C Victor Jongeneel
- 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...
- Comprehensive sampling of gene expression in human cell lines with massively parallel signature sequencingC 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....
- trome, trEST and trGEN: databases of predicted protein sequencesPeter 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...
- Digital expression profiles of human endogenous retroviral families in normal and cancerous tissuesYves Stauffer
Ludwig Institute for Cancer Research, Office of Information Technology, Epalinges, Switzerland
Cancer Immun 4:2. 2004..This study shows that HERV families are more widely expressed than originally thought and that some members of the HERV-K and -H families could encode targets for cancer immunotherapy...
- Identification of tumor-associated antigens by large-scale analysis of genes expressed in human colorectal cancerPedro 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...
- Use of transcriptome data to unravel the fine structure of genes involved in sepsisBrian 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...
- Long-range heterogeneity at the 3' ends of human mRNAsChristian Iseli
Office of Information Technology, Ludwig Institute for Cancer Research, Switzerland
Genome Res 12:1068-74. 2002....
- Establishment of the epithelial-specific transcriptome of normal and malignant human breast cells based on MPSS and array expression dataAnita 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....
- Rapid evolution of cancer/testis genes on the X chromosomeBrian 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...
- Identification of a new cancer/testis gene family, CT47, among expressed multicopy genes on the human X chromosomeYao Tseng Chen
Weill Medical College of Cornell University, New York, New York 10021, USA
Genes Chromosomes Cancer 45:392-400. 2006..The only species other than human in which a gene homologous to CT47 has been detected is the chimpanzee, with the predicted protein showing approximately 80% identity in its carboxy terminal region...
- Gene expression variation and expression quantitative trait mapping of human chromosome 21 genesSamuel Deutsch
Department of Genetic Medicine and Development, Geneva University Medical School, Geneva, Switzerland
Hum Mol Genet 14:3741-9. 2005..5-fold in control samples, are unlikely to be involved in DS-phenotypes present in all affected individuals...
- Similarities and differences of polyadenylation signals in human and flyDorota Retelska
Swiss Institute of Bioinformatics, Batiment Genopode, UNIL, 1015 Lausanne, Switzerland
BMC Genomics 7:176. 2006..The signal recognized by the cleavage enzyme complex has been characterized as an A rich region upstream of the cleavage site containing a motif with consensus AAUAAA, followed by a U or UG rich region downstream of the cleavage site...
- Identification of cancer/testis-antigen genes by massively parallel signature sequencingYao 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...
- Rapid and selective surveillance of Arabidopsis thaliana genome annotations with CentrifugeFlorence Armand
Gene Expression Laboratory, Plant Molecular Biology, University of Lausanne, Biology Building, 1015 Lausanne, Switzerland
Bioinformatics 21:2906-8. 2005..In these cases, a summary table of principal predicted protein features for all genes is given followed by more detailed reports for each individual gene. Centrifuge can also be used for single gene analysis or in a word search mode...
- The generation and utilization of a cancer-oriented representation of the human transcriptome by using expressed sequence tagsHelena 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....
- Identification of 9 novel transcripts and two RGSL genes within the hereditary prostate cancer region (HPC1) at 1q25Ana 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...
- eVOC: a controlled vocabulary for unifying gene expression dataJanet Kelso
South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa
Genome Res 13:1222-30. 2003..Both the vocabularies and the vocabulary-annotated libraries can be retrieved from http://www.sanbi.ac.za/evoc/. Several groups are involved in developing this resource with the aim of unifying transcript expression information...
- Nineteen additional unpredicted transcripts from human chromosome 21Alexandre Reymond
Division of Medical Genetics, University of Geneva Medical School, 1211 Geneva, Switzerland
Genomics 79:824-32. 2002....