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Omics-based approaches for the systematic profiling of mitochondrial biology

MOLECULAR CELL (2023)

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Review Chemistry, Multidisciplinary

Proximity Labeling Techniques: A Multi-Omics Toolbox

Olha Shkel et al.

Summary: Proximity labeling techniques provide a high-throughput approach to study protein-protein, protein-RNA, and protein-DNA interactions with precision. These methods utilize enzymes that can covalently label biomolecules, allowing for the identification of weak or transient interactions. The applications of proximity labeling extend to the analysis of organelle interactomes and spatial composition of macromolecular complexes.

CHEMISTRY-AN ASIAN JOURNAL (2022)

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Article Biochemistry & Molecular Biology

Post-translational modifications on mitochondrial metabolic enzymes in cancer

Yunhua Peng et al.

Summary: Mitochondria play a crucial role in the initiation and development of tumor cells, with metabolic proteins serving as key mediators in tumorigenesis. Understanding mitochondria-related post-translational modifications is important for the future of cancer treatment.

FREE RADICAL BIOLOGY AND MEDICINE (2022)

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Article Biochemistry & Molecular Biology

Low-input RNase footprinting for simultaneous quantification of cytosolic and mitochondrial translation

Qianru Li et al.

Summary: We developed a low-input RNase footprinting technique for rapid quantification of ribosome-protected fragments, applicable to small samples and translation studies under different physiological conditions.

GENOME RESEARCH (2022)

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Article Biochemistry & Molecular Biology

Global mitochondrial protein import proteomics reveal distinct regulation by translation and translocation machinery

Jasmin Adriana Schaefer et al.

Summary: In this study, we introduced a proteomics approach called mePROD(mt), which enables global dynamic analysis of mitochondrial protein uptake. Our results showed that protein uptake into mitochondria is regulated by import and translation machineries, and is influenced by the activation of the integrated stress response.

MOLECULAR CELL (2022)

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Article Biotechnology & Applied Microbiology

Single-cell profiling of proteins and chromatin accessibility using PHAGE-ATAC

Evgenij Fiskin et al.

Summary: The study introduces a novel method called PHAGE-ATAC for simultaneous single-cell measurements of protein levels and chromatin accessibility profiles, using mitochondrial DNA-based clonal tracing. PHAGE-ATAC is utilized for multimodal analysis in primary human immune cells, sample multiplexing, intracellular protein analysis, and detection of SARS-CoV-2 spike protein. Additionally, a synthetic high-complexity phage library is constructed for selection of antigen-specific nanobodies, enabling protein detection, cell characterization, and screening with single-cell genomics.

NATURE BIOTECHNOLOGY (2022)

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Review Medicine, General & Internal

Comprehensive summary of mitochondrial DNA alterations in the postmortem human brain: A systematic review

Alba Valiente-Palleja et al.

Summary: Mitochondrial DNA alterations in human brain tissue can impact brain functioning and are linked to various neurological and psychiatric diseases as well as the aging process. Studies have shown variability in the types of mtDNA alterations across different brain regions and disease categories. More research is needed to fully understand the role of mtDNA in these conditions.

EBIOMEDICINE (2022)

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Review Cell Biology

Complexome Profiling-Exploring Mitochondrial Protein Complexes in Health and Disease

Alfredo Cabrera-Orefice et al.

Summary: Complexome profiling is an advanced method for studying the composition and abundance of protein complexes in biological samples, as well as their dynamics and the impact of mutations. It has been used to discover novel protein interactors and investigate pathophysiological mechanisms.

FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY (2022)

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Review Chemistry, Multidisciplinary

Molecular Spatiomics by Proximity Labeling

Myeong-Gyun Kang et al.

Summary: Proximity labeling is an enzymatic chemical reaction that modifies biomolecules in live cells based on their proximity. It has been used to characterize local proteomes and spatiotemporal interactome information in live cells. The method can also be applied for profiling local RNA and DNA and is promising for studying spatial cell-cell interaction networks in live animal models.

ACCOUNTS OF CHEMICAL RESEARCH (2022)

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Article Biochemistry & Molecular Biology

Ultra-high sensitivity mass spectrometry quantifies single-cell proteome changes upon perturbation

Andreas-David Brunner et al.

Summary: Single-cell technologies have a huge impact on biology, mainly limited to imaging and deep sequencing. This study presents a robust workflow combining miniaturized sample preparation, low flow-rate chromatography, and a novel trapped ion mobility mass spectrometer to improve sensitivity. The technology allows precise and robust quantification of proteomes and their changes in single cells, providing insights into cellular heterogeneity in health and disease.

MOLECULAR SYSTEMS BIOLOGY (2022)

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Article Multidisciplinary Sciences

Defining mitochondrial protein functions through deep multiomic profiling

Jarred W. Rensvold et al.

Summary: Mitochondria, as the epicentres of eukaryotic metabolism and bioenergetics, are linked to numerous diseases. However, the functions of many mitochondrial proteins are still unclear, and the genetic basis of many mitochondrial disorders remains unresolved. Through mass spectrometry-based multiomics analyses, we have established a comprehensive functional compendium of human mitochondrial proteins, providing a foundation for mechanistic investigations and genetic diagnosis of mitochondrial diseases. Our findings have identified specific proteins associated with mitochondrial function and disorders, and defined a rich cell signature of mitochondrial dysfunction.

