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Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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bioRxiv2022

DBERlibR: Automated Data Analysis for Discipline-Based Education Research

Discipline-Based Education Research (DBER) scientists repeatedly analyze assessment data to ensure question items reliability and examine the efficacy of a new educational intervention. Analyzing assessment data comprises multiple steps and statistical techniques that consume much of researchers time and are error-prone. While education research continues to grow across many disciplines of science, technology, engineering, and mathematics (STEM), the DBER community lacks tools to streamline education research data analysis. DBERlibR--an R package to streamline and automate DBER data processing and analysis--fills this gap. The package reads user-provided assessment data, cleans them, merges multiple datasets (as necessary), checks assumption(s) for specific statistical techniques (as necessary), applies various statistical tests (e.g., one-way analysis of covariance, one-way repeated-measures analysis of variance), and presents and interprets the results all at once. By providing the most frequently used analytic techniques, this package will contribute to DBER by facilitating the creation and widespread use of evidence-based knowledge and practices. The outputs contain a sample interpretation of the results for users convenience. User inputs are minimal; they only need to prepare the data files as instructed and type a function in RStudio to conduct a specific data analysis.

scientific communication and education↗

bioRxiv2026

Leveraging a hybrid cross-disciplinary training model to accelerate global bioinformatics capacity

Disparities in formal bioinformatics training exacerbate the global skills gap, impeding the democratized application of advanced genomic technologies. To bridge this divide, we introduce a scalable, hybrid training framework designed to rapidly accelerate regional bioinformatics capacity. We exemplify this approach through the Eastern European Bioinformatics and Genomics (EEBG) workshop series -- a cross-disciplinary initiative that pairs international faculty with local institutions to deliver modular, hands-on curricula. Functioning as a structured knowledge-transfer pipeline, the series has catalyzed a sustainable educational ecosystem, evidenced by the establishment of multiple independent summer schools across the region. The assessment of the 2025 EEBG workshop in Krakow, Poland, validates the models viability; participant metrics confirm high efficacy in skill acquisition (mean satisfaction: 4.4/5.0) and community building. Crucially, the hybrid delivery mode dismantled geographic barriers, serving as a vital mechanism for maintaining scientific continuity for researchers facing displacement and crisis. Synthesizing these outcomes, we define the core features of a replicable blueprint for scientific readiness in resource-constrained environments. We conclude by presenting a strategic roadmap -- organized around infrastructure standardization, governance sustainability, and geographical expansion -- for adapting this regional proof-of-concept into a global export-ready model, offering a critical path toward ensuring universal access to genomic innovation.

scientific communication and education↗

bioRxiv2019

Strategies for building computing skills to support microbiome analysis: a five-year perspective from the EDAMAME workshop

Here, we report our educational approach and learner evaluations of the first five years of the Explorations in Data Analysis for Metagenomic Advances in Microbial Ecology (EDAMAME) workshop, held annually at Michigan State Universitys Kellogg Biological Station from 2014-2018. We hope this information will be useful for others who want to organize computing-intensive workshops and encourage quantitative skill development among microbiologists.\n\nImportanceHigh-throughput sequencing and related statistical and bioinformatic analyses have become routine in microbiology in the past decade, but there are few formal training opportunities to develop these skills. A week-long workshop can offer sufficient time for novices to become introduced to best computing practices and common workflows in sequence analysis. We report our experiences in executing such a workshop targeted to professional learners (graduate students, post-doctoral scientists, faculty, and research staff).

scientific communication and education↗

bioRxiv2021

Remote teaching versus blended learning: exploring discourse richness and learning effectiveness

The Internet has changed the way teachers and students access information and build knowledge. The recent COVID-19 pandemic has created challenges for both teachers and students and a demand for new methodologies of remote learning. In the life sciences, mixing online content with practical activities represents an even greater challenge. In microbiology, the implementation of an active teaching methodology, the #Adopt project, based on the social network Facebook(R), represents an excellent option for connecting remote education with classroom activities. In 2020, the version applied in high school, "Adopt a Microorganism", was adapted to meet the demands of emergency remote education owing to the suppression of face-to-face activities caused by the pandemic. In the present study, we assessed how the change in methodology impacted the discourse richness of students from high school integrated with technical education in the Business Administration program of the Federal Institute of Sao Paulo, Sorocaba Campus. Three questionnaires related to the groups of microorganisms (Archaea, Bacteria, Virus, Fungi, and Protozoan) were applied. The students responses in the 2019 and 2020 classes were compared concerning content richness and multiplicity of concepts through the application of the Shannon diversity index, an approach that is generally used to assess biodiversity in different environments. The observed results suggest that remote learning provided students with a conceptual basis and richness of content equivalent to that achieved by students subjected to the hybrid teaching model. In conclusion, this study suggests that the #Adopt project methodology increases students discourse richness in microbiology even without face-to-face traditional classes.

