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  1. Article ; Online: Surveying the experience of postdocs in the United States before and during the COVID-19 pandemic.

    Morin, Andréanne / Helling, Britney A / Krishnan, Seetha / Risner, Laurie E / Walker, Nykia D / Schwartz, Nancy B

    eLife

    2022  Volume 11

    Abstract: In the interest of advocating for the postdoctoral community in the United States (US), we compared the results of surveys of postdocs carried out in 2019 and in late 2020. We found that respondents' mental health and wellness were significantly impacted ...

    Abstract In the interest of advocating for the postdoctoral community in the United States (US), we compared the results of surveys of postdocs carried out in 2019 and in late 2020. We found that respondents' mental health and wellness were significantly impacted by the pandemic irrespective of their gender, race, citizenship, or other identities. Career trajectories and progression were also affected, as respondents reported being less confident about achieving career goals, and having more negative perceptions of the job market compared to before the pandemic. Postdocs working in the US on temporary visas reported experiencing increased stress levels due to changes in immigration policy. Access to institutional Postdoctoral Offices or Associations positively impacted well-being and helped mitigate some of the personal and professional stresses caused by the pandemic.
    MeSH term(s) COVID-19/epidemiology ; Gender Identity ; Humans ; Pandemics ; Research Personnel ; Surveys and Questionnaires ; United States/epidemiology
    Language English
    Publishing date 2022-07-26
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2687154-3
    ISSN 2050-084X ; 2050-084X
    ISSN (online) 2050-084X
    ISSN 2050-084X
    DOI 10.7554/eLife.75705
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  2. Article ; Online: Two-stage genome-wide association study of chronic rhinosinusitis and disease subphenotypes highlights mucosal immunity contributing to risk.

    Soliai, Marcus / Sundaresan, Agnes S / Morin, Andréanne / Hirsch, Annemarie G / Stanhope, Catherine / Kuiper, Jordan / Schwartz, Brian S / Ober, Carole / Pinto, Jayant M

    International forum of allergy & rhinology

    2021  Volume 11, Issue 4, Page(s) 814–817

    MeSH term(s) Chronic Disease ; Genome-Wide Association Study ; Humans ; Immunity, Mucosal ; Rhinitis/genetics ; Sinusitis/genetics
    Language English
    Publishing date 2021-01-03
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2625826-2
    ISSN 2042-6984 ; 2042-6976
    ISSN (online) 2042-6984
    ISSN 2042-6976
    DOI 10.1002/alr.22731
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  3. Article ; Online: The Effect of COVID-19 on the Postdoctoral Experience: a comparison of pre-pandemic and pandemic surveys.

    Morin, Andréanne / Helling, Britney A / Krishnan, Seetha / Risner, Laurie E / Walker, Nykia D / Schwartz, Nancy B

    bioRxiv

    Abstract: In the interest of advocating for the postdoctoral community in the United States, we present results from survey data collected before and during the COVID-19 pandemic on the same population of postdocs. In 2019, 5,929 postdocs in the US completed a ... ...

    Abstract In the interest of advocating for the postdoctoral community in the United States, we present results from survey data collected before and during the COVID-19 pandemic on the same population of postdocs. In 2019, 5,929 postdocs in the US completed a comprehensive survey, and in 2020, a subset completed a follow-up survey several months into the pandemic. The results show that the pandemic has substantially impacted postdocs9 mental health and wellness irrespective of gender, race, citizenship, or other identities. Postdocs also reported a significant impact on their career trajectories and progression, reduced confidence in achieving career goals, and negative perceptions of the job market compared to pre-COVID-19. International postdocs also reported experiencing distinct stressors due to the changes in immigration policy. Notably, having access to Postdoctoral Associations and Postdoctoral Offices positively impacted postdocs9 overall well-being and helped mitigate the personal and professional stresses and career uncertainties caused by the pandemic.
    Keywords covid19
    Language English
    Publishing date 2021-11-21
    Publisher Cold Spring Harbor Laboratory
    Document type Article ; Online
    DOI 10.1101/2021.11.19.468693
    Database COVID19

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  4. Article ; Online: Exposures to perfluoroalkyl substances and asthma phenotypes in childhood: an investigation of the COPSAC2010 cohort.

