Publications of the Comparative genomics group

  • 2017 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., 2017 Mar;1858(3):208-17 Details

  • 2017 Zazo Seco C, 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, Tranebjaerg L, van Wijk E, Scheffer-de Gooyert JM, Siddique S, Baets J, de Jonghe P, Kazmi SA, Sadananthan SA, van de Warrenburg BP, Khor CC, Gopfert MC, Qamar R, Schenck A, Kremer H, Siddiqi S.
    A homozygous FITM2 mutation causes a deafness-dystonia syndrome with motor regression and signs of ichthyosis and sensory neuropathy
    Dis Model Mech., 2017 Feb 01;10(2):105-18 Details

  • 2017 Adriaenssens EM, Krupovic M, Knezevic P, Ackermann HW, Barylski J, Brister JR, Clokie MR, Duffy S, Dutilh BE, Edwards RA, Enault F, Jang HB, Klumpp J, Kropinski AM, Lavigne R, Poranen MM, Prangishvili D, Rumnieks J, Sullivan MB, Wittmann J, Oksanen HM, Gillis A, Kuhn JH.
    Taxonomy of prokaryotic viruses: 2016 update from the ICTV bacterial and archaeal viruses subcommittee
    Arch Virol., 2017 Apr;162(4):1153-7 Details

  • 2017 Motlagh AM, Bhattacharjee AS, Coutinho FH, Dutilh BE, Casjens SR, Goel RK.
    Insights of Phage-Host Interaction in Hypersaline Ecosystem through Metagenomics Analyses.
    Front Microbiol., 2017;8:352 Details

  • 2017 van Kruijsbergen I, Hontelez S, Elurbe DM, van Heeringen SJ, Huynen MA, Veenstra GJ.
    Heterochromatic histone modifications at transposons in Xenopus tropicalis embryos.
    Dev Biol., 2016 Sep 14. pii: S0012-1606(16)30221-4 Details

  • 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, Pierquin G, Doray B, Gilbert-Dussardier B, Reversade B, Steichen-Gersdorf E, Baumann C, Panigrahi I, Fargeot-Espaliat A, Dieux A, David A, Goldenberg A, Bongers E, Gaillard D, Argente J, Aral B, Gigot N, St-Onge J, Birnbaum D, Phadke SR, Cormier-Daire V, Eguether T, Pazour GJ, Herranz-Perez V, Goldstein JS, Pasquier L, Loget P, Saunier S, Megarbane A, Rosnet O, Leroux MR, Wallingford JB, Blacque OE, Nachury MV, Attie-Bitach T, Riviere JB, Faivre L, Thauvin-Robinet C
    Fifteen years of research on oral-facial-digital syndromes: from 1 to 16 causal genes
    J Med Genet, 2017 Jun;54(6):371-80 Details

  • 2017 Maat DS, Biggs T, Evans C, van Bleijswijk JDL, van der Wel NN, Dutilh BE, Brussaard CPD
    Characterization and Temperature Dependence of Arctic Micromonas polaris Viruses
    Viruses, 2017 Jun 02;9(6) Details

  • 2017 Speth DR, Lagkouvardos I, Wang Y, Qian PY, Dutilh BE, Jetten MSM
    Draft Genome of Scalindua rubra, Obtained from the Interface Above the Discovery Deep Brine in the Red Sea, Sheds Light on Potential Salt Adaptation Strategies in Anammox Bacteria
    Microb Ecol, 2017 Jul;74(1):1-5 Details

  • 2017 van Kruijsbergen I, Hontelez S, Elurbe DM, van Heeringen SJ, Huynen MA, Veenstra GJC
    Heterochromatic histone modifications at transposons in Xenopus tropicalis embryos
    Dev Biol, 2017 Jun 15;426(2):460-71 Details

  • 2017 Coutinho FH, Silveira CB, Gregoracci GB, Thompson CC, Edwards RA, Brussaard CPD, Dutilh BE, Thompson FL.
    Marine viruses discovered via metagenomics shed light on viral strategies throughout the oceans
    Nat Commun, 2017 Jul 05;8:15955 Details

  • 2017 Quainoo S, Coolen JPM, van Hijum S, Huynen MA, Melchers WJG, van Schaik W, Wertheim HFL.
    Whole-Genome Sequencing of Bacterial Pathogens: the Future of Nosocomial Outbreak Analysis
    Clin Microbiol Rev., 2017 Oct;30(4):1015-63 Details

  • 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, Clark TG, Huynen MA, Hermsen CC, Bijker EM, Scholzen A, Sauerwein RW.
    Modest heterologous protection after Plasmodium falciparum sporozoite immunization: a double-blind randomized controlled clinical trial.
    BMC Med., 2017 Sep 13;15(1):168 Details

  • 2017 Zuidscherwoude M, Worah K, van der Schaaf A, Buschow SI, van Spriel AB.
    Differential expression of tetraspanin superfamily members in dendritic cell subsets.
    PLoS One., 2017;12(9):e0184317. Details

  • 2017 van der Lee R., Wiel Laurens, Teunis J.P., Huynen, Martijn A.
    Genome-scale detection of positive selection in nine primates predicts human-virus evolutionary conflicts
    Nucleic Acids Res., 2017 11-08-2017;gkx704 Details

  • 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, Huijben K, Steenbergen G, Quelhas D, Diogo L, Rymen D, Jaeken J, Guffon N, Cheillan D, van den Heuvel LP, Maeda Y, Kaiser O, Schara U, Gerner P, van den Boogert MA, Holleboom AG, Nassogne MC, Sokal E, Salomon J, van den Bogaart G, Drenth JP, Huynen MA, Veltman JA, Wevers RA, Morava E, Matthijs G, Foulquier F, Marquardt T, Lefeber DJ.
    CCDC115 Deficiency Causes a Disorder of Golgi Homeostasis with Abnormal Protein Glycosylation.
    Am J Hum Genet. , 2016 Feb 4;98(2):310-21. doi: 10.1016/j.ajhg.2015.12.010. Epub 2016 Jan 28. Details

  • 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, van den Bogaart G, Salomon J, Holleboom AG, Rodenburg RJ, Drenth JP, Huynen MA, Wevers RA, Morava E, Foulquier F, Veltman JA, Lefeber DJ.
    TMEM199 Deficiency Is a Disorder of Golgi Homeostasis Characterized by Elevated Aminotransferases, Alkaline Phosphatase, and Cholesterol and Abnormal Glycosylation.
    Am J Hum Genet., 2016 Feb 4;98(2):322-30. doi: 10.1016/j.ajhg.2015.12.011. Epub 2016 Jan 28. Details

  • 2016 Barr JJ, Dutilh BE, Skennerton CT, Fukushima T, Hastie ML, Gorman JJ, Tyson GW, Bond PL
    Metagenomic and metaproteomic analyses of Accumulibacter phosphatis-enriched floccular and granular biofilm
    Environ Microbiol., 2016 Jan;18(1):273-87 Details

  • 2016 Chevrier V, Bruel AL, Van Dam TJ, Franco B, Lo Scalzo M, Lembo F, Audebert S, Baudelet E, Isnardon D, Bole A, Borg JP, Kuentz P, Thevenon J, Burglen L, Faivre L, Riviere JB, Huynen MA, Birnbaum D, Rosnet O, Thauvin-Robinet C
    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
    Hum Mol Genet., 2016 Feb 1;25(3):497-513 Details

  • 2016 Edwards RA, McNair K, Faust K, Raes J, Dutilh BE
    Computational approaches to predict bacteriophage-host relationships
    FEMS Microbiol Rev, 2016 Mar;40(2):258-72 Details

  • 2016 Huynen MA, Muhlmeister 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, 2016 Jan;1863(1):91-101 Details

  • 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
    Am J Hum Genet, 2016 Jan 7;98(1):149-64 Details

  • 2016 Kortman GA, Dutilh BE, Maathuis AJ, Engelke UF, Boekhorst J, Keegan KP, Nielsen FG, Betley J, Weir JC, Kingsbury Z, Kluijtmans LA, Swinkels DW, Venema K, Tjalsma H
    Microbial Metabolism Shifts Towards an Adverse Profile with Supplementary Iron in the TIM-2 In vitro Model of the Human Colon
    Front Microbiol, 2015;6:1481 Details

  • 2016 Krupovic M, Dutilh BE, Adriaenssens EM, Wittmann J, Vogensen FK, Sullivan MB, Rumnieks J, Prangishvili D, Lavigne R, Kropinski AM, Klumpp J, Gillis A, Enault F, Edwards RA, Duffy S, Clokie MR, Barylski J, Ackermann HW, Kuhn JH
    Taxonomy of prokaryotic viruses: update from the ICTV bacterial and archaeal viruses subcommittee
    Arch Virol, 2016 Apr;161(4):1095-9 Details

  • 2016 Lambacher NJ, Bruel AL, van Dam TJ, Szymanska K, Slaats GG, Kuhns S, McManus GJ, Kennedy JE, Gaff K, Wu KM, van der Lee R, Burglen L, Doummar D, Riviere JB, Faivre L, Attie-Bitach T, Saunier S, Curd A, Peckham M, Giles RH, Johnson CA, Huynen MA, Thauvin-Robinet C, Blacque OE
    TMEM107 recruits ciliopathy proteins to subdomains of the ciliary transition zone and causes Joubert syndrome
    Nat Cell Biol, 2016 Jan;18(1):122-31 Details

  • 2016 Oti M, Falck J, Huynen MA, Zhou H
    CTCF-mediated chromatin loops enclose inducible gene regulatory domains
    BMC Genomics, 2016;17(1):252 Details

  • 2016 Silva GG, Green KT, Dutilh BE, Edwards RA
    SUPER-FOCUS: a tool for agile functional analysis of shotgun metagenomic data
    Bioinformatics, 2016 Feb 1;32(3):354-61 Details

  • 2016 Speth DR, In 't Zandt MH, Guerrero-Cruz S, Dutilh BE, Jetten MS
    Genome-based microbial ecology of anammox granules in a full-scale wastewater treatment system
    Nat Commun, 2016;7:11172 Details

  • 2016 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 Res, 2016 Jan 4;44(D1):D567-73 Details

  • 2016 Szappanos B, Fritzemeier J, Csorgo B, Lazar V, Lu X, Fekete G, Balint B, Herczeg R, Nagy I, Notebaart RA, Lercher MJ, Pal C, Papp B.
    Adaptive evolution of complex innovations through stepwise metabolic niche expansion
    Nat Commun, 2016;7:11607 Details

