Publications in international journals 2015
  • Dingemanse C, Belzer C, van Hijum SA, Gunthel M, Salvatori D, den Dunnen JT, Kuijper EJ, Devilee P, de Vos WM, van Ommen GB, Robanus-Maandag EC.
    Akkermansia muciniphila and Helicobacter typhlonius modulate intestinal tumor development in mice.
    Carcinogenesis, Nov;36(11):1388-96. doi: 10.1093/carcin/bgv120. , 2015 , PDF


  • Ercan O, Wels M, Smid EJ, Kleerebezem M.
    Genome-Wide Transcriptional Responses to Carbon Starvation in Nongrowing Lactococcus lactis
    Appl Environ Microbiol, Apr 1;81(7):2554-61. doi: 10.1128/AEM.03748-14., 2015 , PDF


  • Fleuren WW, Alkema W.
    Application of text mining in the biomedical domain
    Methods, Mar;74:97-106. doi: 10.1016/j.ymeth.2015.01.015, 2015 , PDF


  • Isberg V, de Graaf C, Bortolato A, Cherezov V, Katritch V, Marshall FH, Mordalski S, Pin JP, Stevens RC, Vriend G, Gloriam DE.
    Generic GPCR residue numbers - aligning topology maps while minding the gaps.
    Trends Pharmacol Sci., Jan;36(1):22-31. doi: 10.1016/j.tips.2014.11.001., 2015 , PDF


  • Touw WG, Baakman C, Black J, Te Beek TA, Krieger TA, Joosten RP, Vriend G.
    A series of PDB-related databanks for everyday needs.
    Nucleic Acids Res., Jan 28;43(Database issue):D364-8. doi: 10.1093/nar/gku1028., 2015 , PDF


  • Ercan O, Wels M, Smid EJ, Kleerebezem M.
    Molecular and metabolic adaptations of Lactococcus lactis at near-zero growth rates.
    Appl Environ Microbiol., Jan;81(1):320-31. doi: 10.1128/AEM.02484-14., 2015 , PDF


  • Renkema GH, Wortmann SB, Smeets RJ, Venselaar H, Antoine M, Visser G, Ben-Omran T, van den Heuvel LP, Timmers HJ, Smeitink JA, Rodenburg RJ.
    SDHA mutations causing a multisystem mitochondrial disease: novel mutations and genetic overlap with hereditary tumors.
    Eur J Hum Genet., Feb;23(2):202-9. doi: 10.1038/ejhg.2014.80., 2015 , PDF


  • 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, 2015 , PDF


  • 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], 2015 , PDF


  • Iqbal Z, Willemsen MH, Papon MA, Musante L, Benevento M, Hu H, Venselaar H, Wissink-Lindhout WM, Vulto-van Silfhout AT, Vissers LE, de Brouwer AP, Marouillat S, Wienker TF, Ropers HH, Kahrizi K, Nadif Kasri N, Najmabadi H, Laumonnier F, Kleefstra T, van Bokhoven H.
    Homozygous SLC6A17 Mutations Cause Autosomal-Recessive Intellectual Disability with Progressive Tremor, Speech Impairment, and Behavioral Problems
    Am J Hum Genet, Mar 5;96(3):386-96. doi: 10.1016/j.ajhg.2015.01.010, 2015 , PDF


  • Lambers TT, Gloerich J, van Hoffen E, Alkema W, Hondmann DH, van Tol EA.
    Clustering analyses in peptidomics revealed that peptide profiles of infant formulae are descriptive
    Food Sci Nutr, Jan;3(1):81-90. doi: 10.1002/fsn3.196., 2015 , PDF


  • Lamontanara A, Caggianiello G, Orru L, Capozzi V, Michelotti V, Bayjanov JR, Renckens B, van Hijum SA, Cattivelli L, Spano G.
    Draft Genome Sequence of Lactobacillus plantarum Lp90 Isolated from Wine
    Genome Announc, Mar 12;3(2). pii: e00097-15. doi: 10.1128/genomeA.00097-15., 2015 , PDF


  • Maria Oonk AM, van Huet RA, Leijendeckers JM, Oostrik J, Venselaar H, van Wijk E, Beynon A, Kunst HP, Hoyng CB, Kremer H, Schraders M, Pennings RJ.
    Nonsyndromic Hearing Loss Caused by USH1G Mutations: Widening the USH1G Disease Spectrum
    Ear Hear, Mar-Apr;36(2):205-11. doi: 10.1097/AUD.0000000000000095., 2015 , PDF