    Sevelsted, Astrid / Pedersen, Casper-Emil Tingskov / Gürdeniz, Gözde / Rasmussen, Morten Arendt / Schullehner, Jörg / Sdougkou, Kalliroi / Martin, Jonathan W / Lasky-Su, Jessica / Morin, Andreanne / Ober, Carole / Schoos, Ann-Marie Malby / Stokholm, Jakob / Bønnelykke, Klaus / Chawes, Bo / Bisgaard, Hans

    EBioMedicine

    2023  Volume 94, Page(s) 104699

    Abstract: Background: Exposure to perfluoroalkyl substances may affect offspring immune development and thereby increase risk of childhood asthma, but the underlying mechanisms and asthma phenotype affected by such exposure is unknown.: Methods: In the Danish ... ...

    Abstract Background: Exposure to perfluoroalkyl substances may affect offspring immune development and thereby increase risk of childhood asthma, but the underlying mechanisms and asthma phenotype affected by such exposure is unknown.
    Methods: In the Danish COPSAC2010 cohort of 738 unselected pregnant women and their children plasma PFOS and PFOA concentrations were semi-quantified by untargeted metabolomics analyses and calibrated using a targeted pipeline in mothers (gestation week 24 and 1 week postpartum) and children (age ½, 1½ and 6 years). We examined associations between pregnancy and childhood PFOS and PFOA exposure and childhood infections, asthma, allergic sensitization, atopic dermatitis, and lung function measures, and studied potential mechanisms by integrating data on systemic low-grade inflammation (hs-CRP), functional immune responses, and epigenetics.
    Findings: Higher maternal PFOS and PFOA exposure during pregnancy showed association with a non-atopic asthma phenotype by age 6, a protection against sensitization, and no association with atopic asthma or lung function, or atopic dermatitis. The effect was primarily driven by prenatal exposure. There was no association with infection proneness, low-grade inflammation, altered immune responses or epigenetic changes.
    Interpretations: Prenatal exposure to PFOS and PFOA, but not childhood exposure, specifically increased the risk of low prevalent non-atopic asthma, whereas there was no effect on atopic asthma, lung function, or atopic dermatitis.
    Funding: All funding received by COPSAC are listed on www.copsac.com. The Lundbeck Foundation (Grant no R16-A1694); The Novo Nordic Foundation (Grant nos NNF20OC0061029, NNF170C0025014, NNF180C0031764); The Ministry of Health (Grant no 903516); Danish Council for Strategic Research (Grant no 0603-00280B); and The Capital Region Research Foundation have provided core support to the COPSAC research center. COPSAC acknowledges the National Facility for Exposomics (SciLifeLab, Sweden) for supporting calibration of the untargeted metabolomics PFAS data. BC and AS has received funding for this project from the European Union's Horizon 2020 research and innovation programme (BC: grant agreement No. 946228 DEFEND; AS: grant agreement No. 864764 HEDIMED).
    MeSH term(s) Female ; Pregnancy ; Humans ; Dermatitis, Atopic ; Prenatal Exposure Delayed Effects ; Asthma/etiology ; Mothers ; Phenotype ; Inflammation/complications ; Fluorocarbons/toxicity
    Chemical Substances Fluorocarbons
    Language English
    Publishing date 2023-07-08
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 2851331-9
    ISSN 2352-3964
    ISSN (online) 2352-3964
    DOI 10.1016/j.ebiom.2023.104699
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  5. Article ; Online: Atopic and non-atopic effects of fish oil supplementation during pregnancy.

    Bisgaard, Hans / Mikkelsen, Marianne / Rasmussen, Morten Arendt / Sevelsted, Astrid / Schoos, Ann-Marie Malby / Brustad, Nicklas / Eliasen, Anders U / Thorsen, Jonathan / Chawes, Bo / Gürdeniz, Gözde / Morin, Andreanne / Stark, Ken / Stokholm, Jakob / Ober, Carole / Pedersen, Casper Emil Tingskov / Bønnelykke, Klaus

    Thorax

    2023  Volume 78, Issue 12, Page(s) 1168–1174

    Abstract: Background: We recently conducted a double-blinded randomised controlled trial showing that fish-oil supplementation during pregnancy reduced the risk of persistent wheeze or asthma in the child by 30%. Here, we explore the mechanisms of the ... ...

