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Publications

Published in peer-reviewed journals

Conrad DF, Pinto D, Redon R, Feuk L, Gokcumen O, Zhang Y, Aerts J, Andrews TD, Barnes C, Campbell P, Fitzgerald T, Hu M, Ihm CH, Kristiansson K, Macarthur DG, Macdonald JR, Onyiah I, Pang AW, Robson S, Stirrups K, Valsesia A, Walter K, Wei J; Wellcome Trust Case Control Consortium, Tyler-Smith C, Carter NP, Lee C, Scherer SW, Hurles ME. (2010) Origins and functional impact of copy number variation in the human genome. Nature 2010 Apr 1;464(7289):704-12.


Wellcome Trust Case Control Consortium, Craddock N, Hurles ME, Cardin N, Pearson RD, Plagnol V, Robson S, Vukcevic D, Barnes C, Conrad DF, Giannoulatou E, Holmes C, Marchini JL, Stirrups K, Tobin MD, Wain LV, Yau C, Aerts J, Ahmad T, Andrews TD, Arbury H, Attwood A, Auton A, Ball SG, Balmforth AJ, Barrett JC, Barroso I, Barton A, Bennett AJ, Bhaskar S, Blaszczyk K, Bowes J, Brand OJ,Braund PS, Bredin F, Breen G, Brown MJ, Bruce IN, Bull J, Burren OS, Burton J, Byrnes J, Caesar S, Clee CM, Coffey AJ, Connell JM,Cooper JD, Dominiczak AF, Downes K, Drummond HE, Dudakia D, Dunham A, Ebbs B, Eccles D, Edkins S, Edwards C, Elliot A,Emery P, Evans DM, Evans G, Eyre S, Farmer A, Ferrier IN, Feuk L, Fitzgerald T, Flynn E, Forbes A, Forty L, Franklyn JA, Freathy RM,Gibbs P, Gilbert P, Gokumen O, Gordon-Smith K, Gray E, Green E, Groves CJ, Grozeva D, Gwilliam R, Hall A, Hammond N, Hardy M,Harrison P, Hassanali N, Hebaishi H, Hines S, Hinks A, Hitman GA, Hocking L, Howard E, Howard P, Howson JM, Hughes D, Hunt S,Isaacs JD, Jain M, Jewell DP, Johnson T, Jolley JD, Jones IR, Jones LA, Kirov G, Langford CF, Lango-Allen H, Lathrop GM, Lee J, Lee KL, Lees C, Lewis K, Lindgren CM, Maisuria-Armer M, Maller J, Mansfield J, Martin P, Massey DC, McArdle WL, McGuffin P, McLay KE,Mentzer A, Mimmack ML, Morgan AE, Morris AP, Mowat C, Myers S, Newman W, Nimmo ER, O'Donovan MC, Onipinla A, Onyiah I,Ovington NR, Owen MJ, Palin K, Parnell K, Pernet D, Perry JR, Phillips A, Pinto D, Prescott NJ, Prokopenko I, Quail MA, Rafelt S,Rayner NW, Redon R, Reid DM, Renwick, Ring SM, Robertson N, Russell E, St Clair D, Sambrook JG, Sanderson JD, Schuilenburg H,Scott CE, Scott R, Seal S, Shaw-Hawkins S, Shields BM, Simmonds MJ, Smyth DJ, Somaskantharajah E, Spanova K, Steer S,Stephens J, Stevens HE, Stone MA, Su Z, Symmons DP, Thompson JR, Thomson W, Travers ME, Turnbull C, Valsesia A, Walker M,Walker NM, Wallace C, Warren-Perry M, Watkins NA, Webster J, Weedon MN, Wilson AG, Woodburn M, Wordsworth BP, Young AH,Zeggini E, Carter NP, Frayling TM, Lee C, McVean G, Munroe PB, Palotie A, Sawcer SJ, Scherer SW, Strachan DP, Tyler-Smith C,Brown MA, Burton PR, Caulfield MJ, Compston A, Farrall M, Gough SC, Hall AS, Hattersley AT, Hill AV, Mathew CG, Pembrey M,Satsangi J, Stratton MR, Worthington J, Deloukas P, Duncanson A, Kwiatkowski DP, McCarthy MI, Ouwehand W, Parkes M, Rahman N, Todd JA, Samani NJ, Donnelly P. (2010) Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls. Nature 2010 Apr 1;464(7289):713-20.

