Coding and non-coding roles of MOCCI (C15ORF48) coordinate to regulate host inflammation and immunity

Mitochondrial stress is relayed to the cytosol by an OMA1–DELE1–HRI pathway

(2020) Xiaoyan Guo et al.   NATURE

A pathway coordinated by DELE1 relays mitochondrial stress to the cytosol

(2020) Evelyn Fessler et al.   NATURE

Coxfa4l3, a novel mitochondrial electron transport chain Complex 4 subunit protein, switches from Coxfa4 during spermatogenesis

(2020) Masahiro Endou et al.   MITOCHONDRION

Mitochondrial peptide BRAWNIN is essential for vertebrate respiratory complex III assembly

(2020) Shan Zhang et al.   Nature Communications

Signatures of host–pathogen evolutionary conflict reveal MISTR—A conserved MItochondrial STress Response network

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Maternal immunity and antibodies to dengue virus promote infection and Zika virus–induced microcephaly in fetuses

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Inflammation and its resolution in atherosclerosis: mediators and therapeutic opportunities

(2019) Magnus Bäck et al.   Nature Reviews Cardiology

SignalP 5.0 improves signal peptide predictions using deep neural networks

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Contractile activity-specific transcriptome response to acute endurance exercise and training in human skeletal muscle

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Comprehensive Integration of Single-Cell Data

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Widespread Translational Control of Fibrosis in the Human Heart by RNA-Binding Proteins

(2019) Sonia Chothani et al.   CIRCULATION

Atheroprotective roles of smooth muscle cell phenotypic modulation and the TCF21 disease gene as revealed by single-cell analysis

(2019) Robert C. Wirka et al.   NATURE MEDICINE

miRDB: an online database for prediction of functional microRNA targets

(2019) Yuhao Chen et al.   NUCLEIC ACIDS RESEARCH

Monomeric structure of an active form of bovine cytochrome c oxidase

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Identifying gene function and module connections by the integration of multispecies expression compendia

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Reversible dimerization of cytochrome c oxidase regulates mitochondrial respiration

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A Mitochondrial Micropeptide Is Required for Activation of the Nlrp3 Inflammasome

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Immune Response to Dengue and Zika

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Structure of the intact 14-subunit human cytochrome c oxidase

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De novo annotation and characterization of the translatome with ribosome profiling data

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STING-dependent translation inhibition restricts RNA virus replication

(2018) Kate M. Franz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dissection of Influenza Infection In Vivo by Single-Cell RNA Sequencing

(2018) Yael Steuerman et al.   Cell Systems

Krebs Cycle Reimagined: The Emerging Roles of Succinate and Itaconate as Signal Transducers

(2018) Michael P. Murphy et al.   CELL

UniProt: a worldwide hub of protein knowledge

(2018)   NUCLEIC ACIDS RESEARCH

The PRIDE database and related tools and resources in 2019: improving support for quantification data

(2018) Yasset Perez-Riverol et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2019

(2018) Fiona Cunningham et al.   NUCLEIC ACIDS RESEARCH

miRBase: from microRNA sequences to function

(2018) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

Multiplexed droplet single-cell RNA-sequencing using natural genetic variation

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Regulation of Mammalian 13-Subunit Cytochrome c Oxidase and Binding of other Proteins: Role of NDUFA4

(2017) Bernhard Kadenbach   TRENDS IN ENDOCRINOLOGY AND METABOLISM

Germline NLRP1 Mutations Cause Skin Inflammatory and Cancer Susceptibility Syndromes via Inflammasome Activation

(2016) Franklin L. Zhong et al.   CELL

Mitochondrial reactive oxygen species and inflammation: Molecular mechanisms, diseases and promising therapies

(2016) Alessandro Rimessi et al.   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY

Mitochondrial Protein Interaction Mapping Identifies Regulators of Respiratory Chain Function

(2016) Brendan J. Floyd et al.   MOLECULAR CELL

TCA Cycle and Mitochondrial Membrane Potential Are Necessary for Diverse Biological Functions

(2016) Inmaculada Martínez-Reyes et al.   MOLECULAR CELL

Mechanism of super-assembly of respiratory complexes III and IV

(2016) Sara Cogliati et al.   NATURE

Accessory subunits are integral for assembly and function of human mitochondrial complex I

(2016) David A. Stroud et al.   NATURE

A multifunctional AAV–CRISPR–Cas9 and its host response

(2016) Wei Leong Chew et al.   NATURE METHODS

The Perseus computational platform for comprehensive analysis of (prote)omics data

(2016) Stefka Tyanova et al.   NATURE METHODS

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

(2016) Maxim V. Kuleshov et al.   NUCLEIC ACIDS RESEARCH

Resolution of Inflammation: What Controls Its Onset?