  • 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, Rodenburg RJ, Adamowicz M, Crushell E, Koenen H, Adams D, Vodopiutz J, Greber-Platzer S, Muller T, Dueckers G, Morava E, Sykut-Cegielska J, Martens GJ, Wevers RA, Niehues T, Huynen MA, Veltman JA, Stevens TH, Lefeber DJ
    ATP6AP1 deficiency causes an immunodeficiency with hepatopathy, cognitive impairment and abnormal protein glycosylation
    Nat Commun., 2016;7:11600 Details

  • 2016 Boldt K, van Reeuwijk J, Lu Q, Koutroumpas K, Nguyen TM, Texier Y, van Beersum SE, Horn N, Willer JR, Mans DA, Dougherty G, Lamers IJ, Coene KL, Arts HH, Betts MJ, Beyer T, Bolat E, Gloeckner CJ, Haidari K, Hetterschijt L, Iaconis D, Jenkins D, Klose F, Knapp B, Latour B, Letteboer SJ, Marcelis CL, Mitic D, Morleo M, Oud MM, Riemersma M, Rix S, Terhal PA, Toedt G, van Dam TJ, de Vrieze E, Wissinger Y, Wu KM, Apic G, Beales PL, Blacque OE, Gibson TJ, Huynen MA, Katsanis N, Kremer H, Omran H, van Wijk E, Wolfrum U, Kepes F, Davis EE, Franco B, Giles RH, Ueffing M, Russell RB, Roepman R
    An organelle-specific protein landscape identifies novel diseases and molecular mechanisms
    Nat Commun., 2016;7:11491 Details

  • 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., 2016 Jul;1857(7):971-9 Details

  • 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-gamma therapy
    J Allergy Clin Immunol, 2016 Apr 7 Details

  • 2016 Di Blasio S, Wortel IM, van Bladel DA, de Vries LE, Duiveman-de Boer T, Worah K, de Haas N, Buschow SI, de Vries IJ, Figdor CG, Hato SV
    Human CD1c(+) DCs are critical cellular mediators of immune responses induced by immunogenic cell death
    Oncoimmunology, 2016 Aug;5(8):e1192739 Details

  • 2016 Worah K, Mathan TS, Vu Manh TP, Keerthikumar S, Schreibelt G, Tel J, Duiveman-de Boer T, Skold AE, van Spriel AB, de Vries IJ, Huynen MA, Wessels HJ, Gloerich J, Dalod M, Lasonder E, Figdor CG, Buschow SI
    Proteomics of Human Dendritic Cell Subsets Reveals Subset-Specific Surface Markers and Differential Inflammasome Function
    Cell Rep, 2016 Sep 13;16(11):2953-66 Details

  • 2016 Yan R, Friemel M, Aloisi C, Huynen M, Taylor IA, Leimkuhler S, Pastore A
    The Eukaryotic-Specific ISD11 Is a Complex-Orphan Protein with Ability to Bind the Prokaryotic IscS
    PLoS One, 2016;11(7):e0157895 Details

  • 2016 Fróes AM, Dutilh BE
    Bioinformatics for studying environmental microorganisms
    Molecular Diversity of Environmental Prokaryotes, Eds. Thiago B. Rodrigues and Amaro E. Trindade Silva. CRC Press Details

  • 2016 Coutinho FH, Dutilh BE, Thompson CC, Thompson FL
    Proposal of fifteen new species of Parasynechococcus based on genomic, physiological and ecological features
    Arch Microbiol., 2016 Dec;198(10):973-86 Details

  • 2016 Gambelli L, Cremers G, Mesman R, Guerrero S, Dutilh BE, Jetten MS, Op den Camp HJ, van Niftrik L
    Ultrastructure and Viral Metagenome of Bacteriophages from an Anaerobic Methane Oxidizing Methylomirabilis Bioreactor Enrichment Culture
    Front Microbiol., 2016;7:1740 Details

  • 2016 Roux S, Brum JR, Dutilh BE, Sunagawa S, Duhaime MB, Loy A, Poulos BT, Solonenko N, Lara E, Poulain J, Pesant S, Kandels-Lewis S, Dimier C, Picheral M, Searson S, Cruaud C, Alberti A, Duarte CM, Gasol JM, Vaque D, Bork P, Acinas SG, Wincker P, Sullivan MB
    Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses
    Nat New Biol., 2016 Sep 29;537(7622):689-93 Details

  • 2015 Novotny R, Vitasek R, Bartoskova A, Cizek P, Prinosilova P, Novakova K.
    Azoospermia with variable testicular histology after 7 months of treatment with a deslorelin implant in toms
    Theriogenology, Apr 15;83(7):1188-93. doi: 10.1016/j.theriogenology.2014.12.026.

  • 2015 Speth DR, Russ L, Kartal B, Op den Camp HJ, Dutilh BE, Jetten MS.
    Draft Genome Sequence of Anammox Bacterium "Candidatus Scalindua brodae," Obtained Using Differential Coverage Binning of Sequencing Data from Two Reactor Enrichments
    Genome Announc, Jan 8;3(1). pii: e01415-14. doi: 10.1128/genomeA.01415-14. Details

  • 2015 Thompson CC, Amaral GR, Campeao M, Edwards RA, Polz MF, Dutilh BE, Ussery DW, Sawabe T, Swings J, Thompson FL.
    Microbial taxonomy in the post-genomic era: Rebuilding from scratch?
    Arch Microbiol., Apr;197(3):359-70. doi: 10.1007/s00203-014-1071-2. Details

  • 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
    Biochim Biophys Acta, 1847(6-7):526-33. doi: 10.1016/j.bbabio.2015.02.006. Details

  • 2015 Busch J, Nascimento JR, Magalhaes AC, Dutilh BE, Dinsdale E
    Copper tolerance and distribution of epibiotic bacteria associated with giant kelp Macrocystis pyrifera in southern California
    Ecotoxicology, Jul;24(5):1131-40. doi: 10.1007/s10646-015-1460-6. Details

  • 2015 Hall RJ, Draper JL, Nielsen FG, Dutilh BE.
    Beyond research: a primer for considerations on using viral metagenomics in the field and clinic
    Front Microbiol., Mar 25;6:224. doi: 10.3389/fmicb.2015.00224. Details

  • 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, Fitzgeral K, Joosten LA, Perfect JR, Wijmenga C, van de Veerdonk FL, Huynen MA, Xavier RJ, Kullberg BJ, Netea MG.
    The RIG-I-like helicase receptor MDA5 (IFIH1) is involved in the host defense against Candida infections
    Eur J Clin Microbiol Infect Dis, May;34(5):963-74. doi: 10.1007/s10096-014-2309-2. Details

  • 2015 Lu X, Megchelenbrink W, Notebaart RA, Huynen MA
    Predicting human genetic interactions from cancer genome evolution
    PLoS One, May 1;10(5):e0125795. doi: 10.1371/journal.pone.0125795 Details

  • 2015 Matthews TD, Schmieder R, Silva GG, Busch J, Cassman N, Dutilh BE, Green D, Matlock B, Heffernan B, Olsen GJ, Farris Hanna L, Schifferli DM, Maloy S, Dinsdale EA, Edwards RA
    Genomic Comparison of the Closely-Related Salmonella enterica Serovars Enteritidis, Dublin and Gallinarum
    PLoS One, Jun 3;10(6):e0126883. doi: 10.1371/journal.pone.0126883. Details

  • 2015 Zoll J, Rahamat-Langendoen J, Ahout I, de Jonge MI, Jans J, Huijnen MA, Ferwerda G, Warris A, Melchers WJ.
    Direct multiplexed whole genome sequencing of respiratory tract samples reveals full viral genomic information
    J Clin Virol, May;66:6-11. doi: 10.1016/j.jcv.2015.02.010. Details

  • 2015 Wheway G, Schmidts M, Mans DA, Szymanska K, Nguyen TM, Racher H, Phelps IG, Toedt G, Kennedy J, Wunderlich KA, Sorusch N, Abdelhamed ZA, Natarajan S, Herridge W, van Reeuwijk J, Horn N, Boldt K, Parry DA, Letteboer SJ, Roosing S, Adams M, Bell SM, Bond J, Higgins J, Morrison EE, Tomlinson DC, Slaats GG, van Dam TJ, Huang L, Kessler K, Giessl A, Logan CV, Boyle EA, Shendure J, Anazi S, Aldahmesh M, Al Hazzaa S, Hegele RA, Ober C, Frosk P, Mhanni AA, Chodirker BN, Chudley AE, Lamont R, Bernier FP, Beaulieu CL, Gordon P, Pon RT, Donahue C, Barkovich AJ, Wolf L, Toomes C, Thiel CT, Boycott KM, McKibbin M, Inglehearn CF, Stewart F, Omran H, Huynen MA, Sergouniotis PI, Alkuraya FS, Parboosingh JS, Innes AM, Willoughby CE, Giles RH, Webster AR, Ueffing M, Blacque O, Gleeson JG, Wolfrum U, Beales PL, Gibson T, Doherty D, Mitchison HM, Roepman R, Johnson CA.
    An siRNA-based functional genomics screen for the identification of regulators of ciliogenesis and ciliopathy genes
    nat cell biol, Aug;17(8):1074-87. doi: 10.1038/ncb3201. Details

  • 2015 Coutinho FH, Meirelles PM, Moreira AP, Paranhos RP, Dutilh BE, Thompson FL.
    Niche distribution and influence of environmental parameters in marine microbial communities: a systematic review.
    PeerJ., Jun 16;3:e1008. doi: 10.7717/peerj.1008. Details

  • 2015 Megchelenbrink W, Katzir R, Lu X, Ruppin E, Notebaart RA.
    Synthetic dosage lethality in the human metabolic network is highly predictive of tumor growth and cancer patient survival
    Proc Natl Acad Sci U S A, Sep 29;112(39):12217-22. doi: 10.1073/pnas.1508573112. Details

  • 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.
    Prog Retin Eye Res., Sep;48:137-59. doi: 10.1016/j.preteyeres.2015.04.004. Details

  • 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., Sep 15;16(1):691. doi: 10.1186/s12864-015-1883-8. Details

  • 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 Res., Nov 17. pii: gkv1228. Details

  • 2015 Lambacher N.J., Bruel A., van Dam T.J.P, et al.
    TMEM107 recruits ciliopathy proteins to subdomains of the ciliary transition zone and causes Joubert syndrome
    Nat Cell Biol., In Press

  • 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, Rivière JB, Huynen MA, Birnbaum D, Rosnet O, Thauvin-Robinet C.
    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.
    Hum Mol Genet, Dec 7. pii: ddv488. [Epub ahead of print] Details

  • 2015 Bezemer D, Cori A, Ratmann O, van Sighem A, Hermanides HS, Dutilh BE, Gras L, Rodrigues Faria N, van den Hengel R, Duits AJ, Reiss P, de Wolf F, Fraser C.
    Dispersion of the HIV-1 Epidemic in Men Who Have Sex with Men in the Netherlands: A Combined Mathematical Model and Phylogenetic Analysis.
    PLoS Med, Nov 3;12(11):e1001898. Details

