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Publications


http://www.ncbi.nlm.nih.gov/myncbi/browse/collection/


JOURNAL PUBLICATIONS

Stubbs B.J., Gopaulakrishnan S., Glass K., Pochet N., Everaert C., Raby B., Carey V. (2019) TFutils: Data structures for transcription factor bioinformatics. F1000Research 2019, 8:152.

Lupberger J., Croonenborghs T., Roca Suarez A.A., Van Renne N., Jühling F., Oudot M.A., Virzì A., Bandiera S., Jamey C., Meszaros G., Brumaru D., Mukherji A., Durand S.C., Heydmann L., Verrier E.R., El Saghire H., Hamdane N., Bartenschlager R., Fereshetian S., Ramberger E., Sinha R., Nabian M., Everaert C., Jovanovic M., Mertins P., Carr S.A., Chayama K., Dali-Youcef N., Ricci R., Bardeesy N.M., Fujiwara N., Gevaert O., Zeisel M.B., Hoshida Y., Pochet N.*, Baumert T.F.* (2019) Combined Analysis of Metabolomes, Proteomes, and Transcriptomes of HCV-infected Cells and Liver to Identify Pathways Associated With Disease Development. Gastroenterology, pii:S0016-5085(19)35670-7. *co-last co-corresponding authors.

Van Renne N., Wei R., Pochet N., Nauwynck H. (2018) PorSignDB: a database of in vivo perturbation signatures for dissecting clinical outcome of PCV2 infection. bioRxiv 341644. BMC Genomics, 19(1):831.
http://www.vetvirology.ugent.be/PorSignDB/
http://software.broadinstitute.org/gsea/msigdb/contributed_genesets.jsp

Verrier E.R., Yim S.A., Heydmann L., El Saghire H., Bach C., Turon-Lagot V., Mailly L., Durand S.C., Lucifora J., Durantel D., Pessaux P., Manel N., Hirsch I., Zeisel M.B., Pochet N., Schuster C., Baumert T.F. (2018) Hepatitis B virus evasion from cyclic guanosine monophosphate-adenosine monophosphate synthase sensing in human hepatocytes. Hepatology, 68(5):1695-1709.

Champion M., Brennan K., Croonenborghs T., Gentles A.J., Pochet N., Gevaert O. (2018) Module Analysis Captures Genetically and Epigenetically Deregulated Cancer Driver Genes for Smoking and Antiviral Response. bioRxiv 216754. EBioMedicine, 27:156-166.
https://bitbucket.org/gevaertlab/pancanceramaretto/src
https://github.com/gevaertlab/AMARETTO
https://github.com/broadinstitute/CommunityAMARETTO

Hu D., Notarbartolo S., Croonenborghs T., Patel B., Cialic R., Yang T.H., Aschenbrenner D., Andersson K.M., Gattorno M., Pham M., Kivisakk P., Pierre I.V., Lee Y., Kiani K., Bokarewa M., Tjon E., Pochet N., Sallusto F., Kuchroo V.K., Weiner H.L. (2017) Transcriptional signature of human pro-inflammatory TH17 cells identifies reduced IL10 gene expression in multiple sclerosis. Nature Communications, 8(1):1600.

Haas B., Dobin A., Stransky N., Li B., Yang X., Tickle T., Bankapur A., Ganote C., Doak T., Pochet N., Sun J., Wu C., Gingeras T., Regev A. (2017) STAR-Fusion: Fast and Accurate Fusion Transcript Detection from RNA-Seq. bioRxiv 120295.
https://github.com/NCIP/Trinity_CTAT

Patrick E., Rajagopal S., Wong H.A., McCabe C., Xu J., Tang A., Imboywa S.H., Schneider J.A., Pochet N., Krichevsky A.M., Chibnik L.B., Bennett D.A., De Jager P.L. (2017) Dissecting the role of non-coding RNAs in the accumulation of amyloid and tau neuropathologies in Alzheimer’s disease. bioRxiv 095067. Molecular Neurodegeneration, 12(1):51.

