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  1. Article ; Online: A Computational Approach: The Functional Effects of Thyroid Peroxidase Variants in Thyroid Cancer and Genetic Disorders.

    Sobitan, Adebiyi / Gebremedhin, Brhan / Yao, Qiaobin / Xie, Guiqin / Gu, Xinbin / Li, Jiang / Teng, Shaolei

    JCO clinical cancer informatics

    2024  Volume 8, Page(s) e2300140

    Abstract: Purpose: Thyroid peroxidase (TPO) is essential for the synthesis of thyroid hormones. However, specific mutations render TPO antigenic and prone to autoimmune attacks leading to thyroid cancer, TPO deficiency, and congenital hypothyroidism (CH). Despite ...

    Abstract Purpose: Thyroid peroxidase (TPO) is essential for the synthesis of thyroid hormones. However, specific mutations render TPO antigenic and prone to autoimmune attacks leading to thyroid cancer, TPO deficiency, and congenital hypothyroidism (CH). Despite technological advancement, most experimental procedures cannot quickly identify the genetic causes of CH nor detect thyroid cancer in the early stages.
    Methods: We performed saturated computational mutagenesis to calculate the folding energy changes (∆∆G) caused by missense mutations and analyzed the mutations involved in post-translational modifications (PTMs).
    Results: Our results showed that the functional important missense mutations occurred in the heme peroxidase domain. Through computational saturation mutagenesis, we identified the TPO mutations in G393 and G348 affecting protein stability and PTMs. Our folding energy calculations revealed that seven of nine somatic thyroid cancer mutations destabilized TPO.
    Conclusion: These findings highlight the impact of these specific mutations on TPO stability, linking them to thyroid cancer and other genetic thyroid-related disorders. Our results show that computational mutagenesis of proteins provides a quick insight into rare mutations causing Mendelian disorders and cancers in humans.
    MeSH term(s) Humans ; Congenital Hypothyroidism/genetics ; Mutation ; Iodide Peroxidase/genetics ; Iodide Peroxidase/metabolism ; Thyroid Neoplasms/genetics ; Mass Screening
    Chemical Substances Iodide Peroxidase (EC 1.11.1.8)
    Language English
    Publishing date 2024-01-31
    Publishing country United States
    Document type Journal Article
    ISSN 2473-4276
    ISSN (online) 2473-4276
    DOI 10.1200/CCI.23.00140
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: NGS for Sequence Variants.

    Teng, Shaolei

    Advances in experimental medicine and biology

    2016  Volume 939, Page(s) 1–20

    Abstract: Recent technological advances in next-generation sequencing (NGS) provide unprecedented power to sequence personal genomes, characterize genomic landscapes, and detect a large number of sequence variants. The discovery of disease-causing variants in ... ...

    Abstract Recent technological advances in next-generation sequencing (NGS) provide unprecedented power to sequence personal genomes, characterize genomic landscapes, and detect a large number of sequence variants. The discovery of disease-causing variants in patients' genomes has dramatically changed our perspective on precision medicine. This chapter provides an overview of sequence variant detection and analysis in NGS study. We outline the general methods for identifying different types of sequence variants from NGS data. We summarize the common approaches for analyzing and visualizing casual variants associated with complex diseases on precision medicine informatics.
    MeSH term(s) Computational Biology/methods ; Genetic Variation ; Genome, Human ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Internet ; Precision Medicine ; Quality Control ; Sequence Analysis, DNA/statistics & numerical data ; Software
    Language English
    Publishing date 2016
    Publishing country United States
    Document type Journal Article
    ISSN 2214-8019 ; 0065-2598
    ISSN (online) 2214-8019
    ISSN 0065-2598
    DOI 10.1007/978-981-10-1503-8_1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Impact of SARS-CoV-2 on Host Factors Involved in Mental Disorders.

    Rhoades, Raina / Solomon, Sarah / Johnson, Christina / Teng, Shaolei

    Frontiers in microbiology

    2022  Volume 13, Page(s) 845559

    Abstract: COVID-19, caused by SARS-CoV-2, is a systemic illness due to its multiorgan effects in patients. The disease has a detrimental impact on respiratory and cardiovascular systems. One early symptom of infection is anosmia or lack of smell; this implicates ... ...

    Abstract COVID-19, caused by SARS-CoV-2, is a systemic illness due to its multiorgan effects in patients. The disease has a detrimental impact on respiratory and cardiovascular systems. One early symptom of infection is anosmia or lack of smell; this implicates the involvement of the olfactory bulb in COVID-19 disease and provides a route into the central nervous system. However, little is known about how SARS-CoV-2 affects neurological or psychological symptoms. SARS-CoV-2 exploits host receptors that converge on pathways that impact psychological symptoms. This systemic review discusses the ways involved by coronavirus infection and their impact on mental health disorders. We begin by briefly introducing the history of coronaviruses, followed by an overview of the essential proteins to viral entry. Then, we discuss the downstream effects of viral entry on host proteins. Finally, we review the literature on host factors that are known to play critical roles in neuropsychiatric symptoms and mental diseases and discuss how COVID-19 could impact mental health globally. Our review details the host factors and pathways involved in the cellular mechanisms, such as systemic inflammation, that play a significant role in the development of neuropsychological symptoms stemming from COVID-19 infection.
    Language English
    Publishing date 2022-04-04
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2587354-4
    ISSN 1664-302X
    ISSN 1664-302X
    DOI 10.3389/fmicb.2022.845559
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: A phenome-wide investigation of risk factors for severe COVID-19.

