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  1. Book ; Thesis: Die Expression von Monozytenoberflächenmarkern und Wachstumsfaktoren in kultivierten Endothelvorläuferzellen aus peripherem Blut

    Rehman, Jalees

    2004  

    Author's details vorgelegt von Jalees Rehman
    Language German
    Size 68 S. : Ill., graph. Darst.
    Publishing country Germany
    Document type Book ; Thesis
    Thesis / German Habilitation thesis Marburg, Univ., Diss., 2004
    HBZ-ID HT014576558
    Database Catalogue ZB MED Medicine, Health

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    In stock of ZB MED Cologne/Königswinter

    Shelf markLoan statusLocation
    2004 D 2251 order for loan Magazin

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  2. Article ; Online: MitoSwap - Mitophagy partnered with compensatory mitochondrial biogenesis during stem cell differentiation.

    Gajwani, Priyanka / Rehman, Jalees

    Autophagy reports

    2022  Volume 1, Issue 1, Page(s) 210–213

    Abstract: Differentiating stem cells must adapt their mitochondrial metabolism to fit the needs of the mature differentiated cell. In a recent study, we observed that during differentiation to an endothelial phenotype, pluripotent stem cell mitochondria are ... ...

    Abstract Differentiating stem cells must adapt their mitochondrial metabolism to fit the needs of the mature differentiated cell. In a recent study, we observed that during differentiation to an endothelial phenotype, pluripotent stem cell mitochondria are removed by mitophagy, triggering compensatory mitochondrial biogenesis to replenish the mitochondrial pool. We identified the mitochondrial phosphatase PGAM5 as the link between mitophagy and transcription of the mitochondrial biogenesis regulator PPARGC1A/PGC1α in the nucleus. Swapping of mitochondria through the coupled processes of mitophagy and mitochondrial biogenesis lead to enhanced metabolic reprogramming in the differentiated cell.
    Language English
    Publishing date 2022-05-04
    Publishing country United States
    Document type Journal Article
    ISSN 2769-4127
    ISSN (online) 2769-4127
    DOI 10.1080/27694127.2022.2071549
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Assessing comparative importance of DNA sequence and epigenetic modifications on gene expression using a deep convolutional neural network.

    Gao, Shang / Rehman, Jalees / Dai, Yang

    Computational and structural biotechnology journal

    2022  Volume 20, Page(s) 3814–3823

    Abstract: Gene expression is regulated at both transcriptional and post-transcriptional levels. DNA sequence and epigenetic modifications are key factors which regulate gene transcription. Understanding their complex interactions and their respective contributions ...

    Abstract Gene expression is regulated at both transcriptional and post-transcriptional levels. DNA sequence and epigenetic modifications are key factors which regulate gene transcription. Understanding their complex interactions and their respective contributions to gene expression regulation remains a challenge in biological studies. We have developed iSEGnet, a framework of deep convolutional neural network to predict mRNA abundance using the information on DNA sequences as well as epigenetic modifications within genes and their
    Language English
    Publishing date 2022-07-13
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 2694435-2
    ISSN 2001-0370
    ISSN 2001-0370
    DOI 10.1016/j.csbj.2022.07.014
    Database MEDical Literature Analysis and Retrieval System OnLINE

    Full text online

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  4. Article: Systematic temporal analysis of peripheral blood transcriptomes using

    Wang, Xinge / Sanborn, Mark / Dai, Yang / Rehman, Jalees

    bioRxiv : the preprint server for biology

    2021  

    Abstract: Studying temporal gene expression shifts during disease progression provides important insights into the biological mechanisms that distinguish adaptive and maladaptive responses. Existing tools for the analysis of time course transcriptomic data are not ...

    Abstract Studying temporal gene expression shifts during disease progression provides important insights into the biological mechanisms that distinguish adaptive and maladaptive responses. Existing tools for the analysis of time course transcriptomic data are not designed to optimally identify distinct temporal patterns when analyzing dynamic differentially expressed genes (DDEGs). Moreover, there is a lack of methods to assess and visualize the temporal progression of biological pathways mapped from time course transcriptomic datasets. In this study, we developed an open-source R package
    Language English
    Publishing date 2021-12-07
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2021.05.04.442617
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: The importance of patient-partnered research in addressing long COVID: Takeaways for biomedical research study design from the RECOVER Initiative's Mechanistic Pathways taskforce.

    Kim, C / Chen, Benjamin / Mohandas, Sindhu / Rehman, Jalees / Sherif, Zaki A / Coombs, K

    eLife

    2023  Volume 12

    Abstract: The NIH-funded RECOVER study is collecting clinical data on patients who experience a SARS-CoV-2 infection. As patient representatives of the RECOVER Initiative's Mechanistic Pathways task force, we offer our perspectives on patient motivations for ... ...

