Fabien Campagne

Summary

Affiliation: Cornell University
Country: USA

Publications

  1. pmc Mining expressed sequence tags identifies cancer markers of clinical interest
    Fabien Campagne
    Institute for Computational Biomedicine and Dept of Physiology and Biophysics, Weill Medical College of Cornell University, New York, NY 10021, USA
    BMC Bioinformatics 7:481. 2006
  2. pmc Objective and automated protocols for the evaluation of biomedical search engines using No Title Evaluation protocols
    Fabien Campagne
    HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY 10021, USA
    BMC Bioinformatics 9:132. 2008
  3. ncbi request reprint Quantitative information management for the biochemical computation of cellular networks
    Fabien Campagne
    Department of Physiology and Biophysics and Institute for Computational Biomedicine, Weill Medical College of Cornell University, New York, NY, 10021, USA
    Sci STKE 2004:pl11. 2004
  4. pmc Building a protein name dictionary from full text: a machine learning term extraction approach
    Lei Shi
    Institute for Computational Biomedicine, Dept of Physiology and Biophysics, Weill Cornell Medical College, 1300 York Ave, New York, NY 10021, USA
    BMC Bioinformatics 6:88. 2005
  5. pmc Critical evaluation of the JDO API for the persistence and portability requirements of complex biological databases
    Marko Srdanovic
    Weill Cornell Medical College, 1300 York Ave, New York, NY 10021, USA
    BMC Bioinformatics 6:5. 2005
  6. pmc Beyond tissueInfo: functional prediction using tissue expression profile similarity searches
    Daniel Aguilar
    HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Medical College of Cornell University, 1305 York Ave, New York, NY 10021, USA
    Nucleic Acids Res 36:3728-37. 2008
  7. pmc GPCR-OKB: the G Protein Coupled Receptor Oligomer Knowledge Base
    George Khelashvili
    Department of Physiology and Biophysics, Weill Medical College of Cornell University, New York, NY, USA
    Bioinformatics 26:1804-5. 2010
  8. pmc Requirements and ontology for a G protein-coupled receptor oligomerization knowledge base
    Lucy Skrabanek
    Department of Physiology and Biophysics, Weill Medical College of Cornell University, New York, NY, USA
    BMC Bioinformatics 8:177. 2007
  9. ncbi request reprint Batch mode generation of residue-based diagrams of proteins
    Fabien Campagne
    Institute for Computational Biomedicine and Department of Physiology and Biophysics, Mount Sinai School of Medicine, Box 1218, New York, NY 10029, USA
    Bioinformatics 19:1854-5. 2003
  10. pmc BDVal: reproducible large-scale predictive model development and validation in high-throughput datasets
    Kevin C Dorff
    Department of Physiology and Biophysics, Weill Medical College of Cornell University, New York, NY, USA
    Bioinformatics 26:2472-3. 2010

