Campagne laboratory


[ research emphases ]

Our laboratory develops computational methods and tools to facilitate new biological discoveries. We apply a variety of computational techniques, including data mining, visualization, information and knowledge management, machine learning and statistics to contribute to significant biomedical problems. The current focus of the lab is:

Reliable protocols for biomarker discovery and biomarker candidate model selection (in collaboration with the MAQC-II consortium).

TEPSS: Tissue Expression Profile Similarity Searches and application to the prioritization of candidate risk genes for neurodegenerative diseases (i.e., late onset-Alzheimer’s disease, in collaboration with Dr. Philippe Marambaud and prioritization of ataxia gene candidates).

Knowledge base about GPCR oligomerization: GPCROKB (collaboration with Marta Filizola at the Mount Sinai School of Medicine).

Previous projects:

TissueInfo Mining of EST data for biomarker discovery.

Twease: Biomedical search engine (Twease/Medline searching abstracts from the Medline database and Twease/OTMI searching an OTMI text corpus).

Furthermore, the lab participates in collaborations to develop:

Ways to predict the selective site of cysteine S-Nitrosylation in proteins (Collaboration with Steven Gross at Weill Cornell who develops proteomics methods to identify sites of S-nitrosylation and provides the data used in the machine learning approach).


[ research opportunities in the laboratory ]

Students enrolled in one of following Weill Cornell graduate programs can apply for rotations in the lab:
The Tri-I Training Program in Computational Biology and Medicine

The Physiology, Biophysics and Systems Biology PhD Program

The Tri-Institutional MD-PhD Program

Other students interested in joining the laboratory are encouraged to apply to these programs and mention the laboratory in their application package.


[ recent publications ]

Dreses-Werringloer U, Lambert JC, Vingtdeux V, Zhao H, Vais H, Siebert A, Jain A, Koppel J, Rovelet-Lecrux A, Hannequin D, Pasquier F, Galimberti D, Scarpini E, Mann D, Lendon C, Campion D, Amouyel P, Davies P, Foskett JK, Campagne F, Marambaud P. A polymorphism in CALHM1 influences Ca2+ homeostasis, Abeta levels, and Alzheimer's disease risk. Cell. 2008 Jun 27;133(7):1149-61. [PubMed]

Aguilar D, Skrabanek L, Gross SS, Oliva B, Campagne F. Beyond tissueInfo: functional prediction using tissue expression profile similarity searches. Nucleic Acids Res. 2008 Jun;36(11):3728-37. Epub 2008 May 15. [PubMed]

List of publications in PubMed.

Book chapters and other publications:

Filizola M, Visiers I, Skrabanek L, Campagne F, Weinstein H. Functional mechanisms of GPCRs in a structural context. In Molecular Neuropharmacology, Strategies and Methods, Eds., A. Schousboe and H. Bräuner-Osborne, Humana Press. Dec. 2003,

Chan E, Campagne F, Applications, Representation and Management of Signaling Pathway Information: Introduction to the SigPath Project. In Introduction to Systems Biology, chapter 19, Ed. Sangdun Choi, Humana Press. ISBN13: 978-1-58829-706-8

Deng X, and Campagne F. Biomarker discovery and validation with high-throughput measurement technologies. Statistical Methods in Molecular Biology. Editors: Bang H, Zhou XK, Van Epps HL, Mazumdar M, Human Press, in press.

News
Jul, 2009; ChIPseeqer, a comprehensive framework for analysis of ChIP-seq data developed in the Elemento lab, is now available for download. [More]
Apr, 2009; The BDVal program developed by the Campagne laboratory for MAQC-II is now available from http://bdval.org. The software supports the development and evaluation of predictive biomarker models from high-throughput data. The web site offers binary and source distributions. [More]
Jan, 2009; Twease now supports searching MEDLINE articles by Author, Journal, and Publication Year. Examples for performing these searches can be found in the updated Twease tutorial. [More]

[News Archives] [Mailing List]


Events
Mar 9th; 4:00pm-5:00pm: Engineering Virtual Cardiac Tissue - Craig S. Henriquez, Ph.D.; Duke University; C-200 [Physiology, Biophysics and Systems Biology (PBSB) Seminar Series]