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Representing DNA for Machine Learning Algorithms: A Primer on One-Hot, Binary, and Integer Encodings
Peer reviewed
Direct linkYash Munnalal Gupta; Satwika Nindya Kirana; Somjit Homchan – Biochemistry and Molecular Biology Education, 2025
This short paper presents an educational approach to teaching three popular methods for encoding DNA sequences: one-hot encoding, binary encoding, and integer encoding. Aimed at bioinformatics and computational biology students, our learning intervention focuses on developing practical skills in implementing these essential techniques for…
Descriptors: Science Instruction, Teaching Methods, Genetics, Molecular Biology
Download full textGabriella Roby Dodd; Cedric Gondro; Tasia M.Taxis; Margaret Young; Breno Fragomeni – NACTA Journal, 2024
The objectives of this study were to identify gaps in educational training for undergraduate and graduate students in agricultural data science, propose paths for filling these gaps, and provide an annotated list of resources currently available to different training levels. Data in this study was collected through three voluntary surveys catered…
Descriptors: Data Science, Statistics Education, Agriculture, Genetics
Gao, Lei; Guo, Miao – Biochemistry and Molecular Biology Education, 2023
With rapid development of sequencing technology and the continuous accumulation of biological big data, people who are capable of using bioinformatic skills to analyze omics data and work out biological problems are urgently needed in the workforce, which highlights the importance of developing bioinformatics skills early in the undergraduate…
Descriptors: Undergraduate Students, Student Research, Student Experience, Biology
Poolman, Toryn M.; Townsend-Nicholson, Andrea; Cain, Amanda – Biochemistry and Molecular Biology Education, 2022
The final year of a biochemistry degree is usually a time to experience research. However, laboratory-based research projects were not possible during COVID-19. Instead, we used open datasets to provide computational research projects in metagenomics to biochemistry undergraduates (80 students with limited computing experience). We aimed to give…
Descriptors: Genetics, Undergraduate Students, Biological Sciences, Internet
Tapprich, William E.; Reichart, Letitia; Simon, Dawn M.; Duncan, Garry; McClung, William; Grandgenett, Neal; Pauley, Mark A. – Biochemistry and Molecular Biology Education, 2021
The lack of an instructional definition of bioinformatics delays its effective integration into biology coursework. Using an iterative process, our team of biologists, a mathematician/computer scientist, and a bioinformatician together with an educational evaluation and assessment specialist, developed an instructional definition of the…
Descriptors: Scoring Rubrics, Definitions, Genetics, Biology
Wilhelmina van Dijk; Cynthia U. Norris; Sara A. Hart – Grantee Submission, 2022
Randomized control trials are considered the pinnacle for causal inference. In many cases, however, randomization of participants in social work research studies is not feasible or ethical. This paper introduces the co-twin control design study as an alternative quasi-experimental design to provide evidence of causal mechanisms when randomization…
Descriptors: Twins, Research Design, Randomized Controlled Trials, Quasiexperimental Design
Zeke T. Spooner; Angela M. Encerrado-Manriquez; Tina T. Truong; Sascha C. T. Nicklisch – Biochemistry and Molecular Biology Education, 2024
We created a 2-week, dual-module summer course introducing high school students to environmental toxicology by teaching them quantitative polymerase chain reaction (qPCR) as a way to quantify gene expression of chemical defense proteins in response to exposure to environmental pollutants. During the course, students are guided through the various…
Descriptors: High School Students, Science Instruction, Quality Control, Genetics
M. C. Morsink; E. N. van Schaik; K. Bossers; D. A. Duijker; A. G. C. L. Speksnijder – Biochemistry and Molecular Biology Education, 2025
Abstract Targeted metagenomics is a rapidly expanding technology to analyze complex biological samples and genetic monitoring of environmental samples. In this research field, data analytical aspects play a crucial role. In order to teach targeted metagenomics data analysis, we developed a 4-week inquiry-driven modular course-based undergraduate…
Descriptors: Genetics, Microbiology, College Science, Science Process Skills
Burian, Alexis N.; Zhao, Wufan; Lo, Te-Wen; Thurtle-Schmidt, Deborah M. – Biochemistry and Molecular Biology Education, 2021
To fully appreciate genetics, one must understand the link between genotype (DNA sequence) and phenotype (observable characteristics). Advances in high-throughput genomic sequencing technologies and applications, so-called "-omics," have made genetic sequencing readily available across fields in biology from applications in…
Descriptors: Genetics, Science Instruction, Teaching Methods, Biology
Mansolf, Maxwell; Vreeker, Annabel; Reise, Steven P.; Freimer, Nelson B.; Glahn, David C.; Gur, Raquel E.; Moore, Tyler M.; Pato, Carlos N.; Pato, Michele T.; Palotie, Aarno; Holm, Minna; Suvisaari, Jaana; Partonen, Timo; Kieseppä, Tuula; Paunio, Tiina; Boks, Marco; Kahn, René; Ophoff, Roel A.; Bearden, Carrie E.; Loohuis, Loes Olde; Teshiba, Terri; deGeorge, Daniella; Bilder, Robert M. – Educational and Psychological Measurement, 2020
Large-scale studies spanning diverse project sites, populations, languages, and measurements are increasingly important to relate psychological to biological variables. National and international consortia already are collecting and executing mega-analyses on aggregated data from individuals, with different measures on each person. In this…
Descriptors: Item Response Theory, Data Analysis, Measurement, Validity
Kocemba-Pilarczyk, Kinga A.; Bentke-Imiolek, Anna; Dudzik, Paulina – Biochemistry and Molecular Biology Education, 2021
The aim of this online workshop is to familiarize biomedical faculties students with the principle of RT-PCR method. The following assumption is made, students participating in the workshop: (1) are already familiar with the principle of PCR reaction; (2) can distinguish PCR from RT-PCR; (3) know the basic possibilities of using the above…
Descriptors: Medical Students, Biochemistry, Genetics, COVID-19
Naicker, Ramona – Education for Information, 2022
Racial bias in research impacts a study's relevancy, validity and reliability, though presently this aspect is not addressed in critical appraisal tools, and consequently appraisers may not take racial bias into account when assessing a paper's quality. Drawing on critical race theory (CRT) tenets that racism is ubiquitous and race a social…
Descriptors: Racism, Critical Race Theory, Disproportionate Representation, Minority Groups
Roy, Brandon G.; Ryndock, Eric; Lappas, Courtney M. – Biochemistry and Molecular Biology Education, 2021
The amplification of nucleic acids is a fundamental tool utilized in various scientific disciplines, including Molecular Biology, Immunology, Microbiology, and Genetics. However, due to the time and technology required for traditional polymerase chain reaction and its derivatives, it is not always possible to include such methodologies in…
Descriptors: Undergraduate Students, College Science, Science Laboratories, Laboratory Experiments
Ageitos, Noa; Puig, Blanca – Journal of Biological Education, 2021
Though argumentation is a key component of scientific knowledge construction practices, it rarely occurs in classrooms worldwide. Moreover, related literature in the context of genetics and evolution learning primarily addresses them separately. In contrast, this paper is part of broader research on genetics and evolution instruction taught…
Descriptors: Diseases, Genetics, Science Instruction, Biology
Lockwood, Svetlana – ProQuest LLC, 2016
The goal of biological sciences is to understand the biomolecular mechanics of living organisms. Proteins serve as the foundation for organisms functional analysis and sequence analysis has shown to be invaluable in answering questions about individual organisms. The first step in any sequence analysis is alignment and it is common that even…
Descriptors: Data, Microbiology, Comparative Analysis, Identification