Walters RG, Jacquemont S, Valsesia A, de Smith AJ, Martinet D, Andersson J, Falchi M, Chen F, Andrieux J, Lobbens S, Delobel B,Stutzmann F, El-Sayed Moustafa JS, Chèvre JC, Lecoeur C, Vatin V, Bouquillon S, Buxton JL, Boute O, Holder-Espinasse M, Cuisset JM, Lemaitre MP, Ambresin AE, Brioschi A, Gaillard M, Giusti V, Fellmann F, Ferrarini A, Hadjikhani N, Campion D, Guilmatre A,Goldenberg A, Calmels N, Mandel JL, Le Caignec C, David A, Isidor B, Cordier MP, Dupuis-Girod S, Labalme A, Sanlaville D, Béri-Dexheimer M, Jonveaux P, Leheup B, Ounap K, Bochukova EG, Henning E, Keogh J, Ellis RJ, Macdermot KD, van Haelst MM,Vincent-Delorme C, Plessis G, Touraine R, Philippe A, Malan V, Mathieu-Dramard M, Chiesa J, Blaumeiser B, Kooy RF, Caiazzo R,Pigeyre M, Balkau B, Sladek R, Bergmann S, Mooser V, Waterworth D, Reymond A, Vollenweider P, Waeber G, Kurg A, Palta P, Esko T, Metspalu A, Nelis M, Elliott P, Hartikainen AL, McCarthy MI, Peltonen L, Carlsson L, Jacobson P, Sjöström L, Huang N, Hurles ME,O'Rahilly S, Farooqi IS, Männik K, Jarvelin MR, Pattou F, Meyre D, Walley AJ, Coin LJ, Blakemore AI, Froguel P, Beckmann JS. (2010) A new highly penetrant form of obesity due to deletions on chromosome 16p11.2. Nature 2010 Feb 4;463(7281):671-5.

Nikolaev SI, Iseli C, Sharp AJ, Robyr D, Rougemont J, Gehrig C, Farinelli L, Antonarakis SE. (2009) Detection of genomic variation by selection of a 9 mb DNA region and high throughput sequencing. PLoS One. 4:e6659.

Rio Frio T, McGee TL, Wade NM, Iseli C, Beckmann JS, Berson EL, Rivolta C. (2009) A single-base substitution within an intronic repetitive element causes dominant retinitis pigmentosa with reduced penetrance. Hum Mutat. 30:1340-7.

Wurm Y, Uva P, Ricci F, Wang J, Jemielity S, Iseli C, Falquet L, Keller L. (2009) Fourmidable: a database for ant genomics. BMC Genomics. 10:5.

Kröber M, Bekel T, Diaz NN, Goesmann A, Jaenicke S, Krause L, Miller D, Runte KJ, Viehöver P, Pühler A, Schlüter A. (2009) Phylogenetic characterization of a biogas plant microbial community integrating clone library 16S-rDNA sequences and metagenome sequence data obtained by 454-pyrosequencing. J Biotechnol. 142:38-49.

Diaz NN, Krause L, Goesmann A, Niehaus K, Nattkemper TW. (2009) TACOA: taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach. BMC Bioinformatics. 10:56.

Conrad DF, Pinto D, Redon R, Feuk L, Gokcumen O, Zhang Y, Aerts J, Andrews TD, Barnes C, Campbell P, Fitzgerald T, Hu M, Ihm CH, Kristiansson K, Macarthur DG, Macdonald JR, Onyiah I, Pang AW, Robson S, Stirrups K, Valsesia A, Walter K, Wei J; The Wellcome Trust Case Control Consortium, Tyler-Smith C, Carter NP, Lee C, Scherer SW, Hurles ME. (2009) Origins and functional impact of copy number variation in the human genome. Nature [Epub ahead of print]. 

Zhao Q, Caballero OL, Levy S, Stevenson BJ, Iseli C, de Souza SJ, Galante PA, Busam D, Leversha MA, Chadalavada K, Rogers YH, Venter JC, Simpson AJ, Strausberg RL. (2009) Transcriptome-guided characterization of genomic rearrangements in a breast cancer cell line. Proc Natl Acad Sci U S A. 106:1886-91.

Martin O, Valsesia A, Telenti A, Xenarios I, Stevenson BJ. (2009) AssociationViewer: a scalable and integrated software tool for visualization of large-scale variation data in genomic context. Bioinformatics. 25:662-3.

Hofmann O, Caballero OL, Stevenson BJ, Chen YT, Cohen T, Chua R, Maher CA, Panji S, Schaefer U, Kruger A, Lehvaslaiho M, Carninci P, Hayashizaki Y, Jongeneel CV, Simpson AJ, Old LJ, Hide W. (2008) Genome-wide analysis of cancer/testis gene expression. Proc Natl Acad Sci U S A. 105:20422-7.

