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Items: 1 to 50 of 98

1.

Developing reproducible bioinformatics analysis workflows for heterogeneous computing environments to support African genomics.

Baichoo S, Souilmi Y, Panji S, Botha G, Meintjes A, Hazelhurst S, Bendou H, Beste E, Mpangase PT, Souiai O, Alghali M, Yi L, O'Connor BD, Crusoe M, Armstrong D, Aron S, Joubert F, Ahmed AE, Mbiyavanga M, Heusden PV, Magosi LE, Zermeno J, Mainzer LS, Fadlelmola FM, Jongeneel CV, Mulder N.

BMC Bioinformatics. 2018 Nov 29;19(1):457. doi: 10.1186/s12859-018-2446-1.

2.

Assessing computational genomics skills: Our experience in the H3ABioNet African bioinformatics network.

Jongeneel CV, Achinike-Oduaran O, Adebiyi E, Adebiyi M, Adeyemi S, Akanle B, Aron S, Ashano E, Bendou H, Botha G, Chimusa E, Choudhury A, Donthu R, Drnevich J, Falola O, Fields CJ, Hazelhurst S, Hendry L, Isewon I, Khetani RS, Kumuthini J, Kimuda MP, Magosi L, Mainzer LS, Maslamoney S, Mbiyavanga M, Meintjes A, Mugutso D, Mpangase P, Munthali R, Nembaware V, Ndhlovu A, Odia T, Okafor A, Oladipo O, Panji S, Pillay V, Rendon G, Sengupta D, Mulder N.

PLoS Comput Biol. 2017 Jun 1;13(6):e1005419. doi: 10.1371/journal.pcbi.1005419. eCollection 2017 Jun.

3.

H3ABioNet, a sustainable pan-African bioinformatics network for human heredity and health in Africa.

Mulder NJ, Adebiyi E, Alami R, Benkahla A, Brandful J, Doumbia S, Everett D, Fadlelmola FM, Gaboun F, Gaseitsiwe S, Ghazal H, Hazelhurst S, Hide W, Ibrahimi A, Jaufeerally Fakim Y, Jongeneel CV, Joubert F, Kassim S, Kayondo J, Kumuthini J, Lyantagaye S, Makani J, Mansour Alzohairy A, Masiga D, Moussa A, Nash O, Ouwe Missi Oukem-Boyer O, Owusu-Dabo E, Panji S, Patterton H, Radouani F, Sadki K, Seghrouchni F, Tastan Bishop Ö, Tiffin N, Ulenga N; H3ABioNet Consortium.

Genome Res. 2016 Feb;26(2):271-7. doi: 10.1101/gr.196295.115. Epub 2015 Dec 1.

4.

Identification and validation of copy number variants using SNP genotyping arrays from a large clinical cohort.

Valsesia A, Stevenson BJ, Waterworth D, Mooser V, Vollenweider P, Waeber G, Jongeneel CV, Beckmann JS, Kutalik Z, Bergmann S.

BMC Genomics. 2012 Jun 15;13:241. doi: 10.1186/1471-2164-13-241.

5.

Exome sequencing identifies recurrent somatic MAP2K1 and MAP2K2 mutations in melanoma.

Nikolaev SI, Rimoldi D, Iseli C, Valsesia A, Robyr D, Gehrig C, Harshman K, Guipponi M, Bukach O, Zoete V, Michielin O, Muehlethaler K, Speiser D, Beckmann JS, Xenarios I, Halazonetis TD, Jongeneel CV, Stevenson BJ, Antonarakis SE.

Nat Genet. 2011 Dec 25;44(2):133-9. doi: 10.1038/ng.1026.

PMID:
22197931
6.

Network-guided analysis of genes with altered somatic copy number and gene expression reveals pathways commonly perturbed in metastatic melanoma.

Valsesia A, Rimoldi D, Martinet D, Ibberson M, Benaglio P, Quadroni M, Waridel P, Gaillard M, Pidoux M, Rapin B, Rivolta C, Xenarios I, Simpson AJ, Antonarakis SE, Beckmann JS, Jongeneel CV, Iseli C, Stevenson BJ.

PLoS One. 2011 Apr 8;6(4):e18369. doi: 10.1371/journal.pone.0018369.

7.

Judging the Archon Genomics X PRIZE for whole human genome sequencing.

Kedes L, Liu E, Jongeneel CV, Sutton G.

Nat Genet. 2011 Mar;43(3):175. doi: 10.1038/ng0311-175. No abstract available.

PMID:
21350493
8.

