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Results: 24
Cohort profile of the Biomarkers of Acute Serious Illness in Children (BASIC) study
Yael Feinstein, Jennifer Claire Walker, Mark J Peters, Simon Nadel, Nazima Pathan, Naomi Edmonds, Jethro Herberg, Myrsini Kaforou, Victoria Wright, Michael Levin, Padmanabhan Ramnarayan
Dec 12, 2018
Biomarkers children multi-omics retreival Acute Disease Adolescent Bacterial Infections Biomarkers Child Child Preschool Cohort Studies Critical Care Critical Illness Emergency Medical Services England Female Follow-Up Studies Humans Infant Infant Newborn Male Multiple Organ Failure Prospective Studies
Decoding mechanism of action and sensitivity to drug candidates from integrated transcriptome and chromatin state.
Caterina Carraro, Lorenzo Bonaguro, Jonas Schulte-Schrepping, Arik Horne, Marie Oestreich, Stefanie Warnat-Herresthal, Tim Helbing, Michele De Franco, Kristian Haendler, Sach Mukherjee, Thomas Ulas, Valentina Gandin, Richard Goettlich, Anna C Aschenbrenner, Joachim L Schultze, Barbara Gatto
Sep 02, 2022
Omics-based technologies are driving major advances in precision medicine, but efforts are still required to consolidate their use in drug discovery. In this work, we exemplify the use of multi-omics to support the development...
Causal integration of multi-omics data with prior knowledge to generate mechanistic hypotheses.
Aurelien Dugourd, Christoph Kuppe, Marco Sciacovelli, Enio Gjerga, Attila Gabor, Kristina B Emdal, Vitor Vieira, Dorte B Bekker-Jensen, Jennifer Kranz, Eric MJ Bindels, Ana SH Costa, Abel Sousa, Pedro Beltrao, Miguel Rocha, Jesper V Olsen, Christian Frezza, Rafael Kramann, Julio Saez-Rodriguez
Mar 12, 2021
Multi-omics datasets can provide molecular insights beyond the sum of individual omics. Various tools have been recently developed to integrate such datasets, but there are limited strategies to systematically extract...
Multi-Omics and Genome-Scale Modeling Reveal a Metabolic Shift During C. elegans Aging.
Janna Hastings, Abraham Mains, Bhupinder Virk, Nicolas Rodriguez, Sharlene Murdoch, Juliette Pearce, Sven Bergmann, Nicolas Le Novère, Olivia Casanueva
Jul 01, 2019
In this contribution, we describe a multi-omics systems biology study of the metabolic changes that occur during aging in Caenorhabditis elegans. Sampling several time points from young adulthood until early old age, our study...
MOFA+
Ricard Argelaguet, Damien Arnol, Danila Bredikhin, Yonatan Deloro, Britta Velten, John C Marioni, Oliver Stegle
Jan 25, 2021
Technological advances have enabled the profiling of multiple molecular layers at single-cell resolution, assaying cells from multiple samples or conditions. Consequently, there is a growing need for computational strategies to...
MOFA+
Ricard Argelaguet, Damien Arnol, Danila Bredikhin, Yonatan Deloro, Britta Velten, John C. Marioni, Oliver Stegle
May 11, 2021
Abstract: Technological advances have enabled the profiling of multiple molecular layers at single-cell resolution, assaying cells from multiple samples or conditions. Consequently, there is a growing need for computational...
Decoding mechanism of action and sensitivity to drug candidates from integrated transcriptome and chromatin state.
Caterina Carraro, Lorenzo Bonaguro, Jonas Schulte-Schrepping, Arik Horne, Marie Oestreich, Stefanie Warnat-Herresthal, Tim Helbing, Michele De Franco, Kristian Haendler, Sach Mukherjee, Thomas Ulas, Valentina Gandin, Richard Goettlich, Anna C Aschenbrenner, Joachim L Schultze, Barbara Gatto
Sep 30, 2022
Omics-based technologies are driving major advances in precision medicine, but efforts are still required to consolidate their use in drug discovery. In this work, we exemplify the use of multi-omics to support the development...
