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 …

Adaptive immune receptor repertoire analysis

V Mhanna, H Bashour, K Lê Quý, P Barennes… - Nature Reviews …, 2024 - nature.com
B cell and T cell receptor repertoires compose the adaptive immune receptor repertoire
(AIRR) of an individual. The AIRR is a unique collection of antigen-specific receptors that …

Multi-omics data integration using ratio-based quantitative profiling with Quartet reference materials

Y Zheng, Y Liu, J Yang, L Dong, R Zhang, S Tian… - Nature …, 2023 - nature.com
Abstract Characterization and integration of the genome, epigenome, transcriptome,
proteome and metabolome of different datasets is difficult owing to a lack of ground truth …

A review of the current state of single-cell proteomics and future perspective

R Ahmad, B Budnik - Analytical and Bioanalytical Chemistry, 2023 - Springer
Single-cell methodologies and technologies have started a revolution in biology which until
recently has primarily been limited to deep sequencing and imaging modalities. With the …

Epigenetic mechanisms underlying sex differences in the brain and behavior

M Kundakovic, M Tickerhoof - Trends in neurosciences, 2024 - cell.com
Sex differences are found across brain regions, behaviors, and brain diseases. Sexual
differentiation of the brain is initiated prenatally but it continues throughout life, as a result of …

Delineating mouse β-cell identity during lifetime and in diabetes with a single cell atlas

K Hrovatin, A Bastidas-Ponce, M Bakhti, L Zappia… - Nature …, 2023 - nature.com
Although multiple pancreatic islet single-cell RNA-sequencing (scRNA-seq) datasets have
been generated, a consensus on pancreatic cell states in development, homeostasis and …

[HTML][HTML] An atlas of cells in the human tonsil

R Massoni-Badosa, S Aguilar-Fernández, JC Nieto… - Immunity, 2024 - cell.com
Palatine tonsils are secondary lymphoid organs (SLOs) representing the first line of
immunological defense against inhaled or ingested pathogens. We generated an atlas of …

What is a cell type?

JS Fleck, JG Camp, B Treutlein - Science, 2023 - science.org
International efforts are underway to provide a comprehensive survey of cells across the
human life span (,). These efforts assign cell “types” on the basis of a set of information-rich …

Single-cell epigenetic, transcriptional, and protein profiling of latent and active HIV-1 reservoir revealed that IKZF3 promotes HIV-1 persistence

Y Wei, TC Davenport, JA Collora, HK Ma… - Immunity, 2023 - cell.com
Understanding how HIV-1-infected cells proliferate and persist is key to HIV-1 eradication,
but the heterogeneity and rarity of HIV-1-infected cells hamper mechanistic interrogations …

Pooled Genome-Scale CRISPR Screens in Single Cells

D Schraivogel, LM Steinmetz… - Annual Review of …, 2023 - annualreviews.org
Assigning functions to genes and learning how to control their expression are part of the
foundation of cell biology and therapeutic development. An efficient and unbiased method to …