  • 2015 Megchelenbrink W, Rossell S, Huynen MA, Notebaart RA, Marchiori E.
    Estimating Metabolic Fluxes Using a Maximum Network Flexibility Paradigm.
    PLoS One, Oct 12;10(10):e0139665. Details

  • 2015 Garza DR, Dutilh BE
    From cultured to uncultured genome sequences: metagenomics and modeling microbial ecosystems.
    Cell Mol Life Sci, Nov;72(22):4287-308. Details

  • 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 Comput Biol., Oct 20;11(10):e1004553. Details

  • 2015 Sanders AA, de Vrieze E, Alazami AM, Alzahrani F, Malarkey EB, Sorusch N, Tebbe L, Kuhns S, van Dam TJ, Alhashem A, Tabarki B, Lu Q, Lambacher NJ, Kennedy JE, Bowie RV, Hetterschijt L, van Beersum S, van Reeuwijk J, Boldt K, Kremer H, Kesterson RA, Monies D, Abouelhoda M, Roepman R, Huynen MH, Ueffing M, Russell RB, Wolfrum U, Yoder BK, van Wijk E, Alkuraya FS, Blacque OE.
    KIAA0556 is a novel ciliary basal body component mutated in Joubert syndrome.
    Genome Biol., Dec 29;16(1):293. Details

  • 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, Oct 8;16:325. Details

  • 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, Rivière JB, Huynen MA, Birnbaum D, Rosnet O, Thauvin-Robinet C
    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
    Hum Mol Genet, 2016 Feb 1;25(3):497-513 Details

  • 2015 Megchelenbrink W, Katzir R, Lu X, Ruppin E, Notebaart RA
    Synthetic dosage lethality in the human metabolic network is highly predictive of tumor growth and cancer patient survival
    Proc Natl Acad Sci U S A, 2015 Sep 29;112(39):12217-22 Details

  • 2015 Appenzeller S, Gilissen C, Rijntjes J, Tops BB, Kastner-van Raaij A, Hebeda KM, Nissen L, Dutilh BE, van Krieken JH, Groenen PJ
    Immunoglobulin rearrangement analysis from multiple lesions in the same patient using next-generation sequencing
    Histopathology, 2015 Dec;67(6):843-58 Details

  • 2014 Ballouz S, Liu JY, Oti M, Gaeta B, Fatkin D, Bahlo M, Wouters MA.
    Candidate disease gene prediction using Gentrepid: application to a genome-wide association study on coronary artery disease.
    Mol Genet Genomic Med, Jan;2(1):44-57. doi: 10.1002/mgg3.40. Details

  • 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.
    Eur J Protistol, Apr;50(2):166-73. doi: 10.1016/j.ejop.2014.01.004. Details

  • 2014 Szklarczyk R, Nooteboom M, Osiewacz HD.
    Control of mitochondrial integrity in ageing and disease.
    Philos Trans R Soc Lond B Biol Sci, Jul 5;369(1646). pii: 20130439. Review. Details

  • 2014 Speijer D, Manjeri GR, Szklarczyk R.
    How to deal with oxygen radicals stemming from mitochondrial fatty acid oxidation.
    Philos Trans R Soc Lond B Biol Sci, Jul 5;369(1646). pii: 20130446. Review. Details

  • 2014 Notebaart RA, Szappanos B, Kintses B, Pál F, Györkei A, Bogos B, Lázár V, Spohn R, Csörg? B, Wagner A, Ruppin E, Pál C, Papp B.
    Network-level architecture and the evolutionary potential of underground metabolism.
    Proc Natl Acad Sci USA, 2014 Aug 12;111(32):11762-7. doi: 10.1073/pnas.1406102111. Epub 2014 Jul 28. Details

  • 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 Res., Jul;42(13):8500-15. doi: 10.1093/nar/gku513 Details

  • 2014 Du Y, Cai KF, Chen S, Cizek P, Lin T.
    Facile preparation and thermoelectric properties of BI2 Te3 based alloy nanosheet/PEDOT:PSS composite films.
    ACS Appl Mater Interfaces., Apr 23;6(8):5735-43. doi: 10.1021/am5002772.

  • 2014 Dutilh BE, Cassman N, McNair K, Sanchez SE, Silva GG, Boling L, Barr JJ, Speth DR, Sequritan V, Aziz RK, Felts B, Dinsdale EA, Mokili JL, Edwards RA.
    A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes.
    Nat Commun, Jul 24;5:4498. doi: 10.1038/ncomms5498. Details

  • 2014 Dutilh BE, Thompson CC, Vicente AC, Marin MA, Lee C, Silva GG, Schmieder R, Andrade BG, Chimetto L, Cuevas D, Garza DR, Okeke IN, Aboderin AO, Spangler J, Ross T, Dinsdale EA, Thompson FL, Harkins TT, Edwards RA.
    Comparative genomics of 274 Vibrio cholerae genomes reveals mobile functions structuring three niche dimensions.
    BMC Genomics, Aug 5;15:654. doi: 10.1186/1471-2164-15-654. Details

  • 2014 ElRakaiby M, Dutilh BE, Rizkallah MR, Boleij A, Cole JN, Aziz RK.
    Pharmacomicrobiomics: the impact of human microbiome variations on systems pharmacology and personalized therapeutics.
    OMICS, Jul;18(7):402-14. doi: 10.1089/omi.2014.0018. Details

  • 2014 Ghamrawi S, Renier G, Saulnier P, Cuenot S, Zykwinska A, Dutilh BE, Thornton C, Faure S, Bouchara JP.
    Cell wall modifications during conidial maturation of the human pathogenic fungus Pseudallescheria boydii.
    PLoS One., Jun 20;9(6):e100290. doi: 10.1371/journal.pone.0100290. Details

  • 2014 Lim YW, Cuevas DA, Silva GG, Aquinaldo K, Dinsdale EA, Haas AF, Hatay M, Sanchez SE, Wegley-Kelly L, Dutilh BE, Harkins TT, Lee CC, Tom W, Sandin SA, Smith JE, Zgliczynski B, Vermeij MJ, Rohwer F, Edwards RA.
    Sequencing at sea: challenges and experiences in Ion Torrent PGM sequencing during the 2013 Southern Line Islands Research Expedition.
    PeerJ., Aug 19;2:e520. doi: 10.7717/peerj.520. Details

  • 2014 Madrigal I, Alvarez-Mora MI, Karlberg O, Rodriguez-Revenga L, Elurbe DM, Rabionet R, Mur A, Pie J, Ballesta F, Sauer S, Syvanen AC, Mila M.
    Efficient application of next-generation sequencing for the diagnosis of rare genetic syndromes.
    J Clin Pathol, Dec;67(12):1099-103. doi: 10.1136/jclinpath-2014-202537. Details

  • 2014 Silva GG, Cuevas DA, Dutilh BE, Edwards RA.
    FOCUS: an alignment-free model to identify organisms in metagenomes using non-negative least squares.
    PeerJ, Jun 5;2:e425. doi: 10.7717/peerj.425. Details

  • 2014 van der Lee R, Buljan M, Lang B, Weatheritt RJ, Daughdrill GW, Dunker AK, Fuxreiter M, Gough J, Gsponer J, Jones DT, Kim PM, Kriwacki RW, Oldfield CJ, Pappu RV, Tompa P, Uversky VN, Wright PE, Babu MM.
    Classification of intrinsically disordered regions and proteins.
    Chem Rev., Jul 9;114(13):6589-631. doi: 10.1021/cr400525m. Details

  • 2014 van der Lee R, Lang B, Kruse K, Gsponer J, Sanchez 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 Rep., Sep 25;8(6):1832-44. doi: 10.1016/j.celrep.2014.07.055. Details

  • 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.
    Hum Mol Genet., Dec 1;23(23):6356-65. doi: 10.1093/hmg/ddu357. Details

  • 2014 Lagemaat LN, Van de Nijhof B, Bosch DGM, Kohansal-Nodehi M, Keerthikumar S, Heimel JA.
    Age-related decreased inhibitory vs. excitatory gene expression in the adult autistic brain
    Frontiers in Neuroscience, 8, 1-9. doi: 10.3389/fnins.2014.00394

  • 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.
    Antioxid Redox Signal, Jan 10;18(2):129-38. doi: 10.1089/ars.2011.4253. Details

  • 2013 van de Vossenberg J, Woebken D, Maalcke WJ, Wessels HJ, Dutilh BE, Kartal B, Janssen-Megens EM, Roeselers G, Yan J, Speth D, Gloerich J, Geerts W, van der Biezen E, Pluk W, Francoijs KJ, Russ L, Lam P, Malfatti SA, Tringe SG, Haaijer SC, Op den Camp HJ, Stunnenberg HG, Amann R, Kuypers MM, Jetten MS.
    The metagenome of the marine anammox bacterium 'Candidatus Scalindua profunda' illustrates the versatility of this globally important nitrogen cycle bacterium.
    Environ Microbiol, May;15(5):1275-1289. doi: 10.1111/j.1462-2920.2012.02774.x. Details

  • 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, van den Heuvel LP.
    A mutation in the FAM36A gene, the human ortholog of COX20, impairs cytochrome c oxidase assembly and is associated with ataxia and muscle hypotonia.
    Hum Mol Genet, Feb 15;22(4):656-667. doi: 10.1093/hmg/dds473. Details

  • 2013 Huynen MA, Duarte I, Szklarczyk R.
    Loss, replacement and gain of proteins at the origin of the mitochondria.
    Biochim Biophys Acta, Feb;1827(2):224-231. doi: 10.1016/j.bbabio.2012.08.001. Details

  • 2013 Rossell S, Huynen MA, Notebaart RA.
    Inferring metabolic States in uncharacterized environments using gene-expression measurements.
    PLoS Comput Biol, Mar;9(3):e1002988. doi: 10.1371/journal.pcbi.1002988. Details

  • 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, May 31;2(1):7. doi: 10.1186/2046-2530-2-7. Details

  • 2013 Lu X, Kensche PR, Huynen MA, Notebaart RA.
    Genome evolution predicts genetic interactions in protein complexes and reveals cancer drug targets.
    Nat Commun, Jul 11;4:2124. doi: 10.1038/ncomms3124. Details

  • 2013 Mokili JL, Dutilh BE, Lim YW, Schneider BS, Taylor T, Haynes MR, Metzgar D, Myers CA, Blair PJ, Nosrat B, Wolfe ND, Rohwer F.
    Identification of a novel human papillomavirus by metagenomic analysis of samples from patients with febrile respiratory illness.
    PLoS One, 8(3):e58404. doi: 10.1371/journal.pone.0058404. Details