Pathway-based integration of multi-omics data reveals lipidomics alterations validated in an Alzheimer's disease mouse model and risk loci carriers.
Monica Emili Garcia-Segura, Brenan R Durainayagam, Sonia Liggi, Gonçalo Graça, Beatriz Jimenez, Abbas Dehghan, Ioanna Tzoulaki, Ibrahim Karaman, Paul Elliott, Julian L Griffin
Dec 12, 2022
ATP-binding-cassette subfamily-a member-7 gene (ABCA7) Alzheimer's Disease lipidomics metabolome-wide association study (MWAS) multi-omics pathway-based integration Humans Mice Animals Alzheimer Disease lipidomics Genome-Wide Association Study multiomics Mice Knockout Lipids ATP-Binding Cassette Transporters
Ascorbic acid metabolites are involved in intraocular pressure control in the general population.
Pirro G Hysi, Anthony P Khawaja, Cristina Menni, Bani Tamraz, Nick Wareham, Kay-Tee Khaw, Paul J Foster, Leslie Z Benet, Tim D Spector, Chris J Hammond
Dec 12, 2018
A study on multi-omic oscillations in Escherichia coli metabolic networks.
BACKGROUND: Two important challenges in the analysis of molecular biology information are data (multi-omic information) integration and the detection of patterns across large scale molecular networks and sequences. They are are...
Discovery of CD80 and CD86 as recent activation markers on regulatory T cells by protein-RNA single-cell analysis.
Dominik Trzupek, Melanie Dunstan, Antony J Cutler, Mercede Lee, Leila Godfrey, Lorna Jarvis, Daniel B Rainbow, Dominik Aschenbrenner, Joanne L Jones, Holm H Uhlig, Linda S Wicker, John A Todd, Ricardo C Ferreira
Sep 09, 2020
BACKGROUND: Traditionally, the transcriptomic and proteomic characterisation of CD4+ T cells at the single-cell level has been performed by two largely exclusive types of technologies: single-cell RNA sequencing (scRNA-seq) and...
AbSeq C-C chemokine receptor type 9 (CCR9) CD4+ T cells CD80 CD86 Immunophenotyping multi-omics regulatory T cells (tregs) Single-cell RNA sequencing (scRNA-seq) Adolescent Adult B7-1 Antigen B7-2 Antigen Female Forkhead Transcription Factors Humans Male Proteome RNA RNA-seq Single-Cell Analysis T-Lymphocytes Regulatory Transcriptome
Combined single-cell profiling of expression and DNA methylation reveals splicing regulation and heterogeneity.
Stephanie M Linker, Lara Urban, Stephen J Clark, Mariya Chhatriwala, Shradha Amatya, Davis J McCarthy, Ingo Ebersberger, Ludovic Vallier, Wolf Reik, Oliver Stegle, Marc Jan Bonder
Apr 10, 2019
BACKGROUND: Alternative splicing is a key regulatory mechanism in eukaryotic cells and increases the effective number of functionally distinct gene products. Using bulk RNA sequencing, splicing variation has been studied across...
Adaptive laboratory evolution of microbial co-cultures for improved metabolite secretion.
Dimitrios Konstantinidis, Filipa Pereira, Eva-Maria Geissen, Kristina Grkovska, Eleni Kafkia, Paula Jouhten, Yongkyu Kim, Saravanan Devendran, Michael Zimmermann, Kiran Raosaheb Patil
Sep 24, 2021
Adaptive laboratory evolution has proven highly effective for obtaining microorganisms with enhanced capabilities. Yet, this method is inherently restricted to the traits that are positively linked to cell fitness, such as...
Transcriptional, epigenetic and metabolic signatures in cardiometabolic syndrome defined by extreme phenotypes.
