Nathalie Pochet

Postdoc
(Group member from 2007 until 2011)


+ 32 (0) 9 33 13 823

VIB / Ghent University
Bioinformatics & Systems Biology
Technologiepark 927
B-9052 Gent
BELGIUM

CV

Birthdate: 23 April 1977, Antwerp, Belgium.
November 2007 now: Postdoctoral research in the groups of Yves Van de Peer and Marnik Vuylsteke at the VIB Department of Plant Systems Biology at Ghent University (Belgium) as a VIB Postdoctoral Fellow of the Flanders Interuniversity Institute for Biotechnology.
September 2006 August 2007: Postdoctoral research in the groups of Aviv Regev and Jill Mesirov at the Broad Institute of MIT and Harvard, and in the group of Kevin Verstrepen at the Bauer Laboratory of the FAS Center for Systems Biology, Harvard University, Boston, USA, as a Henri Benedictus BAEF Postdoctoral Fellow of the King Baudouin Foundation and the Belgian American Educational Foundation for postdoctoral research in bioinformatics and biomedical engineering.
June 2006 August 2006: Postdoctoral research in the Bioinformatics group of Bart De Moor at the Electrical Engineering Department (ESAT-SCD) at Katholieke Universiteit Leuven (K.U.Leuven), Belgium.
October 2002 May 2006: Ph.D. research (title Microarray data analysis using support vector machines and kernel methods) under the supervision of Bart De Moor, Johan Suykens and Frank De Smet in the Bioinformatics group at ESAT-SCD, K.U.Leuven, as a IWT Research Assistant of the IWT-Vlaanderen (Institute for the encouragement of Innovation by Science and Technology in Flanders).
October 2001 June 2002: Master of Science in Bioinformatics at K.U.Leuven, with thesis project (title HIV Structural Genomics) at Tibotec-Virco, Johnson&Johnson, Mechelen, Belgium.
October 2000 June 2001: Master in Artificial Intelligence at K.U.Leuven, with thesis project (title Detailed 3D visualization derived from 2D images) at ESAT-ACCA, K.U.Leuven.
October 1996 June 2000: Master of Science in Industrial Engineering in Electronics (option Information and Communication Technology) at De Nayer Instituut, Sint-Katelijne-Waver, Belgium, with thesis project (title Multi-resolution OpenGL 3D browser for Computational Graceful Degradation) at IMEC, Leuven.

Reviewer for Bioinformatics, BMC Bioinformatics, Nucleic Acids Research (NAR), Ultrasound in Obstetrics and Gynecology (UOG), Engineering Applications of Artificial Intelligence (EAAI), Artificial Intelligence in Medicine (AAIM), Journal of Intelligent and Fuzzy Systems (JIFS).

Research

Research in bioinformatics / computational biology / biomedical engineering, specialized in biomedical data analysis:
  • Identifying regulatory mechanisms perturbing the regulatory network by an GERONIMO-like approach using diallel expression data of the model plant Arabidopsis thaliana;
  • Microarray data analysis using gene set enrichment analysis (GSEA), among others for the malaria parasite Plasmodium falciparum and the model yeast Saccharomyces cerevisiae;
  • Comparative analysis between malaria and yeast using non-negative matrix factorization (NMF) and support vector machines (SVM);
  • Predictive modeling of tandem repeat variability based on biological data derived from the yeast genome towards a broad range of species, among others for neurodegenerative diseases in human;
  • Microarray data analysis using support vector machines and kernel methods, among others in oncology and/or gynecology;
  • Prediction of HIV resistance using support vector machines;
  • Clinical studies: study design and data analysis using advanced methods from biostatistics.

Papers

(28) Klochendler, A., Weinberg-Corem, N., Moran, M., Swisa, A., Pochet, N., Savova, V., Vikesa, J., Van de Peer, Y., Brandeis, M., Regev, A., Nielsen, FC., Dor, Y., Eden, A. (2012) A Transgenic Mouse Marking Live Replicating Cells Reveals In Vivo Transcriptional Program of Proliferation. Dev. Cell 23(4):681-90.

(27) Milner, DA Jr., Pochet, N., Krupka, M., Williams, C., Seydel, K., Taylor, J.S., Van de Peer, Y., Regev, A., Wirth, D., Daily, J.P., Mesirov, J.P. (2012) Transcriptional Profiling of Plasmodium falciparum Parasites from Patients with Severe Malaria Identifies Distinct Low vs. High Parasitemic Clusters. PLoS One 7(7):e40739.

(26) Brown, M.T., Hanna, M., Tesar, B., Pochet, N., Vartanov, A., Fernandes, M., Werner, G., Ash, M., Roden, C., MacConaill, L., Hainz, U., Longtine, J., Wang, X., Correll, M., Van de Peer, Y., Regev, A., Wu, C., Neuberg, D., Freedman, A. (2012) Germline Copy Number Variation Associated with Mendelian Inheritance of CLL in Two Families. Leukemia 26, 1710-3.

