My current list of publications

Articles

Authors.
"Title."
Journal.
Van Moerbeke M, Kasim A, Talloen W, Reumers J, Göhlmann HWH, Shkedy Z.
"A random effects model for the identification of differential splicing (REIDS) using exon and HTA arrays."
BMC Bioinformatics. 2017 May 25;18(1):273. doi: 10.1186/s12859-017-1687-8.
Stroobants S, Van Acker NG, Verheijen FW, Goris I, Daneels GF, Schot R, Verbeek E, Knaapen MW, De Bondt A, Göhlmann HW, Crauwels ML, Mancini GM, Andries LJ, Moechars DW, D'Hooge R.
"Progressive leukoencephalopathy impairs neurobehavioral development in sialin-deficient mice."
Exp Neurol. 2017 Feb 9;291:106-119. doi: 10.1016/j.expneurol.2017.02.009.
Perualila-Tan N, Shkedy Z, Talloen W, Göhlmann HW, QSTAR Consortium, Van Moerbeke M, Kasim A.
"Weighted similarity-based clustering of chemical structure and bioactivity data in early drug discovery."
J Bioinform Comput Biol. 2016 Aug;14(4):1650018. doi: 10.1142/S0219720016500189.
Perualila-Tan N, Shkedy Z, Talloen W, Göhlmann HW, Kasim A.
"A joint modeling approach for uncovering associations between gene expression, bioactivity and chemical structure in early drug discovery to guide lead selection and genomic biomarker development."
Stat Appl Genet Mol Biol. 2016 May 25. pii: /j/sagmb.ahead-of-print/sagmb-2014-0086/sagmb-2014-0086.xml. doi: 10.1515/sagmb-2014-0086. [Epub ahead of print].
De Wolf H, De Bondt A, Turner H, Göhlmann HW.
"Transcriptional characterization of Compounds: Lessons learned from the public LINCS data."
Assay Drug Dev Technol. 2016 May;14(4):252-60. doi: 10.1089/adt.2016.715.
Uhr K, Prager-van der Smissen WJ, Heine AA, Ozturk B, Smid M, Göhlmann HW, Jager A, Foekens JA, Martens JW.
"Understanding drugs in breast cancer through drug sensitivity screening."
Springerplus 2015 Oct 15;4:611. doi: 10.1186/s40064-015-1406-8. eCollection 2015.
Verbist BM, Verheyen GR, Vervoort L, Crabbe M, Beerens D, Bosmans C, Jaensch S, Osselaer S, Talloen W, Van Den Wyngaert I, Van Hecke G, Wuyts D, Van Goethem F, Göhlmann HW.
"Integrating high-dimensional transcriptomics and image analysis tools into early safety screening: a proof-of-concept for a new early drug development strategy."
Chem Res Toxicol. Chem Res Toxicol. 2015 Oct 19;28(10):1914-25. doi: 10.1021/acs.chemrestox.5b00103. Epub 2015 Sep 15.
Kasim A, Shkedy Z, Lin D, Van Sanden S, Abrahantes JC, Göhlmann HW, Bijnens L, Yekutieli D, Aerssens J, Camilleri M, Talloen W.
"Translation of Disease Associated Gene Signatures across Tissues."
Int. J. Data Mining and Bioinformatics, 2015, Vol. 11, No. 3.
Verbist B, Klambauer G, Vervoort L, Talloen W; QSTAR Consortium, Shkedy Z, Thas O, Bender A, Göhlmann HW, Hochreiter S.
"Using transcriptomics to guide lead optimization in drug discovery projects."
Drug Discov Today. 2015 May;20(5):505-13. doi: 10.1016/j.drudis.2014.12.014. Epub 2015 Jan 10.
Ravindranath AC, Perualila-Tan N, Kasim A, Drakakis G, Liggi S, Brewerton SC, Mason D, Bodkin MJ, Evans DA, Bhagwat A, Talloen W, Göhlmann HW, QSTAR Consortium, Shkedy Z, Bender A.
"Connecting gene expression data from connectivity map and in silico target predictions for small molecule mechanism-of-action analysis."
Molecular BioSystems. 2014 16 Sep 2014.
Liu H, Park J, Manning C, Göhlmann HW, Marshall DJ.
"Metastatic signature in lung cancer is associated with sensitivity to anti-integrin αV monoclonal antibody intetumumab."
Genes Chromosomes Cancer. 2014 Apr;53(4):349-57.
Koul A, Vranckx L, Dhar N, Göhlmann HW, Ozdemir E, Neefs JM, Schulz M, Lu P, Mørtz E, McKinney JD, Andries K, Bald D.
"Delayed bactericidal response of Mycobacterium tuberculosis to bedaquiline involves remodelling of bacterial metabolism."
Nat Commun. 2014 Feb 26;5:3369.
Khamiakova T, Shkedy Z, Amaratunga D, Talloen W, Göhlmann HW, Bijnens L, Kasim A.
"Quality Control of Platinum Spike Dataset by Probe-Level Mixed Models."
Math Biosci. 2014 Feb;248:1-10.
Otava O, Shkedy Z, Lin D, Göhlmann HW, Bijnens L, Talloen W, Kasim A.
"Dose-Response Modeling Under Simple Order Restrictions Using Bayesian Variable Selection Methods."
Statistics in Biopharmaceutical Research. 2013 Published online: 27 Nov 2013. doi: 10.1080/19466315.2013.855472.
Forcheh AC, Verbeke G, Kasim A, Lin D, Shkedy Z, Talloen W, Göhlmann HW, Clement L.
"beadarrayFilter: An R Package to Filter Beads."
