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Postdoctoral Researcher in Computational Biology, Bioinformatics and Biomedical Engineering |
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Nathalie Pochet |
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Contact Information
Broad Institute of MIT and Harvard 7 Cambridge Center, NE30-6027 Cambridge, MA 02142 USA
Current research activities
01/09/2006-now: Postdoctoral research in the groups of Prof. Dr. Aviv Regev and Prof. Dr. Jill Mesirov at the Broad Institute, MIT and Harvard, and in the group of Prof. Dr. Kevin Verstrepen at the Bauer Laboratory of the FAS Center for Systems Biology, Harvard University (Boston, USA).
01/06/2006-31/08/2006: Postdoctoral research in the bioinformatics group of Prof. Dr. Ir. Bart De Moor at the Electrical Engineering Department (ESAT-SCD), Katholieke Universiteit Leuven (K.U.Leuven).
01/10/2002-31/05/2006: Ph.D. research (with defense, for text see further) under the supervision of Prof. Dr. Ir. Bart De Moor, Prof. Dr. Ir. Johan Suykens and Dr. Ir., Dr.(med) Frank De Smet in the bioinformatics group at ESAT-SCD, K.U.Leuven.
Research in bioinformatics / computational biology / biomedical engineering, specialized in biomedical data analysis: · 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.
Associated activities: · Author and co-author of publications and conference contributions. · Responsible and co-responsible for several research projects. · Extensive cooperation with clinicians, i.e., on the malaria parasite Plasmodium falciparum (with Prof. Dyann Wirth and Dr. Johanna Daily, Harvard School of Public Health, Boston), on ovarian cancer (with Prof. Ignace Vergote, head of the Department of Obstetrics and Gynecology, U.Z.Leuven), on endometriosis (with Prof. Thomas D'Hooghe, coordinator Leuven University Fertility Center), and on breast cancer (with Prof. Patrick Neven). · Reviewer for Bioinformatics, BMC Bioinformatics, Nucleic Acids Research (NAR), Engineering Applications of Artificial Intelligence (EAAI), Artificial Intelligence in Medicine (AAIM), Journal of Intelligent and Fuzzy Systems (JIFS) . · Teaching in Electrical Engineering courses and ombudsman for Master of Science in Bioinformatics. · Responsible for the supervision of several PhD and Master students.
Education
Doctor in Engineering Sciences, K.U.Leuven. Research on statistical and advanced data mining techniques for analysis of microarray data in oncology (title ‘Microarray data analysis using support vector machines and kernel methods’, promotors Prof. Dr. Ir. Bart De Moor and Prof. Dr. Ir. Johan Suykens) at ESAT-SCD, K.U.Leuven. 2001-2002: Master of Science in Bioinformatics, K.U.Leuven. Cum laude. Thesis project on the prediction of HIV resistance (title ‘HIV Structural Genomics’) at Tibotec-Virco, Johnson&Johnson, Mechelen, Belgium. Student representative in the Committee for Educational Coordination.
2000-2001: Master in Artificial Intelligence, K.U.Leuven. Magna cum laude. Thesis project on the 3D visualization of 2D images (title ‘Detailed 3D visualization derived from 2D images’) at ESAT-ACCA, K.U.Leuven.
1996-2000: Master of Science in Industrial Engineering in Electronics (option Information and Communication Technology), De Nayer Instituut, Sint-Katelijne-Waver, Belgium. Cum laude. Thesis project on MPEG-4 (title ‘Multi-resolution OpenGL 3D browser for Computational Graceful Degradation’) at IMEC, Leuven.
1995-1996: 1st Bachelor in Physics, RUCA, Antwerp, Belgium.
1993-1995: 3rd Grade Science-Mathematics, Instituut Dames van het Christelijk Onderwijs, Antwerp.
1989-1993: 1st and 2nd Grade Latin-Mathematics, Instituut Dames van het Christelijk Onderwijs.
Fellowships
01/09/2006-31/08/2007: Henri Benedictus Fellow of the King Baudouin Foundation for postdoctoral research in bioinformatics and biomedical engineering.
01/09/2006-31/08/2007: BAEF Fellow of the Belgian American Educational Foundation for postdoctoral research in bioinformatics and biomedical engineering.
01/10/2002-31/08/2006: Research Assistant of the IWT-Vlaanderen (Institute for the encouragement of Innovation by Science and Technology in Flanders).
Publications in international journals
Daily J.P., Pochet N., Scanfeld D., Le Roch K., Plouffe D., Kamal M., Sarr O., Mboup S., Ndir O., Wypij D., Levasseur K., Thomas E., Tamayo P., Dong C., Zhou Y., 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. Accepted for publication in Nature, DOI:10.1038/nature06311.