Rougemont J, Amzallag A, Iseli C, Farinelli L, Xenarios I, Naef F. (2008) Probabilistic base calling of Solexa sequencing data. BMC Bioinformatics. 9:431.

Sauvain MO, Dorr AP, Stevenson B, Quazzola A, Naef F, Wiznerowicz M, Schütz F, Jongeneel V, Duboule D, Spitz F, Trono D. (2008) Genotypic features of lentivirus transgenic mice. J Virol. 82:7111-9.

Alves PM, Lévy N, Stevenson BJ, Bouzourene H, Theiler G, Bricard G, Viatte S, Ayyoub M, Vuilleumier H, Givel JC, Rimoldi D, Speiser DE, Jongeneel CV, Romero PJ, Lévy F. (2008) Identification of tumor-associated antigens by large-scale analysis of genes expressed in human colorectal cancer. Cancer Immun. 8:11.

Retelska D, Beaudoing E, Notredame C, Jongeneel CV, Bucher P. (2007) Vertebrate conserved non coding DNA regions have a high persistence length and a short persistence time. BMC Genomics. 8:398.

Moretti S, Armougom F, Wallace IM, Higgins DG, Jongeneel CV, Notredame C. (2007) The M-Coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment methods. Nucleic Acids Res. 35(Web Server issue):W645-8.

Pagni M, Ioannidis V, Cerutti L, Zahn-Zabal M, Jongeneel CV, Hau J, Martin O, Kuznetsov D, Falquet L. MyHits: improvements to an interactive resource for analyzing protein sequences. (2007) Nucleic Acids Res. 35(Web Server issue):W433-7.

Iseli C, Ambrosini G, Bucher P, Jongeneel CV. (2007). Indexing strategies for rapid searches of short words in genome sequences. PLoS ONE. 2:e579.

Stevenson BJ, Iseli C, Panji S, Zahn-Zabal M, Hide W, Old LJ, Simpson AJ, Jongeneel CV. Rapid evolution of cancer/testis genes on the X chromosome. (2007) BMC Genomics. 8:129.

Grigoriadis A, Mackay A, Reis-Filho JS, Steele D, Iseli C, Stevenson B, Jongeneel CV, Valgeirsson H, Fenwick K, Iravani M, Leao M, Simpson AS, Strausberg RL, Jat PJ, Ashworth A, Neville AM, O'hare MJ (2006). Establishment of the epithelial-specific transcriptome of normal and malignant human breast cells based on MPSS and array expression data. Breast Cancer Res.8:R56.

Retelska D, Iseli C, Bucher P, Jongeneel CV, Naef F (2006). Similarities and differences of polyadenylation signals in human and fly. BMC Genomics. 7:176.

Chen YT, Iseli C, Venditti CA, Old LJ, Simpson AJ, Jongeneel CV (2006). Identification of a new cancer/testis gene family, CT47, among expressed multicopy genes on the human X chromosome. Genes Chromosomes Cancer. 45:392.

Deutsch S, Lyle R, Dermitzakis ET, Attar H, Subrahmanyan L, Gehrig C, Parand L, Gagnebin M, Rougemont J, Jongeneel CV, Antonarakis SE (2005) Gene expression variation and expression quantitative trait mapping of human chromosome 21 genes. Hum Mol Genet. 14: 3741.

Chen YT, Scanlan MJ, Venditti CA, Chua R, Theiler G, Stevenson BJ, Iseli C, Gure AO, Vasicek T, Strausberg RL, Jongeneel CV, Old LJ, Simpson AJ (2005). Identification of cancer/testis-antigen genes by massively parallel signature sequencing. Proc Natl Acad Sci USA 102:7940.

Chen YT, Venditti CA, Theiler G, Stevenson BJ, Iseli C, Gure AO, Jongeneel CV, Old LJ, Simpson AJ (2005). Identification of CT46/HORMAD1, an immunogenic cancer/testis antigen encoding a putative meiosis-related protein. Cancer Immun. 7:5.

Jongeneel CV, Delorenzi M, Iseli C, Zhou D, Haudenschild CD, Khrebtukova I, Kuznetsov D, Stevenson BJ, Strausberg RL, Simpson AJ, Vasicek TJ (2005). An atlas of human gene expression from massively parallel signature sequencing (MPSS). Genome Res. 15:1007.

Armand F, Bucher P, Jongeneel CV, Farmer EE (2005). Rapid and selective surveillance of Arabidopsis thaliana genome annotations with Centrifuge. Bioinformatics 21: 2906.

Lee SY, Williamson B, Caballero OL, Chen YT, Scanlan MJ, Ritter G, Jongeneel CV, Simpson AJ, Old LJ (2004). Identification of the gonad-specific anion transporter SLCO6A1 as a cancer/testis (CT) antigen expressed in human lung cancer. Cancer Immun.17:4.