The R Journal. 2013 Jun;5(1)171-180.
Lin D, Tilahun A, Abrahantes JC, Shkedy Z, Molenberghs G, Gohlmann HW, Talloen W, Bijnens L.
"Comparison of methods for the selection of genomic biomarkers."
Int J Data Min Bioinform. 2013 Jan 1;8(1)24-41.
Forcheh AC, Verbeke G, Kasim A, Lin D, Shkedy Z, Talloen W, Göhlmann HW, Clement L.
"Gene Filtering in the Analysis of Illumina Microarray Experiments."
Statistical Applications in Genetics and Molecular Biology. 2012 Jan;11(2):1-17.
Van Sanden S, Shkedy Z, Burzykowski T, Göhlmann HW, Talloen W, Bijnens L.
"Genomic biomarkers for a binary clinical outcome in early drug development microarray experiments."
J Biopharm Stat. 2012 Jan;22(1):72-92.
Clevert DA, Mitterecker A, Mayr A, Klambauer G, Tuefferd M, De Bondt A, Talloen W, Göhlmann HW, Hochreiter S.
"cn.FARMS: a latent variable model to detect copy number variations in microarray data with a low false discovery rate."
Nucleic Acids Res. 2011 Jul;39(12):e79.
Talloen W, Hochreiter S, Bijnens L, Kasim A, Shkedy Z, Amaratunga D, Göhlmann HW.
"Filtering data from high-throughput experiments based on measurement reliability."
Proc Natl Acad Sci U S A. 2010 Nov 16;107(46):E173-4.
Tilahun A, Lin D, Shkedy Z, Geys H, Alonso A, Peeters P, Talloen W, Drinkenburg W, Göhlmann HW, Gorden E, Bijnens L, Molenberghs G.
"Genomic Biomarkers for Depression: Feature-Specific and Joint Biomarkers."
Statistics in Biopharmaceutical Research. 2010 August 1 2(3): 419-434.
Pramana S, Lin D, Haldermans P, Shkedy Z, Verbeke T, Göhlmann HW, De Bondt A, Talloen W, Bijnens L.
"IsoGene: An R Package for Analyzing Dose-response Studies in Microarray Experiments."
The R Journal. 2010 June, Volume 2/1.
Hochreiter S, Bodenhofer U, Heusel M, Mayr A, Mitterecker A, Kasim A, Khamiakova T, Van Sanden S, Lin D, Talloen W, Bijnens L, Göhlmann HW, Shkedy Z, Clevert DA.
"FABIA: factor analysis for bicluster acquisition."
Bioinformatics. 2010 Jun 15;26(12):1520-7. Epub 2010 Apr 23.
Lin D, Skhedy Z, Molenberghs G, Talloen W, Göhlmann HW, Bijnens L.
"Selection and Evaluation of Gene-specific Biomarkers in Pre-clinical and Clinical Microarray Experiments."
Online Journal of Bioinformatics. 2010 Volume 11 (1): 106-127.
Kasim AS, Lin D, Van Sanden S, Clevert DA, Bijnens L, Göhlmann HW, Amaratunga D, Hochreiter S, Shkedy Z, Talloen W.
"Informative or noninformative calls for gene expression: a latent variable approach."
Stat Appl Genet Mol Biol. 2010 9(1):Article 4. Epub 2010 Jan 6.
Versele M, Talloen W, Rockx C, Geerts T, Janssen B, Lavrijssen T, King P, Göhlmann HW, Page M, Perera T.
"Response prediction to a multitargeted kinase inhibitor in cancer cell lines and xenograft tumors using high-content tyrosine peptide arrays with a kinetic read-out."
Molecular cancer therapeutics. 2009 Jul;8(7):1846-55. Epub 2009 Jul 7.
Lin D, Shkedy Z, Burzykowski T, Yekutieli D, De Bondt A, Göhlmann HW, Talloen W, Bijnens L.
"Multiple contrast test for detecting monotonic dose-response relationship and FDR-adjusted confidence intervals for selected parameters in a microarray Setting."
Online Journal of Bioinformatics. 2009 Volume 10 (1):67-73
Tuefferd M, De Bondt A, Van Den Wyngaert I, Talloen W, Verbeke T, Carvalho B, Clevert DA, Alifano M, Raghavan N, Amaratunga D, Göhlmann HW, Broët P, Camilleri-Broët S.
"Genome-wide copy number alterations detection in fresh frozen and matched FFPE samples using SNP 6.0 arrays."
Genes Chromosomes Cancer. 2008 Nov;47(11):957-64.
Lin D, Shkedy Z, Burzykowski T, Ion R, Göhlmann HW, Bondt AD, Perer T, Geerts T, Van den Wyngaert I, Bijnens L.
"An investigation on performance of Significance Analysis of Microarray (SAM) for the comparisons of several treatments with one control in the presence of small-variance genes."
Biom J. 2008 Oct;50(5):801-23.
Koul A, Vranckx L, Dendouga N, Balemans W, Den Wyngaert IV, Vergauwen K, Göhlmann HW, Willebrords R, Poncelet A, Guillemont J, Bald D, Andries K.
"Diarylquinolines are bactericidal for dormant mycobacteria as a result of disturbed ATP homeostasis."
J Biol Chem. 2008 Sep 12;283(37):25273-80. Epub 2008 Jul 14.
Aerssens J, Camilleri M, Talloen W, Thielemans L, Göhlmann HW, Van Den Wyngaert I, Thielemans T, De Hoogt R, Andrews CN, Bharucha AE, Carlson PJ, Busciglio I, Burton DD, Smyrk T, Urrutia R, Coulie B.
