Ibel Carri,Jason Greenbaum,Zhen Yan et al.
Ibel Carri et al.
Accurate identification of immunogenic cancer epitopes remains a central challenge in immuno-oncology. The Cancer Epitope Database and Analysis Resource (CEDAR, https://cedar.iedb.org/) was developed to provide comprehensive curation of exp...
InSituPREP enables 3D single-cell mapping of interaction-associated gene programs in the breast cancer tumor microenvironment [0.03%]
Tal Goldberg,Michal Danino-Levi,Modi Safra et al.
Tal Goldberg et al.
Cell-cell interactions influence gene expression in the tumor microenvironment, yet despite advances in spatial transcriptomics that enable in situ expression profiling, current computational tools remain limited in quantitatively resolving...
A viral noncoding RNA is a master regulator of gene expression that defines host cell identity and function [0.03%]
Carlos Gorbea,Donald Yuhui Sim,Xavier Roca et al.
Carlos Gorbea et al.
Viruses extensively reprogram the host cell to promote infection and persistence, yet the contribution of noncoding RNAs (ncRNAs) to this viral reengineering remains largely unknown. Here, we show that HSUR1, a viral Sm-class ncRNA abundant...
Jiayi Li,Kamilla Vandsø Petersen,Henning Ummethum et al.
Jiayi Li et al.
TOPBP1 is a scaffold protein with multiple functions in genome integrity. During mitosis, TOPBP1 is coordinating DNA repair and genome maintenance, thereby reducing carry-over of DNA damage to daughter cells. This function emerges as a crit...
Ian K Gingerich,Brittany A Goods,Hildreth Robert Frost
Ian K Gingerich
High-throughput spatial transcriptomics (ST) now profiles hundreds of thousands of cells or locations per section, creating computational bottlenecks for routine analysis. Sketching, or intelligent sub-sampling, addresses scale by selecting...
Hyeonjun Kim,Manho Lim,Youngshang Pak
Hyeonjun Kim
Maintaining genome stability requires accurate recognition of oxidative DNA damage. MutY glycosylase prevents mutagenic G:C→T:A transversions by excising adenine mispaired with 8-oxoguanine (8OG). While crystal structures have captured two...
Hariz Nizal,Anthony Mittermaier
Hariz Nizal
Guanine quadruplexes (G4s) are non-canonical DNA secondary structures thought to play critical regulatory roles in cells. Notably, G4s are implicated in oncogenesis, making them attractive therapeutic targets. Thus, understanding G4/ligand ...
GEAR Genomics: a user-friendly, open-source web platform enabling interactive genomic analysis for molecular biologists [0.03%]
Andreas Untergasser,Markus Hsi-Yang Fritz,Vladimir Benes et al.
Andreas Untergasser et al.
Many routine genomics tasks in molecular biology still depend on heterogeneous and proprietary software tools that hinder accessibility, reproducibility, and seamless laboratory use. We present GEAR (https://www.gear-genomics.com/), a unifi...
TridentSynth: a webtool for the retrosynthesis of molecules using chimeric type I polyketide synthases and chemoenzymatic pathways [0.03%]
Yash Chainani,Margaret Guilarte-Silva,Kenna Roberts et al.
Yash Chainani et al.
The design of pathways to synthesize valuable molecules remains a central challenge in chemistry and biotechnology. Several computational retrosynthesis tools have been developed to address this problem, but their scope is often confined on...
SNPnexus: an enhanced web platform for large-scale and multi-sample variant analysis (2025 update) [0.03%]
Jorge Oscanoa,Qianqian Zhu,Emanuela Gadaleta et al.
Jorge Oscanoa et al.
SNPnexus is a long-standing web-based platform for the functional annotation and prioritization of genetic variants. Since its previous release, SNPnexus has undergone substantial backend re-engineering resulting in major performance improv...