Pan-cancer analysis of transcripts encoding novel open-reading frames (nORFs) and their potential biological functions

[1]  E. Greco,et al.  The microproteome of cancer: From invisibility to relevance. , 2020, Experimental cell research.

[2]  Jun Yu,et al.  Analyses of non-coding somatic drivers in 2,658 cancer whole genomes , 2020, Nature.

[3]  E. Robert McDonald,et al.  Quantitative Proteomics of the Cancer Cell Line Encyclopedia , 2020, Cell.

[4]  G. Pertea,et al.  GFF Utilities: GffRead and GffCompare. , 2020, F1000Research.

[5]  M. Leslie New universe of miniproteins is upending cell biology and genetics , 2019, Science.

[6]  Song Zhu,et al.  ncRNA-Encoded Peptides or Proteins and Cancer. , 2019, Molecular therapy : the journal of the American Society of Gene Therapy.

[7]  Joshua M. Korn,et al.  Next-generation characterization of the Cancer Cell Line Encyclopedia , 2019, Nature.

[8]  Simon C. Potter,et al.  The EMBL-EBI search and sequence analysis tools APIs in 2019 , 2019, Nucleic Acids Res..

[9]  Laurent Gatto,et al.  ensembldb: an R package to create and use Ensembl-based annotation resources , 2019, Bioinform..

[10]  Gerben Menschaert,et al.  Using the sORFs.Org Database , 2018, Current protocols in bioinformatics.

[11]  Martin Eisenacher,et al.  The PRIDE database and related tools and resources in 2019: improving support for quantification data , 2018, Nucleic Acids Res..

[12]  Alex Bateman,et al.  RNAcentral: a hub of information for non-coding RNA sequences , 2018, Nucleic Acids Res..

[13]  Gregory M. Cooper,et al.  CADD: predicting the deleteriousness of variants throughout the human genome , 2018, Nucleic Acids Res..

[14]  Mark Gerstein,et al.  GENCODE reference annotation for the human and mouse genomes , 2018, Nucleic Acids Res..

[15]  Zhi Xie,et al.  RPFdb v2.0: an updated database for genome-wide information of translated mRNA generated from ribosome profiling , 2018, Nucleic Acids Res..

[16]  Aïda Ouangraoua,et al.  OpenProt: a more comprehensive guide to explore eukaryotic coding potential and proteomes , 2018, Nucleic Acids Res..

[17]  P. Wei,et al.  A peptide encoded by circular form of LINC-PINT suppresses oncogenic transcriptional elongation in glioblastoma , 2018, Nature Communications.

[18]  B. Benayoun,et al.  The Mitochondrial-Encoded Peptide MOTS-c Translocates to the Nucleus to Regulate Nuclear Gene Expression in Response to Metabolic Stress. , 2018, Cell metabolism.

[19]  Zhe Ji Rfoot: Transcriptome‐Scale Identification of RNA‐Protein Complexes from Ribosome Profiling Data , 2018, Current protocols in molecular biology.

[20]  Pooja Jadiya,et al.  Mitoregulin: A lncRNA-Encoded Microprotein that Supports Mitochondrial Supercomplexes and Respiratory Efficiency , 2018, Cell reports.

[21]  T. Yada,et al.  Micropeptides Encoded in Transcripts Previously Identified as Long Noncoding RNAs: A New Chapter in Transcriptomics and Proteomics , 2018, Front. Genet..

[22]  M. Albà,et al.  Translation of neutrally evolving peptides provides a basis for de novo gene evolution , 2018, Nature Ecology & Evolution.

[23]  M. Huss,et al.  Discovery of coding regions in the human genome by integrated proteogenomics analysis workflow , 2018, Nature Communications.

[24]  Lin Zhang,et al.  The role of long noncoding RNAs in cancer: the dark matter matters. , 2018, Current opinion in genetics & development.

[25]  Gerben Menschaert,et al.  An update on sORFs.org: a repository of small ORFs identified by ribosome profiling , 2017, Nucleic Acids Res..

[26]  Lili Zhang,et al.  SmProt: a database of small proteins encoded by annotated coding and non‐coding RNA loci , 2017, Briefings Bioinform..

[27]  Gerben Menschaert,et al.  In Search of Lost Small Peptides. , 2017, Annual review of cell and developmental biology.

[28]  Guang-Rong Yan,et al.  A Peptide Encoded by a Putative lncRNA HOXB-AS3 Suppresses Colon Cancer Growth. , 2017, Molecular cell.

[29]  D. Baker,et al.  Global analysis of protein folding using massively parallel design, synthesis, and testing , 2017, Science.

[30]  Albin Sandelin,et al.  The Landscape of Isoform Switches in Human Cancers , 2017, Molecular Cancer Research.

