Use of preprint peer review to educate and enculturate science undergraduates

McDowell, Gary S.; Fankhauser, Sarah C.; Saderi, Daniela; Balgopal, Meena M.; Lijek, Rebeccah S.

doi:10.1002/leap.1472

Cited by 10 publications

(12 citation statements)

References 62 publications

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“…We observe that open chromatin in blood (E116, GM12878 Lymphoblastoid Cells; E124, Monocytes-CD14+ RO01746 Primary Cells; E041, Primary T helper cells PMA-I stimulated) and rectum (E102, Rectal Mucosa Donor 31) is positively associated with SNP-disease association in both diseases; this is consistent with a previous study where blood cell types are found to be relevant in many autoimmune diseases, including UC and CD [33]. In addition, symptoms or complications in rectum is also observed in UC and CD [34]. Interestingly, open chromatin in GI-intestine (E085, fetal intestine small) is negatively associated with SNP-disease association, along with ohter intestine tissues (E084, fetal intestine large and E109, small intestine, with the 61th and 86th smallest tissue weight, respectively, amongst 127 contexts).…”

Section: Resultssupporting

confidence: 89%

Disease-specific prioritization of non-coding GWAS variants based on chromatin accessibility

Liang,

Abraham,

Capra

et al. 2023

Preprint

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Non-protein-coding genetic variants are a major driver of the genetic risk for human disease; however, identifying which non-coding variants contribute to which diseases, and their mechanisms, remains challenging. In-silico variant prioritization methods quantify a variant's severity in the context of having a phenotypic effect; but for most methods the specific phenotype and disease context of the prediction are poorly defined. For example, many commonly used methods provide a single organism-wide score for each variant, while other methods summarize a variant's impact specifically in certain tissues and/or cell-types. Here we propose a complementary disease-specific variant prioritization scheme, which is motivated by the observation that the variants contributing to different diseases often operate through different biological mechanisms. We combine tissue/cell-type specific scores into disease-specific scores with a logistic regression approach and apply it to 25,000 non-coding variants spanning 111 diseases. We show that disease-specific aggregation of tissue/cell-type specific scores (GenoSkyline, Fit- Cons2, DNA accessibility) signifiantly improves the association of common non-coding genetic variants with disease (average precision: 0.151, baseline=0.09), compared with organism-wide scores (GenoCanyon, LINSIGHT, GWAVA, eigen, CADD; average precision: 0.129, base- line=0.09). Calculating disease similarities based on data-driven aggregation weights highlights meaningful disease groups (e.g., immune system related diseases and mental/behavioral disorders), and it provides information about tissues and cell-types that drive these similarities (e.g., lymphoblastoid T-cells for immune-system diseases). We also show that so-learned similarities are complementary to genetic similarities as quantified by genetic correlation. Overall, our aggregation approach demonstrates the strengths of disease-specific variant prioritization, leads to improvement in non-coding variant prioritization, and it enables interpretable models that link variants to disease via specific tissues and/or cell-types.

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Section: Resultssupporting

confidence: 89%

Disease-specific prioritization of non-coding GWAS variants based on chromatin accessibility

Liang,

Abraham,

Capra

et al. 2023

Preprint

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“…This knowledge has demystified for these students a critical component of success in STEM fields, that of contributing to scientific knowledge through publication. In line with our overarching goal, the broader data in the literature suggests that such efforts lead to increased development of scholarly identity and, therefore, better STEM engagement and retention, particularly for underrepresented and minoritized students (Burt et al, 2023; Hernandez et al, 2017; McDowell et al, 2022; Perez et al, 2014).…”

Section: Discussionsupporting

confidence: 61%

“…There are practices that engage students in authentic authorship experiences with publishable products (Burks & Chumchal, 2009; Giuliano et al, 2019; Guilford, 2001), though none have been described in the field of synthetic biology. Fewer tools exist to measure learning gains with respect to writing, or that teach the more abstract processes of peer review and scientific publishing (McDowell et al, 2019), and more development is needed in these areas(McDowell et al, 2022). Demystifying authorship and publication processes was shown to improve student learning outcomes and foster a greater sense of scientific identity among graduate students (Sletto et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

Empowering Student Authorship in Synthetic Biology

Roberts,

Farny

2024

Preprint

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Women and racial minorities are underrepresented in the synthetic biology community. Developing a scholarly identity by engaging in a scientific community through writing and communication is an important component for STEM retention, particularly for underrepresented individuals. Several excellent pedagogical tools have been developed to teach scientific literacy and to measure competency in reading and interpreting scientific literature. However, fewer tools exist to measure learning gains with respect to writing, or that teach the more abstract processes of peer review and scientific publishing, which are essential for developing scholarly identity and publication currency. Here we describe our approach to teaching scientific writing and publishing to undergraduate students within a synthetic biology course. Using gold standard practices in project-based learning, we created a writing project in which students became experts in a specific application area of synthetic biology with relevance to an important global problem or challenge. To measure learning gains associated with our learning outcomes, we adapted and expanded the Student Attitudes, Abilities, and Beliefs (SAAB) concept inventory to include additional questions about the process of scientific writing, authorship, and peer review. Our results suggest the project-based approach was effective in achieving the learning objectives with respect to writing and peer reviewed publication, and resulted in high student satisfaction and student self-reported learning gains. We propose that these educational practices will contribute directly to the development of scientific identity of undergraduate students as synthetic biologists, and will be useful in creating a more diverse synthetic biology research enterprise.

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“…Therefore, peer review represents part of science, technology, engineering, and math (STEM) education’s “hidden curriculum” of unstated norms, values, skills, and expectations that are untaught yet required for success ( 14 ). Since peer review is integral to the scientific process and central to the identity of a scientist, we envision a paradigm shift that makes teaching peer review integral to undergraduate science education ( 15 ). Just as early research experiences help students form a scientific identity ( 16 ) and develop scientific literacy ( 17 ), so too can early scholarship experiences in peer review.…”

Section: Introductionmentioning

confidence: 99%