mitoXplorer, a visual data mining platform to systematically analyze and visualize mitochondrial expression dynamics and mutations

Integrative analysis and machine learning on cancer genomics data using the Cancer Systems Biology Database (CancerSysDB)

(2018) Rasmus Krempel et al.   BMC BIOINFORMATICS

Mitochondrial dysfunction in down syndrome: molecular mechanisms and therapeutic targets

(2018) Antonella Izzo et al.   MOLECULAR MEDICINE

Kinetics and Mechanism of Mammalian Mitochondrial Ribosome Assembly

(2018) Daniel F. Bogenhagen et al.   Cell Reports

A transcriptomics resource reveals a transcriptional transition during ordered sarcomere morphogenesis in flight muscle

(2018) Maria L Spletter et al.   eLife

FlyBase 2.0: the next generation

(2018) Jim Thurmond et al.   NUCLEIC ACIDS RESEARCH

Defective Mitochondrial Cardiolipin Remodeling Dampens HIF-1α Expression in Hypoxia

(2018) Arpita Chowdhury et al.   Cell Reports

Barth Syndrome: Connecting Cardiolipin to Cardiomyopathy

(2017) Nikita Ikon et al.   LIPIDS

The proteome of baker's yeast mitochondria

(2017) Humberto Gonczarowska-Jorge et al.   MITOCHONDRION

Mitochondrial diseases: the contribution of organelle stress responses to pathology

(2017) Anu Suomalainen et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Expression Atlas: gene and protein expression across multiple studies and organisms

(2017) Irene Papatheodorou et al.   NUCLEIC ACIDS RESEARCH

Database resources of the National Center for Biotechnology Information

(2017) et al.   NUCLEIC ACIDS RESEARCH

Systematic proteome and proteostasis profiling in human Trisomy 21 fibroblast cells

(2017) Yansheng Liu et al.   Nature Communications

Trisomy 21 causes changes in the circulating proteome indicative of chronic autoinflammation

(2017) Kelly D. Sullivan et al.   Scientific Reports

Definition of a High-Confidence Mitochondrial Proteome at Quantitative Scale

(2017) Marcel Morgenstern et al.   Cell Reports

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

(2017) Inge Kühl et al.   eLife

Mitochondrial Heterogeneity: Evaluating Mitochondrial Subpopulation Dynamics in Stem Cells

(2017) D. C. Woods   Stem Cells International

Mitochondria and Cancer

(2016) Wei-Xing Zong et al.   MOLECULAR CELL

Down Syndrome Developmental Brain Transcriptome Reveals Defective Oligodendrocyte Differentiation and Myelination

(2016) Jose Luis Olmos-Serrano et al.   NEURON

UniProt: the universal protein knowledgebase

(2016)   NUCLEIC ACIDS RESEARCH

The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible

(2016) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

KEGG: new perspectives on genomes, pathways, diseases and drugs

(2016) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Mitochondrial Dynamics and Metabolic Regulation

(2016) Timothy Wai et al.   TRENDS IN ENDOCRINOLOGY AND METABOLISM

The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins

(2016) Andrew D. Rouillard et al.   Database-The Journal of Biological Databases and Curation

Trisomy 21 consistently activates the interferon response

(2016) Kelly D Sullivan et al.   eLife

Molecular Characterization of Down Syndrome Embryonic Stem Cells Reveals a Role for RUNX1 in Neural Differentiation

(2016) Tomer Halevy et al.   Stem Cell Reports

Fundamentals of cancer metabolism

(2016) R. J. DeBerardinis et al.   Science Advances

Quantitative analysis of mitochondrial morphology and membrane potential in living cells using high-content imaging, machine learning, and morphological binning

(2015) Anthony P. Leonard et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

Virtual pathway explorer (viPEr) and pathway enrichment analysis tool (PEANuT): creating and analyzing focus networks to identify cross-talk between molecules and pathways

