The status of the human gene catalogue
暂无分享,去创建一个
Francisco M. De La Vega | J. Harrow | A. Frankish | R. Guigó | K. Pruitt | T. Gingeras | A. Hatzigeorgiou | Rory Johnson | I. Ulitsky | M. Yandell | Hazuki Takahashi | Terence D. Murphy | P. Carninci | S. Pujar | Ales Varabyou | Tiago Faial | SL Salzberg | M. Perțea | Silvia Carbonell-Sala | Paulo Amaral | Christine A. Wells | Sílvia Carbonell-Sala | Tiago Faial
[1] Robert J. Weatheritt,et al. Global detection of human variants and isoforms by deep proteome sequencing , 2023, Nature Biotechnology.
[2] D. Hafler,et al. High-plex protein and whole transcriptome co-mapping at cellular resolution with spatial CITE-seq , 2023, Nature Biotechnology.
[3] James D. Johnson,et al. Transcriptomics for Clinical and Experimental Biology Research: Hang on a Seq , 2023, Advanced genetics.
[4] Howard Y. Chang,et al. Long non-coding RNAs: definitions, functions, challenges and recommendations , 2023, Nature Reviews Molecular Cell Biology.
[5] Jay W. Shin,et al. Antisense-oligonucleotide-mediated perturbation of long non-coding RNA reveals functional features in stem cells and across cell types. , 2022, Cell reports.
[6] James C. Wright,et al. GENCODE: reference annotation for the human and mouse genomes in 2023 , 2022, Nucleic Acids Res..
[7] S. Salzberg,et al. The first gapless, reference-quality, fully annotated genome from a Southern Han Chinese individual , 2022, bioRxiv.
[8] William T. Harvey,et al. A draft human pangenome reference , 2022, bioRxiv.
[9] A. Hutchins,et al. The effects of sequencing depth on the assembly of coding and noncoding transcripts in the human genome , 2022, BMC Genomics.
[10] Jonathan M. Mudge,et al. Standardized annotation of translated open reading frames , 2022, Nature Biotechnology.
[11] Jonathan M. Mudge,et al. A joint NCBI and EMBL-EBI transcript set for clinical genomics and research , 2022, Nature.
[12] Jay W. Shin,et al. Antisense oligonucleotide-mediated perturbation of long non-coding RNA reveals functional features in stem cells and across cell types , 2022, bioRxiv.
[13] Alan M. Moses,et al. Developmental Dynamics of RNA Translation in the Human Brain , 2021, bioRxiv.
[14] S. Salzberg,et al. PhyloCSF++: A fast and user-friendly implementation of PhyloCSF with annotation tools , 2021, bioRxiv.
[15] C. Hon,et al. Systematic functional interrogation of human pseudogenes using CRISPRi , 2021, Genome Biology.
[16] Xuerui Yang,et al. Identification of the cross-strand chimeric RNAs generated by fusions of bi-directional transcripts , 2021, Nature Communications.
[17] Fiona Cunningham,et al. Annotating and prioritizing genomic variants using the Ensembl Variant Effect Predictor—A tutorial , 2021, Human mutation.
[18] S. Salzberg,et al. A reference-quality, fully annotated genome from a Puerto Rican individual , 2021, bioRxiv.
[19] Aaron M. Streets,et al. The complete sequence of a human genome , 2021, bioRxiv.
[20] G. Faulkner,et al. Long-read cDNA sequencing identifies functional pseudogenes in the human transcriptome , 2021, Genome Biology.
[21] Beryl B. Cummings,et al. Transcriptome variation in human tissues revealed by long-read sequencing , 2021, Nature.
[22] Leon N. Schulte,et al. Disease-Causing Mutations and Rearrangements in Long Non-coding RNA Gene Loci , 2020, Frontiers in Genetics.
[23] Peter B. McGarvey,et al. UniProt: the universal protein knowledgebase in 2021 , 2020, Nucleic Acids Res..
[24] Hugh E. Olsen,et al. Identification of high-confidence human poly(A) RNA isoform scaffolds using nanopore sequencing , 2020, bioRxiv.
[25] Shunmin He,et al. NONCODEV6: an updated database dedicated to long non-coding RNA annotation in both animals and plants , 2020, Nucleic Acids Res..
[26] Robert D. Finn,et al. RNAcentral 2021: secondary structure integration, improved sequence search and new member databases , 2020, Nucleic Acids Res..
[27] Nimrod D. Rubinstein,et al. The Tug1 lncRNA locus is essential for male fertility , 2020, Genome Biology.
[28] J. Rinn,et al. Myosin 7b is a regulatory long noncoding RNA (lncMYH7b) in the human heart , 2020, bioRxiv.
[29] Jordan A. Ramilowski,et al. Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network , 2020, Nature Communications.
[30] M. Z. Cader,et al. Targeted RNA sequencing enhances gene expression profiling of ultra-low input samples , 2020, RNA biology.
[31] Q. K. Tan,et al. Alternative transcripts in variant interpretation: the potential for missed diagnoses and misdiagnoses , 2020, Genetics in Medicine.
[32] Nathan D. Olson,et al. Assembly and annotation of an Ashkenazi human reference genome , 2020, bioRxiv.
[33] Ruth L. Seal,et al. A guide to naming human non‐coding RNA genes , 2020, The EMBO journal.
[34] Jonathan M. Mudge,et al. Re-annotation of 191 developmental and epileptic encephalopathy-associated genes unmasks de novo variants in SCN1A , 2019, npj Genomic Medicine.
[35] Christopher D. Brown,et al. The GTEx Consortium atlas of genetic regulatory effects across human tissues , 2019, Science.
[36] James C. Wright,et al. Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci , 2019, Genome research.
[37] Catherine L. Worth,et al. The Translational Landscape of the Human Heart , 2019, Cell.
