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Martijn A. Huynen - Publications

Affiliations: 
Nijmegen Center for Molecular Life Science University of Nijmegen, Nijmegen, Gelderland, Netherlands 
Website:
http://www.ncmls.nl/NCMLS/MenuStructures/PI/theme2/MartijnHuynen.asp

166 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
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  0.32
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  0.76
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  0.8
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  0.76
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  0.76
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  0.76
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  0.8
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  0.48
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  1
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  0.32
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  1
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  1
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  1
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  1
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  1
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  0.48
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
2014 Moon-van der Staay SY, van der Staay GW, Michalowski T, Jouany JP, Pristas P, Javorský P, KiÅ¡idayová 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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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: 10.1093/bioinformatics/btr316  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
2010 Szklarczyk R, Huynen MA. Mosaic origin of the mitochondrial proteome. Proteomics. 10: 4012-24. PMID 21080492 DOI: 10.1002/pmic.201000329  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
2008 Gabaldón T, Huynen MA. Reconstruction of ancestral proteomes Ancestral Sequence Reconstruction. DOI: 10.1093/acprof:oso/9780199299188.003.0012  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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: 10.1016/S0378-1097(02)00720-6  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
2000 Huynen MA, Snel B. Gene and context: integrative approaches to genome analysis. Advances in Protein Chemistry. 54: 345-79. PMID 10829232  1
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  1
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  1
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: 10.1042/0264-6021:3430115  1
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  1
1999 Snel B, Bork P, Huynen MA. Genome phylogeny based on gene content. Nature Genetics. 21: 108-10. PMID 9916801 DOI: 10.1038/5052  1
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  1
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  1
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  1
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  1
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  1
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  1
1997 Huynen MA, Diaz-Lazcoz Y, Bork P. Differential genome display. Trends in Genetics : Tig. 13: 389-90. PMID 9351339  1
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  1
1996 Huynen MA. Exploring phenotype space through neutral evolution. Journal of Molecular Evolution. 43: 165-9. PMID 8703081  1
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  1
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  1
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  1
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  1
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  1
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