(2015) Marius Garmhausen et al.   BMC GENOMICS

MitoMiner v3.1, an update on the mitochondrial proteomics database

(2015) Anthony C. Smith et al.   NUCLEIC ACIDS RESEARCH

MitoCarta2.0: an updated inventory of mammalian mitochondrial proteins

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

Mosaic nature of the mitochondrial proteome: Implications for the origin and evolution of mitochondria

(2015) Michael W. Gray   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetic basis of transcriptome diversity inDrosophila melanogaster

(2015) Wen Huang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The structure of the human mitochondrial ribosome

(2015) A. Amunts et al.   SCIENCE

Oncogenomic portals for the visualization and analysis of genome-wide cancer data

(2015) Katarzyna Klonowska et al.   Oncotarget

Unique features of the transcriptional response to model aneuploidy in human cells

(2014) Milena Dürrbaum et al.   BMC GENOMICS

Making Proteins in the Powerhouse

(2014) B. Martin Hällberg et al.   Cell Metabolism

GABP Transcription Factor (Nuclear Respiratory Factor 2) Is Required for Mitochondrial Biogenesis

(2014) Z.-F. Yang et al.   MOLECULAR AND CELLULAR BIOLOGY

Domains of genome-wide gene expression dysregulation in Down’s syndrome

(2014) Audrey Letourneau et al.   NATURE

Hypoxia regulates Hippo signalling through the SIAH2 ubiquitin E3 ligase

(2014) Biao Ma et al.   NATURE CELL BIOLOGY

Mitochondrial dysfunction as a central actor in intellectual disability-related diseases: An overview of Down syndrome, autism, Fragile X and Rett syndrome

(2014) Daniela Valenti et al.   NEUROSCIENCE AND BIOBEHAVIORAL REVIEWS

Defective Mitochondrial Function In Vivo in Skeletal Muscle in Adults with Down’s Syndrome: A 31P-MRS Study

(2014) Alexander C. Phillips et al.   PLoS One

Deletion of conserved protein phosphatases reverses defects associated with mitochondrial DNA damage in Saccharomyces cerevisiae

(2014) G. Garipler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Barth syndrome

(2013) John L. Jefferies   AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS

Diversity of mitochondrial genome organization

(2013) A. A. Kolesnikov et al.   BIOCHEMISTRY-MOSCOW

Adaptive Downregulation of Mitochondrial Function in Down Syndrome

(2013) Pablo Helguera et al.   Cell Metabolism

Modelling and rescuing neurodevelopmental defect of Down syndrome using induced pluripotent stem cells from monozygotic twins discordant for trisomy 21

(2013) Youssef Hibaoui et al.   EMBO Molecular Medicine

Characterization, Design, and Function of the Mitochondrial Proteome: From Organs to Organisms

(2013) Christopher Lotz et al.   JOURNAL OF PROTEOME RESEARCH

Significant Modifications of the Salivary Proteome Potentially Associated with Complications of Down Syndrome Revealed by Top-down Proteomics

(2013) Tiziana Cabras et al.   MOLECULAR & CELLULAR PROTEOMICS

Translating dosage compensation to trisomy 21

(2013) Jun Jiang et al.   NATURE

The Cancer Genome Atlas Pan-Cancer analysis project

(2013) John N Weinstein et al.   NATURE GENETICS

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Cardiolipin remodeling and the function of tafazzin

(2012) Michael Schlame   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR AND CELL BIOLOGY OF LIPIDS

Lymphocyte respiration in children with Trisomy 21

(2012) Elhadi H Aburawi et al.   BMC Pediatrics

Mitochondria: In Sickness and in Health

(2012) Jodi Nunnari et al.   CELL

Chronic pro-oxidative state and mitochondrial dysfunctions are more pronounced in fibroblasts from Down syndrome foeti with congenital heart defects

