Definition of the transcriptional units of inherited retinal disease genes by meta-analysis of human retinal transcriptome data

[1]  S. Ovchinnikov,et al.  ColabFold: making protein folding accessible to all , 2022, Nature Methods.

[2]  Lin Chen,et al.  Single-Cell RNA Sequencing of Retina:New Looks for Gene Marker and Old Diseases , 2021, Frontiers in Molecular Biosciences.

[3]  Oriol Vinyals,et al.  Highly accurate protein structure prediction with AlphaFold , 2021, Nature.

[4]  P. Humphries,et al.  Next-Generation Sequencing Applications for Inherited Retinal Diseases , 2021, International journal of molecular sciences.

[5]  D. Swarbreck,et al.  Long read sequencing reveals novel isoforms and insights into splicing regulation during cell state changes , 2021, BMC Genomics.

[6]  Chung-May Yang,et al.  Genetic characteristics and epidemiology of inherited retinal degeneration in Taiwan , 2021, NPJ genomic medicine.

[7]  G. Marfany,et al.  The Alter Retina: Alternative Splicing of Retinal Genes in Health and Disease , 2021, International journal of molecular sciences.

[8]  M. Tress,et al.  An analysis of tissue-specific alternative splicing at the protein level , 2020, PLoS Comput. Biol..

[9]  J. N. Kay,et al.  Comprehensive identification of mRNA isoforms reveals the diversity of neural cell-surface molecules with roles in retinal development and disease , 2020, Nature Communications.

[10]  B. Wissinger,et al.  Splicing mutations in inherited retinal diseases , 2020, Progress in Retinal and Eye Research.

[11]  R. C. Wong,et al.  Using single cell transcriptomics to study the complexity of human retina , 2020, Neural regeneration research.

[12]  A. Cideciyan,et al.  Progress in treating inherited retinal diseases: Early subretinal gene therapy clinical trials and candidates for future initiatives , 2019, Progress in Retinal and Eye Research.

[13]  Narmada Thanki,et al.  CDD/SPARCLE: the conserved domain database in 2020 , 2019, Nucleic Acids Res..

[14]  Jose Davila-Velderrain,et al.  Single-cell transcriptomic atlas of the human retina identifies cell types associated with age-related macular degeneration , 2019, Nature Communications.

[15]  K. Nagashima,et al.  Improved Retinal Organoid Differentiation by Modulating Signaling Pathways Revealed by Comparative Transcriptome Analyses with Development In Vivo , 2019, Stem cell reports.

[16]  Peng-Yuan Wang,et al.  A single‐cell transcriptome atlas of the adult human retina , 2019, The EMBO journal.

[17]  Alexis Battle,et al.  Retinal transcriptome and eQTL analyses identify genes associated with age-related macular degeneration , 2019, Nature Genetics.

[18]  H. Kremer,et al.  Homozygous variants in KIAA1549, encoding a ciliary protein, are associated with autosomal recessive retinitis pigmentosa , 2018, Journal of Medical Genetics.

[19]  J. Sahel,et al.  Inherited Retinal Degenerations: Current Landscape and Knowledge Gaps , 2018, Translational vision science & technology.

[20]  Robert D. Finn,et al.  HMMER web server: 2018 update , 2018, Nucleic Acids Res..

[21]  Geet Duggal,et al.  Salmon: fast and bias-aware quantification of transcript expression using dual-phase inference , 2017, Nature Methods.

[22]  Jeffrey T Leek,et al.  Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown , 2016, Nature Protocols.

[23]  Maria Nicoletta Moretti,et al.  An atlas of gene expression and gene co-regulation in the human retina , 2016, Nucleic acids research.

[24]  M. Robinson,et al.  Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences , 2015, F1000Research.

[25]  D. di Bernardo,et al.  High-resolution analysis of the human retina miRNome reveals isomiR variations and novel microRNAs , 2016, Nucleic acids research.

[26]  Anna Skorczyk-Werner,et al.  Fundus albipunctatus: review of the literature and report of a novel RDH5 gene mutation affecting the invariant tyrosine (p.Tyr175Phe) , 2015, Journal of Applied Genetics.

[27]  D. Zack,et al.  Alternative splicing and retinal degeneration , 2013, Clinical genetics.

[28]  G. Grant,et al.  Transcriptome analyses of the human retina identify unprecedented transcript diversity and 3.5 Mb of novel transcribed sequence via significant alternative splicing and novel genes , 2013, BMC Genomics.

[29]  G. Holder,et al.  Biallelic mutations in PLA2G5, encoding group V phospholipase A2, cause benign fleck retina. , 2011, American journal of human genetics.

