Synergistically acting agonists and antagonists of G protein–coupled receptors prevent photoreceptor cell degeneration

Celastrol protects mouse retinas from bright light-induced degeneration through inhibition of oxidative stress and inflammation

(2016) Minjuan Bian et al.   Journal of Neuroinflammation

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Vision from next generation sequencing: Multi-dimensional genome-wide analysis for producing gene regulatory networks underlying retinal development, aging and disease

(2015) Hyun-Jin Yang et al.   PROGRESS IN RETINAL AND EYE RESEARCH

Distinct profiles of functional discrimination among G proteins determine the actions of G protein–coupled receptors

(2015) Ikuo Masuho et al.   Science Signaling

Transcriptome Dynamics of Developing Photoreceptors in Three-Dimensional Retina Cultures Recapitulates Temporal Sequence of Human Cone and Rod Differentiation Revealing Cell Surface Markers and Gene Networks

(2015) Rossukon Kaewkhaw et al.   STEM CELLS

Distinct profiles of functional discrimination among G proteins determine the actions of G protein–coupled receptors

(2015) Ikuo Masuho et al.   Science Signaling

Age-Related Macular Degeneration: Genetics and Biology Coming Together

(2014) Lars G. Fritsche et al.   Annual Review of Genomics and Human Genetics

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Noninvasive two-photon microscopy imaging of mouse retina and retinal pigment epithelium through the pupil of the eye

(2014) Grazyna Palczewska et al.   NATURE MEDICINE

Two-photon microscopy reveals early rod photoreceptor cell damage in light-exposed mutant mice

(2014) A. Maeda et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Updating RNA-Seq analyses after re-annotation

(2013) Adam Roberts et al.   BIOINFORMATICS

RDAVIDWebService: a versatile R interface to DAVID

(2013) C. Fresno et al.   BIOINFORMATICS

Complex diseases require complex therapies

(2013) Ravi Iyengar   EMBO REPORTS

Photoreceptor phagocytosis is mediated by phosphoinositide signaling

(2013) Debarshi Mustafi et al.   FASEB JOURNAL

Photoreceptor Proteins Initiate Microglial Activation via Toll-like Receptor 4 in Retinal Degeneration Mediated by All-trans-retinal

(2013) Hideo Kohno et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Systems pharmacology identifies drug targets for Stargardt disease–associated retinal degeneration

(2013) Yu Chen et al.   JOURNAL OF CLINICAL INVESTIGATION

Human retinal gene therapy for Leber congenital amaurosis shows advancing retinal degeneration despite enduring visual improvement

(2013) A. V. Cideciyan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Systems Pharmacology of Adverse Event Mitigation by Drug Combinations

(2013) S. Zhao et al.   Science Translational Medicine

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

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Systems pharmacology of complex diseases

(2012) Jens Hansen et al.   Annals of the New York Academy of Sciences

Structure-Function of the G Protein–Coupled Receptor Superfamily

(2012) Vsevolod Katritch et al.   Annual Review of Pharmacology and Toxicology

Developing New Drug Treatments in the Era of Network Medicine

(2012) E K Silverman et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

Streaming fragment assignment for real-time analysis of sequencing experiments

(2012) Adam Roberts et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

APCluster: an R package for affinity propagation clustering

(2011) U. Bodenhofer et al.   BIOINFORMATICS

Mechanism of All-trans-retinal Toxicity with Implications for Stargardt Disease and Age-related Macular Degeneration

(2011) Yu Chen et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Progression of neuronal and synaptic remodeling in therd10mouse model of retinitis pigmentosa

(2010) M. Joseph Phillips et al.   JOURNAL OF COMPARATIVE NEUROLOGY

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

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

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

The c-terminus of GRK3 indicates rapid dissociation of G protein heterotrimers

(2009) Bettye Hollins et al.   CELLULAR SIGNALLING

Involvement of All-trans-retinal in Acute Light-induced Retinopathy of Mice

(2009) Akiko Maeda et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Retinopathy in Mice Induced by Disrupted All-trans-retinal Clearance

(2008) Akiko Maeda et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Functional and structural modifications during retinal degeneration in the rd10 mouse

(2008) R. Barhoum et al.   NEUROSCIENCE

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH

Human gene therapy for RPE65 isomerase deficiency activates the retinoid cycle of vision but with slow rod kinetics

(2008) A. V. Cideciyan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA