MoCoLo: a testing framework for motif co-localization
Q Xu, IMA Del Mundo, M Zewail-Foote… - Briefings in …, 2024 - academic.oup.com
Sequence-level data offers insights into biological processes through the interaction of two
or more genomic features from the same or different molecular data types. Within motifs, this …
or more genomic features from the same or different molecular data types. Within motifs, this …
Non-B DNA-informed mutation burden as a marker of treatment response and outcome in cancer
Q Xu, J Kowalski - British Journal of Cancer, 2024 - nature.com
Background Genomic instability is crucial in tumorigenesis, with Tumour Mutation Burden
(TMB) being a biomarker to indicate therapeutic effectiveness, particularly in …
(TMB) being a biomarker to indicate therapeutic effectiveness, particularly in …
Special Issue “Bioinformatics of Unusual DNA and RNA Structures”
Nucleic acids are not only static carriers of genetic information but also play vital roles in
controlling cellular lifecycles through their fascinating structural diversity. Gone are the days …
controlling cellular lifecycles through their fascinating structural diversity. Gone are the days …
RAG1/2 induces double‐stranded DNA breaks at non‐Ig loci in the proximity of single sequence repeats in developing B cells
K Ochodnicka‐Mackovicova, M Mokry… - European Journal of …, 2024 - Wiley Online Library
In developing B cells, V (D) J gene recombination is initiated by the RAG1/2 endonuclease
complex, introducing double‐stranded DNA breaks (DSBs) in V, D, and J genes and …
complex, introducing double‐stranded DNA breaks (DSBs) in V, D, and J genes and …
PACMIDS: Patient-Centered, AI-Enabled, Molecular-Informed Data Fabric for Clinical Treatment Decision Support
J Kowalski, Q Xu, M Ylagan… - AI in Precision …, 2024 - liebertpub.com
Introduction: The demand for comprehensive data resources has surged due to
advancements in research aimed at tackling complex questions. Data integration techniques …
advancements in research aimed at tackling complex questions. Data integration techniques …
NBBC: Quantifying the Prevalence of Non-B DNA Motifs as a Marker of Non-B Burden in Cancer
Q Xu, J Kowalski - bioRxiv, 2024 - biorxiv.org
Alternative DNA structures, such as Z-DNA, G-quadruplexes, and mirror repeats, have
shown potential involvement in cancer etiology. NBBC (Non-B DNA Burden in Cancer) is a …
shown potential involvement in cancer etiology. NBBC (Non-B DNA Burden in Cancer) is a …
Motif-informed analysis of phenotype heterogeneity in cancer
Q Xu - 2023 - repositories.lib.utexas.edu
The landscape of cancer genomics harbors a wealth of DNA motifs, whose thorough
analysis and integration provide a pivotal method to decipher the complex molecular …
analysis and integration provide a pivotal method to decipher the complex molecular …