Nathalie Pochet

Postdoctoral Researcher in Computational Biology,

Bioinformatics and Biomedical Engineering

Contact Information

Broad Institute

7 Cambridge Center, NE30-6027

Cambridge, MA 02142, USA

npochet@broadinstitute.org

Current research activities

01/10/2008-30/09/2011:

Postdoctoral research in the group of Prof. Dr. Yves Van de Peer at the VIB Department of Plant Systems Biology, Ghent University (Belgium), and in collaboration with the group of Prof. Dr. Aviv Regev at the Broad Institute of MIT and Harvard (Boston, USA).

19/11/2007-30/09/2008:

Postdoctoral research in the groups of Prof. Dr. Yves Van de Peer and Dr. Marnik Vuylsteke at the VIB Department of Plant Systems Biology at Ghent University.

01/09/2006-31/08/2007:

Postdoctoral research in the groups of Prof. Dr. Aviv Regev and Prof. Dr. Jill Mesirov at the Broad Institute of 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. Bart De Moor at the Electrical Engineering Department (ESAT-SCD), Katholieke Universiteit Leuven (K.U.Leuven, Belgium).

01/10/2002-31/05/2006:

Ph.D. research under the supervision of Prof. Dr. Bart De Moor, Prof. Dr. Johan Suykens and Dr. 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:

·     Integrated analysis of high-throughput transcriptome and genome data for modeling molecular pathways underlying interactions between the malaria parasite Plasmodium falciparum and the human host;

·     Comparative analysis between Plasmodium falciparum and the model yeast Saccharomyces cerevisiae;

·     Enrichment analyses to support the hypothesis that FLO1 is a variable green beard gene that drives biofilm-like cooperation in budding yeast;

·     Predictive modeling of tandem repeat variability based on biological data derived from the yeast genome towards a broad range of species;

·     Identifying regulatory genetic variants underlying dominance expression patterns in the model plant Arabidopsis thaliana by module-based probabilistic graphical models;

·     Microarray data analysis using support vector machines and kernel methods in oncology and/or gynecology;

·     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 malaria (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, Engineering Applications of Artificial Intelligence, Artificial Intelligence in Medicine, Journal of Intelligent and Fuzzy Systems.

·     Teaching in Electrical Engineering courses and ombudsman for Master of Science in Bioinformatics.

·     Responsible for the supervision of several Ph.D. and Master students.

Fellowships

01/10/2008-30/09/2011:

FWO Postdoctoral Fellow of the Research Foundation – Flanders (FWO).

19/11/2007-30/09/2008:

VIB Postdoctoral Fellow of the Flanders Interuniversity Institute for Biotechnology (VIB).

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 Institute for the encouragement of Innovation by Science and Technology in Flanders (IWT-Vlaanderen).

Education

2002-2006:       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.

Publications in international journals

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 K.R., Verstrepen K.J. (2008) FLO1 is a hyper-variable green beard gene that drives a transition to multicellularity in budding yeast. Cell, 135(4), 726-737. *contributed equally (IF 31.253)

Discussed in:

·     Cell Minireview: Brown S.P., Buckling A. (2008) A social life for discerning microbes. Cell, 135 (4), 600-603.

·     Nature News and Views: Queller D.C. (2008) Behavioural ecology: The social side of wild yeast. Nature, 456 (7222), 589-590.

·     Faculty of 1000 Biology: F1000 factor of 8.5 (Exceptional) by Mark Rose, Lukasz Kozubowski and Joe Heitman, Romain Libbrecht and Laurent Keller, Gerhard Braus, Vincent Jansen.