  • 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 Res Notes, Apr 4;6:133. doi: 10.1186/1756-0500-6-133. Details

  • 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.
    Proc Natl Acad Sci U S A, Apr 23;110(17):6943-6948. doi: 10.1073/pnas.1221011110. Details

  • 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, Collavin L, Huynen MA, Asztalos Z, Verstreken P, Rodenburg RJ, Smeitink JA, de Vries BB, Schenck A.
    CEP89 is required for mitochondrial metabolism and neuronal function in man and fly.
    Hum Mol Genet, Aug 1;22(15):3138-3151. doi: 10.1093/hmg/ddt170. Details

  • 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, May;136(Pt 5):1544-1554. doi: 10.1093/brain/awt086. Details

  • 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, May 6;8(5):e62447. doi: 10.1371/journal.pone.0062447. Details

  • 2013 Gregor A, Oti M, Kouwenhoven EN, Hoyer J, Sticht H, Ekici AB, Kjaergaard S, Rauch A, Stunnenberg HG, Uebe S, Vasileiou G, Reis A, Zhou H, Zweier C.
    De Novo Mutations in the Genome Organizer CTCF Cause Intellectual Disability.
    Am J Hum Genet, Jul 11;93(1):124-131. doi: 10.1016/j.ajhg.2013.05.007. Details

  • 2013 Silva GG, Dutilh BE, Matthews TD, Elkins K, Schmieder R, Dinsdale EA, Edwards RA.
    Combining de novo and reference-guided assembly with scaffold_builder.
    Source Code Biol Med, Nov 22;8(1):23. Details

  • 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, Verstreken P, Huynen MA, Schenck A.
    Human intellectual disability genes form conserved functional modules in Drosophila.
    PLoS Genet, Oct;9(10):e1003911. doi: 10.1371/journal.pgen.1003911. Details

  • 2013 Ljosa V, Caie PD, Ter Horst R, Sokolnicki KL, Jenkins EL, Daya S, Roberts ME, Jones TR, Singh S, Genovesio A, Clemons PA, Carragher NO, Carpenter AE.
    Comparison of methods for image-based profiling of cellular morphological responses to small-molecule treatment.
    J Biomol Screen, Dec;18(10):1321-1329. doi: 10.1177/1087057113503553. Details

  • 2013 Ballouz S, Liu JY, George RA, Bains N, Liu A, Oti M, Gaeta B, Fatkin D, Wouters MA.
    Gentrepid V2.0: a web server for candidate disease gene prediction.
    BMC Bioinformatics, Aug 16;14:249. doi: 10.1186/1471-2105-14-249. Details

  • 2013 Tucker EJ, Wanschers BF, Szklarczyk R, Mountford HS, Wijeyeratne XW, van den Brand MA, Leenders AM, Rodenburg RJ, Relji? B, Compton AG, Frazier AE, Bruno DL, Christodoulou J, Endo H, Ryan MT, Nijtmans LG, Huynen MA, Thorburn DR.
    Mutations in the UQCC1-Interacting Protein, UQCC2, Cause Human Complex III Deficiency Associated with Perturbed Cytochrome b Protein Expression.
    PLoS Genet, Dec;9(12):e1004034. doi: 10.1371/journal.pgen.1004034. Details

  • 2012 Prasad TS, Harsha HC, Keerthikumar S, Sekhar NR, Selvan LD, Kumar P, Pinto SM, Muthusamy B, Subbannayya Y, Renuse S, Chaerkady R, Mathur PP, Ravikumar R, Pandey A.
    Proteogenomic Analysis of Candida glabrata using High Resolution Mass Spectrometry.
    J Proteome Res, Jan 1;11(1):247-260. Details

  • 2012 Suijkerbuijk SJ, van Dam TJ, Karagöz GE, von Castelmur E, Hubner NC, Duarte AM, Vleugel M, Perrakis A, Rüdiger SG, Snel B, Kops GJ.
    The Vertebrate Mitotic Checkpoint Protein BUBR1 Is an Unusual Pseudokinase.
    Dev Cell, Jun 12;22(6):1321-1329. Details

  • 2012 Lasonder E, Treeck M, Alam M, Tobin AB.
    Insights into the Plasmodium falciparum schizont phospho-proteome.
    Microbes Infect, Aug;14(10):811-819. Details

  • 2012 Balsa E, Marco R, Perales-Clemente E, Szklarczyk R, Calvo E, Landázuri MO, Enríquez JA.
    NDUFA4 Is a Subunit of Complex IV of the Mammalian Electron Transport Chain.
    Cell Metab, Sep 5;16(3):378-386. Details

  • 2012 Huynen MA, Duarte I, Szklarczyk R.
    Loss, replacement and gain of proteins at the origin of the mitochondria.
    Biochim Biophys Acta, Aug 10. [Epub ahead of print] Details

  • 2012 Kensche PR, Duarte I, Huynen MA.
    A three-dimensional topology of complex I inferred from evolutionary correlations.
    BMC Struct Biol, Aug 3;12:19. Details

  • 2012 Trindade-Silva AE, Rua C, Silva GG, Dutilh BE, Moreira AP, Edwards RA, Hajdu E, Lobo-Hajdu G, Vasconcelos AT, Berlinck RG, Thompson FL.
    Taxonomic and functional microbial signatures of the endemic marine sponge Arenosclera brasiliensis.
    PLoS One, 7(7):e39905. Details

  • 2012 Tjalsma H, Boleij A, Marchesi JR, Dutilh BE.
    A bacterial driver-passenger model for colorectal cancer: beyond the usual suspects.
    Nat Rev Microbiol, Jun 25;10(8):575-582. doi: 10.1038/nrmicro2819. Details

  • 2012 Boleij A, Dutilh BE, Kortman GA, Roelofs R, Laarakkers CM, Engelke UF, Tjalsma H.
    Bacterial responses to a simulated colon tumor microenvironment.
    Mol Cell Proteomics, Oct;11(10):851-862.

  • 2012 Duarte I, Nabuurs SB, Magno R, Huynen M.
    Evolution and Diversification of the Organellar Release Factor Family.
    Mol Biol Evol, Nov;29(11):3497-512. doi: 10.1093/molbev/mss157. Details

  • 2012 de Kleijn S, Kox M, Sama IE, Pillay J, van Diepen A, Huijnen MA, van der Hoeven JG, Ferwerda G, Hermans PW, Pickkers P.
    Transcriptome kinetics of circulating neutrophils during human experimental endotoxemia.
    PLoS One, 7(6):e38255. Details

  • 2012 Bosman GJ, Lasonder E, Groenen-Döpp YA, Willekens FL, Werre JM.
    The proteome of erythrocyte-derived microparticles from plasma: new clues for erythrocyte aging and vesiculation.
    J Proteomics, Dec;76 Spec No.:203-10. doi: 10.1016/j.jprot.2012.05.031. Details

  • 2012 Garza DR, Thompson CC, Loureiro EC, Dutilh BE, Inada DT, Junior EC, Cardoso JF, Nunes MR, de Lima CP, Silvestre RV, Nunes KN, Santos EC, Edwards RA, Vicente AC, de Sá Morais LL.
    Genome-wide study of the defective sucrose fermenter strain of Vibrio cholerae from the Latin American cholera epidemic.
    PLoS One, 7(5):e37283. Details

  • 2012 Greupink R, Nabuurs SB, Zarzycka B, Verweij V, Monshouwer M, Huisman MT, Russel FG.
    In Silico Identification of Potential Cholestasis-Inducing Agents via Modeling of Na+-Dependent Taurocholate Cotransporting Polypeptide Substrate Specificity.
    Toxicol Sci, Sep;129(1):35-48. Details

  • 2012 de Beer RJ, Zarzycka B, Mariman M, Amatdjais-Groenen HI, Mulders MJ, Quaedflieg PJ, van Delft FL, Nabuurs SB, Rutjes FP.
    Papain-specific activating esters in aqueous dipeptide synthesis.
    Chembiochem, Jun 18;13(9):1319-1326. doi: 10.1002/cbic.201200017. Details

  • 2012 Farhoud MH, Nijtmans LG, Wanders RJ, Wessels HJ, Lasonder E, Janssen AJ, Rodenburg RR, van den Heuvel LP, Smeitink JA.
    Impaired ubiquitin-proteasome-mediated PGC-1α protein turnover and induced mitochondrial biogenesis secondary to complex-I deficiency.
    Proteomics, May;12(9):1349-1362. doi: 10.1002/pmic.201100326. Details

  • 2012 Luckwu de Lucena BT, Silva GG, Manoel Dos Santos B, Dias GM, Amaral GR, Moreira AP, de Morais Júnior MA, Dutilh BE, Edwards RA, Balbino V, Thompson CC, Thompson FL.
    Genome sequences of the ethanol-tolerant Lactobacillus vini strains LMG 23202T and JP7.8.9.
    J Bacteriol, Jun;194(11):3018. Details

  • 2012 Huynen MA, Duarte I, Chrzanowska-Lightowlers ZM, Nabuurs SB.
    Structure based hypothesis of a mitochondrial ribosome rescue mechanism.
    Biol Direct, May 8;7:14. Details

  • 2012 Pawar H, Sahasrabuddhe NA, Renuse S, Keerthikumar S, Sharma J, Kumar GS, Venugopal A, Sekhar NR, Kelkar DS, Nemade H, Khobragade SN, Muthusamy B, Kandasamy K, Harsha HC, Chaerkady R, Patole MS, Pandey A.
    A proteogenomic approach to map the proteome of an unsequenced pathogen - Leishmania donovani.
    Proteomics, Mar;12(6):832-844. doi: 10.1002/pmic.201100505. Details

  • 2012 Mokili JL, Rohwer F, Dutilh BE.
    Metagenomics and future perspectives in virus discovery.
    Curr Opin Virol, Feb;2(1):63-77. Details

  • 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 Biol, Feb 22;13(2):R12. Details

  • 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 Res, May;40(9):4040-4051. Details

  • 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.
    Mol Immunol, Feb;50(1-2):66-73. Details

  • 2012 Buschow SI, Lasonder E, Szklarczyk R, Oud MM, de Vries IJ, Figdor CG.
    Unraveling the human dendritic cell phagosome proteome by organellar enrichment ranking.
    J Proteomics, Feb 16;75(5):1547-1562. Details

  • 2012 Lasonder E, Green JL, Camarda G, Talabani H, Holder AA, Langsley G, Alano P.
    The Plasmodium falciparum schizont phospho-proteome reveals extensive phosphatidylinositol and cAMP-Protein Kinase A signalling.
    J Proteome Res, Nov 2;11(11):5323-37. doi: 10.1021/pr300557m. Details

