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  1. Article ; Online: Editorial: Beneficial and pathological roles of myeloid cells during COVID-19.

    Sharma, Lokesh / Sengupta, Shaon / Roger, Thierry

    Frontiers in immunology

    2023  Volume 14, Page(s) 1194826

    MeSH term(s) Humans ; COVID-19 ; Myeloid Cells ; SARS-CoV-2
    Language English
    Publishing date 2023-04-04
    Publishing country Switzerland
    Document type Editorial ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 2606827-8
    ISSN 1664-3224 ; 1664-3224
    ISSN (online) 1664-3224
    ISSN 1664-3224
    DOI 10.3389/fimmu.2023.1194826
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  2. Article: The story of COVID-19: A comparative analysis

    Sengupta, Shaon

    Sci. Transl. Med.

    Abstract: COVID-19 induces a distinct host transcriptome. ...

    Abstract COVID-19 induces a distinct host transcriptome.
    Keywords covid19
    Publisher WHO
    Document type Article
    Note WHO #Covidence: #620796
    Database COVID19

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  3. Article ; Online: The story of COVID-19

    Sengupta, Shaon

    Science Translational Medicine

    A comparative analysis

    2020  Volume 12, Issue 547, Page(s) eabc8943

    Abstract: COVID-19 induces a distinct host transcriptome. ...

    Abstract COVID-19 induces a distinct host transcriptome.
    Keywords General Medicine ; covid19
    Language English
    Publisher American Association for the Advancement of Science (AAAS)
    Publishing country us
    Document type Article ; Online
    ZDB-ID 2518854-9
    ISSN 1946-6242 ; 1946-6234
    ISSN (online) 1946-6242
    ISSN 1946-6234
    DOI 10.1126/scitranslmed.abc8943
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: MIS-Cing pieces of the puzzle

    Sengupta, Shaon

    Science Translational Medicine

    2020  Volume 12, Issue 563, Page(s) eabe6023

    Abstract: Multisystem inflammatory syndrome in children associated with COVID-19 is distinct from other hyperinflammatory conditions in children. ...

    Abstract Multisystem inflammatory syndrome in children associated with COVID-19 is distinct from other hyperinflammatory conditions in children.
    Keywords General Medicine ; covid19
    Language English
    Publisher American Association for the Advancement of Science (AAAS)
    Publishing country us
    Document type Article ; Online
    ZDB-ID 2518854-9
    ISSN 1946-6242 ; 1946-6234
    ISSN (online) 1946-6242
    ISSN 1946-6234
    DOI 10.1126/scitranslmed.abe6023
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  5. Article ; Online: BEERS2: RNA-Seq simulation through high fidelity in silico modeling.

    Brooks, Thomas G / Lahens, Nicholas F / Mrčela, Antonijo / Sarantopoulou, Dimitra / Nayak, Soumyashant / Naik, Amruta / Sengupta, Shaon / Choi, Peter S / Grant, Gregory R

    Briefings in bioinformatics

    2024  Volume 25, Issue 3

    Abstract: Simulation of RNA-seq reads is critical in the assessment, comparison, benchmarking and development of bioinformatics tools. Yet the field of RNA-seq simulators has progressed little in the last decade. To address this need we have developed BEERS2, ... ...

    Abstract Simulation of RNA-seq reads is critical in the assessment, comparison, benchmarking and development of bioinformatics tools. Yet the field of RNA-seq simulators has progressed little in the last decade. To address this need we have developed BEERS2, which combines a flexible and highly configurable design with detailed simulation of the entire library preparation and sequencing pipeline. BEERS2 takes input transcripts (typically fully length messenger RNA transcripts with polyA tails) from either customizable input or from CAMPAREE simulated RNA samples. It produces realistic reads of these transcripts as FASTQ, SAM or BAM formats with the SAM or BAM formats containing the true alignment to the reference genome. It also produces true transcript-level quantification values. BEERS2 combines a flexible and highly configurable design with detailed simulation of the entire library preparation and sequencing pipeline and is designed to include the effects of polyA selection and RiboZero for ribosomal depletion, hexamer priming sequence biases, GC-content biases in polymerase chain reaction (PCR) amplification, barcode read errors and errors during PCR amplification. These characteristics combine to make BEERS2 the most complete simulation of RNA-seq to date. Finally, we demonstrate the use of BEERS2 by measuring the effect of several settings on the popular Salmon pseudoalignment algorithm.
    MeSH term(s) RNA-Seq ; Sequence Analysis, RNA ; Computer Simulation ; RNA/genetics ; Genome ; High-Throughput Nucleotide Sequencing
    Chemical Substances RNA (63231-63-0)
    Language English
    Publishing date 2024-04-25
    Publishing country England
    Document type Journal Article
    ZDB-ID 2068142-2
    ISSN 1477-4054 ; 1467-5463
    ISSN (online) 1477-4054
    ISSN 1467-5463
    DOI 10.1093/bib/bbae164
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  6. Article: Microbiota-derived inosine programs protective CD8

    Stevens, Joseph / Culberson, Erica / Kinder, Jeremy / Ramiriqui, Alicia / Gray, Jerilyn / Bonfield, Madeline / Shao, Tzu-Yu / Al Gharabieh, Faris / Peterson, Laura / Steinmeyer, Shelby / Zacharias, William / Pryhuber, Gloria / Paul, Oindrila / Sengupta, Shaon / Alenghat, Theresa / Way, Sing Sing / Deshmukh, Hitesh

    bioRxiv : the preprint server for biology

    2024  

    Abstract: The immunological defects causing susceptibility to severe viral respiratory infections due to early-life dysbiosis remain ill-defined. Here, we show that influenza virus susceptibility in dysbiotic infant mice is caused by ... ...

    Abstract The immunological defects causing susceptibility to severe viral respiratory infections due to early-life dysbiosis remain ill-defined. Here, we show that influenza virus susceptibility in dysbiotic infant mice is caused by CD8
    Language English
    Publishing date 2024-04-13
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2024.04.09.588427
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: BEERS2: RNA-Seq simulation through high fidelity

    Brooks, Thomas G / Lahens, Nicholas F / Mrčela, Antonijo / Sarantopoulou, Dimitra / Nayak, Soumyashant / Naik, Amruta / Sengupta, Shaon / Choi, Peter S / Grant, Gregory R

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Simulation of RNA-seq reads is critical in the assessment, comparison, benchmarking, and development of bioinformatics tools. Yet the field of RNA-seq simulators has progressed little in the last decade. To address this need we have developed BEERS2, ... ...

    Abstract Simulation of RNA-seq reads is critical in the assessment, comparison, benchmarking, and development of bioinformatics tools. Yet the field of RNA-seq simulators has progressed little in the last decade. To address this need we have developed BEERS2, which combines a flexible and highly configurable design with detailed simulation of the entire library preparation and sequencing pipeline. BEERS2 takes input transcripts (typically fully-length mRNA transcripts with polyA tails) from either customizable input or from CAMPAREE simulated RNA samples. It produces realistic reads of these transcripts as FASTQ, SAM, or BAM formats with the SAM or BAM formats containing the true alignment to the reference genome. It also produces true transcript-level quantification values. BEERS2 combines a flexible and highly configurable design with detailed simulation of the entire library preparation and sequencing pipeline and is designed to include the effects of polyA selection and RiboZero for ribosomal depletion, hexamer priming sequence biases, GC-content biases in PCR amplification, barcode read errors, and errors during PCR amplification. These characteristics combine to make BEERS2 the most complete simulation of RNA-seq to date. Finally, we demonstrate the use of BEERS2 by measuring the effect of several settings on the popular Salmon pseudoalignment algorithm.
    Language English
    Publishing date 2023-04-24
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.04.21.537847
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Circadian regulation of lung repair and regeneration.

    Naik, Amruta / Forrest, Kaitlyn M / Paul, Oindrila / Issah, Yasmine / Valekunja, Utham K / Tang, Soon Y / Reddy, Akhilesh B / Hennessy, Elizabeth J / Brooks, Thomas G / Chaudhry, Fatima / Babu, Apoorva / Morley, Michael / Zepp, Jarod A / Grant, Gregory R / FitzGerald, Garret A / Sehgal, Amita / Worthen, G Scott / Frank, David B / Morrisey, Edward E /
    Sengupta, Shaon

    JCI insight

    2024  Volume 9, Issue 5

    MeSH term(s) Circadian Rhythm ; Regeneration ; Lung
    Language English
    Publishing date 2024-03-08
    Publishing country United States
    Document type Journal Article ; Published Erratum
    ISSN 2379-3708
    ISSN (online) 2379-3708
    DOI 10.1172/jci.insight.179745
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  9. Article ; Online: The roles of lipids in SARS-CoV-2 viral replication and the host immune response.