(25) Brown, M.T., Hanna, M., Tesar, B., Werner, G., Pochet, N., Asara, J., Wang, X., dal Cin, P., Fernandes, M., Thompson, C., MacConaill, L., Wu, C., Van de Peer, Y., Correll, M., Regev, A., Neuberg, D., Freedman, A. (2012) Integrative Genomic Analysis Implicates Gain of PIK3CA at 3q26 and MYC at 8q24 in Chronic Lymphocytic Leukemia. Clin. Cancer Res. 18, 3791-3802.

(24) * Smukalla, S., * Caldara, M., * Pochet, N., Beauvais, A., Guadagnini, S., Yan, C., Vinces, M.D., Jansen, A., Prevost, M.C., Latgé, J.-P., Fink, G.R., Foster, P.G., Verstrepen, K.J. (2008) FLO1 Is a Variable Green Beard Gene that Drives Biofilm-like Cooperation in Budding Yeast. Cell 135(4):726-37. *contributed equally

(23) Van Calster, B., Vanden Bempt, I., Drijkoningen, M., Pochet, N., Cheng, Y.-Y., Van Huffel, S., Hendrickx, K., Decock, J., Huang, H.J., Leunen, K., Amant, F., Berteloot, P., Paridaens, R., Wildiers, H., Van Limbergen, E., Weltens, C., Timmerman, D., Van Gorp, T., Smeets, A., Van den Bogaert, W., Vergote, I., Christiaens, M., Neven, P. (2008) Axillary lymph node status of operable breast cancers by combined steroid receptor and HER-2 status: triple positive tumours are more likely lymph node positive. Breast Cancer Res. Treat. 113(1):181-7.

(22) Daily, J.P., * Scanfeld, D., * Pochet, N., * Le Roch, K., Plouffe, D., Kamal, M., Sarr, O., Mboup, S., Ndir, O., Wypij, D., Levasseur, K., Thomas, E., Tamayo, P., Dong, C., Zhou, K., Lander, E.S., Ndiaye, D., Wirth, D., Winzeler, E.A., Mesirov, J.P., Regev, A. (2007) Distinct physiological states of Plasmodium falciparum in malaria infected patients. Nature 450(7172):1091-5. *contributed equally

(21) De Maeyer, L., Van Limbergen, E., De Nys, K., Moerman, P., Pochet, N., Hendrickx, K., Wildiers, H., Paridaens, R., Smeets, A., Christiaens, M., Vergote, I., Leunen, K., Amant, F., Neven, P. (2007) Does ER-PR+ breast carcinoma exist?. J. Clin. Oncol. 26, 335-336.

(20) * Legendre, M., * Pochet, N., Pak, T., Verstrepen, K.J. (2007) Sequence-based estimation of minisatellite and microsatellite repeat variability. Genome Res. 17(12):1787-96. *contributed equally

(19) Van den Bosch, T., Daemen, A., Van Schoubroeck, D., Pochet, N., De Moor, B., Timmerman, D. (2007) Occurrence and outcome of residual trophoblastic tissue: a prospective study. J. Ultrasound Med. 27, 357-361.

(18) Van Mieghem, T., Leunen, K., Pochet, N., De Moor, B., De Smet, F., Amant, F., Berteloot, P., Timmerman, D., Vanden Bempt, I., Drijkoningen, M., Wildiers, H., Paridaens, R., Smeets, A., Hendrickx, K., Van Limbergen, E., Christiaens, M., Vergote, I., Neven, P. (2007) Body mass index and HER-2 overexpression in breast cancer patients over 50 years of age. Breast Cancer Res. Treat. 106, 127-133.

(17) Gevaert, O., De Smet, F., Van Gorp, T., Pochet, N., Engelen, K., Amant, F., De Moor, B., Timmerman, D., Vergote, I. (2007) Expression profiling to predict the clinical behaviour of ovarian cancer fails independent evaluation. BMC Cancer 8, 18.

(16) Van Mieghem, T., Leunen, K., Pochet, N., De Moor, B., Amant, F., Vanden Bempt, I., Drijkoningen, M., Christiaens, M., Vergote, I., Neven, P. (2006) Weight and body mass index (BMI) affect HER-2 expression in postmenopausal breast cancer. European Journal of Cancer Supplements (EBCC) 4, 68.

(15) De Maeyer, L., Neven, P., Drijkoningen, M., Woestenborghs, H., Pochet, N., De Moor, B., Amant, F., Berteloot, P., Leunen, K., Van Limbergen, E., Smeets, A., Wildiers, H., Paridaens, R., Christiaens, M., Vergote, I. (2006) The oestrogen receptor has a prognostic value in progesterone receptor-positive breast cancer. Int. J. Gynecol. Cancer 16, 589-590.