  • 2012 Cassman N, Prieto-Davó A, Walsh K, Silva GG, Angly F, Akhter S, Barott K, Busch J, McDole T, Haggerty JM, Willner D, Alarcón G, Ulloa O, Delong EF, Dutilh BE, Rohwer F, Dinsdale EA.
    Oxygen minimum zones harbour novel viral communities with low diversity.
    Environ Microbiol, Sep 11. doi: 10.1111/j.1462-2920.2012.02891.x. [Epub ahead of print] Details

  • 2012 Dutilh BE, Schmieder R, Nulton J, Felts B, Salamon P, Edwards RA, Mokili JL.
    Reference-independent comparative metagenomics using cross-assembly: crAss.
    Bioinformatics, http://bioinformatics.oxfordjournals.org/content/28/24/3225.full.pdf Details

  • 2012 Moran R, Kuilenburg AB, Duley J, Nabuurs SB, Retno-Fitri A, Christodoulou J, Roelofsen J, Yntema HG, Friedman NR, van Bokhoven H, de Brouwer AP.
    Phosphoribosylpyrophosphate synthetase superactivity and recurrent infections is caused by a p.Val142Leu mutation in PRS-I.
    Am J Med Genet A, Feb;158A(2):455-460. doi: 10.1002/ajmg.a.34428. Details

  • 2012 Dessimoz C, Gabaldón T, Roos DS, Sonnhammer EL, Herrero J; Quest for Orthologs Consortium.
    Toward community standards in the quest for orthologs.
    Bioinformatics, Mar 15;28(6):900-904. Details

  • 2012 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, van den Heuvel LP.
    A mutation in the FAM36A gene, the human ortholog of COX20, impairs cytochrome c oxidase assembly and is associated with ataxia and muscle hypotonia.
    Hum Mol Genet, Nov 2. [Epub ahead of print] Details

  • 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(11):e50034. doi: 10.1371/journal.pone.0050034. Details

  • 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, Oct 11;120(15):3058-68. doi: 10.1182/blood-2011-10-386086. Details

  • 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.
    Am J Hum Genet, Apr 8;88(4):488-493. Details

  • 2011 van Dam TJ, Bos JL, Snel B.
    Evolution of the Ras-like small GTPases and their regulators.
    Small Gtpases, Jan;2(1):4-16. Details

  • 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, Jun 27;12(1):330. Details

  • 2011 Huerta-Cepas J, Dopazo J, Huynen MA, Gabaldon T.
    Evidence for short-time divergence and long-time conservation of tissue-specific expression after gene duplication.
    Brief Bioinform, Sep;12(5):442-448. Details

  • 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.
    Mol Biol Evol, Aug;28(8):2379-2391. Details

  • 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 Res, May 1;39(10):4284-4299. Details

  • 2011 Kip N, Dutilh BE, Pan Y, Bodrossy L, Neveling K, Kwint MP, Jetten MSM and Op den Camp HJM.
    Ultra-deep pyrosequencing of pmoA amplicons confirms prevalence of Methylomonas and Methylocystis in Sphagnum mosses from a Dutch peat bog.
    Environmental Microbiology Reports, Mar;3(6):667–673. Details

  • 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, Chapter 43:379-385. Details

  • 2011 Emons J, Dutilh BE, Decker E, Pirzer H, Sticht C, Gretz N, Rappold G, Cameron ER, Neil JC, Stein GS, van Wijnen AJ, Wit JM, Post JN, Karperien M.
    Genome wide screening in human growth plates during puberty in one patient suggests a role for RUNX2 in epiphyseal maturation.
    Journal of Endocrinology , May;209(2):245-254. Details

  • 2011 Marchesi JR, Dutilh BE, Hall N, Peters WH, Roelofs R, Boleij A, Tjalsma H.
    Towards the Human Colorectal Cancer Microbiome.
    PLoS One, 6(5):e20447. Details

  • 2011 Papp B, Notebaart RA, Pál C.
    Systems-biology approaches for predicting genomic evolution.
    Nat Rev Genet, Aug 2;12(9):591-602. Details

  • 2011 Papp B, Szappanos B, Notebaart RA.
    Use of genome-scale metabolic models in evolutionary systems biology.
    Methods Mol Biol, 759(3):483-497. Details

  • 2011 de Bok FA, Janssen PW, Bayjanov JR, Sieuwerts S, Lommen A, van Hylckama Vlieg JE, Molenaar D.
    Volatile compound fingerprinting of mixed-culture fermentations.
    Appl Environ Microbiol, Sep;77(17):6233-6239. Details

  • 2011 Rossell S, Solem C, Jensen PR, Heijnen JJ.
    Towards a quantitative prediction of the fluxome from the proteome.
    Metab Eng, May;13(3):253-262. Details

  • 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, Nov;11(6):954-963. Details

  • 2011 Thompson CC, Marin MA, Dias GM, Dutilh BE, Edwards RA, Iida T, Thompson FL, Vicente AC.
    Genome Sequence of the Human Pathogen Vibrio cholerae Amazonia.
    J Bacteriol, 193(20):5877-5878. Details

  • 2011 van Eunen K, Rossell S, Bouwman J, Westerhoff HV, Bakker BM.
    Quantitative analysis of flux regulation through hierarchical regulation analysis.
    Methods Enzymol, 500:571-595. Details

  • 2011 van Kessel MA, Dutilh BE, Neveling K, Kwint MP, Veltman JA, Flik G, Jetten MS, Klaren PH, Op den Camp HJ.
    Pyrosequencing of 16S rRNA gene amplicons to study the microbiota in the gastrointestinal tract of carp (Cyprinus carpio L.).
    AMB Express, Nov 18;1:41. Details

  • 2011 van Dam TJ, Zwartkruis FJ, Bos JL, Snel B.
    Evolution of the TOR Pathway.
    J Mol Evol, Oct;73(3-4):209-220. Details

  • 2011 Buschow SI, Lasonder E, Szklarczyk R, Oud MM, de Vries IJ, Figdor CG.
    Unraveling the human dendritic cell phagosome proteome by organellar enrichment ranking.
    J Proteomics, Feb 16;75(5):1547-1562. Details

  • 2011 Babu MM, van der Lee R, de Groot NS, Gsponer J.
    Intrinsically disordered proteins: regulation and disease.
    Curr Opin Struct Biol, Jun;21(3):432-440. Details

  • 2011 Ballouz S, Liu JY, Oti M, Gaeta B, Fatkin D, Bahlo M, Wouters MA.
    Analysis of genome-wide association study data using the protein knowledge base.
    BMC Genet, Nov 13;12(1):98. Details

  • 2011 Oti M, Ballouz S, Wouters MA.
    Web tools for the prioritization of candidate disease genes.
    Methods Mol Biol, 760:189-206. Details

  • 2011 Barbhuiya MA, Sahasrabuddhe NA, Pinto SM, Muthusamy B, Singh TD, Nanjappa V, Keerthikumar S, Delanghe B, Harsha HC, Chaerkady R, Jalaj V, Gupta S, Shrivastav BR, Tiwari PK, Pandey A.
    Comprehensive proteomic analysis of human bile.
    Proteomics, Dec;11(23):4443-4453. Details

  • 2011 Kumar GS, Venugopal AK, Selvan LD, Marimuthu A, Keerthikumar S, Pathare S, Dikshit JB, Tata P, Hariharan R, Prasad TS, Harsha HC, Ramachandra YL, Mahadevan A, Chaerkady R, Shankar SK, Pandey A.
    Gene Expression Profiling of Tuberculous Meningitis.
    Journal of Proteomics and Bioinformatics, 4:98-105. Details

  • 2011 Marimuthu A, Jacob HK, Jakharia A, Subbannayya Y, Keerthikumar S, Kashyap MK, Goel R, Balakrishnan L, Dwivedi S, Pathare S, Dikshit JB, Maharudraiah J, Singh S, Kumar GS, Vijayakumar M, Veerendra Kumar KV, Premalatha CS, Tata P, Hariharan R, Roa JC, Prasad TS, Chaerkady R, Kumar RV, Pandey A.
    Gene Expression Profiling of Gastric Cancer.
    J Proteomics Bioinform, 4:074-082. Details

  • 2011 De Franceschi L, Tomelleri C, Matte A, Brunati AM, Bovee-Geurts PH, Bertoldi M, Lasonder E, Tibaldi E, Danek A, Walker RH, Jung HH, Bader B, Siciliano A, Ferru E, Mohandas N, Bosman GJ.
    Erythrocyte membrane changes of chorea-acanthocytosis are the result of altered Lyn kinase activity.
    Blood, Nov 17;118(20):5652-5663. Details

  • 2011 Kartal B, Maalcke WJ, de Almeida NM, Cirpus I, Gloerich J, Geerts W, Op den Camp HJ, Harhangi HR, Janssen-Megens EM, Francoijs KJ, Stunnenberg HG, Keltjens JT, Jetten MS, Strous M.
    Molecular mechanism of anaerobic ammonium oxidation.
    Nature, Oct 2;479(7371):127-130. Details

  • 2011 Laurentino EC, Taylor S, Mair GR, Lasonder E, Bartfai R, Stunnenberg HG, Kroeze H, Ramesar J, Franke-Fayard B, Khan SM, Janse CJ, Waters AP.
    Experimentally controlled downregulation of the histone chaperone FACT in Plasmodium berghei reveals that it is critical to male gamete fertility.
    Cell Microbiol, Dec;13(12):1956-1974. Details

  • 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 Lett, Mar 9;585(5):737-743. Details

  • 2010 Bosman GJ, Lasonder E, Groenen-Döpp YA, Willekens FL, Werre JM, Novotný VM.
    Comparative proteomics of erythrocyte aging in vivo and in vitro.
    J Proteomics, Jan;73(3):396-402. Details

  • 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.
    J Proteome Res, Apr 5;9(4):1727-1737. Details

  • 2010 van Diepen A, Brand HK, Sama I, Lambooy LH, van den Heuvel LP, van der Well L, Huynen M, Osterhaus AD, Andeweg AC, Hermans PW.
    Quantitative proteome profiling of respiratory virus-infected lung epithelial cells.
    J Proteomics, Aug 5;73(9):1680-1693. Details

  • 2010 Ettwig KF, Butler MK, Le Paslier D, Pelletier E, Mangenot S, Kuypers MM, Schreiber F, Dutilh BE, Zedelius J, de Beer D, Gloerich J, Wessels HJ, van Alen T, Luesken F, Wu ML, van de Pas-Schoonen KT, Op den Camp HJ, Janssen-Megens EM, Francoijs KJ, Stunnenberg H, Weissenbach J, Jetten MS, Strous M.
    Nitrite-driven anaerobic methane oxidation by oxygenic bacteria.
    Nature, Mar 25;464(7288):543-548. Details

  • 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, Brunner HG, Roscioli T, Oates E, Wilson M, Manzanares M, Gómez-Skarmeta JL, Stunnenberg HG, Lohrum M, van Bokhoven H, Zhou H.
    Genome-wide profiling of p63 DNA-binding sites identifies an element that regulates gene expression during limb development in the 7q21 SHFM1 locus.
    PLoSGenetics, 6:e1001065 Details

  • 2010 Sama IE, Huynen MA.
    Measuring the physical cohesiveness of proteins using Physical Interaction Enrichment (PIE).
    Bioinformatics, Nov 1;26(21):2737-2743. Details

  • 2010 Szklarczyk R, Huynen MA.
    Mosaic origin of the mitochondrial proteome.
    Proteomics, Nov;10(22):4012-4024. Details

  • 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, Vogel RO.
    Acyl-CoA dehydrogenase 9 is required for the biogenesis of oxidative phosphorylation complex I.
    Cell Metab, Sep 8;12(3):283-294. Details

  • 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.
    EMBO J, Mar 17;29(6):1116-1125. Details

  • 2010 Silvestrini F, Lasonder E, Olivieri A, Camarda G, van Schaijk B, Sanchez M, Younis Younis S, Sauerwein R, Alano P.
    Protein export marks the early phase of gametocytogenesis of the human malaria parasite Plasmodium falciparum.
    Mol Cell Proteomics, Jul;9(7):1437-1448. Details

  • 2010 Mair GR, Lasonder E, Garver LS, Franke-Fayard BM, Carret CK, Wiegant JC, Dirks RW, Dimopoulos G, Janse CJ, Waters AP.
    Universal features of post-transcriptional gene regulation are critical for Plasmodium zygote development.
    PLoS Pathog, Feb 12;6(2):e1000767. Details

  • 2010 van der Voort R, Verweij V, de Witte TM, Lasonder E, Adema GJ, Dolstra H.
    An alternatively spliced CXCL16 isoform expressed by dendritic cells is a secreted chemoattractant for CXCR6+ cells.
    J Leukoc Biol, Jun;87(6):1029-1039. Details

  • 2010 Hijikata A, Raju R, Keerthikumar S, Ramabadran S, Balakrishnan L, Ramadoss SK, Pandey A, Mohan S, Ohara O.
    Mutation@A Glance: an integrative web application for analysing mutations from human genetic diseases.
    DNA Res, Jun;17(3):197-208. Details

  • 2010 Kandasamy K, Mohan SS, Raju R, Keerthikumar S, Kumar GS, Venugopal AK, Telikicherla D, Navarro JD, Mathivanan S, Pecquet C, Gollapudi SK, Tattikota SG, Mohan S, Padhukasahasram H, Subbannayya Y, Goel R, Jacob HK, Zhong J, Sekhar R, Nanjappa V, Balakrishnan L, Subbaiah R, Ramachandra YL, Rahiman BA, Prasad TS, Lin JX, Houtman JC, Desiderio S, Renauld JC, Constantinescu SN, Ohara O, Hirano T, Kubo M, Singh S, Khatri P, Draghici S, Bader GD, Sander C, Leonard WJ, Pandey A.
    NetPath: a public resource of curated signal transduction pathways.
    Genome Biol, Jan 12;11(1):R3 Details

  • 2010 Kashyap MK, Harsha HC, Renuse S, Pawar H, Sahasrabuddhe NA, Kim MS, Marimuthu A, Keerthikumar S, Muthusamy B, Kandasamy K, Subbannayya Y, Prasad TS, Mahmood R, Chaerkady R, Meltzer SJ, Kumar RV, Rustgi AK, Pandey A.
    SILAC-based quantitative proteomic approach to identify potential biomarkers from the esophageal squamous cell carcinoma secretome.
    Cancer Biol Ther, Oct 15;10(8):796-810. Details

  • 2010 Prasad TSK, Keerthikumar S, Chaerkady R, Kandasamy K, Renuse S, Marimuthu A, Venugopal AK, Thomas JK, Jacob HKC, et al.
    Comparative Proteomic Analysis of Candida albicans and Candida glabrata.
    Clinical Proteomics, 6(4):163-173. Details

  • 2009 Papp B, Teusink B, Notebaart RA.
    A critical view of metabolic network adaptations.
    HFSP J, Feb;3(1):24-35. Details

  • 2009 Verouden MPH, Notebaart RA, Westerhuis JA, van der Werf MJ, Teusink B, Smilde AK.
    Multi-way analysis of flux distributions across multiple conditions.
    J. Chemometrics, 23(7-8):406-420. Details

  • 2009 Teusink B, Wiersma A, Jacobs L, Notebaart RA, Smid EJ.
    Understanding the adaptive growth strategy of Lactobacillus plantarum by in silico optimisation.
    PLoS Comput Biol, Jun;5(6):e1000410. Details

  • 2009 Dutilh BE, Huynen MA, Strous M.
    Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly.
    Bioinformatics, Nov 1;25(21):2878-2881. Details

  • 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.
    Am J Hum Genet, Jun;84(6):718-727. Details

  • 2009 Notebaart RA, Kensche PR, Huynen MA, Dutilh BE.
    Asymmetric relationships between proteins shape genome evolution.
    Genome Biol, Feb 12;10(2):R19. Details

  • 2009 Szklarczyk R, Huynen MA.
    Expansion of the human mitochondrial proteome by intra- and inter-compartmental protein duplication.
    Genome Biol, Nov 24;10(11):R135. Details

  • 2009 Parmley JL, Huynen MA.
    Clustering of codons with rare cognate tRNAs in human genes suggests an extra level of expression regulation.
    PLoS Genet, Jul;5(7):e1000548. Details

  • 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, Nov 6;10:514. Details

  • 2009 Huynen MA, de Hollander M, Szklarczyk R.
    Mitochondrial proteome evolution and genetic disease.
    Biochim Biophys Acta, Dec;1792(12):1122-1129. Details

  • 2009 Jurgelenaite R, Dijkstra TMH, Kocken CHM, Heskes T.
    Gene regulation in the intraerythrocytic cycle of Plasmodium falciparum.
    Bioinformatics, 25(12):1484-1491. Details

  • 2009 Doerig C, Baker D, Billker O, Blackman MJ, Chitnis C, Dhar Kumar S, Heussler V, Holder AA, Kocken C, Krishna S, Langsley G, Lasonder E, Menard R, Meissner M, Pradel G, Ranford-Cartwright L, Sharma A, Sharma P, Tardieux T, Tatu U, Alano P.
    Signalling in malaria parasites. The MALSIG consortium.
    Parasite, Sep;16(3):169-182. Details

  • 2009 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, Mar;67(6):875-890. Details

  • 2009 Oti M, Huynen MA, Brunner HG.
    The biological coherence of human phenome databases.
    Am J Hum Genet, Dec;85(6):801-808. Details

  • 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 Evol Biol, Dec 9;9:287. Details

  • 2008 Notebaart RA, Teusink B, Siezen RJ, Papp B.
    Co-regulation of metabolic genes is better explained by flux coupling than by network distance.
    PLoS Comput Biol, 4(1):e26 Details

  • 2008 Dutilh BE, Snel B, Ettema TJG, Huynen MA.
    Signature genes as a phylogenomic tool.
    Molecular Biology and Evolution, Aug;25(8):1659-1667. Details

  • 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, Jul 1;36(Web Server issue):W470-474. Details

  • 2008 Kensche PR, Oti M, Dutilh BE, Huynen MA.
    Conservation of divergent transcription in fungi.
    Trends in Genetics, May;24(5):207-211. Details

  • 2008 Franck E, Hulsen T, Huynen MA, de Jong WW, Lubsen NH, Madsen O.
    Evolution of closely linked gene pairs in vertebrate genomes.
    Mol Biol Evol, Sep;25(9):1909-1921. Details

  • 2008 Oti M, van Reeuwijk J, Huynen MA, Brunner HG.
    Co-expression for candidate disease gene prioritization.
    BMC Bioinformatics, Apr 23;9:208. Details

  • 2008 Ala U, Piro RM, Grassi E, Damasco C, Silengo L, Oti M, Provero P, Di Cunto F.
    Prediction of human disease genes by human-mouse conserved coexpression analysis.
    PLoS Comput Biol, Mar 28;4(3):e1000043. Details

  • 2008 Oti M, Huynen MA, Brunner HG.
    Phenome connections.
    Trends Genet, Mar;24(3):103-106. Details

  • 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.
    J R Soc Interface, Feb 6;5(19):151-170. Details

  • 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.
    EMBO J, 27(12):1736-1746. Details

  • 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.
    Pflugers Arch, 457(1):91-101. Details

  • 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 Pathog, 4(10):e1000195. Details

  • 2008 Warnecke T, JL Parmley, Hurst LD.
    Finding exonic islands in a sea of non-coding sequence: splicing related constraints on protein composition and evolution are common in intron-rich genomes.
    Genome Biol, 9(2):R29. Details

  • 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, Dec 5;9:587. Details

  • 2008 Szklarczyk R, Huynen MA, Snel B.
    Complex fate of paralogs.
    BMC Evol Biol, Dec 18;8:337. Details

  • 2008 Hatzis P, van der Flier LG, van Driel MA, Guryev V, Nielsen F, Denissov S, Nijman IJ, Koster J, Santo EE, Welboren W, Versteeg R, Cuppen E, van de Wetering M, Clevers H, Stunnenberg HG.
    Genome-wide pattern of TCF7L2/TCF4 chromatin occupancy in colorectal cancer cells.
    Mol Cell Biol, Apr;28(8):2732-2744. Details

  • 2008 Clark K, Middelbeek J, Dorovkov MV, Figdor CG, Ryazanov AG, Lasonder E, van Leeuwen FN.
    The alpha-kinases TRPM6 and TRPM7, but not eEF-2 kinase, phosphorylate the assembly domain of myosin IIA, IIB and IIC.
    FEBS , Lett. 582:2993-29977. Details

  • 2008 Clark K, Middelbeek J, Lasonder E, Dulyaninova N, Morrice NA, Ryazanov AG, Bresnick AR, Figdor CG, van Leeuwen FN.
    Trpm7 regulates myosin IIA filament stability and protein localization by heavy chain phosphorylation.
    J Mol Biol , May 9;378(4):790-803. Details

  • 2008 Clark K, Middelbeek J, Morrice N. Figdor CG, Lasonder E, van Leeuwen FN.
    Massive Autophosphorylation of the Ser/Thr-Rich Domain Controls Protein Kinase Activity of TRPM6 and TRPM7.
    PLoS ONE 3 , Mar 26;3(3):e1876. Details

  • 2008 Bosman GJCGM, Lasonder E, Luten M, Roerdinkholder-Stoelwinder B, Novotny VMJ, Bos H, De Grip WJ.
    The proteome of erythrocyte membranes and vesicles during storage in blood bank conditions.
    Transfusion, May;48(5):827-835. Details

