Publications in international journals 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, 2016 , PDF


  • 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., 2016 , PDF


  • 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., 2016 , PDF


  • Alkema W, Boekhorst J, Wels M, van Hijum SA
    Microbial bioinformatics for food safety and production
    Brief Bioinform., 2016 Mar;17(2):283-92, 2016 , PDF


  • Bron PA, Lee IC, Backus L, van Hijum SA, Wels M, Kleerebezem M
    Draft Genome Sequence of Lactobacillus plantarum SF2A35B
    Genome announcements, 2016;4(1), 2016 , PDF


  • 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, 2016 , PDF


  • 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, 2016 , PDF


  • Cnossen WR, Te Morsche RH, Hoischen A, Gilissen C, Venselaar H, Mehdi S, Bergmann C, Losekoot M, Breuning MH, Peters DJ, Veltman JA, Drenth JP
    LRP5 variants may contribute to ADPKD
    Eur J Hum Genet, 2016 Feb;24(2):237-42, 2016 , PDF


  • de Voer RM, Hahn MM, Weren RD, Mensenkamp AR, Gilissen C, van Zelst-Stams WA, Spruijt L, Kets CM, Zhang J, Venselaar H, Vreede L, Schubert N, Tychon M, Derks R, Schackert HK, Geurts van Kessel A, Hoogerbrugge N, Ligtenberg MJ, Kuiper RP
    Identification of Novel Candidate Genes for Early-Onset Colorectal Cancer Susceptibility
    PLoS Genet, 2016 Feb;12(2):e1005880, 2016 , PDF


  • 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, 2016 , PDF


  • 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, 2016 , PDF


  • Isberg V, Mordalski S, Munk C, Rataj K, Harpsoe K, Hauser AS, Vroling B, Bojarski AJ, Vriend G, Gloriam DE
    GPCRdb: an information system for G protein-coupled receptors
    Nucleic Acids Res , 2016 Jan 4;44(D1):D356-64, 2016 , PDF


  • Ison J, Rapacki K, Menager H, Kalas M, Rydza E, Chmura P, Anthon C, Beard N, Berka K, Bolser D, Booth T, Bretaudeau A, Brezovsky J, Casadio R, Cesareni G, Coppens F, Cornell M, Cuccuru G, Davidsen K, Vedova GD, Dogan T, Doppelt-Azeroual O, Emery L, Gasteiger E, Gatter T, Goldberg T, Grosjean M, Gruning B, Helmer-Citterich M, Ienasescu H, Ioannidis V, Jespersen MC, Jimenez R, Juty N, Juvan P, Koch M, Laibe C, Li JW, Licata L, Mareuil F, Micetic I, Friborg RM, Moretti S, Morris C, Moller S, Nenadic A, Peterson H, Profiti G, Rice P, Romano P, Roncaglia P, Saidi R, Schafferhans A, Schwammle V, Smith C, Sperotto MM, Stockinger H, Varekova RS, Tosatto SC, de la Torre V, Uva P, Via A, Yachdav G, Zambelli F, Vriend G, Rost B, Parkinson H, Longreen P, Brunak S
    Tools and data services registry: a community effort to document bioinformatics resources
    Nucleic Acids Res, 2016 Jan 4;44(D1):D38-47, 2016 , PDF


  • 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, 2016 , PDF


  • Munk C, Isberg V, Mordalski S, Harpsoe K, Rataj K, Hauser AS, Kolb P, Bojarski AJ, Vriend G, Gloriam DE
    GPCRdb: the G protein-coupled receptor database - an introduction
    Br J Pharmacol., 2016 Jul;173(14):2195-207, 2016 , PDF


  • Kuipers K, Gallay C, Martinek V, Rohde M, Martinkova M, van der Beek SL, Jong WS, Venselaar H, Zomer A, Bootsma H, Veening JW, de Jonge MI
    Highly conserved nucleotide phosphatase essential for membrane lipid homeostasis in Streptococcus pneumoniae
    Mol Microbiol., 2016 Jul;101(1):12-26, 2016 , PDF


  • 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, 2016 , PDF


  • 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, 2016 , PDF


  • 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, 2016 , PDF


  • Labbe CM, Kuenemann MA, Zarzycka B, Vriend G, Nicolaes GA, Lagorce D, Miteva MA, Villoutreix BO, Sperandio O
    iPPI-DB: an online database of modulators of protein-protein interactions
    Nucleic Acids Res, 2016 Jan 4;44(D1):D542-7, 2016 , PDF


  • 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, 2016 , PDF


  • Micheal S, Siddiqui SN, Zafar SN, Venselaar H, Qamar R, Khan MI, den Hollander AI
    Whole exome sequencing identifies a heterozygous missense variant in the PRDM5 gene in a family with Axenfeld-Rieger syndrome
    Neurogenetics, 2016 Jan;17(1):17-23, 2016 , PDF


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


  • Rutten JW, Dauwerse HG, Peters DJ, Goldfarb A, Venselaar H, Haffner C, van Ommen GJ, Aartsma-Rus AM, Lesnik Oberstein SA
    Therapeutic NOTCH3 cysteine correction in CADASIL using exon skipping: in vitro proof of concept
    Brain, 2016 Apr;139(Pt 4):1123-35, 2016 , PDF


  • 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, 2016 , PDF


  • 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, 2016 , PDF


  • 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, 2016 , PDF


  • Zarzycka B, Kuenemann MA, Miteva MA, Nicolaes GA, Vriend G, Sperandio O
    Stabilization of protein-protein interaction complexes through small molecules
    Drug Discov Today, 2016 Jan;21(1):48-57, 2016 , PDF


