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).

Goby: a next-gen data management framework that facilitates the implementation of efficient and scalable analysis pipelines.

Development of a robust analysis pipleline for epigenomic HELP data.

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

Previous projects:

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).

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).

You can find Fabien Campagne's NIH biosketch here.

[ 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 ]

Figueroa et al., DNA Methylation Signatures Identify Biologically Distinct Subtypes in Acute Myeloid Leukemia, Cancer Cell (2010), doi:10.1016/j.ccr.2009.11.020

Discovery and Validation of Urine Markers of Acute Pediatric Appendicitis Using High-Accuracy Mass Spectrometry. Kentsis A, Lin YY, Kurek K, Calicchio M, Wang YY, Monigatti F, Campagne F, Lee R, Horwitz B, Steen H, Bachur R. Ann Emerg Med. 2009 Jun 25.

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.