Long-Read RNA Sequencing Identifies Polyadenylation Elongation and Differential Transcript Usage of Host Transcripts During SARS-CoV-2 In Vitro Infection

Palindromic target site identification in SARS-CoV-2, MERS-CoV and SARS-CoV-1 by adopting CRISPR-Cas technique

(2022) Nimisha Ghosh et al.   GENE

Transcriptome of nasopharyngeal samples from COVID-19 patients and a comparative analysis with other SARS-CoV-2 infection models reveal disparate host responses against SARS-CoV-2

(2021) Abul Bashar Mir Md. Khademul Islam et al.   Journal of Translational Medicine

Dynamic competition between SARS-CoV-2 NSP1 and mRNA on the human ribosome inhibits translation initiation

(2021) Christopher P. Lapointe et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Meta-analysis of host transcriptional responses to SARS-CoV-2 infection reveals their manifestation in human tumors

(2021) Fengju Chen et al.   Scientific Reports

Transcriptomic profiling of SARS-CoV-2 infected human cell lines identifies HSP90 as target for COVID-19 therapy

(2021) Emanuel Wyler et al.   iScience

Gene signatures and potential therapeutic targets of Middle East respiratory syndrome coronavirus (MERS-CoV)-infected human lung adenocarcinoma epithelial cells

(2021) Yen-Hung Wu et al.   JOURNAL OF MICROBIOLOGY IMMUNOLOGY AND INFECTION

Transcriptional and epi-transcriptional dynamics of SARS-CoV-2 during cellular infection

(2021) Jessie J.-Y. Chang et al.   Cell Reports

Network Analysis and Transcriptome Profiling Identify Autophagic and Mitochondrial Dysfunctions in SARS-CoV-2 Infection

(2021) Komudi Singh et al.   Frontiers in Genetics

Cell-type-resolved quantitative proteomics map of interferon response against SARS-CoV-2

(2021) Elisa Saccon et al.   iScience

Correction: SARS-CoV-2 engages inflammasome and pyroptosis in human primary monocytes

(2021) André C. Ferreira et al.   Cell Death Discovery

Comparative transcriptomic analysis of SARS-CoV-2 infected cell model systems reveals differential innate immune responses

(2021) Guihua Sun et al.   Scientific Reports

Systematic analysis of SARS-CoV-2 infection of an ACE2-negative human airway cell

(2021) Maritza Puray-Chavez et al.   Cell Reports

Transcriptomic Signature Differences Between SARS-CoV-2 and Influenza Virus Infected Patients

(2021) Stéphanie Bibert et al.   Frontiers in Immunology

Isoform Age - Splice Isoform Profiling Using Long-Read Technologies

(2021) Ricardo De Paoli-Iseppi et al.   Frontiers in Molecular Biosciences

Air-liquid interphase culture confers SARS-CoV-2 susceptibility to A549 alveolar epithelial cells

(2021) Michihito Sasaki et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Accurate expression quantification from nanopore direct RNA sequencing with NanoCount

(2021) Josie Gleeson et al.   NUCLEIC ACIDS RESEARCH

Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19

(2020) Daniel Blanco-Melo et al.   CELL

SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor

(2020) Markus Hoffmann et al.   CELL

Olfactory and Gustatory Dysfunction in Coronavirus Disease 19 (COVID-19)

(2020) Jan C Luers et al.   CLINICAL INFECTIOUS DISEASES

A first case of meningitis/encephalitis associated with SARS-Coronavirus-2

(2020) Takeshi Moriguchi et al.   INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES

Granzyme A from cytotoxic lymphocytes cleaves GSDMB to trigger pyroptosis in target cells

(2020) Zhiwei Zhou et al.   SCIENCE

Expression of the SARS-CoV-2 cell receptor gene ACE2 in a wide variety of human tissues

(2020) Meng-Yuan Li et al.   Infectious Diseases of Poverty

Differential immune activation profile of SARS-CoV-2 and SARS-CoV infection in human lung and intestinal cells: Implications for treatment with IFN-β and IFN inducer

(2020) Huiping Shuai et al.   JOURNAL OF INFECTION

Overview of Immune Response During SARS-CoV-2 Infection: Lessons From the Past

(2020) Vibhuti Kumar Shah et al.   Frontiers in Immunology

SARS-CoV-2 Nsp1 binds the ribosomal mRNA channel to inhibit translation

(2020) Katharina Schubert et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Transcriptional and proteomic insights into the host response in fatal COVID-19 cases

(2020) Meng Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A nanoluciferase SARS-CoV-2 for rapid neutralization testing and screening of anti-infective drugs for COVID-19

(2020) Xuping Xie et al.   Nature Communications

Evasion of Type I Interferon by SARS-CoV-2

(2020) Hongjie Xia et al.   Cell Reports

In vivo antiviral host transcriptional response to SARS-CoV-2 by viral load, sex, and age

(2020) Nicole A. P. Lieberman et al.   PLOS BIOLOGY

Upper airway gene expression reveals suppressed immune responses to SARS-CoV-2 compared with other respiratory viruses

(2020) Eran Mick et al.   Nature Communications

tailfindr: Alignment-free poly(A) length measurement for Oxford Nanopore RNA and DNA sequencing

(2019) Maximilian Krause et al.   RNA

Dynamics of IFN-β Responses During Respiratory Viral Infection: Insights for Therapeutic Strategies

(2019) Alastair Watson et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

Nanopore native RNA sequencing of a human poly(A) transcriptome

(2019) Rachael E. Workman et al.   NATURE METHODS

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Translational Control in Virus-Infected Cells

(2018) Noam Stern-Ginossar et al.   Cold Spring Harbor Perspectives in Biology

lmerTest Package: Tests in Linear Mixed Effects Models

(2017) Alexandra Kuznetsova et al.   Journal of Statistical Software

Detecting DNA cytosine methylation using nanopore sequencing

(2017) Jared T Simpson et al.   NATURE METHODS

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

Regulation of Poly(A) Tail and Translation during the Somatic Cell Cycle

(2016) Jong-Eun Park et al.   MOLECULAR CELL

Spliced synthetic genes as internal controls in RNA sequencing experiments

(2016) Simon A Hardwick et al.   NATURE METHODS

Implications of polyadenylation in health and disease

(2014) Ana Curinha et al.   Nucleus

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

From Cis-Regulatory Elements to Complex RNPs and Back

(2012) F. Gebauer et al.   Cold Spring Harbor Perspectives in Biology

Murine Coronavirus Induces Type I Interferon in Oligodendrocytes through Recognition by RIG-I and MDA5

(2010) J. Li et al.   JOURNAL OF VIROLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Aberrant Herpesvirus-Induced Polyadenylation Correlates With Cellular Messenger RNA Destruction

(2009) Yeon J. Lee et al.   PLOS BIOLOGY

Alternative splicing and disease

(2008) Jamal Tazi et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE