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  1. AU=Vlachos Ioannis S.
  2. AU=Grundy Scott M
  3. AU="Koumoutsea, Evangelia Vlachodimitropoulou"
  4. AU="Almen, Aimee"
  5. AU="Howard, Dianna S."
  6. AU="Elizete Rizzo"
  7. AU="El Sayegh, Suzanne"
  8. AU="Vaittinen, Tiina"
  9. AU="Khir, Amir S"
  10. AU=Patterson Andrew D
  11. AU="Kim, Joyce Mary"
  12. AU="Saribay, S Adil"
  13. AU="Couderc, M."
  14. AU="Macerlane de Lira Silva"
  15. AU=Neal Michael S
  16. AU="Nakai, Kozo"
  17. AU="Debatin, Jörg F."
  18. AU="Plant, Laura"
  19. AU="Manuel Tisminetzky"
  20. AU="Monaco, Carlo"
  21. AU="Srivastava, Rupesh"
  22. AU="Nathan, Jaimie D"
  23. AU="Schnegelberger, Regina D"
  24. AU=Doshi Paresh
  25. AU="Cecilia Hognon"
  26. AU="Mason, Jeremy K."
  27. AU=Hasumi Hisashi
  28. AU="Swati Sethi"
  29. AU="Martin G. Myers, Jr."
  30. AU="Marcus-Sekura, Carol"
  31. AU="Petagine, Lucy"
  32. AU="Jessa R. Alexander"
  33. AU=Rauner Martina
  34. AU="Richlen, Mindy L"
  35. AU="Merghani, Nada M"
  36. AU=Splitt M P
  37. AU="Zlatanović, Gordana"

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  1. Artikel ; Online: Polycomb-mediated silencing of miR-8 is required for maintenance of intestinal stemness in Drosophila melanogaster.

    Veneti, Zoe / Fasoulaki, Virginia / Kalavros, Nikolaos / Vlachos, Ioannis S / Delidakis, Christos / Eliopoulos, Aristides G

    Nature communications

    2024  Band 15, Heft 1, Seite(n) 1924

    Abstract: Balancing maintenance of self-renewal and differentiation is a key property of adult stem cells. The epigenetic mechanisms controlling this balance remain largely unknown. Herein, we report that the Polycomb Repressive Complex 2 (PRC2) is required for ... ...

    Abstract Balancing maintenance of self-renewal and differentiation is a key property of adult stem cells. The epigenetic mechanisms controlling this balance remain largely unknown. Herein, we report that the Polycomb Repressive Complex 2 (PRC2) is required for maintenance of the intestinal stem cell (ISC) pool in the adult female Drosophila melanogaster. We show that loss of PRC2 activity in ISCs by RNAi-mediated knockdown or genetic ablation of the enzymatic subunit Enhancer of zeste, E(z), results in loss of stemness and precocious differentiation of enteroblasts to enterocytes. Mechanistically, we have identified the microRNA miR-8 as a critical target of E(z)/PRC2-mediated tri-methylation of histone H3 at Lys27 (H3K27me3) and uncovered a dynamic relationship between E(z), miR-8 and Notch signaling in controlling stemness versus differentiation of ISCs. Collectively, these findings uncover a hitherto unrecognized epigenetic layer in the regulation of stem cell specification that safeguards intestinal homeostasis.
    Mesh-Begriff(e) Female ; Animals ; Drosophila melanogaster/genetics ; Drosophila Proteins/genetics ; Polycomb-Group Proteins ; Intestines ; Polycomb Repressive Complex 2/genetics ; MicroRNAs/genetics
    Chemische Substanzen Drosophila Proteins ; Polycomb-Group Proteins ; Polycomb Repressive Complex 2 (EC 2.1.1.43) ; MicroRNAs
    Sprache Englisch
    Erscheinungsdatum 2024-03-02
    Erscheinungsland England
    Dokumenttyp Journal Article
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-024-46119-9
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  2. Artikel ; Online: Identifying and profiling structural similarities between Spike of SARS-CoV-2 and other viral or host proteins with Machaon.

    Kakoulidis, Panos / Vlachos, Ioannis S / Thanos, Dimitris / Blatch, Gregory L / Emiris, Ioannis Z / Anastasiadou, Ema

    Communications biology

    2023  Band 6, Heft 1, Seite(n) 752

    Abstract: ... ranks, as well as host proteins, such as ACE2 receptor. Machaon's meta-analysis of the results ...