scientific communication and education↗

bioRxiv2018

Developing Future Biologists: creating and assessing a portable short course to engage underrepresented undergraduate students in developmental biology

Many barriers discourage underrepresented students from pursuing science careers. To access graduate education, undergraduate students must first gain exposure to a particular subject and subsequently accumulate related coursework and research experience. Many underrepresented students lack exposure to developmental biology due to limited undergraduate course offerings and finite resources at smaller institutions. To address this disparity, a group of University of Michigan graduate students and postdoctoral fellows created a portable short course focusing on developmental biology, titled \"Developing Future Biologists\" (DFB). This weeklong educational initiative provides hands-on laboratory sessions, interactive lectures, and professional development workshops to teach students about developmental biology and increase awareness of scientific career options. To evaluate course effectiveness, we developed a pre-post assessment, incorporating main ideas from the BioCore Guide. Student understanding of basic concepts and perceived experience in developmental biology increased in DFB participants, despite the abbreviated nature of the course. Here, we provide all course materials and an in-depth analysis of the assessment we created. The DFB portable short course model is an easily adaptable tool that connects undergraduate students with opportunities for advanced study and lowers barriers for underrepresented students in science, technology, engineering, and mathematics.

scientific communication and education↗

bioRxiv2024

Seeing isn't believing? Mixed effects of a perspective-getting intervention to improve mentoring relationships for science doctoral students

Science doctoral students can experience negative interactions with faculty mentors and internalize these experiences, potentially leading to self-blame and undermining their research self-efficacy. Helping students perceive these interactions adaptively may protect their research self-efficacy and maintain functional mentoring relationships. We conducted a pre-registered, longitudinal field experiment of a novel perspective-getting intervention combined with attribution retraining to help students avoid self-blame and preserve research self-efficacy. Science doctoral students (n = 155) were randomly assigned to read about mentor perspectives on negative interactions (i.e., Perspective-getting Condition) or about mentoring with no mentor perspective (i.e., control condition). Contrary to our hypotheses, we found no main effects of the intervention on students self-blame or research self-efficacy. However, for students with lower pre-intervention mentorship relationship satisfaction, the intervention preserved research self-efficacy six months later. This study provides evidence that perspective getting may be protective for students who are most in need of relationship intervention. Educational Relevance and Implications StatementEffective mentoring relationships are fundamental for promoting the success of doctoral students in science, yet not all mentoring relationships are high quality. This study assessed the effectiveness of a brief perspective-getting intervention (where students are given the perspective of what it is like to be a research mentor) that aimed to protect science doctoral students from blaming themselves for negative interactions with faculty mentors and maintain their research self-efficacy. Results showed that on average across all students, the intervention did not affect students self-blame for negative interactions or their research self-efficacy. However, the intervention did help students with less satisfying mentoring relationships maintain their self-efficacy. Thus, perspective-getting shows some promise for protecting science doctoral students from harm that can be caused by negative interactions with faculty mentors.

scientific communication and education↗

bioRxiv2020

The aggregate effect of implementation strength of family planning programs on modern contraceptive use at the health systems level in rural Malawi

Background To explore the association between the strength of implementation of family planning (FP) programs on the use of modern contraceptives. Specifically, how strongly these programs are being implemented across a health facility’s catchment area in Malawi and the odds of a woman in that catchment area is using modern contraceptives. This information can be used to assess whether the combined impact of multiple large-scale FP programs is leading to change in the health outcomes they aim to improve.Methods and findings We used data from the 2017 Implementation Strength Assessment (ISA) that quantified how much of family planning programs at the health facility and community health worker levels were being implemented across every district of Malawi. We used a summary measure developed in a previous study that employs quantitative methods to combine data across FP domains and health system levels. We tested the association of this summary measure for implementation strength with household data from the 2015 Malawi Demographic Health Survey (DHS). We found that areas with stronger implementation of FP programs had higher odds of women using modern contraceptives compared with areas with weaker implementation. The association of ISA with use of modern contraception was different by education, marital status, and geography. After controlling for these factors, we found that the adjusted odds of using a modern contraceptive was three times higher in catchment areas with high implementation strength compared to those with lower strength.Conclusion Metrics that summarize how strongly FP programs are being implemented were used to show a statistically significantly positive relationship between increasing implementation strength and higher rates of modern contraceptive use. Decisionmakers at the various levels of health authority can use this type of summary measure to better understand the combined impact of their diverse FP programming and inform future programmatic and policy decisions. The findings also reinforce the idea that having a well-supported and supplied cadre of community health workers supplementing FP provision at the health facility can be an important health systems mechanism, especially in rural settings and to target youth populations.View Full Text

scientific communication and education↗

bioRxiv2026

A Comparative Study of MBTI and Learning Style- Based Grouping for Enhancing Group Effectiveness and Balance in a Pedagogical Setting