  • 2008 Pandithage R, Lilischkis R, Harting K, Wolf A, Jedamzik B, Lüscher_Firzlaff J, Vervoorts J, Lasonder E, Kremmer E, Knöll B, Lüscher B.
    The regulation of SIRT2 function by cyclin-dependent kinases affects cell motility.
    J Cell Biol, Mar 10;180(5):915-929. Details

  • 2008 Cao G, Thébault S, van der Wijst J, van der Kemp A, Lasonder E, Bindels RJ, Hoenderop JG.
    RACK1 inhibits TRPM6 Activity via Phosphorylation of the Fused alpha-Kinase Domain.
    Curr Biol, Feb 12;18(3):168-176. Details

  • 2007 van der Heijden RT, Snel B, van Noort V, Huynen MA.
    Orthology prediction at Scalable Resolution by phylogenetic Tree analysis.
    BMC Bioinformatics, 8(1):83. Details

  • 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, Apr 1;23(7):815-824. Details

  • 2007 van den Hondel CA, van der Heijden RT, van der Kaaij RM, Klis FM, Kools, HJ, Kubicek CP, van Kuyk PA, Lauber J, Lu X, van der Maarel MJ, Meulenberg, R, Menke H, Mortimer MA, Nielsen J, Oliver SG, Olsthoorn M, Pal K, van Peij NN, Ram AF, Rinas U, Roubos JA, Sagt CM, Schmoll M, Sun J, Ussery D, Varga J, Vervecken W, van de Vondervoort PJ, Wedler H, Wosten HA, Zeng AP, van Ooyen AJ, Visser J, Stam H.Pel HJ, de Winde JH, Archer DB, Dyer PS, Hofmann G, Schaap PJ, Turner G, de Vries RP, Albang R, Albermann K, Andersen MR, Bendtsen JD, Benen JA, van den Berg M, Breestraat S, Caddick MX, Contreras R, Cornell M, Coutinho PM, Danchin EG, Debets AJ, Dekker P, van Dijck PW, van Dijk A, Dijkhuizen L, Driessen AJ, d'Enfert C, Geysens S, Goosen C, Groot GS, de Groot PW, Guillemette T, Henrissat B, Herweijer M, van den Hombergh JP.
    Genome sequencing and analysis of the versatile cell actory Aspergillus niger CBS 513.88.
    Nat Biotechnol, 25(2):221-231. Details

  • 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, Hackstein JH.
    The [FeFe] hydrogenase of Nyctotherus ovalis has a chimeric origin.
    BMC Evol Biol , Nov 16;7:230. Details

  • 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, Jun 25;8:190. Details

  • 2007 Gabaldón T, Huynen MA.
    From Endosymbiont to Host-Controlled Organelle: The Hijacking of Mitochondrial Protein Synthesis and Metabolism.
    PLoS Comput Biol, Nov;3(11):e219. Details

  • 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, Jul 1;23(13):i195-204. Details

  • 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.
    J Biol Chem , Aug 3;282(31):22481-22491. Details

  • 2007 Smits P, Smeitink JA, van den Heuvel LP, Huynen MA, Ettema TJ.
    Reconstructing the evolution of the mitochondrial ribosomal proteome.
    Nucleic Acids Res, 35(14):4686-4703. Details

  • 2007 van Noort V, Snel B, Huynen MA.
    Exploration of the omics evidence landscape: adding qualitative labels to predicted protein-protein interactions.
    Genome Biol, 8(9):R197. Details

  • 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, Jun 25;8:190. Details

  • 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, Jan 19;7:10. Details

  • 2006 Ettema TJ, Brinkman AB, Lamers PP, Kornet NG, de Vos WM, van der Oost J.
    Molecular characterization of a conserved archaeal copper resistance (cop) gene cluster and its copper-responsive regulator in Sulfolobus solfataricus P2.
    Microbiology , Jul;152(Pt 7):1969-1979. Details

  • 2006 Oti M, Snel B, Huynen MA, Brunner HG.
    Predicting disease genes using protein-protein interactions.
    J Med Genet, Aug;43(8):691-698. Details

  • 2006 Tiffin N, Adie E, Turner F, Brunner HG, van Driel MA, Oti M, Lopez-Bigas N, Ouzounis C, Perez-Iratxeta C, Andrade-Navarro MA, Adeyemo A, Patti ME, Semple CA, Hide W.
    Computational disease gene identification: a concert of methods prioritizes type 2 diabetes and obesity candidate genes.
    Nucleic Acids Res, Jun 6;34(10):3067-3081. Details

  • 2006 Ricard G, McEwan NR, Dutilh BE, Jouany J-P, Macheboeuf D, Mitsumori M, McIntosh FM, Michalowski T., Nagamine T, Nelson N, Newbold ChJ, Nsabimana E, Takenaka A, Thomas NA, Ushida K, Hackstein JHP, Huynen MA.
    Horizontal Gene Transfer from Bacteria to rumen Ciliates indicates adaptation to their anaerobic carbohydrates, rich-environment.
    BMC Genomics , Feb 10;7:22. Details

  • 2006 Strous M, Pelletier E, Mangenot S, Rattei Th, Lehner A, Taylor MW, Horn M, Daims H, Bartol-Mavel D, Wincker P, Barbe V, Fonknechten N, Vallenet D, Segurens B, Schenowitz-Truong C, Médigue C, Collingro A, Snel B, Dutilh BE, Op den Camp HJM, van der Drift Ch, Cirpus I, van de Pas-Schoonen KT, Harhangi HR, van Niftrik L, Schmid M, Keltjens J, van de Vossenberg J, Kartal B, Meier H, Frishman D, Huynen MA, Mewes H-W, Weissenbach J, Jetten MSM, Wagner M, Le Paslier D.
    Deciphering the evolution and metabolism of an anammox bacterium from a community genome.
    Nature, Apr 6;440(7085):790-794. Details

  • 2006 von Mering C, Huynen M, Jaeggi D, Schmidt S, Bork P, Snel B.
    STRING: a database of predicted functional associations between proteins.
    Nucleic Acids Res, Jan 1;31(1):258-261. Details

  • 2006 Hackstein JH, Tjaden J, Huynen M.
    Mitochondria, hydrogenosomes and mitosomes: products of evolutionary tinkering!
    Curr Genet., Oct;50(4):225-245. Details

  • 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, May;14(5):857-867. Details

  • 2006 Oti M, Snel B, Huynen MA, Brunner HG.
    Predicting disease genes using protein-protein interactions.
    J Med Genet., Aug;43(8):691-698. Details

  • 2006 Gabaldon T, Snel B, van Zimmeren F, Hemrika W, Tabak H, Huynen MA.
    Origin and evolution of the peroxisomal proteome.
    Biol Direct, Mar 23;1:8. Details

  • 2006 van Noort V, Huynen MA.
    Combinatorial gene regulation in Plasmodium falciparum.
    Trends Genet, Feb;22(2):73-78. Details

  • 2006 Kuramae EE, Robert V, Snel B, Boekhout T.
    Conflicting phylogenetic position of Schizosaccharomyces pombe.
    Genomics, Oct;88(4):387-393. Details

  • 2006 Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P.
    Toward automatic reconstruction of a highly resolved tree of life.
    Science, Mar 3;311(5765):1283-1287. Details

  • 2006 Tabak HF, Hoepfner D, Zand AV, Geuze HJ, Braakman I, Huynen MA.
    Formation of peroxisomes: Present and past.
    Biochim Biophys Acta, Dec;1763(12):1647-1654. Details

  • 2006 Tjalsma H, Scholler-Guinard M, Lasonder E, Ruers TJ, Willems HL, Swinkels DW.
    Profiling the humoral immune response in colon cancer patients: diagnostic antigens from Streptococcus bovis.
    Int J Cancer, Nov 1;119(9):2127-2135. Details

  • 2006 Vermeulen M, Walter W, Le Guezennec X, Kim J, Edayathumangalam RS, Lasonder E, Luger K, Roeder RG, Logie C, Berger SL, Stunnenberg HG.
    A feed-forward repression mechanism anchors the Sin3/histone deacetylase and N-CoR/SMRT corepressors on chromatin.
    Mol Cell Biol, Jul;26(14):5226-5236. Details

  • 2006 Le Guezennec X, Vermeulen M, Brinkman AB, Hoeijmakers WA, Cohen A, Lasonder E, Stunnenberg HG.
    MBD2/NuRD and MBD3/NuRD, two distinct complexes with different biochemical and functional properties.
    Mol Cell Biol, Feb;26(3):843-851. Details

  • 2006 Wessels E, Notebaart RA, Duijsings D, Lanke K, Vergeer B, Melchers WJ, van Kuppeveld FJ.
    Structure-function analysis of the coxsackievirus protein 3A: identification of residues important for dimerization, viral rna replication, and transport inhibition.
    J Biol Chem, Sep 22;281(38):28232-28243. Details

  • 2005 Ahmed H, Ettema TJ, Tjaden B, Geerling AC, van der Oost J, Siebers B.
    The semi-phosphorylative Entner-Doudoroff pathway in hyperthermophilic archaea: a re-evaluation.
    Biochem J, Sep 1;390(Pt 2):529-540. Details

  • 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, Mar 3;434(7029):74-79. Details

  • 2005 Ettema TJ, de Vos WM, van der Oost J.
    Discovering novel biology by in silico archaeology.
    Nat Rev Microbiol, Nov;3(11):859-869. Details

  • 2005 Gabaldón T, Huynen MA.
    Lineage-specific gene loss following mitochondrial endosymbiosis and its potential for function prediction in eukaryotes.
    Bioinformatics, Sep 1;21 Suppl 2:ii144-150. Details

  • 2005 Gabaldón T, Rainey D, Huynen MA.
    Tracing the evolution of a large protein complex in the eukaryotes, NADH: ubiquinone oxidoreductase (Complex I).
    J Mol Biol, May 13;348(4):857-870. Details

  • 2005 Huynen MA, Gabaldón T, Snel B.
    Variation and evolution of biomolecular systems: searching for functional relevance.
    FEBS Lett, Mar 21;579(8):1839-1845. Details

  • 2005 Huynen MA, Spronk CA, Gabaldon T, Snel B.
    Combining data from genomes, Y2H and 3D structure indicates that BolA is a reductase interacting with a glutaredoxin.
    FEBS Lett, Jan 31;579(3):591-596. Details

  • 2005 Kaper T, Talik B, Ettema TJ, Bos H, van der Maarel MJ, Dijkhuizen L.
    Amylomaltase of Pyrobaculum aerophilum IM2 produces thermoreversible starch gels.
    Appl Environ Microbiol, Sep;71(9):5098-5106. Details

