Enablers and challenges of spatial omics, a melting pot of technologies
Mol Syst Biol. 2023 Oct 16:e10571. doi: 10.15252/msb.202110571. Online ahead of print.ABSTRACTSpatial omics has emerged as a rapidly growing and fruitful field with hundreds of publications presenting novel methods for obtaining spatially resolved information for any omics data type on spatial scales ranging from subcellular to organismal. From a technology development perspective, spatial omics is a highly interdisciplinary field that integrates imaging and omics, spatial and molecular analyses, sequencing and mass spectrometry, and image analysis and bioinformatics. The emergence of this field has not only opened a windo...
Source: Genomics Proteomics ... - October 16, 2023 Category: Genetics & Stem Cells Authors: Theodore Alexandrov Julio Saez-Rodriguez Sinem K Saka Source Type: research
Enablers and challenges of spatial omics, a melting pot of technologies
Mol Syst Biol. 2023 Oct 16:e10571. doi: 10.15252/msb.202110571. Online ahead of print.ABSTRACTSpatial omics has emerged as a rapidly growing and fruitful field with hundreds of publications presenting novel methods for obtaining spatially resolved information for any omics data type on spatial scales ranging from subcellular to organismal. From a technology development perspective, spatial omics is a highly interdisciplinary field that integrates imaging and omics, spatial and molecular analyses, sequencing and mass spectrometry, and image analysis and bioinformatics. The emergence of this field has not only opened a windo...
Source: Genomics Proteomics ... - October 16, 2023 Category: Genetics & Stem Cells Authors: Theodore Alexandrov Julio Saez-Rodriguez Sinem K Saka Source Type: research
Enablers and challenges of spatial omics, a melting pot of technologies
Mol Syst Biol. 2023 Oct 16:e10571. doi: 10.15252/msb.202110571. Online ahead of print.ABSTRACTSpatial omics has emerged as a rapidly growing and fruitful field with hundreds of publications presenting novel methods for obtaining spatially resolved information for any omics data type on spatial scales ranging from subcellular to organismal. From a technology development perspective, spatial omics is a highly interdisciplinary field that integrates imaging and omics, spatial and molecular analyses, sequencing and mass spectrometry, and image analysis and bioinformatics. The emergence of this field has not only opened a windo...
Source: Genomics Proteomics ... - October 16, 2023 Category: Genetics & Stem Cells Authors: Theodore Alexandrov Julio Saez-Rodriguez Sinem K Saka Source Type: research
From BIG Data Center to China National Center for Bioinformation
Genomics Proteomics Bioinformatics. 2023 Oct 11:S1672-0229(23)00109-2. doi: 10.1016/j.gpb.2023.10.001. Online ahead of print.NO ABSTRACTPMID:37832784 | DOI:10.1016/j.gpb.2023.10.001 (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - October 13, 2023 Category: Genetics & Stem Cells Authors: Yiming Bao Yongbiao Xue Source Type: research
From BIG Data Center to China National Center for Bioinformation
Genomics Proteomics Bioinformatics. 2023 Oct 11:S1672-0229(23)00109-2. doi: 10.1016/j.gpb.2023.10.001. Online ahead of print.NO ABSTRACTPMID:37832784 | DOI:10.1016/j.gpb.2023.10.001 (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - October 13, 2023 Category: Genetics & Stem Cells Authors: Yiming Bao Yongbiao Xue Source Type: research
Advancing microbiome research with machine learning: key findings from the ML4Microbiome COST action
Front Microbiol. 2023 Sep 25;14:1257002. doi: 10.3389/fmicb.2023.1257002. eCollection 2023.ABSTRACTThe rapid development of machine learning (ML) techniques has opened up the data-dense field of microbiome research for novel therapeutic, diagnostic, and prognostic applications targeting a wide range of disorders, which could substantially improve healthcare practices in the era of precision medicine. However, several challenges must be addressed to exploit the benefits of ML in this field fully. In particular, there is a need to establish "gold standard" protocols for conducting ML analysis experiments and improve interact...
Source: Genomics Proteomics ... - October 9, 2023 Category: Genetics & Stem Cells Authors: Domenica D'Elia Jaak Truu Leo Lahti Magali Berland Georgios Papoutsoglou Michelangelo Ceci Aldert Zomer Marta B Lopes Eliana Ibrahimi Aleksandra Gruca Alina Nechyporenko Marcus Frohme Thomas Klammsteiner Enrique Carrillo-de Santa Pau Laura Judith Marcos-Z Source Type: research
Advancing microbiome research with machine learning: key findings from the ML4Microbiome COST action
Front Microbiol. 2023 Sep 25;14:1257002. doi: 10.3389/fmicb.2023.1257002. eCollection 2023.ABSTRACTThe rapid development of machine learning (ML) techniques has opened up the data-dense field of microbiome research for novel therapeutic, diagnostic, and prognostic applications targeting a wide range of disorders, which could substantially improve healthcare practices in the era of precision medicine. However, several challenges must be addressed to exploit the benefits of ML in this field fully. In particular, there is a need to establish "gold standard" protocols for conducting ML analysis experiments and improve interact...
Source: Genomics Proteomics ... - October 9, 2023 Category: Genetics & Stem Cells Authors: Domenica D'Elia Jaak Truu Leo Lahti Magali Berland Georgios Papoutsoglou Michelangelo Ceci Aldert Zomer Marta B Lopes Eliana Ibrahimi Aleksandra Gruca Alina Nechyporenko Marcus Frohme Thomas Klammsteiner Enrique Carrillo-de Santa Pau Laura Judith Marcos-Z Source Type: research
Advancing microbiome research with machine learning: key findings from the ML4Microbiome COST action
Front Microbiol. 2023 Sep 25;14:1257002. doi: 10.3389/fmicb.2023.1257002. eCollection 2023.ABSTRACTThe rapid development of machine learning (ML) techniques has opened up the data-dense field of microbiome research for novel therapeutic, diagnostic, and prognostic applications targeting a wide range of disorders, which could substantially improve healthcare practices in the era of precision medicine. However, several challenges must be addressed to exploit the benefits of ML in this field fully. In particular, there is a need to establish "gold standard" protocols for conducting ML analysis experiments and improve interact...
Source: Genomics Proteomics ... - October 9, 2023 Category: Genetics & Stem Cells Authors: Domenica D'Elia Jaak Truu Leo Lahti Magali Berland Georgios Papoutsoglou Michelangelo Ceci Aldert Zomer Marta B Lopes Eliana Ibrahimi Aleksandra Gruca Alina Nechyporenko Marcus Frohme Thomas Klammsteiner Enrique Carrillo-de Santa Pau Laura Judith Marcos-Z Source Type: research
Advancing microbiome research with machine learning: key findings from the ML4Microbiome COST action
Front Microbiol. 2023 Sep 25;14:1257002. doi: 10.3389/fmicb.2023.1257002. eCollection 2023.ABSTRACTThe rapid development of machine learning (ML) techniques has opened up the data-dense field of microbiome research for novel therapeutic, diagnostic, and prognostic applications targeting a wide range of disorders, which could substantially improve healthcare practices in the era of precision medicine. However, several challenges must be addressed to exploit the benefits of ML in this field fully. In particular, there is a need to establish "gold standard" protocols for conducting ML analysis experiments and improve interact...
Source: Genomics Proteomics ... - October 9, 2023 Category: Genetics & Stem Cells Authors: Domenica D'Elia Jaak Truu Leo Lahti Magali Berland Georgios Papoutsoglou Michelangelo Ceci Aldert Zomer Marta B Lopes Eliana Ibrahimi Aleksandra Gruca Alina Nechyporenko Marcus Frohme Thomas Klammsteiner Enrique Carrillo-de Santa Pau Laura Judith Marcos-Z Source Type: research
Advancing microbiome research with machine learning: key findings from the ML4Microbiome COST action
Front Microbiol. 2023 Sep 25;14:1257002. doi: 10.3389/fmicb.2023.1257002. eCollection 2023.ABSTRACTThe rapid development of machine learning (ML) techniques has opened up the data-dense field of microbiome research for novel therapeutic, diagnostic, and prognostic applications targeting a wide range of disorders, which could substantially improve healthcare practices in the era of precision medicine. However, several challenges must be addressed to exploit the benefits of ML in this field fully. In particular, there is a need to establish "gold standard" protocols for conducting ML analysis experiments and improve interact...