    Abstract Using protein structure to predict function, interactions, and evolutionary history is still an open challenge, with existing approaches relying extensively on protein homology and families. Here, we present Machaon, a data-driven method combining orientation invariant metrics on phi-psi angles, inter-residue contacts and surface complexity. It can be readily applied on whole structures or segments-such as domains and binding sites. Machaon was applied on SARS-CoV-2 Spike monomers of native, Delta and Omicron variants and identified correlations with a wide range of viral proteins from close to distant taxonomy ranks, as well as host proteins, such as ACE2 receptor. Machaon's meta-analysis of the results highlights structural, chemical and transcriptional similarities between the Spike monomer and human proteins, indicating a multi-level viral mimicry. This extended analysis also revealed relationships of the Spike protein with biological processes such as ubiquitination and angiogenesis and highlighted different patterns in virus attachment among the studied variants. Available at: https://machaonweb.com .
    Mesh-Begriff(e) Humans ; SARS-CoV-2/genetics ; SARS-CoV-2/metabolism ; COVID-19 ; Binding Sites ; Receptors, Virus/metabolism
    Chemische Substanzen Receptors, Virus
    Sprache Englisch
    Erscheinungsdatum 2023-07-19
    Erscheinungsland England
    Dokumenttyp Meta-Analysis ; Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 2399-3642
    ISSN (online) 2399-3642
    DOI 10.1038/s42003-023-05076-7
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  3. Artikel: The Role of Sclerostin in Bone Diseases.

    Vasiliadis, Elias S / Evangelopoulos, Dimitrios-Stergios / Kaspiris, Angelos / Benetos, Ioannis S / Vlachos, Christos / Pneumaticos, Spyros G

    Journal of clinical medicine

    2022  Band 11, Heft 3

    Abstract: ... Many studies have been published in the last few years regarding sclerostin's origin, regulation, and mechanism ...

    Abstract Sclerostin has been identified as an important regulator of bone homeostasis through inhibition of the canonical Wnt-signaling pathway, and it is involved in the pathogenesis of many different skeletal diseases. Many studies have been published in the last few years regarding sclerostin's origin, regulation, and mechanism of action. The ongoing research emphasizes the potential therapeutic implications of sclerostin in many pathological conditions with or without skeletal involvement. Antisclerostin antibodies have recently been approved for the treatment of osteoporosis, and several animal studies and clinical trials are currently under way to evaluate the effectiveness of antisclerostin antibodies in the treatment of other than osteoporosis skeletal disorders and cancer with promising results. Understanding the exact role of sclerostin may lead to new therapeutic approaches for the treatment of skeletal disorders.
    Sprache Englisch
    Erscheinungsdatum 2022-02-02
    Erscheinungsland Switzerland
    Dokumenttyp Journal Article ; Review
    ZDB-ID 2662592-1
    ISSN 2077-0383
    ISSN 2077-0383
    DOI 10.3390/jcm11030806
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  4. Artikel ; Online: DIANA-miTED: a microRNA tissue expression database.

    Kavakiotis, Ioannis / Alexiou, Athanasios / Tastsoglou, Spyros / Vlachos, Ioannis S / Hatzigeorgiou, Artemis G

    Nucleic acids research

    2021  Band 50, Heft D1, Seite(n) D1055–D1061

    Abstract: microRNAs (miRNAs) are short (∼23nt) single-stranded non-coding RNAs that act as potent post-transcriptional gene expression regulators. Information about miRNA expression and distribution across cell types and tissues is crucial to the understanding of ... ...