    Abstract The NIH-funded RECOVER study is collecting clinical data on patients who experience a SARS-CoV-2 infection. As patient representatives of the RECOVER Initiative's Mechanistic Pathways task force, we offer our perspectives on patient motivations for partnering with researchers to obtain results from mechanistic studies. We emphasize the challenges of balancing urgency with scientific rigor. We recognize the importance of such partnerships in addressing post-acute sequelae of SARS-CoV-2 infection (PASC), which includes 'long COVID,' through contrasting objective and subjective narratives. Long COVID's prevalence served as a call to action for patients like us to become actively involved in efforts to understand our condition. Patient-centered and patient-partnered research informs the balance between urgency and robust mechanistic research. Results from collaborating on protocol design, diverse patient inclusion, and awareness of community concerns establish a new precedent in biomedical research study design. With a public health matter as pressing as the long-term complications that can emerge after SARS-CoV-2 infection, considerate and equitable stakeholder involvement is essential to guiding seminal research. Discussions in the RECOVER Mechanistic Pathways task force gave rise to this commentary as well as other review articles on the current scientific understanding of PASC mechanisms.
    MeSH term(s) Humans ; Post-Acute COVID-19 Syndrome ; COVID-19 ; SARS-CoV-2 ; Disease Progression ; Biomedical Research
    Language English
    Publishing date 2023-09-22
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2687154-3
    ISSN 2050-084X ; 2050-084X
    ISSN (online) 2050-084X
    ISSN 2050-084X
    DOI 10.7554/eLife.86043
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Bone marrow tinctures for cardiovascular disease: lost in translation.

    Rehman, Jalees

    Circulation

    2013  Volume 127, Issue 19, Page(s) 1935–1937

    MeSH term(s) Bone Marrow Cells/physiology ; Bone Marrow Transplantation/methods ; Female ; Humans ; Leukocytes, Mononuclear/transplantation ; Male ; Myocardial Infarction/surgery ; Ventricular Function, Left/physiology
    Language English
    Publishing date 2013-04-17
    Publishing country United States
    Document type Editorial ; Research Support, N.I.H., Extramural ; Comment
    ZDB-ID 80099-5
    ISSN 1524-4539 ; 0009-7322 ; 0069-4193 ; 0065-8499
    ISSN (online) 1524-4539
    ISSN 0009-7322 ; 0069-4193 ; 0065-8499
    DOI 10.1161/CIRCULATIONAHA.113.002775
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Ui IV Zs.60: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
    ab Jg. 2022: Lesesaal (EG)

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  7. Article ; Online: A Bayesian inference transcription factor activity model for the analysis of single-cell transcriptomes.

    Gao, Shang / Dai, Yang / Rehman, Jalees

    Genome research

    2021  Volume 31, Issue 7, Page(s) 1296–1311

    Abstract: Single-cell RNA sequencing (scRNA-seq) has emerged as a powerful experimental approach to study cellular heterogeneity. One of the challenges in scRNA-seq data analysis is integrating different types of biological data to consistently recognize discrete ... ...

    Abstract Single-cell RNA sequencing (scRNA-seq) has emerged as a powerful experimental approach to study cellular heterogeneity. One of the challenges in scRNA-seq data analysis is integrating different types of biological data to consistently recognize discrete biological functions and regulatory mechanisms of cells, such as transcription factor activities and gene regulatory networks in distinct cell populations. We have developed an approach to infer transcription factor activities from scRNA-seq data that leverages existing biological data on transcription factor binding sites. The Bayesian inference transcription factor activity model (BITFAM) integrates ChIP-seq transcription factor binding information into scRNA-seq data analysis. We show that the inferred transcription factor activities for key cell types identify regulatory transcription factors that are known to mechanistically control cell function and cell fate. The BITFAM approach not only identifies biologically meaningful transcription factor activities, but also provides valuable insights into underlying transcription factor regulatory mechanisms.
    Language English
    Publishing date 2021-06-11
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1284872-4
    ISSN 1549-5469 ; 1088-9051 ; 1054-9803
    ISSN (online) 1549-5469
    ISSN 1088-9051 ; 1054-9803
    DOI 10.1101/gr.265595.120
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 3729: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)
    Zs.MG 8: Show issues

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  8. Article: Assessing comparative importance of DNA sequence and epigenetic modifications on gene expression using a deep convolutional neural network

    Gao, Shang / Rehman, Jalees / Dai, Yang

    Computational and Structural Biotechnology Journal. 2022, v. 20

    2022  

    Abstract: Gene expression is regulated at both transcriptional and post-transcriptional levels. DNA sequence and epigenetic modifications are key factors which regulate gene transcription. Understanding their complex interactions and their respective contributions ...