EuroDia: a beta-cell gene expression resource.

Liechti R, Csárdi G, Bergmann S, Schütz F, Sengstag T, Boj SF, Servitja JM, Ferrer J, Van Lommel L, Schuit F, Klinger S, Thorens B, Naamane N, Eizirik DL, Marselli L, Bugliani M, Marchetti P, Lucas S, Holm C, Jongeneel CV, Xenarios I.

Database (Oxford). 2010 Oct 12;2010:baq024. doi: 10.1093/database/baq024.

9.

Genome-wide analysis of cancer/testis gene expression.

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.

Proc Natl Acad Sci U S A. 2008 Dec 23;105(51):20422-7. doi: 10.1073/pnas.0810777105. Epub 2008 Dec 16.

10.

Identification of tumor-associated antigens by large-scale analysis of genes expressed in human colorectal cancer.

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.

Cancer Immun. 2008 Jun 27;8:11.

11.

Vertebrate conserved non coding DNA regions have a high persistence length and a short persistence time.

Retelska D, Beaudoing E, Notredame C, Jongeneel CV, Bucher P.

BMC Genomics. 2007 Oct 31;8:398.

12.

Indexing strategies for rapid searches of short words in genome sequences.

Iseli C, Ambrosini G, Bucher P, Jongeneel CV.

PLoS One. 2007 Jun 27;2(6):e579.

13.

MyHits: improvements to an interactive resource for analyzing protein sequences.

Pagni M, Ioannidis V, Cerutti L, Zahn-Zabal M, Jongeneel CV, Hau J, Martin O, Kuznetsov D, Falquet L.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W433-7. Epub 2007 Jun 1.

14.

The M-Coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment methods.

Moretti S, Armougom F, Wallace IM, Higgins DG, Jongeneel CV, Notredame C.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W645-8. Epub 2007 May 25.

15.

Rapid evolution of cancer/testis genes on the X chromosome.

Stevenson BJ, Iseli C, Panji S, Zahn-Zabal M, Hide W, Old LJ, Simpson AJ, Jongeneel CV.

BMC Genomics. 2007 May 23;8:129.

16.

Establishment of the epithelial-specific transcriptome of normal and malignant human breast cells based on MPSS and array expression data.

Grigoriadis A, Mackay A, Reis-Filho JS, Steele D, Iseli C, Stevenson BJ, Jongeneel CV, Valgeirsson H, Fenwick K, Iravani M, Leao M, Simpson AJ, Strausberg RL, Jat PS, Ashworth A, Neville AM, O'Hare MJ.

Breast Cancer Res. 2006;8(5):R56.

17.

Similarities and differences of polyadenylation signals in human and fly.

Retelska D, Iseli C, Bucher P, Jongeneel CV, Naef F.

BMC Genomics. 2006 Jul 12;7:176.

18.

Identification of a new cancer/testis gene family, CT47, among expressed multicopy genes on the human X chromosome.

Chen YT, Iseli C, Venditti CA, Old LJ, Simpson AJ, Jongeneel CV.

Genes Chromosomes Cancer. 2006 Apr;45(4):392-400.

PMID:
16382448
19.

Gene expression variation and expression quantitative trait mapping of human chromosome 21 genes.

Deutsch S, Lyle R, Dermitzakis ET, Attar H, Subrahmanyan L, Gehrig C, Parand L, Gagnebin M, Rougemont J, Jongeneel CV, Antonarakis SE.

Hum Mol Genet. 2005 Dec 1;14(23):3741-9. Epub 2005 Oct 26.

PMID:
16251198
20.

Identification of CT46/HORMAD1, an immunogenic cancer/testis antigen encoding a putative meiosis-related protein.

Chen YT, Venditti CA, Theiler G, Stevenson BJ, Iseli C, Gure AO, Jongeneel CV, Old LJ, Simpson AJ.

Cancer Immun. 2005 Jul 7;5:9.

21.

An atlas of human gene expression from massively parallel signature sequencing (MPSS).

Jongeneel CV, Delorenzi M, Iseli C, Zhou D, Haudenschild CD, Khrebtukova I, Kuznetsov D, Stevenson BJ, Strausberg RL, Simpson AJ, Vasicek TJ.

Genome Res. 2005 Jul;15(7):1007-14.

22.

Identification of cancer/testis-antigen genes by massively parallel signature sequencing.

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.

Proc Natl Acad Sci U S A. 2005 May 31;102(22):7940-5. Epub 2005 May 19.

23.

Rapid and selective surveillance of Arabidopsis thaliana genome annotations with Centrifuge.