  • 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


  • Zarzycka B, Seijkens T, Nabuurs SB, Ritschel T, Grommes J, Soehnlein O, Schrijver R, van Tiel CM, Hackeng TM, Weber C, Giehler F, Kieser A, Lutgens E, Vriend G, Nicolaes GA.
    Discovery of Small Molecule CD40-TRAF6 Inhibitors
    J Chem Inf Model, Feb 23;55(2):294-307. doi: 10.1021/ci500631e., 2015 , PDF


  • Atwood TK, Bongcam-Rudloff E, Brazas ME, Corpas M, Gaudet P, Lewitter F, Mulder N, Palagi PM, Schneider MV, van Gelder CW, GOBLET Consortium
    GOBLET: The Global Organisation for Bioinformatics Learning, Education and Training
    PLoS Comput Biol., Apr 9;11(4):e1004143. doi: 10.1371/journal.pcbi.1004143., 2015 , PDF


  • Roifman M., Marcelis CL, Paton T, Marshall C, Silver R, Lohr JL, Yntema HG, Venselaar H, Kayserili H, van Bon B, Seaward G, Brunner HG, Chitayat D.
    De novo WNT5A-associated autosomal dominant Robinow syndrome suggests specificity of genotype and phenotype
    Clin Genet, Jan;87(1):34-41. doi: 10.1111/cge.12401., 2015 , PDF


  • Roland WS, Sanders MP, van Buren L, Gouka RJ, Gruppen H, Vincken JP, Ritschel T.
    Snooker structure-based pharmacophore model explains differences in agonist and blocker binding to bitter receptor hTAS2R39
    PLoS One, Mar 2;10(3):e0118200. doi: 10.1371/journal.pone.0118200, 2015 , PDF


  • Sanders JW, Oomes SJ, Membre JM, Wegkamp A, Wels M.
    Biodiversity of spoilage lactobacilli: phenotypic characterisation
    Food Microbiol, Feb;45(Pt A):34-44. doi: 10.1016/j.fm.2014.03.013, 2015 , PDF


  • 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., 2015 , PDF


  • 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. , 2015 , PDF


  • van den Kieboom CH, Ahout IM, Zomer A, Brand KH, de Groot R, Ferwerda G, de Jonge MI.
    Nasopharyngeal gene expression, a novel approach to study the course of respiratory syncytial virus infection.
    Eur Respir J., Mar;45(3):718-25. doi: 10.1183/09031936.00085614., 2015 , PDF


  • Venter G, Polling S, Pluk H, Venselaar H, Wijers M, Willemse M, Fransen JA, Wieringa B.
    Submembranous recruitment of creatine kinase B supports formation of dynamic actin-based protrusions of macrophages and relies on its C-terminal flexible loop
    Eur J Cell Biol, Feb;94(2):114-27. doi: 10.1016/j.ejcb.2014.11.002., 2015 , PDF


  • Wortmann SB, Zietkiewicz S, Kousi M, Szklarczyk R, Haack TB, Gersting SW, Muntau AC, Rakovic A, Renkema GH, Rodenburg RJ, Strom TM, Meitinger T, Rubio-Gozalbo ME, Chrusciel E, Distelmaier F, Golzio C, Jansen JH, van Karnebeek C, Lillguist Y, Lucke T, Ounap K, Zordania R, Yaplito-Lee J, van Bokhoven H, Spelbrink JN, Vaz FM, Pras-Raves M, Ploski R, Pronicka E, Klein C, Willemsen MA, de Brouwer AP, Prokisch H, Katsanis N, Wevers RA.
    CLPB mutations cause 3-methylglutaconic aciduria, progressive brain atrophy, intellectual disability, congenital neutropenia, cataracts, movement disorder
    Am J Hum Genet, Feb 5;96(2):245-57. doi: 10.1016/j.ajhg.2014.12.013., 2015 , PDF


  • Wu J, Pipathsouk A, Keizer-Gunnink A, Fusetti F, Alkema W, Liu S, Altschuler S, Wu L, Kortholt A, Weiner OD. 
    Homer3 regulates the establishment of neutrophil polarity
    Molecular Biology of the Cell, Mar 4;26(9): 1629-1639, 2015


  • Lusher S, Ritschel T.
    Finding the right approach to big data-driven medicinal chemistry.
    Future Med Chem, Jul;7(10):1213-6. doi: 10.4155/fmc.15.58., 2015 , PDF