(2016) Michelle A. Sugimoto et al.   Frontiers in Immunology

MicroRNAs miR-146a/b negatively modulate the senescence-associated inflammatory mediators IL-6 and IL-8

(2016) Dipa Bhaumik et al.   Aging-US

Hypoxia Inducible Factors Modulate Mitochondrial Oxygen Consumption and Transcriptional Regulation of Nuclear-Encoded Electron Transport Chain Genes

(2015) Hye Jin Hwang et al.   BIOCHEMISTRY

MAVS Coordination of Antiviral Innate Immunity

(2015) Christine Vazquez et al.   JOURNAL OF VIROLOGY

The subunit composition and function of mammalian cytochrome c oxidase

(2015) Bernhard Kadenbach et al.   MITOCHONDRION

MitoFates: Improved Prediction of Mitochondrial Targeting Sequences and Their Cleavage Sites

(2015) Yoshinori Fukasawa et al.   MOLECULAR & CELLULAR PROTEOMICS

The I-TASSER Suite: protein structure and function prediction

(2015) Jianyi Yang et al.   NATURE METHODS

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

MitoCarta2.0: an updated inventory of mammalian mitochondrial proteins

(2015) Sarah E. Calvo et al.   NUCLEIC ACIDS RESEARCH

Higd1ais a positive regulator of cytochromecoxidase

(2015) Takaharu Hayashi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Predicting effective microRNA target sites in mammalian mRNAs

(2015) Vikram Agarwal et al.   eLife

The Molecular Signatures Database Hallmark Gene Set Collection

(2015) Arthur Liberzon et al.   Cell Systems

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Apoptotic Caspases Prevent the Induction of Type I Interferons by Mitochondrial DNA

(2014) Anthony Rongvaux et al.   CELL

Improved vectors and genome-wide libraries for CRISPR screening

(2014) Neville E Sanjana et al.   NATURE METHODS

Easy quantitative assessment of genome editing by sequence trace decomposition

(2014) Eva K. Brinkman et al.   NUCLEIC ACIDS RESEARCH

Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool

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Mitochondrial Cardiolipin Is Required for Nlrp3 Inflammasome Activation

(2013) Shankar S. Iyer et al.   IMMUNITY

Lentiviral Delivery of RNAi for In Vivo Lineage-Specific Modulation of Gene Expression in Mouse Lung Macrophages

(2013) Andrew A Wilson et al.   MOLECULAR THERAPY

The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote

(2013) Yang Liao et al.   NUCLEIC ACIDS RESEARCH

Early Host Responses of Seasonal and Pandemic Influenza A Viruses in Primary Well-Differentiated Human Lung Epithelial Cells

(2013) Rachael L. Gerlach et al.   PLoS One

NDUFA4 Mutations Underlie Dysfunction of a Cytochrome c Oxidase Subunit Linked to Human Neurological Disease

(2013) Robert D.S. Pitceathly et al.   Cell Reports

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

NDUFA4 Is a Subunit of Complex IV of the Mammalian Electron Transport Chain

(2012) Eduardo Balsa et al.   Cell Metabolism

Assessment of mitochondrial respiratory chain enzymatic activities on tissues and cultured cells

(2012) Marco Spinazzi et al.   Nature Protocols

Camera: a competitive gene set test accounting for inter-gene correlation

(2012) Di Wu et al.   NUCLEIC ACIDS RESEARCH

Universal Real-Time PCR for the Detection and Quantification of Adeno-Associated Virus Serotype 2-Derived Inverted Terminal Repeat Sequences

(2012) Christine Aurnhammer et al.   Human Gene Therapy Methods

The Cell-Non-Autonomous Nature of Electron Transport Chain-Mediated Longevity

(2011) Jenni Durieux et al.   CELL

Induction of the Mitochondrial NDUFA4L2 Protein by HIF-1α Decreases Oxygen Consumption by Inhibiting Complex I Activity

(2011) Daniel Tello et al.   Cell Metabolism

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

Immune surveillance by mast cells during dengue infection promotes natural killer (NK) and NKT-cell recruitment and viral clearance

(2011) A. L. St. John et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

I-TASSER: a unified platform for automated protein structure and function prediction

(2010) Ambrish Roy et al.   Nature Protocols

Jalview Version 2--a multiple sequence alignment editor and analysis workbench

(2009) A. M. Waterhouse et al.   BIOINFORMATICS

Restriction of Chlamydia pneumoniae replication in human dendritic cell by activation of indoleamine 2,3-dioxygenase

(2009) Florence Njau et al.   MICROBES AND INFECTION

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

miR-147, a microRNA that is induced upon Toll-like receptor stimulation, regulates murine macrophage inflammatory responses

(2009) G. Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

How mitochondria produce reactive oxygen species

(2008) Michael P. Murphy   BIOCHEMICAL JOURNAL

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

I-TASSER server for protein 3D structure prediction

(2008) Yang Zhang   BMC BIOINFORMATICS

Regional variation in gene expression in the healthy colon is dysregulated in ulcerative colitis

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Suppression of inflammatory signaling in monocytes from patients with coronary artery disease

(2008) Stephan H. Schirmer et al.   JOURNAL OF MOLECULAR AND CELLULAR CARDIOLOGY

Transcriptome of Hypoxic Immature Dendritic Cells: Modulation of Chemokine/Receptor Expression

(2008) A. Ricciardi et al.   MOLECULAR CANCER RESEARCH

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH

Type I Interferon: Potential Therapeutic Target for Psoriasis?

(2008) Yihong Yao et al.   PLoS One