Effective group work is central to Problem-Based Learning (PBL) in higher education, yet the optimal strategy for forming student groups remains unclear. This study compared MBTI-based grouping, informed by personality types and Keirsey temperaments, with Learning Style-Based (LSB) grouping, grounded in Kolbs Experiential Learning Theory, to assess their impact on group functioning and role performance. Participants were undergraduate students enrolled in Cell Biology (Fall 2022 and Fall 2023) and Introduction to Biology Laboratory (Fall 2023) courses. Students completed MBTI and Kolb Learning Style assessments, and groups and roles (Leader, Communicator, Organizer) were assigned accordingly. Results indicated that LSB-based groups consistently outperformed MBTI-based groups across multiple performance metrics, including productivity, listening, sense of safety, belonging, and overall satisfaction. All metrics showed statistically significant decreases in MBTI-based groups except contribution, which did not differ significantly between grouping strategies. Role performance ratings were significantly higher for Leaders and Communicators in LSB groups, while no significant differences were observed for the Organizer role. Correlation analyses revealed that satisfaction was strongly associated with perceived productivity in MBTI-based groups, whereas in LSB-based groups, satisfaction was more strongly correlated with psychological safety. These findings suggest that learning style alignment may better support effective collaboration and group climate in PBL settings than personality-based grouping.

scientific communication and education↗

bioRxiv2020

The Ph.D. Panic: Examining the relationships among teaching anxiety, teaching self-efficacy, and coping in Biology graduate teaching assistants (GTAs)

Anxiety among graduate students in the United States has increased over the last several decades, affecting not only their overall mental health but also reducing retention in graduate programs. Teachers with high teaching anxiety can negatively impact student learning, yet the impacts of teaching anxiety on graduate teaching assistants (GTAs) is not well studied. Biology GTAs teach most introductory Biology labs and discussions nationally, thus broadly influencing the quality of undergraduate education. In Fall 2016, we investigated Biology GTA teaching anxiety at a large research-intensive southeastern university by (1) measuring teaching anxiety of Biology GTAs, and (2) exploring the relationships among teaching anxiety, self-efficacy, and coping. Using multiple linear regressions, we found that greater teaching self-efficacy is related to lower teaching anxiety in Biology GTAs (R2adi =0.65, p<0.001). Coping strategies and frequencies did not significantly contribute to teaching anxiety in our models. We found similar levels of teaching anxiety across genders, ethnicities, student citizenship status (domestic vs. international) and teaching experience level. However, there were significant differences among student subgroups in teaching self-efficacy and coping strategies. Effective coping may contribute to the lack of anxiety differences among some of the student subgroups. These results can inform teaching professional development for GTAs, and encourage greater awareness and dialogue about the impacts of mental health issues in academia.

scientific communication and education↗

bioRxiv2017

Is Democracy the Right System? Collaborative Approaches to Building an Engaged RDM Community

When developing new products, tools or services, one always need to think about the end users to ensure a wide-spread adoption. While this applies equally to services developed at higher education institutions, sometimes these services are driven by policies and not by needs of end users. This policy-driven approach can prove challenging for building effective community engagement. The initial development of Research Data Management support services at the University of Cambridge was policy-driven and subsequently failed in the first instance to engage the community of researchers for whom these services were created.\n\nIn this practice paper we will describe the initial approach undertaken at Cambridge when developing RDM services, the results of this approach and lessons learnt. We will then provide an overview of alternative, democratic strategies employed and their positive effects on community engagement. We will summarise by performing a cost-benefit analysis of the two approaches. This paper might be a useful case study for any institutions aiming to develop central support services for researchers, with conclusions applicable to the wide sector, and extending beyond Research Data Management services.

scientific communication and education↗

bioRxiv2021

The Influence of Public Health Faculty on College and University Plans during the COVID-19 Pandemic