    Baranova, Ancha / Cao, Hongbao / Teng, Shaolei / Zhang, Fuquan

    Journal of medical virology

    2022  Volume 95, Issue 1, Page(s) e28264

    Abstract: With the continued spread of COVID-19 globally, it is crucial to identify the potential risk or protective factors associated with COVID-19. Here, we performed genetic correlation analysis and Mendelian randomization analysis to examine genetic ... ...

    Abstract With the continued spread of COVID-19 globally, it is crucial to identify the potential risk or protective factors associated with COVID-19. Here, we performed genetic correlation analysis and Mendelian randomization analysis to examine genetic relationships between COVID-19 hospitalization and 405 health conditions and lifestyle factors in 456 422 participants from the UK Biobank. The genetic correlation analysis revealed 134 positive and 65 negative correlations, including those with intakes of a variety of dietary components. The MR analysis indicates that a set of body fat-related traits, maternal smoking around birth, basal metabolic rate, lymphocyte count, peripheral enthesopathies and allied syndromes, blood clots in the leg, and arthropathy are causal risk factors for severe COVID-19, while higher education attainment, physical activity, asthma, and never smoking status protect against the illness. Our findings have implications for risk stratification in patients with COVID-19 and the prevention of its severe outcomes.
    MeSH term(s) Humans ; Genome-Wide Association Study ; COVID-19/epidemiology ; Risk Factors ; Phenotype ; Smoking ; Polymorphism, Single Nucleotide
    Language English
    Publishing date 2022-11-08
    Publishing country United States
    Document type Journal Article
    ZDB-ID 752392-0
    ISSN 1096-9071 ; 0146-6615
    ISSN (online) 1096-9071
    ISSN 0146-6615
    DOI 10.1002/jmv.28264
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    In stock of ZB MED Cologne/Königswinter

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  5. Article: ACE2 enhance viral infection or viral infection aggravate the underlying diseases.

    Teng, Shaolei / Tang, Qiyi

    Computational and structural biotechnology journal

    2020  Volume 18, Page(s) 2100–2106

    Abstract: ACE2 plays a critical role in SARS-CoV-2 infection to cause COVID-19 and SARS-CoV-2 spike protein binds to ACE2 and probably functionally inhibits ACE2 to aggravate the underlying diseases of COVID-19. The important factors that affect the severity and ... ...

    Abstract ACE2 plays a critical role in SARS-CoV-2 infection to cause COVID-19 and SARS-CoV-2 spike protein binds to ACE2 and probably functionally inhibits ACE2 to aggravate the underlying diseases of COVID-19. The important factors that affect the severity and fatality of COVID-19 include patients' underlying diseases and ages. Therefore, particular care to the patients with underlying diseases is needed during the treatment of COVID-19 patients.
    Keywords covid19
    Language English
    Publishing date 2020-08-06
    Publishing country Netherlands
    Document type Journal Article ; Review
    ZDB-ID 2694435-2
    ISSN 2001-0370
    ISSN 2001-0370
    DOI 10.1016/j.csbj.2020.08.002
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  6. Article ; Online: ACE2 enhance viral infection or viral infection aggravate the underlying diseases

    Shaolei Teng / Qiyi Tang

    Computational and Structural Biotechnology Journal, Vol 18, Iss , Pp 2100-

    2020  Volume 2106

    Abstract: ACE2 plays a critical role in SARS-CoV-2 infection to cause COVID-19 and SARS-CoV-2 spike protein binds to ACE2 and probably functionally inhibits ACE2 to aggravate the underlying diseases of COVID-19. The important factors that affect the severity and ... ...

    Abstract ACE2 plays a critical role in SARS-CoV-2 infection to cause COVID-19 and SARS-CoV-2 spike protein binds to ACE2 and probably functionally inhibits ACE2 to aggravate the underlying diseases of COVID-19. The important factors that affect the severity and fatality of COVID-19 include patients' underlying diseases and ages. Therefore, particular care to the patients with underlying diseases is needed during the treatment of COVID-19 patients.
    Keywords Coronavirus Infectious Disease-19 ; Severe Acute Respiratory Syndrome Coronavirus −2 ; Angiotensin converting enzyme 2 ; Single Nucleotide Polymorphism ; Underlying diseases ; Health disparity ; Biotechnology ; TP248.13-248.65 ; covid19
    Language English
    Publishing date 2020-01-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: Corrigendum to: Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity.