NATURE (2022)

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Article Biotechnology & Applied Microbiology

Mitochondrial variant enrichment from high-throughput single-cell RNA sequencing resolves clonal populations

Tyler E. Miller et al.

Summary: The combination of single-cell transcriptomics and mitochondrial DNA variant detection is useful for establishing lineage relationships in primary human cells, but current methods are not suitable for analyzing complex tissues. In this study, researchers combined common 3' single-cell RNA-sequencing protocols with mitochondrial transcriptome enrichment to significantly increase coverage and enable high-confidence mutation detection. This method successfully identified skewed immune cell expansions in primary human clonal hematopoiesis.

NATURE BIOTECHNOLOGY (2022)

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Review Genetics & Heredity

Into the multiverse: advances in single-cell multiomic profiling

Silvia Ogbeide et al.

Summary: Single-cell transcriptomic approaches have revolutionised the study of complex biological systems, enabling construction of whole-organism cell atlases. By linking measurements from different layers, the potential to reveal regulatory and functional mechanisms underlying cell behaviour in healthy development and disease is enhanced.

TRENDS IN GENETICS (2022)

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Review Cell Biology

Single-Cell Multiomics Techniques: From Conception to Applications

Maria A. Dimitriu et al.

Summary: Recent advances in single-cell analyses have led to comprehensive characterization of cellular and molecular states, with the development of multiplexed assays offering simultaneous analysis of multiple factors and processes. These technologies have rapidly evolved, providing better specificity, precision, and resolution. This review summarizes recent progress in single-cell multiomics approaches, focusing on innovative techniques that integrate genome, epigenome, and transcriptome profiling.

FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY (2022)

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Article Multidisciplinary Sciences

Insights into protein post-translational modification landscapes of individual human cells by trapped ion mobility time-of-flight mass spectrometry

Benjamin C. Orsburn et al.

Summary: Single-cell proteomics is a powerful tool for studying cellular heterogeneity and quantifying post-translational modifications. The authors developed a method with improved protein sequence coverage and demonstrated its application in characterizing the effects of inhibitor treatment in single human cells. This approach allows for the detection of multiple classes of post-translational modifications and provides insight into cell-to-cell variability in drug response that is missed by traditional proteomics.

NATURE COMMUNICATIONS (2022)

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Article Multidisciplinary Sciences

Mitochondrial RNA modifications shape metabolic plasticity in metastasis

Sylvain Delaunay et al.

Summary: The study reveals that the NSUN3-dependent RNA modifications of mitochondrial mRNA can impact metabolic plasticity, thus affecting the metastatic potential of cancer cells, providing new therapeutic targets for combating cancer metastasis.

NATURE (2022)

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Article Multidisciplinary Sciences

Protein import motor complex reacts to mitochondrial misfolding by reducing protein import and activating mitophagy

Jonas Benjamin Michaelis et al.

Summary: Mitophagy activation can be induced by mitochondrial protein misfolding through the reduction of protein import, without requiring mitochondrial depolarization. This discovery expands our understanding of the induction of mitophagy and explains how mitophagy can be activated under conditions that do not affect membrane polarization.

NATURE COMMUNICATIONS (2022)

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Article Genetics & Heredity

Free Fatty Acid Overload Targets Mitochondria: Gene Expression Analysis of Palmitic Acid-Treated Endothelial Cells

Afraz Ahmad Raja et al.

Summary: This study investigates the impact of lipotoxicity on endothelial cells and identifies differentially expressed genes associated with processes such as mitochondrial dysfunction and apoptosis. The findings provide insights for future experiments on the role of fatty acids in endothelial cell damage.

GENES (2022)

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Article Multidisciplinary Sciences

A method for multiplexed full-length single-molecule sequencing of the human mitochondrial genome

Ieva Keraite et al.

Summary: Accurate analysis of mitochondrial DNA is crucial for clinical research and diagnostics of mitochondrial diseases. This study presents a method that utilizes Cas9 cleavage, nanopore sequencing, and a custom pipeline to identify pathogenic variants and accurately quantify heteroplasmy. The authors demonstrate that their method is capable of detecting complex deletions, determining the phase of variants, and achieving high coverage of the mitochondrial genome, overcoming the limitations of short-read sequencing. The developed workflow provides a powerful tool for studying mtDNA variation and will greatly accelerate mitochondrial research.

NATURE COMMUNICATIONS (2022)

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Article Biotechnology & Applied Microbiology

Balanced mitochondrial and cytosolic translatomes underlie the biogenesis of human respiratory complexes

Iliana Soto et al.

Summary: This study shows that human OXPHOS complexes are synthesized proportionally to each other, and the balance between mitochondrial and nuclear genes relies on the regulation of OXPHOS subunit translation across cellular compartments.

GENOME BIOLOGY (2022)

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Review Biochemistry & Molecular Biology

A systematic review of post-translational modifications in the mitochondrial permeability transition pore complex associated with cardiac diseases

H. Alves-Figueiredo et al.

Summary: PTMs play a crucial role in regulating mPTP in the pathophysiology of cardiac diseases, potentially altering mitochondrial function. Further investigation into this regulatory mechanism may lead to the discovery of new therapeutic targets and treatment approaches.

BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE (2021)

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Article Cell Biology

Identification of long-lived proteins in the mitochondria reveals increased stability of the electron transport chain

Shefali Krishna et al.