Pagni M, Ioannidis V, Cerutti L, Zahn-Zabal M, Jongeneel CV, Falquet L (2004). MyHits: a new interactive resource for protein annotation and domain identification. Nucleic Acids Res. 32:W332.

Stauffer Y, Theiler G, Sperisen P, Lebedev Y, Jongeneel CV (2004). Digital expression profiles of human endogenous retroviral families in normal and cancerous tissues. Cancer Immun. 4:2.

Sperisen P, Iseli C, Pagni M, Stevenson BJ, Bucher P, Jongeneel CV (2004). trome, trEST and trGEN: databases of predicted protein sequences. Nucleic Acids Res. 32: D509.

Brentani H, Caballero OL, Camargo AA, da Silva AM, da Silva WA Jr, Dias Neto E, Grivet M, Gruber A, Guimaraes PE, Hide W, Iseli C, Jongeneel CV, Kelso J, Nagai MA, Ojopi EP, Osorio EC, Reis EM, Riggins GJ, Simpson AJ, de Souza S, Stevenson BJ, Strausberg RL, Tajara EH, Verjovski-Almeida S, Human Cancer Genome Project/Cancer Genome Anatomy Project Annotation Consortium; Human Cancer Genome Project Sequencing Consortium (2003). The generation and utilization of a cancer-oriented representation of the human transcriptome by using expressed sequence tags. Proc Natl Acad Sci USA 100:13418.

Lottaz C, Iseli C, Jongeneel CV, Bucher P (2003). Modeling sequencing errors by combining Hidden Markov models. Bioinformatics 19:II103.

Favre M, Butticaz C, Stevenson B, Jongeneel CV, Telenti A (2003). High frequency of alternative splicing of human genes participating in the HIV-1 life cycle: a model using TSG101, betaTrCP, PPIA, INI1, NAF1, and PML. J Acquir Immune Defic Syndr. 34:127.

Falquet L, Bordoli L, Ioannidis V, Pagni M, Jongeneel CV (2003). Swiss EMBnet node web server. Nucleic Acids Res. 31:3782.

Stevenson BJ, Iseli C, Beutler B, Jongeneel CV (2003). Use of transcriptome data to unravel the fine structure of genes involved in sepsis. J Infect Dis. 187:S308.

Kelso J, Visagie J, Theiler G, Christoffels A, Bardien S, Smedley D, Otgaar D, Greyling G, Jongeneel CV, McCarthy MI, Hide T, Hide W (2003). eVOC: a controlled vocabulary for unifying gene expression data. Genome Res. 13:1222.

Silva AP, Salim AC, Bulgarelli A, de Souza JE, Osorio E, Caballero OL, Iseli C, Stevenson BJ, Jongeneel CV, de Souza SJ, Simpson AJ, Camargo AA (2003). Identification of 9 novel transcripts and two RGSL genes within the hereditary prostate cancer region (HPC1) at 1q25. Gene 310:49.

Jongeneel CV, Iseli C, Stevenson BJ, Riggins GJ, Lal A, Mackay A, Harris RA, O'Hare MJ, Neville AM, Simpson AJ, Strausberg RL (2003). Comprehensive sampling of gene expression in human cell lines with massively parallel signature sequencing. Proc Natl Acad Sci U S A. 100:4702.

Dermitzakis ET, Reymond A, Lyle R, Scamuffa N, Ucla C, Deutsch S, Stevenson BJ, Flegel V, Bucher P, Jongeneel CV, Antonarakis SE (2002). Numerous potentially functional but non-genic conserved sequences on human chromosome 21. Nature 420:578.

Iseli C, Stevenson BJ, de Souza SJ, Samaia HB, Camargo AA, Buetow KH, Strausberg RL, Simpson AJ, Bucher P, Jongeneel CV (2002). Long-range heterogeneity at the 3' ends of human mRNAs. Genome Res. 12:1068.

Reymond A, Camargo AA, Deutsch S, Stevenson BJ, Parmigiani RB, Ucla C, Bettoni F, Rossier C, Lyle R, Guipponi M, de Souza S, Iseli C, Jongeneel CV, Bucher P, Simpson AJ, Antonarakis SE (2002). Nineteen additional unpredicted transcripts from human chromosome 21. Genomics 79:824.

Jongeneel V (2001). Towards a cancer immunome database. Cancer Immun. 1:3.

Pagni M, Jongeneel CV (2001). Making sense of score statistics for sequence alignments. Brief Bioinform. 2:51.