Denis Seyres, Alessandra Cabassi, John J Lambourne, Frances Burden, Samantha Farrow, Harriet McKinney, Joana Batista, Carly Kempster, Maik Pietzner, Oliver Slingsby, Thong Huy Cao, Paulene A Quinn, Luca Stefanucci, Matthew C Sims, Karola Rehnstrom, Claire L Adams, Amy Frary, Bekir Ergüener, Roman Kreuzhuber, Gabriele Mocciaro, Simona D'Amore, Albert Koulman, Luigi Grassi, Julian L Griffin, Leong Loke Ng, Adrian Park, David B Savage, Claudia Langenberg, Christoph Bock, Kate Downes, Nicholas Wareham, Michael Allison, Michele Vacca, Paul Kirk, Mattia Frontini
Mar 12, 2022
MOFA+
Ricard Argelaguet, Damien Arnol, Danila Bredikhin, Yonatan Deloro, Britta Velten, John C. Marioni, Oliver Stegle
Jun 06, 2020
Abstract: Technological advances have enabled the profiling of multiple molecular layers at single-cell resolution, assaying cells from multiple samples or conditions. Consequently, there is a growing need for computational...
Energy Metabolites as Biomarkers in Ischemic and Dilated Cardiomyopathy
Jan Haas, Karen S. Frese, Farbod Sedaghat-Hamedani, Elham Kayvanpour, Rewati Tappu, Rouven Nietsch, Oguz Firat Tugrul, Michael Wisdom, Carsten Dietrich, Ali Amr, Tanja Weis, Torsten Niederdränk, Michael P. Murphy, Thomas Krieg, Marcus Dörr, Uwe Völker, Jens Fielitz, Norbert Frey, Stephan B. Felix, Andreas Keller, Hugo A. Katus, Benjamin Meder
Feb 20, 2021
With more than 25 million people affected, heart failure (HF) is a global threat. As energy production pathways are known to play a pivotal role in HF, we sought here to identify key metabolic changes in ischemic- and...
Complex Networks of Prion-Like Proteins Reveal Cross Talk Between Stress and Memory Pathways in Plants.
Sampurna Garai, Citu, Sneh L Singla-Pareek, Sudhir K Sopory, Charanpreet Kaur, Gitanjali Yadav
Aug 11, 2021
Prions are often considered as molecular memory devices, generating reproducible memory of a conformational change. Prion-like proteins (PrLPs) have been widely demonstrated to be present in plants, but their role in plant...
Four groups of type 2 diabetes contribute to the etiological and clinical heterogeneity in newly diagnosed individuals
A Wesolowska-Andersen, CA Brorsson, R Bizzotto, A Mari, A Tura, R Koivula, A Mahajan, A Vinuela, JF Tajes, S Sharma, M Haid, C Prehn, A Artati, MG Hong, PB Musholt, A Kurbasic, F De Masi, K Tsirigos, HK Pedersen, V Gudmundsdottir, CE Thomas, K Banasik, C Jennison, A Jones, G Kennedy, J Bell, L Thomas, G Frost, H Thomsen, K Allin, TH Hansen, H Vestergaard, T Hansen, F Rutters, P Elders, L t'Hart, A Bonnefond, M Canouil, S Brage, T Kokkola, A Heggie, D McEvoy, A Hattersley, T McDonald, H Teare, M Ridderstrale, M Walker, I Forgie, GN Giordano, P Froguel, I Pavo, H Ruetten, O Pedersen, E Dermitzakis, PW Franks, JM Schwenk, J Adamski, E Pearson, MI McCarthy, S Brunak
Mar 05, 2022
The presentation and underlying pathophysiology of type 2 diabetes (T2D) is complex and heterogeneous. Recent studies attempted to stratify T2D into distinct subgroups using data-driven approaches, but their clinical utility may...
