Biology subjects

Reyes, R.-J.

Publications and source records attributed to Reyes, R.-J..

3 recordsLinked to original sources

bioRxiv2023

Microsatellites used in forensics are located in regions unusually rich in trait-associated variants

The 20 short tandem repeat (STR) markers of the combined DNA index system (CODIS) are the basis of the vast majority of forensic genetics in the United States. One argument for permissive rules about the collection of CODIS genotypes is that the CODIS markers are thought to contain information relevant to identification only (such as a human fingerprint would), with little information about ancestry or traits. However, in the past 20 years, a quickly growing field has identified hundreds of thousands of genotype-trait associations. Here we conduct a survey of the landscape of such associations surrounding the CODIS loci as compared with non-CODIS STRs. We find that the regions around the CODIS markers are enriched for both known pathogenic variants (>90th percentile) and for SNPs identified as trait-associated in genome-wide association studies (GWAS) ([≥]95th percentile in 10kb and 100kb flanking regions), compared with other random sets of autosomal tetranucleotide-repeat STRs. Although it is not obvious how much phenotypic information CODIS would need to convey to strain the "DNA fingerprint" analogy, the CODIS markers, considered as a set, are in regions unusually dense with variants with known phenotypic associations.

genetics↗

bioRxiv2022

SCIP: A self-paced, community-based summer coding program creates community and increases coding confidence

In 2020, many students lost summer opportunities due to the COVID-19 pandemic. We wanted to offer students an opportunity to learn computational skills and be part of a community while they were stuck at home. Because the pandemic was very isolating, it was important to support students to learn and build community online. We used lessons learned from literature and our own experience to design, run and test an online program for students called the Science Coding Immersion Program (SCIP). In our program, students worked in small teams for 8 hours a week spread over the week, with one participant as the team leader and Zoom host. Teams worked on an online R or Python class at their own pace with support on Slack from the organizing team. For motivation and career advice, we hosted a weekly webinar with guest speakers. We used pre- and post-program surveys to determine how different aspects of the program impacted students. We were able to recruit a large and diverse group of participants who were happy with the program, found community in their team, and improved their coding confidence. We hope that our work will inspire others to start their own version of SCIP.

scientific communication and education↗

bioRxiv2018

Illuminating women’s hidden contribution to the foundation of theoretical population genetics

Plentiful evidence shows an historic and continuing gender gap in participation and success in scientific research. However, less attention has been directed at clarifying obscured contributions of women to science. The lack of visible women role models (particularly in computational fields) contributes to a reduced sense of belonging and retention among women. We seek to counteract this cycle by illuminating the contribution of women programmers to the foundation of our own fields--population and evolutionary genetics. We consider past acknowledged programmers (APs), who developed, ran, and sometimes analyzed the results of early computer programs. Due to authorship norms at the time, these programmers were credited in the acknowledgments sections of manuscripts, rather than being recognized as authors. For example, one acknowledgement reads \"I thanks Mrs. M. Wu for help with the numerical work, and in particular for computing table I.\". We identified APs in Theoretical Population Biology articles published between 1970 and 1990. While only 7% of authors were women, 43% of APs were women. This significant difference (p = 4.0x10-10) demonstrates a substantial proportion of womens contribution to foundational computational population genetics has been unrecognized. The proportion of women APs, as well as number of APs decreased over time. These observations correspond to the masculinization of computer programming, and the shifting of programming responsibilities to individuals credited as authors (likely graduate students). Finally, we note recurrent APs who contributed to several highly-cited manuscripts. We conclude that, while previously overlooked, historically, women have made substantial contributions to computational biology.

scientific communication and education↗