| Year |
Citation |
Score |
| 2023 |
Lezcano OM, Fuhrmann L, Ramakrishnan G, Beerenwinkel N, Huynen MA, van Rij RP. Parallel evolution and enhanced virulence upon passage of an RNA virus in . Virus Evolution. 9: vead074. PMID 38162315 DOI: 10.1093/ve/vead074 |
0.583 |
|
| 2023 |
Ramakrishnan G, Baakman C, Heijl S, Vroling B, van Horck R, Hiraki J, Xue LC, Huynen MA. Understanding structure-guided variant effect predictions using 3D convolutional neural networks. Frontiers in Molecular Biosciences. 10: 1204157. PMID 37475887 DOI: 10.3389/fmolb.2023.1204157 |
0.592 |
|
| 2022 |
Garza DR, von Meijenfeldt FAB, van Dijk B, Boleij A, Huynen MA, Dutilh BE. Nutrition or nature: using elementary flux modes to disentangle the complex forces shaping prokaryote pan-genomes. Bmc Ecology and Evolution. 22: 101. PMID 35974327 DOI: 10.1186/s12862-022-02052-3 |
0.398 |
|
| 2020 |
Sánchez-Caballero L, Elurbe DM, Baertling F, Guerrero-Castillo S, van den Brand M, van Strien J, van Dam TJP, Rodenburg R, Brandt U, Huynen MA, Nijtmans LGJ. TMEM70 functions in the assembly of complexes I and V. Biochimica Et Biophysica Acta. Bioenergetics. 148202. PMID 32275929 DOI: 10.1016/J.Bbabio.2020.148202 |
0.334 |
|
| 2020 |
Cremers AJH, Coolen JPM, Bleeker-Rovers CP, van der Geest-Blankert ADJ, Haverkate D, Hendriks H, Henriet SSV, Huynen MA, Kolwijck E, Liem D, Melchers WJG, Rossen JW, Zoll J, van Heijst A, Hopman J, et al. Surveillance-embedded genomic outbreak resolution of methicillin-susceptible Staphylococcus aureus in a neonatal intensive care unit. Scientific Reports. 10: 2619. PMID 32060342 DOI: 10.1038/S41598-020-59015-1 |
0.335 |
|
| 2020 |
Garza DR, Taddese R, Wirbel J, Zeller G, Boleij A, Huynen MA, Dutilh BE. Metabolic models predict bacterial passengers in colorectal cancer. Cancer & Metabolism. 8: 3. PMID 32055399 DOI: 10.1186/S40170-020-0208-9 |
0.501 |
|
| 2019 |
van Esveld SL, Cansız-Arda Ş, Hensen F, van der Lee R, Huynen MA, Spelbrink JN. A Combined Mass Spectrometry and Data Integration Approach to Predict the Mitochondrial Poly(A) RNA Interacting Proteome. Frontiers in Cell and Developmental Biology. 7: 283. PMID 31803741 DOI: 10.3389/Fcell.2019.00283 |
0.347 |
|
| 2019 |
Lenting K, van den Heuvel CNAM, van Ewijk A, ElMelik D, de Boer R, Tindall E, Wei G, Kusters B, Te Dorsthorst M, Ter Laan M, Huynen MA, Leenders WP. Mapping actionable pathways and mutations in brain tumours using targeted RNA next generation sequencing. Acta Neuropathologica Communications. 7: 185. PMID 31747973 DOI: 10.1186/S40478-019-0826-Z |
0.313 |
|
| 2019 |
van Dam TJP, Kennedy J, van der Lee R, de Vrieze E, Wunderlich KA, Rix S, Dougherty GW, Lambacher NJ, Li C, Jensen VL, Leroux MR, Hjeij R, Horn N, Texier Y, Wissinger Y, ... ... Huynen MA, et al. CiliaCarta: An integrated and validated compendium of ciliary genes. Plos One. 14: e0216705. PMID 31095607 DOI: 10.1371/Journal.Pone.0216705 |
0.553 |
|
| 2019 |
Dirks RAM, van Mierlo G, Kerstens HHD, Bernardo AS, Kobolák J, Bock I, Maruotti J, Pedersen RA, Dinnyés A, Huynen MA, Jouneau A, Marks H. Allele-specific RNA-seq expression profiling of imprinted genes in mouse isogenic pluripotent states. Epigenetics & Chromatin. 12: 14. PMID 30767785 DOI: 10.1186/S13072-019-0259-8 |
0.36 |
|
| 2019 |
Van Strien J, Guerrero-Castillo S, Chatzispyrou IA, Houtkooper RH, Brandt U, Huynen MA. COmplexome Profiling ALignment (COPAL) reveals remodeling of mitochondrial protein complexes in Barth syndrome. Bioinformatics (Oxford, England). PMID 30649188 DOI: 10.1093/Bioinformatics/Btz025 |
0.304 |
|
| 2018 |
Joosten J, Miesen P, Tasköprü E, Pennings B, Jansen PW, Huynen MA, Vermeulen M, Van Rij RP. The Tudor protein Veneno assembles the ping-pong amplification complex that produces viral piRNAs in Aedes mosquitoes. Nucleic Acids Research. PMID 30566680 DOI: 10.1093/Nar/Gky1266 |
0.393 |
|
| 2018 |
Ligas J, Pineau E, Bock R, Huynen MA, Meyer EH. The assembly pathway of Complex I in Arabidopsis thaliana. The Plant Journal : For Cell and Molecular Biology. PMID 30347487 DOI: 10.1111/Tpj.14133 |
0.308 |
|
| 2018 |
van Esveld SL, Huynen MA. Does mitochondrial DNA evolution in metazoa drive the origin of new mitochondrial proteins? Iubmb Life. 70: 1240-1250. PMID 30281911 DOI: 10.1002/Iub.1940 |
0.395 |
|
| 2018 |
Mallik M, Catinozzi M, Hug CB, Zhang L, Wagner M, Bussmann J, Bittern J, Mersmann S, Klämbt C, Drexler HCA, Huynen MA, Vaquerizas JM, Storkebaum E. genetically interacts with the ALS-associated orthologue and mediates its toxicity. The Journal of Cell Biology. PMID 30209068 DOI: 10.1083/Jcb.201802151 |
0.331 |
|
| 2018 |
Bernardo AS, Jouneau A, Marks H, Kensche P, Kobolak J, Freude K, Hall V, Feher A, Polgar Z, Sartori C, Bock I, Louet C, Faial T, Kerstens HHD, Bouissou C, ... ... Huynen M, et al. Mammalian embryo comparison identifies novel pluripotency genes associated with the naïve or primed state. Biology Open. PMID 30026265 DOI: 10.1242/Bio.033282 |
0.398 |
|
| 2018 |
Wesdorp M, de Koning Gans PAM, Schraders M, Oostrik J, Huynen MA, Venselaar H, Beynon AJ, van Gaalen J, Piai V, Voermans N, van Rossum MM, Hartel BP, Lelieveld SH, Wiel L, Verbist B, et al. Heterozygous missense variants of LMX1A lead to nonsyndromic hearing impairment and vestibular dysfunction. Human Genetics. PMID 29754270 DOI: 10.1007/S00439-018-1880-5 |
0.313 |
|
| 2018 |
Garza DR, van Verk MC, Huynen MA, Dutilh BE. Towards predicting the environmental metabolome from metagenomics with a mechanistic model. Nature Microbiology. PMID 29531366 DOI: 10.1038/S41564-018-0124-8 |
0.407 |
|
| 2018 |
Meerstein-Kessel L, van der Lee R, Stone W, Lanke K, Baker DA, Alano P, Silvestrini F, Janse CJ, Khan SM, van de Vegte-Bolmer M, Graumans W, Siebelink-Stoter R, Kooij TWA, Marti M, Drakeley C, ... ... Huynen MA, et al. Probabilistic data integration identifies reliable gametocyte-specific proteins and transcripts in malaria parasites. Scientific Reports. 8: 410. PMID 29323249 DOI: 10.1038/S41598-017-18840-7 |
0.371 |
|
| 2018 |
Quainoo S, Coolen JPM, van Hijum SAFT, Huynen MA, Melchers WJG, van Schaik W, Wertheim HFL. Correction for Quainoo et al., "Whole-Genome Sequencing of Bacterial Pathogens: the Future of Nosocomial Outbreak Analysis". Clinical Microbiology Reviews. 31. PMID 29092893 DOI: 10.1128/Cmr.00082-17 |
0.304 |
|
| 2017 |
Roncaglia P, van Dam TJP, Christie KR, Nacheva L, Toedt G, Huynen MA, Huntley RP, Gibson TJ, Lomax J. The Gene Ontology of eukaryotic cilia and flagella. Cilia. 6: 10. PMID 29177046 DOI: 10.1186/S13630-017-0054-8 |
0.36 |
|
| 2017 |
Elurbe DM, Paranjpe SS, Georgiou G, van Kruijsbergen I, Bogdanovic O, Gibeaux R, Heald R, Lister R, Huynen MA, van Heeringen SJ, Veenstra GJC. Regulatory remodeling in the allo-tetraploid frog Xenopus laevis. Genome Biology. 18: 198. PMID 29065907 DOI: 10.1186/S13059-017-1335-7 |
0.507 |
|
| 2017 |
van der Lee R, Wiel L, van Dam TJP, Huynen MA. Genome-scale detection of positive selection in nine primates predicts human-virus evolutionary conflicts. Nucleic Acids Research. PMID 28977405 DOI: 10.1093/Nar/Gkx704 |
0.416 |
|
| 2017 |
Quainoo S, Coolen JPM, van Hijum SAFT, Huynen MA, Melchers WJG, van Schaik W, Wertheim HFL. Whole-Genome Sequencing of Bacterial Pathogens: the Future of Nosocomial Outbreak Analysis. Clinical Microbiology Reviews. 30: 1015-1063. PMID 28855266 DOI: 10.1128/Cmr.00016-17 |
0.348 |
|
| 2017 |
Bruel AL, Franco B, Duffourd Y, Thevenon J, Jego L, Lopez E, Deleuze JF, Doummar D, Giles RH, Johnson CA, Huynen MA, Chevrier V, Burglen L, Morleo M, Desguerres I, et al. Fifteen years of research on oral-facial-digital syndromes: from 1 to 16 causal genes. Journal of Medical Genetics. PMID 28289185 DOI: 10.1136/Jmedgenet-2016-104436 |
0.424 |
|
| 2016 |
Guerrero-Castillo S, Cabrera-Orefice A, Huynen MA, Arnold S. Identification and evolutionary analysis of tissue-specific isoforms of mitochondrial complex I subunit NDUFV3. Biochimica Et Biophysica Acta. PMID 27988283 DOI: 10.1016/J.Bbabio.2016.12.004 |
0.311 |
|
| 2016 |
van Kruijsbergen I, Hontelez S, Elurbe DM, van Heeringen SJ, Huynen MA, Veenstra GJ. Heterochromatic histone modifications at transposons in Xenopus tropicalis embryos. Developmental Biology. PMID 27639284 DOI: 10.1016/J.Ydbio.2016.08.031 |
0.355 |
|
| 2016 |
Worah K, Mathan TS, Vu Manh TP, Keerthikumar S, Schreibelt G, Tel J, Duiveman-de Boer T, Sköld AE, van Spriel AB, de Vries IJ, Huynen MA, Wessels HJ, Gloerich J, Dalod M, Lasonder E, et al. Proteomics of Human Dendritic Cell Subsets Reveals Subset-Specific Surface Markers and Differential Inflammasome Function. Cell Reports. 16: 2953-66. PMID 27626665 DOI: 10.1016/J.Celrep.2016.08.023 |
0.307 |
|
| 2016 |
Yan R, Friemel M, Aloisi C, Huynen M, Taylor IA, Leimkühler S, Pastore A. The Eukaryotic-Specific ISD11 Is a Complex-Orphan Protein with Ability to Bind the Prokaryotic IscS. Plos One. 11: e0157895. PMID 27427956 DOI: 10.1371/Journal.Pone.0157895 |
0.343 |
|
| 2016 |