The purpose of this study was to determine whether the institutional presence of public health faculty within colleges and universities influenced operational plans for the fall semester of 2020. Using cross-sectional data collected by the College Crisis Initiative of Davidson College, six levels of instructional modalities (ranked from least to most restrictive) were compared between Council on Education of Public Health (CEPH)-accredited and non-CEPH-accredited 4-year institutions. Institutions with CEPH-accredited schools and programs were more likely to select some restrictive teaching modalities: 63.8% more likely to use hybrid/hyflex or more restrictive and 66.9% more likely to be primarily online (with some in person) or more restrictive. However, having CEPH-accredited programs did not push institutions to the most restrictive modalities. COVID-19 cases in county, enrollment, and political affiliation of the state governor were also found to influence instructional modality selection. While any ecological study has certain limitations, this study demonstrates that college and university fall plans appear to have been influenced by the presence of CEPH-accredited schools and programs of public health, and/or the input of their faculty. The influence of relevant faculty expertise on institutional decision-making can help inform college and university responses to future crises.

scientific communication and education↗

bioRxiv2022

Community engagement through student-led science for dengue prevention during the COVID-19 pandemic in Cordoba, Argentina.

BackgroundDuring 2019-2020 while COVID-19 pandemic, the Americas were facing the biggest dengue fever epidemic in recent history. Traditional vector control programs, based on insecticide application have been insufficient to control the spread of dengue fever. Several studies suggest refocusing on education with the aim of an integrated vector management strategy within the local ecological-community context. We aim to assess community perceptions, knowledge, attitude, preventive practice, and action through student-led science assignments regarding dengue fever, prevention, and socio-ecological factors in temperate Cordoba, Argentina. MethodsThe study was conducted during the COVID-19 quarantine when schools switched to online education for the first time. Several activities through Google Classroom platform included a survey to one students family member, and an outdoor activity to assess their attitudes and to clean the backyard and gardens. ResultsSignificant number of respondents developed good preventive practices and increased their knowledge about the vector and disease highlighting that 75% of responders knew that dengue fever was transmitted by a mosquito, 81.96% declared having obtained knowledge regarding dengue and vector through television, 56% affirm that dengue is a severe illness, 67% of respondents admitted that individuals play an important role in the prevention of dengue. Regarding mosquito control activities, 90% of respondents reported turning containers. ConclusionsThis highlights the need for school programs with curricula to address vector biology and the prevention of vector-borne diseases not only during activity periods when mosquitoes batter people but all year long to do real prevention.

scientific communication and education↗

bioRxiv2023

Building the Next Generation Workforce: Why We Need Science Policy Training at the Undergraduate Level

Diverse pathways into the science policy workforce are necessary for providing opportunities to students at all levels to engage in the field and to bring their talents to the future of policymaking. Both classroom and experiential training opportunities are essential to achieving this goal. In this publication, we assessed the current landscape of science policy training for undergraduate students in the United States by conducting a keyword search for experiential career training opportunities at varying levels of education. We also reviewed existing science policy publications for undergraduate opportunities, an area that has been largely unexplored to date. From these assessments, we found that most experiential training opportunities are geared towards Science, Technology, Engineering and Math (STEM) students in PhDs program or recent PhD graduates, followed by Masters-level students or graduates, and fewer opportunities exist for undergraduate students and Bachelor-degree holders. We then conducted focus group-style interviews with early career scientists involved in science policy, including undergraduate students, to discuss their experiences and ideas for change. Based on our findings, we recommend that universities, organizations, and funding agencies expand upon their existing resources for curriculum, academic advising, training opportunities, and funding, and dedicate resources toward raising awareness and creating additional opportunities in science policy at the undergraduate level. These steps can help create pathways for undergraduate students to enter and contribute to the science policy workforce.

scientific communication and education↗

bioRxiv2020

Active learning tools improve the learning outcomes, scientific attitude and critical thinking in higher education: Experiences in an online course during the COVID-19 pandemic

Active teaching methodologies have been placed as a hope for changing education at different levels, transiting from passive lecture-centered to student-centered learning. With the health measures of social distance, the COVID-19 pandemic forced a strong shift to remote education. With the challenge of delivering quality education through a computer screen, we validated and applied an online course model using active teaching tools for higher education. We incorporated published active-learning strategies into an online construct, with problem-based inquiry and design of inquiry research projects to serve as our core active-learning tool. The gains related to students science learning experiences and their attitudes towards science were assessed by applying questionnaires before, during and after the course. The course counted on the participation of 83 students, most of them (60,8%) from post-graduate students. Our results show that engagement provided by active learning methods can improve performance both in hard and soft skills. Students participation seems to be more relevant when activities require interaction of information, prediction and reasoning, such as open-ended questions and design of research projects. Therefore, our data shows that, in pandemic, active learning tools benefit students and improve their critical thinking and their motivation and positive positioning in science.