    Abstract Background: We recently conducted a double-blinded randomised controlled trial showing that fish-oil supplementation during pregnancy reduced the risk of persistent wheeze or asthma in the child by 30%. Here, we explore the mechanisms of the intervention.
    Methods: 736 pregnant women were given either placebo or n-3 long-chain polyunsaturated fatty acids (LCPUFAs) in the third trimester in a randomised controlled trial. Deep clinical follow-up of the 695 children in the trial was done at 12 visits until age 6 years, including assessment of genotype at the fatty acid desaturase (FADS) locus, plasma fatty acids, airway DNA methylation, gene expression, microbiome and metabolomics.
    Results: Supplementation with n-3 LCPUFA reduced the overall risk of non-atopic asthma by 73% at age 6 (relative risk (RR) 0.27 (95% CI 0.06 to 0.85), p=0.042). In contrast, there was no overall effect on asthma with atopic traits (RR 1.42 (95% CI 0.63 to 3.38), p=0.40), but this was significantly modified by maternal FADS genotype and LCPUFA blood levels (interaction p<0.05), and supplementation did reduce the risk of atopic asthma in the subgroup of mothers with FADS risk variants and/or low blood levels of n-3 LCPUFA before the intervention (RR 0.31 (95% CI 0.11 to 0.75), p=0.016). Furthermore, n-3 LCPUFA significantly reduced the number of infections (croup, gastroenteritis, tonsillitis, otitis media and pneumonia) by 16% (incidence rate ratio 0.84 (95% CI 0.74 to 0.96), p=0.009).
    Conclusions: n-3 LCPUFA supplementation in pregnancy showed protective effects on non-atopic asthma and infections. Protective effects on atopic asthma depended on maternal FADS genotype and n-3 LCPUFA levels. This indicates that the fatty acid pathway is involved in multiple mechanisms affecting the risk of asthma subtypes and infections.
    Trial registration number: NCT00798226.
    MeSH term(s) Child ; Female ; Humans ; Pregnancy ; Fish Oils/therapeutic use ; Dietary Supplements ; Fatty Acids, Omega-3 ; Asthma/prevention & control ; Fatty Acids
    Chemical Substances Fish Oils ; Fatty Acids, Omega-3 ; Fatty Acids
    Language English
    Publishing date 2023-09-11
    Publishing country England
    Document type Randomized Controlled Trial ; Journal Article
    ZDB-ID 204353-1
    ISSN 1468-3296 ; 0040-6376
    ISSN (online) 1468-3296
    ISSN 0040-6376
    DOI 10.1136/thorax-2022-219725
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  6. Article: Optimizing ChIP-seq peak detectors using visual labels and supervised machine learning

    Hocking, Toby Dylan / Goerner-Potvin, Patricia / Morin, Andreanne / Shao, Xiaojian / Pastinen, Tomi / Bourque, Guillaume

    Bioinformatics. 2017 Feb. 15, v. 33, no. 4

    2017  

    Abstract: Motivation: Many peak detection algorithms have been proposed for ChIP-seq data analysis, but it is not obvious which algorithm and what parameters are optimal for any given dataset. In contrast, regions with and without obvious peaks can be easily ... ...