archetypes Disease Progression glycaemic deterioration multi-omics patient clustering patient stratification Precision Medicine soft-clustering Type 2 diabetes Adult Diabetes mellitus Type 2 Disease Progression Female Follow-Up Studies Genetic Predisposition to Disease Genomics Humans Male Middle Aged Phenotype Risk Factors
Discovery of CD80 and CD86 as recent activation markers on regulatory T cells by protein-RNA single-cell analysis
Dominik Trzupek, Melanie Dunstan, Antony J. Cutler, Mercede Lee, Leila Godfrey, Lorna Jarvis, Daniel B. Rainbow, Dominik Aschenbrenner, Joanne L. Jones, Holm H. Uhlig, Linda S. Wicker, John A. Todd, Ricardo C. Ferreira
Jun 24, 2021
Abstract: Background: Traditionally, the transcriptomic and proteomic characterisation of CD4+ T cells at the single-cell level has been performed by two largely exclusive types of technologies: single-cell RNA sequencing...
Secreted Toxins From Staphylococcus aureus Strains Isolated From Keratinocyte Skin Cancers Mediate Pro-tumorigenic Inflammatory Responses in the Skin.
Annika Krueger, Julian Zaugg, Sarah Chisholm, Richard Linedale, Nancy Lachner, Siok Min Teoh, Zewen K Tuong, Samuel W Lukowski, Mark Morrison, H Peter Soyer, Philip Hugenholtz, Michelle M Hill, Ian H Frazer
Feb 08, 2022
Squamous cell carcinoma (SCC) is a common type of skin cancer that typically arises from premalignant precursor lesions named actinic keratoses (AK). Chronic inflammation is a well-known promoter of skin cancer progression. AK...
Improving prediction of disease outcome for inflammatory bowel disease
Introduction: Inflammatory bowel diseases (IBDs) are lifelong conditions causing relapsing inflammation of the intestine. In the absence of a cure, clinical management of IBDs is extremely challenging since they present with a...
Discovery of CD80 and CD86 as recent activation markers on regulatory T cells by protein-RNA single-cell analysis
Dominik Trzupek, Melanie Dunstan, Antony J. Cutler, Mercede Lee, Leila Godfrey, Lorna Jarvis, Daniel B. Rainbow, Dominik Aschenbrenner, Joanne L. Jones, Holm H. Uhlig, Linda S. Wicker, John A. Todd, Ricardo C. Ferreira
Jun 25, 2020
Abstract: Background: Traditionally, the transcriptomic and proteomic characterisation of CD4+ T cells at the single-cell level has been performed by two largely exclusive types of technologies: single-cell RNA sequencing...
Transcriptional, epigenetic and metabolic signatures in cardiometabolic syndrome defined by extreme phenotypes.
Denis Seyres, Alessandra Cabassi, John J Lambourne, Frances Burden, Samantha Farrow, Harriet McKinney, Joana Batista, Carly Kempster, Maik Pietzner, Oliver Slingsby, Thong Huy Cao, Paulene A Quinn, Luca Stefanucci, Matthew C Sims, Karola Rehnstrom, Claire L Adams, Amy Frary, Bekir Ergüener, Roman Kreuzhuber, Gabriele Mocciaro, Simona D'Amore, Albert Koulman, Luigi Grassi, Julian L Griffin, Leong Loke Ng, Adrian Park, David B Savage, Claudia Langenberg, Christoph Bock, Kate Downes, Nicholas J Wareham, Michael Allison, Michele Vacca, Paul DW Kirk, Mattia Frontini
Apr 13, 2022
Energy Metabolites as Biomarkers in Ischemic and Dilated Cardiomyopathy.
Jan Haas, Karen S Frese, Farbod Sedaghat-Hamedani, Elham Kayvanpour, Rewati Tappu, Rouven Nietsch, Oguz Firat Tugrul, Michael Wisdom, Carsten Dietrich, Ali Amr, Tanja Weis, Torsten Niederdränk, Michael P Murphy, Thomas Krieg, Marcus Dörr, Uwe Völker, Jens Fielitz, Norbert Frey, Stephan B Felix, Andreas Keller, Hugo A Katus, Benjamin Meder
Feb 25, 2021
With more than 25 million people affected, heart failure (HF) is a global threat. As energy production pathways are known to play a pivotal role in HF, we sought here to identify key metabolic changes in ischemic- and...