Computational oncology in the multi-omics era: state of the art

G de Anda-Jáuregui, E Hernández-Lemus - Frontiers in oncology, 2020 - frontiersin.org
Cancer is the quintessential complex disease. As technologies evolve faster each day, we
are able to quantify the different layers of biological elements that contribute to the …

Federated benchmarking of medical artificial intelligence with MedPerf

A Karargyris, R Umeton, MJ Sheller… - Nature machine …, 2023 - nature.com
Medical artificial intelligence (AI) has tremendous potential to advance healthcare by
supporting and contributing to the evidence-based practice of medicine, personalizing …

Advances in systems biology modeling: 10 years of crowdsourcing DREAM challenges

P Meyer, J Saez-Rodriguez - Cell Systems, 2021 - cell.com
Computational and mathematical models are key to obtain a system-level understanding of
biological processes, but their limitations have to be clearly defined to allow their proper …

[HTML][HTML] State-of-the-art methods for exposure-health studies: results from the exposome data challenge event

L Maitre, JB Guimbaud, C Warembourg… - Environment …, 2022 - Elsevier
The exposome recognizes that individuals are exposed simultaneously to a multitude of
different environmental factors and takes a holistic approach to the discovery of etiological …

NCT/DKFZ MASTER handbook of interpreting whole-genome, transcriptome, and methylome data for precision oncology

A Mock, MV Teleanu, S Kreutzfeldt, CE Heilig… - NPJ Precision …, 2023 - nature.com
Abstract Analysis of selected cancer genes has become an important tool in precision
oncology but cannot fully capture the molecular features and, most importantly …

Profiling the baseline performance and limits of machine learning models for adaptive immune receptor repertoire classification

C Kanduri, M Pavlović, L Scheffer, K Motwani… - …, 2022 - academic.oup.com
Background Machine learning (ML) methodology development for the classification of
immune states in adaptive immune receptor repertoires (AIRRs) has seen a recent surge of …

[HTML][HTML] A community challenge to evaluate RNA-seq, fusion detection, and isoform quantification methods for cancer discovery

A Creason, D Haan, K Dang, KE Chiotti, M Inkman… - Cell systems, 2021 - cell.com
The accurate identification and quantitation of RNA isoforms present in the cancer
transcriptome is key for analyses ranging from the inference of the impacts of somatic …

Prediagnostic image data, artificial intelligence, and pancreatic cancer: a tell-tale sign to early detection

MR Young, N Abrams, S Ghosh, JAS Rinaudo… - Pancreas, 2020 - journals.lww.com
Pancreatic cancer continues to be one of the deadliest malignancies and is the third leading
cause of cancer-related mortality in the United States. Based on several models, it is …

[HTML][HTML] Bringing code to data: Do not forget governance

C Suver, A Thorogood, M Doerr, J Wilbanks… - Journal of Medical …, 2020 - jmir.org
Developing or independently evaluating algorithms in biomedical research is difficult
because of restrictions on access to clinical data. Access is restricted because of privacy …

Metapipeline-DNA: A comprehensive germline & somatic genomics Nextflow pipeline

Y Patel, C Zhu, TN Yamaguchi, NK Wang, N Wiltsie… - BioRxiv, 2024 - pmc.ncbi.nlm.nih.gov
DNA sequencing is becoming more affordable and faster through advances in high-
throughput technologies. This rise in data availability has contributed to the development of …