    Abstract Motivation: Many peak detection algorithms have been proposed for ChIP-seq data analysis, but it is not obvious which algorithm and what parameters are optimal for any given dataset. In contrast, regions with and without obvious peaks can be easily labeled by visual inspection of aligned read counts in a genome browser. We propose a supervised machine learning approach for ChIP-seq data analysis, using labels that encode qualitative judgments about which genomic regions contain or do not contain peaks. The main idea is to manually label a small subset of the genome, and then learn a model that makes consistent peak predictions on the rest of the genome. Results: We created 7 new histone mark datasets with 12 826 visually determined labels, and analyzed 3 existing transcription factor datasets. We observed that default peak detection parameters yield high false positive rates, which can be reduced by learning parameters using a relatively small training set of labeled data from the same experiment type. We also observed that labels from different people are highly consistent. Overall, these data indicate that our supervised labeling method is useful for quantitatively training and testing peak detection algorithms. Availability and Implementation: Labeled histone mark data http://cbio.ensmp.fr/~thocking/chip-seq-chunk-db/, R package to compute the label error of predicted peaks https://github.com/tdhock/PeakError Contacts: toby.hocking@mail.mcgill.ca or guil.bourque@mcgill.ca Supplementary information: Supplementary data are available at Bioinformatics online.
    Keywords algorithms ; artificial intelligence ; bioinformatics ; computer software ; data collection ; detectors ; genome ; genomics ; histones ; models ; people ; prediction ; transcription factors
    Language English
    Dates of publication 2017-0215
    Size p. 491-499.
    Publishing place Oxford University Press
    Document type Article
    ZDB-ID 1468345-3
    ISSN 1460-2059 ; 1367-4811 ; 1367-4803
    ISSN (online) 1460-2059 ; 1367-4811
    ISSN 1367-4803
    DOI 10.1093/bioinformatics/btw672
    Database NAL-Catalogue (AGRICOLA)

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  7. Article ; Online: Combining omics data to identify genes associated with allergic rhinitis.

    Morin, Andréanne / Laviolette, Michel / Pastinen, Tomi / Boulet, Louis-Philippe / Laprise, Catherine

    Clinical epigenetics

    2017  Volume 9, Page(s) 3

    Abstract: Allergic rhinitis is a common chronic disorder characterized by immunoglobulin E-mediated inflammation. To identify new genes associated with this trait, we performed genome- and epigenome-wide association studies and linked marginally significant CpGs ... ...

    Abstract Allergic rhinitis is a common chronic disorder characterized by immunoglobulin E-mediated inflammation. To identify new genes associated with this trait, we performed genome- and epigenome-wide association studies and linked marginally significant CpGs located in genes or its promoter and SNPs located 1 Mb from the CpGs, by identifying
    MeSH term(s) Adolescent ; Adult ; Aged ; Aged, 80 and over ; Asthma/genetics ; Child ; Child, Preschool ; CpG Islands ; Epigenesis, Genetic ; Female ; Genetic Predisposition to Disease ; Genome-Wide Association Study/methods ; Homeodomain Proteins/genetics ; Humans ; Immediate-Early Proteins/genetics ; Infant ; Male ; Middle Aged ; Polymorphism, Single Nucleotide ; Quantitative Trait Loci ; Rhinitis, Allergic/genetics ; Young Adult
    Chemical Substances CDX1 protein, human ; Homeodomain Proteins ; Immediate-Early Proteins ; RNF39 protein, human
    Language English
    Publishing date 2017
    Publishing country Germany
    Document type Journal Article
    ISSN 1868-7083
    ISSN (online) 1868-7083
    DOI 10.1186/s13148-017-0310-1
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  8. Article ; Online: Optimizing ChIP-seq peak detectors using visual labels and supervised machine learning.

    Hocking, Toby Dylan / Goerner-Potvin, Patricia / Morin, Andreanne / Shao, Xiaojian / Pastinen, Tomi / Bourque, Guillaume

    Bioinformatics (Oxford, England)

    2017  Volume 33, Issue 4, Page(s) 491–499

    Abstract: Motivation: Many peak detection algorithms have been proposed for ChIP-seq data analysis, but it is not obvious which algorithm and what parameters are optimal for any given dataset. In contrast, regions with and without obvious peaks can be easily ... ...