[38] Steven L Salzberg,et al. Next-generation genome annotation: we still struggle to get it right , 2019, Genome Biology.
[39] Gunnar Rätsch,et al. BRCA Challenge: BRCA Exchange as a global resource for variants in BRCA1 and BRCA2 , 2018, PLoS genetics.
[40] S. Salzberg,et al. CHESS: a new human gene catalog curated from thousands of large-scale RNA sequencing experiments reveals extensive transcriptional noise , 2018, Genome Biology.
[41] Alan F. Scott,et al. OMIM.org: leveraging knowledge across phenotype–gene relationships , 2018, Nucleic Acids Res..
[42] Angela N. Brooks,et al. Nanopore native RNA sequencing of a human poly(A) transcriptome , 2018, bioRxiv.
[43] Lennart Martens,et al. LNCipedia 5: towards a reference set of human long non-coding RNAs , 2018, Nucleic Acids Res..
[44] Vladimir B Bajic,et al. LncBook: a curated knowledgebase of human long non-coding RNAs , 2018, Nucleic Acids Res..
[45] A. Frankish,et al. Towards a complete map of the human long non-coding RNA transcriptome , 2018, Nature Reviews Genetics.
[46] Mingjuan Lei,et al. Transcriptional-Readthrough RNAs Reflect the Phenomenon of “A Gene Contains Gene(s)” or “Gene(s) within a Gene” in the Human Genome, and Thus Are Not Chimeric RNAs , 2018, Genes.
[47] J. Mattick,et al. Intergenic disease-associated regions are abundant in novel transcripts , 2017, Genome Biology.
[48] G. Shivashankar,et al. Damage-induced lncRNAs control the DNA damage response through interaction with DDRNAs at individual double-strand breaks , 2017, Nature Cell Biology.
[49] Piero Carninci,et al. The FANTOM5 collection, a data series underpinning mammalian transcriptome atlases in diverse cell types , 2017, Scientific Data.
[50] Ira W. Deveson,et al. Universal alternative splicing of noncoding exons , 2017, bioRxiv.
[51] Jordan A. Ramilowski,et al. An atlas of human long non-coding RNAs with accurate 5′ ends , 2017, Nature.
[52] Jennifer Harrow,et al. High-throughput annotation of full-length long noncoding RNAs with Capture Long-Read Sequencing , 2017, Nature Genetics.
[53] Robert J. Weatheritt,et al. The ribosome-engaged landscape of alternative splicing , 2016, Nature Structural &Molecular Biology.
[54] Reece K. Hart,et al. HGVS Recommendations for the Description of Sequence Variants: 2016 Update , 2016, Human mutation.
[55] Jianzhi Zhang,et al. Are Human Translated Pseudogenes Functional? , 2016, Molecular biology and evolution.
[56] Wen J. Li,et al. Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation , 2015, Nucleic Acids Res..
[57] Jay W. Shin,et al. Paradigm shifts in genomics through the FANTOM projects , 2015, Mammalian Genome.
[58] S. Dhanasekaran,et al. The landscape of long noncoding RNAs in the human transcriptome , 2015, Nature Genetics.
[59] Shenghao Xu,et al. Supplementary Information , 2014, States at War, Volume 3.
[60] Marcel E Dinger,et al. Targeted sequencing for gene discovery and quantification using RNA CaptureSeq , 2014, Nature Protocols.
[61] J. Steitz,et al. The Noncoding RNA Revolution—Trashing Old Rules to Forge New Ones , 2014, Cell.
[62] Cesare Furlanello,et al. A promoter-level mammalian expression atlas , 2015 .
[63] J. Harrow,et al. Transcriptome analysis of human tissues and cell lines reveals one dominant transcript per gene , 2013, Genome Biology.
[64] Shane J. Neph,et al. Systematic Localization of Common Disease-Associated Variation in Regulatory DNA , 2012, Science.
[65] David G. Knowles,et al. The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression , 2012, Genome research.
[66] Raymond K. Auerbach,et al. An Integrated Encyclopedia of DNA Elements in the Human Genome , 2012, Nature.
[67] H. Hakonarson,et al. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data , 2010, Nucleic acids research.
[68] Steven L Salzberg,et al. Between a chicken and a grape: estimating the number of human genes , 2010, Genome Biology.
[69] Jonathan M. Mudge,et al. The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes. , 2009, Genome research.
[70] James A. Cuff,et al. Distinguishing protein-coding and noncoding genes in the human genome , 2007, Proceedings of the National Academy of Sciences.
[71] Tyler S. Alioto,et al. U12DB: a database of orthologous U12-type spliceosomal introns , 2006, Nucleic Acids Res..
[72] S. Batalov,et al. Antisense Transcription in the Mammalian Transcriptome , 2005, Science.
[73] S. Salzberg,et al. The Transcriptional Landscape of the Mammalian Genome , 2005, Science.
[74] D. Haussler,et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. , 2005, Genome research.
[75] J. Bonfield,et al. Finishing the euchromatic sequence of the human genome , 2004, Nature.
[76] S. J. Senn,et al. Competing interests , 2003, Nature Biotechnology.
[77] E. Birney,et al. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs , 2002, Nature.
[78] M. Adams,et al. How many genes in the human genome? , 1994, Nature Genetics.
[79] D. Mccormick. Sequence the Human Genome , 1986, Bio/Technology.
[80] OUP accepted manuscript , 2021, Bioinformatics.
[81] K. Pollard,et al. Detection of nonneutral substitution rates on mammalian phylogenies. , 2010, Genome research.
[82] International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome , 2001, Nature.
[83] Jordan A. Ramilowski,et al. Edinburgh Research Explorer Functional annotation of human long noncoding RNAs via molecular phenotyping , 2020 .