Research Topics
Genomes and Genes | Fabien CampagneSummaryAffiliation: Cornell University Country: USA Publications
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Publications
Mining expressed sequence tags identifies cancer markers of clinical interestFabien 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...- Objective and automated protocols for the evaluation of biomedical search engines using No Title Evaluation protocolsFabien 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... 
Quantitative information management for the biochemical computation of cellular networksFabien 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...- Building a protein name dictionary from full text: a machine learning term extraction approachLei 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... - Critical evaluation of the JDO API for the persistence and portability requirements of complex biological databasesMarko 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... - Beyond tissueInfo: functional prediction using tissue expression profile similarity searchesDaniel 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... - GPCR-OKB: the G Protein Coupled Receptor Oligomer Knowledge BaseGeorge 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.. - Requirements and ontology for a G protein-coupled receptor oligomerization knowledge baseLucy Skrabanek
Department of Physiology and Biophysics, Weill Medical College of Cornell University, New York, NY, USA
BMC Bioinformatics 8:177. 2007.... - Batch mode generation of residue-based diagrams of proteinsFabien 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..AVAILABILITY: Licensed. Royalty free licenses are granted to non-profit institutions for educational and research purposes. http://icb.mssm.edu/crt/RbDg/index.xml.. - BDVal: reproducible large-scale predictive model development and validation in high-throughput datasetsKevin 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... - Crooked tail (Cd) model of human folate-responsive neural tube defects is mutated in Wnt coreceptor lipoprotein receptor-related protein 6Michelle 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... - SNOSID, a proteomic method for identification of cysteine S-nitrosylation sites in complex protein mixturesGang 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... - Gene expression profiling separates chromophobe renal cell carcinoma from oncocytoma and identifies vesicular transport and cell junction proteins as differentially expressed genesStephen 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... - CALHM1 P86L polymorphism modulates CSF Aβ levels in cognitively healthy individuals at risk for Alzheimer's diseaseJeremy 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... 
Introduction to the development and validation of predictive biomarker models from high-throughput data setsXutao 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 /)...- Building protein diagrams on the web with the residue-based diagram editor RbDeLucy 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.. - DNA methylation signatures identify biologically distinct subtypes in acute myeloid leukemiaMaria 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)... - Characterization of the mouse adeno-associated virus AAVS1 orthologNathalie 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... - Pseudomonas aeruginosa SoxR does not conform to the archetypal paradigm for SoxR-dependent regulation of the bacterial oxidative stress adaptive responseMarco 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... - 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.... - GPCRDB information system for G protein-coupled receptorsFlorence 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/... - Interoperability calls for an unusual mix of skillsFabien Campagne
Nature 418:125. 2002 - A polymorphism in CALHM1 influences Ca2+ homeostasis, Abeta levels, and Alzheimer's disease riskUte 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...