RNA-Seq reveals expression signatures of genes involved in oxygen transport, protein synthesis, folding, and degradation in response to heat stress in catfish

Efficient assembly and annotation of the transcriptome of catfish by RNA-Seq analysis of a doubled haploid homozygote

(2012) Shikai Liu et al.   BMC GENOMICS

Transcriptomic signatures of attachment, NF-κB suppression and IFN stimulation in the catfish gill following columnaris bacterial infection

(2012) Fanyue Sun et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

RNA-seq analysis of mucosal immune responses reveals signatures of intestinal barrier disruption and pathogen entry following Edwardsiella ictaluri infection in channel catfish, Ictalurus punctatus

(2012) Chao Li et al.   FISH & SHELLFISH IMMUNOLOGY

Both G3BP1 and G3BP2 contribute to stress granule formation

(2012) Hideaki Matsuki et al.   GENES TO CELLS

A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae

(2012) Intawat Nookaew et al.   NUCLEIC ACIDS RESEARCH

Effects of thermal acclimation on transcriptional responses to acute heat stress in the eurythermal fish Gillichthys mirabilis (Cooper)

(2011) Cheryl A. Logan et al.   AMERICAN JOURNAL OF PHYSIOLOGY-REGULATORY INTEGRATIVE AND COMPARATIVE PHYSIOLOGY

Next-generation transcriptome assembly

(2011) Jeffrey A. Martin et al.   NATURE REVIEWS GENETICS

Thermal Tolerance of Antarctic Notothenioid Fishes Correlates with Level of Circulating Hemoglobin

(2011) Jody M. Beers et al.   PHYSIOLOGICAL AND BIOCHEMICAL ZOOLOGY

Identification of genes associated with heat tolerance in Arctic charr exposed to acute thermal stress

(2011) Nicole L. Quinn et al.   PHYSIOLOGICAL GENOMICS

Ribosomal genes and heat shock proteins as putative markers for chronic, sublethal heat stress in Arctic charr: applications for aquaculture and wild fish

(2011) Nicole L. Quinn et al.   PHYSIOLOGICAL GENOMICS

From RNA-seq reads to differential expression results

(2011) Alicia Oshlack et al.   GENOME BIOLOGY

Transcriptional responses to thermal acclimation in the eurythermal fish Gillichthys mirabilis (Cooper 1864)

(2010) Cheryl A. Logan et al.   AMERICAN JOURNAL OF PHYSIOLOGY-REGULATORY INTEGRATIVE AND COMPARATIVE PHYSIOLOGY

CD-HIT Suite: a web server for clustering and comparing biological sequences

(2010) Ying Huang et al.   BIOINFORMATICS

Relationship among circulating hemoglobin, nitric oxide synthase activities and angiogenic poise in red- and white-blooded Antarctic notothenioid fishes

(2010) Jody M. Beers et al.   COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY A-MOLECULAR & INTEGRATIVE PHYSIOLOGY

Collective Roles of Molecular Chaperones in Protein Degradation Pathways Associated with Neurodegenerative Diseases

(2010) Guang Luo et al.   CURRENT PHARMACEUTICAL BIOTECHNOLOGY

Optimization of de novo transcriptome assembly from next-generation sequencing data

(2010) Y. Surget-Groba et al.   GENOME RESEARCH

Physiological, behavioral and biochemical adaptations of intertidal fishes to hypoxia

(2010) J. G. Richards   JOURNAL OF EXPERIMENTAL BIOLOGY

Transcriptional response to heat stress in the Antarctic bivalve Laternula elliptica

(2010) Manuela Truebano et al.   JOURNAL OF EXPERIMENTAL MARINE BIOLOGY AND ECOLOGY

Molecular characterization and gene expression of the channel catfish ferritin H subunit after bacterial infection and iron treatment

(2010) Hong Liu et al.   Journal of Experimental Zoology Part A-Ecological Genetics and Physiology

Temperature and salmonid reproduction: implications for aquaculture

(2010) N. W. Pankhurst et al.   JOURNAL OF FISH BIOLOGY

De novo assembly and analysis of RNA-seq data

(2010) Gordon Robertson et al.   NATURE METHODS

The rapidly expanding CREC protein family: members, localization, function, and role in disease

(2009) Bent Honoré   BIOESSAYS

Muscle structure responses and lysosomal cathepsins B and L in farmed Atlantic salmon (Salmo salar L.) pre- and post-rigor fillets exposed to short and long-term crowding stress

(2009) D. Bahuaud et al.   FOOD CHEMISTRY

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

Ontologizer 2.0--a multifunctional tool for GO term enrichment analysis and data exploration

(2008) S. Bauer et al.   BIOINFORMATICS

Stability of reference genes for real-time PCR analyses in channel catfish (Ictalurus punctatus) tissues under varying physiological conditions

(2008) Brian C. Small et al.   COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY B-BIOCHEMISTRY & MOLECULAR BIOLOGY

Identification and characterization of hypoxia-induced genes in Carassius auratus blastulae embryonic cells using suppression subtractive hybridization

(2008) Xue-Ping Zhong et al.   COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY B-BIOCHEMISTRY & MOLECULAR BIOLOGY

Rhythms of Gene Expression in a Fluctuating Intertidal Environment

(2008) Andrew Y. Gracey et al.   CURRENT BIOLOGY

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Isolation and analysis of differentially expressed genes in Penicillium glabrum subjected to thermal stress

(2008) L. Nevarez et al.   MICROBIOLOGY-SGM

cDNA microarray analysis reveals the capacity of the cold-adapted Antarctic fish Trematomus bernacchii to alter gene expression in response to heat stress

(2008) Bradley A. Buckley et al.   POLAR BIOLOGY

ECOLOGY: Physiology and Climate Change

(2008) H. O. Portner et al.   SCIENCE