416 results match your criteria interactions multi-omics

TIMEOR: a web-based tool to uncover temporal regulatory mechanisms from multi-omics data.

Nucleic Acids Res 2021 Jun 14. Epub 2021 Jun 14.

Center for Computational and Molecular Biology, Brown University, Providence, RI 02912, USA.

Uncovering how transcription factors regulate their targets at DNA, RNA and protein levels over time is critical to define gene regulatory networks (GRNs) and assign mechanisms in normal and diseased states. RNA-seq is a standard method measuring gene regulation using an established set of analysis stages. However, none of the currently available pipeline methods for interpreting ordered genomic data (in time or space) use time-series models to assign cause and effect relationships within GRNs, are adaptive to diverse experimental designs, or enable user interpretation through a web-based platform. Read More

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Editorial: Application of Systems Biology in Molecular Characterization and Diagnosis of Cancer.

Front Mol Biosci 2021 28;8:668146. Epub 2021 May 28.

Department of Surgery, School of Medicine, University of Maryland, College Park, MD, United States.

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Efficient representations of tumor diversity with paired DNA-RNA aberrations.

PLoS Comput Biol 2021 Jun 11;17(6):e1008944. Epub 2021 Jun 11.

Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America.

Cancer cells display massive dysregulation of key regulatory pathways due to now well-catalogued mutations and other DNA-related aberrations. Moreover, enormous heterogeneity has been commonly observed in the identity, frequency and location of these aberrations across individuals with the same cancer type or subtype, and this variation naturally propagates to the transcriptome, resulting in myriad types of dysregulated gene expression programs. Many have argued that a more integrative and quantitative analysis of heterogeneity of DNA and RNA molecular profiles may be necessary for designing more systematic explorations of alternative therapies and improving predictive accuracy. Read More

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PredTAD: A machine learning framework that models 3D chromatin organization alterations leading to oncogene dysregulation in breast cancer cell lines.

Comput Struct Biotechnol J 2021 7;19:2870-2880. Epub 2021 May 7.

School of Biomedical Informatics, University of Texas Health Science Center, Houston, TX 77054, USA.

Topologically associating domains, or TADs, play important roles in genome organization and gene regulation; however, they are often altered in diseases. High-throughput chromatin conformation capturing assays, such as Hi-C, can capture domains of increased interactions, and TADs and boundaries can be identified using well-established analytical tools. However, generating Hi-C data is expensive. Read More

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Successive High-Resolution (HO)-GCIB and C-SIMS Imaging Integrates Multi-Omics in Different Cell Types in Breast Cancer Tissue.

Anal Chem 2021 Jun 2;93(23):8143-8151. Epub 2021 Jun 2.

Department of Chemistry, Pennsylvania State University, Chemistry Building, Shortlidge Rd, University Park, Pennsylvania 16802, United States.

The temporo-spatial organization of different cells in the tumor microenvironment (TME) is the key to understanding their complex communication networks and the immune landscape that exists within compromised tissues. Multi-omics profiling of single-interacting cells in the native TME is critical for providing further information regarding the reprograming mechanisms leading to immunosuppression and tumor progression. This requires new technologies for biomolecular profiling of phenotypically heterogeneous cells on the same tissue sample. Read More

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Predicting COVID-19-Comorbidity Pathway Crosstalk-Based Targets and Drugs: Towards Personalized COVID-19 Management.

Biomedicines 2021 May 17;9(5). Epub 2021 May 17.

PanTherapeutics, CH 1095 Lutry, Switzerland.

It is well established that pre-existing comorbid conditions such as hypertension, diabetes, obesity, cardiovascular diseases (CVDs), chronic kidney diseases (CKDs), cancers, and chronic obstructive pulmonary disease (COPD) are associated with increased severity and fatality of COVID-19. The increased death from COVID-19 is due to the unavailability of a gold standard therapeutic and, more importantly, the lack of understanding of how the comorbid conditions and COVID-19 interact at the molecular level, so that personalized management strategies can be adopted. Here, using multi-omics data sets and bioinformatics strategy, we identified the pathway crosstalk between COVID-19 and diabetes, hypertension, CVDs, CKDs, and cancers. Read More

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The Impact of Microbiome and Microbiota-Derived Sodium Butyrate on Transcriptome and Metabolome Revealed by Multi-Omics Analysis.

