List of works - Ferhat Ay

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

scientific article

A fast and accurate algorithm for comparative analysis of metabolic pathways.

scientific article

A multi-task graph-clustering approach for chromosome conformation capture data sets identifies conserved modules of chromosomal interactions

scientific article

A predictive modeling approach for cell line-specific long-range regulatory interactions

scientific article published on 3 September 2015

A predictive modeling approach for cell line-specific long-range regulatory interactions.

scientific article published on 5 November 2015

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

scientific article

Accurate identification of centromere locations in yeast genomes using Hi-C.

scientific article published on 4 May 2015

Analysis methods for studying the 3D architecture of the genome

scientific article (publication date: 2015)

Bipartite structure of the inactive mouse X chromosome

scientific article

COVID-19 genetic risk variants are associated with expression of multiple genes in diverse immune cell types

scientific article published on 02 December 2020

Combined RNA-seq and RAT-seq mapping of long noncoding RNAs in pluripotent reprogramming

scientific article published on 20 November 2018

Comparative 3D genome organization in apicomplexan parasites

scientific article published on 05 February 2019

Comprehensive identification and analysis of human accelerated regulatory DNA

scientific article

Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of human lincRNA genes.

scientific article published on December 2014

Form and function of topologically associating genomic domains in budding yeast

scientific article published on 27 March 2017

Genomic interaction profiles in breast cancer reveal altered chromatin architecture

scientific article

Human Eosinophils Express a Distinct Gene Expression Program in Response to IL-3 Compared with Common β-Chain Cytokines IL-5 and GM-CSF

scientific article published on 07 June 2019

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

scientific article published on 18 October 2017

Identification of significant chromatin contacts from HiChIP data by FitHiChIP

scientific article published on 17 September 2019

Identifying multi-locus chromatin contacts in human cells using tethered multiple 3C

scientific article

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

scientific article published on 24 January 2020

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

scientific article published on November 2013

Integrative detection and analysis of structural variation in cancer genomes

scientific article published on 10 September 2018

Intratumoral follicular regulatory T cells curtail anti-PD-1 treatment efficacy

scientific article published on 24 June 2021

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

scientific article

Metabolic network alignment in large scale by network compression

scientific article

Multi-cell type gene coexpression network analysis reveals coordinated interferon response and cross-cell type correlations in systemic lupus erythematosus

scientific article published on 05 March 2021

Multiple dimensions of epigenetic gene regulation in the malaria parasite Plasmodium falciparum: gene regulation via histone modifications, nucleosome positioning and nuclear architecture in P. falciparum

scientific article

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

scientific article published on 30 September 2020

NSD2 overexpression drives clustered chromatin and transcriptional changes in a subset of insulated domains

scientific article published on 24 October 2019

Neocentromeres Provide Chromosome Segregation Accuracy and Centromere Clustering to Multiple Loci along a Candida albicans Chromosome

scientific article

Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks

scientific article

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

scientific article published on 21 December 2020

Scalable steady state analysis of Boolean biological regulatory networks

scientific article

Single-cell transcriptomic analysis of tissue-resident memory T cells in human lung cancer

scientific article published on 21 June 2019

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

scientific article (publication date: 5 February 2014)

TET enzymes augment activation-induced deaminase (AID) expression via 5-hydroxymethylcytosine modifications at the Aicda superenhancer

scientific article published on 01 April 2019

The role of 3D genome organization in disease: From compartments to single nucleotides

scientific article published on 17 July 2018

The tumor suppressor kinase DAPK3 drives tumor-intrinsic immunity through the STING-IFN-β pathway

scientific article published on 25 March 2021

Third-generation sequencing revises the molecular karyotype for <i>Toxoplasma gondii</i> and identifies emerging copy number variants in sexual recombinants

scientific article published on 27 April 2021

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

scientific article

Topologically associating domains and their long-range contacts are established during early G1 coincident with the establishment of the replication-timing program

scientific article published on 20 May 2015

Using DNase Hi-C techniques to map global and local three-dimensional genome architecture at high resolution

scientific article published on 27 January 2018

List of works by Ferhat Ay

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

A fast and accurate algorithm for comparative analysis of metabolic pathways.

A multi-task graph-clustering approach for chromosome conformation capture data sets identifies conserved modules of chromosomal interactions

A predictive modeling approach for cell line-specific long-range regulatory interactions

A predictive modeling approach for cell line-specific long-range regulatory interactions.

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

Accurate identification of centromere locations in yeast genomes using Hi-C.

Analysis methods for studying the 3D architecture of the genome

Bipartite structure of the inactive mouse X chromosome

COVID-19 genetic risk variants are associated with expression of multiple genes in diverse immune cell types

Combined RNA-seq and RAT-seq mapping of long noncoding RNAs in pluripotent reprogramming

Comparative 3D genome organization in apicomplexan parasites

Comprehensive identification and analysis of human accelerated regulatory DNA

Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of human lincRNA genes.

Form and function of topologically associating genomic domains in budding yeast

Genomic interaction profiles in breast cancer reveal altered chromatin architecture

Human Eosinophils Express a Distinct Gene Expression Program in Response to IL-3 Compared with Common β-Chain Cytokines IL-5 and GM-CSF

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

Identification of significant chromatin contacts from HiChIP data by FitHiChIP

Identifying multi-locus chromatin contacts in human cells using tethered multiple 3C

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

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

Integrative detection and analysis of structural variation in cancer genomes

Intratumoral follicular regulatory T cells curtail anti-PD-1 treatment efficacy

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

Metabolic network alignment in large scale by network compression

Multi-cell type gene coexpression network analysis reveals coordinated interferon response and cross-cell type correlations in systemic lupus erythematosus

Multiple dimensions of epigenetic gene regulation in the malaria parasite Plasmodium falciparum: gene regulation via histone modifications, nucleosome positioning and nuclear architecture in P. falciparum

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

NSD2 overexpression drives clustered chromatin and transcriptional changes in a subset of insulated domains

Neocentromeres Provide Chromosome Segregation Accuracy and Centromere Clustering to Multiple Loci along a Candida albicans Chromosome

Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks

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

Scalable steady state analysis of Boolean biological regulatory networks

Single-cell transcriptomic analysis of tissue-resident memory T cells in human lung cancer

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

TET enzymes augment activation-induced deaminase (AID) expression via 5-hydroxymethylcytosine modifications at the Aicda superenhancer

The role of 3D genome organization in disease: From compartments to single nucleotides

The tumor suppressor kinase DAPK3 drives tumor-intrinsic immunity through the STING-IFN-β pathway

Third-generation sequencing revises the molecular karyotype for <i>Toxoplasma gondii</i> and identifies emerging copy number variants in sexual recombinants

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

Topologically associating domains and their long-range contacts are established during early G1 coincident with the establishment of the replication-timing program

Using DNase Hi-C techniques to map global and local three-dimensional genome architecture at high resolution