"Alterations in mucosal immunity identified in the colon of patients with irritable bowel syndrome."
Clin Gastroenterol Hepatol. 2008 Feb;6(2):194-205.
Lin D, Shkedy Z, Yekutieli D, Burzykowski T, Göhlmann HW, De Bondt A, Perera T, Geerts T, Bijnens L.
"Testing for trends in dose-response microarray experiments: a comparison of several testing procedures, multiplicity and resampling-based inference."
Stat Appl Genet Mol Biol. 2007; 6:Article26. Epub 2007 Oct 11.
Raghavan N, De Bondt AM, Talloen W, Moechars D, Göhlmann HW, Amaratunga D.
"The High-level Similarity of Some Disparate Gene Expression Measures."
Bioinformatics. 2007 Nov 15;23(22):3032-8. Epub 2007 Sep 24.
Talloen W, Clevert DA, Hochreiter S, Amaratunga D, Bijnens L, Kass S, Göhlmann HW.
"I/NI-calls for the exclusion of non-informative genes: a highly effective feature filtering tool for microarray data."
Bioinformatics. 2007 Nov 1;23(21):2897-902. Epub 2007 Oct 5.
Aerssens J, Hillsley K, Peeters PJ, de Hoogt R, Stanisz A, Lin JH, Van den Wyngaert I, Göhlmann HW, Grundy D, Stead RH, Coulie B.
"Alterations in the brain-gut axis underlying visceral chemosensitivity in Nippostrongylus brasiliensis-infected mice."
Gastroenterology. 2007 Apr;132(4):1375-87. Epub 2007 Feb 7.
Camilleri M, Andrews CN, Bharucha AE, Carlson PJ, Ferber I, Stephens D, Smyrk TC, Urrutia R, Aerssens J, Thielemans L, Göhlmann HW, van den Wyngaert I, Coulie B.
"Alterations in expression of p11 and SERT in mucosal biopsy specimens of patients with irritable bowel syndrome."
Gastroenterology. 2007 Jan;132(1):17-25. Epub 2006 Nov 17.
Cope L, Hartman SM, Göhlmann HW, Tiesman JP, Irizarry RA.
"Analysis of Affymetrix GeneChip data using amplified RNA."
Biotechniques. 2006 Feb;40(2):165-6, 168, 170.
Peeters PJ, Aerssens J, de Hoogt R, Stanisz A, Göhlmann HW, Hillsley K, Meulemans A, Grundy D,
Stead RH, Coulie B.
"Molecular profiling of murine sensory neurons in the nodose and dorsal root ganglia labeled from the peritoneal cavity."
Physiol Genomics. 2006 Feb 14;24(3):252-63. Epub 2005 Nov 22.
Aliouat-Denis CM, Dendouga N, Van den Wyngaert I, Goehlmann H, Steller U, van de Weyer I, Van Slycken N, Andries L, Kass S, Luyten W, Janicot M, Vialard JE.
"p53-independent regulation of p21Waf1/Cip1 expression and senescence by Chk2."
Mol Cancer Res. 2005 Nov;3(11):627-34.
Andries K, Verhasselt P, Guillemont J, Göhlmann HW, Neefs JM, Winkler H, Van Gestel J, Timmerman P, Zhu M, Lee E, Williams P, de Chaffoy D, Huitric E, Hoffner S, Cambau E, Truffot-Pernot C, Lounis N, Jarlier V.
"A diarylquinoline drug active on the ATP synthase of Mycobacterium tuberculosis."
Science. 2005 Jan 14;307(5707):223-7. Epub 2004 Dec 9.
Peeters PJ, Göhlmann HW, Van den Wyngaert I, Swagemakers SM, Bijnens L, Kass SU, Steckler T.
"Transcriptional response to corticotropin-releasing factor in AtT-20 cells."
Mol Pharmacol. 2004 Nov;66(5):1083-92. Epub 2004 Jul 22.
Peeters PJ, Fierens FL, van den Wyngaert I, Göhlmann HW, Swagemakers SM, Kass SU, Langlois X, Pullan S, Stenzel-Poore MP, Steckler T.
"Gene expression profiles highlight adaptive brain mechanisms in corticotropin releasing factor overexpressing mice."
Brain Res Mol Brain Res. 2004 Oct 22;129(1-2):135-50.
Wouters L, Göhlmann HW, Bijnens L, Kass SU, Molenberghs G, Lewi PJ.
"Graphical exploration of gene expression data: a comparative study of three multivariate methods."
Biometrics. 2003 Dec;59(4):1131-9.
Weiner J 3rd, Zimmerman CU, Göhlmann HW, Herrmann R.
"Transcription profiles of the bacterium Mycoplasma pneumoniae grown at different temperatures."
Nucleic Acids Res. 2003 Nov 1;31(21):6306-20.
Göhlmann HW, Weiner J 3rd, Schon A, Herrmann R.
"Identification of a small RNA within the pdh gene cluster of Mycoplasma pneumoniae and Mycoplasma genitalium."
J Bacteriol. 2000 Jun;182(11):3281-4.
Fisseha M, Göhlmann HW, Herrmann R, Krause DC.
"Identification and complementation of frameshift mutations associated with loss of cytadherence in Mycoplasma pneumoniae."
J Bacteriol. 1999 Jul;181(14):4404-10.
Boles E, Göhlmann HW, Zimmermann FK.
"Cloning of a second gene encoding 5-phosphofructo-2-kinase in yeast, and characterization of mutant strains without fructose-2,6-bisphosphate."
Mol Microbiol. 1996 Apr;20(1):65-76.
  View my collection, "My Bibliography" from NCBI