Kuimov AN, Kuprash DV, Petrov VN, Vdovichenko KK, Scanlan MJ, Jongeneel CV, Lagarkova MA, Nedospasov SA (2001). Cloning and characterization of TNKL, a member of tankyrase gene family. Genes Immun. 2:52.

Pagni M, Iseli C, Junier T, Falquet L, Jongeneel V, Bucher P (2001). trEST, trGEN and Hits: access to databases of predicted protein sequences. Nucleic Acids Res. 29:148.

Dias Neto E, Correa RG, Verjovski-Almeida S, Briones MR, Nagai MA, da Silva W Jr, Zago MA, Bordin S, Costa FF, Goldman GH, Carvalho AF, Matsukuma A, Baia GS, Simpson DH, Brunstein A, de Oliveira PS, Bucher P, Jongeneel CV, O'Hare MJ, Soares F, Brentani RR, Reis LF, de Souza SJ, Simpson AJ (2000). Shotgun sequencing of the human transcriptome with ORF expressed sequence tags. Proc Natl Acad Sci USA 97:3491.

Jongeneel CV (2000). Searching the expressed sequence tag (EST) databases: panning for genes. Brief Bioinform. 1:76.

Scanlan MJ, Gordan JD, Williamson B, Stockert E, Bander NH, Jongeneel V, Gure AO, Jager D, Jager E, Knuth A, Chen YT, Old LJ (1999). Antigens recognized by autologous antibody in patients with renal-cell carcinoma. Int J Cancer 83:456.

Rimoldi D, Salvi S, Reed D, Coulie P, Jongeneel CV, De Plaen E, Brasseur F, Rodriguez AM, Boon T, Cerottini JC (1999). cDNA and protein characterization of human MAGE-10. Int J Cancer.82:901.

Lengacher S, Reed D, Heumann D, Jongeneel CV (1999). Genomic organization and chromosomal localization of the mouse lipopolysaccharide binding protein gene. Immunogenetics.49:553.

Bakker TR, Renno T, Jongeneel CV (1999). Impaired fetal thymocyte development after efficient adenovirus-mediated inhibition of NF-kappa B activation. J Immunol. 162:3456.

Herman J, Jongeneel V, Kuznetsov D, Coulie PG (1999). Differences in the recognition by CTL of peptides presented by the HLA-B*4402 and the HLA-B*4403 molecules which differ by a single amino acid. Tissue Antigens 53:111.

Bakker TR, Reed D, Renno T, Jongeneel CV. Efficient adenoviral transfer of NF-kappaB inhibitor sensitizes melanoma to tumor necrosis factor-mediated apoptosis. Int J Cancer 80:320.

Iseli C, Jongeneel CV, Bucher P (1999). ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. Proc Int Conf Intell Syst Mol Biol. 1999:138.

Poyet JL, Hoeveler A, Jongeneel CV (1998). Analysis of active site residues of the antiviral protein from summer leaves from Phytolacca americana by site-directed mutagenesis. Biochem Biophys Res Commun. 253:582.

Esslinger CW, Jongeneel CV, MacDonald HR (1998). Survival-independent function of NF-kappaB/Rel during late stages of thymocyte differentiation. Mol Immunol. 35:847.

Valmori D, Fonteneau JF, Lizana CM, Gervois N, Lienard D, Rimoldi D, Jongeneel V, Jotereau F, Cerottini JC, Romero P (1998). Enhanced generation of specific tumor-reactive CTL in vitro by selected Melan-A/MART-1 immunodominant peptide analogues. J Immunol. 160:1750.

Reed DS, Romero P, Rimoldi D, Cerottini JC, Schaack J, Jongeneel CV (1997). Construction and characterization of a recombinant adenovirus directing expression of the MAGE-1 tumor-specific antigen. Int J Cancer. 72:1045.

Esslinger CW, Wilson A, Sordat B, Beermann F, Jongeneel CV (1997). Abnormal T lymphocyte development induced by targeted overexpression of IkappaB alpha. J Immunol. 158:5075.

Anjuere F, Kuznetsov D, Romero P, Cerottini JC, Jongeneel CV, Luescher IF (1997). Differential roles of T cell receptor alpha and beta chains in ligand binding among H-2Kd-restricted cytolytic T lymphocyte clones specific for a photoreactive Plasmodium berghei circumsporozoite peptide derivative. J Biol Chem. 272:8505.

Luescher IF, Romero P, Kuznetsov D, Rimoldi D, Coulie P, Cerottini JC, Jongeneel CV (1997). HLA photoaffinity labeling reveals overlapping binding of homologous melanoma-associated gene peptides by HLA-A1, HLA-A29, and HLA-B44. J Biol Chem. 271:12463.