Summary: Research has found that mitochondria in the mouse brain can be long-lived, with specific mitochondrial proteins having half-lives longer than the average proteome. These long-lived mitochondrial proteins are core components of the electron transport chain, and their extended longevity contributes to the maintenance of respiratory supercomplexes.

DEVELOPMENTAL CELL (2021)

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Article Biochemistry & Molecular Biology

Ribosome profiling analysis of human skeletal muscle identifies reduced translation of mitochondrial proteins with age

Ravi Tharakan et al.

Summary: As human muscle ages, the translation of proteins related to oxidative phosphorylation, especially those encoded by the mitochondrial genome, decreases, potentially leading to reduced strength and function in old skeletal muscle.

RNA BIOLOGY (2021)

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Review Biochemistry & Molecular Biology

VDACs Post-Translational Modifications Discovery by Mass Spectrometry: Impact on Their Hub Function

Maria Gaetana Giovanna Pittala et al.

Summary: VDAC (voltage-dependent anion selective channel) proteins, also known as mitochondrial porins, are crucial in cellular processes, metabolism regulation, and survival pathways due to their abundance and function as cellular hubs. Their structural characterization poses challenges due to high hydrophobicity, low solubility, and difficulty in isolation, leading to a need for analysis as components of a complex mixture. Recent advancements in tools such as nano-reversed phase ultra-high performance liquid chromatography (nanoRP-UHPLC) and ultra-sensitive high-resolution mass spectrometry (HRMS) have greatly contributed to the understanding of post-translational modifications (PTMs) of VDAC proteins.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2021)

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Article Multidisciplinary Sciences

Proteome-wide profiling and mapping of post translational modifications in human hearts

Navratan Bagwan et al.

Summary: Post translational modifications (PTMs) are covalent modifications of proteins that regulate protein function and increase proteome diversity. In human hearts, high-resolution mass spectrometry measurements and PTM identification algorithms identified over 150 different PTMs, highlighting the diversity of cardiac protein modifications.

SCIENTIFIC REPORTS (2021)

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Article Biochemistry & Molecular Biology

SILAC-based complexome profiling dissects the structural organization of the human respiratory supercomplexes in SCAFIKO cells

Erika Fernandez-Vizarra et al.

Summary: The study of mitochondrial respiratory chain function in relation to its structural organization is essential for understanding eukaryotic cell metabolism. The complexome profiling technique has provided valuable information on the composition and assembly of MRC complexes, including larger supercomplexes and respirasomes. SCAFI plays a role in connecting individual MRC complexes III and IV, but is not the main player in respirasome formation as previously thought.

BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS (2021)

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Article Biochemistry & Molecular Biology

Self-assembly of multi-component mitochondrial nucleoids via phase separation

Marina Feric et al.

Summary: Mitochondria contain an autonomous genome organized into nucleoids, and the primary physical mechanism for assembly and size control of the mitochondrial nucleoid (mt-nucleoid) is phase separation. The major mtDNA-binding protein TFAM can spontaneously phase separate into droplets with slow internal dynamics in vitro, which recapitulates the dynamics and behavior of mt-nucleoids in vivo. Mt-nucleoids coalesce into larger droplets in response to cellular stress, as seen in patients with Hutchinson-Gilford Progeria Syndrome (HGPS), pointing to phase separation as an evolutionarily conserved mechanism of genome organization.

EMBO JOURNAL (2021)

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Article Biochemical Research Methods

Multiplexed single-cell proteomics using SCoPE2

Aleksandra A. Petelski et al.

Summary: The study introduces the SCoPE2 protocol for single-cell protein analysis, which utilizes isobaric mass tags for labeling and achieves cost-effective quantitative protein analysis.

NATURE PROTOCOLS (2021)

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Review Oncology

The genetics of mitochondrial disease: dissecting mitochondrial pathology using multi-omic pipelines

Charlotte L. Alston et al.

Summary: Mitochondria play essential roles in metabolism, with mitochondrial diseases clinically diverse and genetically heterogeneous. Genetic diagnosis is crucial for genetic counselling and reproductive options, with next-generation sequencing and multi-omics approaches revolutionizing mitochondrial diagnostics. Patient tissues and integrated multi-omics approach are pivotal for understanding molecular mechanisms in challenging cases.

JOURNAL OF PATHOLOGY (2021)

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Review Clinical Neurology

Applying genomic and transcriptomic advances to mitochondrial medicine

William L. Macken et al.

Summary: This article discusses the current genetic testing approach for primary mitochondrial diseases and the opportunities for increased use of whole-genome NGS. It also explores the expanding applications of RNA sequencing.

NATURE REVIEWS NEUROLOGY (2021)

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Review Biochemistry & Molecular Biology

Metabolomics and Lipidomics: Expanding the Molecular Landscape of Exercise Biology

Mehdi R. Belhaj et al.

Summary: Dynamic changes in metabolism and lipid profiles during exercise provide insights into the metabolic responses to different types of exercise. Advances in metabolomics and lipidomics have allowed for a better understanding of the molecular mechanisms underlying the health-promoting effects of exercise, with a focus on human biofluids and tissues in recent years.

METABOLITES (2021)

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Article Biology

Age-dependent changes in protein incorporation into collagen-rich tissues of mice by in vivo pulsed SILAC labelling

Yoanna Ariosa-Morejon et al.

