Michael Kotliar

Gene regulatory network determinants of rapid recall in human memory CD4+ T cells

This study identifies gene regulatory networks in human memory CD4+ T cells that drive rapid recall, linking specific transcription factors to immune-mediated disease risk.

Memory T cell rapid recall is driven by memory-specific AP-1 recruitment determined by epigenome and co-factor interactions

The paper identifies memory-specific AP-1 recruitment in T cells, driven by epigenetic changes and co-factor interactions, and links it to disease risk variants.

Defining the T cell transcriptional landscape in pediatric liver transplant rejection at single cell resolution

This study defines the transcriptional landscape of CD8+ T cells in pediatric liver transplant rejection using single-cell sequencing and identifies persistent CD8+ clones associated with graft failure.

Accelerating Single-Cell Sequencing Data Analysis with SciDAP: A User-Friendly Approach

The paper introduces SciDAP, a platform enabling biologists to analyze single-cell sequencing data without coding expertise using reproducible pipelines.

Long-term Tolerance to Islet Transplantation via Targeted Reduction of beta cell-specific T cells.

This paper demonstrates that targeting islet-reactive T effector cells with a combination therapy improves long-term islet graft acceptance in T1D mice.

Multiome-seq links inflammatory bowel disease polygenic risk to TNF inhibitor response

The paper links IBD polygenic risk to TNFi response using multiome-seq and genetic data from pediatric IBD patients.

maxATAC: genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks

maxATAC provides deep learning models for predicting transcription factor binding sites from ATAC-seq data, improving prediction in primary and single-cell contexts.

CWL-Airflow: a lightweight pipeline manager supporting Common Workflow Language

CWL-Airflow extends Apache Airflow to support Common Workflow Language, enabling portable and reproducible computational workflows across various environments.