Jansen EJ, Timal S, Ryan M, Ashikov A, van Scherpenzeel M, Graham LA, Mandel H, Hoischen A, Iancu TC, Raymond K, Steenbergen G, Gilissen C, Huijben K, van Bakel NH, Maeda Y, ... ... Huynen MA, et al. ATP6AP1 deficiency causes an immunodeficiency with hepatopathy, cognitive impairment and abnormal protein glycosylation. Nature Communications. 7: 11600. PMID 27231034 DOI: 10.1038/Ncomms11600 |
0.31 |
|
| 2016 |
Elurbe DM, Huynen MA. The origin of the supernumerary subunits and assembly factors of complex I: A treasure trove of pathway evolution. Biochimica Et Biophysica Acta. PMID 27048931 DOI: 10.1016/J.Bbabio.2016.03.027 |
0.36 |
|
| 2016 |
Oti M, Falck J, Huynen MA, Zhou H. CTCF-mediated chromatin loops enclose inducible gene regulatory domains. Bmc Genomics. 17: 252. PMID 27004515 DOI: 10.1186/S12864-016-2516-6 |
0.437 |
|
| 2016 |
Jansen JC, Cirak S, van Scherpenzeel M, Timal S, Reunert J, Rust S, Pérez B, Vicogne D, Krawitz P, Wada Y, Ashikov A, Pérez-Cerdá C, Medrano C, Arnoldy A, Hoischen A, ... ... Huynen MA, et al. CCDC115 Deficiency Causes a Disorder of Golgi Homeostasis with Abnormal Protein Glycosylation. American Journal of Human Genetics. PMID 26833332 DOI: 10.1016/J.Ajhg.2015.12.010 |
0.307 |
|
| 2016 |
Jansen JC, Timal S, van Scherpenzeel M, Michelakakis H, Vicogne D, Ashikov A, Moraitou M, Hoischen A, Huijben K, Steenbergen G, van den Boogert MA, Porta F, Calvo PL, Mavrikou M, Cenacchi G, ... ... Huynen MA, et al. TMEM199 Deficiency Is a Disorder of Golgi Homeostasis Characterized by Elevated Aminotransferases, Alkaline Phosphatase, and Cholesterol and Abnormal Glycosylation. American Journal of Human Genetics. PMID 26833330 DOI: 10.1016/J.Ajhg.2015.12.011 |
0.332 |
|
| 2016 |
Kochinke K, Zweier C, Nijhof B, Fenckova M, Cizek P, Honti F, Keerthikumar S, Oortveld MA, Kleefstra T, Kramer JM, Webber C, Huynen MA, Schenck A. Systematic Phenomics Analysis Deconvolutes Genes Mutated in Intellectual Disability into Biologically Coherent Modules. American Journal of Human Genetics. 98: 149-64. PMID 26748517 DOI: 10.1016/J.Ajhg.2015.11.024 |
0.363 |
|
| 2016 |
Roncaglia P, Dam TJPv, Christie KR, Nacheva L, Huynen MA, Huntley RP, Gibson T, Lomax J. Towards the gene ontology of the eukaryotic cilia and flagella F1000research. 5. DOI: 10.7490/F1000Research.1113234.1 |
0.453 |
|
| 2015 |
Lambacher NJ, Bruel AL, van Dam TJ, Szymańska K, Slaats GG, Kuhns S, McManus GJ, Kennedy JE, Gaff K, Wu KM, van der Lee R, Burglen L, Doummar D, Rivière JB, Faivre L, ... ... Huynen MA, et al. TMEM107 recruits ciliopathy proteins to subdomains of the ciliary transition zone and causes Joubert syndrome. Nature Cell Biology. PMID 26595381 DOI: 10.1038/Ncb3273 |
0.343 |
|
| 2015 |
Szklarczyk R, Megchelenbrink W, Cizek P, Ledent M, Velemans G, Szklarczyk D, Huynen MA. WeGET: predicting new genes for molecular systems by weighted co-expression. Nucleic Acids Research. PMID 26582928 DOI: 10.1093/Nar/Gkv1228 |
0.441 |
|
| 2015 |
van der Lee R, Feng Q, Langereis MA, Ter Horst R, Szklarczyk R, Netea MG, Andeweg AC, van Kuppeveld FJ, Huynen MA. Integrative Genomics-Based Discovery of Novel Regulators of the Innate Antiviral Response. Plos Computational Biology. 11: e1004553. PMID 26485378 DOI: 10.1371/Journal.Pcbi.1004553 |
0.484 |
|
| 2015 |
Huynen MA, Mühlmeister M, Gotthardt K, Guerrero-Castillo S, Brandt U. Evolution and structural organization of the mitochondrial contact site (MICOS) complex and the mitochondrial intermembrane space bridging (MIB) complex. Biochimica Et Biophysica Acta. 1863: 91-101. PMID 26477565 DOI: 10.1016/J.Bbamcr.2015.10.009 |
0.418 |
|
| 2015 |
Megchelenbrink W, Rossell S, Huynen MA, Notebaart RA, Marchiori E. Estimating Metabolic Fluxes Using a Maximum Network Flexibility Paradigm. Plos One. 10: e0139665. PMID 26457579 DOI: 10.1371/Journal.Pone.0139665 |
0.326 |
|
| 2015 |
Hou Q, Dutilh BE, Huynen MA, Heringa J, Feenstra KA. Sequence specificity between interacting and non-interacting homologs identifies interface residues - a homodimer and monomer use case. Bmc Bioinformatics. 16: 325. PMID 26449222 DOI: 10.1186/S12859-015-0758-Y |
0.378 |
|
| 2015 |
van der Lee R, Szklarczyk R, Smeitink J, Smeets HJ, Huynen MA, Vogel R. Transcriptome analysis of complex I-deficient patients reveals distinct expression programs for subunits and assembly factors of the oxidative phosphorylation system. Bmc Genomics. 16: 691. PMID 26369791 DOI: 10.1186/S12864-015-1883-8 |
0.415 |
|
| 2015 |
Wheway G, Schmidts M, Mans DA, Szymanska K, Nguyen TT, Racher H, Phelps IG, Toedt G, Kennedy J, Wunderlich KA, Sorusch N, Abdelhamed ZA, Natarajan S, Herridge W, van Reeuwijk J, ... ... Huynen MA, et al. An siRNA-based functional genomics screen for the identification of regulators of ciliogenesis and ciliopathy genes. Nature Cell Biology. PMID 26167768 DOI: 10.1038/Ncb3201 |
0.395 |
|
| 2015 |
Slijkerman RW, Song F, Astuti GD, Huynen MA, van Wijk E, Stieger K, Collin RW. The pros and cons of vertebrate animal models for functional and therapeutic research on inherited retinal dystrophies. Progress in Retinal and Eye Research. PMID 25936606 DOI: 10.1016/J.Preteyeres.2015.04.004 |
0.343 |
|
| 2015 |
Lu X, Megchelenbrink W, Notebaart RA, Huynen MA. Predicting human genetic interactions from cancer genome evolution. Plos One. 10: e0125795. PMID 25933428 DOI: 10.1371/Journal.Pone.0125795 |
0.476 |
|
| 2014 |
van der Lee R, Lang B, Kruse K, Gsponer J, Sánchez de Groot N, Huynen MA, Matouschek A, Fuxreiter M, Babu MM. Intrinsically disordered segments affect protein half-life in the cell and during evolution. Cell Reports. 8: 1832-44. PMID 25220455 DOI: 10.1016/J.Celrep.2014.07.055 |
0.338 |
|
| 2014 |
Wanschers BF, Szklarczyk R, van den Brand MA, Jonckheere A, Suijskens J, Smeets R, Rodenburg RJ, Stephan K, Helland IB, Elkamil A, Rootwelt T, Ott M, van den Heuvel L, Nijtmans LG, Huynen MA. A mutation in the human CBP4 ortholog UQCC3 impairs complex III assembly, activity and cytochrome b stability. Human Molecular Genetics. 23: 6356-65. PMID 25008109 DOI: 10.1093/Hmg/Ddu357 |
0.31 |
|
| 2014 |
Dalla Rosa I, Durigon R, Pearce SF, Rorbach J, Hirst EM, Vidoni S, Reyes A, Brea-Calvo G, Minczuk M, Woellhaf MW, Herrmann JM, Huynen MA, Holt IJ, Spinazzola A. MPV17L2 is required for ribosome assembly in mitochondria. Nucleic Acids Research. 42: 8500-15. PMID 24948607 DOI: 10.1093/Nar/Gku513 |
0.302 |
|
| 2014 |
Moon-van der Staay SY, van der Staay GW, Michalowski T, Jouany JP, Pristas P, Javorský P, Kišidayová S, Varadyova Z, McEwan NR, Newbold CJ, van Alen T, de Graaf R, Schmid M, Huynen MA, Hackstein JH. The symbiotic intestinal ciliates and the evolution of their hosts. European Journal of Protistology. 50: 166-73. PMID 24703617 DOI: 10.1016/J.Ejop.2014.01.004 |
0.335 |
|
| 2013 |
Tucker EJ, Wanschers BF, Szklarczyk R, Mountford HS, Wijeyeratne XW, van den Brand MA, Leenders AM, Rodenburg RJ, Reljić B, Compton AG, Frazier AE, Bruno DL, Christodoulou J, Endo H, Ryan MT, ... ... Huynen MA, et al. Mutations in the UQCC1-interacting protein, UQCC2, cause human complex III deficiency associated with perturbed cytochrome b protein expression. Plos Genetics. 9: e1004034. PMID 24385928 DOI: 10.1371/Journal.Pgen.1004034 |
0.328 |
|
| 2013 |
Oortveld MA, Keerthikumar S, Oti M, Nijhof B, Fernandes AC, Kochinke K, Castells-Nobau A, van Engelen E, Ellenkamp T, Eshuis L, Galy A, van Bokhoven H, Habermann B, Brunner HG, Zweier C, ... ... Huynen MA, et al. Human intellectual disability genes form conserved functional modules in Drosophila. Plos Genetics. 9: e1003911. PMID 24204314 DOI: 10.1371/Journal.Pgen.1003911 |
0.441 |
|
| 2013 |
Lu X, Kensche PR, Huynen MA, Notebaart RA. Genome evolution predicts genetic interactions in protein complexes and reveals cancer drug targets. Nature Communications. 4: 2124. PMID 23851603 DOI: 10.1038/Ncomms3124 |
0.402 |
|
| 2013 |
Vos M, te Beek TA, van Driel MA, Huynen MA, Eyre-Walker A, van Passel MW. ODoSE: a webserver for genome-wide calculation of adaptive divergence in prokaryotes. Plos One. 8: e62447. PMID 23671597 DOI: 10.1371/Journal.Pone.0062447 |
0.411 |
|
| 2013 |
Jonckheere AI, Renkema GH, Bras M, van den Heuvel LP, Hoischen A, Gilissen C, Nabuurs SB, Huynen MA, de Vries MC, Smeitink JA, Rodenburg RJ. A complex V ATP5A1 defect causes fatal neonatal mitochondrial encephalopathy. Brain : a Journal of Neurology. 136: 1544-54. PMID 23599390 DOI: 10.1093/Brain/Awt086 |
0.375 |
|
| 2013 |
van Bon BW, Oortveld MA, Nijtmans LG, Fenckova M, Nijhof B, Besseling J, Vos M, Kramer JM, de Leeuw N, Castells-Nobau A, Asztalos L, Viragh E, Ruiter M, Hofmann F, Eshuis L, ... ... Huynen MA, et al. CEP89 is required for mitochondrial metabolism and neuronal function in man and fly. Human Molecular Genetics. 22: 3138-51. PMID 23575228 DOI: 10.1093/Hmg/Ddt170 |
0.34 |
|
| 2013 |
van Dam TJ, Townsend MJ, Turk M, Schlessinger A, Sali A, Field MC, Huynen MA. Evolution of modular intraflagellar transport from a coatomer-like progenitor. Proceedings of the National Academy of Sciences of the United States of America. 110: 6943-8. PMID 23569277 DOI: 10.1073/Pnas.1221011110 |
0.302 |
|
| 2013 |
Nielsen FG, Kooyman M, Kensche P, Marks H, Stunnenberg H, Huynen M. The PinkThing for analysing ChIP profiling data in their genomic context Bmc Research Notes. 6. PMID 23557140 DOI: 10.1186/1756-0500-6-133 |
