Computational immunogenomic approaches to predict response to cancer immunotherapies
Cancer immunogenomics is an emerging field that bridges genomics and immunology. The
establishment of large-scale genomic collaborative efforts along with the development of …
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 …
noncancerous diseases and aging. While clonally expanded mutations can be studied by …
Hyenadna: Long-range genomic sequence modeling at single nucleotide resolution
Genomic (DNA) sequences encode an enormous amount of information for gene regulation
and protein synthesis. Similar to natural language models, researchers have proposed …
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 …
and thereby regulate spatiotemporal activation of their target genes. It has been a long …
Systematic benchmarking of single-cell ATAC-sequencing protocols
Single-cell assay for transposase-accessible chromatin by sequencing (scATAC-seq) has
emerged as a powerful tool for dissecting regulatory landscapes and cellular heterogeneity …
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 …
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
Enhancers are distal DNA elements believed to loop and contact promoters to control gene
expression. Recently, we found diffraction-sized transcriptional condensates at genes …
expression. Recently, we found diffraction-sized transcriptional condensates at genes …
Chromatin context-dependent regulation and epigenetic manipulation of prime editing
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 …
prime editing, a precise genome engineering tool. Using a highly sensitive method for …
Identification of constrained sequence elements across 239 primate genomes
Noncoding DNA is central to our understanding of human gene regulation and complex
diseases,, and measuring the evolutionary sequence constraint can establish the functional …
diseases,, and measuring the evolutionary sequence constraint can establish the functional …
Epigenetic variation impacts individual differences in the transcriptional response to influenza infection
Humans display remarkable interindividual variation in their immune response to identical
challenges. Yet, our understanding of the genetic and epigenetic factors contributing to such …
challenges. Yet, our understanding of the genetic and epigenetic factors contributing to such …