  • van de Schans MG, Ritschel T, Bovee TF, et al.
    Involvement of a hydrophobic pocket and helix 11 in determining the mode of action of prenylated flavonoids and isoflavonoids in the human estrogen receptor.
    Chembiochem, doi: 10.1002/cbic.201500343., 2015 , PDF


  • 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., 2015 , PDF


  • Attwood TK, Bongcam-Rudloff E, Brazas ME, Corpas M, Gaudet P, Lewitter F, Mulder N, Palagi PM, Schneider MV, van Gelder CW.
    Correction: GOBLET: The Global Organisation for Bioinformatics Learning, Education and Training
    PLoS Comput Biol, May 14;11(5):e1004281. doi: 10.1371/journal.pcbi.1004281., 2015 , PDF


  • Bertoli-Avella AM, Gillis E, Morisaki H, Verhagen JM, de Graaf BM, van de Beek G, Gallo E, Kruithof BP, Venselaar H, Myers LA, Laga S, Doyle AJ, Oswald G, van Cappellen GW, Yamanaka I, van der Helm RM, Beverloo B, de Klein A, Pardo L, Lammens M, Evers C, Devriendt K, Dumoulein M, Timmermans J, Bruggenwirth HT, Verheijen F, Rodrigus I, Baynam G, Kempers M, Saenen J, Van Craenenbroeck EM, Minatoya K, Matsukawa R, Tsukube T, Kubo N, Hofstra R, Goumans MJ, Bekkers JA, Roos-Hesselinks JW, van de Laar IM, Dietz HC, Van Laer L, Morisaki T, Wessels MW, Loeys BL.
    Mutations in a TGF-beta ligand, TGFB3, cause syndromic aortic aneurysms and dissections
    J Am Coll Cardiol, Apr 7;65(13):1324-36. doi: 10.1016/j.jacc.2015.01.040., 2015 , PDF


  • 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., 2015 , PDF


  • Ganapathy S, Becheau O, Venselaar H, Frolich S, van der Steen JB, Chen Q, Radwan S, Lugtenburg J, Hellingwerf KJ, de Groot HJ, de Grip WJ.
    Modulation of spectral properties and pump activity of proteorhodopsins by retinal analogues
    Biochem J, Apr 15;467(2):333-43. doi: 10.1042/BJ20141210., 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., 2015 , PDF


  • Holliday GL, Bairoch A, Bagos PG, Chatonnet A, Craik DJ, Finn RD, Henrissat B, Landsman D, Maning G, Nagano N, O'Donovan C, Pruitt KD, Rawlings ND, Saier M, Sowdhamini R, Spedding M, Srinivasan N, Vriend G, Babbit PC, Bateman A.
    Key challenges for the creation and maintenance of specialist protein resources
    Proteins, Jun;83(6):1005-13. doi: 10.1002/prot.24803., 2015 , PDF


  • 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. , 2015 , PDF


  • Jaeggi T, Kortman GA, Moretti D, Chassard C, Holding P, Dostal A, Boekhorst J, Timmerman HM, Swinkels DW, Tjalsma H, Njenga J, Mwangi A, Kvalsvig J, Lacroix C, Zimmerman MB.
    Iron fortification adversely affects the gut microbiome, increases pathogen abundance and induces intestinal inflammation in Kenyan infants
    Gut, May;64(5):731-42. doi: 10.1136/gutjnl-2014-307720., 2015 , PDF


  • Krieger E, Vriend G.
    New ways to boost molecular dynamics simulations
    J Comput Chem, May 15;36(13):996-1007. doi: 10.1002/jcc.23899. , 2015 , PDF


  • 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, 2015 , PDF


  • Marchegiani S, Davis T, Tessadori F, van Haaften G, Brancati F, Hoischen A, Huang H, Valkanas E, Pusey B, Schanze D, Venselaar H, Vulto-van Silfhout AT, Wolfe LA, Tifft CJ, Zerfas PM, Zambruo G, Kariminejad A, Sabbagh-Kermani F, Lee J, Tsokos MG, Lee CC, Ferraz V, da Silva EM, Stevens CA, Roche N, Bartsch O, Farndon P, Bemejo-Sanchez E, Brooks BP, Maduro V, Dallapiccola B, Ramos FJ, Chung HY, Le Cainec C, Martins F, Jacyk WK, Mazzanti L, Brunner HG, Bakkers J, Lin S, Malicdan MC, Boerkoel CF, Gahl WA, de Vries BB, van Haelst MM, Zenker M, Markello TC.
    Recurrent Mutations in the Basic Domain of TWIST2 Cause Ablepharon Macrostomia and Barber-Say Syndromes
    Am J Hum Genet, Jul 2;97(1):99-110. doi: 10.1016/j.ajhg.2015.05.017., 2015 , PDF