0.41 |
|
| 2013 |
Rossell S, Huynen MA, Notebaart RA. Inferring metabolic states in uncharacterized environments using gene-expression measurements. Plos Computational Biology. 9: e1002988. PMID 23555222 DOI: 10.1371/Journal.Pcbi.1002988 |
0.362 |
|
| 2013 |
Szklarczyk R, Wanschers BF, Nijtmans LG, Rodenburg RJ, Zschocke J, Dikow N, van den Brand MA, Hendriks-Franssen MG, Gilissen C, Veltman JA, Nooteboom M, Koopman WJ, Willems PH, Smeitink JA, Huynen MA, et al. A mutation in the FAM36A gene, the human ortholog of COX20, impairs cytochrome c oxidase assembly and is associated with ataxia and muscle hypotonia. Human Molecular Genetics. 22: 656-67. PMID 23125284 DOI: 10.1093/Hmg/Dds473 |
0.375 |
|
| 2013 |
Huynen MA, Duarte I, Szklarczyk R. Loss, replacement and gain of proteins at the origin of the mitochondria. Biochimica Et Biophysica Acta. 1827: 224-31. PMID 22902511 DOI: 10.1016/J.Bbabio.2012.08.001 |
0.388 |
|
| 2012 |
Camps SM, Dutilh BE, Arendrup MC, Rijs AJ, Snelders E, Huynen MA, Verweij PE, Melchers WJ. Discovery of a HapE mutation that causes azole resistance in Aspergillus fumigatus through whole genome sequencing and sexual crossing. Plos One. 7: e50034. PMID 23226235 DOI: 10.1371/Journal.Pone.0050034 |
0.322 |
|
| 2012 |
Kensche PR, Duarte I, Huynen MA. A three-dimensional topology of complex I inferred from evolutionary correlations. Bmc Structural Biology. 12: 19. PMID 22857522 DOI: 10.1186/1472-6807-12-19 |
0.313 |
|
| 2012 |
Duarte I, Nabuurs SB, Magno R, Huynen M. Evolution and diversification of the organellar release factor family Molecular Biology and Evolution. 29: 3497-3512. PMID 22688947 DOI: 10.1093/Molbev/Mss157 |
0.302 |
|
| 2012 |
Huynen MA, Duarte I, Chrzanowska-Lightowlers ZM, Nabuurs SB. Structure based hypothesis of a mitochondrial ribosome rescue mechanism. Biology Direct. 7: 14. PMID 22569235 DOI: 10.1186/1745-6150-7-14 |
0.338 |
|
| 2012 |
Szklarczyk R, Wanschers BF, Cuypers TD, Esseling JJ, Riemersma M, van den Brand MA, Gloerich J, Lasonder E, van den Heuvel LP, Nijtmans LG, Huynen MA. 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. Genome Biology. 13: R12. PMID 22356826 DOI: 10.1186/Gb-2012-13-2-R12 |
0.471 |
|
| 2012 |
Wanschers BF, Szklarczyk R, Pajak A, van den Brand MA, Gloerich J, Rodenburg RJ, Lightowlers RN, Nijtmans LG, Huynen MA. C7orf30 specifically associates with the large subunit of the mitochondrial ribosome and is involved in translation. Nucleic Acids Research. 40: 4040-51. PMID 22238375 DOI: 10.1093/Nar/Gkr1271 |
0.429 |
|
| 2012 |
Sanecka A, Ansems M, van Hout-Kuijer MA, Looman MW, Prosser AC, Welten S, Gilissen C, Sama IE, Huynen MA, Veltman JA, Jansen BJ, Eleveld-Trancikova D, Adema GJ. Analysis of genes regulated by the transcription factor LUMAN identifies ApoA4 as a target gene in dendritic cells. Molecular Immunology. 50: 66-73. PMID 22209087 DOI: 10.1016/J.Molimm.2011.12.003 |
0.332 |
|
| 2012 |
Roepman R, Ueffing M, Kremer H, Huynen M, Gibson T, Katsanis N, Walz G, Wolfrum U, Franco B, Giles R, Beales P, Johnson C, Blacque O, Pontoglio M, Képès F, et al. SYSCILIA, “A systems biology approach to dissect cilia function and its disruption in human genetic disease” Cilia. 1: 41. DOI: 10.1186/2046-2530-1-S1-P41 |
0.303 |
|
| 2011 |
Jonckheere AI, Huigsloot M, Lammens M, Jansen J, van den Heuvel LP, Spiekerkoetter U, von Kleist-Retzow JC, Forkink M, Koopman WJ, Szklarczyk R, Huynen MA, Fransen JA, Smeitink JA, Rodenburg RJ. Restoration of complex V deficiency caused by a novel deletion in the human TMEM70 gene normalizes mitochondrial morphology. Mitochondrion. 11: 954-63. PMID 21945727 DOI: 10.1016/J.Mito.2011.08.012 |
0.382 |
|
| 2011 |
Dutilh BE, Jurgelenaite R, Szklarczyk R, van Hijum SA, Harhangi HR, Schmid M, de Wild B, Françoijs KJ, Stunnenberg HG, Strous M, Jetten MS, Op den Camp HJ, Huynen MA. FACIL: Fast and Accurate Genetic Code Inference and Logo. Bioinformatics (Oxford, England). 27: 1929-33. PMID 21653513 DOI: 10.7490/F1000Research.1871.1 |
0.324 |
|
| 2011 |
Huerta-Cepas J, Dopazo J, Huynen MA, Gabaldón T. Evidence for short-time divergence and long-time conservation of tissue-specific expression after gene duplication. Briefings in Bioinformatics. 12: 442-8. PMID 21515902 DOI: 10.1093/Bib/Bbr022 |
0.62 |
|
| 2011 |
Huigsloot M, Nijtmans LG, Szklarczyk R, Baars MJ, van den Brand MA, Hendriksfranssen MG, van den Heuvel LP, Smeitink JA, Huynen MA, Rodenburg RJ. A mutation in C2orf64 causes impaired cytochrome c oxidase assembly and mitochondrial cardiomyopathy. American Journal of Human Genetics. 88: 488-93. PMID 21457908 DOI: 10.1016/J.Ajhg.2011.03.002 |
0.331 |
|
| 2011 |
de Graaf RM, Ricard G, van Alen TA, Duarte I, Dutilh BE, Burgtorf C, Kuiper JW, van der Staay GW, Tielens AG, Huynen MA, Hackstein JH. The organellar genome and metabolic potential of the hydrogen-producing mitochondrion of Nyctotherus ovalis. Molecular Biology and Evolution. 28: 2379-91. PMID 21378103 DOI: 10.1093/Molbev/Msr059 |
0.439 |
|
| 2011 |
Dutilh BE, Huynen MA, Bruno WJ, Snel B. The consistent signal in genome trees revealed by reducing the impact of noise F1000research. 2. DOI: 10.7490/F1000Research.826.1 |
0.716 |
|
| 2011 |
Dutilh BE, Noort Vv, Heijden RTvd, Huynen MA, Snel B. A comprehensive comparison of phylogenomics and orthology methods applied to the Fungi F1000research. 2. DOI: 10.7490/F1000Research.813.1 |
0.691 |
|
| 2010 |
Szklarczyk R, Huynen MA. Mosaic origin of the mitochondrial proteome. Proteomics. 10: 4012-24. PMID 21080492 DOI: 10.1002/Pmic.201000329 |
0.405 |
|
| 2010 |
Kouwenhoven EN, van Heeringen SJ, Tena JJ, Oti M, Dutilh BE, Alonso ME, de la Calle-Mustienes E, Smeenk L, Rinne T, Parsaulian L, Bolat E, Jurgelenaite R, Huynen MA, Hoischen A, Veltman JA, et al. Genome-wide profiling of p63 DNA-binding sites identifies an element that regulates gene expression during limb development in the 7q21 SHFM1 locus. Plos Genetics. 6: e1001065. PMID 20808887 DOI: 10.1371/Journal.Pgen.1001065 |
0.4 |
|
| 2010 |
Sama IE, Huynen MA. Measuring the physical cohesiveness of proteins using physical interaction enrichment. Bioinformatics (Oxford, England). 26: 2737-43. PMID 20798171 DOI: 10.1093/Bioinformatics/Btq474 |
0.439 |
|
| 2010 |
Buschow SI, Lasonder E, van Deutekom HW, Oud MM, Beltrame L, Huynen MA, de Vries IJ, Figdor CG, Cavalieri D. Dominant processes during human dendritic cell maturation revealed by integration of proteome and transcriptome at the pathway level. Journal of Proteome Research. 9: 1727-37. PMID 20131907 DOI: 10.1021/Pr9008546 |
0.378 |
|
| 2009 |
Oti M, Huynen MA, Brunner HG. The biological coherence of human phenome databases. American Journal of Human Genetics. 85: 801-8. PMID 20004759 DOI: 10.1016/J.Ajhg.2009.10.026 |
0.362 |
|
| 2009 |
de Graaf RM, Duarte I, van Alen TA, Kuiper JW, Schotanus K, Rosenberg J, Huynen MA, Hackstein JH. The hydrogenosomes of Psalteriomonas lanterna. Bmc Evolutionary Biology. 9: 287. PMID 20003182 DOI: 10.1186/1471-2148-9-287 |
0.335 |
|
| 2009 |
Szklarczyk R, Huynen MA. Expansion of the human mitochondrial proteome by intra- and inter-compartmental protein duplication. Genome Biology. 10: R135. PMID 19930686 DOI: 10.1186/Gb-2009-10-11-R135 |
0.435 |
|
| 2009 |
de Graaf RM, van Alen TA, Dutilh BE, Kuiper JW, van Zoggel HJ, Huynh MB, Görtz HD, Huynen MA, Hackstein JH. The mitochondrial genomes of the ciliates Euplotes minuta and Euplotes crassus. Bmc Genomics. 10: 514. PMID 19895685 DOI: 10.1186/1471-2164-10-514 |
0.468 |
|
| 2009 |
Parmley JL, Huynen MA. Clustering of codons with rare cognate tRNAs in human genes suggests an extra level of expression regulation. Plos Genetics. 5: e1000548. PMID 19578405 DOI: 10.1371/Journal.Pgen.1000548 |
0.44 |
|
| 2009 |
Dutilh BE, Huynen MA, Strous M. Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly. Bioinformatics (Oxford, England). 25: 2878-81. PMID 19542148 DOI: 10.1093/Bioinformatics/Btp377 |
0.419 |
|
| 2009 |
Saada A, Vogel RO, Hoefs SJ, van den Brand MA, Wessels HJ, Willems PH, Venselaar H, Shaag A, Barghuti F, Reish O, Shohat M, Huynen MA, Smeitink JA, van den Heuvel LP, Nijtmans LG. Mutations in NDUFAF3 (C3ORF60), encoding an NDUFAF4 (C6ORF66)-interacting complex I assembly protein, cause fatal neonatal mitochondrial disease. American Journal of Human Genetics. 84: 718-27. PMID 19463981 DOI: 10.1016/J.Ajhg.2009.04.020 |
0.389 |
|
| 2009 |
Huynen MA, de Hollander M, Szklarczyk R. Mitochondrial proteome evolution and genetic disease. Biochimica Et Biophysica Acta. 1792: 1122-9. PMID 19328849 DOI: 10.1016/J.Bbadis.2009.03.005 |
0.404 |
|
| 2009 |
Notebaart RA, Kensche PR, Huynen MA, Dutilh BE. Asymmetric relationships between proteins shape genome evolution. Genome Biology. 10: R19. PMID 19216750 DOI: 10.1186/Gb-2009-10-2-R19 |
0.493 |
|
| 2008 |
Szklarczyk R, Huynen MA, Snel B. Complex fate of paralogs. Bmc Evolutionary Biology. 8: 337. PMID 19094234 DOI: 10.1186/1471-2148-8-337 |
0.761 |
|
| 2008 |
