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  1. Article: Clustering single-cell multimodal omics data with jrSiCKLSNMF.

    Ellis, Dorothy / Roy, Arkaprava / Datta, Susmita

    Frontiers in genetics

    2023  Volume 14, Page(s) 1179439

    Abstract: Introduction: ...

    Abstract Introduction:
    Language English
    Publishing date 2023-06-09
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2606823-0
    ISSN 1664-8021
    ISSN 1664-8021
    DOI 10.3389/fgene.2023.1179439
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: asmbPLS: Adaptive Sparse Multi-block Partial Least Square for Survival Prediction using Multi-Omics Data.

    Zhang, Runzhi / Datta, Susmita

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Background: As high-throughput studies advance, more and more high-dimensional multi-omics data are available and collected from the same patient cohort. Using multi-omics data as predictors to predict survival outcomes is challenging due to the complex ...

    Abstract Background: As high-throughput studies advance, more and more high-dimensional multi-omics data are available and collected from the same patient cohort. Using multi-omics data as predictors to predict survival outcomes is challenging due to the complex structure of such data.
    Results: In this article, we introduce an adaptive sparse multi-block partial least square (asmbPLS) regression method by assigning different penalty factors to different blocks in different PLS components for feature selection and prediction. We compared the proposed method with several competitive algorithms in many aspects including prediction performance, feature selection and computation efficiency. The performance and the efficiency of our method were demonstrated using both the simulated and the real data.
    Conclusions: In summary, asmbPLS achieved a competitive performance in prediction, feature selection, and computation efficiency. We anticipate asmbPLS to be a valuable tool for multi-omics research. An R package called
    Language English
    Publishing date 2023-04-05
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.04.03.535442
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Adaptive Sparse Multi-Block PLS Discriminant Analysis: An Integrative Method for Identifying Key Biomarkers from Multi-Omics Data.

    Zhang, Runzhi / Datta, Susmita

    Genes

    2023  Volume 14, Issue 5

    Abstract: With the growing use of high-throughput technologies, multi-omics data containing various types of high-dimensional omics data is increasingly being generated to explore the association between the molecular mechanism of the host and diseases. In this ... ...

    Abstract With the growing use of high-throughput technologies, multi-omics data containing various types of high-dimensional omics data is increasingly being generated to explore the association between the molecular mechanism of the host and diseases. In this study, we present an adaptive sparse multi-block partial least square discriminant analysis (asmbPLS-DA), an extension of our previous work, asmbPLS. This integrative approach identifies the most relevant features across different types of omics data while discriminating multiple disease outcome groups. We used simulation data with various scenarios and a real dataset from the TCGA project to demonstrate that asmbPLS-DA can identify key biomarkers from each type of omics data with better biological relevance than existing competitive methods. Moreover, asmbPLS-DA showed comparable performance in the classification of subjects in terms of disease status or phenotypes using integrated multi-omics molecular profiles, especially when combined with other classification algorithms, such as linear discriminant analysis and random forest. We have made the R package called
    MeSH term(s) Multiomics ; Biomarkers ; Algorithms ; Computer Simulation ; Phenotype
    Chemical Substances Biomarkers
    Language English
    Publishing date 2023-04-23
    Publishing country Switzerland
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2527218-4
    ISSN 2073-4425 ; 2073-4425
    ISSN (online) 2073-4425
    ISSN 2073-4425
    DOI 10.3390/genes14050961
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Biofilm-producing antibiotic-resistant bacteria in Indian patients: a comprehensive review.

    Datta, Susmita / Nag, Soma / Roy, Dijendra Nath

    Current medical research and opinion

    2024  Volume 40, Issue 3, Page(s) 403–422

    Abstract: For the past few years, microbial biofilms have been emerging as a significant threat to the modern healthcare system, and their prevalence and antibiotic resistance threat gradually increase daily among the human population. The biofilm has a remarkable ...

    Abstract For the past few years, microbial biofilms have been emerging as a significant threat to the modern healthcare system, and their prevalence and antibiotic resistance threat gradually increase daily among the human population. The biofilm has a remarkable impact in the field of infectious diseases, in particular healthcare-associated infections related to indwelling devices such as catheters, implants, artificial heart valves, and prosthetic joints. Bacterial biofilm potentially adheres to any biotic or abiotic surfaces that give specific shelter to the microbial community, making them less susceptible to many antimicrobial agents and even resistant to the immune cells of animal hosts. Around thirty clinical research reports available in PUBMED have been considered to establish the occurrence of biofilm-forming bacteria showing resistance against several regular antibiotics prescribed against infection by clinicians among Indian patients. After the extensive literature review, our observation exhibits a high predominance of biofilm formation among bacteria such as
    MeSH term(s) Animals ; Humans ; Anti-Bacterial Agents/pharmacology ; Anti-Bacterial Agents/therapeutic use ; Biofilms ; Bacteria ; Drug Resistance, Microbial ; Cross Infection
    Chemical Substances Anti-Bacterial Agents
    Language English
    Publishing date 2024-01-27
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 80296-7
    ISSN 1473-4877 ; 0300-7995
    ISSN (online) 1473-4877
    ISSN 0300-7995
    DOI 10.1080/03007995.2024.2305241
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 955: 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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  5. Article ; Online: Adaptive Sparse Multi-Block PLS Discriminant Analysis: An Integrative Method for Identifying Key Biomarkers from Multi-Omics Data