scientific communication and education↗

bioRxiv2022

C.R.E.A.T.E'ing shifts in first year students' science efficacy that are independent of instructor rank and experience in a large, multi-section online introductory course

With a primary objective to engage students in the process of science online, we transformed a long-standing laboratory course for first-year science students into a more accessible, immersive experience of current biological research using a narrow and focused set of primary literature and the CREATE pedagogy. The efficacy of the CREATE approach has been demonstrated in a diversity of higher education settings and courses. It is, however, not yet known if CREATE can be successfully implemented online with a large, diverse team of faculty untrained in the CREATE pedagogy. Here, we present the transformation of a large-enrollment, multi-section, multi-instructor course for first-year students in which instructors follow different biological research questions but work together to reach shared goals and outcomes. We assessed students: (1) science self-efficacy and (2) epistemological beliefs about science throughout an academic year of instruction fully administered online as a result of ongoing threats posed by COVID-19. Our findings demonstrate that novice CREATE instructors with varying levels of teaching experience and ranks can achieve comparable outcomes and improvements in students science efficacy in the virtual classroom as a teaching team. This study extends the use of the CREATE strategy to large, team-taught, multi-section courses and shows its utility in the online teaching and learning environment.

scientific communication and education↗

bioRxiv2023

Inclusive pedagogy strategies to introduce high schoolers to systems biology

Women and non-white racial and ethnic groups remain underrepresented in science, technology, engineering, and math (STEM). To achieve a more diverse and equitable STEM workforce, the recruitment and retention of these historically marginalized communities in postsecondary education will also need to increase. Recently, the lens has turned to pedagogy and how creating a more inclusive classroom environment can foster STEM identity in previously marginalized communities. This work focuses on developing and piloting systems biology education modules designed to promote an inclusive learning environment in a summer outreach program for high school students by (1) utilizing a hybrid of unplugged activities with coded simulation and (2) a female-oriented problem statement. Based on initial findings in our pilot program, we anticipate that these techniques will enable students with limited prior computational experience to feel more comfortable and able to complete tasks, thereby increasing their self-efficacy and STEM identity. These modules could be a valuable tool for practitioners teaching high school or early college-level computational courses who instruct students with varied coding experience. Additionally, our analysis of the use of a female-oriented problem statement on female-identifying students self-efficacy provides potential evidence of the usefulness of representative problem statements in engaging underrepresented student populations. We believe these techniques could be adapted to address a variety of contexts across STEM disciplines and other fields to foster inclusive learning environments.

scientific communication and education↗

bioRxiv2023

Open-loop lab-on-a-chip technology enables remote computer science training in Latinx life sciences students

Despite many interventions, science education remains highly inequitable throughout the world. Among all life sciences fields, Bioinformatics and Computational Biology suffer from the strongest underrepresentation of racial and gender minorities. Internet-enabled project-based learning (PBL) has the potential to reach underserved communities and increase the diversity of the scientific workforce. Here, we demonstrate the use of lab-on-a-chip (LoC) technologies to train Latinx life science undergraduate students in concepts of computer programming by taking advantage of open-loop cloud-integrated LoCs. We developed a context-aware curriculum to train students at over 8,000 km from the experimental site. We showed that this approach was sufficient to develop programming skills and increase the interest of students in continuing careers in Bioinformatics. Altogether, we conclude that LoC-based Internet-enabled PBL can become a powerful tool to train Latinx students and increase the diversity in STEM.

scientific communication and education↗

bioRxiv2021

Virtual meetings promise to eliminate the geographical and administrative barriers and increase accessibility, diversity, and inclusivity

The COVID-19 pandemic brought a new set of unprecedented challenges not only for healthcare, education, and everyday jobs but also in terms of academic conferences. In this study, we investigate the effect of the broad adoption of virtual platforms for academic conferences as a response to COVID-19 restrictions. We show that virtual platforms enable higher participation from underrepresented minority groups, increased inclusion, and broader geographic distribution. We also discuss emerging challenges associated with the virtual conference format resulting in a decreased engagement of social activities, limited possibilities of cross-fertilization between participants, and reduced peer-to-peer interactions. Lastly, we conclude that a novel comprehensive approach needs to be adopted by the conference organizers to ensure increased accessibility, diversity, and inclusivity of post-pandemic conferences. Our findings provide evidence favoring a hybrid format for future conferences, marrying the strength of both in-person and virtual platforms.

scientific communication and education↗