PLOS Computational Biology

by Lin Yuan, Junjie Cao, Shengguo Sun, Siguo Wang, Lan Ye, De-Shuang Huang

A key challenge in single-cell RNA sequencing (scRNA-seq) data analysis is accurately and efficiently identifying the cell type of each cell. Cell type annotation for scRNA-seq data not only needs to overcome batch effects caused by various factors but also requires effective handling of large-sca...

by Nathan Gravel, Zhongliang Zhou, Ruili Fang, Austin Downes, Saber Soleymani, Natarajan Kannan

Post-Translational Modifications (PTMs) are a fundamental mechanism for regulating cellular pathways and increasing the functional diversity of the proteome. Accurately predicting the PTM types that are likely to occur at a given site in the primary sequence is a key challenge...

by Eric Wang, Arup K. Chakraborty

Despite decades of research, an effective HIV vaccine or cure has not yet been developed. An important reason is the virus’s mutability, which allows it to rapidly evade human immune responses. Often, the virus also takes advantage of epistatic pathways to evolve escape mutations through compensatory effects that allow maintaining its fi...

by Mingze Sun, Di Zhang, Zhiyuan Li, Yihan Lin

N6-methyladenosine (m6A), the most abundant mRNA modification in eukaryotes, plays essential roles in gene regulation and disease pathogenesis. Computational prediction of m6A sites offers a scalable alternative to costly experimental approaches, yet current methods rely predominantly on linear sequence features. This overlo...

by Edoh Kodji, Redha Attaoua, Mounsif Haloui, Camil Hishmih, Mirjam Seitz, Mark Woodward, Julie G. Hussin, Pavel Hamet, Johanne Tremblay

Polygenic risk scores (PRS) developed in European populations often show reduced predictive performance in non-European populations, limiting their clinical utility. This lack of transferability across ancestries remains a major challen...