    Zhang, Runzhi / Datta, Susmita

    Genes (Basel). 2023 Apr. 23, v. 14, no. 5

    2023  

    Abstract: With the growing use of high-throughput technologies, multi-omics data containing various types of high-dimensional omics data is increasingly being generated to explore the association between the molecular mechanism of the host and diseases. In this ... ...

    Abstract With the growing use of high-throughput technologies, multi-omics data containing various types of high-dimensional omics data is increasingly being generated to explore the association between the molecular mechanism of the host and diseases. In this study, we present an adaptive sparse multi-block partial least square discriminant analysis (asmbPLS-DA), an extension of our previous work, asmbPLS. This integrative approach identifies the most relevant features across different types of omics data while discriminating multiple disease outcome groups. We used simulation data with various scenarios and a real dataset from the TCGA project to demonstrate that asmbPLS-DA can identify key biomarkers from each type of omics data with better biological relevance than existing competitive methods. Moreover, asmbPLS-DA showed comparable performance in the classification of subjects in terms of disease status or phenotypes using integrated multi-omics molecular profiles, especially when combined with other classification algorithms, such as linear discriminant analysis and random forest. We have made the R package called asmbPLS that implements this method publicly available on GitHub. Overall, asmbPLS-DA achieved competitive performance in terms of feature selection and classification. We believe that asmbPLS-DA can be a valuable tool for multi-omics research.
    Keywords biomarkers ; data collection ; discriminant analysis ; least squares ; multiomics
    Language English
    Dates of publication 2023-0423
    Publishing place Multidisciplinary Digital Publishing Institute
    Document type Article ; Online
    ZDB-ID 2527218-4
    ISSN 2073-4425
    ISSN 2073-4425
    DOI 10.3390/genes14050961
    Database NAL-Catalogue (AGRICOLA)

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  6. Article: Integration of ion transport membrane with conventional powerplant to enhance the plant capacity with improved power production.

    Das, Arnob / Peu, Susmita Datta / Hossain, Md Sanowar / Das, Barun Kumar

    Heliyon

    2023  Volume 9, Issue 6, Page(s) e16387

    Abstract: Ion Transport Membrane (ITM) is an emerging technology for producing ... ...

    Abstract Ion Transport Membrane (ITM) is an emerging technology for producing O
    Language English
    Publishing date 2023-05-17
    Publishing country England
    Document type Journal Article
    ZDB-ID 2835763-2
    ISSN 2405-8440
    ISSN 2405-8440
    DOI 10.1016/j.heliyon.2023.e16387
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: Unraveling T Cell Responses for Long Term Protection of SARS-CoV-2 Infection.

    Wu, Dongyuan / Zhang, Runzhi / Datta, Susmita

    Frontiers in genetics

    2022  Volume 13, Page(s) 871164

    Abstract: Due to the COVID-19 pandemic, the global need for vaccines to prevent the disease is imperative. To date, several manufacturers have made efforts to develop vaccines against SARS-CoV-2. In spite of the success of developing many useful vaccines so far, ... ...

    Abstract Due to the COVID-19 pandemic, the global need for vaccines to prevent the disease is imperative. To date, several manufacturers have made efforts to develop vaccines against SARS-CoV-2. In spite of the success of developing many useful vaccines so far, it will be helpful for future vaccine designs, targetting long-term disease protection. For this, we need to know more details of the mechanism of T cell responses to SARS-CoV-2. In this study, we first detected pairwise differentially expressed genes among the healthy, mild, and severe COVID-19 groups of patients based on the expression of CD4
    Language English
    Publishing date 2022-05-04
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2606823-0
    ISSN 1664-8021
    ISSN 1664-8021
    DOI 10.3389/fgene.2022.871164
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Inferring Cell-Cell Communications from Spatially Resolved Transcriptomics Data Using a Bayesian Tweedie Model.

    Wu, Dongyuan / Gaskins, Jeremy T / Sekula, Michael / Datta, Susmita

    Genes

    2023  Volume 14, Issue 7

    Abstract: Cellular communication through biochemical signaling is fundamental to every biological activity. Investigating cell signaling diffusions across cell types can further help understand biological mechanisms. In recent years, this has become an important ... ...

