Brian J Stevenson

Summary

Affiliation: Ludwig Institute for Cancer Research
Country: Belgium

Publications

  1. pmc AssociationViewer: a scalable and integrated software tool for visualization of large-scale variation data in genomic context
    Olivier Martin
    Swiss Institute of Bioinformatics, Switzerland
    Bioinformatics 25:662-3. 2009
  2. pmc Establishment of the epithelial-specific transcriptome of normal and malignant human breast cells based on MPSS and array expression data
    Anita Grigoriadis
    Ludwig Institute for Cancer Research University College London Breast Cancer Laboratory, 91 Riding House Street, London, W1W 7BS, UK
    Breast Cancer Res 8:R56. 2006
  3. pmc Rapid evolution of cancer/testis genes on the X chromosome
    Brian J Stevenson
    Ludwig Institute for Cancer Research and Swiss Institute of Bioinformatics, Lausanne, Switzerland
    BMC Genomics 8:129. 2007
  4. pmc An atlas of human gene expression from massively parallel signature sequencing (MPSS)
    C Victor Jongeneel
    Office of Information Technology, Ludwig Institute for Cancer Research, and Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
    Genome Res 15:1007-14. 2005
  5. pmc Identification of cancer/testis-antigen genes by massively parallel signature sequencing
    Yao Tseng Chen
    Weill Medical College of Cornell University, New York, NY 10021, USA
    Proc Natl Acad Sci U S A 102:7940-5. 2005
  6. pmc Comprehensive sampling of gene expression in human cell lines with massively parallel signature sequencing
    C Victor Jongeneel
    Office of Information Technology, Ludwig Institute for Cancer Research, and Swiss Institute of Bioinformatics, 1066 Epalinges, Switzerland
    Proc Natl Acad Sci U S A 100:4702-5. 2003
  7. ncbi Nineteen additional unpredicted transcripts from human chromosome 21
    Alexandre Reymond
    Division of Medical Genetics, University of Geneva Medical School, 1211 Geneva, Switzerland
    Genomics 79:824-32. 2002
  8. pmc The generation and utilization of a cancer-oriented representation of the human transcriptome by using expressed sequence tags
    Helena Brentani
    Laboratório de Genética Molecular do Câncer, Departmento de Radiologia, Universidade de Sao Paulo, Travessa da Rua Dr Ovídeo Pires de Campos S N, 4deg, Brazil
    Proc Natl Acad Sci U S A 100:13418-23. 2003
  9. pmc trome, trEST and trGEN: databases of predicted protein sequences
    Peter Sperisen
    Swiss Institute of Bioinformatics, Ludwig Institute for Cancer Research, Chemin des Boveresses 155, 1066 Epalinges s Lausanne, Switzerland
    Nucleic Acids Res 32:D509-11. 2004
  10. ncbi Identification of 9 novel transcripts and two RGSL genes within the hereditary prostate cancer region (HPC1) at 1q25
    Ana Paula M Silva
    Ludwig Institute for Cancer Research, Rua Antonio Prudente 109, 4th Floor, 01509 010, Sao Paulo, SP, Brazil
    Gene 310:49-57. 2003