Armand F, Bucher P, Jongeneel CV, Farmer EE.

Bioinformatics. 2005 Jun 15;21(12):2906-8. Epub 2005 Apr 7.

PMID:
15817689
24.

Identification of the gonad-specific anion transporter SLCO6A1 as a cancer/testis (CT) antigen expressed in human lung cancer.

Lee SY, Williamson B, Caballero OL, Chen YT, Scanlan MJ, Ritter G, Jongeneel CV, Simpson AJ, Old LJ.

Cancer Immun. 2004 Nov 17;4:13.

25.

MyHits: a new interactive resource for protein annotation and domain identification.

Pagni M, Ioannidis V, Cerutti L, Zahn-Zabal M, Jongeneel CV, Falquet L.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W332-5.

26.

Digital expression profiles of human endogenous retroviral families in normal and cancerous tissues.

Stauffer Y, Theiler G, Sperisen P, Lebedev Y, Jongeneel CV.

Cancer Immun. 2004 Feb 11;4:2.

27.

trome, trEST and trGEN: databases of predicted protein sequences.

Sperisen P, Iseli C, Pagni M, Stevenson BJ, Bucher P, Jongeneel CV.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D509-11.

28.

The generation and utilization of a cancer-oriented representation of the human transcriptome by using expressed sequence tags.

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, Acencio ML, Bengtson MH, Bettoni F, Bodmer WF, Briones MR, Camargo LP, Cavenee W, Cerutti JM, Coelho Andrade LE, Costa dos Santos PC, Ramos Costa MC, da Silva IT, Estécio MR, Sa Ferreira K, Furnari FB, Faria M Jr, Galante PA, Guimaraes GS, Holanda AJ, Kimura ET, Leerkes MR, Lu X, Maciel RM, Martins EA, Massirer KB, Melo AS, Mestriner CA, Miracca EC, Miranda LL, Nobrega FG, Oliveira PS, Paquola AC, Pandolfi JR, Campos Pardini MI, Passetti F, Quackenbush J, Schnabel B, Sogayar MC, Souza JE, Valentini SR, Zaiats AC, Amaral EJ, Arnaldi LA, de Araújo AG, de Bessa SA, Bicknell DC, Ribeiro de Camaro ME, Carraro DM, Carrer H, Carvalho AF, Colin C, Costa F, Curcio C, Guerreiro da Silva ID, Pereira da Silva N, Dellamano M, El-Dorry H, Espreafico EM, Scattone Ferreira AJ, Ayres Ferreira C, Fortes MA, Gama AH, Giannella-Neto D, Giannella ML, Giorgi RR, Goldman GH, Goldman MH, Hackel C, Ho PL, Kimura EM, Kowalski LP, Krieger JE, Leite LC, Lopes A, Luna AM, Mackay A, Mari SK, Marques AA, Martins WK, Montagnini A, Mourão Neto M, Nascimento AL, Neville AM, Nobrega MP, O'Hare MJ, Otsuka AY, Ruas de Melo AI, Paco-Larson ML, Guimarães Pereira G, Pereira da Silva N, Pesquero JB, Pessoa JG, Rahal P, Rainho CA, Rodrigues V, Rogatto SR, Romano CM, Romeiro JG, Rossi BM, Rusticci M, Guerra de Sá R, Sant' Anna SC, Sarmazo ML, Silva TC, Soares FA, Sonati Mde F, de Freitas Sousa J, Queiroz D, Valente V, Vettore AL, Villanova FE, Zago MA, Zalcberg H; Human Cancer Genome Project/Cancer Genome Anatomy Project Annotation Consortium; Human Cancer Genome Project Sequencing Consortium.

Proc Natl Acad Sci U S A. 2003 Nov 11;100(23):13418-23. Epub 2003 Oct 30.

29.

Modeling sequencing errors by combining Hidden Markov models.

Lottaz C, Iseli C, Jongeneel CV, Bucher P.

Bioinformatics. 2003 Oct;19 Suppl 2:ii103-12.

PMID:
14534179
30.

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.

Favre M, Butticaz C, Stevenson B, Jongeneel CV, Telenti A.

J Acquir Immune Defic Syndr. 2003 Oct 1;34(2):127-33.

PMID:
14526201
31.

Swiss EMBnet node web server.

Falquet L, Bordoli L, Ioannidis V, Pagni M, Jongeneel CV.

Nucleic Acids Res. 2003 Jul 1;31(13):3782-3.

32.

