Pervasive generation of non-canonical subgenomic RNAs by SARS-CoV-2

[1]  J. Decaprio,et al.  Pervasive generation of non-canonical subgenomic RNAs by SARS-CoV-2 , 2020, Genome Medicine.

[2]  J. Decaprio,et al.  virORF_direct - Pervasive generation of non-canonical subgenomic RNAs by SARS-CoV-2 , 2020 .

[3]  Christian Drosten,et al.  Bulk and single-cell gene expression profiling of SARS-CoV-2 infected human cell lines identifies molecular targets for therapeutic intervention , 2020 .

[4]  D. Matthews,et al.  Characterisation of the transcriptome and proteome of SARS-CoV-2 reveals a cell passage induced in-frame deletion of the furin-like cleavage site from the spike glycoprotein , 2020, Genome Medicine.

[5]  Mark Bathe,et al.  Structure of the full SARS-CoV-2 RNA genome in infected cells , 2020, bioRxiv.

[6]  Takeshi Kobayashi,et al.  Generation of human bronchial organoids for SARS-CoV-2 research , 2020, bioRxiv.

[7]  M. Schwartz,et al.  The coding capacity of SARS-CoV-2 , 2020, Nature.

[8]  M. Alexander,et al.  Bulk and single-cell gene expression profiling of SARS-CoV-2 infected human cell lines identifies molecular targets for therapeutic intervention , 2020, bioRxiv.

[9]  R. Schwartz,et al.  Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19 , 2020, Cell.

[10]  A. Pruijssers,et al.  The coronavirus proofreading exoribonuclease mediates extensive viral recombination , 2020, bioRxiv.

[11]  Joanna Ellis,et al.  Characterisation of the transcriptome and proteome of SARS-CoV-2 using direct RNA sequencing and tandem mass spectrometry reveals evidence for a cell passage induced in-frame deletion in the spike glycoprotein that removes the furin-like cleavage site , 2020, bioRxiv.

[12]  Hyeshik Chang,et al.  The Architecture of SARS-CoV-2 Transcriptome , 2020, Cell.

[13]  Nichollas E. Scott,et al.  Direct RNA sequencing and early evolution of SARS-CoV-2 , 2020, bioRxiv.

[14]  B. Graham,et al.  Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation , 2020, Science.

[15]  B. Graham,et al.  Cryo-EM Structure of the 2019-nCoV Spike in the Prefusion Conformation , 2020, bioRxiv.

[16]  E. Holmes,et al.  A new coronavirus associated with human respiratory disease in China , 2020, Nature.

[17]  C. López,et al.  The Impact of Defective Viruses on Infection and Immunity. , 2019, Annual review of virology.

[18]  Manja Marz,et al.  Direct RNA nanopore sequencing of full-length coronavirus genomes provides novel insights into structural variants and enables modification analysis , 2018, bioRxiv.

[19]  Angela N. Brooks,et al.  Nanopore native RNA sequencing of a human poly(A) transcriptome , 2018, bioRxiv.

[20]  W. Kloosterman,et al.  From squiggle to basepair: computational approaches for improving nanopore sequencing read accuracy , 2018, Genome Biology.

[21]  Heng Li,et al.  Minimap2: pairwise alignment for nucleotide sequences , 2017, Bioinform..

[22]  R. Panettieri,et al.  Immunostimulatory Defective Viral Genomes from Respiratory Syncytial Virus Promote a Strong Innate Antiviral Response during Infection in Mice and Humans , 2015, PLoS pathogens.

[23]  Chao Xie,et al.  Fast and sensitive protein alignment using DIAMOND , 2014, Nature Methods.

[24]  C. Brooke,et al.  Biological activities of 'noninfectious' influenza A virus particles. , 2014, Future virology.

[25]  L. Romão,et al.  Gene Expression Regulation by Upstream Open Reading Frames and Human Disease , 2013, PLoS genetics.

[26]  John Yin,et al.  Population dynamics of an RNA virus and its defective interfering particles in passage cultures , 2010, Virology Journal.

[27]  Miriam L. Land,et al.  Trace: Tennessee Research and Creative Exchange Prodigal: Prokaryotic Gene Recognition and Translation Initiation Site Identification Recommended Citation Prodigal: Prokaryotic Gene Recognition and Translation Initiation Site Identification , 2022 .

[28]  Ning Ma,et al.  BLAST+: architecture and applications , 2009, BMC Bioinformatics.

[29]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[30]  Jonathan D Dinman,et al.  The role of programmed-1 ribosomal frameshifting in coronavirus propagation. , 2008, Frontiers in bioscience : a journal and virtual library.

[31]  Krishna Shankara Narayanan,et al.  SARS coronavirus accessory proteins , 2007, Virus Research.

[32]  Stuart G. Siddell,et al.  A Contemporary View of Coronavirus Transcription , 2006, Journal of Virology.

[33]  D. Garcin,et al.  Sendai virus defective-interfering genomes and the activation of interferon-beta. , 2006, Virology.

[34]  R. Baric,et al.  Severe Acute Respiratory Syndrome Coronavirus Group-Specific Open Reading Frames Encode Nonessential Functions for Replication in Cell Cultures and Mice , 2005, Journal of Virology.

[35]  P. Tien,et al.  Identification of Novel Subgenomic RNAs and Noncanonical Transcription Initiation Signals of Severe Acute Respiratory Syndrome Coronavirus , 2005, Journal of Virology.

[36]  J. Lepault,et al.  Severe acute respiratory syndrome coronavirus (SARS-CoV) infection inhibition using spike protein heptad repeat-derived peptides. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[37]  P. Rottier,et al.  The Group-Specific Murine Coronavirus Genes Are Not Essential, but Their Deletion, by Reverse Genetics, Is Attenuating in the Natural Host , 2002, Virology.

[38]  R Core Team,et al.  R: A language and environment for statistical computing. , 2014 .

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

[40]  H. Wickham.  ggplot2 , 2011 .

[41]  Hervé Abdi,et al.  Wiley Interdisciplinary Reviews: Computational Statistics , 2010 .

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