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List of works by Martijn A Huynen

A Prioritized and Validated Resource of Mitochondrial Proteins in <i>Plasmodium</i> Identifies Unique Biology

scientific article published on 08 September 2021

A complex V ATP5A1 defect causes fatal neonatal mitochondrial encephalopathy

scientific article

A functional peptidyl-tRNA hydrolase, ICT1, has been recruited into the human mitochondrial ribosome

scientific article

A global definition of expression context is conserved between orthologs, but does not correlate with sequence conservation

scientific article

A homozygous FITM2 mutation causes a deafness-dystonia syndrome with motor regression and signs of ichthyosis and sensory neuropathy

scientific article published on 15 December 2016

A hydrogenosomal [Fe]-hydrogenase from the anaerobic chytrid Neocallimastix sp. L2.

scientific article published on February 2002

A mutation in C2orf64 causes impaired cytochrome c oxidase assembly and mitochondrial cardiomyopathy

scientific article

A mutation in the FAM36A gene, the human ortholog of COX20, impairs cytochrome c oxidase assembly and is associated with ataxia and muscle hypotonia.

scientific article published on 2 November 2012

A mutation in the human CBP4 ortholog UQCC3 impairs complex III assembly, activity and cytochrome b stability

scientific article

A three-dimensional topology of complex I inferred from evolutionary correlations.

scientific article

ATP6AP1 deficiency causes an immunodeficiency with hepatopathy, cognitive impairment and abnormal protein glycosylation

scientific article published on 27 May 2016

Acyl-CoA dehydrogenase 9 is required for the biogenesis of oxidative phosphorylation complex I

scientific article

An anaerobic mitochondrion that produces hydrogen

scientific article

An organelle-specific protein landscape identifies novel diseases and molecular mechanisms

scientific journal article

An siRNA-based functional genomics screen for the identification of regulators of ciliogenesis and ciliopathy genes ⬇️

scientific journal article

Analysis of genes regulated by the transcription factor LUMAN identifies ApoA4 as a target gene in dendritic cells.

scientific article

Asymmetric relationships between proteins shape genome evolution.

scientific article published on 12 February 2009

BCG-induced trained immunity enhances acellular pertussis vaccination responses in an explorative randomized clinical trial

scientific article published in 2022

BOLA1 is an aerobic protein that prevents mitochondrial morphology changes induced by glutathione depletion

scientific journal article

Base pairing probabilities in a complete HIV-1 RNA.

scientific article published in January 1996

Benchmarking ortholog identification methods using functional genomics data

scientific article

C7orf30 specifically associates with the large subunit of the mitochondrial ribosome and is involved in translation

scientific article

CATCHprofiles: clustering and alignment tool for ChIP profiles.

scientific article

CCDC115 Deficiency Causes a Disorder of Golgi Homeostasis with Abnormal Protein Glycosylation

scientific journal article

CEP89 is required for mitochondrial metabolism and neuronal function in man and fly.

scientific article published on 10 April 2013

COmplexome Profiling ALignment (COPAL) reveals remodeling of mitochondrial protein complexes in Barth syndrome

scientific article published on 01 September 2019

CTCF-mediated chromatin loops enclose inducible gene regulatory domains.

scientific article

Chromatin accessibility, p300, and histone acetylation define PML-RARα and AML1-ETO binding sites in acute myeloid leukemia

scientific article

CiliaCarta: An Integrated And Validated Compendium Of Ciliary Genes

article

CiliaCarta: An integrated and validated compendium of ciliary genes

scientific article published on 16 May 2019

Clustering of codons with rare cognate tRNAs in human genes suggests an extra level of expression regulation

scientific article published on 3 July 2009

Combinatorial gene regulation in Plasmodium falciparum

scientific article

Combining data from genomes, Y2H and 3D structure indicates that BolA is a reductase interacting with a glutaredoxin

scientific article

Comparative genomics for reliable protein-function prediction from genomic data

scientific article

Complex fate of paralogs

scientific article

Composition and stage dynamics of mitochondrial complexes in Plasmodium falciparum.

scientific article

Conservation of divergent transcription in fungi.

scientific article published on 28 March 2008

Conservation of gene co-regulation in prokaryotes and eukaryotes

article

Conserved co-expression for candidate disease gene prioritization

scientific article

Correction for Quainoo et al., "Whole-Genome Sequencing of Bacterial Pathogens: the Future of Nosocomial Outbreak Analysis".

scientific article published in November 2017

Correlation between sequence conservation and the genomic context after gene duplication

scientific article

Correlation between sequence conservation and the genomic context after gene duplication.

