Transcriptional regulation of photoreceptor development and homeostasis in the mammalian retina

A Swaroop, D Kim, D Forrest - Nature Reviews Neuroscience, 2010 - nature.com
In the developing vertebrate retina, diverse neuronal subtypes originate from multipotent
progenitors in a conserved order and are integrated into an intricate laminated architecture …

Locating mammalian transcription factor binding sites: a survey of computational and experimental techniques

L Elnitski, VX Jin, PJ Farnham, SJM Jones - Genome research, 2006 - genome.cshlp.org
Fields such as genomics and systems biology are built on the synergism between
computational and experimental techniques. This type of synergism is especially important …

Co-expression networks reveal the tissue-specific regulation of transcription and splicing

A Saha, Y Kim, ADH Gewirtz, B Jo, C Gao… - Genome …, 2017 - genome.cshlp.org
Gene co-expression networks capture biologically important patterns in gene expression
data, enabling functional analyses of genes, discovery of biomarkers, and interpretation of …

CRX ChIP-seq reveals the cis-regulatory architecture of mouse photoreceptors

JC Corbo, KA Lawrence, M Karlstetter… - Genome …, 2010 - genome.cshlp.org
Approximately 98% of mammalian DNA is noncoding, yet we understand relatively little
about the function of this enigmatic portion of the genome. The cis-regulatory elements that …

Unravelling the genetics of inherited retinal dystrophies: Past, present and future

S Broadgate, J Yu, SM Downes, S Halford - Progress in retinal and eye …, 2017 - Elsevier
The identification of the genes underlying monogenic diseases has been of interest to
clinicians and scientists for many years. Using inherited retinal dystrophies as an example of …

Transcriptomics resources of human tissues and organs

M Uhlén, BM Hallström, C Lindskog… - Molecular systems …, 2016 - embopress.org
Quantifying the differential expression of genes in various human organs, tissues, and cell
types is vital to understand human physiology and disease. Recently, several large‐scale …

PASTAA: identifying transcription factors associated with sets of co-regulated genes

HG Roider, T Manke, S O'Keeffe, M Vingron… - …, 2009 - academic.oup.com
Motivation: A major challenge in regulatory genomics is the identification of associations
between functional categories of genes (eg tissues, metabolic pathways) and their …

The Cis-regulatory Logic of the Mammalian Photoreceptor Transcriptional Network

THC Hsiau, C Diaconu, CA Myers, J Lee, CL Cepko… - PloS one, 2007 - journals.plos.org
The photoreceptor cells of the retina are subject to a greater number of genetic diseases
than any other cell type in the human body. The majority of more than 120 cloned human …

Eye evolution: common use and independent recruitment of genetic components

P Vopalensky, Z Kozmik - Philosophical Transactions of …, 2009 - royalsocietypublishing.org
Animal eyes can vary in complexity ranging from a single photoreceptor cell shaded by a
pigment cell to elaborate arrays of these basic units, which allow image formation in …

Identification of molecular markers of bipolar cells in the murine retina

DS Kim, SE Ross, JM Trimarchi, J Aach… - Journal of …, 2008 - Wiley Online Library
Retinal bipolar neurons serve as relay interneurons that connect rod and cone
photoreceptor cells to amacrine and ganglion cells. They exhibit diverse morphologies …