    Theken, Katherine N / Tang, Soon Yew / Sengupta, Shaon / FitzGerald, Garret A

    Journal of lipid research

    2021  Volume 62, Page(s) 100129

    Abstract: The significant morbidity and mortality associated with severe acute respiratory syndrome coronavirus 2 infection has underscored the need for novel antiviral strategies. Lipids play essential roles in the viral life cycle. The lipid composition of cell ... ...

    Abstract The significant morbidity and mortality associated with severe acute respiratory syndrome coronavirus 2 infection has underscored the need for novel antiviral strategies. Lipids play essential roles in the viral life cycle. The lipid composition of cell membranes can influence viral entry by mediating fusion or affecting receptor conformation. Upon infection, viruses can reprogram cellular metabolism to remodel lipid membranes and fuel the production of new virions. Furthermore, several classes of lipid mediators, including eicosanoids and sphingolipids, can regulate the host immune response to viral infection. Here, we summarize the existing literature on the mechanisms through which these lipid mediators may regulate viral burden in COVID-19. Furthermore, we define the gaps in knowledge and identify the core areas in which lipids offer therapeutic promise for severe acute respiratory syndrome coronavirus 2.
    MeSH term(s) COVID-19/immunology ; Cell Membrane/immunology ; Eicosanoids/immunology ; Humans ; SARS-CoV-2/physiology ; Sphingolipids/immunology ; Virus Replication/immunology
    Chemical Substances Eicosanoids ; Sphingolipids
    Language English
    Publishing date 2021-09-29
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Review
    ZDB-ID 80154-9
    ISSN 1539-7262 ; 0022-2275
    ISSN (online) 1539-7262
    ISSN 0022-2275
    DOI 10.1016/j.jlr.2021.100129
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  10. Article ; Online: Circadian disruption in lung fibroblasts enhances NF-κB activity to exacerbate neutrophil recruitment.

    Cox, Shannon L / O'Siorain, James R / He, Yan / Lordan, Ronan / Naik, Amruta / Tang, Soon Yew / Sengupta, Shaon / FitzGerald, Garret A / Carroll, Richard G / Curtis, Annie M

    FASEB journal : official publication of the Federation of American Societies for Experimental Biology

    2023  Volume 37, Issue 2, Page(s) e22753

    Abstract: Fibroblasts are stromal cells abundant throughout tissues, including the lungs. Fibroblasts are integral coordinators of immune cell recruitment through chemokine secretion. Circadian rhythms direct the recruitment of immune cells to the lung, which in ... ...

    Abstract Fibroblasts are stromal cells abundant throughout tissues, including the lungs. Fibroblasts are integral coordinators of immune cell recruitment through chemokine secretion. Circadian rhythms direct the recruitment of immune cells to the lung, which in turn impacts response to infection and survival. Although fibroblasts display robust circadian rhythms, the contribution of the fibroblast molecular clock to lung-specific migration of immune cells and recruitment remains to be established. Mice challenged intranasally with lipopolysaccharide (LPS) at dusk showed increased expression of the pro-inflammatory cytokine IL-1β and chemokine CXCL5 in the lung, which was accompanied by increased neutrophil recruitment. Primary lung fibroblasts with knockdown of the core clock gene Bmal1 and immortalized Bmal1
    MeSH term(s) Animals ; Mice ; NF-kappa B ; Neutrophil Infiltration ; ARNTL Transcription Factors/genetics ; Fibroblasts ; Cell Movement ; Circadian Rhythm
    Chemical Substances NF-kappa B ; ARNTL Transcription Factors
    Language English
    Publishing date 2023-01-10
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 639186-2
    ISSN 1530-6860 ; 0892-6638
    ISSN (online) 1530-6860
    ISSN 0892-6638
    DOI 10.1096/fj.202201456R
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