[31]  J. Harrow,et al.  Genome annotation for clinical genomic diagnostics: strengths and weaknesses , 2017, Genome Medicine.

[32]  Mary Goldman,et al.  Toil enables reproducible, open source, big biomedical data analyses , 2017, Nature Biotechnology.

[33]  Akinobu Matsumoto,et al.  mTORC1 and muscle regeneration are regulated by the LINC00961-encoded SPAR polypeptide , 2016, Nature.

[34]  L. Hurst,et al.  Open questions in the study of de novo genes: what, how and why , 2016, Nature Reviews Genetics.

[35]  Jianzhi Zhang,et al.  The Genomic Landscape of Position Effects on Protein Expression Level and Noise in Yeast. , 2016, Cell systems.

[36]  R. Aebersold,et al.  On the Dependency of Cellular Protein Levels on mRNA Abundance , 2016, Cell.

[37]  Emile G Magny,et al.  Hemotin, a Regulator of Phagocytosis Encoded by a Small ORF and Conserved across Metazoans , 2016, PLoS biology.

[38]  Jianzhi Zhang,et al.  Are Human Translated Pseudogenes Functional? , 2016, Molecular biology and evolution.

[39]  Stephen C. Cannon,et al.  A peptide encoded by a transcript annotated as long noncoding RNA enhances SERCA activity in muscle , 2016, Science.

[40]  A. Dreher Modeling Survival Data Extending The Cox Model , 2016 .

[41]  A. Regev,et al.  Many lncRNAs, 5’UTRs, and pseudogenes are translated and some are likely to express functional proteins , 2015, eLife.

[42]  Ying Zhang,et al.  The neXtProt knowledgebase on human proteins: current status , 2014, Nucleic Acids Res..

[43]  G. Kreiman,et al.  Quantitative Profiling of Peptides from RNAs classified as non-coding , 2014, Nature Communications.

[44]  Nicholas T Ingolia,et al.  Ribosome profiling reveals pervasive translation outside of annotated protein-coding genes. , 2014, Cell reports.

[45]  Predrag Radivojac,et al.  The structural and functional signatures of proteins that undergo multiple events of post‐translational modification , 2014, Protein science : a publication of the Protein Society.

[46]  Wenqian Hu,et al.  Translation of small open reading frames within unannotated RNA transcripts in Saccharomyces cerevisiae. , 2014, Cell reports.

[47]  S. Cohen Everything old is new again: (linc)RNAs make proteins! , 2014, The EMBO journal.

[48]  Matthew Fraser,et al.  InterProScan 5: genome-scale protein function classification , 2014, Bioinform..

[49]  François-Michel Boisvert,et al.  Direct Detection of Alternative Open Reading Frames Translation Products in Human Significantly Expands the Proteome , 2013, PloS one.

[50]  Gilles Celeux,et al.  Data-based filtering for replicated high-throughput transcriptome sequencing experiments , 2013, Bioinform..

[51]  Tom R. Gaunt,et al.  Predicting the Functional, Molecular, and Phenotypic Consequences of Amino Acid Substitutions using Hidden Markov Models , 2012, Human mutation.

[52]  D. Tautz,et al.  Phylogenetic patterns of emergence of new genes support a model of frequent de novo evolution , 2013, BMC Genomics.

[53]  Thomas A. Hopf,et al.  Protein structure prediction from sequence variation , 2012, Nature Biotechnology.

[54]  César A. Hidalgo,et al.  Proto-genes and de novo gene birth , 2012, Nature.

[55]  D. Tautz,et al.  The evolutionary origin of orphan genes , 2011, Nature Reviews Genetics.

[56]  D. Hanahan,et al.  Hallmarks of Cancer: The Next Generation , 2011, Cell.

[57]  Henrik Kaessmann,et al.  Origins, evolution, and phenotypic impact of new genes. , 2010, Genome research.

[58]  Aaron R. Quinlan,et al.  Bioinformatics Applications Note Genome Analysis Bedtools: a Flexible Suite of Utilities for Comparing Genomic Features , 2022 .

[59]  Mark D. Robinson,et al.  edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..

[60]  M. Robinson,et al.  A scaling normalization method for differential expression analysis of RNA-seq data , 2010, Genome Biology.

[61]  Zsuzsanna Dosztányi,et al.  ANCHOR: web server for predicting protein binding regions in disordered proteins , 2009, Bioinform..

[62]  James A. Cuff,et al.  Distinguishing protein-coding and noncoding genes in the human genome , 2007, Proceedings of the National Academy of Sciences.

[63]  D. Morris,et al.  Polyamine regulation of ribosome pausing at the upstream open reading frame of S-adenosylmethionine decarboxylase. , 2001, The Journal of biological chemistry.