  • Vollan HS, Tannaes T, Vriend G, Bukholm G
    In Silico Structure and Sequence Analysis of Bacterial Porins and Specific Diffusion Channels for Hydrophilic Molecules: Conservation, Multimericity and Multifunctionality
    Int J Mol Sci., 2016;17(4), 2016 , PDF


  • Lange J, Wyrwicz LS, Vriend G
    KMAD: knowledge-based multiple sequence alignment for intrinsically disordered proteins
    Bioinformatics, 2016 Mar 15;32(6):932-6, 2016 , PDF


  • Warda AK, Siezen RJ, Boekhorst J, Wells-Bennik MH, de Jong A, Kuipers OP, Nierop Groot MN, Abee T
    Linking Bacillus cereus Genotypes and Carbohydrate Utilization Capacity
    PLoS One, 2016;11(6):e0156796, 2016 , PDF


  • Touw WG, Joosten RP, Vriend G
    New Biological Insights from Better Structure Models
    J Mol Biol., 2016 Mar 27;428(6):1375-93, 2016 , PDF


  • 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, 2016 , PDF


  • 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, 2016 , PDF


  • Erkus O, de Jager VC, Geene RT, van Alen-Boerrigter I, Hazelwood L, van Hijum SA, Kleerebezem M, Smid EJ
    Use of propidium monoazide for selective profiling of viable microbial cells during Gouda cheese ripening
    Int J Food Microbiol., 2016 Jul 2;228:1-9, 2016 , PDF


  • 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, 2016 , PDF


  • Bosma EF, Koehorst JJ, van Hijum SA, Renckens B, Vriesendorp B, van de Weijer AH, Schaap PJ, de Vos WM, van der Oost J, van Kranenburg R
    Complete genome sequence of thermophilic Bacillus smithii type strain DSM 4216(T)
    Stand Genomic Sci, 2016;11(1):52, 2016 , PDF


  • 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, 2016 , PDF


  • Durst RF, Huynh C, Lott A, Miller SJ, Palsson EA, Touw W, Vriend G
    The Inverse Gamma Distribution and Benford's Law
    arXiv preprint arXiv:160904106 Mathematics Probability, 2016 Sep 15:1-12, 2016 , PDF


  • van Lith SA, Navis AC, Lenting K, Verrijp K, Schepens JT, Hendriks WJ, Schubert NA, Venselaar H, Wevers RA, van Rooij A, Wesseling P, Molenaar RJ, van Noorden CJ, Pusch S, Tops B, Leenders WP
    Identification of a novel inactivating mutation in Isocitrate Dehydrogenase 1 (IDH1-R314C) in a high grade astrocytoma
    Sci Rep, 2016;6:30486, 2016 , PDF


  • 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, 2016 , PDF


  • 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, 2016 , PDF


  • 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, 2016 , PDF


  • Astuti GD, Arno G, Hull S, Pierrache L, Venselaar H, Carss K, Raymond FL, Collin RW, Faradz SM, van den Born LI, Webster AR, Cremers FP
    Mutations in AGBL5, Encoding alpha-Tubulin Deglutamylase, Are Associated With Autosomal Recessive Retinitis Pigmentosa
    Invest Ophthalmol Vis Sci., 2016 Nov 01;57(14):6180-7, 2016 , PDF


  • 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, 2016 , PDF


  • Dijkstra AR, Alkema W, Starrenburg MJ, Hugenholtz J, van Hijum SA, Bron PA
    Strain-Dependent Transcriptome Signatures for Robustness in Lactococcus lactis
    PLoS One, 2016;11(12):e0167944, 2016 , PDF


  • 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, 2016 , PDF


  • Homberg JR, Olivier JD, VandenBroeke M, Youn J, Ellenbroek AK, Karel P, Shan L, van Boxtel R, Ooms S, Balemans M, Langedijk J, Muller M, Vriend G, Cools AR, Cuppen E, Ellenbroek BA
    The role of the dopamine D1 receptor in social cognition: studies using a novel genetic rat model
    Dis Model Mech., 2016 Oct 01;9(10):1147-58, 2016 , PDF


  • Martino ME, Bayjanov JR, Caffrey BE, Wels M, Joncour P, Hughes S, Gillet B, Kleerebezem M, van Hijum SA, Leulier F
    Nomadic lifestyle of Lactobacillus plantarum revealed by comparative genomics of 54 strains isolated from different habitats
    Environ Microbiol., 2016 Dec;18(12):4974-89, 2016 , PDF


  • 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, 2016 , PDF


  • Touw WG, van Beusekom B, Evers JM, Vriend G, Joosten RP
    Validation and correction of Zn-CysxHisy complexes
    Acta crystallographica Section D, Structural biology, 2016 Oct 01;72(Pt 10):1110-8, 2016 , PDF


  • Urshev Z, Hajo K, Lenoci L, Bron PA, Dijkstra A, Alkema W, Wels M, Siezen RJ, Minkova S, van Hijum SA
    Draft Genome Sequence of Lactobacillus delbrueckii subsp. bulgaricus LBB.B5
    Genome announcements, 2016 Oct 06;4(5), 2016 , PDF


  • van der Krieken DA, Ederveen TH, van Hijum SA, Jansen PA, Melchers WJ, Scheepers PT, Schalkwijk J, Zeeuwen PL
    An In vitro Model for Bacterial Growth on Human Stratum Corneum
    Acta Derm Venereol., 2016 Nov 02;96(7):873-9, 2016 , PDF


  • Vass M, Kooistra AJ, Ritschel T, Leurs R, de Esch IJ, de Graaf C
    Molecular interaction fingerprint approaches for GPCR drug discovery
    Curr Opin Pharmacol., 2016 Oct;30:59-68, 2016 , PDF