    Abstract microRNAs (miRNAs) are short (∼23nt) single-stranded non-coding RNAs that act as potent post-transcriptional gene expression regulators. Information about miRNA expression and distribution across cell types and tissues is crucial to the understanding of their function and for their translational use as biomarkers or therapeutic targets. DIANA-miTED is the most comprehensive and systematic collection of miRNA expression values derived from the analysis of 15 183 raw human small RNA-Seq (sRNA-Seq) datasets from the Sequence Read Archive (SRA) and The Cancer Genome Atlas (TCGA). Metadata quality maximizes the utility of expression atlases, therefore we manually curated SRA and TCGA-derived information to deliver a comprehensive and standardized set, incorporating in total 199 tissues, 82 anatomical sublocations, 267 cell lines and 261 diseases. miTED offers rich instant visualizations of the expression and sample distributions of requested data across variables, as well as study-wide diagrams and graphs enabling efficient content exploration. Queries also generate links towards state-of-the-art miRNA functional resources, deeming miTED an ideal starting point for expression retrieval, exploration, comparison, and downstream analysis, without requiring bioinformatics support or expertise. DIANA-miTED is freely available at http://www.microrna.gr/mited.
    Mesh-Begriff(e) Binding Sites/genetics ; Databases, Genetic ; Databases, Nucleic Acid ; Gene Expression Regulation/genetics ; Genome/genetics ; Humans ; MicroRNAs/classification ; MicroRNAs/genetics ; Software ; Tissue Distribution/genetics ; Transcriptome/genetics
    Chemische Substanzen MicroRNAs
    Sprache Englisch
    Erscheinungsdatum 2021-09-01
    Erscheinungsland England
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gkab733
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  5. Artikel ; Online: Determinants of gastric cancer immune escape identified from non-coding immune-landscape quantitative trait loci.

    Miliotis, Christos / Ma, Yuling / Katopodi, Xanthi-Lida / Karagkouni, Dimitra / Kanata, Eleni / Mattioli, Kaia / Kalavros, Nikolas / Pita-Juárez, Yered H / Batalini, Felipe / Ramnarine, Varune R / Nanda, Shivani / Slack, Frank J / Vlachos, Ioannis S

    Nature communications

    2024  Band 15, Heft 1, Seite(n) 4319

    Abstract: The landscape of non-coding mutations in cancer progression and immune evasion is largely unexplored. Here, we identify transcrptome-wide somatic and germline 3' untranslated region (3'-UTR) variants from 375 gastric cancer patients from The Cancer ... ...

    Abstract The landscape of non-coding mutations in cancer progression and immune evasion is largely unexplored. Here, we identify transcrptome-wide somatic and germline 3' untranslated region (3'-UTR) variants from 375 gastric cancer patients from The Cancer Genome Atlas. By performing gene expression quantitative trait loci (eQTL) and immune landscape QTL (ilQTL) analysis, we discover 3'-UTR variants with cis effects on expression and immune landscape phenotypes, such as immune cell infiltration and T cell receptor diversity. Using a massively parallel reporter assay, we distinguish between causal and correlative effects of 3'-UTR eQTLs in immune-related genes. Our approach identifies numerous 3'-UTR eQTLs and ilQTLs, providing a unique resource for the identification of immunotherapeutic targets and biomarkers. A prioritized ilQTL variant signature predicts response to immunotherapy better than standard-of-care PD-L1 expression in independent patient cohorts, showcasing the untapped potential of non-coding mutations in cancer.
    Mesh-Begriff(e) Humans ; Quantitative Trait Loci ; Stomach Neoplasms/genetics ; Stomach Neoplasms/immunology ; Tumor Escape/genetics ; 3' Untranslated Regions/genetics ; Gene Expression Regulation, Neoplastic ; Mutation ; B7-H1 Antigen/genetics ; B7-H1 Antigen/metabolism ; Immunotherapy/methods ; Female ; Male
    Chemische Substanzen CD274 protein, human
    Sprache Englisch
    Erscheinungsdatum 2024-05-21
    Erscheinungsland England
    Dokumenttyp Journal Article
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-024-48436-5
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  6. Artikel ; Online: Machine learning natural language processing for identifying venous thromboembolism: Systematic review and meta-analysis.

    Lam, Barbara D / Chrysafi, Pavlina / Chiasakul, Thita / Khosla, Harshit / Karagkouni, Dimitra / McNichol, Megan / Adamski, Alys / Reyes, Nimia / Abe, Karon / Mantha, Simon / Vlachos, Ioannis S / Zwicker, Jeffrey I / Patell, Rushad

    Blood advances

    2024  

    Abstract: ... A meta-analysis evaluated the pooled performance of each study's best performing model that evaluated ...