Pochet N., Legendre M., Pak T., Verstrepen K.J. (2007) Sequence-based estimation of minisatellite and microsatellite repeat variability. Genome Research, DOI: 10.1101/gr.6554007. http://hulsweb1.cgr.harvard.edu/SERV/
De Maeyer L. , Moerman P., Van Limbergen E., De Nys K., Pochet N., Hendrickx W., Wildiers H., Paridaens R., Smeets A., Leunen K., Amant F., Christiaens M.R., Vergote I., Neven P. (2007) Does ER-PR+ breast carcinoma exist? Accepted for publication in Journal of Clinical Oncology.
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. Accepted for publication in Journal of Ultrasound in Medicine.
Neven P., Pochet N., Drijkoningen M., Amant F., De Smet F., Paridaens R., Christiaens M.R., Vergote I. (2006) Progesterone receptor in estrogen receptor-positive breast cancer: the association between HER-2 and lymph node involvement is age related. Journal of Clinical Oncology, 24(16), 2595.
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. International Journal of Cancer, 119(6), 1511.
Van Mieghem T., Leunen K., Pochet N., De Moor B., De Smet F., Amant F., Berteloot P., Timmerman D., Vanden Bempt I., Drijkoningen R., Wildiers H., Paridaens R., Smeets A., Hendrickx W., Van Limbergen E., Christiaens M.R., Vergote I., Neven P. (2006) Body mass index and HER-2 overexpression in breast cancer patients over 50 years of age. Breast Cancer Research and Treatment, 106(1), 127-133.
Pochet N.L.M.M., Suykens J.A.K. (2006) Opinion: Support Vector Machines versus Logistic Regression: improving prospective performance in clinical decision making. Ultrasound in Obstetrics and Gynecology, 27(6), 607-608.
De Smet F., De Brabanter J., Konstantinovic M.L., Pochet N., Van den Bosch T., 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(6), 664-671.
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. International Journal of Gynecological Cancer, 16(S1), 147-151.
Van Gorp T., Vergote I.B., Pochet N.L.M.M., Amant F. (2006) Methodology in plasma proteomic pattern experiments. International Journal of Gynecological Cancer, 16(5), 1951-1952.
Pochet N.L.M.M., Janssens F.A.L., De Smet F., Marchal K., Suykens J.A.K., De Moor B.L.R. (2005) M@CBETH: a microarray classification benchmarking tool. Bioinformatics, 21(14), 3185-3186. http://www.esat.kuleuven.be/MACBETH/
De Smet F., Pochet N.L.M.M., Van Gorp T., Timmerman D., De Moor B.L.R., Vergote I.B., Hartmann L.C., Damokosh A.I., Hoersch S. (2005) Independent test set performance in the prediction of early relapse in ovarian cancer with gene expression profiles. Clinical Cancer Research, 11(21), 7958-7959.
Pochet N., De Smet F., Suykens J.A.K., De Moor B.L.R. (2004) Systematic benchmarking of microarray data classification: assessing the role of non-linearity and dimensionality reduction. Bioinformatics, 20(17), 3185-3195.
Book chapter
Pochet N.L.M.M., Ojeda F., De Smet F., De Bie T., Suykens J.A.K., De Moor B.L.R. (2007) ‘Kernel clustering for knowledge discovery in clinical microarray data analysis’, Chapter 3 of Kernel methods in bioengineering, communications and image processing, (Camps-Valls G., Rojo-Alvarez J.L., and Martinez-Ramon M., eds.), Idea Group Inc. (Hershey, Pennsylvania (US)), 65-93.
Abstract in international journal
Van Mieghem T., Leunen K., Pochet N., De Moor B., Amant F., Vanden Bempt I., Drijkoningen R., Christiaens M.R., Vergote I., Neven P. (2006) Weight and body mass index (BMI) affect HER-2 expression in postmenopausal breast cancer. European Journal of Cancer Supplements (European Breast Cancer Conference (EBCC)), 4(2), 68.
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.R., Vergote I. (2006) The oestrogen receptor has a prognostic value in progesterone receptor-positive breast cancer. International Journal of Gynecological Cancer (Flemish Gynecology Oncologic Group (FGOG) Conference), 16(S2), 589-590.
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.R., Vergote I., Neven P. (2006) The progesterone receptor in postmenopausal women with an oestrogen receptor-positive breast cancer: The effect of body composition? International Journal of Gynecological Cancer (Flemish Gynecology Oncologic Group (FGOG) Conference), 16(S2), 592.
Van Mieghem T., Leunen K., Pochet N., Deleyn A., De Moor B., De Smet F., Amant F., Berteloot P., Marquette S., Drijkoningen R., Van Limbergen E., Smeets A., Wildiers H., Paridaens R., Christiaens M.R., 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. International Journal of Gynecological Cancer (Flemish Gynecology Oncologic Group (FGOG) Conference), 16(S2), 596-597.