Metabolites 2021 May 6;11(5). Epub 2021 May 6.

Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China.

The host microbiome plays an important role in regulating physiology through microbiota-derived metabolites during host-microbiome interactions. However, molecular mechanism underly host-microbiome interactions remains to be explored. In this study, we used as the model to investigate the influence of microbiome and microbiota-derived metabolite sodium butyrate on host transcriptome and metabolome. Read More

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Lantern: an integrative repository of functional annotations for lncRNAs in the human genome.

BMC Bioinformatics 2021 May 26;22(1):279. Epub 2021 May 26.

Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University, Informatics and Communications Technology Complex, 535 W Michigan St., IT 475H, Indianapolis, IN, 46202, USA.

Background: With advancements in omics technologies, the range of biological processes where long non-coding RNAs (lncRNAs) are involved, is expanding extensively, thereby generating the need to develop lncRNA annotation resources. Although, there are a plethora of resources for annotating genes, despite the extensive corpus of lncRNA literature, the available resources with lncRNA ontology annotations are rare.

Results: We present a lncRNA annotation extractor and repository (Lantern), developed using PubMed's abstract retrieval engine and NCBO's recommender annotation system. Read More

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Investigation of the hepatic development in the coculture of hiPSCs-derived LSECs and HLCs in a fluidic microenvironment.

APL Bioeng 2021 Jun 10;5(2):026104. Epub 2021 May 10.

Department of Chemical System Engineering, graduate school of Engineering, University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.

Interactions between the different liver cell types are critical to the maintenance or induction of their function . In this work, human-induced Pluripotent Stem Cells (hiPSCs)-derived Liver Sinusoidal Endothelial Cells (LSECs) and Hepatocytes-Like Cells (HLCs) were cultured and matured in a microfluidic environment. Both cell populations were differentiated in Petri dishes, detached, and inoculated in microfluidic biochips. Read More

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From multi-omics integration towards novel genomic interaction networks to identify key cancer cell line characteristics.

Sci Rep 2021 May 18;11(1):10542. Epub 2021 May 18.

Department of Toxicogenomics, GROW School for Oncology and Developmental Biology, Maastricht University, P.O. Box 616, 6200 MD, Maastricht, the Netherlands.

Cancer is a complex disease where cancer cells express epigenetic and transcriptomic mechanisms to promote tumor initiation, progression, and survival. To extract relevant features from the 2019 Cancer Cell Line Encyclopedia (CCLE), a multi-layer nonnegative matrix factorization approach is used. We used relevant feature genes and DNA promoter regions to construct genomic interaction network to study gene-gene and gene-DNA promoter methylation relationships. Read More

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Molecular mechanisms of mutualistic and antagonistic interactions in a plant-pollinator association.

Nat Ecol Evol 2021 May 17. Epub 2021 May 17.

Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China.

Many insects metamorphose from antagonistic larvae into mutualistic adult pollinators, with reciprocal adaptation leading to specialized insect-plant associations. It remains unknown how such interactions are established at molecular level. Here we assemble high-quality genomes of a fig species, Ficus pumila var. Read More

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Integrated OMICs unveil the bone-marrow microenvironment in human leukemia.

Cell Rep 2021 May;35(6):109119

Haematopoietic Stem Cell Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK. Electronic address:

The bone-marrow (BM) niche is the spatial environment composed by a network of multiple stromal components regulating adult hematopoiesis. We use multi-omics and computational tools to analyze multiple BM environmental compartments and decipher their mutual interactions in the context of acute myeloid leukemia (AML) xenografts. Under homeostatic conditions, we find a considerable overlap between niche populations identified using current markers. Read More

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Bradyrhizobium diazoefficiens USDA110 Nodulation of Aeschynomene afraspera Is Associated with Atypical Terminal Bacteroid Differentiation and Suboptimal Symbiotic Efficiency.

mSystems 2021 May 11;6(3). Epub 2021 May 11.

Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France

Legume plants can form root organs called nodules where they house intracellular symbiotic rhizobium bacteria. Within nodule cells, rhizobia differentiate into bacteroids, which fix nitrogen for the benefit of the plant. Depending on the combination of host plants and rhizobial strains, the output of rhizobium-legume interactions varies from nonfixing associations to symbioses that are highly beneficial for the plant. Read More

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Metaproteomics-An Advantageous Option in Studies of Host-Microbiota Interaction.

Microorganisms 2021 Apr 30;9(5). Epub 2021 Apr 30.

Department of Biochemistry and Molecular Biology, UAMS, Little Rock, AR 72205, USA.

Gut microbiome contributes to host health by maintaining homeostasis, increasing digestive efficiency, and facilitating the development of the immune system. Manipulating gut microbiota is being recognized as a therapeutic target to manage various chronic diseases. The therapeutic manipulation of the intestinal microbiome is achieved through diet modification, the administration of prebiotics, probiotics, or antibiotics, and more recently, fecal microbiome transplantation (FMT). Read More

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The Development of Bacteriophage Resistance in Depends on a Complex Metabolic Adaptation Strategy.

Viruses 2021 04 10;13(4). Epub 2021 Apr 10.

Laboratory of Molecular Biology, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 1855 Athens, Greece.

Lytic bacteriophages have been well documented to play a pivotal role in microbial ecology due to their complex interactions with bacterial species, especially in aquatic habitats. Although the use of phages as antimicrobial agents, known as phage therapy, in the aquatic environment has been increasing, recent research has revealed drawbacks due to the development of phage-resistant strains among Gram-negative species. Acquired phage resistance in marine has been proven to be a very complicated process utilizing biochemical, metabolic, and molecular adaptation strategies. Read More

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Mining Synergistic Microbial Interactions: A Roadmap on How to Integrate Multi-Omics Data.

Microorganisms 2021 Apr 14;9(4). Epub 2021 Apr 14.

Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, 04318 Leipzig, Germany.

Mining interspecies interactions remain a challenge due to the complex nature of microbial communities and the need for computational power to handle big data. Our meta-analysis indicates that genetic potential alone does not resolve all issues involving mining of microbial interactions. Nevertheless, it can be used as the starting point to infer synergistic interspecies interactions and to limit the search space (i. Read More

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Deep learning approaches for natural product discovery from plant endophytic microbiomes.

Environ Microbiome 2021 Mar 18;16(1). Epub 2021 Mar 18.

Department of Biological Sciences, Texas Tech University, 2901 Main St, Lubbock, TX, 79409, USA.

Plant microbiomes are not only diverse, but also appear to host a vast pool of secondary metabolites holding great promise for bioactive natural products and drug discovery. Yet, most microbes within plants appear to be uncultivable, and for those that can be cultivated, their metabolic potential lies largely hidden through regulatory silencing of biosynthetic genes. The recent explosion of powerful interdisciplinary approaches, including multi-omics methods to address multi-trophic interactions and artificial intelligence-based computational approaches to infer distribution of function, together present a paradigm shift in high-throughput approaches to natural product discovery from plant-associated microbes. Read More

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Multi-omics integration strategies for animal epigenetic studies.

Anim Biosci 2021 Apr 23. Epub 2021 Apr 23.

Department of Animal Science and Technology, Chung-Ang University, Anseong-si, Gyeonggi-do, 17546, Korea.

Genome-wide studies provide considerable insights into the genetic background of animals; however, the inheritance of several heritable factors cannot be elucidated. Epigenetics explains these heritabilities, including those of genes influenced by environmental factors. Knowledge of the mechanisms underlying epigenetics enables understanding the processes of gene regulation through interactions with the environment. Read More

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Adrenal Hormone Interactions and Metabolism: A Single Sample Multi-Omics Approach.