Ricard G, de Graaf RM, Dutilh BE, Duarte I, van Alen TA, van Hoek AH, Boxma B, van der Staay GW, Moon-van der Staay SY, Chang WJ, Landweber LF, Hackstein JH, Huynen MA. Macronuclear genome structure of the ciliate Nyctotherus ovalis: single-gene chromosomes and tiny introns. Bmc Genomics. 9: 587. PMID 19061489 DOI: 10.1186/1471-2164-9-587 |
0.385 |
|
| 2008 |
Lasonder E, Janse CJ, van Gemert GJ, Mair GR, Vermunt AM, Douradinha BG, van Noort V, Huynen MA, Luty AJ, Kroeze H, Khan SM, Sauerwein RW, Waters AP, Mann M, Stunnenberg HG. Proteomic profiling of Plasmodium sporozoite maturation identifies new proteins essential for parasite development and infectivity. Plos Pathogens. 4: e1000195. PMID 18974882 DOI: 10.1371/Journal.Ppat.1000195 |
0.742 |
|
| 2008 |
Franck E, Hulsen T, Huynen MA, de Jong WW, Lubsen NH, Madsen O. Evolution of closely linked gene pairs in vertebrate genomes. Molecular Biology and Evolution. 25: 1909-21. PMID 18566020 DOI: 10.1093/Molbev/Msn136 |
0.498 |
|
| 2008 |
Dutilh BE, Snel B, Ettema TJ, Huynen MA. Signature genes as a phylogenomic tool. Molecular Biology and Evolution. 25: 1659-67. PMID 18492663 DOI: 10.1093/Molbev/Msn115 |
0.8 |
|
| 2008 |
Dutilh BE, He Y, Hekkelman ML, Huynen MA. Signature, a web server for taxonomic characterization of sequence samples using signature genes. Nucleic Acids Research. 36: W470-4. PMID 18487625 DOI: 10.1093/Nar/Gkn277 |
0.47 |
|
| 2008 |
Oti M, van Reeuwijk J, Huynen MA, Brunner HG. Conserved co-expression for candidate disease gene prioritization. Bmc Bioinformatics. 9: 208. PMID 18433471 DOI: 10.1186/1471-2105-9-208 |
0.438 |
|
| 2008 |
Kensche PR, Oti M, Dutilh BE, Huynen MA. Conservation of divergent transcription in fungi. Trends in Genetics : Tig. 24: 207-11. PMID 18375009 DOI: 10.1016/J.Tig.2008.02.003 |
0.583 |
|
| 2008 |
Kensche PR, van Noort V, Dutilh BE, Huynen MA. Practical and theoretical advances in predicting the function of a protein by its phylogenetic distribution. Journal of the Royal Society, Interface / the Royal Society. 5: 151-70. PMID 17535793 DOI: 10.1098/Rsif.2007.1047 |
0.833 |
|
| 2007 |
Boxma B, Ricard G, van Hoek AH, Severing E, Moon-van der Staay SY, van der Staay GW, van Alen TA, de Graaf RM, Cremers G, Kwantes M, McEwan NR, Newbold CJ, Jouany JP, Michalowski T, Pristas P, ... Huynen MA, et al. The [FeFe] hydrogenase of Nyctotherus ovalis has a chimeric origin. Bmc Evolutionary Biology. 7: 230. PMID 18021395 DOI: 10.1186/1471-2148-7-230 |
0.382 |
|
| 2007 |
Gabaldón T, Huynen MA. From endosymbiont to host-controlled organelle: the hijacking of mitochondrial protein synthesis and metabolism. Plos Computational Biology. 3: e219. PMID 17983265 DOI: 10.1371/Journal.Pcbi.0030219 |
0.55 |
|
| 2007 |
van Noort V, Snel B, Huynen MA. Exploration of the omics evidence landscape: adding qualitative labels to predicted protein-protein interactions. Genome Biology. 8: R197. PMID 17880677 DOI: 10.1186/Gb-2007-8-9-R197 |
0.8 |
|
| 2007 |
Smits P, Smeitink JA, van den Heuvel LP, Huynen MA, Ettema TJ. Reconstructing the evolution of the mitochondrial ribosomal proteome. Nucleic Acids Research. 35: 4686-703. PMID 17604309 DOI: 10.1093/Nar/Gkm441 |
0.421 |
|
| 2007 |
Datson NA, Morsink MC, Atanasova S, Armstrong VW, Zischler H, Schlumbohm C, Dutilh BE, Huynen MA, Waegele B, Ruepp A, de Kloet ER, Fuchs E. Development of the first marmoset-specific DNA microarray (EUMAMA): a new genetic tool for large-scale expression profiling in a non-human primate. Bmc Genomics. 8: 190. PMID 17592630 DOI: 10.1186/1471-2164-8-190 |
0.319 |
|
| 2007 |
van der Heijden RT, Snel B, van Noort V, Huynen MA. Orthology prediction at scalable resolution by phylogenetic tree analysis. Bmc Bioinformatics. 8: 83. PMID 17346331 DOI: 10.1186/1471-2105-8-83 |
0.816 |
|
| 2007 |
Dutilh BE, van Noort V, van der Heijden RT, Boekhout T, Snel B, Huynen MA. Assessment of phylogenomic and orthology approaches for phylogenetic inference. Bioinformatics (Oxford, England). 23: 815-24. PMID 17237036 DOI: 10.1093/Bioinformatics/Btm015 |
0.832 |
|
| 2007 |
Nielsen F, Graef S, Zhang X, Kurtz S, Denissov S, Green R, Birney E, Flicek P, Huynen M, Stunnenberg H. Optimising oligonucleotide array design for ChIP-on-chip Bmc Bioinformatics. 8. DOI: 10.1186/1471-2105-8-S8-P4 |
0.398 |
|
| 2006 |
Hulsen T, Huynen MA, de Vlieg J, Groenen PM. Benchmarking ortholog identification methods using functional genomics data. Genome Biology. 7: R31. PMID 16613613 DOI: 10.1186/Gb-2006-7-4-R31 |
0.504 |
|
| 2006 |
Oti M, Snel B, Huynen MA, Brunner HG. Predicting disease genes using protein-protein interactions. Journal of Medical Genetics. 43: 691-8. PMID 16611749 DOI: 10.1136/Jmg.2006.041376 |
0.765 |
|
| 2006 |
Strous M, Pelletier E, Mangenot S, Rattei T, Lehner A, Taylor MW, Horn M, Daims H, Bartol-Mavel D, Wincker P, Barbe V, Fonknechten N, Vallenet D, Segurens B, Schenowitz-Truong C, ... ... Huynen MA, et al. Deciphering the evolution and metabolism of an anammox bacterium from a community genome. Nature. 440: 790-4. PMID 16598256 DOI: 10.1038/Nature04647 |
0.763 |
|
| 2006 |
Gabaldón T, Snel B, van Zimmeren F, Hemrika W, Tabak H, Huynen MA. Origin and evolution of the peroxisomal proteome. Biology Direct. 1: 8. PMID 16556314 DOI: 10.1186/1745-6150-1-8 |
0.79 |
|
| 2006 |
Ricard G, McEwan NR, Dutilh BE, Jouany JP, Macheboeuf D, Mitsumori M, McIntosh FM, Michalowski T, Nagamine T, Nelson N, Newbold CJ, Nsabimana E, Takenaka A, Thomas NA, Ushida K, ... ... Huynen MA, et al. Horizontal gene transfer from Bacteria to rumen Ciliates indicates adaptation to their anaerobic, carbohydrates-rich environment. Bmc Genomics. 7: 22. PMID 16472398 DOI: 10.1186/1471-2164-7-22 |
0.512 |
|
| 2006 |
Dutilh BE, Huynen MA, Snel B. A global definition of expression context is conserved between orthologs, but does not correlate with sequence conservation. Bmc Genomics. 7: 10. PMID 16423292 DOI: 10.1186/1471-2164-7-10 |
0.77 |
|
| 2006 |
van Noort V, Huynen MA. Combinatorial gene regulation in Plasmodium falciparum. Trends in Genetics : Tig. 22: 73-8. PMID 16380193 DOI: 10.1016/J.Tig.2005.12.002 |
0.797 |
|
| 2005 |
Notebaart RA, Huynen MA, Teusink B, Siezen RJ, Snel B. Correlation between sequence conservation and the genomic context after gene duplication. Nucleic Acids Research. 33: 6164-71. PMID 16257980 DOI: 10.1093/Nar/Gki913 |
0.815 |
|
| 2005 |
Gabaldón T, Huynen MA. Lineage-specific gene loss following mitochondrial endosymbiosis and its potential for function prediction in eukaryotes. Bioinformatics (Oxford, England). 21: ii144-50. PMID 16204094 DOI: 10.1093/Bioinformatics/Bti1124 |
0.67 |
|
| 2005 |
Snel B, Huynen MA, Dutilh BE. Genome trees and the nature of genome evolution. Annual Review of Microbiology. 59: 191-209. PMID 16153168 DOI: 10.1146/Annurev.Micro.59.030804.121233 |
0.789 |
|
| 2005 |
van Reeuwijk J, Janssen M, van den Elzen C, Beltran-Valero de Bernabé D, Sabatelli P, Merlini L, Boon M, Scheffer H, Brockington M, Muntoni F, Huynen MA, Verrips A, Walsh CA, Barth PG, Brunner HG, et al. POMT2 mutations cause alpha-dystroglycan hypoglycosylation and Walker-Warburg syndrome. Journal of Medical Genetics. 42: 907-12. PMID 15894594 DOI: 10.1136/Jmg.2005.031963 |
0.327 |
|
| 2005 |
Gabaldón T, Rainey D, Huynen MA. Tracing the evolution of a large protein complex in the eukaryotes, NADH:ubiquinone oxidoreductase (Complex I). Journal of Molecular Biology. 348: 857-70. PMID 15843018 DOI: 10.1016/J.Jmb.2005.02.067 |
0.63 |
|
| 2005 |
Kunin V, Teichmann SA, Huynen MA, Ouzounis CA. The properties of protein family space depend on experimental design. Bioinformatics (Oxford, England). 21: 2618-22. PMID 15769834 DOI: 10.1093/Bioinformatics/Bti386 |
0.307 |
|
| 2005 |
Huynen MA, Gabaldón T, Snel B. Variation and evolution of biomolecular systems: searching for functional relevance. Febs Letters. 579: 1839-45. PMID 15763561 DOI: 10.1016/J.Febslet.2005.02.004 |
0.796 |
|
| 2005 |
Boxma B, de Graaf RM, van der Staay GW, van Alen TA, Ricard G, Gabaldón T, van Hoek AH, Moon-van der Staay SY, Koopman WJ, van Hellemond JJ, Tielens AG, Friedrich T, Veenhuis M, Huynen MA, Hackstein JH. An anaerobic mitochondrion that produces hydrogen. Nature. 434: 74-9. PMID 15744302 DOI: 10.1038/Nature03343 |
0.555 |
|
| 2005 |
Huynen MA, Spronk CA, Gabaldón T, Snel B. Combining data from genomes, Y2H and 3D structure indicates that BolA is a reductase interacting with a glutaredoxin. Febs Letters. 579: 591-6. PMID 15670813 DOI: 10.1016/J.Febslet.2004.11.111 |
0.807 |
|
| 2005 |
von Mering C, Jensen LJ, Snel B, Hooper SD, Krupp M, Foglierini M, Jouffre N, Huynen MA, Bork P. STRING: known and predicted protein-protein associations, integrated and transferred across organisms. Nucleic Acids Research. 33: D433-7. PMID 15608232 DOI: 10.1093/Nar/Gki005 |
0.792 |
|
| 2004 |
Franck E, Madsen O, van Rheede T, Ricard G, Huynen MA, de Jong WW. Evolutionary diversity of vertebrate small heat shock proteins. Journal of Molecular Evolution. 59: 792-805. PMID 15599511 DOI: 10.1007/S00239-004-0013-Z |
0.427 |
|
| 2004 |
Gabaldón T, Huynen MA. Shaping the mitochondrial proteome. Biochimica Et Biophysica Acta. 1659: 212-20. PMID 15576054 DOI: 10.1016/J.Bbabio.2004.07.011 |
0.576 |
|
| 2004 |