Van Renne N., Suarez A.A.R., Duong F.H.T., Gondeauc C., Calabrese D., Fontaine N., Ababsa A., Bandiera S., Kaukinen P., Chane-Woon-Ming B., Pfeffer S., Croonenborghs T., Pochet N., De Blasi V., Pessaux P., Piardi T., Sommacale D., Hoshida Y., Zeisel M., Heim M.H., Baumert T.F., Lupberger J. (2018) miR-135a-5p-mediated downregulation of protein-tyrosine phosphatase delta is a candidate driver of HCV-associated hepatocarcinogenesis. Gut, 67(5):953-962.

Rothhammer V., Mascanfroni I.D., Bunse L., Takenaka M.C., Kenison J., Mayo, L., Chao C.C., Patel B., Yan R., Blain M., Alvarez J.I., Kébir H., Anandasabapathy N., Izquierdo G., Jung S., Obholzer N., Pochet N., Clish C.B., Prinz M., Prat A., Antel J., Quintana F.J. (2016) Modulation of astrocyte activity by type I interferon and dietary tryptophan limits inflammation in the central nervous system. Nature Medicine, 22(6):586-597.

Qu K., Garamszegi S., Wu F., Thorvaldsdottir H., Liefeld T., Ocana M., Borges-Rivera D., Pochet N., Robinson J.T., Demchak B., Hull T., Ben-Artzi G., Blankenberg D., Barber G.P., Lee B.T., Kuhn R.M., Nekrutenko A., Segal E., Ideker T., Reich M., Regev A., Chang H.Y., Mesirov J.P. (2016) Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace. Nature Methods, 13(3):245-247.
http://www.genomespace.org

Rezende R., da Cunha A., Kuhn C., Rubino S., M'Hamdi H., Gabriely G., Vandeventer T., Liu S., Cialic R., Rosa N., Oliveira R., Gaublomme J., Obholzer N., Kozubek J., Pochet N., de Faria A.M., Weiner H. (2015) Identification and characterization of latency-associated peptide-expressing γδ T cells. Nature Communications, 6:8726.

Colpitts C.C., El-Saghire H., Pochet N., Schuster C., Baumert T.F. (2016) High-throughput approaches to unravel hepatitis C virus-host interactions. Virus Research, 218:18-24.

Verrier E.R., Colpitts C.C., Bach C., Heydmann L., Weiss A., Renaud M., Durand S.C., Habersetzer F., Durantel D., Abou-Jaoudé G., López Ledesma M.M., Felmlee D.J., Soumillon M., Croonenborghs T., Pochet N., Nassal M., Schuster C., Brino L., Sureau C., Zeisel M.B., Baumert T.F. (2016) Hepatology, 63(1):35-48.

Butovsky O., Jedrychowski M.P., Cialic R., Krasemann S., Murugaiyan G., Fanek Z., Greco D.J., Wu P.M., Doykan C.E., Kiner O., Lawson R.J., Frosch M.P., Pochet N., Fatimy R.E., Krichevsky A.M., Gygi S.P., Lassman H., Berry J., Cudkowicz M.E., Weiner H.L. (2015) Targeting miR-155 restores abnormal microglia and attenuates disease in SOD1 mice. Annals of Neurology, 77(1):75-99.

Yu L., Chibnik L.B., Srivastava G., Pochet N., Yang J., Xu J., Kozubek J., Obholzer N., Leurgans S., Schneider J.A., Meissner A., De Jager P.L., Bennett D.A.. (2015) Brain DNA methylation in SORL1, ABCA7, HLA-DRB5, SLC24A4, and BIN1 are associated with pathologic diagnosis of Alzheimer’s disease. JAMA Neurology, 72(1):15-24.

Wang L., Shalek A., Lawrence M., Ding R., Gaublomme J., Pochet N., Stojanov P., Sougnez C., Shukla S., Stevenson K., Zhang W., Wong J., Sievers Q., MacDonald B., Vartanov A., Goldstein N., Neuberg D., He X., Lander E., Hacohen N., Regev A., Getz G., Brown J., Park H., Wu C. (2014) Somatic mutation as a mechanism of Wnt/ß-catenin pathway activation in CLL. Blood, 124(7):1089-1098.