  • 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., 2015 , PDF


  • Metselaar KI, den Besten HM, Boekhorst J, van Hijum SA, Zwietering MH, Abee T
    Diversity of acid stress resistant variants of Listeria monocytogenes and the potential role of ribosomal protein S21 encoded by rpsU
    Front Microbiol, May 8;6:422. doi: 10.3389/fmicb.2015.00422., 2015 , PDF


  • Navis AC, van Lith SA, van Duijnhoven SM, de Pooter M, Yetkin-Arik B, Wesseling P, Hendriks WJ, Venselaar H, Timmer M, van Cleef P, van Bergen En Henegouwen P, Best MG, Wurdinger TD, Tops BB, Leenders WP.
    Identification of a novel MET mutation in high-grade glioma resulting in an auto-active intracellular protein
    Acta Neuropathol, Jul;130(1):131-44. doi: 10.1007/s00401-015-1420-5., 2015 , PDF


  • Oh, SK, Baek JI, Weigand KM, Venselaar H, Swarts HG, Park SH, Hashim Raza M, Jung da J, Choi SY, Lee SH, Friedrich T, Vriend G, Koenderink JB, Kim UK, Lee KY.
    A missense variant of the ATP1A2 gene is associated with a novel phenotype of progressive sensorineural hearing loss associated with migraine
    Eur J Hum Genet, May;23(5):639-45. doi: 10.1038/ejhg.2014.154., 2015 , PDF


  • Wedler HB, Pemberton RP, Lounnas V, Vriend G, Tantillo DJ, Wang SC.
    Quantum chemical study of the isomerization of 24-methylenecycloartanol, a potential marker of olive oil refining
    J Mol Model, May;21(5):111. doi: 10.1007/s00894-015-2652-y., 2015 , PDF


  • Xiao Y, van Hijum SA, Abee T, Wells-Bennik MH.
    Genome-Wide Transcriptional Profiling of Clostridium perfringens SM101 during Sporulation Extends the Core of Putative Sporulation Genes and Genes Determining Spore Properties and Germination Characteristics
    PLoS One, May 15;10(5):e0127036. doi: 10.1371/journal.pone.0127036., 2015 , PDF


  • 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. , 2015 , PDF


  • 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., 2015 , PDF


  • Schirris TJ, Ritschel T, Herma Renkema G, Willems PH, Smeitink JA, Russel FG
    Mitochondrial ADP/ATP exchange inhibition: a novel off-target mechanism underlying ibipinabant-induced myotoxicity
    Sci Rep, Sep 29;5:14533. doi: 10.1038/srep14533., 2015 , PDF


  • Schirris TJ, Ritschel T, Bilos A, Smeitink JA, Russel FG.
    Statin lactonization by uridine 5'-diphospho-glucuronosyltransferases (UGTs).
    Mol Pharm, 12(11):4048-55, 2015 , PDF


  • Babbitt PC, Bagos PG, Bairoch A, Bateman A, Chatonnet A, Chen MJ, Craik DJ, Finn RD, Gloriam D, Haft DH, Henrissat B, Holliday GL, Isberg V, Kaas Q, Landsman D, Lenfant N, Manning G, Nagano N, Srinivasan N, O'Donovan C, Pruitt KD, Sowdhamini R, Rawlings ND, Saier MH Jr, Sharman JL, Spedding M, Tsirigos KD, Vastermark A, Vriend G
    Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat.
    Database (Oxford), Jul 11:bav063. doi: 10.1093/database/bav063. eCollection 2015., 2015 , PDF


  • 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., 2015 , PDF


  • Meester JA, Southgate L, Stittrich AB, Venselaar H, Beekmans SJ, den Hollander N, Bijlsma EK, Helderman-van den Enden A, Verheij JB, Glusman G, Roach JC, Lehman A, Patel MS, de Vries BB, Ruivenkamp C, Itin P, Prescott K, Clarke S, Trembath R, Zenker M, Sukalo M, Van Laer L, Loeys B, Wuyts W.
    Heterozygous Loss-of-Function Mutations in DLL4 Cause Adams-Oliver Syndrome.
    Am J Hum Genet., Sep 3;97(3):475-82. doi: 10.1016/j.ajhg.2015.07.015., 2015 , PDF