Ettema TJ, Makarova KS, Jellema GL, Gierman HJ, Koonin EV, Huynen MA, de Vos WM, van der Oost J. Identification and functional verification of archaeal-type phosphoenolpyruvate carboxylase, a missing link in archaeal central carbohydrate metabolism. Journal of Bacteriology. 186: 7754-62. PMID 15516590 DOI: 10.1128/Jb.186.22.7754-7762.2004 |
0.423 |
|
| 2004 |
Snel B, van Noort V, Huynen MA. Gene co-regulation is highly conserved in the evolution of eukaryotes and prokaryotes. Nucleic Acids Research. 32: 4725-31. PMID 15353560 DOI: 10.1093/Nar/Gkh815 |
0.836 |
|
| 2004 |
Huynen MA, Snel B, van Noort V. Comparative genomics for reliable protein-function prediction from genomic data. Trends in Genetics : Tig. 20: 340-4. PMID 15262404 DOI: 10.1016/J.Tig.2004.06.003 |
0.826 |
|
| 2004 |
Dutilh BE, Huynen MA, Bruno WJ, Snel B. The consistent phylogenetic signal in genome trees revealed by reducing the impact of noise. Journal of Molecular Evolution. 58: 527-39. PMID 15170256 DOI: 10.1007/S00239-003-2575-6 |
0.779 |
|
| 2004 |
van Bakel H, Huynen M, Wijmenga C. Prokaryotic diversity of the Saccharomyces cerevisiae Atx1p-mediated copper pathway. Bioinformatics (Oxford, England). 20: 2644-55. PMID 15145814 DOI: 10.1093/Bioinformatics/Bth298 |
0.382 |
|
| 2004 |
Gabaldón T, Huynen MA. Prediction of protein function and pathways in the genome era. Cellular and Molecular Life Sciences : Cmls. 61: 930-44. PMID 15095013 DOI: 10.1007/S00018-003-3387-Y |
0.678 |
|
| 2004 |
Snel B, Huynen MA. Quantifying modularity in the evolution of biomolecular systems. Genome Research. 14: 391-7. PMID 14993205 DOI: 10.1101/Gr.1969504 |
0.755 |
|
| 2004 |
van Noort V, Snel B, Huynen MA. The yeast coexpression network has a small-world, scale-free architecture and can be explained by a simple model. Embo Reports. 5: 280-4. PMID 14968131 DOI: 10.1038/Sj.Embor.7400090 |
0.793 |
|
| 2003 |
Gabaldón T, Huynen MA. Reconstruction of the proto-mitochondrial metabolism. Science (New York, N.Y.). 301: 609. PMID 12893934 DOI: 10.1126/Science.1085463 |
0.598 |
|
| 2003 |
Ettema TJ, Huynen MA, de Vos WM, van der Oost J. TRASH: a novel metal-binding domain predicted to be involved in heavy-metal sensing, trafficking and resistance. Trends in Biochemical Sciences. 28: 170-3. PMID 12713899 DOI: 10.1016/S0968-0004(03)00037-9 |
0.369 |
|
| 2003 |
van Noort V, Snel B, Huynen MA. Predicting gene function by conserved co-expression. Trends in Genetics : Tig. 19: 238-42. PMID 12711213 DOI: 10.1016/S0168-9525(03)00056-8 |
0.831 |
|
| 2003 |
Huynen MA, Snel B, von Mering C, Bork P. Function prediction and protein networks. Current Opinion in Cell Biology. 15: 191-8. PMID 12648675 DOI: 10.1016/S0955-0674(03)00009-7 |
0.819 |
|
| 2003 |
von Mering C, Huynen M, Jaeggi D, Schmidt S, Bork P, Snel B. STRING: a database of predicted functional associations between proteins. Nucleic Acids Research. 31: 258-61. PMID 12519996 DOI: 10.1093/Nar/Gkg034 |
0.852 |
|
| 2002 |
van der Oost J, Huynen MA, Verhees CH. Molecular characterization of phosphoglycerate mutase in archaea. Fems Microbiology Letters. 212: 111-20. PMID 12076796 DOI: 10.1111/J.1574-6968.2002.Tb11253.X |
0.464 |
|
| 2002 |
Voncken F, Boxma B, Tjaden J, Akhmanova A, Huynen M, Verbeek F, Tielens AG, Haferkamp I, Neuhaus HE, Vogels G, Veenhuis M, Hackstein JH. Multiple origins of hydrogenosomes: functional and phylogenetic evidence from the ADP/ATP carrier of the anaerobic chytrid Neocallimastix sp. Molecular Microbiology. 44: 1441-54. PMID 12067335 DOI: 10.1046/J.1365-2958.2002.02959.X |
0.342 |
|
| 2002 |
Snel B, Bork P, Huynen MA. The identification of functional modules from the genomic association of genes. Proceedings of the National Academy of Sciences of the United States of America. 99: 5890-5. PMID 11983890 DOI: 10.1073/Pnas.092632599 |
0.819 |
|
| 2002 |
Korbel JO, Snel B, Huynen MA, Bork P. SHOT: a web server for the construction of genome phylogenies. Trends in Genetics : Tig. 18: 158-62. PMID 11858840 DOI: 10.1016/S0168-9525(01)02597-5 |
0.845 |
|
| 2002 |
Snel B, Bork P, Huynen MA. Genomes in flux: the evolution of archaeal and proteobacterial gene content. Genome Research. 12: 17-25. PMID 11779827 DOI: 10.1101/Gr.176501 |
0.829 |
|
| 2002 |
Snel B, Bork P, Huynen MA. Conservation of gene co-regulation in prokaryotes and eukaryotes Trends in Biotechnology. 20: 410. DOI: 10.1016/S0167-7799(02)02040-1 |
0.793 |
|
| 2001 |
Hackstein J, Akhmanova A, Voncken F, Hoek Av, Alen Tv, Boxma B, Staay SMd, Staay Gvd, Leunissen J, Huynen M, Rosenberg J, Veenhuis M, Hackstein JHP, Staay SYMd. Hydrogenosomes : convergent adaptations of mitochondria to anaerobic environments Zoology. 104: 290-302. PMID 16351844 DOI: 10.1078/0944-2006-00035 |
0.348 |
|
| 2001 |
Huynen MA, Snel B, Bork P, Gibson TJ. The phylogenetic distribution of frataxin indicates a role in iron-sulfur cluster protein assembly. Human Molecular Genetics. 10: 2463-8. PMID 11689493 DOI: 10.1093/Hmg/10.21.2463 |
0.826 |
|
| 2001 |
Verhees CH, Huynen MA, Ward DE, Schiltz E, de Vos WM, van der Oost J. The phosphoglucose isomerase from the hyperthermophilic archaeon Pyrococcus furiosus is a unique glycolytic enzyme that belongs to the cupin superfamily. The Journal of Biological Chemistry. 276: 40926-32. PMID 11533028 DOI: 10.1074/Jbc.M104603200 |
0.398 |
|
| 2001 |
Ettema T, Oost Jvd, Huynen M. Modularity in the gain and loss of genes: applications for function prediction Trends in Genetics. 17: 485-487. PMID 11525815 DOI: 10.1016/S0168-9525(01)02384-8 |
0.461 |
|
| 2001 |
Huynen MA, Snel B, Bork P. Inversions and the dynamics of eukaryotic gene order. Trends in Genetics : Tig. 17: 304-6. PMID 11377779 DOI: 10.1016/S0168-9525(01)02302-2 |
0.839 |
|
| 2000 |
Snel B, Lehmann G, Bork P, Huynen MA. STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene. Nucleic Acids Research. 28: 3442-4. PMID 10982861 DOI: 10.1093/Nar/28.18.3442 |
0.839 |
|
| 2000 |
Huynen M, Snel B, Lathe W, Bork P. Predicting protein function by genomic context: quantitative evaluation and qualitative inferences. Genome Research. 10: 1204-10. PMID 10958638 DOI: 10.1101/Gr.10.8.1204 |
0.848 |
|
| 2000 |
Dandekar T, Huynen M, Regula JT, Ueberle B, Zimmermann CU, Andrade MA, Doerks T, Sánchez-Pulido L, Snel B, Suyama M, Yuan YP, Herrmann R, Bork P. Re-annotating the Mycoplasma pneumoniae genome sequence: adding value, function and reading frames. Nucleic Acids Research. 28: 3278-88. PMID 10954595 DOI: 10.1093/Nar/28.17.3278 |
0.828 |
|
| 2000 |
Huynen M, Snel B, Lathe W, Bork P. Exploitation of gene context. Current Opinion in Structural Biology. 10: 366-70. PMID 10851194 DOI: 10.1016/S0959-440X(00)00098-1 |
0.838 |
|
| 2000 |
Huynen MA, Snel B. Gene and context: integrative approaches to genome analysis. Advances in Protein Chemistry. 54: 345-79. PMID 10829232 DOI: 10.1016/S0065-3233(00)54010-8 |
0.779 |
|
| 2000 |
van Hoek AH, Akhmanova AS, Huynen MA, Hackstein JH. A mitochondrial ancestry of the hydrogenosomes of Nyctotherus ovalis. Molecular Biology and Evolution. 17: 202-6. PMID 10666720 DOI: 10.1093/Oxfordjournals.Molbev.A026234 |
0.357 |
|
| 2000 |
Snel B, Bork P, Huynen M. Genome evolution. Gene fusion versus gene fission. Trends in Genetics : Tig. 16: 9-11. PMID 10637623 DOI: 10.1016/S0168-9525(99)01924-1 |
0.831 |
|
| 2000 |
Huynen M. Constructing a minimal genome Trends in Genetics. 16: 116. DOI: 10.1016/S0168-9525(99)01972-1 |
0.543 |
|
| 1999 |
Bork P, Huynen M. A point of entry into genomics Nature Genetics. 23: 273-273. PMID 10545945 DOI: 10.1038/15453 |
0.63 |
|
| 1999 |
Dandekar T, Schuster S, Snel B, Huynen M, Bork P. Pathway alignment: application to the comparative analysis of glycolytic enzymes. The Biochemical Journal. 343: 115-24. PMID 10493919 DOI: 10.1042/Bj3430115 |
0.808 |
|
| 1999 |
Huynen MA, Dandekar T, Bork P. Variation and evolution of the citric-acid cycle: a genomic perspective. Trends in Microbiology. 7: 281-91. PMID 10390638 DOI: 10.1016/S0966-842X(99)01539-5 |
0.71 |
|
| 1999 |
Snel B, Bork P, Huynen MA. Genome phylogeny based on gene content. Nature Genetics. 21: 108-10. PMID 9916801 DOI: 10.1038/5052 |
0.844 |
|
| 1999 |
Huynen M. Lateral Gene Transfer, Genome Surveys, and the Phylogeny of Prokaryotes Science. 286: 1443a-1443. DOI: 10.1126/Science.286.5444.1443A |
0.488 |
|
| 1998 |
Bork P, Dandekar T, Diaz-Lazcoz Y, Eisenhaber F, Huynen M, Yuan Y. Predicting function: from genes to genomes and back. Journal of Molecular Biology. 283: 707-25. PMID 9790834 DOI: 10.1006/Jmbi.1998.2144 |
0.77 |
|
| 1998 |
Dandekar T, Snel B, Huynen M, Bork P. Conservation of gene order: a fingerprint of proteins that physically interact. Trends in Biochemical Sciences. 23: 324-8. PMID 9787636 DOI: 10.1016/S0968-0004(98)01274-2 |
0.841 |
|
| 1998 |
Hofacker IL, Fekete M, Flamm C, Huynen MA, Rauscher S, Stolorz PE, Stadler PF. Automatic detection of conserved RNA structure elements in complete RNA virus genomes. Nucleic Acids Research. 26: 3825-36. PMID 9685502 DOI: 10.1093/Nar/26.16.3825 |
0.342 |
|
| 1998 |
Huynen M, Doerks T, Eisenhaber F, Orengo C, Sunyaev S, Yuan Y, Bork P. Homology-based fold predictions for Mycoplasma genitalium proteins. Journal of Molecular Biology. 280: 323-6. PMID 9665839 DOI: 10.1006/Jmbi.1998.1884 |