    Abstract Venous thromboembolism (VTE) is a leading cause of preventable in-hospital mortality. Monitoring VTE cases is limited by the challenges of manual chart review and diagnosis code interpretation. Natural language processing (NLP) can automate the process. Rule-based NLP methods are effective but time consuming. Machine learning (ML)-NLP methods present a promising solution. We conducted a systematic review and meta-analysis of studies published before May 2023 that use ML-NLP to identify VTE diagnoses in the electronic health records. Four reviewers screened all manuscripts, excluding studies that only used a rule-based method. A meta-analysis evaluated the pooled performance of each study's best performing model that evaluated for pulmonary embolism (PE) and/or deep vein thrombosis (DVT). Pooled sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) with confidence interval (CI) were calculated by DerSimonian and Laird method using a random-effects model. Study quality was assessed using an adapted TRIPOD tool. Thirteen studies were included in the systematic review and 8 had data available for meta-analysis. Pooled sensitivity was 0.931 (95% CI 0.881-0.962), specificity 0.984 (95% CI 0.967-0.992), PPV 0.910 (95% CI 0.865-0.941) and NPV 0.985 (95% CI 0.977-0.990). All studies met at least 13 of the 21 NLP-modified TRIPOD items, demonstrating fair quality. The highest performing models used vectorization rather than bag-of-words, and deep learning techniques such as convolutional neural networks. There was significant heterogeneity in the studies and only four validated their model on an external dataset. Further standardization of ML studies can help progress this novel technology towards real-world implementation.
    Sprache Englisch
    Erscheinungsdatum 2024-03-24
    Erscheinungsland United States
    Dokumenttyp Journal Article
    ZDB-ID 2915908-8
    ISSN 2473-9537 ; 2473-9529
    ISSN (online) 2473-9537
    ISSN 2473-9529
    DOI 10.1182/bloodadvances.2023012200
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  7. Artikel ; Online: Functional Analysis of miRNAs Using the DIANA Tools Online Suite.

    Vlachos, Ioannis S / Hatzigeorgiou, Artemis G

    Methods in molecular biology (Clifton, N.J.)

    2017  Band 1517, Seite(n) 25–50

    Abstract: microRNAs (miRNAs) are central regulators of gene expression. They are actively studied for their involvement in numerous physiological and pathological conditions but also as diagnostic biomarkers or promising therapeutic targets. The increased ... ...

    Abstract microRNAs (miRNAs) are central regulators of gene expression. They are actively studied for their involvement in numerous physiological and pathological conditions but also as diagnostic biomarkers or promising therapeutic targets. The increased complexity of the miRNA interactomes hinders straightforward interpretation of miRNA expression differences between states and conditions. To this end, functional analysis web servers process and combine experimental and in silico data, enabling researchers to uncover targeted pathways and transcriptional mechanisms that are hidden within numerous interactions and vast expression datasets. DIANA-tools ( www.microrna.gr ) is a web server hosting state-of-the-art utilities and databases for miRNA functional investigation. Available utilities cover a wide scope of different needs and research scenarios, rendering DIANA website a one-stop-shop for miRNA analyses. The most commonly utilized databases and algorithms include DIANA-microT-CDS, DIANA-TarBase v7.0, DIANA-lncBase v2.0, DIANA-miRGen v3.0, DIANA-miRPath v3.0, and DIANA-mirExTra v2.0.In the presented protocol, we will utilize different online tools in order to explore miRNA functions and to identify probable targets of interest for downstream analyses and wet lab experiments. The combined use of different applications from the DIANA suite can shed light to numerous different aspects of miRNA regulation and regulatory function, without the necessity for extensive bioinformatics expertise or computational infrastructure.
    Sprache Englisch
    Erscheinungsdatum 2017
    Erscheinungsland United States
    Dokumenttyp Journal Article
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-4939-6563-2_2
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  8. Artikel ; Online: Artificial intelligence for venous thromboembolism prophylaxis: Clinician perspectives.

    Lam, Barbara D / Zerbey, Sabrina / Pinson, Amanda / Robertson, William / Rosovsky, Rachel P / Lake, Leslie / Dodge, Laura E / Adamski, Alys / Reyes, Nimia / Abe, Karon / Vlachos, Ioannis S / Zwicker, Jeffrey I / Schonberg, Mara / Patell, Rushad

    Research and practice in thrombosis and haemostasis

    2023  Band 7, Heft 8, Seite(n) 102272

    Sprache Englisch
    Erscheinungsdatum 2023-11-23
    Erscheinungsland United States
    Dokumenttyp Journal Article
    ISSN 2475-0379
    ISSN (online) 2475-0379
    DOI 10.1016/j.rpth.2023.102272
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  9. Artikel ; Online: Manatee: detection and quantification of small non-coding RNAs from next-generation sequencing data.