scientific article

Deciphering the evolution and metabolism of an anammox bacterium from a community genome

scientific article

Development of the first marmoset-specific DNA microarray (EUMAMA): a new genetic tool for large-scale expression profiling in a non-human primate

scientific article

Discovery of a HapE mutation that causes azole resistance in Aspergillus fumigatus through whole genome sequencing and sexual crossing

scientific article

Does mitochondrial DNA evolution in metazoa drive the origin of new mitochondrial proteins?

scientific article published on 03 October 2018

Dominant processes during human dendritic cell maturation revealed by integration of proteome and transcriptome at the pathway level

scientific article published in April 2010

Equal G and C contents in histone genes indicate selection pressures on mRNA secondary structure

scientific article published on April 1, 1992

Estimating Metabolic Fluxes Using a Maximum Network Flexibility Paradigm

scientific article published on 12 October 2015

Evidence for short-time divergence and long-time conservation of tissue-specific expression after gene duplication

scientific article published on 22 April 2011

Evolution and diversification of the organellar release factor family.

scientific article

Evolution and structural organization of the mitochondrial contact site (MICOS) complex and the mitochondrial intermembrane space bridging (MIB) complex.

scientific article published on 15 October 2015

Evolution of closely linked gene pairs in vertebrate genomes

scientific article published on 19 June 2008

Evolution of modular intraflagellar transport from a coatomer-like progenitor.

scientific article published on 8 April 2013

Evolutionary diversity of vertebrate small heat shock proteins.

scientific article published on December 2004

Expansion of the human mitochondrial proteome by intra- and inter-compartmental protein duplication

scientific article

Exploration of the omics evidence landscape: adding qualitative labels to predicted protein-protein interactions

scientific article

FACIL: Fast and Accurate Genetic Code Inference and Logo

scientific article

Fifteen years of research on oral-facial-digital syndromes: from 1 to 16 causal genes ⬇️

scientific article published on 13 March 2017

Formation of peroxisomes: present and past.

scientific article published on 3 September 2006

From endosymbiont to host-controlled organelle: the hijacking of mitochondrial protein synthesis and metabolism

scientific article

Function prediction and protein networks

scientific article

Gene co-regulation is highly conserved in the evolution of eukaryotes and prokaryotes

scientific article

Genome evolution predicts genetic interactions in protein complexes and reveals cancer drug targets.

scientific article published on January 2013

Genome phylogeny based on gene content

scientific article (publication date: 1999)

Genome trees and the nature of genome evolution

scientific article

Genome-scale detection of positive selection in nine primates predicts human-virus evolutionary conflicts

scientific article published on 11 August 2017

Genome-wide analysis in Escherichia coli unravels a high level of genetic homoplasy associated with cefotaxime resistance

scientific article published in 2021

Genome-wide profiling of p63 DNA-binding sites identifies an element that regulates gene expression during limb development in the 7q21 SHFM1 locus.

scientific article

Genomes in Flux: The Evolution of Archaeal and Proteobacterial Gene Content

article

Haemophilus is overrepresented in the nasopharynx of infants hospitalized with RSV infection and associated with increased viral load and enhanced mucosal CXCL8 responses.

scientific article published on 11 January 2018

Heterochromatic histone modifications at transposons in Xenopus tropicalis embryos

scientific article

Horizontal gene transfer from Bacteria to rumen Ciliates indicates adaptation to their anaerobic, carbohydrates-rich environment

scientific article published on 10 February 2006

Human intellectual disability genes form conserved functional modules in Drosophila.

scientific article

Identification and evolutionary analysis of tissue-specific isoforms of mitochondrial complex I subunit NDUFV3.

scientific article published on 14 December 2016

Identification and functional verification of archaeal-type phosphoenolpyruvate carboxylase, a missing link in archaeal central carbohydrate metabolism

scientific article

Identification of Nipsnap1 as a novel auxiliary protein inhibiting TRPV6 activity.

scientific article

Immunologic defects in severe mucocutaneous HSV-2 infections: Response to IFN-γ therapy

scientific article published on 7 April 2016

Inferring metabolic states in uncharacterized environments using gene-expression measurements

scientific article

Integrative Genomics-Based Discovery of Novel Regulators of the Innate Antiviral Response

scientific article published on 20 October 2015

Interspecies differences in PTH-mediated PKA phosphorylation of the epithelial calcium channel TRPV5.

scientific article published on 22 May 2017

Intrinsically disordered segments affect protein half-life in the cell and during evolution

scientific article

Iterative orthology prediction uncovers new mitochondrial proteins and identifies C12orf62 as the human ortholog of COX14, a protein involved in the assembly of cytochrome c oxidase

scientific article

KIAA0556 is a novel ciliary basal body component mutated in Joubert syndrome

scientific article

Lineage-specific gene loss following mitochondrial endosymbiosis and its potential for function prediction in eukaryotes

scientific article published in September 2005

Loss, replacement and gain of proteins at the origin of the mitochondria.