Patents

Grants

Invited reviewer

Awards

  • 2014 Individual Johnson & Johnson Leadership Award
    QSTAR project on integrating transcriptomic, chemical, and bioassay data
  • 2008 Nomination for Janssen Pharmaceutica Business Excellence Awards 2008
    development of a statistical search engine for genes
  • 2007 Innovation Award (Johnson & Johnson Pharmaceutical Research & Development)
    development of a diagnostic tool for response prediction
  • 2004 Philip B. Hofmann Research Scientist Award
    elucidation of the mechanism of action of our novel anti-tuberculosis drug TMC207/R207910
  • 2001 Individual Johnson & Johnson Standards of Leadership Award
    development of an intrasite for the standardized analysis of microarray experiments & presentation of results
  • 1998 Scholarship DFG-Graduiertenkolleg
    "Pathogenic microorganisms: molecular mechanisms and genomes"
    Deutsche Forschungsgemeinschaft (German Research Foundation)

Recent posters & oral presentations

Older presentations can be found here.

Book chapters

Proceedings


Education

2010 - Masterclass BioBusiness at Neyenrode Business University, The Netherlands

1999 - Doctorate in molecular biology at the ZMBH Heidelberg, Germany

1995 - Diplom-Biologe, TU Darmstadt, Germany

1990 - Abitur, Gymnasium Beverungen, Germany

1988 - High School Diploma, William Fremd High School, Palatine, IL, USA