    Abstract Motivation: Many peak detection algorithms have been proposed for ChIP-seq data analysis, but it is not obvious which algorithm and what parameters are optimal for any given dataset. In contrast, regions with and without obvious peaks can be easily labeled by visual inspection of aligned read counts in a genome browser. We propose a supervised machine learning approach for ChIP-seq data analysis, using labels that encode qualitative judgments about which genomic regions contain or do not contain peaks. The main idea is to manually label a small subset of the genome, and then learn a model that makes consistent peak predictions on the rest of the genome.
    Results: We created 7 new histone mark datasets with 12 826 visually determined labels, and analyzed 3 existing transcription factor datasets. We observed that default peak detection parameters yield high false positive rates, which can be reduced by learning parameters using a relatively small training set of labeled data from the same experiment type. We also observed that labels from different people are highly consistent. Overall, these data indicate that our supervised labeling method is useful for quantitatively training and testing peak detection algorithms.
    Availability and implementation: Labeled histone mark data http://cbio.ensmp.fr/~thocking/chip-seq-chunk-db/ , R package to compute the label error of predicted peaks https://github.com/tdhock/PeakError.
    Contacts: toby.hocking@mail.mcgill.ca or guil.bourque@mcgill.ca.
    Supplementary information: Supplementary data are available at Bioinformatics online.
    Language English
    Publishing date 2017-02-15
    Publishing country England
    Document type Journal Article
    ZDB-ID 1422668-6
    ISSN 1367-4811 ; 1367-4803
    ISSN (online) 1367-4811
    ISSN 1367-4803
    DOI 10.1093/bioinformatics/btw672
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  9. Article ; Online: 17q12-q21 variants interact with early-life exposures to modify asthma risk in Black children.

    Gereige, Jessica D / Morin, Andreanne / Calatroni, Agustin / Visness, Cynthia M / Wood, Robert A / Kattan, Meyer / Bacharier, Leonard B / Becker, Patrice / Altman, Matthew C / Gern, James E / Ober, Carole / O'Connor, George T

    Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology

    2021  Volume 52, Issue 4, Page(s) 565–568

    MeSH term(s) Asthma/etiology ; Asthma/genetics ; Child ; Environmental Exposure ; Genetic Predisposition to Disease ; Humans
    Language English
    Publishing date 2021-12-12
    Publishing country England
    Document type Letter ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 645204-8
    ISSN 1365-2222 ; 0954-7894 ; 0960-2178
    ISSN (online) 1365-2222
    ISSN 0954-7894 ; 0960-2178
    DOI 10.1111/cea.14074
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  10. Article ; Online: Prenatal exposure to ambient air pollution is associated with early life immune perturbations.

    Tingskov Pedersen, Casper-Emil / Eliasen, Anders Ulrik / Ketzel, Matthias / Brandt, Jørgen / Loft, Steffen / Frohn, Lise Marie / Khan, Jibran / Brix, Susanne / Rasmussen, Morten A / Stokholm, Jakob / Chawes, Bo / Morin, Andreanne / Ober, Carole / Bisgaard, Hans / Pedersen, Marie / Bønnelykke, Klaus

    The Journal of allergy and clinical immunology

    2022  Volume 151, Issue 1, Page(s) 212–221

    Abstract: Background: Exposure to ambient air pollution has been linked to asthma, allergic rhinitis, and other inflammatory disorders, but little is known about the underlying mechanisms.: Objective: We studied the potential mechanisms leading from prenatal ... ...

    Abstract Background: Exposure to ambient air pollution has been linked to asthma, allergic rhinitis, and other inflammatory disorders, but little is known about the underlying mechanisms.
    Objective: We studied the potential mechanisms leading from prenatal ambient air pollution exposure to asthma and allergy in childhood.
    Methods: Long-term exposure to nitrogen dioxide (NO
    Results: Higher prenatal air pollution exposure with NO
    Conclusion: Prenatal exposure to ambient air pollution was associated with early life immune perturbations conferring risk of allergic rhinitis and asthma. These findings suggest potential mechanisms of prenatal exposure to ambient air pollution on the developing immune system.
    MeSH term(s) Child ; Pregnancy ; Female ; Humans ; Infant ; Air Pollutants/adverse effects ; Air Pollutants/analysis ; Nitrogen Dioxide/adverse effects ; Prenatal Exposure Delayed Effects ; Asthma/etiology ; Asthma/chemically induced ; Particulate Matter/adverse effects ; Rhinitis, Allergic/chemically induced ; Environmental Exposure/adverse effects
    Chemical Substances Air Pollutants ; Nitrogen Dioxide (S7G510RUBH) ; Particulate Matter
    Language English
    Publishing date 2022-09-06
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 121011-7
    ISSN 1097-6825 ; 1085-8725 ; 0091-6749
    ISSN (online) 1097-6825 ; 1085-8725
    ISSN 0091-6749
    DOI 10.1016/j.jaci.2022.08.020
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