[HTML][HTML] Challenges in neoantigen-directed therapeutics

L Lybaert, S Lefever, B Fant, E Smits, B De Geest… - Cancer Cell, 2023 - cell.com
A fundamental prerequisite for the efficacy of cancer immunotherapy is the presence of
functional, antigen-specific T cells within the tumor. Neoantigen-directed therapy is a …

Transcriptomics for clinical and experimental biology research: hang on a seq

T Stokes, HH Cen, P Kapranov, IJ Gallagher… - Advanced …, 2023 - Wiley Online Library
Sequencing the human genome empowers translational medicine, facilitating transcriptome‐
wide molecular diagnosis, pathway biology, and drug repositioning. Initially, microarrays are …

[HTML][HTML] Maternal cecal microbiota transfer rescues early-life antibiotic-induced enhancement of type 1 diabetes in mice

XS Zhang, YS Yin, J Wang, T Battaglia, K Krautkramer… - Cell host & …, 2021 - cell.com
Early-life antibiotic exposure perturbs the intestinal microbiota and accelerates type 1
diabetes (T1D) development in the NOD mouse model. Here, we found that maternal cecal …

[HTML][HTML] TDP-43 loss induces extensive cryptic polyadenylation in ALS/FTD

S Bryce-Smith, AL Brown, PR Mehta, F Mattedi… - BioRxiv, 2024 - ncbi.nlm.nih.gov
Nuclear depletion and cytoplasmic aggregation of the RNA-binding protein TDP-43 is the
hallmark of ALS, occurring in over 97% of cases. A key consequence of TDP-43 nuclear loss …

MAAPER: model-based analysis of alternative polyadenylation using 3′ end-linked reads

WV Li, D Zheng, R Wang, B Tian - Genome biology, 2021 - Springer
Most eukaryotic genes express alternative polyadenylation (APA) isoforms. A growing
number of RNA sequencing methods, especially those used for single-cell transcriptome …

Prediction of transcript structure and concentration using RNA-Seq data

H Sharma, T Pani, U Dasgupta, J Batra… - Briefings in …, 2023 - academic.oup.com
Alternative splicing (AS) is a key post-transcriptional modification that helps in increasing
protein diversity. Almost 90% of the protein-coding genes in humans are known to undergo …

Anti-bias training for (sc) RNA-seq: experimental and computational approaches to improve precision

P Davies, M Jones, J Liu… - Briefings in …, 2021 - academic.oup.com
RNA-seq, including single cell RNA-seq (scRNA-seq), is plagued by insufficient sensitivity
and lack of precision. As a result, the full potential of (sc) RNA-seq is limited. Major factors in …

Comprehensive modular analyses of scar subtypes illuminate underlying molecular mechanisms and potential therapeutic targets

L Liu, L Lu, M Qiu, N Han, S Dai, S Shi… - International Wound …, 2024 - Wiley Online Library
Pathological scarring resulting from traumas and wounds, such as hypertrophic scars and
keloids, pose significant aesthetic, functional and psychological challenges. This study …

Partitioning RNAs by length improves transcriptome reconstruction from short-read RNA-seq data

FR Ringeling, S Chakraborty, C Vissers… - Nature …, 2022 - nature.com
The accuracy of methods for assembling transcripts from short-read RNA sequencing data is
limited by the lack of long-range information. Here we introduce Ladder-seq, an approach …