    Abstract Gene expression is regulated at both transcriptional and post-transcriptional levels. DNA sequence and epigenetic modifications are key factors which regulate gene transcription. Understanding their complex interactions and their respective contributions to gene expression regulation remains a challenge in biological studies. We have developed iSEGnet, a framework of deep convolutional neural network to predict mRNA abundance using the information on DNA sequences as well as epigenetic modifications within genes and their cis-regulatory regions. We demonstrate that our framework outperforms other machine learning models in terms of predicting mRNA abundance using transcriptional and epigenetic profiles from six distinct cell lines/types chosen from the ENCODE. The analysis from the learned models also reveals that specific regions around promotors and transcription termination sites are most important for gene expression regulation. Using the method of Integrated Gradients, we identify narrow segments in these regions which are most likely to impact gene expression for a specific epigenetic modification. We further show that these identified segments are enriched in known active regulatory regions by comparing the transcription factor binding sites obtained via ChIP-seq. Moreover, we demonstrate how iSEGnet can uncover potential transcription factors that have regulatory functions in cancer using two cancer multi-omics data.
    Keywords DNA ; biotechnology ; chromatin immunoprecipitation ; epigenetics ; gene expression ; gene expression regulation ; multiomics ; neural networks ; nucleotide sequences ; transcription factors ; transcription termination
    Language English
    Size p. 3814-3823.
    Publishing place Elsevier B.V.
    Document type Article
    ZDB-ID 2694435-2
    ISSN 2001-0370
    ISSN 2001-0370
    DOI 10.1016/j.csbj.2022.07.014
    Database NAL-Catalogue (AGRICOLA)

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  9. Article ; Online: Temporal transcriptomic analysis using TrendCatcher identifies early and persistent neutrophil activation in severe COVID-19.

    Wang, Xinge / Sanborn, Mark A / Dai, Yang / Rehman, Jalees

    JCI insight

    2022  Volume 7, Issue 7

    Abstract: Studying temporal gene expression shifts during disease progression provides important insights into the biological mechanisms that distinguish adaptive and maladaptive responses. Existing tools for the analysis of time course transcriptomic data are not ...

    Abstract Studying temporal gene expression shifts during disease progression provides important insights into the biological mechanisms that distinguish adaptive and maladaptive responses. Existing tools for the analysis of time course transcriptomic data are not designed to optimally identify distinct temporal patterns when analyzing dynamic differentially expressed genes (DDEGs). Moreover, there are not enough methods to assess and visualize the temporal progression of biological pathways mapped from time course transcriptomic data sets. In this study, we developed an open-source R package TrendCatcher (https://github.com/jaleesr/TrendCatcher), which applies the smoothing spline ANOVA model and break point searching strategy, to identify and visualize distinct dynamic transcriptional gene signatures and biological processes from longitudinal data sets. We used TrendCatcher to perform a systematic temporal analysis of COVID-19 peripheral blood transcriptomes, including bulk and single-cell RNA-Seq time course data. TrendCatcher uncovered the early and persistent activation of neutrophils and coagulation pathways, as well as impaired type I IFN (IFN-I) signaling in circulating cells as a hallmark of patients who progressed to severe COVID-19, whereas no such patterns were identified in individuals receiving SARS-CoV-2 vaccinations or patients with mild COVID-19. These results underscore the importance of systematic temporal analysis to identify early biomarkers and possible pathogenic therapeutic targets.
    MeSH term(s) COVID-19/genetics ; Gene Expression Profiling/methods ; Humans ; Neutrophil Activation ; SARS-CoV-2/genetics ; Transcriptome
    Language English
    Publishing date 2022-04-08
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ISSN 2379-3708
    ISSN (online) 2379-3708
    DOI 10.1172/jci.insight.157255
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Hypoxia Signaling in Vascular Homeostasis.

    Marsboom, Glenn / Rehman, Jalees

    Physiology (Bethesda, Md.)

    2018  Volume 33, Issue 5, Page(s) 328–337

    Abstract: Hypoxia signaling in the vasculature controls vascular permeability, inflammation, vascular growth, and repair of vascular injury. In this review, we summarize recent insights in this burgeoning field and highlight the importance of studying the ... ...

    Abstract Hypoxia signaling in the vasculature controls vascular permeability, inflammation, vascular growth, and repair of vascular injury. In this review, we summarize recent insights in this burgeoning field and highlight the importance of studying the heterogeneity of hypoxia responses among individual patients, distinct vascular beds, and even individual vascular cells.
    MeSH term(s) Animals ; Capillary Permeability/physiology ; Endothelial Cells/physiology ; Homeostasis/physiology ; Humans ; Hypoxia/physiopathology ; Signal Transduction/physiology
    Language English
    Publishing date 2018-08-14
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 2158667-6
    ISSN 1548-9221 ; 1548-9213
    ISSN (online) 1548-9221
    ISSN 1548-9213
    DOI 10.1152/physiol.00018.2018
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 2164: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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