scientific article

MPV17L2 is required for ribosome assembly in mitochondria

scientific article

Macronuclear genome structure of the ciliate Nyctotherus ovalis: single-gene chromosomes and tiny introns

scientific article

Measuring genome evolution

scientific article (publication date: 26 May 1998)

Measuring the physical cohesiveness of proteins using physical interaction enrichment.

scientific article

MicroRNA genes preferentially expressed in dendritic cells contain sites for conserved transcription factor binding motifs in their promoters.

scientific article

Mitochondria, hydrogenosomes and mitosomes: products of evolutionary tinkering!

scientific article published on 9 August 2006

Mitochondrial proteome evolution and genetic disease.

scientific article published on 26 March 2009

Modest heterologous protection after Plasmodium falciparum sporozoite immunization: a double-blind randomized controlled clinical trial

scientific article published on 13 September 2017

Molecular and biochemical analysis of the plastidic ADP-glucose transporter (ZmBT1) from Zea mays.

scientific article published on 11 June 2007

Molecular characterization of phosphoglycerate mutase in archaea

scientific article

Monoclonal antibodies block transmission of genetically diverse Plasmodium falciparum strains to mosquitoes

publication published on 12 August 2021

Mosaic origin of the mitochondrial proteome

scientific article

Multiple coding and the evolutionary properties of RNA secondary structure.

scientific article published in November 1993

Multiple origins of hydrogenosomes: functional and phylogenetic evidence from the ADP/ATP carrier of the anaerobic chytrid Neocallimastix sp.

scientific article

Mutations in NDUFAF3 (C3ORF60), encoding an NDUFAF4 (C6ORF66)-interacting complex I assembly protein, cause fatal neonatal mitochondrial disease

scientific article

Mutations in the UQCC1-interacting protein, UQCC2, cause human complex III deficiency associated with perturbed cytochrome b protein expression

scientific article

NDUFB7 and NDUFA8 are located at the intermembrane surface of complex I

scientific article

Novel insights from the Plasmodium falciparum sporozoite-specific proteome by probabilistic integration of 26 studies

scientific article published on 30 April 2021

ODoSE: a webserver for genome-wide calculation of adaptive divergence in prokaryotes

scientific article

OFIP/KIAA0753 forms a complex with OFD1 and FOR20 at pericentriolar satellites and centrosomes and is mutated in one individual with oral-facial-digital syndrome.

scientific article published on 7 December 2015

Optimized design and assessment of whole genome tiling arrays.

scientific article published on July 2007

Origin and evolution of the peroxisomal proteome

scientific article

Orthology prediction at scalable resolution by phylogenetic tree analysis

scientific article

POMT2 mutations cause alpha-dystroglycan hypoglycosylation and Walker-Warburg syndrome

scientific article

Phenome connections

scientific article published on 19 February 2008

Practical and theoretical advances in predicting the function of a protein by its phylogenetic distribution ⬇️

scientific article published on February 2008

Predicting disease genes using protein-protein interactions.

scientific article published on 12 April 2006

Predicting human genetic interactions from cancer genome evolution

scientific article

Prediction of protein function and pathways in the genome era.

scientific article

Prior exposure to B. pertussis shapes the mucosal antibody response to acellular pertussis booster vaccination

scientific article published in 2022

Probabilistic data integration identifies reliable gametocyte-specific proteins and transcripts in malaria parasites

scientific article published on 11 January 2018

Probabilistic data integration identifies reliable gametocyte-specific proteins and transcripts in malaria parasites

scholarly article published 10 October 2017

Prokaryotic diversity of the Saccharomyces cerevisiae Atx1p-mediated copper pathway

scientific article published on 14 May 2004

Proteomic profiling of Plasmodium sporozoite maturation identifies new proteins essential for parasite development and infectivity

scientific article

Proteomics of Human Dendritic Cell Subsets Reveals Subset-Specific Surface Markers and Differential Inflammasome Function

scientific article

Quantifying modularity in the evolution of biomolecular systems

scientific article published on March 2004

Quantitative proteome profiling of respiratory virus-infected lung epithelial cells

scientific article

Rate of killing of HIV-infected T cells and disease progression

scientific article published on 01 June 1996

Reconstructing the evolution of the mitochondrial ribosomal proteome.

scientific article published on 29 June 2007

Reconstruction of the proto-mitochondrial metabolism

scientific article (publication date: August 2003)