0.791 |
|
| 1998 |
Huynen MA, Bork P. Measuring genome evolution. Proceedings of the National Academy of Sciences of the United States of America. 95: 5849-56. PMID 9600883 DOI: 10.1073/Pnas.95.11.5849 |
0.719 |
|
| 1998 |
Huynen M, Dandekar T, Bork P. Differential genome analysis applied to the species-specific features of Helicobacter pylori. Febs Letters. 426: 1-5. PMID 9598967 DOI: 10.1016/S0014-5793(98)00276-2 |
0.757 |
|
| 1998 |
Huynen MA, van Nimwegen E. The frequency distribution of gene family sizes in complete genomes. Molecular Biology and Evolution. 15: 583-9. PMID 9580988 DOI: 10.1093/Oxfordjournals.Molbev.A025959 |
0.449 |
|
| 1997 |
Huynen MA, Diaz-Lazcoz Y, Bork P. Differential genome display. Trends in Genetics : Tig. 13: 389-90. PMID 9351339 DOI: 10.1016/S0168-9525(97)01255-9 |
0.591 |
|
| 1994 |
Huynen MA, Hogeweg P. Pattern generation in molecular evolution: exploitation of the variation in RNA landscapes. Journal of Molecular Evolution. 39: 71-9. PMID 7520506 DOI: 10.1007/Bf00178251 |
0.56 |
|
| 1993 |
Huynen MA, Konings DA, Hogeweg P. Multiple coding and the evolutionary properties of RNA secondary structure. Journal of Theoretical Biology. 165: 251-67. PMID 7507189 DOI: 10.1006/Jtbi.1993.1188 |
0.599 |
|
| 1992 |
Huynen MA, Konings DA, Hogeweg P. Equal G and C contents in histone genes indicate selection pressures on mRNA secondary structure. Journal of Molecular Evolution. 34: 280-91. PMID 1569583 DOI: 10.1007/Bf00160235 |
0.538 |
|
| Low-probability matches (unlikely to be authored by this person) |
| 1996 |
Huynen MA, Perelson A, Vieira WA, Stadler PF. Base pairing probabilities in a complete HIV-1 RNA. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 3: 253-74. PMID 8811486 DOI: 10.1089/Cmb.1996.3.253 |
0.3 |
|
| 2013 |
van Dam TJ, Wheway G, Slaats GG, Huynen MA, Giles RH. The SYSCILIA gold standard (SCGSv1) of known ciliary components and its applications within a systems biology consortium. Cilia. 2: 7. PMID 23725226 DOI: 10.1186/2046-2530-2-7 |
0.299 |
|
| 2018 |
Chaidir L, Ruesen C, Dutilh BE, Ganiem AR, Andryani A, Apriani L, Huynen MA, Ruslami R, Hill PC, Crevel RV, Alisjahbana B. Use of whole genome sequencing to predict Mycobacterium tuberculosis drug resistance in Indonesia. Journal of Global Antimicrobial Resistance. PMID 30172045 DOI: 10.1016/J.Jgar.2018.08.018 |
0.299 |
|
| 2010 |
Richter R, Rorbach J, Pajak A, Smith PM, Wessels HJ, Huynen MA, Smeitink JA, Lightowlers RN, Chrzanowska-Lightowlers ZM. A functional peptidyl-tRNA hydrolase, ICT1, has been recruited into the human mitochondrial ribosome. The Embo Journal. 29: 1116-25. PMID 20186120 DOI: 10.1038/Emboj.2010.14 |
0.296 |
|
| 2007 |
Kirchberger S, Leroch M, Huynen MA, Wahl M, Neuhaus HE, Tjaden J. Molecular and biochemical analysis of the plastidic ADP-glucose transporter (ZmBT1) from Zea mays. The Journal of Biological Chemistry. 282: 22481-91. PMID 17562699 DOI: 10.1074/Jbc.M702484200 |
0.294 |
|
| 1998 |
Zheng ZM, Huynen M, Baker CC. A pyrimidine-rich exonic splicing suppressor binds multiple RNA splicing factors and inhibits spliceosome assembly Proceedings of the National Academy of Sciences of the United States of America. 95: 14088-14093. PMID 9826658 DOI: 10.1073/Pnas.95.24.14088 |
0.293 |
|
| 2013 |
Willems P, Wanschers BF, Esseling J, Szklarczyk R, Kudla U, Duarte I, Forkink M, Nooteboom M, Swarts H, Gloerich J, Nijtmans L, Koopman W, Huynen MA. BOLA1 is an aerobic protein that prevents mitochondrial morphology changes induced by glutathione depletion. Antioxidants & Redox Signaling. 18: 129-38. PMID 22746225 DOI: 10.1089/Ars.2011.4253 |
0.292 |
|
| 1996 |
Huynen MA, Stadler PF, Fontana W. Smoothness within ruggedness: the role of neutrality in adaptation. Proceedings of the National Academy of Sciences of the United States of America. 93: 397-401. PMID 8552647 DOI: 10.1073/Pnas.93.1.397 |
0.29 |
|
| 2008 |
Schoeber JP, Topala CN, Lee KP, Lambers TT, Ricard G, van der Kemp AW, Huynen MA, Hoenderop JG, Bindels RJ. Identification of Nipsnap1 as a novel auxiliary protein inhibiting TRPV6 activity. PflüGers Archiv : European Journal of Physiology. 457: 91-101. PMID 18392847 DOI: 10.1007/S00424-008-0494-5 |
0.287 |
|
| 2007 |
Smits P, Smeitink JA, van den Heuvel LP, Huynen MA, Ettema TJ. 24 Reconstructing the tempestuous evolution of the mitochondrial ribosomal proteome Mitochondrion. 7: 410-411. DOI: 10.1016/J.Mito.2007.08.028 |
0.287 |
|
| 2015 |
Chevrier V, Bruel AL, van Dam TJ, Franco B, Scalzo ML, Lembo F, Audebert S, Baudelet E, Isnardon D, Bole A, Borg JP, Kuentz P, Thevenon J, Burglen L, Faivre L, ... ... Huynen MA, et al. 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. Human Molecular Genetics. PMID 26643951 DOI: 10.1093/Hmg/Ddv488 |
0.286 |
|
| 1996 |
Huynen MA. Exploring phenotype space through neutral evolution. Journal of Molecular Evolution. 43: 165-9. PMID 8703081 DOI: 10.1007/Bf02338823 |
0.285 |
|
| 2006 |
Hackstein JHP, Tjaden J, Huynen M. Mitochondria, hydrogenosomes and mitosomes: Products of evolutionary tinkering! Current Genetics. 50: 225-245. PMID 16897087 DOI: 10.1007/S00294-006-0088-8 |
0.285 |
|
| 2012 |
Nielsen FGG, Markus KG, Friborg RM, Favrholdt LM, Stunnenberg HG, Huynen M. CATCHprofiles: Clustering and alignment tool for chip profiles Plos One. 7. DOI: 10.1371/Journal.Pone.0028272 |
0.284 |
|
| 2011 |
Szklarczyk R, Wanschers BF, Nabuurs SB, Nouws J, Nijtmans LG, Huynen MA. NDUFB7 and NDUFA8 are located at the intermembrane surface of complex I. Febs Letters. 585: 737-43. PMID 21310150 DOI: 10.1016/J.Febslet.2011.01.046 |
0.284 |
|
| 2007 |
Gräf S, Nielsen FG, Kurtz S, Huynen MA, Birney E, Stunnenberg H, Flicek P. Optimized design and assessment of whole genome tiling arrays. Bioinformatics (Oxford, England). 23: i195-204. PMID 17646297 DOI: 10.1093/bioinformatics/btm200 |
0.283 |
|
| 2004 |
Tjaden J, Haferkamp I, Boxma B, Tielens AG, Huynen M, Hackstein JH. A divergent ADP/ATP carrier in the hydrogenosomes of Trichomonas gallinae argues for an independent origin of these organelles. Molecular Microbiology. 51: 1439-46. PMID 14982636 DOI: 10.1111/J.1365-2958.2004.03918.X |
0.277 |
|
| 2012 |
Saeed S, Logie C, Francoijs KJ, Frigè G, Romanenghi M, Nielsen FG, Raats L, Shahhoseini M, Huynen M, Altucci L, Minucci S, Martens JH, Stunnenberg HG. Chromatin accessibility, p300, and histone acetylation define PML-RARα and AML1-ETO binding sites in acute myeloid leukemia. Blood. 120: 3058-68. PMID 22923494 DOI: 10.1182/Blood-2011-10-386086 |
0.277 |
|
| 2023 |
Potter A, Hangas A, Goffart S, Huynen MA, Cabrera-Orefice A, Spelbrink JN. Uncharacterized protein C17orf80: A novel interactor of human mitochondrial nucleoids. Journal of Cell Science. PMID 37401363 DOI: 10.1242/jcs.260822 |
0.276 |
|
| 2011 |
Minczuk M, He J, Duch AM, Ettema TJ, Chlebowski A, Dzionek K, Nijtmans LG, Huynen MA, Holt IJ. TEFM (c17orf42) is necessary for transcription of human mtDNA. Nucleic Acids Research. 39: 4284-99. PMID 21278163 DOI: 10.1093/Nar/Gkq1224 |
0.273 |
|
| 2019 |
Heuvel CNAMvd, Ewijk Av, Zeelen C, Bitter Td, Huynen M, Mulders P, Oosterwijk E, Leenders WPJ. Molecular Profiling of Druggable Targets in Clear Cell Renal Cell Carcinoma Through Targeted RNA Sequencing Frontiers in Oncology. 9: 117. PMID 30881919 DOI: 10.3389/Fonc.2019.00117 |
0.272 |
|
| 2008 |
Bych K, Kerscher S, Netz DJ, Pierik AJ, Zwicker K, Huynen MA, Lill R, Brandt U, Balk J. The iron-sulphur protein Ind1 is required for effective complex I assembly. The Embo Journal. 27: 1736-46. PMID 18497740 DOI: 10.1038/Emboj.2008.98 |
0.272 |
|
| 2002 |
Voncken FGJ, Boxma B, Hoek AHAMv, Akhmanova AS, Vogels GD, Huynen M, Veenhuis M, Hackstein JHP. A hydrogenosomal [Fe]-hydrogenase from the anaerobic chytrid Neocallimastix sp. L2 Gene. 284: 103-112. PMID 11891051 DOI: 10.1016/S0378-1119(02)00388-8 |
0.271 |
|
| 2015 |
Jaeger M, van der Lee R, Cheng SC, Johnson MD, Kumar V, Ng A, Plantinga TS, Smeekens SP, Oosting M, Wang X, Barchet W, Fitzgerald K, Joosten LA, Perfect JR, Wijmenga C, ... ... Huynen MA, et al. The RIG-I-like helicase receptor MDA5 (IFIH1) is involved in the host defense against Candida infections. European Journal of Clinical Microbiology & Infectious Diseases : Official Publication of the European Society of Clinical Microbiology. 34: 963-74. PMID 25579795 DOI: 10.1007/S10096-014-2309-2 |
0.27 |
|
| 2014 |
Megchelenbrink W, Huynen M, Marchiori E. optGpSampler: An improved tool for uniformly sampling the solution-space of genome-scale metabolic networks Plos One. 9. PMID 24551039 DOI: 10.1371/Journal.Pone.0086587 |
0.27 |
|
| 1997 |
Huynen M, Gutell R, Konings D. Assessing the reliability of RNA folding using statistical mechanics. Journal of Molecular Biology. 267: 1104-1112. PMID 9150399 DOI: 10.1006/Jmbi.1997.0889 |
0.269 |
|
| 2016 |
Seco CZ, Castells-Nobau A, Joo SH, Schraders M, Foo JN, van der Voet M, Velan SS, Nijhof B, Oostrik J, de Vrieze E, Katana R, Mansoor A, Huynen M, Szklarczyk R, Oti M, et al. A homozygous FITM2 mutation causes a deafness-dystonia syndrome with motor regression and signs of ichthyosis and sensory neuropathy. Disease Models & Mechanisms. PMID 28067622 DOI: 10.1242/Dmm.026476 |