Horm Metab Res 2021 May 26;53(5):326-334. Epub 2021 Apr 26.

Institute of Clinical Chemistry and Laboratory Medicine, Technische Universität Dresden, Dresden, Germany.

The adrenal gland is important for many physiological and pathophysiological processes, but studies are often restricted by limited availability of sample material. Improved methods for sample preparation are needed to facilitate analyses of multiple classes of adrenal metabolites and macromolecules in a single sample. A procedure was developed for preparation of chromaffin cells, mouse adrenals, and human chromaffin tumors that allows for multi-omics analyses of different metabolites and preservation of native proteins. Read More

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Multi-omics study reveals that statin therapy is associated with restoration of gut microbiota homeostasis and improvement in outcomes in patients with acute coronary syndrome.

Theranostics 2021 31;11(12):5778-5793. Epub 2021 Mar 31.

Department of Cardiology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, 100730, Beijing, China.

Prior chronic treatment with statins has been shown to be associated with more favorable outcomes in patients with acute coronary syndrome (ACS). Specific changes in the gut microbiota and microbial metabolites have been shown to influence the progression of coronary artery disease. However, the critical microbial and metabolomic changes associated with the cardiovascular protective effects of statins in ACS remain elusive. Read More

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Modeling transcriptional regulation using gene regulatory networks based on multi-omics data sources.

BMC Bioinformatics 2021 Apr 19;22(1):200. Epub 2021 Apr 19.

Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA.

Background: Transcriptional regulation is complex, requiring multiple cis (local) and trans acting mechanisms working in concert to drive gene expression, with disruption of these processes linked to multiple diseases. Previous computational attempts to understand the influence of regulatory mechanisms on gene expression have used prediction models containing input features derived from cis regulatory factors. However, local chromatin looping and trans-acting mechanisms are known to also influence transcriptional regulation, and their inclusion may improve model accuracy and interpretation. Read More

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Genetics of Food Allergy.

Immunol Allergy Clin North Am 2021 May 26;41(2):301-319. Epub 2021 Mar 26.

Division of Asthma Research, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, 3333 Burnet Avenue, Cincinnati, OH 45229-3026, USA. Electronic address:

The risk factors for food allergy (FA) include both genetic variants and environmental factors. Advances using both candidate-gene association studies and genome-wide approaches have led to the identification of FA-associated genes involved in immune responses and skin barrier functions. Epigenetic changes have also been associated with the risk of FA. Read More

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Synthetic lethality-mediated precision oncology via the tumor transcriptome.

Cell 2021 Apr 14;184(9):2487-2502.e13. Epub 2021 Apr 14.

Cancer Data Science Lab, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA. Electronic address:

Precision oncology has made significant advances, mainly by targeting actionable mutations in cancer driver genes. Aiming to expand treatment opportunities, recent studies have begun to explore the utility of tumor transcriptome to guide patient treatment. Here, we introduce SELECT (synthetic lethality and rescue-mediated precision oncology via the transcriptome), a precision oncology framework harnessing genetic interactions to predict patient response to cancer therapy from the tumor transcriptome. Read More

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Advanced single-cell technologies to guide the development of bioengineered lungs.

Am J Physiol Lung Cell Mol Physiol 2021 Jun 14;320(6):L1101-L1117. Epub 2021 Apr 14.

Department of Pediatrics, University of Connecticut Health Center, Farmington, Connecticut.

Lung transplantation remains the only viable option for individuals suffering from end-stage lung failure. However, a number of current limitations exist including a continuing shortage of suitable donor lungs and immune rejection following transplantation. To address these concerns, engineering a decellularized biocompatible lung scaffold from cadavers reseeded with autologous lung cells to promote tissue regeneration is being explored. Read More

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iNetModels 2.0: an interactive visualization and database of multi-omics data.

Nucleic Acids Res 2021 Apr 13. Epub 2021 Apr 13.

Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm SE-171 21, Sweden.

