Results 41 to 50 of about 53,428 (254)

Statistical single cell multi-omics integration

Current Opinion in Systems Biology, 2018
Single cell high throughput genomic measurements are revolutionizing the fields of biology and medicine, providing a means to tackle biological problems that have thus far been inaccessible, such as the systematic discovery of new cell types, the identification of cellular heterogeneity in health and disease, or the cell-fate decisions taking place ...
Colomé-Tatché, M., Theis, F.J.
openaire   +3 more sources

A multivariate approach to the integration of multi-omics datasets [PDF]

BMC Bioinformatics, 2014
To leverage the potential of multi-omics studies, exploratory data analysis methods that provide systematic integration and comparison of multiple layers of omics information are required. We describe multiple co-inertia analysis (MCIA), an exploratory data analysis method that identifies co-relationships between multiple high dimensional datasets ...
Chen Meng, Bernhard Küster, Aedín C. Culhane, Amin Moghaddas Gholami   +3 more
openaire   +4 more sources

Community-led, integrated, reproducible multi-omics with anvi’o [PDF]

Nature Microbiology, 2020
Big data abound in microbiology, but the workflows designed to enable researchers to interpret data can constrain the biological questions that can be asked. Five years after anvi’o was first published, this community-led multi-omics platform is maturing into an open software ecosystem that reduces constraints in ‘omics data analyses.
A. Murat Eren, Evan Kiefl, Alon Shaiber, Iva Veseli, Samuel E. Miller, Matthew S. Schechter, Isaac Fink, Jessica N. Pan, Mahmoud Yousef, Emily C. Fogarty, Florian Trigodet, Andrea R. Watson, Özcan C. Esen, Ryan M. Moore, Quentin Clayssen, Michael D. Lee, Veronika Kivenson, Elaina D. Graham, Bryan D. Merrill, Antti Karkman, Daniel Blankenberg, John M. Eppley, Andreas Sjödin, Jarrod J. Scott, Xabier Vázquez-Campos, Luke J. McKay, Elizabeth A. McDaniel, Sarah L. R. Stevens, Rika E. Anderson, Jessika Fuessel, Antonio Fernandez-Guerra, Lois Maignien, Tom O. Delmont, Amy D. Willis   +33 more
openaire   +5 more sources

Modelling stem cell differentiation related processes—A practical overview for biologists

FEBS Letters, EarlyView.
Stem cell differentiation is complex and difficult to control experimentally. This review introduces suitable computational modelling approaches that can support stem cell research, from mechanistic ODE and abstract models to multiscale and deep learning methods.
Ricco Zeegelaar, Xinqi Yan, Lucas F. Jansen Klomp, Stefano Schivo, Janine N. Post   +4 more
wiley   +1 more source

OmniPath: integrated knowledgebase for multi-omics analysis

Nucleic Acids Research
Abstract Analysis and interpretation of omics data largely benefit from the use of prior knowledge. However, this knowledge is fragmented across resources and often is not directly accessible for analytical methods.
Dénes Türei, Jonathan Schaul, Nicolàs Palacio-Escat, Balázs Bohár, Yunfan Bai, Francesco Ceccarelli, Elif Çevrim, Macabe Daley, Melih Darcan, Daniel Dimitrov, Tunca Doğan, Daniel Domingo-Fernández, Aurelien Dugourd, Attila Gábor, Lejla Gul, Benjamin A Hall, Charles Tapley Hoyt, Olga Ivanova, Michal Klein, Toby Lawrence, Diego Mañanes, Dezső Módos, Sophia Müller-Dott, Márton Ölbei, Christina Schmidt, Bünyamin Şen, Fabian J Theis, Atabey Ünlü, Erva Ulusoy, Alberto Valdeolivas, Tamás Korcsmáros, Julio Saez-Rodriguez   +31 more
openaire   +4 more sources

Design and analysis strategies for robust microbiome ageing research

FEBS Letters, EarlyView.
The gut microbiome changes with age and associates with age‐related morbidity and mortality, establishing it as a potential biomarker and intervention target for ageing. Realising this potential requires methodological rigour, yet distinguishing biological signals from methodological artefacts remains challenging across cohorts. This review provides an
Mark Olenik, İsmail Güderer, Yi Wang, Tayyaba Alvi, Prasoon Pandey, Handan Melike Dönertaş   +5 more
wiley   +1 more source

Editorial: Multi-omic Data Integration in Oncology [PDF]

Frontiers in Oncology, 2020
Non peer ...
Finotello, Francesca, Calura, Enrica, Risso, Davide, Hautaniemi, Sampsa, Romualdi, Chiara   +4 more
openaire   +5 more sources

Microbiome‐blood–brain barrier interactions in aging — mechanisms and therapeutic potential

FEBS Letters, EarlyView.
Aging reshapes the gut microbiome (↓SCFA‐producing commensals; ↑pro‐inflammatory outputs), shifting circulating metabolites (↓SCFAs; ↑LPS, ↑TMAO, ↑PAA) that act at the BBB to increase nonspecific transcytosis, alter transport, and promote astrocyte reactivity, heightening brain vulnerability.
Daniel Cuervo‐Zanatta, Hari Baskar Balasubramanian, Amir Pasokh, Marietta Zille   +3 more
wiley   +1 more source

Epigenetic heterogeneity and plasticity in therapy‐induced tumor states through single‐cell multi‐omics

Molecular Oncology, EarlyView.
Single‐cell multi‐omics reveals epigenetic heterogeneity across therapy‐adaptive tumor states, including quiescent/dormant, drug‐tolerant persister, and EMT‐like phenotypes. By linking regulatory features with state‐associated biomarkers, these approaches inform biomarker‐guided therapeutic strategies for evolving tumors.
Hee Jung Kim, Hwiyeong Lee, Jin Hong, Daechan Park   +3 more
wiley   +1 more source

MoAGL-SA: a multi-omics adaptive integration method with graph learning and self attention for cancer subtype classification

BMC Bioinformatics
Background The integration of multi-omics data through deep learning has greatly improved cancer subtype classification, particularly in feature learning and multi-omics data integration.
Lei Cheng, Qian Huang, Zhengqun Zhu, Yanan Li, Shuguang Ge, Longzhen Zhang, Ping Gong   +6 more
doaj   +1 more source