Summary: By using in vivo pulsed SILAC labelling, the study found reduced new protein incorporation in cartilage, bone, and skin with age. Age-related diseases may be associated with changes in epigenetic modulators, decreased growth factors, mitochondrial dysregulation, and reduced collagen synthesis.

ELIFE (2021)

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Article Biology

Mitochondrial-nuclear cross-talk in the human brain is modulated by cell type and perturbed in neurodegenerative disease

Aine Fairbrother-Browne et al.

Summary: Fairbrother-Browne and collaborators analyzed the relationship between nuclear and mitochondrial gene expression in the human brain, finding correlations governed by regional patterns that are disrupted in neurodegenerative diseases. The study shows that interactions between mitochondrial and nuclear genes are vital for normal brain function, and disruptions in these relationships may contribute to the pathogenesis of diseases like AD. The research presents a tool called MitoNuclearCOEXPlorer to explore crucial mitochondria-nuclear relationships in multi-dimensional brain data.

COMMUNICATIONS BIOLOGY (2021)

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Review Biotechnology & Applied Microbiology

Computational principles and challenges in single-cell data integration

Ricard Argelaguet et al.

Summary: The development of single-cell multimodal assays has provided a powerful tool for investigating cellular heterogeneity in multiple dimensions. Data integration is a key challenge in analyzing single-cell multimodal data, with existing strategies utilizing similar mathematical ideas but having distinct goals and principles.

NATURE BIOTECHNOLOGY (2021)

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Review Oncology

Current Methods of Post-Translational Modification Analysis and Their Applications in Blood Cancers

Katie Dunphy et al.

Summary: This review discusses techniques used for PTM analysis and their applications in blood cancer research. Mass spectrometry-based techniques are at the forefront of PTM analysis due to their ability to detect large numbers of modified proteins with high sensitivity and specificity. Immuno-based techniques remain popular, with improvements in the quality of commercially available modification-specific antibodies facilitating the detection of modified proteins with high affinity. PTM-focused studies on blood cancers have provided information on altered cellular processes that contribute to the malignant phenotype, while many blood cancer therapies target protein modifications to exert their anti-cancer effects. Continued optimization of protocols and techniques for PTM analysis in blood cancer research will lead to novel insights into mechanisms of malignant transformation and the identification of new biomarkers and therapeutic targets.

CANCERS (2021)

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Review Biochemistry & Molecular Biology

RNA Granules in the Mitochondria and Their Organization under Mitochondrial Stresses

Vanessa Joanne Xavier et al.

Summary: The human mitochondrial genome regulates its transcription products in specialized ways through mtDNA, with RNA regulation organized within the Mitochondrial RNA Granules. Recent findings show that dsRNA species can form granules in the mitochondria matrix. Dysfunctions in mitochondria, such as RNA processing defects, may lead to loss or aberrant accumulation of these RNA granules, emphasizing the link between mitochondrial maintenance and proper gene expression.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2021)

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Review Biochemistry & Molecular Biology

The extensive and functionally uncharacterized mitochondrial phosphoproteome

Natalie M. Niemi et al.

Summary: The importance of phosphorylation within mitochondria has been widely recognized, but the majority of modifications remains poorly characterized, with disruption of mitochondrial protein phosphatases causing metabolic dysfunction. While current data suggests critical importance of mitochondrial phosphorylation, significant gaps exist in understanding how these modifications influence organellar function.

JOURNAL OF BIOLOGICAL CHEMISTRY (2021)

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Article Biotechnology & Applied Microbiology

Scalable, multimodal profiling of chromatin accessibility, gene expression and protein levels in single cells

Eleni P. Mimitou et al.

Summary: ASAP-seq is a new tool that can simultaneously profile chromatin accessibility and protein levels in single cells. It uses a bridging approach that repurposes antibody:oligonucleotide conjugates originally designed for protein measurements paired with single-cell RNA sequencing. Together with DOGMA-seq, it demonstrates the utility of systematic multi-omic profiling by revealing coordinated and distinct changes in chromatin, RNA, and surface proteins in single cells.

NATURE BIOTECHNOLOGY (2021)

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Review Cell Biology

Functions and Mechanisms of Lysine Glutarylation in Eukaryotes

Longxiang Xie et al.

Summary: Lysine glutarylation is a newly discovered post-translational modification involved in metabolism regulation, oxidative damage, chromatin dynamics, and disease development. The process is reversible and evolving computational tools enable better prediction of modification sites.

FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY (2021)

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Review Cell Biology

Mitochondrial Protein Translation: Emerging Roles and Clinical Significance in Disease

Fei Wang et al.

Summary: Mitochondria in cells are crucial organelles with their own genetic system, and their protein translation process is regulated by various factors that, when abnormal, can lead to diseases. The balance between mitochondrial protein translation and cytoplasmic translation is also important for physiological and pathological processes in the body.

FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY (2021)

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Review Biochemistry & Molecular Biology

Metabolomics: A Scoping Review of Its Role as a Tool for Disease Biomarker Discovery in Selected Non-Communicable Diseases

Adewale Victor Aderemi et al.

Summary: Metabolomics is a branch of omics sciences that aims to identify and assess small molecules in samples for their diagnostic and therapeutic potentials. It has been utilized in various aspects of life and has shown potential in biomarker discovery for disease diagnosis and management. However, challenges remain in translating laboratory discoveries to clinical applications.

METABOLITES (2021)

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Article Biotechnology & Applied Microbiology

Complete vertebrate mitogenomes reveal widespread repeats and gene duplications

Giulio Formenti et al.

