Ay, Ferhat

Integrative detection and analysis of structural variation in cancer genomes

Dixon, J. R., Xu, J., Dileep, V., Zhan, Y., Song, F., Le, V. T., Yardımcı, G. G., Chakraborty, A., Bann, D. V., Wang, Y., et al. (2018) · Nature Genetics

Genomic variations and chromosomal abnormalitiesCancer Genomics and Diagnostics

Cited by 452

Mustache: multi-scale detection of chromatin loops from Hi-C and Micro-C maps using scale-space representation

Roayaei Ardakany, A., Gezer, H. T., Lonardi, S., & Ay, F. (2020) · Genome Biology

Genomics and Chromatin DynamicsChromosomal and Genetic Variations

Cited by 250

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

Varoquaux, N., Ay, F., Noble, W. S., & Vert, J.-P. (2014) · Bioinformatics

Genomics and Chromatin DynamicsProtein Structure and Dynamics

Cited by 246

Identification of significant chromatin contacts from HiChIP data by FitHiChIP

Bhattacharyya, S., Chandra, V., Vijayanand, P., & Ay, F. (2019) · Nature Communications

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 238

Identifying statistically significant chromatin contacts from Hi-C data with FitHiC2

Kaul, A., Bhattacharyya, S., & Ay, F. (2020) · Nature Protocols

Genomics and Chromatin DynamicsChromosomal and Genetic Variations

Cited by 226

17q21 asthma-risk variants switch CTCF binding and regulate IL-2 production by T cells

Schmiedel, B. J., Seumois, G., Samaniego-Castruita, D., Cayford, J., Schulten, V., Chavez, L., Ay, F., Sette, A., Peters, B., & Vijayanand, P. (2016) · Nature Communications

Asthma and respiratory diseasesGenomics and Chromatin Dynamics

Cited by 127

Promoter-interacting expression quantitative trait loci are enriched for functional genetic variants

Chandra, V., Bhattacharyya, S., Schmiedel, B. J., Madrigal, A., Gonzalez-Colin, C., Fotsing, S., Crinklaw, A., Seumois, G., Mohammadi, P., Kronenberg, M., et al. (2021) · Nature Genetics

Genomics and Chromatin DynamicsGenetic Associations and Epidemiology

Cited by 122

Identification of copy number variations and translocations in cancer cells from Hi-C data

Chakraborty, A., & Ay, F. (2018) · Bioinformatics

Genomic variations and chromosomal abnormalitiesGenomics and Chromatin Dynamics

Cited by 94

Joint annotation of chromatin state and chromatin conformation reveals relationships among domain types and identifies domains of cell-type-specific expression

Libbrecht, M. W., Ay, F., Hoffman, M. M., Gilbert, D. M., Bilmes, J. A., & Noble, W. S. (2015) · Genome Research

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 84

The Evf2 ultraconserved enhancer lncRNA functionally and spatially organizes megabase distant genes in the developing forebrain

Cajigas, I., Chakraborty, A., Swyter, K. R., Luo, H., Bastidas, M., Nigro, M., Morris, E. R., Chen, S., VanGompel, M. J. W., Leib, D., et al. (2018) · Molecular Cell

Cancer-related molecular mechanisms researchGenomics and Chromatin Dynamics

Cited by 82