Maryanski JL, Jongeneel CV, Bucher P, Casanova JL, Walker PR (1996). Single-cell PCR analysis of TCR repertoires selected by antigen in vivo: a high magnitude CD8 response is comprised of very few clones. Immunity 4:47.

Romero P, Pannetier C, Herman J, Jongeneel CV, Cerottini JC, Coulie PG (1995). Multiple specificities in the repertoire of a melanoma patient's cytolytic T lymphocytes directed against tumor antigen MAGE-1.A1. J Exp Med. 182:1019.

Buchmuller-Rouiller Y, Corrandin SB, Smith J, Schneider P, Ransijn A, Jongeneel CV, Mauel J (1995). Role of glutathione in macrophage activation: effect of cellular glutathione depletion on nitrite production and leishmanicidal activity. Cell Immunol. 164:73.

Luescher IF, Anjuere F, Peitsch MC, Jongeneel CV, Cerottini JC, Romero P (1995). Structural analysis of TCR-ligand interactions studied on H-2Kd-restricted cloned CTL specific for a photoreactive peptide derivative. Immunity. 3:51.

Lisby S, Muller KM, Jongeneel CV, Saurat JH, Hauser C (1995). Nickel and skin irritants up-regulate tumor necrosis factor-alpha mRNA in keratinocytes by different but potentially synergistic mechanisms. Int. Immunol. 7:343.

Lengacher S, Jongeneel CV, Le Roy D, Lee JD, Kravchenko V, Ulevitch RJ, Glauser MP, Heumann D (1995). Reactivity of murine and human recombinant LPS-binding protein (LBP) within LPS and gram negative bacteria. J Inflamm. 47:165.

Albrecht H, Schook LB, Jongeneel CV (1995). Nuclear migration of NF-kappa B correlates with TNF-alpha mRNA accumulation. J Inflamm. 45:64.

Derkx HHF, Bruin KF, Jongeneel CV, de Waal LP, Brinkman BMN, Verweij CL, Houwing-Duistermaat JJ, Rosendaal FR, van Deventer SJH (1995). Familial differences in endotoxin-induced TNF release in whole blood and peripheral blood mononuclear cells in vitro: relationship to TNF gene polymorphism. J. Endotox. Res. 2 :19.

Schook LB, Albrecht H, Gallay P, Jongeneel CV (1994). Cytokine regulation of TNF-alpha mRNA and protein production by unprimed macrophages from C57Bl/6 and NZW mice. J Leukoc Biol. 56:514.

Albrecht H, Tschopp J, Jongeneel CV (1994). Bcl-2 protects from oxidative damage and apoptotic cell death without interfering with activation of NF-kappa B by TNF. FEBS Lett. 351:45.

Bazzoni F, Kruys V, Shakhov A, Jongeneel CV, Beutler B (1994). Analysis of tumor necrosis factor promoter responses to ultraviolet light. J Clin Invest. 93:56.

Gallay P, Jongeneel CV, Barras C, Burnier M, Baumgartner JD, Glauser MP, Heumann D (1993). Short time exposure to lipopolysaccharide is sufficient to activate human monocytes. J Immunol. 150:5086.

Peitsch MC, Jongeneel CV (1993). A 3-D model for the CD40 ligand predicts that it is a compact trimer similar to the tumor necrosis factors. Int Immunol. 5:233.

Pociot F, Briant L, Jongeneel CV, Molvig J, Worsaae H, Abbal M, Thomsen M, Nerup J, Cambon-Thomsen A (1993). Association of tumor necrosis factor (TNF) and class II major histocompatibility complex alleles with the secretion of TNF-alpha and TNF-beta by human mononuclear cells: a possible link to insulin-dependent diabetes mellitus. Eur J Immunol. 23:224.

Albrecht H, Shakhov AN, Jongeneel CV (1992). trans activation of the tumor necrosis factor alpha promoter by the human -cell leukemia virus type I Tax1 protein. J Virol. 66:6191.

Rothe H, Schuller I, Richter G, Jongeneel CV, Kiesel U, Diamantstein T, Blankenstein T, Kolb H (1992). Abnormal TNF production in prediabetic BB rats is linked to defective CD45R expression. Immunology 77:1.

Kruys V, Kemmer K, Shakhov A, Jongeneel V, Beutler B (1992). Constitutive activity of the tumor necrosis factor promoter is canceled by the 3' untranslated region in nonmacrophage cell lines; a trans-dominant factor overcomes this suppressive effect. Proc Natl Acad Sci USA 89:673.

Crouau-Roy B, Bouissou C, Clayton J, Jongeneel CV (1992). Identification of microsatellite alleles on individual sperm. Methods Mol. Cell. Biol. 3:239.