It is essential to reveal the associations between various omics data for a comprehensive understanding of the altered biological process in human wellness and disease. To date, very few studies have focused on collecting and exhibiting multi-omics associations in a single database. Here, we present iNetModels, an interactive database and visualization platform of Multi-Omics Biological Networks (MOBNs). Read More

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Multilevel proteomics reveals host perturbations by SARS-CoV-2 and SARS-CoV.

Nature 2021 06 12;594(7862):246-252. Epub 2021 Apr 12.

Technical University of Munich, School of Medicine, Institute of Virology, Munich, Germany.

The emergence and global spread of SARS-CoV-2 has resulted in the urgent need for an in-depth understanding of molecular functions of viral proteins and their interactions with the host proteome. Several individual omics studies have extended our knowledge of COVID-19 pathophysiology. Integration of such datasets to obtain a holistic view of virus-host interactions and to define the pathogenic properties of SARS-CoV-2 is limited by the heterogeneity of the experimental systems. Read More

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mTOR/EGFR/iNOS/MAP2K1/FGFR/TGFB1 Are Druggable Candidates for N-(2,4-Difluorophenyl)-2',4'-Difluoro-4-Hydroxybiphenyl-3-Carboxamide (NSC765598), With Consequent Anticancer Implications.

Front Oncol 2021 26;11:656738. Epub 2021 Mar 26.

PhD Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei, Taiwan.

Background: The application of computational and multi-omics approaches has aided our understanding of carcinogenesis and the development of therapeutic strategies. NSC765598 is a novel small molecule derivative of salicylanilide. This study aims to investigate the ligand-protein interactions of NSC765598 with its potential targets and to evaluate its anticancer activities

Methods: We used multi-computational tools and clinical databases, respectively, to identify the potential drug target for NSC765598 and analyze the genetic profile and prognostic relevance of the targets in multiple cancers. Read More

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The ecology of wine fermentation: a model for the study of complex microbial ecosystems.

Appl Microbiol Biotechnol 2021 Apr 9;105(8):3027-3043. Epub 2021 Apr 9.

Department of Viticulture and Oenology, South African Grape and Wine Research Institute, Stellenbosch University, Private Bag X1, Stellenbosch, 7600, South Africa.

The general interest in microbial ecology has skyrocketed over the past decade, driven by technical advances and by the rapidly increasing appreciation of the fundamental services that these ecosystems provide. In biotechnology, ecosystems have many more functionalities than single species, and, if properly understood and harnessed, will be able to deliver better outcomes for almost all imaginable applications. However, the complexity of microbial ecosystems and of the interactions between species has limited their applicability. Read More

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Molecular subgroup of periodontitis revealed by integrated analysis of the microbiome and metabolome in a cross-sectional observational study.

J Oral Microbiol 2021 Mar 25;13(1):1902707. Epub 2021 Mar 25.

Department of Oral Microbiology, School of Dentistry, Pusan National University, Busan, South Korea.

: Periodontitis (PT) is a multifactorial, chronic inflammatory disease that can have heterogeneous clinical presentations. The oral microbiome and its metabolites have been implicated as the causes and regulators of PT pathogenesis. In this study, we assessed the oral microbiome and its metabolome in PT patients to clarify the interactions between the microbiome and its metabolites. Read More

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DeepDRK: a deep learning framework for drug repurposing through kernel-based multi-omics integration.

Brief Bioinform 2021 Apr 5. Epub 2021 Apr 5.

Division of Life Science, Department of Chemical and Biological Engineering, and State Key Laboratory of Molecular Neuroscience at The Hong Kong University of Science and Technology, China.

Recent pharmacogenomic studies that generate sequencing data coupled with pharmacological characteristics for patient-derived cancer cell lines led to large amounts of multi-omics data for precision cancer medicine. Among various obstacles hindering clinical translation, lacking effective methods for multimodal and multisource data integration is becoming a bottleneck. Here we proposed DeepDRK, a machine learning framework for deciphering drug response through kernel-based data integration. Read More

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