Summary: This study developed a fully automated pipeline that successfully assembled complete mitochondrial genomes of 100 vertebrate species, and found that tissue type and library size selection significantly impact mitochondrial genome sequencing and assembly. Comparison with reference mitochondrial genomes based on short-read sequencing revealed errors, missing sequences, and incomplete genes in the references.

GENOME BIOLOGY (2021)

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Article Biotechnology & Applied Microbiology

Single-cell proteomic and transcriptomic analysis of macrophage heterogeneity using SCoPE2

Harrison Specht et al.

Summary: The SCoPE2 technology was developed to improve the accuracy and throughput of single-cell proteomics through automated sample preparation, revealing the gradual differences in the proteome of macrophages during the enhancement of heterogeneity and allowing differentiation of cell states.

GENOME BIOLOGY (2021)

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Ultrasensitive single-cell proteomics workflow identifies >1000 protein groups per mammalian cell

Yongzheng Cong et al.

Summary: The combination of nanodroplet sample preparation, ultra-low-flow nanoLC, high-field asymmetric ion mobility spectrometry (FAIMS), and the latest-generation Orbitrap Eclipse Tribrid mass spectrometer led to greatly improved single-cell proteome profiling. FAIMS effectively filtered out singly charged ions, allowing for more effective MS analysis of multiply charged peptides, resulting in a significantly higher number of protein groups identified from single HeLa cells compared to traditional methods. Differential analysis also showed similar proteome coverage for single microdissected motor neurons and interneurons from human spinal tissue, with the ability to differentiate between the two subpopulations based on label-free quantification.

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MitoCarta3.0: an updated mitochondrial proteome now with sub-organelle localization and pathway annotations

Sneha Rath et al.

Summary: MitoCarta3.0 is a catalog of over 1000 genes encoding the mammalian mitochondrial proteome, with 1136 human genes after manual review. It includes annotations of sub-mitochondrial localization and hierarchical 'MitoPathways', serving as a valuable resource for mitochondrial biology and medicine.

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Real-Time NMR Spectroscopy for Studying Metabolism

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ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2020)

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ANNUAL REVIEW OF BIOCHEMISTRY, VOL 89 (2020)

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Mitochondrial DNA heteroplasmy in disease and targeted nuclease-based therapeutic approaches

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Functional Translatome Proteomics Reveal Converging and Dose-Dependent Regulation by mTORC1 and eIF2α

Kevin Klann et al.

MOLECULAR CELL (2020)

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

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NATURE (2020)

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A pathway coordinated by DELE1 relays mitochondrial stress to the cytosol

Evelyn Fessler et al.

NATURE (2020)

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Mitochondrial TCA cycle metabolites control physiology and disease

Inmaculada Martinez-Reyes et al.

NATURE COMMUNICATIONS (2020)

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Rapid and site-specific deep phosphoproteome profiling by data-independent acquisition without the need for spectral libraries

Dorte B. Bekker-Jensen et al.

NATURE COMMUNICATIONS (2020)

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Review Biochemistry & Molecular Biology

Mitochondrial OXPHOS Biogenesis: Co-Regulation of Protein Synthesis, Import, and Assembly Pathways

Jia Xin Tang et al.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2020)

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Contact-ID, a tool for profiling organelle contact sites, reveals regulatory proteins of mitochondrial-associated membrane formation

Chulhwan Kwak et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

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A salvage pathway maintains highly functional respiratory complex I

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NATURE COMMUNICATIONS (2020)

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Comprehensive analysis of posttranslational protein modifications in aging of subcellular compartments

Tim Baldensperger et al.

SCIENTIFIC REPORTS (2020)

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The Mouse Heart Mitochondria N Terminome Provides Insights into ClpXP-Mediated Proteolysis

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Phase Separation in Membrane Biology: The Interplay between Membrane-Bound Organelles and Membraneless Condensates

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TMEM70 functions in the assembly of complexes I and V

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The Mitochondrial Proteomic Signatures of Human Skeletal Muscle Linked to Insulin Resistance

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Growth Factor Receptor Signaling Inhibition Prevents SARS-CoV-2 Replication

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A High-Density Human Mitochondrial Proximity Interaction Network

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Why All the Fuss about Oxidative Phosphorylation (OXPHOS)?

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Stuart J. Hesketh et al.

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Mass-spectrometric multi-omics linked to function - State-of-the-art investigations of mitochondria in systems medicine

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TRAC-TRENDS IN ANALYTICAL CHEMISTRY (2019)

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Article Biochemistry & Molecular Biology

Calcium, mitochondria and cell metabolism: A functional triangle in bioenergetics

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BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH (2019)

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Article Multidisciplinary Sciences

MITO-Tag Mice enable rapid isolation and multimodal profiling of mitochondria from specific cell types in vivo

Erol C. Bayraktar et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)

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Article Biochemistry & Molecular Biology

A Chemical Strategy for Protease Substrate Profiling

Andrew R. Griswold et al.

CELL CHEMICAL BIOLOGY (2019)

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Review Biochemistry & Molecular Biology

Communication between mitochondria and other organelles: a brand-new perspective on mitochondria in cancer

MengFang Xia et al.

CELL AND BIOSCIENCE (2019)

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Review Cell Biology

The multifaceted contributions of mitochondria to cellular metabolism

Jessica B. Spinelli et al.

