Computational immunogenomic approaches to predict response to cancer immunotherapies

V Addala, F Newell, JV Pearson, A Redwood… - Nature Reviews …, 2024 - nature.com
Cancer immunogenomics is an emerging field that bridges genomics and immunology. The
establishment of large-scale genomic collaborative efforts along with the development of …

Analyzing somatic mutations by single-cell whole-genome sequencing

L Zhang, M Lee, AY Maslov, C Montagna, J Vijg… - Nature …, 2024 - nature.com
Somatic mutations are the cause of cancer and have been implicated in other,
noncancerous diseases and aging. While clonally expanded mutations can be studied by …

Hyenadna: Long-range genomic sequence modeling at single nucleotide resolution

E Nguyen, M Poli, M Faizi, A Thomas… - Advances in neural …, 2024 - proceedings.neurips.cc
Genomic (DNA) sequences encode an enormous amount of information for gene regulation
and protein synthesis. Similar to natural language models, researchers have proposed …

Cell-type-directed design of synthetic enhancers

II Taskiran, KI Spanier, H Dickmänken, N Kempynck… - Nature, 2024 - nature.com
Transcriptional enhancers act as docking stations for combinations of transcription factors
and thereby regulate spatiotemporal activation of their target genes. It has been a long …

Systematic benchmarking of single-cell ATAC-sequencing protocols

FV De Rop, G Hulselmans, C Flerin, P Soler-Vila… - Nature …, 2024 - nature.com
Single-cell assay for transposase-accessible chromatin by sequencing (scATAC-seq) has
emerged as a powerful tool for dissecting regulatory landscapes and cellular heterogeneity …

The chemotherapeutic drug CX-5461 is a potent mutagen in cultured human cells

GCC Koh, S Boushaki, SJ Zhao, AM Pregnall… - Nature Genetics, 2024 - nature.com
The chemotherapeutic agent CX-5461, or pidnarulex, has been fast-tracked by the United
States Food and Drug Administration for early-stage clinical studies of BRCA1-, BRCA2-and …

[HTML][HTML] Direct observation of a condensate effect on super-enhancer controlled gene bursting

M Du, SH Stitzinger, JH Spille, WK Cho, C Lee, M Hijaz… - Cell, 2024 - cell.com
Enhancers are distal DNA elements believed to loop and contact promoters to control gene
expression. Recently, we found diffraction-sized transcriptional condensates at genes …

Chromatin context-dependent regulation and epigenetic manipulation of prime editing

X Li, W Chen, BK Martin, D Calderon, C Lee, J Choi… - Cell, 2024 - cell.com
We set out to exhaustively characterize the impact of the cis-chromatin environment on
prime editing, a precise genome engineering tool. Using a highly sensitive method for …

Identification of constrained sequence elements across 239 primate genomes

LFK Kuderna, JC Ulirsch, S Rashid, M Ameen… - Nature, 2024 - nature.com
Noncoding DNA is central to our understanding of human gene regulation and complex
diseases,, and measuring the evolutionary sequence constraint can establish the functional …

Epigenetic variation impacts individual differences in the transcriptional response to influenza infection

KA Aracena, YL Lin, K Luo, A Pacis, S Gona, Z Mu… - Nature …, 2024 - nature.com
Humans display remarkable interindividual variation in their immune response to identical
challenges. Yet, our understanding of the genetic and epigenetic factors contributing to such …