Jongeneel CV, Briant L, Udalova IA, Sevin A, Nedospasov SA, Cambon-Thomsen A (1991). Extensive genetic polymorphism in the human tumor necrosis factor region and relation to extended HLA haplotypes. Proc Natl Acad Sci USA 88: 9717.

Drouet C, Shakhov AN, Jongeneel CV (1991). Enhancers and transcription factors controlling the inducibility of the tumor necrosis factor-alpha promoter in primary macrophages. J Immunol. 147:1694.

Viville S, Jongeneel V, Koch W, Mantovani R, Benoist C, Mathis D (1991). The E alpha promoter: a linker-scanning analysis. J Immunol. 146:3211.

Shakhov AN, Kuprash DV, Azizov MM, Jongeneel CV, Nedospasov SA (1990). Structural analysis of the rabbit TNF locus, containing the genes encoding TNF-beta (lymphotoxin) and TNF-alpha (tumor necrosis factor). Gene 95:215.

Jongeneel CV, Acha-Orbea H, Blankenstein T (1990). A polymorphic microsatellite in the tumor necrosis factor alpha promoter identifies an allele unique to the NZW mouse strain. J Exp Med. 171:2141.

Shakhov AN, Collart MA, Vassalli P, Nedospasov SA, Jongeneel CV (1990). Kappa B-type enhancers are involved in lipopolysaccharide-mediated transcriptional activation of the tumor necrosis factor alpha gene in primary macrophages. J Exp Med. 171:35.

Monod L, Diserens AC, Jongeneel CV, Carrel S, Ronco P, Verroust P, de Tribolet N (1989). Human glioma cell lines expressing the common acute lymphoblastic leukemia antigen (cALLa) have neutral endopeptidase activity. Int J Cancer 44:948.

Jongeneel CV, Shakhov AN, Nedospasov SA, Cerottini JC (1989). Molecular control of tissue-specific expression at the mouse TNF locus. Eur J Immunol. 19:549.

Jongeneel CV, Quackenbush EJ, Ronco P, Verroust P, Carrel S, Letarte M (1989). Common acute lymphoblastic leukemia antigen expressed on leukemia and melanoma cell lines has neutral endopeptidase activity. J Clin Invest. 83:713.

Jongeneel CV, Bouvier J, Bairoch A (1989). A unique signature identifies a family of zinc-dependent metallopeptidases. FEBS Lett. 242:211.

Letarte M, Vera S, Tran R, Addis JB, Onizuka RJ, Quackenbush EJ, Jongeneel CV, McInnes RR (1988). Common acute lymphocytic leukemia antigen is identical to neutral endopeptidase. J Exp Med. 168:1247.

Jongeneel CV, Nedospasov SA, Plaetinck G, Naquet P, Cerottini JC (1988). Expression of the tumor necrosis factor locus is not necessary for the cytolytic activity of T lymphocytes. J Immunol. 140:1916.

Semon D, Kawashima E, Jongeneel CV, Shakhov AN, Nedospasov SA (1987). Nucleotide sequence of the murine TNF locus, including the TNF-alpha (tumor necrosis factor) and TNF-beta (lymphotoxin) genes. Nucleic Acids Res. 15:9083.

Muller U, Jongeneel CV, Nedospasov SA, Lindahl KF, Steinmetz M (1987). Tumour necrosis factor and lymphotoxin genes map close to H-2D in the mouse major histocompatibility complex. Nature 325:265.

Nedospasov SA, Jongeneel CV (1987). Molecular cloning of genes coding for tumor necrosis factors: tandem localization of alpha and beta genes on mouse chromosome 17. Dokl. Akad. Nauk SSSR 295: 749.

Nedospasov SA, Hirt B, Shakhov AN, Dobrynin VN, Kawashima E, Accolla RS, Jongeneel CV (1986). The genes for tumor necrosis factor (TNF-alpha) and lymphotoxin (TNF-beta) are tandemly arranged on chromosome 17 of the mouse. Nucleic Acids Res. 14:7713.

Jongeneel CV, Sahli R, McMaster GK, Hirt B (1986). A precise map of splice junctions in the mRNAs of minute virus of mice, an autonomous parvovirus. J Virol. 59:564.

Kimsey PB, Engers HD, Hirt B, Jongeneel CV (1986). Pathogenicity of fibroblast- and lymphocyte-specific variants of minute virus of mice. J Virol. 59:8.

Jongeneel CV, Bedinger P, Alberts BM (1984). Effects of the bacteriophage T4 dda protein on DNA synthesis catalyzed by purified T4 replication proteins. J Biol Chem. 259:12933.

