Harnessing multimodal data integration to advance precision oncology

KM Boehm, P Khosravi, R Vanguri, J Gao… - Nature Reviews …, 2022 - nature.com
Advances in quantitative biomarker development have accelerated new forms of data-driven
insights for patients with cancer. However, most approaches are limited to a single mode of …

Computational principles and challenges in single-cell data integration

R Argelaguet, ASE Cuomo, O Stegle… - Nature biotechnology, 2021 - nature.com
The development of single-cell multimodal assays provides a powerful tool for investigating
multiple dimensions of cellular heterogeneity, enabling new insights into development …

[HTML][HTML] Integration strategies of multi-omics data for machine learning analysis

M Picard, MP Scott-Boyer, A Bodein, O Périn… - Computational and …, 2021 - Elsevier
Increased availability of high-throughput technologies has generated an ever-growing
number of omics data that seek to portray many different but complementary biological …

State of the field in multi-omics research: from computational needs to data mining and sharing

M Krassowski, V Das, SK Sahu, BB Misra - Frontiers in Genetics, 2020 - frontiersin.org
Multi-omics, variously called integrated omics, pan-omics, and trans-omics, aims to combine
two or more omics data sets to aid in data analysis, visualization and interpretation to …

Multi-omics data integration using ratio-based quantitative profiling with Quartet reference materials

Y Zheng, Y Liu, J Yang, L Dong, R Zhang, S Tian… - Nature …, 2024 - nature.com
Abstract Characterization and integration of the genome, epigenome, transcriptome,
proteome and metabolome of different datasets is difficult owing to a lack of ground truth …

Web-based multi-omics integration using the analyst software suite

JD Ewald, G Zhou, Y Lu, J Kolic, C Ellis, JD Johnson… - Nature …, 2024 - nature.com
The growing number of multi-omics studies demands clear conceptual workflows coupled
with easy-to-use software tools to facilitate data analysis and interpretation. This protocol …

A benchmark study of deep learning-based multi-omics data fusion methods for cancer

D Leng, L Zheng, Y Wen, Y Zhang, L Wu, J Wang… - Genome biology, 2022 - Springer
Background A fused method using a combination of multi-omics data enables a
comprehensive study of complex biological processes and highlights the interrelationship of …

Advancing CAR T cell therapy through the use of multidimensional omics data

J Yang, Y Chen, Y Jing, MR Green, L Han - Nature Reviews Clinical …, 2023 - nature.com
Despite the notable success of chimeric antigen receptor (CAR) T cell therapies in the
treatment of certain haematological malignancies, challenges remain in optimizing CAR …

Challenges and best practices in omics benchmarking

TG Brooks, NF Lahens, A Mrčela, GR Grant - Nature Reviews Genetics, 2024 - nature.com
Technological advances enabling massively parallel measurement of biological features—
such as microarrays, high-throughput sequencing and mass spectrometry—have ushered in …

Integrating and formatting biomedical data as pre-calculated knowledge graph embeddings in the Bioteque

A Fernández-Torras, M Duran-Frigola, M Bertoni… - Nature …, 2022 - nature.com
Biomedical data is accumulating at a fast pace and integrating it into a unified framework is a
major challenge, so that multiple views of a given biological event can be considered …