Aristotelis Tsirigos

This study introduces C.Origami, a deep learning model that predicts cell type-specific 3D chromatin organization, enabling in silico genetic screening to identify genomic regions affecting chromatin structure.

This study uses single-cell RNA-seq to map cell fates in human cornea organoids and identifies developmental states of corneal cell types.

The paper identifies a bipartite imprinting control region at the Dlk1-Dio3 locus that maintains imprint stability through allele-specific regulation of DNA methylation and chromatin structure.

This study shows that H3K27 acetylation retention during mitosis accelerates transcriptional and topological resetting of stem cell genes in mouse pluripotent stem cells upon G1 entry.

This paper proposes a machine learning approach to estimate drug development risk more accurately than traditional models.

The paper investigates the distinct and combined roles of CTCF and CTCFL in chromosome organization and transcription by analyzing their binding sites and functional domains.

The paper introduces KNetL, a graph drawing-based dimensionality reduction method to better identify hidden cell communities in single-cell sequencing data.

The paper introduces two batch alignment methods for single-cell RNA sequencing to address drop-out issues and improve clustering accuracy across batches.

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

This study shows that reducing EHMT1/2 activity during reprogramming with ascorbic acid impairs iPSC formation and viability, highlighting the role of H3K9 methylation in reprogramming efficiency.

This study investigates the role of KLF4 in chromatin reorganization and 3D enhancer rewiring during reprogramming of mouse embryonic fibroblasts to pluripotent stem cells.

This paper introduces a simplified CNN architecture for efficient pan-cancer whole-slide image classification and outlier detection.

The paper shows that learning regulates protein synthesis in adult rat amygdala axons, identified through TRAP-RNASeq, revealing upregulated mitochondrial and translation-related genes and downregulated synaptic genes.

ChIPSeqSpike provides tools for normalizing, assessing, and analyzing ChIP-Seq data using spike-in controls, producing scaled bigwig files and scaling factors.

The paper improves Hi-C contact matrix reproducibility using fused two-dimensional lasso, identifies TAD boundaries with varying insulation strength, and shows super-enhancers are preferentially insulated by strong boundaries, which are frequently co-duplicated in cancer.

lncRNA-screen is a pipeline for computationally screening lncRNAs in large genomics datasets, generating interactive reports for further experimental validation.

HiC-bench provides a comprehensive and reproducible platform for Hi-C data analysis, enabling parameter exploration and benchmarking of different tools and methods.