Biology subjects

Wiggins, G.

Publications and source records attributed to Wiggins, G..

3 recordsLinked to original sources

bioRxiv2021

Enhancing Quantitative and Data Science Education for Graduate Students in Biomedical Science

Substantial guidance is available on undergraduate quantitative training for biologists, including reports focused on biomedical science, but far less attention has been paid to the graduate curriculum. In this setting, we propose an innovative approach to quantitative education that goes beyond recommendations of a course or set of courses or activities. Due to the diversity of quantitative methods, it is infeasible to expect that biomedical PhD students can be exposed to more than a minority of the quantitative concepts and techniques employed in modern biology. We developed a novel prioritization approach in which we mined and analyzed quantitative concepts and skills from publications that faculty in relevant units deemed central to the scientific comprehension of their field. The analysis provides a prioritization of quantitative skills and concepts and could represent an effective method to drive curricular focus based upon program-specific faculty input for biological science programs of all types. Our results highlight the disconnect between typical undergraduate quantitative education for life science students, focused on continuous mathematics, and the concepts and skills in graphics, statistics, and discrete mathematics that arise from priorities established by biomedical science faculty. One Sentence SummaryWe developed a novel approach to prioritize quantitative concepts and methods for inclusion in a graduate biomedical science curriculum based upon approaches included in faculty-identified key publications.

scientific communication and education↗

bioRxiv2020

Estimating invasion dynamics with geopolitical-unit level records: performance and similarity of common methods using both simulated data and a real case

Estimating invasion dynamic is important to the management of invasive species, and geopolitical-unit level data are usually the most abundant and available records of invasive species. Here, for the first time we evaluated performances and similarities of eight common methods to estimate spread pattern and spread dynamic of invasive species with geopolitical-unit level data, and assessed impacts of variations in geopolitical-units on each method using simulated spread data. We also formulated a concave hull boundary displacement method (i.e., CEB) and an area-based regression method (i.e., AER) for estimating spread with geopolitical-unit data. Three regions with different sized counties in the United States (U.S.) were selected to conduct simulations and three spread scenarios were simulated. R2 and root mean square error were used to evaluate the abilities of all methods to estimate spread. Correlation coefficients were used to assess the similarity pattern of all methods. Finally, kudzu bug Megacopta cribraria, an invasive insect in the U.S., was used as a case study to test the generality of some results concluded from the simulated research. We found the CEB and two regression methods consistently estimated the right expansion patterns. Two boundary displacement and two area-based regression methods estimated highly correlated spread and were the best four methods, among which CEB had the best estimation. Distance-based regression methods are sensitive to irregularity and stochasticity in spread, and the minimum spread distance method had low ability to estimate spread. The case study showed consistent results with the simulated research. Both regression and boundary displacement methods can estimate spread patterns, overall rate, and spread dynamics of invasive species. Boundary displacement methods best estimate spread rates and dynamics; however, for spread without clear infestation outlines, area-based regression methods can be good alternatives.

ecology↗

bioRxiv2017

Nanopore sequencing of full-length BRCA1 mRNA transcripts reveals co-occurrence of known exon skipping events

Laboratory assays evaluating the effect of DNA sequence variants on BRCA1 mRNA splicing may contribute to classification by providing molecular evidence. However, our knowledge of normal and aberrant BRCA1 splicing events to date has been limited to data derived from assays targeting partial transcript sequences. For the first time, we resolve the exon structure of whole BRCA1 transcripts using MinION nanopore sequencing of long-range PCR amplicons. Our study identified 32 BRCA1 isoforms, including 18 novel isoforms which comprised skipping of multiple contiguous and/or non-contiguous exons. Furthermore, we show that known BRCA1 exon skipping events, such as {Delta}(9,10) and {Delta}21, can co-occur in a single transcript, with some isoforms containing four or more alternative splice junctions. Our results highlight complexity in BRCA1 transcript structure that has not previously been described. This finding has key implications for predicting translation frame of splicing transcripts, important for interpreting the clinical significance of spliceogenic variants. Future research is warranted to quantitatively assess full length BRCA1 transcript levels, and to assess the application of nanopore sequencing for routine evaluation of potential spliceogenic variants.

genomics↗