Identification of 9 novel transcripts and two RGSL genes within the hereditary prostate cancer region (HPC1) at 1q25.

Silva AP, Salim AC, Bulgarelli A, de Souza JE, Osório E, Caballero OL, Iseli C, Stevenson BJ, Jongeneel CV, de Souza SJ, Simpson AJ, Camargo AA.

Gene. 2003 May 22;310:49-57.

PMID:
12801632
33.

eVOC: a controlled vocabulary for unifying gene expression data.

Kelso J, Visagie J, Theiler G, Christoffels A, Bardien S, Smedley D, Otgaar D, Greyling G, Jongeneel CV, McCarthy MI, Hide T, Hide W.

Genome Res. 2003 Jun;13(6A):1222-30.

34.

Use of transcriptome data to unravel the fine structure of genes involved in sepsis.

Stevenson BJ, Iseli C, Beutler B, Jongeneel CV.

J Infect Dis. 2003 Jun 15;187 Suppl 2:S308-14.

PMID:
12792844
35.

Comprehensive sampling of gene expression in human cell lines with massively parallel signature sequencing.

Jongeneel CV, Iseli C, Stevenson BJ, Riggins GJ, Lal A, Mackay A, Harris RA, O'Hare MJ, Neville AM, Simpson AJ, Strausberg RL.

Proc Natl Acad Sci U S A. 2003 Apr 15;100(8):4702-5. Epub 2003 Apr 1.

36.

Numerous potentially functional but non-genic conserved sequences on human chromosome 21.

Dermitzakis ET, Reymond A, Lyle R, Scamuffa N, Ucla C, Deutsch S, Stevenson BJ, Flegel V, Bucher P, Jongeneel CV, Antonarakis SE.

Nature. 2002 Dec 5;420(6915):578-82.

PMID:
12466853
37.

Long-range heterogeneity at the 3' ends of human mRNAs.

Iseli C, Stevenson BJ, de Souza SJ, Samaia HB, Camargo AA, Buetow KH, Strausberg RL, Simpson AJ, Bucher P, Jongeneel CV.

Genome Res. 2002 Jul;12(7):1068-74.

38.

Nineteen additional unpredicted transcripts from human chromosome 21.

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.

Genomics. 2002 Jun;79(6):824-32.

PMID:
12036297
39.

Searching the expressed sequence tag (EST) databases: panning for genes.

Jongeneel CV.

Brief Bioinform. 2000 Feb;1(1):76-92.

PMID:
11466975
40.

Making sense of score statistics for sequence alignments.

Pagni M, Jongeneel CV.

Brief Bioinform. 2001 Mar;2(1):51-67.

PMID:
11465063
41.

Cloning and characterization of TNKL, a member of tankyrase gene family.

Kuimov AN, Kuprash DV, Petrov VN, Vdovichenko KK, Scanlan MJ, Jongeneel CV, Lagarkova MA, Nedospasov SA.

Genes Immun. 2001 Feb;2(1):52-5.

42.

The need for a human gene index.

Jongeneel CV.

Bioinformatics. 2000 Dec;16(12):1059-61. No abstract available.

PMID:
11159324
43.

ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences.

Iseli C, Jongeneel CV, Bucher P.

Proc Int Conf Intell Syst Mol Biol. 1999:138-48.

PMID:
10786296
44.

Shotgun sequencing of the human transcriptome with ORF expressed sequence tags.

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.

Proc Natl Acad Sci U S A. 2000 Mar 28;97(7):3491-6.

45.

Genomic organization and chromosomal localization of the mouse lipopolysaccharide binding protein gene.

Lengacher S, Reed D, Heumann D, Jongeneel CV.

Immunogenetics. 1999 Jun;49(6):553-6. No abstract available.

PMID:
10380702
46.
47.
48.

Analysis of active site residues of the antiviral protein from summer leaves from Phytolacca americana by site-directed mutagenesis.

Poyet JL, Hoeveler A, Jongeneel CV.

Biochem Biophys Res Commun. 1998 Dec 30;253(3):582-7.

PMID:
9918771
49.

Survival-independent function of NF-kappaB/Rel during late stages of thymocyte differentiation.

Esslinger CW, Jongeneel CV, MacDonald HR.

Mol Immunol. 1998 Sep;35(13):847-52.

PMID:
9839553
50.

The pathogenic role of LBP in gram-negative sepsis and septic shock.

Heumann D, Lengacher S, Le Roy D, Jongeneel CV, Glauser MP.

Prog Clin Biol Res. 1998;397:379-86. Review. No abstract available.

PMID:
9575578

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