Collaborators

  • C Victor Jongeneel
  • A J G Simpson
  • R L Strausberg
  • Yao Tseng Chen
  • J Quackenbush
  • Alan Ashworth
  • Xin Lu
  • Pedro A F Galante
  • Sandro J de Souza
  • Daniel E Speiser
  • Peter Sperisen
  • S E Antonarakis
  • Sergio Verjovski-Almeida
  • Ali O Gure
  • M J Scanlan
  • Jorge S Reis-Filho
  • BRUCE A BEUTLER
  • Maria Aparecida Nagai
  • Emmanouil T Dermitzakis
  • Christian Iseli
  • Olivier Martin
  • Anamaria A Camargo
  • Pedro M S Alves
  • Anita Grigoriadis
  • Alan Mackay
  • A Munro Neville
  • Ana Paula M Silva
  • Otavia L Caballero
  • Helena Brentani
  • Fabiana Bettoni
  • Alexandre Reymond
  • Armand Valsesia
  • Ioannis Xenarios
  • Amalio Telenti
  • Sebastien Viatte
  • Frédéric Lévy
  • Henri Vuilleumier
  • Jean Claude R Givel
  • Pedro J Romero
  • Gabriel Bricard
  • Donata Rimoldi
  • Gregory Theiler
  • Hanifa Bouzourene
  • Nicole Lévy
  • Maha Ayyoub
  • Haukur Valgeirsson
  • Michael J O'Hare
  • Dawn Steele
  • Maria Leao
  • Kerry Fenwick
  • Parmjit S Jat
  • Marjan Iravani
  • Pedro Edson Moreira Guimaraes
  • Jose E Krieger
  • Alex F Carvalho
  • Mike J O'Hare
  • Elisabete Cristina Miracca
  • Andre Luiz Vettore
  • Webster Cavenee
  • Apua C M Paquola
  • Jorge Estefano S de Souza
  • Maria Lúcia C C Giannella
  • Francisco G Nobrega
  • Helaine Carrer
  • Ana Mercedes S C Luna
  • Andre Montagnini
  • Eloiza H Tajara
  • Dirce Maria Carraro
  • Frank B Furnari
  • Luiz Paulo Kowalski
  • Monica Rusticci
  • Miriam L Sarmazo
  • Fabio Passetti
  • Israel Tojal da Silva
  • Diana Queiroz
  • Maarten R Leerkes
  • Marcelo R S Briones
  • Maria Angela H Z Fortes
  • Gustavo S Guimaraes
  • Anna Izabel Ruas de Melo
  • Márcia Dellamano
  • Audrey Yumi Otsuka
  • Aline M da Silva
  • Suely Kazue Nagahashi Mari
  • Cristiane Ayres Ferreira
  • Elisabete Jorge Amaral
  • Eduardo M R Reis
  • David C Bicknell
  • Hamza El-Dorry
  • Elisson Osório

