Nathalie Pochet
Postdoctoral Researcher in
Computational Biology,
Bioinformatics and Biomedical
Engineering
Contact Information
Address: Broad Institute of MIT and Harvard
7 Cambridge Center, NE30-6027
Cambridge, MA 02142, USA
Work phone: +1 617 714 8662
Cell phone: +1 617 901 6040 (USA), +32 475 413832
(Belgium)
E-mail: npochet@broadinstitute.org
Homepage: http://www.broadinstitute.org/~npochet/
Research
activities
2010-…:
Broad Fellow in the group of Prof. Dr. Aviv Regev at the Broad Institute of MIT and Harvard (Cambridge, USA).
2007-…:
Postdoctoral Fellow in the group of Prof. Dr. Yves Van de Peer at
the VIB Department of Plant Systems Biology, Ghent University, Belgium, and in the
group of Prof. Dr. Aviv Regev at the Broad Institute of MIT and Harvard.
2006-2007:
Postdoctoral Fellow in the group of Prof.
Dr. Kevin Verstrepen at the FAS Center for Systems Biology, Harvard University,
and in the group of Prof. Dr. Aviv Regev at the Broad Institute of MIT and Harvard.
2002-2006:
Ph.D. Research Assistant 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:
· Next-generation sequencing data analysis: whole exome and whole genome (DNA-Seq), transcriptome (RNA-Seq), nucleosome sequencing,…
o Aligning reads to genome, transcriptome or nucleosome; alternative splicing and expression abundance estimation; polymorphisms, insertions and deletions calling; de novo transcriptome reconstruction; and nucleosome calling;
o Developing novel algorithms to detect genetic and epigenetic structural variants (polymorphisms, insertions and deletions, and rearrangements such as gene fusions, trans-splicing, novel transcripts and splice isoforms, intron retention) from de novo reconstructed transcriptomes, e.g., in chronic lymphocytic leukemia (CLL);
o Predictive modeling of tandem repeat variability using support vector machines on biological data derived from yeast genome sequences towards a broad range of species;
· Microarray data analysis:
o Using support vector machines and kernel methods, e.g., in oncology and/or gynecology;
o Comparative analysis between the malaria parasite Plasmodium falciparum and the model yeast Saccharomyces cerevisiae using non-negative matrix factorization and support vector machines;
o Pathway enrichment analyses, e.g., to support the hypothesis that FLO1 is a variable green beard gene that drives biofilm-like cooperation in budding yeast;
· Clinical studies: study design and data analysis using advanced methods from biostatistics;
· Integrated analysis of high-throughput transcriptome and genome, as well as other biomedical data sources, using module-based probabilistic graphical algorithms for modeling molecular pathways underlying e.g. disease mechanisms in chronic lymphocytic leukemia (CLL).
Associated activities:
·
Author
and co-author of publications and conference contributions.
·
Responsible
and co-responsible for several research projects.
·
Extensive
cooperation with highly
distinguished computational and biomedical experts, i.e., on the rare Mendelian kidney disease MCKD1
(with Prof. Eric Lander, Founding Director of the Broad Institute, Co-chair of
U.S. President Barack Obama's Council of Advisors on Science and Technology),
on malaria (with Prof. Jill Mesirov, Director Computational Biology and Bioinformatics,
Broad Institute, and Prof. Dyann Wirth, Director
Harvard Malaria Initiative, Harvard School of
Public Health, Co-director Infectious Disease Initiative, Broad Institute), on chronic lymphocytic leukemia
(with Prof. Nir Hacohen, Broad Institute, Mass General Hospital, and Prof. Catherine
Wu, Harvard Medical School, Dana Farber Cancer Institute), on ovarian cancer
(with Prof. Ignace Vergote, Head of the Department of Obstetrics and
Gynecology, U.Z.Leuven, and Prof. Dirk
Timmerman, U.Z.Leuven), on endometriosis (with Prof. Thomas D'Hooghe,
U.Z.Leuven), and on breast cancer (with Prof. Patrick Neven, U.Z.Leuven).
·
Reviewer
for Nucleic Acids Research, Bioinformatics, BMC Bioinformatics, Journal of Machine Learning Research,
Engineering Applications of Artificial Intelligence, Artificial Intelligence in
Medicine,…
·
Teaching
in Electrical Engineering courses (2002-2006) and ombudsman for Master of
Science in Bioinformatics.
·
Responsible
for training of computational research assistants, and supervision of Ph.D. and
Master students.
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. Bart De Moor and Prof. Dr. 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.
Fellowships
01/01/2010-…:
Broad Fellow of the Broad Institute of MIT and Harvard.
01/10/2008-30/09/2014:
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 – BAEF Fellow of the King
Baudouin Foundation and 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).
Publications in preparation
Pochet N., Haas B.J., Yassour M.,
Grabherr M., Sivachenko A., Robinson J., Getz G., Brown J.R., Van de Peer Y.,
Friedman N., Hacohen N., Wu C.J., Regev A. (2011) Detection of structural
variants from de novo RNA-Seq assembly to understand their role in chronic lymphocytic leukemia tumorigenesis. In preparation.