Source: Genomics Proteomics ... - October 9, 2023 Category: Genetics & Stem Cells Authors: Domenica D'Elia Jaak Truu Leo Lahti Magali Berland Georgios Papoutsoglou Michelangelo Ceci Aldert Zomer Marta B Lopes Eliana Ibrahimi Aleksandra Gruca Alina Nechyporenko Marcus Frohme Thomas Klammsteiner Enrique Carrillo-de Santa Pau Laura Judith Marcos-Z Source Type: research
OBIA: An Open Biomedical Imaging Archive
Genomics Proteomics Bioinformatics. 2023 Oct 6:S1672-0229(23)00108-0. doi: 10.1016/j.gpb.2023.09.003. Online ahead of print.ABSTRACTWith the development of artificial intelligence (AI) technologies, biomedical imaging data play an important role in scientific research and clinical application, but the available resources are limited. Here we present Open Biomedical Imaging Archive (OBIA), a repository for archiving biomedical imaging and related clinical data. OBIA adopts five data objects (Collection, Individual, Study, Series, and Image) for data organization, accepts the submission of biomedical images of multiple modal...
Source: Genomics Proteomics ... - October 8, 2023 Category: Genetics & Stem Cells Authors: Enhui Jin Dongli Zhao Gangao Wu Junwei Zhu Zhonghuang Wang Zhiyao Wei Sisi Zhang Anke Wang Bixia Tang Xu Chen Yanling Sun Zhe Zhang Wenming Zhao Yuanguang Meng Source Type: research
Disrupted Binding of Cystathionine γ-Lyase to p53 Promotes Endothelial Senescence
CONCLUSIONS: Aging-associated impairment of vascular repair is partly determined by the vasoprotective enzyme CSE.PMID:37800327 | DOI:10.1161/CIRCRESAHA.123.323084 (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - October 6, 2023 Category: Genetics & Stem Cells Authors: Jiong Hu Matthias S Leisegang Mario Looso Maria-Kyriaki Drekolia Janina Wittig Janina Mettner Christina Karantanou Anastasia Kyselova Gabrjela Dumbovic Xiaoming Li Yuanyuan Li Stefan Guenther David John Mauro Siragusa Sven Zukunft James Oo Ilka Wittig Sus Source Type: research
α-ketoglutarate-dependent KDM6 histone demethylases regulate Interferon Stimulated Gene expression in Lupus
CONCLUSION: Our study suggests chronic IFNα exposure alters epigenetic regulation of ISG expression in SLE monocytes via changes in immunometabolism, a mechanism reflecting trained immunity to type I IFN. Importantly, it opens the possibility that targeting histone modifying enzymes such as KDM6A/B may reduce IFN responses in SLE.PMID:37800478 | DOI:10.1002/art.42724 (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - October 6, 2023 Category: Genetics & Stem Cells Authors: Erica N Montano Moumita Bose Lihong Huo Gantsetseg Tumurkhuu Gabriela De Los Santos Brianna Simental Aleksandr B Stotland Janet Wei C Noel Bairey Merz Jo Suda Gislaine Martins Sarfaraz Lalani Kate Lawrenson Yizhou Wang Sarah Parker Swamy Venuturupalli Mar Source Type: research
The non-ribosomal peptide synthetase-independent siderophore (NIS) rhizobactin produced by < em > Caballeronia mineralivorans < /em > PML1(12) confers the ability to weather minerals
This study provides the first demonstration of the synthesis of a NIS in the genus Caballeronia and its involvement in mineral weathering. Our conclusions reinforce the idea that strain PML1(12) is particularly well adapted to nutrient-poor environments. IMPORTANCE This work deciphers the molecular and genetic bases used by strain PML1(12) of Caballeronia mineralivorans to mobilize iron and weather minerals. Through the combination of bioinformatics, chemical, and phylogenetic analyses, we characterized the siderophore produced by strain PML1(12) and the related genes. This siderophore was identified as rhizobactin and cla...
Source: Genomics Proteomics ... - October 6, 2023 Category: Genetics & Stem Cells Authors: Cintia Blanco Nouche C édric Paris Tiphaine Dhalleine Philippe Oger Marie-Pierre Turpault St éphane Uroz Source Type: research
Emerging Trends in Big Data Analysis in Computational Biology and Bioinformatics in Health Informatics: A Case Study on Epilepsy and Seizures
This study might provide insight into the workings of the disease and shows the importance of continued research into epilepsy and other conditions that can trigger seizure activity.PMID:37803114 | DOI:10.1007/978-1-0716-3461-5_6 (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - October 6, 2023 Category: Genetics & Stem Cells Authors: Usha Chouhan Rakesh Kumar Sahu Shaifali Bhatt Sonu Kurmi Jyoti Kant Choudhari Source Type: research
