| 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 |
0.58 |
|
| 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 |
0.589 |
|
| 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 |
0.346 |
|
| 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 |
0.325 |
|
| 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 |
0.409 |
|
| 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 |
0.617 |
|
| 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 |
0.715 |
|
| 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 |
0.69 |
|
| 2010 |
Szklarczyk R, Huynen MA. Mosaic origin of the mitochondrial proteome. Proteomics. 10: 4012-24. PMID 21080492 DOI: 10.1002/Pmic.201000329 |
0.404 |
|
| 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 |
0.334 |
|
| 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 |
0.741 |
|
| 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 |
0.799 |
|
| 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 |
0.469 |
|
| 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 |
0.832 |
|
| 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 |
0.381 |
|
| 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 |
0.546 |
|
| 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 |
0.397 |
|
| 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 |
0.764 |
|
| 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 |
0.788 |
|
| 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 |
0.769 |
|
| 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 |
0.796 |
|
| 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 |
0.667 |
|
| 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 |
0.627 |
|
| 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 |
0.795 |
|
| 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 |
0.552 |
|
| 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 |
0.806 |
|
| 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 |
0.572 |
|
| 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 |
0.422 |
|
| 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 |
0.778 |
|
| 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 |
0.675 |
|
| 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 |
0.754 |
|
| 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 |
0.594 |
|
| 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 |
0.778 |
|
| 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 |
0.629 |
|
| 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 |
0.843 |
|
| 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 |
0.756 |
|
| 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 |
0.59 |
|
| 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 |
|
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