Ferhat Ay

IL-27 induces a cytotoxic state in CD4+ T cells distinct from the Th1 lineage

This study identifies IL-27 as an inducer of a distinct CD4+ cytotoxic T cell program that differs from Th1 lineage.

Genomic Language Model for Predicting Enhancers and Their Allele-Specific Activity in the Human Genome

The paper develops DNABERT-Enhancer, a genomic language model for enhancer prediction, achieving high accuracy and identifying allele-specific activity and candidate SNPs.

An Open Benchmark for Systems Vaccinology: Insights from the CMI-PB Challenges

The paper benchmarks computational models predicting B. pertussis booster vaccine responses using multi-omics data from three cohorts, identifying key predictors of immunity and establishing a community resource for systems vaccinology.

CTCF directly binds G-quadruplex structures to regulate genome topology and gene expression

This study identifies CTCF as a strong G4 DNA binder and shows its role in genome topology and gene expression through chromatin looping and CTCF occupancy.

EpiExpr: Predicting gene expression using epigenetic data and chromatin interactions

EpiExpr predicts gene expression using epigenetic data and chromatin interactions, achieving performance comparable to sequence-based models without requiring sequence embeddings.

DiffHiChIP: Identifying differential chromatin contacts from HiChIP data

DiffHiChIP identifies differential chromatin contacts from HiChIP data by addressing limitations in existing methods through improved statistical modeling and distance correction.

Loss of TET function in T regulatory cells yields ex-Treg cells biased toward T follicular helper cells, causingautoimmune diseases through autoantibody production

This study shows that loss of TET function in Treg cells leads to ex-Treg cells that differentiate into Tfh cells, promoting autoantibody production and autoimmune disease.

Master transcription factor binding sites constitute the core of early replication control elements

The paper identifies subERCEs as master transcription factor binding sites that drive early replication timing and transcription in mESCs, functioning as both enhancers and structural chromatin organizers.

Soffritto: a deep-learning model for predicting high-resolution replication timing

Soffritto predicts high-resolution replication timing using two-fraction RT data and other genomic features, achieving accurate 16-fraction RT signals across cell lines.

Loop Catalog: a comprehensive HiChIP database of human and mouse samples

Loop Catalog compiles HiChIP data from 1000+ human and mouse samples to provide a resource for analyzing chromatin loops and their regulatory roles.

Distinct interferon response patterns link to increased transposable element expression in leukocytes of systemic lupus erythematosus patients

This study links increased transposable element (TE) expression in SLE patients to IFN responses, showing strong correlations with disease activity and splicing alterations.

Putting computational models of immunity to the test - an invited challenge to predict B. pertussis vaccination outcomes

The paper benchmarks 49 algorithms for predicting B. pertussis vaccination outcomes, finding that purpose-built models outperform literature-based ones due to better handling of nonlinearities and data preprocessing.

nipalsMCIA: Flexible Multi-Block Dimensionality Reduction in R via Nonlinear Iterative Partial Least Squares

The paper introduces nipalsMCIA, a tool for multi-omics dimensionality reduction that improves speed and flexibility over existing methods for single-cell data.

Chromatin structure and var2csa - a tango in regulation of var gene expression in the human malaria parasite Plasmodium falciparum?

The paper investigates how var2csa influences var gene expression in Plasmodium falciparum by analyzing chromatin structure changes after gene deletion.

Brd2 is dispensable for genome compartmentalization and replication timing

This study shows that Brd2 depletion does not alter genome replication timing or A/B compartmentalization in mouse embryonic stem cells.

MuDCoD: Multi-Subject Community Detection in Personalized Dynamic Gene Networks from Single Cell RNA Sequencing

MuDCoD detects dynamic gene communities across multiple subjects and time points in scRNA-seq data, revealing subject- and time-specific network variations.

A systems vaccinology resource to develop and test computational models of immunity

The paper evaluates computational models predicting immune responses to Pertussis Booster vaccinations using a new community resource, finding that existing models perform poorly and new models show variable performance based on features and strategies.

ExTraMapper: Exon- and Transcript-level mappings for orthologous gene pairs

ExTraMapper improves transcript-level orthology mapping between human and mouse by identifying more exon and transcript mappings than previous methods.

Third generation sequencing revises the molecular karyotype for Toxoplasma gondii and identifies emerging copy number variants in sexual recombinants.

This paper uses third-generation sequencing to revise the molecular karyotype of Toxoplasma gondii, identifying chromosome fusions and copy number variants in sexual recombinants.

Integrative transcriptomic analysis of SLE reveals IFN-driven cross-talk between immune cells

This paper identifies IFN-driven cross-talk between immune cell types in SLE using gene expression analysis and a novel integrative method.

Sox2-RNA mechanisms of chromosome topological control in developing forebrain

The paper shows Evf2 RNA regulates gene expression in mouse forebrain by interacting with Sox2 to control enhancer interactions and chromosome topology.

dcHiC: differential compartment analysis of Hi-C datasets

dcHiC identifies significant changes in chromatin compartmentalization across multiple Hi-C datasets, revealing biologically relevant differences in gene regulation and chromatin states.

Mustache: Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation

MO_SCPLOWUSTACHEC_SCPLOW detects chromatin loops from Hi-C and Micro-C data using scale-space theory, identifying more loops than HiCCUPS and showing strong agreement between datasets.

Severely ill COVID-19 patients display augmented functional properties in SARS-CoV-2-reactive CD8+ T cells

This study analyzes single-cell transcriptomes of SARS-CoV-2-reactive CD8+ T cells from COVID-19 patients and healthy controls, revealing differences in functional properties between mild and severe cases.

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

The paper shows NSD2 overexpression alters chromatin structure and gene expression by affecting CTCF and H3K27ac in specific chromatin domains.

FitHiChIP: Identification of significant chromatin contacts from HiChIP data

FitHiChIP identifies significant chromatin contacts from HiChIP data by modeling coverage and distance scaling, validating enhancer interactions, and enabling differential contact analysis between immune cell types.

Replication Timing Networks: a novel class of gene regulatory networks

The paper constructs replication timing networks from human cell types and identifies master regulators and novel trans interactions between transcription factors and RT changes.

Selfish: Discovery of Differential Chromatin Interactions via a Self-Similarity Measure

Selfish identifies differential chromatin interactions by comparing Hi-C contact maps using a self-similarity measure, showing improved accuracy over existing methods.

Measuring the reproducibility and quality of Hi-C data

The paper evaluates reproducibility and quality measures for Hi-C data using real and simulated datasets, showing that specialized methods outperform simple correlation analysis.

Identification of cis elements for spatio-temporal control of DNA replication

The paper identifies cis-regulatory elements (ERCEs) that control domain-wide replication timing, chromatin compartmentalization, and transcription in mouse embryonic stem cells.