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  • 1
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    Pluripotent stem cells induced from adult neural stem cells by reprogramming with two factors (2008)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2008-07-03
    Description: Reprogramming of somatic cells is a valuable tool to understand the mechanisms of regaining pluripotency and further opens up the possibility of generating patient-specific pluripotent stem cells. Reprogramming of mouse and human somatic cells into pluripotent stem cells, designated as induced pluripotent stem (iPS) cells, has been possible with the expression of the transcription factor quartet Oct4 (also known as Pou5f1), Sox2, c-Myc and Klf4 (refs 1-11). Considering that ectopic expression of c-Myc causes tumorigenicity in offspring and that retroviruses themselves can cause insertional mutagenesis, the generation of iPS cells with a minimal number of factors may hasten the clinical application of this approach. Here we show that adult mouse neural stem cells express higher endogenous levels of Sox2 and c-Myc than embryonic stem cells, and that exogenous Oct4 together with either Klf4 or c-Myc is sufficient to generate iPS cells from neural stem cells. These two-factor iPS cells are similar to embryonic stem cells at the molecular level, contribute to development of the germ line, and form chimaeras. We propose that, in inducing pluripotency, the number of reprogramming factors can be reduced when using somatic cells that endogenously express appropriate levels of complementing factors.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kim, Jeong Beom -- Zaehres, Holm -- Wu, Guangming -- Gentile, Luca -- Ko, Kinarm -- Sebastiano, Vittorio -- Arauzo-Bravo, Marcos J -- Ruau, David -- Han, Dong Wook -- Zenke, Martin -- Scholer, Hans R -- England -- Nature. 2008 Jul 31;454(7204):646-50. doi: 10.1038/nature07061. Epub 2008 Jun 29.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Rontgenstrasse 20, 48149 Munster, NRW, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18594515" target="_blank"〉PubMed〈/a〉
    Keywords: Adult Stem Cells/*cytology/metabolism ; Animals ; Cell Differentiation/genetics ; Cells, Cultured ; *Cellular Reprogramming ; Chimera ; DNA-Binding Proteins/genetics/metabolism ; Female ; Gene Expression Profiling ; Genes, myc/genetics ; HMGB Proteins/genetics/metabolism ; Homeodomain Proteins/genetics ; Kruppel-Like Transcription Factors/genetics/metabolism ; Male ; Mice ; Mice, Nude ; Mice, Transgenic ; Neurons/*cytology ; Octamer Transcription Factor-3/genetics/metabolism ; Pluripotent Stem Cells/*cytology/*metabolism ; Proteins/genetics ; Proto-Oncogene Proteins c-myc/metabolism ; RNA, Untranslated ; SOXB1 Transcription Factors ; Transcription Factors/genetics/metabolism ; Transduction, Genetic
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 2
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    Constrained transcription factor spacing is prevalent and important for transcriptional control of mouse blood cells (2014)
    Oxford University Press
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    Publication Date: 2014-12-17
    Description: Combinatorial transcription factor (TF) binding is essential for cell-type-specific gene regulation. However, much remains to be learned about the mechanisms of TF interactions, including to what extent constrained spacing and orientation of interacting TFs are critical for regulatory element activity. To examine the relative prevalence of the ‘enhanceosome’ versus the ‘TF collective’ model of combinatorial TF binding, a comprehensive analysis of TF binding site sequences in large scale datasets is necessary. We developed a motif-pair discovery pipeline to identify motif co-occurrences with preferential distance(s) between motifs in TF-bound regions. Utilizing a compendium of 289 mouse haematopoietic TF ChIP-seq datasets, we demonstrate that haematopoietic-related motif-pairs commonly occur with highly conserved constrained spacing and orientation between motifs. Furthermore, motif clustering revealed specific associations for both heterotypic and homotypic motif-pairs with particular haematopoietic cell types. We also showed that disrupting the spacing between motif-pairs significantly affects transcriptional activity in a well-known motif-pair—E-box and GATA, and in two previously unknown motif-pairs with constrained spacing—Ets and Homeobox as well as Ets and E-box. In this study, we provide evidence for widespread sequence-specific TF pair interaction with DNA that conforms to the ‘enhanceosome’ model, and furthermore identify associations between specific haematopoietic cell-types and motif-pairs.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 3
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    TRES predicts transcription control in embryonic stem cells (2014)
    Oxford University Press
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    Publication Date: 2014-10-04
    Description: : Unraveling transcriptional circuits controlling embryonic stem cell maintenance and fate has great potential for improving our understanding of normal development as well as disease. To facilitate this, we have developed a novel web tool called ‘TRES’ that predicts the likely upstream regulators for a given gene list. This is achieved by integrating transcription factor (TF) binding events from 187 ChIP-sequencing and ChIP-on-chip datasets in murine and human embryonic stem (ES) cells with over 1000 mammalian TF sequence motifs. Using 114 TF perturbation gene sets, as well as 115 co-expression clusters in ES cells, we validate the utility of this approach. Availability and implementation: TRES is freely available at http://www.tres.roslin.ed.ac.uk . Contact: Anagha.Joshi@roslin.ed.ac.uk or bg200@cam.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 4
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    CODEX: a next-generation sequencing experiment database for the haematopoietic and embryonic stem cell communities (2015)