    Handzlik, Joanna E / Tastsoglou, Spyros / Vlachos, Ioannis S / Hatzigeorgiou, Artemis G

    Scientific reports

    2020  Band 10, Heft 1, Seite(n) 705

    Abstract: Small non-coding RNAs (sncRNAs) play important roles in health and disease. Next Generation Sequencing (NGS) technologies are considered as the most powerful and versatile methodologies to explore small RNA (sRNA) transcriptomes in diverse experimental ... ...

    Abstract Small non-coding RNAs (sncRNAs) play important roles in health and disease. Next Generation Sequencing (NGS) technologies are considered as the most powerful and versatile methodologies to explore small RNA (sRNA) transcriptomes in diverse experimental and clinical studies. Small RNA-Seq (sRNA-Seq) data analysis proved to be challenging due to non-unique genomic origin, short length, and abundant post-transcriptional modifications of sRNA species. Here, we present Manatee, an algorithm for the quantification of sRNA classes and the detection of novel expressed non-coding loci. Manatee combines prior annotation of sRNAs with reliable alignment density information and extensive rescue of usually neglected multimapped reads to provide accurate transcriptome-wide sRNA expression quantification. Comparison of Manatee against state-of-the-art implementations using real and simulated data demonstrates its high accuracy across diverse sRNA classes. Manatee also goes beyond common pipelines by identifying and quantifying expression from unannotated loci and microRNA isoforms (isomiRs). It is user-friendly, can be easily incorporated in pipelines, and provides a simplified output suitable for direct usage in downstream analyses and functional studies.
    Mesh-Begriff(e) Algorithms ; Computational Biology/methods ; Gene Expression Profiling ; Hep G2 Cells ; High-Throughput Nucleotide Sequencing ; Humans ; MCF-7 Cells ; Molecular Sequence Annotation ; Neoplasms/genetics ; RNA, Small Untranslated/classification ; RNA, Small Untranslated/genetics ; Sequence Analysis, RNA/methods
    Chemische Substanzen RNA, Small Untranslated
    Sprache Englisch
    Erscheinungsdatum 2020-01-20
    Erscheinungsland England
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-020-57495-9
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  10. Artikel ; Online: Serine and arginine rich splicing factor 1 deficiency alters pathways involved in IL-17A expression and is implicated in human psoriasis.

    Su, Shi / Katopodi, Xanthi-Lida / Pita-Juarez, Yered H / Maverakis, Emanual / Vlachos, Ioannis S / Adamopoulos, Iannis E

    Clinical immunology (Orlando, Fla.)

    2022  Band 240, Seite(n) 109041

    Abstract: Serine and Arginine Rich Splicing Factor 1 (SRSF1) is a splicing factor that binds to exonic enhancers and stimulates splicing and is previously implicated with autoimmunity. Herein, we investigate the role of SRSF1 in regulating innate immune functions ... ...

    Abstract Serine and Arginine Rich Splicing Factor 1 (SRSF1) is a splicing factor that binds to exonic enhancers and stimulates splicing and is previously implicated with autoimmunity. Herein, we investigate the role of SRSF1 in regulating innate immune functions that are pertinent in the pathogenesis of auto-inflammatory diseases. Specifically, we show that conditional deletion of SRSF1 in mature lymphocytes resulted in higher expression of il-17a and il-17 f and an expansion of IL17A
    Mesh-Begriff(e) Alternative Splicing ; Animals ; Arginine/genetics ; Arginine/metabolism ; Humans ; Interleukin-17/metabolism ; Mice ; Psoriasis/genetics ; RNA Splicing Factors/genetics ; RNA Splicing Factors/metabolism ; Serine/genetics ; Serine/metabolism ; Serine-Arginine Splicing Factors/genetics ; Serine-Arginine Splicing Factors/metabolism
    Chemische Substanzen Interleukin-17 ; RNA Splicing Factors ; SRSF1 protein, human ; Serine-Arginine Splicing Factors (170974-22-8) ; Serine (452VLY9402) ; Arginine (94ZLA3W45F)
    Sprache Englisch
    Erscheinungsdatum 2022-05-22
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Meta-Analysis ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 1459903-x
    ISSN 1521-7035 ; 1521-6616
    ISSN (online) 1521-7035
    ISSN 1521-6616
    DOI 10.1016/j.clim.2022.109041
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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