  • 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. , 2015 , PDF


  • Overmars L, Siezen RJ, Francke C.
    A Novel Quality Measure and Correction Procedure for the Annotation of Microbial Translation Initiation Sites.
    PLoS One., Jul 23;10(7):e0133691. doi: 10.1371/journal.pone.0133691, 2015 , PDF


  • Overmars L, van Hijum SA, Siezen RJ, Francke C.
    CiVi: circular genome visualization with unique features to analyze sequence elements.
    Bioinformatics. , Sep 1;31(17):2867-9. doi: 10.1093/bioinformatics/btv249., 2015 , PDF


  • Schirris TJ, Renkema GH, Ritschel T, Voermans NC, Bilos A, van Engelen BG, Brandt U, Koopman WJ, Beyrath JD, Rodenburg RJ, Willems PH, Smeitink JA, Russel FG.
    Statin-Induced Myopathy Is Associated with Mitochondrial Complex III Inhibition.
    Cell Metab., Sep 1;22(3):399-407. doi: 10.1016/j.cmet., 2015 , PDF


  • 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., 2015 , PDF


  • Snijders Blok L, Madsen E, Juusola J, Gilissen C, Baralle D, Reijnders MR, Venselaar H, Helsmoortel C, Cho MT, Hoischen A, Vissers LE, Koemans TS, Wissink-Lindhout W, Eichler EE, Romano C, Van Esch H, Stumpel C, Vreeburg M, Smeets E, Oberndorff K, van Bon BW, Shaw M, Gecz J, Haan E, Bienek M, Jensen C, Loeys BL, Van Dijck A, Innes AM, Racher H, Vermeer S, Di Donato N, Rump A, Tatton-Brown K, Parker MJ, Henderson A, Lynch SA, Fryer A, Ross A, Vasudevan P, Kini U, Newbury-Ecob R, Chandler K, Male A, Dijkstra S, Schieving J, Giltay J, van Gassen KL, Schuurs-Hoeijmakers J, Tan PL, Pediaditakis I, Haas SA, Retterer K, Reed P, Monaghan KG, Haverfield E, Natowicz M, Myers A, Kruer MC, Stein Q, Strauss KA, Brigatti KW, Keating K, Burton BK, Kim KH, Charrow J, Norman J, Foster-Barber A, Kline AD, Kimball A, Zackai E, Harr M, Fox J, McLaughlin J, Lindstrom K, Haude KM, van Roozendaal K, Brunner H, Chung WK, Kooy RF, Pfundt R, Kalscheuer V, Mehta SG, Katsanis N, Kleefstra T.
    Mutations in DDX3X Are a Common Cause of Unexplained Intellectual Disability with Gender-Specific Effects on Wnt Signaling.
    Am J Hum Genet. , Aug 6;97(2):343-52. doi: 10.1016/j.ajhg.2015.07.004., 2015 , PDF


  • Touw WG, Joosten RP, Vriend G.
    Detection of trans-cis flips and peptide-plane flips in protein structures.
    Acta Crystallogr D Biol Crystallogr, Aug;71(Pt 8):1604-14. doi: 10.1107/S1399004715008263, 2015 , PDF


  • 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., 2015 , PDF


  • Ison J, Rapacki K, Ménager H, Kalaš 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, Grüning 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, Mi?eti? I, Friborg RM, Moretti S, Morris C, Möller S, Nenadic A, Peterson H, Profiti G, Rice P, Romano P, Roncaglia P, Saidi R, Schafferhans A, Schwämmle V, Smith C, Sperotto MM, Stockinger H, Va?eková RS, Tosatto SC, de la Torre V, Uva P, Via A, Yachdav G, Zambelli F, Vriend G, Rost B, Parkinson H, Løngreen P, Brunak S.
    Tools and data services registry: a community effort to document bioinformatics resources.
    Necleic Acids Res., Nov 3. pii: gkv1116, 2015 , PDF


  • Alkema W, Boekhorst J, Wels M, van Hijum SA.
    Microbial bioinformatics for food safety and production.
    Brief Bioinform., 2015 Jun 16. pii: bbv034., 2015 , PDF


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