Collaborators

Detail Information

Publications24

  1. pmc Mining expressed sequence tags identifies cancer markers of clinical interest
    Fabien Campagne
    Institute for Computational Biomedicine and Dept of Physiology and Biophysics, Weill Medical College of Cornell University, New York, NY 10021, USA
    BMC Bioinformatics 7:481. 2006
    ..Gene expression data are a rich source of information about the transcriptional dis-regulation of genes in cancer. Genes that display differential regulation in cancer are a subtype of cancer biomarkers...
  2. pmc Objective and automated protocols for the evaluation of biomedical search engines using No Title Evaluation protocols
    Fabien Campagne
    HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY 10021, USA
    BMC Bioinformatics 9:132. 2008
    ..The TREC Genomics Track has recently been introduced to measure the performance of information retrieval for biomedical applications...
  3. ncbi request reprint Quantitative information management for the biochemical computation of cellular networks
    Fabien Campagne
    Department of Physiology and Biophysics and Institute for Computational Biomedicine, Weill Medical College of Cornell University, New York, NY, 10021, USA
    Sci STKE 2004:pl11. 2004
    ..We anticipate that, when appropriately populated, such a system will be useful for large-scale quantitative studies of cell-signaling networks and other cellular networks. SigPath is distributed under the GNU General Public License...
  4. pmc Building a protein name dictionary from full text: a machine learning term extraction approach
    Lei Shi
    Institute for Computational Biomedicine, Dept of Physiology and Biophysics, Weill Cornell Medical College, 1300 York Ave, New York, NY 10021, USA
    BMC Bioinformatics 6:88. 2005
    ..This is a limitation, because such databases have low coverage of the many name variants which are used to refer to biological entities in the literature...
  5. pmc Critical evaluation of the JDO API for the persistence and portability requirements of complex biological databases
    Marko Srdanovic
    Weill Cornell Medical College, 1300 York Ave, New York, NY 10021, USA
    BMC Bioinformatics 6:5. 2005
    ..SigPath is an example of a complex biological database that needs to store various types of information connected by many relationships...
  6. pmc Beyond tissueInfo: functional prediction using tissue expression profile similarity searches
    Daniel Aguilar
    HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Medical College of Cornell University, 1305 York Ave, New York, NY 10021, USA
    Nucleic Acids Res 36:3728-37. 2008
    ..Since the approach does not use sequence similarity, we expect that TEPSS will be useful for various gene discovery applications. TEPSS programs and data are distributed at http://icb.med.cornell.edu/crt/tepss/index.xml...
  7. pmc GPCR-OKB: the G Protein Coupled Receptor Oligomer Knowledge Base
    George Khelashvili
    Department of Physiology and Biophysics, Weill Medical College of Cornell University, New York, NY, USA
    Bioinformatics 26:1804-5. 2010
    ..Availability and Implementation: The GPCR-OKB web application is freely available at http://www.gpcr-okb.org..
  8. pmc Requirements and ontology for a G protein-coupled receptor oligomerization knowledge base
    Lucy Skrabanek
    Department of Physiology and Biophysics, Weill Medical College of Cornell University, New York, NY, USA
    BMC Bioinformatics 8:177. 2007
    ....
  9. ncbi request reprint Batch mode generation of residue-based diagrams of proteins
    Fabien Campagne
    Institute for Computational Biomedicine and Department of Physiology and Biophysics, Mount Sinai School of Medicine, Box 1218, New York, NY 10029, USA
    Bioinformatics 19:1854-5. 2003
    ....
  10. pmc BDVal: reproducible large-scale predictive model development and validation in high-throughput datasets
    Kevin C Dorff
    Department of Physiology and Biophysics, Weill Medical College of Cornell University, New York, NY, USA
    Bioinformatics 26:2472-3. 2010
    ..AVAILABILITY AND IMPLEMENTATION: The BDVal programs are implemented in Java, provided under the GNU General Public License and freely available at http://bdval.campagnelab.org...
  11. pmc Crooked tail (Cd) model of human folate-responsive neural tube defects is mutated in Wnt coreceptor lipoprotein receptor-related protein 6
    Michelle Carter
    Department of Neurology, Weill Medical College of Cornell University, New York, NY 10021, USA
    Proc Natl Acad Sci U S A 102:12843-8. 2005
    ..The Lrp6 mutation in Cd mice provides evidence for a functional connection between Wnt signaling and folate rescue of neural tube defects...
  12. pmc SNOSID, a proteomic method for identification of cysteine S-nitrosylation sites in complex protein mixtures
    Gang Hao
    Department of Pharmacology, Weill Medical College of Cornell University, 1300 York Avenue, New York, NY 10021, USA
    Proc Natl Acad Sci U S A 103:1012-7. 2006
    ..SNOSID provides the first effective tool for unbiased elucidation of the SNO proteome, identifying Cys residues that undergo reversible S-nitrosylation...
