Analysis and visualization of longitudinal genomic and clinical data from the AACR project GENIE biopharma collaborative in cBioPortal

I de Bruijn, R Kundra, B Mastrogiacomo, TN Tran… - Cancer research, 2023 - AACR
International cancer registries make real-world genomic and clinical data available, but their
joint analysis remains a challenge. AACR Project GENIE, an international cancer registry …

Colon cancer transcriptome

K Mokhtari, M Peymani, M Rashidi… - Progress in biophysics …, 2023 - Elsevier
Over the last four decades, methodological innovations have continuously changed
transcriptome profiling. It is now feasible to sequence and quantify the transcriptional outputs …

In silico resources help combat cancer drug resistance mediated by target mutations

YQ Huang, S Wang, DH Gong, V Kumar, YW Dong… - Drug Discovery …, 2023 - Elsevier
Drug resistance causes catastrophic cancer treatment failures. Mutations in target proteins
with altered drug binding indicate a main mechanism of cancer drug resistance (CDR) …

Ku70 senses cytosolic DNA and assembles a tumor-suppressive signalosome

A Pandey, C Shen, S Feng, D Enosi Tuipulotu… - Science …, 2024 - science.org
The innate immune response contributes to the development or attenuation of acute and
chronic diseases, including cancer. Microbial DNA and mislocalized DNA from damaged …

MarkerDB 2.0: a comprehensive molecular biomarker database for 2025

H Jackson, E Oler, C Torres-Calzada… - Nucleic Acids …, 2024 - academic.oup.com
Abstract MarkerDB (https://markerdb. ca) has become a leading resource for comprehensive
information on molecular biomarkers. Over the past 3 years, the database has evolved …

Longitudinal ultra-sensitive mutation burden sequencing for precise minimal residual disease assessment in AML

Y Wu, S Zhang, R Feng, K Xiao, T Wang, J Bai… - Nature …, 2024 - nature.com
Relapse is one of the major challenges in clinical treatment of acute myeloid leukemia
(AML). Though minimal residual disease (MRD) monitoring plays a crucial role in …

MRE11: p. K464R mutation mediates olaparib resistance by enhancing DNA damage repair in HGSOC

X Zhuang, R Xiao, Y Fu, B Yang, J Fan, F Lu, T Qin… - Cell & Bioscience, 2023 - Springer
Background Although the clinical application of PARP inhibitors has brought hope to ovarian
cancer, the problem of its resistance has become increasingly prominent. Therefore, clinical …

[HTML][HTML] Identification of neoepitope reactive T-cell receptors guided by HLA-A* 03: 01 and HLA-A* 11: 01 immunopeptidomics

CM Ade, MJ Sporn, S Das, Z Yu, K Hanada… - … for Immunotherapy of …, 2023 - ncbi.nlm.nih.gov
Background Tumor-specific mutated proteins can create immunogenic non-self, mutation-
containing 'neoepitopes' that are attractive targets for adoptive T-cell therapies. To avoid the …

Screen Them All: High-Throughput Pan-Cancer Genetic and Phenotypic Biomarker Screening from H&E Whole Slide Images

YK Wang, L Tydlitatova, JD Kunz, G Oakley… - arXiv preprint arXiv …, 2024 - arxiv.org
Many molecular alterations serve as clinically prognostic or therapy-predictive biomarkers,
typically detected using single or multi-gene molecular assays. However, these assays are …

Identifying actionable variants in cancer–the dual web and batch processing tool MTB-Report

NS Kurz, J Perera-Bel, C Höltermann… - … Data Sciences 2022 …, 2022 - ebooks.iospress.nl
Next-generation sequencing methods continuously provide clinicians and researchers in
precision oncology with growing numbers of genomic variants found in cancer. However …