Publications

Nov 1, 2014 Bioessays

Multiple dimensions of epigenetic gene regulation in the malaria parasite Plasmodium falciparum

F. Ay, EM. Bunnik, N. Varoquax, JP. Vert, WS. Noble, KG. Le Roch

Jun 24, 2014 Genome Research

Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts

F. Ay, T. L. Bailey and W. S. Noble.

Jun 15, 2014 Bioinformatics

A statistical approach for inferring the 3D structure of the genome.

N. Varoquaux, F. Ay, J.-P. Vert and W. S. Noble

Mar 26, 2014 Genome Research

Three-dimensional modeling of the P. falciparum genome during the erythrocytic cycle reveals a strong connection between genome architecture and gene expression.

F. Ay*, E. M. Bunnik*, N. Varoquaux*, S. M. Bol, J. Prudhomme, J.-P. Vert, W. S. Noble and K. G. Le Roch.

Dec 4, 2013 Nucleus

Implications of COMT long-range interactions on the phenotypic variability of 22q11.2 deletion syndrome.

M. J. Zeitz, P. L. Lerner, F. Ay , E. V. Nostrand, J. D. Heidmann, W. S. Noble and A. R. Ho man.

Sep 3, 2013 PLoS ONE

Genomic interaction profiles in breast cancer reveal altered chromatin architecture.

M. J. Zeitz, F. Ay , J. D. Heidmann, P. L. Lerner, W. S. Noble, B. N. Steelman and A. R. Ho man.

Jul 22, 2012 Genome Research

Predictive regulatory models in Drosophila Melanogaster by integrative inference of transcriptional networks.

D. Marbach, S. Roy, F. Ay, P. Meyer, R. Candeias, T. Kahveci, C. Bristow and M. Kellis.

Mar 21, 2012 BMC Bioinformatics

Metabolic Network Alignment in Large Scale by Network Compression.

F. Ay, M. Dang and T. Kahveci

Mar 18, 2011 Journal of Computational Biology (JCB)

SubMAP: Aligning metabolic pathways with subnetwork mappings.

F. Ay, M. Kellis and T. Kahveci.

Dec 24, 2010 Science

Identification of functional elements and regulatory circuits by Drosophila modENCODE

The modENCODE Consortium, S. Roy*, J. Ernst*, P.V. Kharchenko*, P. Kheradpour*, N. Negre*, M.L. Eaton*, J.M. Landolin*, C.A. Bristow*, L. Ma*, M.F. Lin*, S. Washiet*, B.I. Arshino *, F. Ay*, P.E. Meyer*, N. Robine*, N. L Washington*, L.D. Stefano*, et. al., S.E. Celniker, S. Heniko , G.H. Karpen, E.C. Lai, D.M. MacAlpine, L.D. Stein, K.P. White and M.Kellis.

Dec 1, 2009 PLoS ONE

Scalable steady state analysis of Boolean biological regulatory networks.

F. Ay, F. Xu, and T. Kahveci.

Jun 7, 2009 Journal of Bioinformatics and Computational Biology (JBCB)

A fast and accurate algorithm for comparative analysis of metabolic pathways

F. Ay, T. Kahveci, and V. de Crecy-Lagard.