Haas B.J., Papanicolaou A., Yassour M., Grabherr M., Blood P.D., Bowden J., Couger M.B., Eccles D., Li B., Lieber M., MacManes M.D., Ott M., Orvis J., Pochet N., Strozzi F., Weeks N., Westerman R., William T., Dewey C.N., Henschel R., LeDuc R.D., Friedman N., Regev A. (2013) De novo transcript sequence reconstruction from RNA-Seq using the Trinity platform for reference generation and analysis. Nature Protocols, 8(8):1494-1512.
http://trinityrnaseq.github.io

Adiconis X.*, Borges-Rivera D.*, Satija R., Deluca D.S., Busby M.A., Berlin A.M., Sivachenko A., Thompson D.A., Wysoker A., Fennell T., Gnirke A., Pochet N., Regev A., Levin J.Z. (2013) Comparative analysis of RNA sequencing methods for degraded or low-input samples. Nature Methods, 10(7):623-629. *contributed equally.
Discussed in:
• Faculty of 1000: recommendation by Christine Clayton.

Kirby A., Gnirke A., Jaffe D.B., Barešová V., Pochet N., Blumenstiel B., Ye C., Aird D., Stevens C., Robinson J.T., Cabili M.N., Gat-Viks I., Kelliher E., Daza R., DeFelice M., Hulková H., Sovová J., Vyletal P., Antignac C., Guttman M., Handsaker R.E., Perrin D., Steelman S., Sigurdsson S., Scheinman S.J., Sougnez C., Cibulskis K., Parkin M., Green T., Rossin E., Zody M.C., Xavier R.J., Pollak M.R., Alper S.L., Lindblad-Toh K., Gabriel S., Hart S.P., Regev A., Nusbaum C., Kmoch S., Bleyer A.J., Lander E.S., Daly M.J. (2013) Mutations causing medullary cystic kidney disease type 1 (MCKD1) lie in a large VNTR in MUC1 missed by massively parallel sequencing. Nature Genetics, 45(3):299-303.

Shalek A.K., Gaublomme J.T., Wang L., Yosef N., Chevrier N., Andersen M.S., Robinson J.T., Pochet N., Neuberg D., Gertner R.S., Amit I., Brown J.R., Hacohen N., Regev A., Wu C.J., Park H. (2012) Nanowire-mediated delivery enables functional interrogation of primary immune cells: application to the analysis of chronic lymphocytic leukemia. Nano Letters, 12(12):6498-6504.

Klochendler A., Weinberg-Corem N., Moran M., Swisa A., Pochet N., Savova V., Vikeså J., Van de Peer Y., Brandeis M., Regev A., Nielsen F.C., Dor Y., Eden A. (2012) A transgenic mouse marking live replicating cells reveals in vivo transcriptional program of proliferation. Developmental Cell, 23(4):681-690.

Milner D.A. Jr.*, Pochet N.*, Krupka M., Williams C., Seydel K., Taylor T.E., 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 versus high parasitemic clusters. PLoS One, 7(7):e40739. *contributed equally.

Brown J.R., Hanna M., Tesar B., Werner L., Pochet N., Asara J.M., Wang Y.E., Dal Cin P., Fernandes S.M., Thompson C., Macconaill L., Wu C.J., Van de Peer Y., Correll M., Regev A., Neuberg D., Freedman A.S. (2012) Integrative genomic analysis implicates gain of PIK3CA at 3q26 and MYC at 8q24 in chronic lymphocytic leukemia. Clinical Cancer Research, 18(14):3791-3802.

Brown J.R., Hanna M., Tesar B., Pochet N., Vartanov A., Fernandes S.M., Werner L., Ash M., Roden C.A., MacConaill L., Hainz U., Longtine J., Wang Y.E., Correll M., Van de Peer Y., Regev A., Wu C., Neuberg D., Freedman A.S. (2012) Germline copy number variation associated with Mendelian inheritance of chronic lymphocytic leukemia in two families. Leukemia, 26(7):1710-1713.

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):654-664.

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.
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: recommendations 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.

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.

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.

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.

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.
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: recommendation 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.
http://www.igs.cnrs-mrs.fr/SERV/
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.

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.

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.

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.

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.

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.

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.

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.

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.
ftp://ftp.esat.kuleuven.be/sista/npochet/tutorial.pdf
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.


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.


PH.D. THESIS

Pochet N. (2006) Microarray data analysis using support vector machines and kernel methods. Ph.D. thesis, Faculty of Engineering Sciences, KU Leuven. (ftp://ftp.esat.kuleuven.be/pub/SISTA/npochet/PhD_Nathalie_Pochet.pdf)