(2012) C. Piccoli et al.   HUMAN MOLECULAR GENETICS

Mitochondrial diseases

(2012) Anthony HV Schapira   LANCET

Global analysis of genome, transcriptome and proteome reveals the response to aneuploidy in human cells

(2012) Silvia Stingele et al.   Molecular Systems Biology

Mitochondrial disorders as windows into an ancient organelle

(2012) Scott B. Vafai et al.   NATURE

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

NIH Image to ImageJ: 25 years of image analysis

(2012) Caroline A Schneider et al.   NATURE METHODS

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

NCBI GEO: archive for functional genomics data sets—update

(2012) Tanya Barrett et al.   NUCLEIC ACIDS RESEARCH

Molecular Signatures of Cardiac Defects in Down Syndrome Lymphoblastoid Cell Lines Suggest Altered Ciliome and Hedgehog Pathways

(2012) Clémentine Ripoll et al.   PLoS One

Genome-Wide Expression Analysis in Down Syndrome: Insight into Immunodeficiency

(2012) Chong Li et al.   PLoS One

Deficit of complex I activity in human skin fibroblasts with chromosome 21 trisomy and overproduction of reactive oxygen species by mitochondria: involvement of the cAMP/PKA signalling pathway

(2011) Daniela Valenti et al.   BIOCHEMICAL JOURNAL

Mitochondrial dysfunction and Down's syndrome: Is there a role for coenzyme Q10?

(2011) Luca Tiano et al.   BIOFACTORS

MotifMap: integrative genome-wide maps of regulatory motif sites for model species

(2011) Kenneth Daily et al.   BMC BIOINFORMATICS

Down syndrome: searching for the genetic culprits

(2011) E. Lana-Elola et al.   Disease Models & Mechanisms

T Lymphocytes Apoptosis and Mitochondrial Membrane Potential in Down's Syndrome

(2011) Nagla Abu Faddan et al.   Fetal and Pediatric Pathology

D³ Data-Driven Documents

(2011) M. Bostock et al.   IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS

The DNA Data Bank of Japan launches a new resource, the DDBJ Omics Archive of functional genomics experiments

(2011) Y. Kodama et al.   NUCLEIC ACIDS RESEARCH

Saccharomyces Genome Database: the genomics resource of budding yeast

(2011) J. M. Cherry et al.   NUCLEIC ACIDS RESEARCH

International Cancer Genome Consortium Data Portal--a one-stop shop for cancer genomics data

(2011) J. Zhang et al.   Database-The Journal of Biological Databases and Curation

Structural Diversity of Mitochondria

(2010) Carmen A. Mannella   Annals of the New York Academy of Sciences

Impairment of F1F0-ATPase, adenine nucleotide translocator and adenylate kinase causes mitochondrial energy deficit in human skin fibroblasts with chromosome 21 trisomy

(2010) Daniela Valenti et al.   BIOCHEMICAL JOURNAL

Mitochondrial energy metabolism and ageing

(2010) Ivana Bratic et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments

(2010) H. Parkinson et al.   NUCLEIC ACIDS RESEARCH

Importing Mitochondrial Proteins: Machineries and Mechanisms

(2009) Agnieszka Chacinska et al.   CELL

HUMMR, a hypoxia- and HIF-1α–inducible protein, alters mitochondrial distribution and transport

(2009) Yan Li et al.   JOURNAL OF CELL BIOLOGY

The Mitochondrial Proteome: From Inventory to Function

(2008) Chris Meisinger et al.   CELL

A Mitochondrial Protein Compendium Elucidates Complex I Disease Biology

(2008) David J. Pagliarini et al.   CELL

Overexpression of Mitochondrial Methionine Sulfoxide Reductase B2 Protects Leukemia Cells from Oxidative Stress-induced Cell Death and Protein Damage

(2008) Filipe Cabreiro et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Gene expression variation increase in trisomy 21 tissues

(2008) Ching Yu Chou et al.   MAMMALIAN GENOME