies by oligonucleotide microarrays

(2008) Maria Ravo et al.   LABORATORY INVESTIGATION

Gene Expression in Fixed Tissues and Outcome in Hepatocellular Carcinoma

(2008) Yujin Hoshida et al.   NEW ENGLAND JOURNAL OF MEDICINE

PID: the Pathway Interaction Database

(2008) Carl F. Schaefer et al.   NUCLEIC ACIDS RESEARCH