  13. ncbi request reprint Gene expression profiling separates chromophobe renal cell carcinoma from oncocytoma and identifies vesicular transport and cell junction proteins as differentially expressed genes
    Stephen Rohan
    Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, New York, New York 10021, USA
    Clin Cancer Res 12:6937-45. 2006
    ..To compare gene expression profiles of chromophobe renal cell carcinoma (RCC) and benign oncocytoma, aiming at identifying differentially expressed genes...
  14. pmc GobyWeb: Simplified Management and Analysis of Gene Expression and DNA Methylation Sequencing Data
    Kevin C Dorff
    The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, the Weill Cornell Medical College, New York, New York, United States of America
    PLoS ONE 8:e69666. 2013
    ..GobyWeb plugins are distributed in source code and licensed under the open source LGPL3 license to facilitate code inspection, reuse and independent extensions http://github.com/CampagneLaboratory/gobyweb2-plugins. ..
  15. pmc CALHM1 P86L polymorphism modulates CSF Aβ levels in cognitively healthy individuals at risk for Alzheimer's disease
    Jeremy Koppel
    Litwin Zucker Research Center for the Study of Alzheimer s Disease, The Feinstein Institute for Medical Research, Manhasset, New York, USA
    Mol Med 17:974-9. 2011
    ..These data further demonstrate the utility of endophenotype-based approaches focusing on CSF biomarkers for the identification or validation of risk factors for AD...
  16. doi request reprint Introduction to the development and validation of predictive biomarker models from high-throughput data sets
    Xutao Deng
    HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Medical College of Cornell University, New York, NY, USA
    Methods Mol Biol 620:435-70. 2010
    ..This example leverages BDVal, a suite of biomarker model development programs developed as an open-source project (see http://bdval.org /)...
  17. pmc Building protein diagrams on the web with the residue-based diagram editor RbDe
    Lucy Skrabanek
    Mount Sinai School of Medicine, Institute for Computational Biomedicine and Department of Physiology and Biophysics, New York, NY, USA
    Nucleic Acids Res 31:3856-8. 2003
    ..Users can now import custom-diagram layouts, use them to render members of any protein family and generate high-quality output for publication purposes. RbDe is available free over the web, at http://icb.mssm.edu/crt/RbDe..
  18. pmc DNA methylation signatures identify biologically distinct subtypes in acute myeloid leukemia
    Maria E Figueroa
    Department of Medicine, Hematology Oncology Division, Weill Cornell Medical College, New York, NY 10065, USA
    Cancer Cell 17:13-27. 2010
    ..We report a 15 gene methylation classifier predictive of overall survival in an independent patient cohort (p < 0.001, adjusted for known covariates)...
  19. pmc Characterization of the mouse adeno-associated virus AAVS1 ortholog
    Nathalie Dutheil
    Carl C Icahn Institute for Gene Therapy and Molecular Medicine, Mount Sinai School of Medicine, One Gustave L Levy Pl, Box 1496, New York, NY 10029, USA
    J Virol 78:8917-21. 2004
    ..Furthermore, these signals can serve as a minimal origin for Rep-dependent DNA replication. In addition, we isolated the mouse Mbs85 proximal promoter and show transcriptional activity in three mouse cell lines...
  20. pmc Pseudomonas aeruginosa SoxR does not conform to the archetypal paradigm for SoxR-dependent regulation of the bacterial oxidative stress adaptive response
    Marco Palma
    Microbiology and Immunology, Medical College of Cornell University, 1300 York Avenue, Box 62, W 706, New York, NY 10021, USA
    Infect Immun 73:2958-66. 2005
    ..These results demonstrate that the E. coli-based SoxRS paradigm does not hold in P. aeruginosa and foster new hypotheses for the possible physiological role of P. aeruginosa SoxR...
  21. pmc GPCRDB information system for G protein-coupled receptors
    Florence Horn
    Department of Cellular and Molecular Pharmacology, UCSF, San Francisco, California, USA
    Nucleic Acids Res 31:294-7. 2003
    ..The GPCRDB is updated automatically once every 4-5 months and is freely accessible at http://www.gpcr.org/7tm/...
  22. ncbi request reprint Minimum information requested in the annotation of biochemical models (MIRIAM)
    Nicolas Le Novère
    European Bioinformatics Institute, Hinxton, CB10 1SD, UK
    Nat Biotechnol 23:1509-15. 2005
    ....
  23. ncbi request reprint Interoperability calls for an unusual mix of skills
    Fabien Campagne
    Nature 418:125. 2002
  24. pmc A polymorphism in CALHM1 influences Ca2+ homeostasis, Abeta levels, and Alzheimer's disease risk
    Ute Dreses-Werringloer
    Litwin Zucker Research Center for the Study of Alzheimer s Disease, The Feinstein Institute for Medical Research, North Shore LIJ, Manhasset, NY 11030, USA
    Cell 133:1149-61. 2008
    ..We propose that CALHM1 encodes an essential component of a previously uncharacterized cerebral Ca(2+) channel that controls Abeta levels and susceptibility to late-onset AD...