    Teng, Shaolei / Sobitan, Adebiyi / Rhoades, Raina / Liu, Dongxiao / Tang, Qiyi

    Briefings in bioinformatics

    2021  Volume 22, Issue 5

    Language English
    Publishing date 2021-04-09
    Publishing country England
    Document type Published Erratum
    ZDB-ID 2068142-2
    ISSN 1477-4054 ; 1467-5463
    ISSN (online) 1477-4054
    ISSN 1467-5463
    DOI 10.1093/bib/bbab176
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 6262: Show issues Location:
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  8. Article: ACE2 enhance viral infection or viral infection aggravate the underlying diseases

    Teng, Shaolei / Tang, Qiyi

    Computational and Structural Biotechnology Journal. 2020, v. 18

    2020  

    Abstract: ACE2 plays a critical role in SARS-CoV-2 infection to cause COVID-19 and SARS-CoV-2 spike protein binds to ACE2 and probably functionally inhibits ACE2 to aggravate the underlying diseases of COVID-19. The important factors that affect the severity and ... ...

    Abstract ACE2 plays a critical role in SARS-CoV-2 infection to cause COVID-19 and SARS-CoV-2 spike protein binds to ACE2 and probably functionally inhibits ACE2 to aggravate the underlying diseases of COVID-19. The important factors that affect the severity and fatality of COVID-19 include patients' underlying diseases and ages. Therefore, particular care to the patients with underlying diseases is needed during the treatment of COVID-19 patients.
    Keywords COVID-19 infection ; Severe acute respiratory syndrome coronavirus 2 ; biotechnology ; death
    Language English
    Size p. 2100-2106.
    Publishing place Elsevier B.V.
    Document type Article
    Note NAL-AP-2-clean
    ZDB-ID 2694435-2
    ISSN 2001-0370
    ISSN 2001-0370
    DOI 10.1016/j.csbj.2020.08.002
    Database NAL-Catalogue (AGRICOLA)

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  9. Article ; Online: Computational Saturation Mutagenesis to Investigate the Effects of Neurexin-1 Mutations on AlphaFold Structure.

    Rhoades, Raina / Henry, Brianna / Prichett, Dominique / Fang, Yayin / Teng, Shaolei

    Genes

    2022  Volume 13, Issue 5

    Abstract: Neurexin-1 (NRXN1) is a membrane protein essential in synapse formation and cell signaling as a cell-adhesion molecule and cell-surface receptor. NRXN1 and its binding partner neuroligin have been associated with deficits in cognition. Recent genetics ... ...

    Abstract Neurexin-1 (NRXN1) is a membrane protein essential in synapse formation and cell signaling as a cell-adhesion molecule and cell-surface receptor. NRXN1 and its binding partner neuroligin have been associated with deficits in cognition. Recent genetics research has linked NRXN1 missense mutations to increased risk for brain disorders, including schizophrenia (SCZ) and autism spectrum disorder (ASD). Investigation of the structure-function relationship in NRXN1 has proven difficult due to a lack of the experimental full-length membrane protein structure. AlphaFold, a deep learning-based predictor, succeeds in high-quality protein structure prediction and offers a solution for membrane protein model construction. In the study, we applied a computational saturation mutagenesis method to analyze the systemic effects of missense mutations on protein functions in a human NRXN1 structure predicted from AlphaFold and an experimental
    MeSH term(s) Animals ; Autism Spectrum Disorder/genetics ; Calcium-Binding Proteins/metabolism ; Cattle ; Humans ; Membrane Proteins/genetics ; Mutagenesis ; Mutation ; Nerve Tissue Proteins/genetics ; Neural Cell Adhesion Molecules/metabolism ; Reproducibility of Results
    Chemical Substances Calcium-Binding Proteins ; Membrane Proteins ; NRXN1 protein, human ; Nerve Tissue Proteins ; Neural Cell Adhesion Molecules
    Language English
    Publishing date 2022-04-28
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2527218-4
    ISSN 2073-4425 ; 2073-4425
    ISSN (online) 2073-4425
    ISSN 2073-4425
    DOI 10.3390/genes13050789
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article: ACE2 enhance viral infection or viral infection aggravate the underlying diseases

    Teng, Shaolei / Tang, Qiyi

    Comput Struct Biotechnol J

    Abstract: ACE2 plays a critical role in SARS-CoV-2 infection to cause COVID-19 and SARS-CoV-2 spike protein binds to ACE2 and probably functionally inhibits ACE2 to aggravate the underlying diseases of COVID-19. The important factors that affect the severity and ... ...

    Abstract ACE2 plays a critical role in SARS-CoV-2 infection to cause COVID-19 and SARS-CoV-2 spike protein binds to ACE2 and probably functionally inhibits ACE2 to aggravate the underlying diseases of COVID-19. The important factors that affect the severity and fatality of COVID-19 include patients' underlying diseases and ages. Therefore, particular care to the patients with underlying diseases is needed during the treatment of COVID-19 patients.
    Keywords covid19
    Publisher WHO
    Document type Article
    Note WHO #Covidence: #696802
    Database COVID19

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