    Oxford University Press
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    Publication Date: 2015-01-16
    Description: CODEX ( http://codex.stemcells.cam.ac.uk/ ) is a user-friendly database for the direct access and interrogation of publicly available next-generation sequencing (NGS) data, specifically aimed at experimental biologists. In an era of multi-centre genomic dataset generation, CODEX provides a single database where these samples are collected, uniformly processed and vetted. The main drive of CODEX is to provide the wider scientific community with instant access to high-quality NGS data, which, irrespective of the publishing laboratory, is directly comparable. CODEX allows users to immediately visualize or download processed datasets, or compare user-generated data against the database's cumulative knowledge-base. CODEX contains four types of NGS experiments: transcription factor chromatin immunoprecipitation coupled to high-throughput sequencing (ChIP-Seq), histone modification ChIP-Seq, DNase-Seq and RNA-Seq. These are largely encompassed within two specialized repositories, HAEMCODE and ESCODE, which are focused on haematopoiesis and embryonic stem cell samples, respectively. To date, CODEX contains over 1000 samples, including 221 unique TFs and 93 unique cell types. CODEX therefore provides one of the most complete resources of publicly available NGS data for the direct interrogation of transcriptional programmes that regulate cellular identity and fate in the context of mammalian development, homeostasis and disease.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 5
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    Cocultures of Umbilical Cord Blood Hematopoietic Progenitor Cells and Umbilical Cord Endothelium. (2005)
    American Society of Hematology
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    Publication Date: 2005-11-16
    Description: Purpose. The expansion of hematopoietic progenitor cells (HPC) from cord blood is limited so far. For HPC expansion and differentiation we evaluated a coculture model of cord blood-derived HPC and endothelial cells (EC) isolated from the umbilical cord. Methods. CD34(+) HPC were cultured directly in contact with the endothelial monolayer or indirectly using a 0.4μm microporous transmembrane. EC were stimulated by various cytokines including TPO, interleukin (IL) 1β, IL4, and IL6. After 1 and 2 weeks, the HPC were counted and analyzed by flow cytometry. Their plating efficiencies were determined by methylcellulose assays, and their reconstitutive potential was analyzed by cobblestone assays. DNA microarrays on the expanding cells as well as on cytokine-stimulated EC were also performed. Results. EC stimulation with thrombopoietin and IL4 had no significant effect on mononuclear cell expansion. In contrast, IL1β stimulation resulted in a 10 and 100fold increase of the cell number after one and two weeks, respectively. More than 90% of these cells were CD33(+) and had a plating efficiency equivalent to that of HPC post isolation (7.3 ±1.2 versus 8.3±0.68%). The number of 5-wk cobblestone-area forming cells among these expanded cells was diminished, whereas the number of 2-wk cobblestone areas did not change (10.6 versus 8.5). The expanded cells could further mature into functional granulocytes. Time-course DNA microarrays of IL1β-stimulated EC demonstrated an increased expression of genes encoding tumor necrosis factor-induced proteins, interleukins, and endothelial adhesion molecules. When IL1β was replaced by IL6, a 7-fold expansion of morphologically progenitor-like cells took place. 10–13% of these cells were positive for CD133, had a plating efficiency of 10.2±1.7%, and showed on average 14.5 five-week cobblestone areas. Conclusion. Cocultures of cord blood-derived HPC with umbilical cord-derived EC offer alternative methods for the expansion and differentiation of hematopoietic cells.
    Print ISSN: 0006-4971
    Electronic ISSN: 1528-0020
    Topics: Biology , Medicine
    Published by American Society of Hematology
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  • 6
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    Update of NUREBASE: nuclear hormone receptor functional genomics (2004)
    Oxford University Press
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    Publication Date: 2004-01-01
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 7
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    Discovering Key Topics From Short, Real-World Medical Inquiries via Natural Language Processing (2021)
    Frontiers Media
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    Publication Date: 2021-09-22
    Description: Millions of unsolicited medical inquiries are received by pharmaceutical companies every year. It has been hypothesized that these inquiries represent a treasure trove of information, potentially giving insight into matters regarding medicinal products and the associated medical treatments. However, due to the large volume and specialized nature of the inquiries, it is difficult to perform timely, recurrent, and comprehensive analyses. Here, we combine biomedical word embeddings, non-linear dimensionality reduction, and hierarchical clustering to automatically discover key topics in real-world medical inquiries from customers. This approach does not require ontologies nor annotations. The discovered topics are meaningful and medically relevant, as judged by medical information specialists, thus demonstrating that unsolicited medical inquiries are a source of valuable customer insights. Our work paves the way for the machine-learning-driven analysis of medical inquiries in the pharmaceutical industry, which ultimately aims at improving patient care.
    Electronic ISSN: 2624-9898
    Topics: Computer Science
    Published by Frontiers Media
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