Van den Bosch T., Daemen A., Van Schoubroeck D., Pochet N., De Moor B., Timmerman D. (2008) Occurrence and outcome of residual trophoblastic tissue: a prospective study. Journal of Ultrasound in Medicine, 27(3), 357-361. (IF 1.087)

Van Calster B., Vanden Bempt I., Drijkoningen M., Pochet N., Cheng J., 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.R., Neven P. (2009) 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 Research and Treatment, 113, 181-187. (IF 5.684)

Gevaert O., De Smet F., Van Gorp T., Pochet N., Engelen K., Amant F., De Moor B., Timmerman D., Vergote I. (2008) Expression profiling to predict the clinical behaviour of ovarian cancer fails independent evaluation. BMC Cancer, 8, 18. (IF 3.087)

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. (2008) Does estrogen receptor negative/progesterone receptor positive breast carcinoma exist? Journal of Clinical Oncology, 26(2), 335-336. (IF 17.157)

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 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. Nature, 450 (7172), 1091-1095. *contributed equally (IF 31.434)

Discussed in:

·     Nature News and Views: van Dooren G.G., McFadden G.I. (2007) Malaria: Differential parasite drive. Nature, 450 (7172), 955-956.

·     Faculty of 1000 Biology: F1000 factor of 9.0 (Exceptional) by Roberto Docampo.

Legendre M.*, Pochet N.*, Pak T., Verstrepen K.J. (2007) Sequence-based estimation of minisatellite and microsatellite repeat variability. Genome Research, 17(12), 1787-1796. *contributed equally (IF 10.176)

http://hulsweb1.cgr.harvard.edu/SERV/

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. (2007) 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. (IF 5.684)

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. (IF 1.932)

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. (IF 17.157)

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. (IF 2.690)

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(6), 664-671. (IF 2.690)

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. (IF 4.734)

De Smet F., Pochet N.L.M.M., Engelen K., Van Gorp T., Van Hummelen P., Marchal K., Amant F., Timmerman D., De Moor B.L.R., Vergote I.B. (2006) Predicting the clinical behaviour of ovarian cancer from gene expression profiles. International Journal of Gynecological Cancer, 16(S1), 147-151. (IF 1.932)

De Smet F., Pochet N.L.M.M., De Moor B.L.R., Van Gorp T., Timmerman D., 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. (IF 6.488)

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. (IF 4.328)

http://www.esat.kuleuven.be/MACBETH/

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. (IF 4.328)

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. (IF 4.475)

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. (IF 1.932)

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. (IF 1.932)

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. (IF 1.932)

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. (IF 1.932)

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. (IF 1.932)

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.

ftp://ftp.esat.kuleuven.be/pub/SISTA/npochet/PhD_Nathalie_Pochet.pdf

Talks at international meetings

National Institute of Health’s (NIH) Bioinformatics Summit 2008 of the Division of Allergy, Immunology, and Transplantation (DAIT) of the National Institute of Allergy and Infectious Diseases (NIAID) on ‘Meeting the Challenges of a Systems Approach for Personalized Medicine’, Washington DC/Rockville, Washington (USA). Presentation on ‘Distinct physiological states of Plasmodium falciparum in malaria-infected patients’.

MIT Biology Retreat 2007, Cape Cod, Massachusetts (USA). Presentation on ‘Distinct physiological states of the parasite Plasmodium falciparum in malaria infected patients’.

Bertinoro Computational Biology Meeting 2007 (BCB2007), Bertinoro (Forlì-Cesena), Italy. Presentation on ‘Characterizing the expression response of the malaria parasite, Plasmodium falciparum, by comparative analysis with the model yeast, Saccharomyces cerevisiae‘.

Computational Biology and Bioinformatics Meeting in 2006, Broad Institute of MIT and Harvard, Cambridge, Massachusetts (USA). Presentation on ‘Predictive SVM-based models to support clinical management decisions in oncology’.

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:              1^st Bachelor Violin, Koninklijk Muziek Conservatorium, Brussels, Belgium.

         Teacher: Valery Oistrakh.

1995-1996:              Contract-student Violin, Koninklijk Muziek Conservatorium, Brussels.

         Teacher: Philippe Hirshhorn.

1992-1995:              1^st 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.

·     Laureate of several music competitions (violin, piano and chamber music).

·     Musical participation in several TV programs and productions.