NATURE CELL BIOLOGY (2018)

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Article Biochemistry & Molecular Biology

Fatiguing contractions increase protein S-glutathionylation occupancy in mouse skeletal muscle

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REDOX BIOLOGY (2018)

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Article Biochemistry & Molecular Biology

Integration of Multi-omics Data from Mouse Diversity Panel Highlights Mitochondrial Dysfunction in Non-alcoholic Fatty Liver Disease

Karthickeyan Chella Krishnan et al.

CELL SYSTEMS (2018)

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Article Biochemistry & Molecular Biology

Barth syndrome cells display widespread remodeling of mitochondrial complexes without affecting metabolic flux distribution

Iliana A. Chatzispyrou et al.

BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE (2018)

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Article Cell Biology

Disease-Linked Glutarylation Impairs Function and Interactions of Mitochondrial Proteins and Contributes to Mitochondrial Heterogeneity

Jessica Schmiesing et al.

CELL REPORTS (2018)

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Review Chemistry, Analytical

Recent advances in using mass spectrometry for mitochondrial metabolomics and lipidomics - A review

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ANALYTICA CHIMICA ACTA (2018)

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Review Biochemistry & Molecular Biology

Chemical and Physiological Features of Mitochondrial Acylation

Alison E. Ringel et al.

MOLECULAR CELL (2018)

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Review Biotechnology & Applied Microbiology

Mitochondria as a therapeutic target for common pathologies

Michael P. Murphy et al.

NATURE REVIEWS DRUG DISCOVERY (2018)

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Article Biochemistry & Molecular Biology

Single-nucleotide-resolution sequencing of human N6-methyldeoxyadenosine reveals strand-asymmetric clusters associated with SSBP1 on the mitochondrial genome

Casslynn W. Q. Koh et al.

NUCLEIC ACIDS RESEARCH (2018)

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Article Multidisciplinary Sciences

Differential regulation of cysteine oxidative post-translational modifications in high and low aerobic capacity

Rodrigo W. A. Souza et al.

SCIENTIFIC REPORTS (2018)

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Article Biotechnology & Applied Microbiology

SCoPE-MS: mass spectrometry of single mammalian cells quantifies proteome heterogeneity during cell differentiation

Bogdan Budnik et al.

GENOME BIOLOGY (2018)

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Article Biochemistry & Molecular Biology

A homozygous missense mutation in ERAL1, encoding a mitochondrial rRNA chaperone, causes Perrault syndrome

Iliana A. Chatzispyrou et al.

HUMAN MOLECULAR GENETICS (2017)

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Review Biochemistry & Molecular Biology

Iron-sulfur cluster biogenesis and trafficking in mitochondria

Joseph J. Braymer et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2017)

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Article Cell Biology

Multi-omics analysis identifies ATF4 as a key regulator of the mitochondrial stress response in mammals

Pedro M. Quiros et al.

JOURNAL OF CELL BIOLOGY (2017)

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Article Cell Biology

Coi1 is a novel assembly factor of the yeast complex III-complex IV supercomplex

Ravi K. Singhal et al.

MOLECULAR BIOLOGY OF THE CELL (2017)

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Article Biochemistry & Molecular Biology

Multi-omic Mitoprotease Profiling Defines a Role for Oct1p in Coenzyme Q Production

Mike T. Veling et al.

MOLECULAR CELL (2017)

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Article Multidisciplinary Sciences

A subcellular map of the human proteome

Peter J. Thul et al.

SCIENCE (2017)

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Review Biochemistry & Molecular Biology

Regulation of Mammalian Mitochondrial Gene Expression: Recent Advances

Sarah F. Pearce et al.

TRENDS IN BIOCHEMICAL SCIENCES (2017)

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Article Cell Biology

MR-1S Interacts with PET100 and PET117 in Module-Based Assembly of Human Cytochrome c Oxidase

Sara Vidoni et al.

CELL REPORTS (2017)

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Article Genetics & Heredity

Integrated genomic analysis of mitochondrial RNA processing in human cancers

Youssef Idaghdour et al.

GENOME MEDICINE (2017)

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Article Biology

Transcriptomic and proteomic landscape of mitochondrial dysfunction reveals secondary coenzyme Q deficiency in mammals

Inge Kuehl et al.

ELIFE (2017)

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Article Chemistry, Analytical

Phosphoproteomics with Activated Ion Electron Transfer Dissociation

Nicholas M. Riley et al.

ANALYTICAL CHEMISTRY (2017)

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Article Cell Biology

The Assembly Pathway of Mitochondrial Respiratory Chain Complex I

Sergio Guerrero-Castillo et al.

CELL METABOLISM (2017)

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Article Cell Biology

Age modifies respiratory complex I and protein homeostasis in a muscle type-specific manner

Shane E. Kruse et al.

AGING CELL (2016)

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Article Genetics & Heredity

Mutations in Complex I Assembly Factor TMEM126B Result in Muscle Weakness and Isolated Complex I Deficiency

Laura Sanchez-Caballero et al.

AMERICAN JOURNAL OF HUMAN GENETICS (2016)

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Article Genetics & Heredity

Biallelic Mutations in TMEM126B Cause Severe Complex I Deficiency with a Variable Clinical Phenotype

Charlotte L. Alston et al.