Detail Information

Publications14

  1. pmc AssociationViewer: a scalable and integrated software tool for visualization of large-scale variation data in genomic context
    Olivier Martin
    Swiss Institute of Bioinformatics, Switzerland
    Bioinformatics 25:662-3. 2009
    ..AssociationViewer integrates functionalities that enable the aggregation or intersection of data tracks. It implements an efficient cache system and allows the display of several, very large-scale genomic datasets...
  2. pmc Establishment of the epithelial-specific transcriptome of normal and malignant human breast cells based on MPSS and array expression data
    Anita Grigoriadis
    Ludwig Institute for Cancer Research University College London Breast Cancer Laboratory, 91 Riding House Street, London, W1W 7BS, UK
    Breast Cancer Res 8:R56. 2006
    ....
  3. pmc Rapid evolution of cancer/testis genes on the X chromosome
    Brian J Stevenson
    Ludwig Institute for Cancer Research and Swiss Institute of Bioinformatics, Lausanne, Switzerland
    BMC Genomics 8:129. 2007
    ..While it has been shown that some CT genes are under diversifying selection, this question has not been addressed before for the class as a whole...
  4. pmc An atlas of human gene expression from massively parallel signature sequencing (MPSS)
    C Victor Jongeneel
    Office of Information Technology, Ludwig Institute for Cancer Research, and Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
    Genome Res 15:1007-14. 2005
    ..The data are available on the Web at http://mpss.licr.org and http://sgb.lynxgen.com...
  5. pmc Identification of cancer/testis-antigen genes by massively parallel signature sequencing
    Yao Tseng Chen
    Weill Medical College of Cornell University, New York, NY 10021, USA
    Proc Natl Acad Sci U S A 102:7940-5. 2005
    ..Thus, MPSS analysis has resulted in a significant extension of our knowledge of CT antigens, leading to the discovery of a distinctive X-linked CT-antigen gene family...
  6. pmc Comprehensive sampling of gene expression in human cell lines with massively parallel signature sequencing
    C Victor Jongeneel
    Office of Information Technology, Ludwig Institute for Cancer Research, and Swiss Institute of Bioinformatics, 1066 Epalinges, Switzerland
    Proc Natl Acad Sci U S A 100:4702-5. 2003
    ....
  7. ncbi Nineteen additional unpredicted transcripts from human chromosome 21
    Alexandre Reymond
    Division of Medical Genetics, University of Geneva Medical School, 1211 Geneva, Switzerland
    Genomics 79:824-32. 2002
    ....
  8. pmc The generation and utilization of a cancer-oriented representation of the human transcriptome by using expressed sequence tags
    Helena Brentani
    Laboratório de Genética Molecular do Câncer, Departmento de Radiologia, Universidade de Sao Paulo, Travessa da Rua Dr Ovídeo Pires de Campos S N, 4deg, Brazil
    Proc Natl Acad Sci U S A 100:13418-23. 2003
    ....
  9. pmc trome, trEST and trGEN: databases of predicted protein sequences
    Peter Sperisen
    Swiss Institute of Bioinformatics, Ludwig Institute for Cancer Research, Chemin des Boveresses 155, 1066 Epalinges s Lausanne, Switzerland
    Nucleic Acids Res 32:D509-11. 2004
    ..These new databases are in a Swiss-Prot-like format and are updated on a weekly basis (trEST and trGEN) or every 3 months (trome). They can be downloaded by anonymous ftp from ftp://ftp.isrec.isb-sib.ch/pub/databases...
  10. ncbi Identification of 9 novel transcripts and two RGSL genes within the hereditary prostate cancer region (HPC1) at 1q25
    Ana Paula M Silva
    Ludwig Institute for Cancer Research, Rua Antonio Prudente 109, 4th Floor, 01509 010, Sao Paulo, SP, Brazil
    Gene 310:49-57. 2003
    ..RGSL1 and RGLS2 expression was detected by real-time polymerase chain reaction in normal prostate tissue, but could not be detected in prostate tumor cell lines, suggesting they might have a role in prostate cancer...
  11. ncbi Use of transcriptome data to unravel the fine structure of genes involved in sepsis
    Brian J Stevenson
    Office of Information Technology, Ludwig Institute for Cancer Research, and Swiss Institute of Bioinformatics, Epalinges, Switzerland
    J Infect Dis 187:S308-14. 2003
    ..These findings have implications for the analysis of TLR gene expression and for the diversity of the proteins encoded by these genes...
  12. ncbi Identification of CT46/HORMAD1, an immunogenic cancer/testis antigen encoding a putative meiosis-related protein
    Yao Tseng Chen
    Weill Medical College, Cornell University, New York, NY 10021, USA
    Cancer Immun 5:9. 2005
    ..The CT46/HORMAD1 protein was found to be homologous to the prototype HORMA domain-containing protein, Hop1, a yeast meiosis-specific protein, as well as to asy1, a meiotic synaptic mutant protein in Arabidopsis thaliana...
  13. ncbi Numerous potentially functional but non-genic conserved sequences on human chromosome 21
    Emmanouil T Dermitzakis
    Division of Medical Genetics, 1 rue Michel Servet, University of Geneva Medical School and University Hospitals of Geneva, CH 1211 Geneva, Switzerland
    Nature 420:578-82. 2002
    ....
  14. pmc Identification of tumor-associated antigens by large-scale analysis of genes expressed in human colorectal cancer
    Pedro M S Alves
    National Center of Competence in Research, Molecular Oncology, ISREC, Ch des Boveresses 155, 1066 Epalinges, Switzerland
    Cancer Immun 8:11. 2008
    ..Our data suggest that this sequence should be considered as a target of immunological interventions against colorectal cancer...