Milner D.A.*, Pochet N.*, Krupka M., Williams C., Seydel K., Taylor T.E., Van de Peer Y., Regev A., Wirth D., Daily J., Mesirov J.P. (2011) Transcriptional profiling of Plasmodium falciparum parasites from patients with severe malaria identifies distinct low versus high parasitemic clusters. Submitted. *contributed equally
Wang L.*, Pochet N.*, Lawrence M., Sougnez C., Shalek A.,
Neuberg D., Cibulskis K., Zhang W., Sievers Q.L., Goldstein N., Van de Peer Y.,
Shefler E., Gabriel S., He X., Park H., Regev A., Getz G., Brown J.R., Hacohen
N., Wu C.J. (2011) Whole genome sequencing of chronic lymphocytic leukemia
identifies functional mutations in the Wnt pathway. Submitted. *contributed
equally
Brown J.R., Hanna M., Tesar B., Pochet
N., Ash M., Werner L., Fernandes S.M., MacConaill L., Hainz U., Longtine
J., Wang Y.E., Van de Peer Y., Correll M., Regev A., Wu C.J., Neuberg D.,
Freedman A.S. (2011) Germline copy number variation in
familial chronic lymphocytic leukemia. Submitted.
Brown J.R., Hanna M., Tesar B.,
Werner L., Pochet N., Asara J., Wang Y.E., Cin P.D., Fernandes S.M.,
Thompson C., Macconnaill L., Wu C.J., Van de Peer Y., Correll M., Regev A.,
Neuberg D., Freedman A.S. (2011) Integrative genomic
analysis implicates PIK3CA and MYC in chronic lymphocytic leukemia. Submitted.
Publications in international journals
Mihalyi A., Gevaert O., Kyama C.M., Simsa P., Pochet N., De Smet F., De Moor B., Meuleman C., Billen J.,
Blanckaert N., Vodolazkaia A., Fulop V., D'Hooghe T.M. (2010) Non-invasive
diagnosis of endometriosis based on a combined analysis of six plasma
biomarkers. Human
Reproduction, 25(3), 654-64. (IF 4.357)
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 4.859)
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 variable green beard gene that drives biofilm-like cooperation in budding
yeast. Cell,
135(4), 726-737. *contributed equally
(IF 32.401)
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 FFa17 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 1.246)
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 3.150)
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 18.970)
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 36.101)
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 FFa10 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 13.588)
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 4.859)
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 1.558)
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 18.970)
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 & Gynecology, 27(6), 607-608. (IF 3.163)
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 & Gynecology, 27(6), 664-671.
(IF 3.163)
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 4.926)
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 1.558)
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 7.338)
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 4.877)
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 4.877)
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
Wang L., Pochet N., Cibulskis K., Zhang W.,
Lawrence M., Sievers Q.L., Shefler E., Neuberg D., Gabriel S., Sougnez C.,
Regev A., Getz G., Hacohen N., Brown J.R., Wu C.J. (2010) Whole Genome
Sequencing Identifies Functional Mutations In the Wnt Pathway In CLL. Blood (52nd Annual Meeting of the
American-Society-of-Hematology (ASH)), 116(21), 305-306. (IF 10.558)
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. American Journal of Tropical Medicine and Hygiene (56th Annual Meeting
of the American Society of Tropical Medicine and Hygiene), 77(5S), 106. (IF
2.446)
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 4.944)
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 1.558)
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 1.558)
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 1.558)
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 1.558)
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 1.558)
International
conferences
Cold
Spring Harbor Laboratories’ (CSHL) Genome Informatics
2011 meeting, Cold Spring Harbor, New York (USA). Submitted for presentation or
poster on ‘Detection of structural variants from de novo RNA-Seq
assembly to understand their role in CLL tumorigenesis’ and ‘Leveraging RNA-Seq
for genome-free transcriptome studies’.
Keystone Symposium on Changing
Landscape of the Cancer Genome 2011, in Boston, Massachusetts (USA). Poster on
‘Using de novo RNA-Seq assembly in CLL to understand the role of splicing in
CLL tumorigenesis’ and ‘Whole genome sequencing identifies functional mutations
in the Wnt pathway in CLL’.
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, 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 2006, Broad Institute of MIT and Harvard, Cambridge, Massachusetts (USA). Presentation on ‘Predictive SVM-based models to support clinical management decisions in oncology’.
Computational
Systems Bioinformatics Conference 2005, Stanford University, Palo Alto, California
(USA). Poster on ‘M@CBETH: optimizing clinical microarray classification’ with
publication in Proceedings of the 2005 IEEE Computational Systems
Bioinformatics Conference (CSB2005), 89-90.
Benelux
Bioinformatics Conference in 2005, Ghent, Belgium. Presentation on ‘M@CBETH:
optimizing clinical microarray classification’.
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.
(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.