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 R., Van Limbergen E., Smeets A., Wildiers H., Paridaens R., Christiaens M.R., Vergote I., Neven P. (2006) Weight and body mass index affect HER-2 expression in postmenopausal women with breast cancer. International Journal of Gynecological Cancer (Flemish Gynecology Oncologic Group (FGOG) Conference), 16(S2), 597.
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. International Journal of Gynecological Cancer (14th International meeting of the ESGO), 15(S2), 66.
International conferences
Pochet N., Daily J.P., Scanfeld D., Le Roch K., Plouffe D., Kamal M., Sarr O., Mboup S., Ndir O., Wypij D., Levasseur K., Thomas E., Tamayo P., Dong C., Zhou Y., Lander E.S., Ndiaye D., Wirth D., Winzeler E.A., Mesirov J.P., Regev A. (2007) Distinct physiological states of the parasite Plasmodium falciparum in malaria infected patients, MIT Biology Retreat, Cape Cod, Massachusetts (USA), presentation.
Pochet N., Daily J.P., Scanfeld D., Le Roch K., Plouffe D., Kamal M., Sarr O., Mboup S., Ndir O., Wypij D., Levasseur K., Thomas E., Tamayo P., Dong C., Zhou Y., Lander E.S., Ndiaye D., Wirth D., Winzeler E.A., Mesirov J.P., Regev A. (2007) Characterizing the expression response of the malaria parasite, Plasmodium falciparum, by comparative analysis with the model yeast, Saccharomyces cerevisiae, Bertinoro Computational Biology Meeting (BCB2007), Bertinoro (Forlì-Cesena), Italy, presentation.
Pochet N. (2006) Predictive SVM-based models to support clinical management decisions in oncology, Computational Biology and Bioinformatics Meeting, Broad Institute of MIT and Harvard, Cambridge, Massachusetts (USA), presentation.
Ordoñez R., Pochet N., Daily J.P., Scanfeld D., Le Roch K., Plouffe D., Kamal M., Sarr O., Mboup S., Ndir O., Wypij D., Levasseur K., Tamayo P., Dong C., Zhou Y., Lander E.S., Ndiaye D., Wirth D., Winzeler E.A., Mesirov J.P., Regev A. (2007) Characterization of host-pathogen interactions through in vivo expression profiling of Plasmodium falciparum in malaria infected patients, MIT Summer Research Program, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts (USA), poster.
Pochet N.L.M.M., Janssens F.A.L., De Smet F., Marchal K., Vergote I.B., Suykens J.A.K., De Moor B.L.R. (2005) M@CBETH: optimizing clinical microarray classification, in Proceedings of the 2005 IEEE Computational Systems Bioinformatics Conference (CSB2005), Stanford, Palo Alto, California (USA), 89-90 (publication with poster).
Pochet N.L.M.M., Janssens F.A.L., De Smet F., Marchal K., Vergote I.B., Suykens J.A.K., De Moor B.L.R. (2005) M@CBETH: optimizing clinical microarray classification, Benelux Bioinformatics Conference 2005 (BBC2005), Ghent, Belgium, presentation.
Ph.D. manuscript
Pochet N. (2006) Microarray data analysis using support vector machines and kernel methods. Ph.D. thesis, Faculty of Engineering, K.U.Leuven. (for complete text, see: ftp://ftp.esat.kuleuven.be/pub/SISTA/npochet/PhD_Nathalie_Pochet.pdf)
Miscellaneous
Member of the student committee (E-kring, De Nayer Instituut): vice-president (1998-1999), treasurer (1999-2000); start-up of the non-profit organization (VZW) E-kring (2000).
Musical education:
2004-2005 1st Bachelor Violin, Koninklijk Muziek Conservatorium, Brussels, Belgium.Teacher: Valery Oistrakh.
1995-1996 Contract-student Violin, Koninklijk Muziek Conservatorium, Brussels.Teacher: Philippe Hirshhorn.
1992-1995 1st Price Violin, Koninklijk Vlaams Muziek Conservatorium, Antwerp.
1994-1995 Final exam Piano, Muziekacademie van het Gemeenschapsonderwijs, Antwerp.
1991-1992 Final exam Violin, Muziekacademie van het Gemeenschapsonderwijs, Antwerp.
Master Classes, among others ‘Cours International de Musique’ in Morges (Switzerland), ‘Holland Music Sessions’ in Alkmaar, and ‘International Festival’ in Banff (Canada).
Scholarship for Master Class in Blue Lake (Michigan): concert master of Symphonic Orchestra, first violin of string quartet and laureate of Concerto Competition for solo-instruments.
Laureate of several music competitions (violin, piano and chamber music).
Musical participation in several TV programs and productions.
Concerts, among others in Belgium, The Netherlands, France, Germany, Poland, Austria, Switzerland, Italy, United States and Canada.
Extended orchestra experience, among others in ‘Filharmonisch Jeugdorkest van Vlaanderen’ conducted by Robert Groslot.
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