(14) Leunen, K., Van Mieghem, T., Pochet, N., De, Smet F., De Moor, B., DeLeyn, A., Van Limbergen, E., Amant, F., Berteloot, P., Wildiers, H., Paridaens, R., Smeets, A., Christiaens, M., Vergote, I., Neven, P. (2006) The progesterone receptor in postmenopausal women with an oestrogen receptor-positive breast cancer: The effect of body composition?. Int. J. Gynecol. Cancer 16, 592.

(13) Van Mieghem, T., Leunen, K., Pochet, N., DeLeyn, A., De Moor, B., De, Smet F., Amant, F., Berteloot, P., Marquette, S., Drijkoningen, M., Van Limbergen, E., Smeets, A., Wildiers, H., Paridaens, R., Christiaens, M., Vergote, I., Neven, P. (2006) The influence of body composition and hormone replacement therapy on progesterone receptor expression in postmenopausal women with an estrogen receptor-positive breast cancer. Int. J. Gynecol. Cancer 16, 596-597.

(12) Van Mieghem, T., Leunen, K., Pochet, N., DeLeyn, A., De Moor, B., De Smet, F., Amant, F., Berteloot, P., Marquette, S., Vanden Bempt, I., Drijkoningen, M., Van Limbergen, E., Smeets, A., Wildiers, H., Paridaens, R., Christiaens, M., Vergote, I., Neven, P. (2006) Weight and body mass index affect HER-2 expression in postmenopausal women with breast cancer. Int. J. Gynecol. Cancer 16, 597.

(11) Neven, P., Pochet, N., Drijkoningen, M., Amant, F., De Smet, F., Paridaens, R., Christiaens, M., Vergote, I. (2006) Progesterone receptor in estrogen receptor-positive breast cancer: the association between HER-2 and lymph node involvement is age related. J. Clin. Oncol. 24, 2595-7.

(10) Gevaert, O., Pochet, N., De Smet, F., Van Gorp, T., De Moor, B., Timmerman, D., Amant, F., Vergote, I. (2006) Molecular profiling of platinum resistant ovarian cancer: use of the model in clinical practice. Int. J. Cancer 119, 1511..

(9) Pochet, N., Suykens, J. (2006) Opinion: Support Vector Machines versus Logistic Regression: improving prospective performance in clinical decision making. Ultrasound in Obstetrics and Gynecology 27, 607-608.

(8) De Smet, F., De Brabanter, J., Van den Bosch, T., Pochet, N., Amant, F., Van Holsbeke, C., Moerman, P., De Moor, B., Vergote, I., Timmerman, D. (2006) New models to predict depth of infiltration in endometrial carcinoma based on transvaginal sonography. Ultrasound in Obstetrics and Gynecology 27, 664-671.

(7) De Smet, F., Pochet, N., Engelen, K., Van Gorp, T., Van Hummelen, P., Marchal, K., Amant, F., Timmerman, D., De Moor, B., Vergote, I. (2006) Predicting the clinical behaviour of ovarian cancer from gene expression profiles. Int. J. Gynecol. Cancer 16, 147-151.

(6) Van Gorp, T., Vergote, I., Pochet, N., Amant, F. (2006) Methodology in plasma proteomic pattern experiments. Int. J. Gynecol. Cancer 16, 1951-1952.

(5) Van Gorp, T., De Smet, F., Pochet, N., Engelen, K., Van Hummelen, P., Suykens, J., Marchal, K., Amant, F., Moreau, Y., Timmerman, D., De Moor, B., Vergote, I. (2005) Predicting the clinical behavior of ovarian cancer from gene expression profiles. Int. J. Gynecol. Cancer 15, 66.

(4) Pochet, N., Janssens, F., De Smet, F., Marchal, K., Suykens, J., De Moor, B. (2005) M@CBETH: a microarray classification benchmarking tool. Bioinformatics 21(14):3185-6.

(3) De Smet, F., Pochet, N., De Moor, B., Van Gorp, T., Timmerman, D., Vergote, I., Hartmann, L., Damokosh, A., Hoersch, S. (2005) Independent test set performance in the prediction of early relapse in ovarian cancer with gene expression profiles. Clin. Cancer Res. 11, 7958-7959.

(2) Pochet, N., Janssens, F., De Smet, F., Marchal, K., Vergote, I., Suykens, J., De Moor, B. (2005) M@CBETH: optimizing clinical microarray classification. In : Proc. of the 2005 IEEE Computational Systems Bioinformatics Conference (CSB2005). 2005 IEEE Computational Systems Bioinformatics Conference (CSB2005), Stanford, California (US), Aug. 2005 pp. 89-90.

(1) Pochet, N., De Smet, F., Suykens, J., De Moor, B. (2004) Systematic benchmarking of microarray data classification: assessing the role of non-linearity and dimensionality reduction. Bioinformatics 20, 3185-3195.











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