AMERICAN JOURNAL OF HUMAN GENETICS (2016)

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Article Biochemistry & Molecular Biology

Mitochondrial Sirtuin Network Reveals Dynamic SIRT3-Dependent Deacetylation in Response to Membrane Depolarization

Wen Yang et al.

CELL (2016)

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Article Biochemistry & Molecular Biology

Absolute Quantification of Matrix Metabolites Reveals the Dynamics of Mitochondrial Metabolism

Walter W. Chen et al.

CELL (2016)

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Review Biochemistry & Molecular Biology

Post-translational modifications in mitochondria: protein signaling in the powerhouse

Amanda R. Stram et al.

CELLULAR AND MOLECULAR LIFE SCIENCES (2016)

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Article Biochemical Research Methods

Simultaneous Metabolite, Protein, Lipid Extraction (SIMPLEX): A Combinatorial Multimolecular Omics Approach for Systems Biology

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MOLECULAR & CELLULAR PROTEOMICS (2016)

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Article Multidisciplinary Sciences

Mitochondrial unfolded protein response controls matrix pre-RNA processing and translation

Christian Munch et al.

NATURE (2016)

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Review Cell Biology

Metabolomics: beyond biomarkers and towards mechanisms

Caroline H. Johnson et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2016)

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Article Multidisciplinary Sciences

Systems proteomics of liver mitochondria function

Evan G. Williams et al.

SCIENCE (2016)

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Review Biochemistry & Molecular Biology

Mechanisms and Dynamics of Protein Acetylation in Mitochondria

Josue Baeza et al.

TRENDS IN BIOCHEMICAL SCIENCES (2016)

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Article Multidisciplinary Sciences

Deficient methylation and formylation of mt- tRNAMet wobble cytosine in a patient carrying mutations in NSUN3

Lindsey Van Haute et al.

NATURE COMMUNICATIONS (2016)

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Article Multidisciplinary Sciences

Purity matters: A workflow for the valid high-resolution lipid profiling of mitochondria from cell culture samples

Lisa Kappler et al.

SCIENTIFIC REPORTS (2016)

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Article Cell Biology

Simultaneous Multiplexed Measurement of RNA and Proteins in Single Cells

Spyros Darmanis et al.

CELL REPORTS (2016)

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Article Cell Biology

COX7A2L Is a Mitochondrial Complex III Binding Protein that Stabilizes the III2+IV Supercomplex without Affecting Respirasome Formation

Rafael Perez-Perez et al.

CELL REPORTS (2016)

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Article Biology

Global, quantitative and dynamic mapping of protein subcellular localization

Daniel N. Itzhak et al.

ELIFE (2016)

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Article Multidisciplinary Sciences

The Role of Mitochondrial Non-Enzymatic Protein Acylation in Ageing

Shin Yee Hong et al.

PLOS ONE (2016)

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Article Biotechnology & Applied Microbiology

Multiplexed, targeted profiling of single-cell proteomes and transcriptomes in a single reaction

Alex S. Genshaft et al.

GENOME BIOLOGY (2016)

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Article Cell Biology

Maximal Oxidative Capacity during Exercise Is Associated with Skeletal Muscle Fuel Selection and Dynamic Changes in Mitochondrial Protein Acetylation

Katherine A. Overmyer et al.

CELL METABOLISM (2015)

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Article Biochemical Research Methods

Proteomic and Biochemical Studies of Lysine Malonylation Suggest Its Malonic Aciduria-associated Regulatory Role in Mitochondrial Function and Fatty Acid Oxidation

Gozde Colak et al.

MOLECULAR & CELLULAR PROTEOMICS (2015)

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Article Biochemistry & Molecular Biology

SIRT5 Regulates both Cytosolic and Mitochondrial Protein Malonylation with Glycolysis as a Major Target

Yuya Nishida et al.

MOLECULAR CELL (2015)

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Review Cell Biology

New roles for mitochondrial proteases in health, ageing and disease

Pedro M. Quiros et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2015)

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Article Multidisciplinary Sciences

Extensive tissue-related and allele-related mtDNA heteroplasmy suggests positive selection for somatic mutations

Mingkun Li et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)

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Review Cell & Tissue Engineering

Connecting Mitochondria, Metabolism, and Stem Cell Fate

Anais Wanet et al.

STEM CELLS AND DEVELOPMENT (2015)

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Review Biochemistry & Molecular Biology

Mass Spectrometry-Based Detection and Assignment of Protein Posttranslational Modifications

Sophia Doll et al.

ACS CHEMICAL BIOLOGY (2015)

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Review Geriatrics & Gerontology

Post-translational modification of mitochondria as a novel mode of regulation

Annette Hofer et al.

EXPERIMENTAL GERONTOLOGY (2014)

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Article Biochemistry & Molecular Biology

Proteomic Mapping of the Human Mitochondrial Intermembrane Space in Live Cells via Ratiometric APEX Tagging

Victoria Hung et al.

MOLECULAR CELL (2014)

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Article Biochemical Research Methods

Genome-wide identification and quantification of protein synthesis in cultured cells and whole tissues by puromycin-associated nascent chain proteomics (PUNCH-P)

Ranen Aviner et al.

NATURE PROTOCOLS (2014)

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Article Medicine, Research & Experimental

Differential Gene Expression Reveals Mitochondrial Dysfunction in an Imprinting Center Deletion Mouse Model of Prader-Willi Syndrome

Puya G. Yazdi et al.