0.268 |
|
| 2018 |
Lenting K, Khurshed M, Peeters TH, van den Heuvel CNAM, van Lith SAM, de Bitter T, Hendriks W, Span PN, Molenaar RJ, Botman D, Verrijp K, Heerschap A, Ter Laan M, Kusters B, van Ewijk A, ... Huynen MA, et al. Isocitrate dehydrogenase 1-mutated human gliomas depend on lactate and glutamate to alleviate metabolic stress. Faseb Journal : Official Publication of the Federation of American Societies For Experimental Biology. fj201800907RR. PMID 30001166 DOI: 10.1096/Fj.201800907Rr |
0.267 |
|
| 2018 |
Ruesen C, Chaidir L, van Laarhoven A, Dian S, Ganiem AR, Nebenzahl-Guimaraes H, Huynen MA, Alisjahbana B, Dutilh BE, van Crevel R. Large-scale genomic analysis shows association between homoplastic genetic variation in Mycobacterium tuberculosis genes and meningeal or pulmonary tuberculosis. Bmc Genomics. 19: 122. PMID 29402222 DOI: 10.1186/S12864-018-4498-Z |
0.264 |
|
| 2006 |
Tabak HF, Hoepfner D, Zand Av, Geuze HJ, Braakman I, Huynen MA. Formation of peroxisomes: present and past. Biochimica Et Biophysica Acta. 1763: 1647-54. PMID 17030445 DOI: 10.1016/J.Bbamcr.2006.08.045 |
0.261 |
|
| 2021 |
Meerstein-Kessel L, Venhuizen J, Garza D, Proellochs NI, Vos EJ, Obiero JM, Felgner PL, Sauerwein RW, Peters M, Yang ASP, Huynen MA. Novel insights from the Plasmodium falciparum sporozoite-specific proteome by probabilistic integration of 26 studies. Plos Computational Biology. 17: e1008067. PMID 33930021 DOI: 10.1371/journal.pcbi.1008067 |
0.26 |
|
| 2023 |
van Strien J, Evers F, Lutikurti M, Berendsen SL, Garanto A, van Gemert GJ, Cabrera-Orefice A, Rodenburg RJ, Brandt U, Kooij TWA, Huynen MA. Comparative Clustering (CompaCt) of eukaryote complexomes identifies novel interactions and sheds light on protein complex evolution. Plos Computational Biology. 19: e1011090. PMID 37549177 DOI: 10.1371/journal.pcbi.1011090 |
0.256 |
|
| 2015 |
Alam MT, Manjeri GR, Rodenburg RJ, Smeitink JA, Notebaart RA, Huynen M, Willems PH, Koopman WJ. Skeletal muscle mitochondria of NDUFS4(-/-) mice display normal maximal pyruvate oxidation and ATP production. Biochimica Et Biophysica Acta. 1847: 526-33. PMID 25687896 DOI: 10.1016/J.Bbabio.2015.02.006 |
0.255 |
|
| 1999 |
Van Nimwegen E, Crutchfield JP, Huynen M. Neutral evolution of mutational robustness Proceedings of the National Academy of Sciences of the United States of America. 96: 9716-9720. PMID 10449760 DOI: 10.1073/Pnas.96.17.9716 |
0.25 |
|
| 2010 |
Nouws J, Nijtmans L, Houten SM, van den Brand M, Huynen M, Venselaar H, Hoefs S, Gloerich J, Kronick J, Hutchin T, Willems P, Rodenburg R, Wanders R, van den Heuvel L, Smeitink J, et al. Acyl-CoA dehydrogenase 9 is required for the biogenesis of oxidative phosphorylation complex I. Cell Metabolism. 12: 283-94. PMID 20816094 DOI: 10.1016/J.Cmet.2010.08.002 |
0.249 |
|
| 2011 |
Jansen BJ, Sama IE, Eleveld-Trancikova D, van Hout-Kuijer MA, Jansen JH, Huynen MA, Adema GJ. MicroRNA genes preferentially expressed in dendritic cells contain sites for conserved transcription factor binding motifs in their promoters. Bmc Genomics. 12: 330. PMID 21708028 DOI: 10.1186/1471-2164-12-330 |
0.248 |
|
| 2017 |
van Goor MK, Verkaart S, van Dam TJ, Huynen MA, van der Wijst J. Interspecies differences in PTH-mediated PKA phosphorylation of the epithelial calcium channel TRPV5. Pflugers Archiv : European Journal of Physiology. PMID 28534087 DOI: 10.1007/S00424-017-1996-9 |
0.242 |
|
| 2021 |
van Esveld SL, Meerstein-Kessel L, Boshoven C, Baaij JF, Barylyuk K, Coolen JPM, van Strien J, Duim RAJ, Dutilh BE, Garza DR, Letterie M, Proellochs NI, de Ridder MN, Venkatasubramanian PB, de Vries LE, ... ... Huynen MA, et al. A Prioritized and Validated Resource of Mitochondrial Proteins in Identifies Unique Biology. Msphere. e0061421. PMID 34494883 DOI: 10.1128/mSphere.00614-21 |
0.242 |
|
| 2020 |
Heuvel CNAMvd, Loopik DL, Ebisch RMF, Elmelik D, Andralojc KM, Huynen M, Bulten J, Bekkers RLM, Massuger LFAG, Melchers WJG, Siebers AG, Leenders WPJ. RNA-based high-risk HPV genotyping and identification of high-risk HPV transcriptional activity in cervical tissues. Modern Pathology. 33: 748-757. PMID 31537894 DOI: 10.1038/S41379-019-0369-7 |
0.235 |
|
| 2010 |
Middelbeek J, Clark K, Venselaar H, Huynen MA, van Leeuwen FN. The alpha-kinase family: an exceptional branch on the protein kinase tree. Cellular and Molecular Life Sciences : Cmls. 67: 875-90. PMID 20012461 DOI: 10.1007/S00018-009-0215-Z |
0.235 |
|
| 2018 |
Ederveen THA, Ferwerda G, Ahout IM, Vissers M, de Groot R, Boekhorst J, Timmerman HM, Huynen MA, van Hijum SAFT, de Jonge MI. Haemophilus is overrepresented in the nasopharynx of infants hospitalized with RSV infection and associated with increased viral load and enhanced mucosal CXCL8 responses. Microbiome. 6: 10. PMID 29325581 DOI: 10.1186/S40168-017-0395-Y |
0.235 |
|
| 2010 |
van Diepen A, Brand HK, Sama I, Lambooy LHJ, van den Heuvel LP, van der Well L, Huynen M, Osterhaus ADME, Andeweg AC, Hermans PWM. Quantitative proteome profiling of respiratory virus-infected lung epithelial cells Journal of Proteomics. 73: 1680-1693. PMID 20470912 DOI: 10.1016/J.Jprot.2010.04.008 |
0.229 |
|
| 2013 |
Jonckheere A, Renkema G, Bras M, van den Heuvel L, Hoischen A, Gilissen C, Huynen M, de Vries M, Smeitink J, Rodenburg R. PP6.8 – 1911 A complex V ATP5A1 defect causes fatal neonatal mitochondrial encephalopathy European Journal of Paediatric Neurology. 17: S47. DOI: 10.1016/S1090-3798(13)70158-2 |
0.228 |
|
| 2004 |
Boxma B, Voncken F, Jannink S, van Alen T, Akhmanova A, van Weelden SW, van Hellemond JJ, Ricard G, Huynen M, Tielens AG, Hackstein JH. The anaerobic chytridiomycete fungus Piromyces sp. E2 produces ethanol via pyruvate:formate lyase and an alcohol dehydrogenase E. Molecular Microbiology. 51: 1389-99. PMID 14982632 DOI: 10.1046/J.1365-2958.2003.03912.X |
0.22 |
|
| 2021 |
Andralojc KM, Molina MA, Qiu M, Spruijtenburg B, Rasing M, Pater B, Huynen MA, Dutilh BE, Ederveen THA, Elmelik D, Siebers AG, Loopik D, Bekkers RLM, Leenders WPJ, Melchers WJG. Novel high-resolution targeted sequencing of the cervicovaginal microbiome. Bmc Biology. 19: 267. PMID 34915863 DOI: 10.1186/s12915-021-01204-z |
0.219 |
|
| 2011 |
Dutilh BE, Huynen MA, Gloerich J, Strous M. Iterative Read Mapping and Assembly Allows the Use of a More Distant Reference in Metagenome Assembly Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches. 379-385. DOI: 10.1002/9781118010518.Ch43 |
0.219 |
|
| 2016 |
Boldt K, van Reeuwijk J, Lu Q, Koutroumpas K, Nguyen TT, Texier Y, van Beersum SE, Horn N, Willer JR, Mans DA, Dougherty G, Lamers IJ, Coene KL, Arts HH, Betts MJ, ... ... Huynen MA, et al. An organelle-specific protein landscape identifies novel diseases and molecular mechanisms. Nature Communications. 7: 11491. PMID 27173435 DOI: 10.1038/ncomms11491 |
0.217 |
|
| 2021 |
Dudás EF, Huynen MA, Lesk AM, Pastore A. Invisible leashes: the tethering VAP proteins from infectious diseases to neurodegeneration. The Journal of Biological Chemistry. 100421. PMID 33609524 DOI: 10.1016/j.jbc.2021.100421 |
0.2 |
|
| 2022 |
Brischigliaro M, Cabrera-Orefice A, Sturlese M, Elurbe DM, Frigo E, Fernandez-Vizarra E, Moro S, Huynen MA, Arnold S, Viscomi C, Zeviani M. CG7630 is the Drosophila melanogaster homolog of the cytochrome c oxidase subunit COX7B. Embo Reports. e54825. PMID 35699132 DOI: 10.15252/embr.202254825 |
0.194 |
|
| 2021 |
van Strien J, Haupt A, Schulte U, Braun HP, Cabrera-Orefice A, Choudhary JS, Evers F, Fernandez-Vizarra E, Guerrero-Castillo S, Kooij TWA, Páleníková P, Pardo M, Ugalde C, Wittig I, Wöhlbrand L, ... ... Huynen MA, et al. CEDAR, an online resource for the reporting and exploration of complexome profiling data. Biochimica Et Biophysica Acta. Bioenergetics. 1862: 148411. PMID 33722514 DOI: 10.1016/j.bbabio.2021.148411 |
0.193 |
|
| 2017 |
Walk J, Reuling IJ, Behet MC, Meerstein-Kessel L, Graumans W, van Gemert GJ, Siebelink-Stoter R, van de Vegte-Bolmer M, Janssen T, Teelen K, de Wilt JHW, de Mast Q, van der Ven AJ, Diez Benavente E, Campino S, ... ... Huynen MA, et al. Modest heterologous protection after Plasmodium falciparum sporozoite immunization: a double-blind randomized controlled clinical trial. Bmc Medicine. 15: 168. PMID 28903777 DOI: 10.1186/S12916-017-0923-4 |
0.192 |
|
| 2016 |
Arts P, van de Veerdonk FL, van der Lee R, Langereis MA, Gilissen C, van Zelst-Stams WA, Huynen MA, van der Meer JW, van Kuppeveld FJ, Veltman JA, Kullberg BJ, Hoischen A, Netea MG. Immunologic defects in severe mucocutaneous HSV-2 infections: Response to IFN-γ therapy. The Journal of Allergy and Clinical Immunology. PMID 27132219 DOI: 10.1016/J.Jaci.2016.02.025 |
0.183 |
|
| 2006 |
Pastore C, Adinolfi S, Huynen MA, Rybin V, Martin S, Mayer M, Bukau B, Pastore A. YfhJ, a molecular adaptor in iron-sulfur cluster formation or a frataxin-like protein? Structure (London, England : 1993). 14: 857-67. PMID 16698547 DOI: 10.1016/J.Str.2006.02.010 |
0.182 |