Regulatory remodeling in the allo-tetraploid frog Xenopus laevis

scientific article published on 24 October 2017

Restoration of complex V deficiency caused by a novel deletion in the human TMEM70 gene normalizes mitochondrial morphology

article

SHOT: a web server for the construction of genome phylogenies

scientific article published on 01 March 2002

STRING: a database of predicted functional associations between proteins

scientific article

STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene

scientific article

STRING: known and predicted protein-protein associations, integrated and transferred across organisms

scientific article

Sequence specificity between interacting and non-interacting homologs identifies interface residues--a homodimer and monomer use case

scientific article

Shaping the mitochondrial proteome

scientific article

Signature genes as a phylogenomic tool

scientific article (publication date: August 2008)

Signature, a web server for taxonomic characterization of sequence samples using signature genes.

scientific article published on 17 May 2008

Skeletal muscle mitochondria of NDUFS4-/- mice display normal maximal pyruvate oxidation and ATP production

scientific article published on 14 February 2015

Smoothness within ruggedness: the role of neutrality in adaptation.

scientific article

Structure based hypothesis of a mitochondrial ribosome rescue mechanism

scientific article

Systematic Phenomics Analysis Deconvolutes Genes Mutated in Intellectual Disability into Biologically Coherent Modules.

scientific article

TEFM (c17orf42) is necessary for transcription of human mtDNA

scientific article

TMEM107 recruits ciliopathy proteins to subdomains of the ciliary transition zone and causes Joubert syndrome ⬇️

scientific journal article

TMEM199 Deficiency Is a Disorder of Golgi Homeostasis Characterized by Elevated Aminotransferases, Alkaline Phosphatase, and Cholesterol and Abnormal Glycosylation

scientific journal article

TRASH: a novel metal-binding domain predicted to be involved in heavy-metal sensing, trafficking and resistance

scientific article published on 01 April 2003

The Eukaryotic-Specific ISD11 Is a Complex-Orphan Protein with Ability to Bind the Prokaryotic IscS

scientific article

The Gene Ontology of eukaryotic cilia and flagella

scientific article published on 16 November 2017

The PinkThing for analysing ChIP profiling data in their genomic context

scientific article

The RIG-I-like helicase receptor MDA5 (IFIH1) is involved in the host defense against Candida infections

scientific article published on 13 January 2015

The SYSCILIA gold standard (SCGSv1) of known ciliary components and its applications within a systems biology consortium

scientific article published on 31 May 2013

The [FeFe] hydrogenase of Nyctotherus ovalis has a chimeric origin

scientific article

The alpha-kinase family: an exceptional branch on the protein kinase tree.

scientific article published on 12 December 2009

The consistent phylogenetic signal in genome trees revealed by reducing the impact of noise

scientific article published in May 2004

The hydrogenosomes of Psalteriomonas lanterna

scientific article published in 2009

The identification of functional modules from the genomic association of genes

scientific article

The iron-sulphur protein Ind1 is required for effective complex I assembly

scientific article published on 22 May 2008

The mitochondrial genomes of the ciliates Euplotes minuta and Euplotes crassus

scientific article

The organellar genome and metabolic potential of the hydrogen-producing mitochondrion of Nyctotherus ovalis.

scientific article

The origin of the supernumerary subunits and assembly factors of complex I: A treasure trove of pathway evolution.

scientific article published on 2 April 2016

The phosphoglucose isomerase from the hyperthermophilic archaeon Pyrococcus furiosus is a unique glycolytic enzyme that belongs to the cupin superfamily.

scientific article published on 30 August 2001

The phylogenetic distribution of frataxin indicates a role in iron-sulfur cluster protein assembly

scientific article published on 01 October 2001

The properties of protein family space depend on experimental design

scientific article

The pros and cons of vertebrate animal models for functional and therapeutic research on inherited retinal dystrophies

scientific article published on 30 April 2015

The symbiotic intestinal ciliates and the evolution of their hosts

scientific article

The yeast coexpression network has a small-world, scale-free architecture and can be explained by a simple model

scientific article

Tracing the evolution of a large protein complex in the eukaryotes, NADH:ubiquinone oxidoreductase (Complex I).

scientific article

Transcriptome analysis of complex I-deficient patients reveals distinct expression programs for subunits and assembly factors of the oxidative phosphorylation system

scientific article published on 15 September 2015

Variation and evolution of biomolecular systems: searching for functional relevance

scientific article

Variation and evolution of the citric-acid cycle: a genomic perspective.

scientific article

WeGET: predicting new genes for molecular systems by weighted co-expression.

scientific article

Whole-Genome Sequencing of Bacterial Pathogens: the Future of Nosocomial Outbreak Analysis

scientific article published on October 2017

YfhJ, a Molecular Adaptor in Iron-Sulfur Cluster Formation or a Frataxin-like Protein?

scientific article published on 01 May 2006

genetically interacts with the ALS-associated orthologue and mediates its toxicity

article

optGpSampler: an improved tool for uniformly sampling the solution-space of genome-scale metabolic networks

scientific article

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