CTS-CLINICAL AND TRANSLATIONAL SCIENCE (2013)

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Article Biochemical Research Methods

Unambiguous Phosphosite Localization using Electron-Transfer/Higher-Energy Collision Dissociation (EThcD)

Christian K. Frese et al.

JOURNAL OF PROTEOME RESEARCH (2013)

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Article Biochemistry & Molecular Biology

SIRT5-Mediated Lysine Desuccinylation Impacts Diverse Metabolic Pathways

Jeongsoon Park et al.

MOLECULAR CELL (2013)

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Article Multidisciplinary Sciences

Proteomic Mapping of Mitochondria in Living Cells via Spatially Restricted Enzymatic Tagging

Hyun-Woo Rhee et al.

SCIENCE (2013)

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Article Multidisciplinary Sciences

Ribosome profiling reveals features of normal and disease-associated mitochondrial translation

Koos Rooijers et al.

NATURE COMMUNICATIONS (2013)

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Article Cell Biology

Complexome Profiling Identifies TMEM126B as a Component of the Mitochondrial Complex I Assembly Complex

Heinrich Heide et al.

CELL METABOLISM (2012)

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Review Cell Biology

Metabolomics: the apogee of the omics trilogy

Gary J. Patti et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2012)

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Article Multidisciplinary Sciences

Proteomic Investigations of Lysine Acetylation Identify Diverse Substrates of Mitochondrial Deacetylase Sirt3

Eri Maria Sol et al.

PLOS ONE (2012)

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Review Biochemical Research Methods

Electron transfer dissociation mass spectrometry in proteomics

Min-Sik Kim et al.

PROTEOMICS (2012)

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Article Cell Biology

Principles of Translational Control: An Overview

John W. B. Hershey et al.

COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY (2012)

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Article Genetics & Heredity

Protective Coupling of Mitochondrial Function and Protein Synthesis via the eIF2α Kinase GCN-2

Brooke M. Baker et al.

PLOS GENETICS (2012)

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Article Cell Biology

Regulating mitochondrial outer membrane proteins by ubiquitination and proteasomal degradation

Mariusz Karbowski et al.

CURRENT OPINION IN CELL BIOLOGY (2011)

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Article Cell Biology

Protein localization in disease and therapy

Mien-Chie Hung et al.

JOURNAL OF CELL SCIENCE (2011)

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Global quantification of mammalian gene expression control

Bjoern Schwanhaeusser et al.

NATURE (2011)

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Article Biochemical Research Methods

A large-scale method to measure absolute protein phosphorylation stoichiometries

Ronghu Wu et al.

NATURE METHODS (2011)

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Article Biochemical Research Methods

The SILAC Fly Allows for Accurate Protein Quantification in Vivo

Matthias D. Sury et al.

MOLECULAR & CELLULAR PROTEOMICS (2010)

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Article Biotechnology & Applied Microbiology

Isotopic labeling of terminal amines in complex samples identifies protein N-termini and protease cleavage products

Oded Kleifeld et al.

NATURE BIOTECHNOLOGY (2010)

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Review Genetics & Heredity

The Role of Mitochondria in Apoptosis

Chunxin Wang et al.

ANNUAL REVIEW OF GENETICS (2009)

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Review Biochemistry & Molecular Biology

Assembly of the oxidative phosphorylation system in humans: What we have learned by studying its defects

Erika Fernandez-Vizarra et al.

BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH (2009)

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Article Biochemical Research Methods

Turnover of the Human Proteome: Determination of Protein Intracellular Stability by Dynamic SILAC

Mary K. Doherty et al.

JOURNAL OF PROTEOME RESEARCH (2009)

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Article Biochemical Research Methods

Global analysis of cellular protein translation by pulsed SILAC

Bjoern Schwanhaeusser et al.

PROTEOMICS (2009)

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Article Multidisciplinary Sciences

Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling

Nicholas T. Ingolia et al.

SCIENCE (2009)

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Article Biochemistry & Molecular Biology

Global Sequencing of proteolytic cleavage sites in apoptosis by specific Labeling of protein N termini

Sami Mahrus et al.

CELL (2008)

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Article Biochemistry & Molecular Biology

SILAC mouse for quantitative proteomics uncovers kindlin-3 as an essential factor for red blood cell function

Marcus Krueger et al.

CELL (2008)

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Review Biochemistry & Molecular Biology

The mitochondrial serine protease HtrA2/Omi: an overview

L. Vande Walle et al.

CELL DEATH AND DIFFERENTIATION (2008)

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Review Cell Biology

Signal integration in the endoplasmic reticulum unfolded protein response

David Ron et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2007)

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Article Multidisciplinary Sciences

Selective identification of newly synthesized proteins in mammalian cells using bioorthogonal noncanonical amino acid tagging (BONCAT)

Daniela C. Dieterich et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)

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Review Genetics & Heredity

Mitochondrial DNA mutations in human disease

RW Taylor et al.

NATURE REVIEWS GENETICS (2005)

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Article Biotechnology & Applied Microbiology

Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides

K Gevaert et al.

NATURE BIOTECHNOLOGY (2003)

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Review Physiology

Import of nuclear-encoded proteins into mitochondria

D Stojanovski et al.

EXPERIMENTAL PHYSIOLOGY (2003)

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Review Genetics & Heredity

The genetics and pathology of oxidative phosphorylation

J Smeitink et al.

NATURE REVIEWS GENETICS (2001)

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