  • 2005 Kunin V, Teichmann SA, Huynen MA, Ouzounis CA.
    The properties of protein family space depend on experimental design.
    Bioinformatics, Jun 1;21(11):2618-2622. Details

  • 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 Res, Jan 1;33(Database issue):D433-437. Details

  • 2005 Notebaart RA, Huynen MA, Teusink B, Siezen RJ, Snel B.
    Correlation between sequence conservation and the genomic context after gene duplication .
    Nucleic Acids Res, Oct 27;33(19):6164-6171. Details

  • 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, van Bokhoven H.
    POMT2 mutations cause {alpha}-dystroglycan hypoglycosylation and Walker-Warburg syndrome.
    J Med Genet, Dec;42(12):907-912. Details

  • 2005 Snel B, Huynen MA, Dutilh BE.
    Genome trees and the nature of genome evolution.
    Annu Rev Microbiol, 59:191-209. Details

  • 2005 Wessels E, Duijsings D, Notebaart RA, Melchers WJ, van Kuppeveld FJ.
    A proline-rich region in the coxsackievirus 3A protein is required for the protein to inhibit endoplasmic reticulum-to-golgi transport.
    J Virol, Apr;79(8):5163-5173. Details

  • 2005 Notebaart RA, Huynen MA, Teusink B, Siezen RJ, Snel B.
    Correlation between sequence conservation and the genomic context after gene duplication.
    Nucleic Acids Res, Oct 27;33(19):6164-6171. Details

  • 2004 van Bakel H, Huynen M, Wijmenga C.
    Prokaryotic diversity of the Saccharomyces cerevisiae Atx1p-mediated copper pathway.
    Bioinformatics, Nov 1;20(16):2644-2655. Details

  • 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.
    Mol Microbiol, Mar;51(5):1389-1399. Details

  • 2004 Dutilh BE, Huynen MA, Bruno WJ, Snel B.
    The Consistent Phylogenetic Signal in Genome Trees Revealed by Reducing the Impact of Noise.
    J Mol Evol, May;58(5):527-539. Details

  • 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.
    J Bacteriol, Nov;186(22):7754-7762. Details

  • 2004 Franck E, Madsen O, van Rheede T, Ricard G, Huynen MA, de Jong WW.
    Evolutionary diversity of vertebrate small heat shock proteins.
    J Mol Evol, Dec;59(6):792-805. Details

  • 2004 Gabaldón T, Huynen MA.
    Prediction of protein function and pathways in the genome era.
    Cell Mol Life Sci, Apr;61(7-8):930-944. Details

  • 2004 Gabaldón T, Huynen MA.
    Shaping the mitochondrial proteome.
    Biochim Biophys Acta, Dec 6;1659(2-3):212-220. Details

  • 2004 Huynen MA, Snel B, van Noort V.
    Comparative Genomics for reliable protein-function prediction from genomic data.
    Trends Genet , Aug;20(8):340-344. Details

  • 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 Rep, Mar;5(3):280-284. Details

  • 2004 Snel B, Huynen MA.
    Quantifying modularity in the evolution of biomolecular systems.
    Genome Res , Mar;14(3):391-397. Details

  • 2004 Snel B, van Noort V, Huynen MA.
    Gene co-regulation is highly conserved in the evolution of eukaryotes and prokaryotes.
    Nucleic Acids Res, Sep 7;32(16):4725-4731. Details

  • 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.
    Mol Microbiol , Mar;51(5):1439-1446. Details

  • 2003 Dutilh BE, de Boer RJ.
    Decline in excision circles requires homeostatic renewal or homeostatic death of naive T cells.
    J Theor Biol , Oct 7;224(3):351-358. Details

  • 2003 Gabaldon T, Huynen MA.
    Reconstruction of the proto-mitochondrial metabolism.
    Science, Aug 1;301(5633):609. Details

  • 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 Biochem Sci, Apr;28(4):170-173. Details

  • 2003 Huynen MA, Snel B.
    Exploiting the variations in the genomic associations of genes to predict pathways and reconstruct their evolution.
    Frontiers in Computational Genomics, Caister Academic Press:145-166.

  • 2003 Huynen MA, Snel B, von Mering C, Bork P.
    Function prediction and protein networks.
    Curr Opin Cell Biol, Apr;15(2):191-198. Details

  • 2003 Kesmir C, Van Noort V, De Boer RJ, Hogeweg P.
    Bioinformatic analysis of functional differences between the immunoproteasome and the constitutive proteasome.
    Immunogenetics, Oct;55(7):437-449. Details

  • 2003 van Noort V, Snel B, Huynen MA.
    Predicting gene function by conserved co-expression.
    Trends in Genetic , May;19(5):238-242. Details

  • 2003 van Noort V, Worning P, Ussery DW, Rosche WA, Sinden RR.
    Strand misalingments lead to quasipalindrome correction.
    Trends in Genetics , Jul;19(7):365-369. Details

  • 2003 Morett E, Korbel JO, Rajan E, Saab-Rincon G, Olvera L, Olvera M, Schmidt S, Snel B, Bork P.
    Systematic discovery of analogous enzymes in thiamin biosynthesis.
    Nat. Biotechnol, Jul;21(7):790-795. Details

  • 2002 Dandekar T, Snel B, Schmidt S, Lathe W, Suyama M, Huynen M, Bork P.
    Comparative Genome Analysis of the Mollicutes.
    Molecular Biology and Pathogenity of Mycoplasmas , Edited by Razin and Herrmann, Kluwer Academic/Plenum Publishers, New York, 255-278. Details

  • 2002 Hackstein JH, van Hoek AH, Leunissen JA, Huynen M.
    Anaerobic ciliates and their methanogenic endosymbionts.
    Symbiosis: Mechanisms and Model Systems, Edited by J. Seckbach, Kluwer, Dordrecht, The Netherlands, 451-464. Details

  • 2002 Kappé G, Leunissen JA, de Jong WW.
    Evolution and diversity of prokaryotic small heat shock proteins.
    Prog Mol Subcell Biol, 28:1-17. Details

  • 2002 Korbel J, Snel B, Huynen MA, Bork P.
    SHOT: a web server for the construction of genome phylogenies.
    Trends in Genetics, Mar;18(3):158-162. Details

  • 2002 von Mering C, Krause R, Snel B, Cornell M, Oliver SG, Fields S, Bork P.
    Comparative assessment of large-scale data sets of protein-protein interactions.
    Nature, May 23;417(6887):399-403. Details

  • 2002 van der Oost J, Huynen MA, Verhees CH.
    Molecular characterization of phosphoglycerate mutase in archaea.
    FEMS Microbiol Lett , Jun 18;212(1):111-120. Details

  • 2002 Schell MA, Karmirantzou M, Snel B, Vilanova D, Berger B, Pessi G, Zwahlen MC, Desiere F, Bork P, Delley M, Pridmore RD, Arigoni F.
    The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract.
    Proc Natl Acad Sci U S A, Oct 29;99(22):14422-14427. Details

  • 2002 Snel B, Bork P, Huynen MA.
    Conservation of gene co-regulation in prokaryotes and eukaryotes.
    Trends Biotechnol, Oct 1;20(10):410. Details

  • 2002 Snel B, Bork P, Huynen MA.
    The identification of functional modules from the genomic association of genes.
    Proc Natl Acad Sci U S A, Apr 30;99(9):5890-5895. Details

  • 2002 Snel B, Bork P, Huynen MA.
    Genomes in flux: the evolution of archaeal and proteobacterial gene content.
    Genome Research , Jan;12(1):17-25. Details

  • 2002 Voncken FG, Boxma B, van Hoek AH, Akhmanova AS, Vogels GD, Huynen M, Veenhuis M, Hackstein JH.
    A hydrogenosomal [Fe]-hydrogenase from the anaerobic chytrid Neocallimastix sp. L2.
    Gene, Feb 6;284(1-2):103-112. Details

  • 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: A mitochondrial-type ADP/ATP carrier from the hydrogenosomes of the anaerobic chytrid Neocallimastix sp. L2.
    Molecular Microbiology, Jun;44(6):1441-1454. Details

  • 2001 Ettema T, van der Oost J, Huynen M.
    Modularity in the gain and loss of genes: applications for function prediction.
    Trends in Genetics , Sep;17(9):485-487. Details

  • 2001 Hackstein JH, Akhmanova A, Voncken F, van Hoek A, van Alen T, Boxma B, Moon-van der Staay SY, van der Staay G, Leunissen J, Huynen M, Rosenberg J, Veenhuis M.
    Hydrogenosomes: convergent adaptations of mitochondria to anaerobic environments.
    Zoology , 104(3-4):290-302. Details

  • 2001 Huynen MA.
    Using comparative genome analysis to find interaction partners for frataxin.
    Proceedings of ESF Cardiovascular Genomics: New Pathophysiological Concepts, Edited by Doevendans PA, Kääb S. Issue 4.

  • 2001 Huynen MA, Snel B, Bork P.
    Inversions and the dynamics of eukaryotic gene order.
    Trends in Genetics , Jun;17(6):304-306. Details

  • 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, Oct 1;10(21):2463-2468. Details

  • 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.
    Journal of Biological Chemistry , Nov 2;276(44):40926-40932. Details

  • 2000 van Hoek AH, van Alen TA, Sprakel VS, Leunissen JA, Brigge T, Vogels GD, Hackstein JH.
    Multiple acquisition of methanogenic archaeal symbionts by anaerobic ciliates.
    Mol Biol Evol, Feb;17(2):251-258. Details

  • 2000 van Kampen AH, van Schaik BD, Pauws E, Michiels EM, Ruijter JM, Caron HN, Versteeg R, Heisterkamp SH, Leunissen JA, Baas F, van der Mee M.
    AGE: a web-based approach towards the analysis of SAGE data. Serial Analysis of Gene Expression.
    Bioinformatics, Oct;16(10):899-905. Details

  • 2000 Kersten MASH, van der Drift C, Op den Camp HJM, Baars JJP, van Griensven LJLD, Schaap PJ, Müller Y, Visser J, Leunissen JAM
    The glutamine synthetase from the edible mushroom Agaricus bisporus.
    Science and clutivation of edible fungi - Proceedings of the 15th international congress, Edited by van Griensven LJLD. Balkema Publishers, Rotterdam/Brookfield, pp 71-78.

  • 2000 Leunissen JAM.
    De Gene Machine vindt al uw genen.
    BioNieuws, Interview by Rinze Benedictus, July.

  • 1999 Wang J, Bakkers JM, Galama JM, Bruins Slot HJ, Pilipenko EV, Agol VI, Melchers WJ.
    Structural requirements of the higher order RNA kissing element in the enteroviral 3'UTR.
    Nucleic Acids Res, Jan 15;27(2):485-490. Details