[30]  Adam P. DeLuca,et al.  Exome sequencing and analysis of induced pluripotent stem cells identify the cilia-related gene male germ cell-associated kinase (MAK) as a cause of retinitis pigmentosa , 2011, Proceedings of the National Academy of Sciences.

[31]  J. Abril,et al.  High transcriptional complexity of the retinitis pigmentosa CERKL gene in human and mouse. , 2011, Investigative ophthalmology & visual science.

[32]  T. Rosenberg,et al.  A novel MERTK deletion is a common founder mutation in the Faroe Islands and is responsible for a high proportion of retinitis pigmentosa cases , 2011, Molecular vision.

[33]  Marcel Martin Cutadapt removes adapter sequences from high-throughput sequencing reads , 2011 .

[34]  Vineet K. Sharma,et al.  Expression of Conjoined Genes: Another Mechanism for Gene Regulation in Eukaryotes , 2010, PloS one.

[35]  W. Berger,et al.  The molecular basis of human retinal and vitreoretinal diseases , 2010, Progress in Retinal and Eye Research.

[36]  Kang Zhang,et al.  A splice-site mutation in a retina-specific exon of BBS8 causes nonsyndromic retinitis pigmentosa. , 2010, American journal of human genetics.

[37]  Shomi S. Bhattacharya,et al.  Photoreceptor degeneration: genetic and mechanistic dissection of a complex trait , 2010, Nature Reviews Genetics.

[38]  T. Nilsen,et al.  Expansion of the eukaryotic proteome by alternative splicing , 2010, Nature.

[39]  B. Frey,et al.  Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing , 2008, Nature Genetics.

[40]  Eric T. Wang,et al.  Alternative Isoform Regulation in Human Tissue Transcriptomes , 2008, Nature.

[41]  William Stafford Noble,et al.  Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project , 2007, Nature.

[42]  Jack A. M. Leunissen,et al.  Turning CFCs into salt. , 1996, Nucleic Acids Res..

[43]  Warren A. Kibbe,et al.  The issue of amalgams. , 1996, Nucleic Acids Res..

[44]  T. Meitinger,et al.  Mutations in the CEP290 (NPHP6) gene are a frequent cause of Leber congenital amaurosis. , 2006, American journal of human genetics.

[45]  H. Fong,et al.  Exon-skipping variant of RGR opsin in human retina and pigment epithelium. , 2006, Experimental eye research.

[46]  M. Schaller,et al.  Phosphorylation of GRK1 and GRK7 by cAMP-dependent Protein Kinase Attenuates Their Enzymatic Activities* , 2005, Journal of Biological Chemistry.

[47]  W. J. Kent,et al.  BLAT--the BLAST-like alignment tool. , 2002, Genome research.

[48]  S. Jacobson,et al.  Mutations in MERTK, the human orthologue of the RCS rat retinal dystrophy gene, cause retinitis pigmentosa , 2000, Nature Genetics.

[49]  A. Ciccodicola,et al.  Mutational hot spot within a new RPGR exon in X-linked retinitis pigmentosa , 2000, Nature Genetics.

[50]  I. Longden,et al.  EMBOSS: the European Molecular Biology Open Software Suite. , 2000, Trends in genetics : TIG.

[51]  T. Dryja,et al.  Mutations in the gene encoding 11-cis retinol dehydrogenase cause delayed dark adaptation and fundus albipunctatus , 1999, Nature Genetics.

[52]  Thomas L. Madden,et al.  PowerBLAST: a new network BLAST application for interactive or automated sequence analysis and annotation. , 1997, Genome research.

[53]  T. Dryja,et al.  Defects in the rhodopsin kinase gene in the Oguchi form of stationary night blindness , 1997, Nature Genetics.

[54]  Alan Bird,et al.  Mutations in the human retinal degeneration slow (RDS) gene can cause either retinitis pigmentosa or macular dystrophy , 1993, Nature Genetics.

[55]  T. Dryja,et al.  Mutations in the human retinal degeneration slow gene in autosomal dominant retinitis pigmentosa , 1991, Nature.

[56]  J. Sutcliffe,et al.  The retinal degeneration slow (rds) gene product is a photoreceptor disc membrane-associated glycoprotein , 1991, Neuron.

[57]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[58]  N. L. Brown,et al.  Specification of retinal cell types , 2020, Patterning and Cell Type Specification in the Developing CNS and PNS.

[59]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

[60]  John L.R. Rubenstein,et al.  Patterning and Cell Type Specification in the Developing CNS and PNS , 2013 .

[61]  Hilde van der Togt,et al.  Publisher's Note , 2003, J. Netw. Comput. Appl..

[62]  V. Sheffield,et al.  A 2 base pair deletion in the RDS gene associated with butterfly-shaped pigment dystrophy of the fovea. , 1993, Human molecular genetics.