|
| 2021 |
Coolen JPM, den Drijver EPM, Verweij JJ, Schildkraut JA, Neveling K, Melchers WJG, Kolwijck E, Wertheim HFL, Kluytmans JAJW, Huynen MA. Genome-wide analysis in unravels a high level of genetic homoplasy associated with cefotaxime resistance. Microbial Genomics. 7. PMID 33843573 DOI: 10.1099/mgen.0.000556 |
0.181 |
|
| 2019 |
Ruesen C, Chaidir L, Ugarte-Gil C, van Ingen J, Critchley JA, Hill PC, Ruslami R, Santoso P, Huynen MA, Dockrell HM, Moore DAJ, Alisjahbana B, van Crevel R. Diabetes is associated with genotypically drug-resistant tuberculosis. The European Respiratory Journal. PMID 31831585 DOI: 10.1183/13993003.01891-2019 |
0.179 |
|
| 1996 |
Huynen MA, Neumann AU. Rate of killing of HIV-infected T cells and disease progression. Science (New York, N.Y.). 272: 1962. PMID 8658174 DOI: 10.1126/Science.272.5270.1962 |
0.174 |
|
| 2022 |
van Esveld SL, Rodenburg RJ, Al-Murshedi F, Al-Ajmi E, Al-Zuhaibi S, Huynen MA, Spelbrink JN. Mitochondrial RNA processing defect caused by a SUPV3L1 mutation in two siblings with a novel neurodegenerative syndrome. Journal of Inherited Metabolic Disease. PMID 35023579 DOI: 10.1002/jimd.12476 |
0.16 |
|
| 2021 |
Evers F, Cabrera-Orefice A, Elurbe DM, Kea-Te Lindert M, Boltryk SD, Voss TS, Huynen MA, Brandt U, Kooij TWA. Composition and stage dynamics of mitochondrial complexes in Plasmodium falciparum. Nature Communications. 12: 3820. PMID 34155201 DOI: 10.1038/s41467-021-23919-x |
0.15 |
|
| 2012 |
Nielsen FG, Markus KG, Friborg RM, Favrholdt LM, Stunnenberg HG, Huynen M. CATCHprofiles: clustering and alignment tool for ChIP profiles. Plos One. 7: e28272. PMID 22238575 DOI: 10.1371/journal.pone.0028272 |
0.143 |
|
| 2022 |
Molina MA, Andralojc KM, Huynen MA, Leenders WPJ, Melchers WJG. In-depth insights into cervicovaginal microbial communities and hrHPV infections using high-resolution microbiome profiling. Npj Biofilms and Microbiomes. 8: 75. PMID 36171433 DOI: 10.1038/s41522-022-00336-6 |
0.134 |
|
| 2012 |
van Dam J, Field M, Huynen M. Origin and extension of the IFT complex in early eukaryotic evolution Cilia. 1. DOI: 10.1186/2046-2530-1-S1-P56 |
0.121 |
|
| 2022 |
Huynen MA, Elurbe DM. Mitochondrial complex complexification. Science (New York, N.Y.). 376: 794-795. PMID 35587988 DOI: 10.1126/science.abq0368 |
0.12 |
|
| 2024 |
Gillard J, Suffiotti M, Brazda P, Venkatasubramanian PB, Versteegen P, de Jonge MI, Kelly D, Bibi S, Pinto MV, Simonetti E, Babiceanu M, Kettring A, Teodosio C, de Groot R, Berbers G, ... ... Huynen MA, et al. Antiviral responses induced by Tdap-IPV vaccination are associated with persistent humoral immunity to Bordetella pertussis. Nature Communications. 15: 2133. PMID 38459022 DOI: 10.1038/s41467-024-46560-w |
0.111 |
|
| 2008 |
Gabaldón T, Huynen MA. Reconstruction of ancestral proteomes Ancestral Sequence Reconstruction. DOI: 10.1093/acprof:oso/9780199299188.003.0012 |
0.111 |
|
| 2020 |
Schirris TJJ, Rossell S, de Haas R, Frambach SJCM, Hoogstraten CA, Renkema GH, Beyrath JD, Willems PHGM, Huynen MA, Smeitink JAM, Russel FGM, Notebaart RA. Stimulation of cholesterol biosynthesis in mitochondrial complex I-deficiency lowers reductive stress and improves motor function and survival in mice. Biochimica Et Biophysica Acta. Molecular Basis of Disease. 166062. PMID 33385517 DOI: 10.1016/j.bbadis.2020.166062 |
0.11 |
|
| 2021 |
Goldmann JM, Hampstead JE, Wong WSW, Wilfert AB, Turner TN, Jonker MA, Bernier R, Huynen MA, Eichler EE, Veltman JA, Maxwell GL, Gilissen C. Differences in the number of de novo mutations between individuals are due to small family-specific effects and stochasticity. Genome Research. PMID 34301630 DOI: 10.1101/gr.271809.120 |
0.094 |
|
| 2022 |
Andralojc KM, Elmelik D, Rasing M, Pater B, Siebers AG, Bekkers R, Huynen MA, Bulten J, Loopik D, Melchers WJG, Leenders WPJ. Targeted RNA next generation sequencing analysis of cervical smears can predict the presence of hrHPV-induced cervical lesions. Bmc Medicine. 20: 206. PMID 35676700 DOI: 10.1186/s12916-022-02386-1 |
0.09 |
|
| 2008 |
Oti M, Huynen MA, Brunner HG. Phenome connections. Trends in Genetics : Tig. 24: 103-6. PMID 18243400 DOI: 10.1016/j.tig.2007.12.005 |
0.084 |
|
| 2021 |
de Jong RM, Meerstein-Kessel L, Da DF, Nsango S, Challenger JD, van de Vegte-Bolmer M, van Gemert GJ, Duarte E, Teyssier N, Sauerwein RW, Churcher TS, Dabire RK, Morlais I, Locke E, Huynen MA, et al. Monoclonal antibodies block transmission of genetically diverse Plasmodium falciparum strains to mosquitoes. Npj Vaccines. 6: 101. PMID 34385463 DOI: 10.1038/s41541-021-00366-9 |
0.077 |
|
| 2020 |
Huynen M, Kapusuz KY, Sun X, Van der Plas G, Beyne E, De Zutter D, Vande Ginste D. Entire Domain Basis Function Expansion of the Differential Surface Admittance for Efficient Broadband Characterization of Lossy Interconnects Ieee Transactions On Microwave Theory and Techniques. 68: 1217-1233. DOI: 10.1109/TMTT.2019.2957485 |
0.075 |
|
| 2011 |
Megchelenbrink W, Huynen M, Marchiori E. Flux measurement selection in metabolic networks Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 7036: 214-224. DOI: 10.1007/978-3-642-24855-9_19 |
0.068 |
|
| 2021 |
Fröberg J, Gillard J, Philipsen R, Lanke K, Rust J, van Tuijl D, Teelen K, Bousema T, Simonetti E, van der Gaast-de Jongh CE, Bos M, van Kuppeveld FJ, Bosch BJ, Nabuurs-Franssen M, van der Geest-Blankert N, ... ... Huynen MA, et al. SARS-CoV-2 mucosal antibody development and persistence and their relation to viral load and COVID-19 symptoms. Nature Communications. 12: 5621. PMID 34556667 DOI: 10.1038/s41467-021-25949-x |
0.067 |
|
| 2022 |
Molina MA, Coenen BA, Leenders WPJ, Andralojc KM, Huynen MA, Melchers WJG. Assessing the Cervicovaginal Microbiota in the Context of hrHPV Infections: Temporal Dynamics and Therapeutic Strategies. Mbio. e0161922. PMID 35980030 DOI: 10.1128/mbio.01619-22 |
0.065 |
|
| 2023 |
Rademaker DT, Koopmans JJ, Thyen GMSM, Piruska A, Huck WTS, Vriend G, 't Hoen PAC, Kooij TWA, Huynen MA, Proellochs NI. Quantifying the deformability of malaria-infected red blood cells using deep learning trained on synthetic cells. Iscience. 26: 108542. PMID 38089575 DOI: 10.1016/j.isci.2023.108542 |
0.062 |
|
| 2023 |
Molina MA, Melchers WJG, Andralojc KM, Leenders WPJ, Huynen MA. Longitudinal analysis on the ecological dynamics of the cervicovaginal microbiome in hrHPV infection. Computational and Structural Biotechnology Journal. 21: 4424-4431. PMID 37731597 DOI: 10.1016/j.csbj.2023.09.011 |
0.059 |
|
| 2007 |
Hackstein JHP, Tjaden J, Koopman W, Huynen M. Hydrogenosomes (and related organelles, either) are not the same Origin of Mitochondria and Hydrogenosomes. 135-159. DOI: 10.1007/978-3-540-38502-8_7 |
0.05 |
|
| 2020 |
Lambert EE, Corbière V, van Gaans-van den Brink JAM, Duijst M, Venkatasubramanian PB, Simonetti E, Huynen M, Diavatopoulos DD, Versteegen P, Berbers GAM, Mascart F, van Els CACM. Uncovering Distinct Primary Vaccination-Dependent Profiles in Human Specific CD4+ T-Cell Responses Using a Novel Whole Blood Assay. Vaccines. 8. PMID 32429152 DOI: 10.3390/vaccines8020225 |
0.038 |
|
| 2022 |
van Schuppen E, Fröberg J, Venkatasubramanian PB, Versteegen P, de Graaf H, Holubová J, Gillard J, van Gageldonk PGM, Joosten I, de Groot R, Šebo P, Berbers GAM, Read RC, Huynen MA, de Jonge MI, et al. Prior exposure to B. pertussis shapes the mucosal antibody response to acellular pertussis booster vaccination. Nature Communications. 13: 7429. PMID 36460655 DOI: 10.1038/s41467-022-35165-w |
0.035 |
|
| 2023 |
Papadimitriou TI, Singh P, van Caam A, Walgreen B, Gorris MAJ, Vitters EL, van Ingen IL, Koenders MI, Smeets RL, Vonk M, de Vries JM, van der Kraan PM, van Oosterhout Y, Huynen MA, Koenen HJPM, et al. CD7 activation regulates cytotoxicity-driven pathology in systemic sclerosis, yielding a target for selective cell depletion. Annals of the Rheumatic Diseases. PMID 38123919 DOI: 10.1136/ard-2023-224827 |
0.033 |
|
| 2023 |
Fröberg J, Koomen VJCH, van der Gaast-de Jongh CE, Philipsen R, GeurtsvanKessel CH, de Vries RD, Baas MC, van der Molen RG, de Jonge MI, Hilbrands LB, Huynen MA, Diavatopoulos DA. Primary exposure to SARS-CoV-2 via infection or vaccination determines mucosal antibody-dependent ACE2 binding inhibition. The Journal of Infectious Diseases. PMID 37675756 DOI: 10.1093/infdis/jiad385 |
0.031 |
|
| 2023 |
van Woudenbergh E, van Rooijen DM, Veldman-Wolf JJ, Nicolaie MA, Huynen MA, van der Klis FRM, de Jonge MI, den Hartog G. Effect of age and season on respiratory mucosal immune marker profiles. The Journal of Allergy and Clinical Immunology. PMID 38142822 DOI: 10.1016/j.jaci.2023.12.009 |
0.023 |
|
| 2022 |
Gillard J, Blok BA, Garza DR, Venkatasubramanian PB, Simonetti E, Eleveld MJ, Berbers GAM, van Gageldonk PGM, Joosten I, de Groot R, de Bree LCJ, van Crevel R, de Jonge MI, Huynen MA, Netea MG, et al. BCG-induced trained immunity enhances acellular pertussis vaccination responses in an explorative randomized clinical trial. Npj Vaccines. 7: 21. PMID 35177621 DOI: 10.1038/s41541-022-00438-4 |
0.016 |
|
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