    Abstract Cellular communication through biochemical signaling is fundamental to every biological activity. Investigating cell signaling diffusions across cell types can further help understand biological mechanisms. In recent years, this has become an important research topic as single-cell sequencing technologies have matured. However, cell signaling activities are spatially constrained, and single-cell data cannot provide spatial information for each cell. This issue may cause a high false discovery rate, and using spatially resolved transcriptomics data is necessary. On the other hand, as far as we know, most existing methods focus on providing an ad hoc measurement to estimate intercellular communication instead of relying on a statistical model. It is undeniable that descriptive statistics are straightforward and accessible, but a suitable statistical model can provide more accurate and reliable inference. In this way, we propose a generalized linear regression model to infer cellular communications from spatially resolved transcriptomics data, especially spot-based data. Our BAyesian Tweedie modeling of COMmunications (BATCOM) method estimates the communication scores between cell types with the consideration of their corresponding distances. Due to the properties of the regression model, BATCOM naturally provides the direction of the communication between cell types and the interaction of ligands and receptors that other approaches cannot offer. We conduct simulation studies to assess the performance under different scenarios. We also employ BATCOM in a real-data application and compare it with other existing algorithms. In summary, our innovative model can fill gaps in the inference of cell-cell communication and provide a robust and straightforward result.
    MeSH term(s) Transcriptome/genetics ; Bayes Theorem ; Gene Expression Profiling ; Cell Communication/genetics ; Signal Transduction
    Language English
    Publishing date 2023-06-28
    Publishing country Switzerland
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2527218-4
    ISSN 2073-4425 ; 2073-4425
    ISSN (online) 2073-4425
    ISSN 2073-4425
    DOI 10.3390/genes14071368
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article: Single-Cell Differential Network Analysis with Sparse Bayesian Factor Models.

    Sekula, Michael / Gaskins, Jeremy / Datta, Susmita

    Frontiers in genetics

    2022  Volume 12, Page(s) 810816

    Abstract: Differential network analysis plays an important role in learning how gene interactions change under different biological conditions, and the high resolution of single-cell RNA (scRNA-seq) sequencing provides new opportunities to explore these changing ... ...

    Abstract Differential network analysis plays an important role in learning how gene interactions change under different biological conditions, and the high resolution of single-cell RNA (scRNA-seq) sequencing provides new opportunities to explore these changing gene-gene interactions. Here, we present a sparse hierarchical Bayesian factor model to identify differences across network structures from different biological conditions in scRNA-seq data. Our methodology utilizes latent factors to impact gene expression values for each cell to help account for zero-inflation, increased cell-to-cell variability, and overdispersion that are unique characteristics of scRNA-seq data. Condition-dependent parameters determine which latent factors are activated in a gene, which allows for not only the calculation of gene-gene co-expression within each group but also the calculation of the co-expression differences between groups. We highlight our methodology's performance in detecting differential gene-gene associations across groups by analyzing simulated datasets and a SARS-CoV-2 case study dataset.
    Language English
    Publishing date 2022-02-04
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2606823-0
    ISSN 1664-8021
    ISSN 1664-8021
    DOI 10.3389/fgene.2021.810816
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Association of air pollution with postmenopausal breast cancer risk in UK Biobank.

    Smotherman, Carmen / Sprague, Brian / Datta, Susmita / Braithwaite, Dejana / Qin, Huaizhen / Yaghjyan, Lusine

    Breast cancer research : BCR

    2023  Volume 25, Issue 1, Page(s) 83

    Abstract: Background: We investigated the association of several air pollution measures with postmenopausal breast cancer (BCa) risk.: Methods: This study included 155,235 postmenopausal women (of which 6146 with BCa) from UK Biobank. Cancer diagnoses were ... ...

    Abstract Background: We investigated the association of several air pollution measures with postmenopausal breast cancer (BCa) risk.
    Methods: This study included 155,235 postmenopausal women (of which 6146 with BCa) from UK Biobank. Cancer diagnoses were ascertained through the linkage to the UK National Health Service Central Registers. Annual exposure averages were available from 2005, 2006, 2007, and 2010 for NO
    Results: PM
    Conclusion: Our findings suggest a positive association of 2007 PM
    MeSH term(s) Humans ; Female ; Air Pollutants/adverse effects ; Particulate Matter/adverse effects ; Breast Neoplasms/etiology ; Breast Neoplasms/chemically induced ; Postmenopause ; Biological Specimen Banks ; State Medicine ; Environmental Exposure ; Air Pollution/adverse effects ; Air Pollution/analysis ; United Kingdom/epidemiology
    Chemical Substances Air Pollutants ; Particulate Matter
    Language English
    Publishing date 2023-07-13
    Publishing country England
    Document type Journal Article
    ZDB-ID 2015059-3
    ISSN 1465-542X ; 1465-5411
    ISSN (online) 1465-542X
    ISSN 1465-5411
    DOI 10.1186/s13058-023-01681-w
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 5494: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
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