Jongeneel CV, Formosa T, Alberts BM (1984). Purification and characterization of the bacteriophage T4 dda protein. A DNA helicase that associates with the viral helix-destabilizing protein. J Biol Chem. 259:12925.

Bedinger P, Hochstrasser M, Jongeneel CV, Alberts BM (1983). Properties of the T4 bacteriophage DNA replication apparatus: the T4 dda DNA helicase is required to pass a bound RNA polymerase molecule. Cell 34:115.

Jongeneel CV, Bachenheimer SL (1981). Structure of replicating herpes simplex virus DNA. J Virol. 39:656.

Jongeneel CV, Bachenheimer SL (1980). Replication of herpes simplex virus type I DNA in permeabilized infected cells. Nucleic Acids Res. 8:1661.

Plata F, Jongeneel CV (1977). Characterization to effector lymphocytes associated with immunity to murine sarcoma virus (MSV)-induced tumors. II. Repeated stimulation and proliferation in vitro of specific cytolytic T lymphocytes. J Immunol.119:623.

Plata F, Jongeneel V, Cerottini JC, Brunner KT (1976). Antigenic specificity of the cytolytic T lymphocyte (CTL) response to murine sarcoma virus-induced tumors. I. Preferential reactivity of in vitro generated secondary CTL with syngeneic tumor cells. Eur J Immunol. 6:823.

 

Published without peer review

Jongeneel CV (2000). The need for a human gene index. Bioinformatics 16:1059.

Jongeneel CV, Beutler B (1996). Genetic polymorphism in the human TNF region: correlation or causation? J Inflamm. 46:3.

Jongeneel CV (1995). Transcriptional regulation of the TNFa gene. Immunobiology 193:210.

Tschopp J, Jongeneel CV (1988). Cytotoxic T lymphocyte mediated cytolysis. Biochemistry 27: 2641.

reuzer KN, Jongeneel CV (1983). Escherichia coli phage T4 topoisomerase. Methods Enzymol. 100:144.

Alberts BM, Barry J, Bedinger P, Formosa T, Jongeneel CV, Kreuzer KN (1983). Studies on DNA replication in the bacteriophage T4 in vitro system. Cold Spring Harb Symp Quant Biol. 47:655.

Published in books

Jongeneel CV(2003). Bioinformatics: technical aspects. In "Encyclopedia of the Human Genome", Macmillan Publishers Inc, Nature Publishing Group.

Jongeneel CV(1993). Regulation of the TNF-? gene. In "Bacterial Endotoxins: Basic Science to Anti-Sepsis Strategies", J. Levin, A. Sturk, T. van der Poll, and S.J.H. van Deventer, eds., John Wiley, New York, pp. 367-381.

Briant L, Jongeneel CV, Sommer E, Sevin A, Abbal M, Ohayon E, Cambon-Thomsen E (1993). HLA extended haplotypes including three tumour necrosis factor polymorphic microsatellites in normal Caucasoids and in families with insulin-dependent diabetes mellitus. In "Histocompatibility Testing 1992", K. Tsugi, M. Aizawa, T. Sasazuki, Eds., Oxford Science Publishers, Oxford, UK, pp. 492-495.

Jongeneel CV, Briant L, Sevin A, Cambon-Thomsen A (1992). Genetic polymorphism in the human TNF region: relation to extended HLA haplotypes and potential involvement in IDDM. In: "Pathophysiology and pharmacology of cytokines", P. Ghezzi and A. Mantovani, eds., Biomedical Press, Augusta, USA, pp. 29-35.

Jongeneel CV(1991). The TNF and lymphotoxin promoters. In: "Tumor Necrosis Factors: The Molecules and Their Emerging Role in Medicine", B. Beutler, ed., Raven Press, New York, pp. 539-559.

Shakhov AN, Turetskaya RL, Kuprash DV, Nedospasov SA, Collart MA, Drouet C, Jongeneel CV (1990). Sequences involved in the regulation of TNF gene expression. In: "Molecular and cellular biology of cytokines". Powanda, Oppenheim, Kluger and Dinarello, eds. Alan R. Liss, New York, pp. 21-25.

Jongeneel CV, Formosa T, Munn M, Alberts BM (1984). Enzymological studies of the T4 replication proteins. In: "Proteins involved in DNA replication" (Advances in Experimental Medicine and Biology, vol. 179), pp. 17-33. U. Huebscher and S. Spadari, eds., Plenum Press, NY.

Plata F, Jongeneel CV (1977). Regeneration and proliferation in vitro of cytolytic T lymphocytes specific for MSV-associated tumor antigens. In "Regulatory Mechanisms in Lymphocyte Action" (Proceedings of the 11th Leukocyte Culture Conference) pp. 533-535. Academic Press, NY.

 

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