A bioinformatics-driven CURE extension increases student self-efficacy and interest in biomedical research

ABSTRACT

The biology workforce has a need for undergraduate students trained in bioinformatics. Although bioinformatics is a critical sub-discipline of biology, it is not required in all biology degree programs. In parallel, there is a need to increase student access to research experiences. To address these needs, we offer a one-credit bioinformatics-focused and computational biology course-based undergraduate research experience (CURE), here called the CB-CURE. Preliminary data suggest the CB-CURE increased student interest, knowledge, and self-efficacy, but also reveal a shortage of access to undergraduate research experiences (UREs) in faculty labs at our large institution. To provide a more URE-like experience for a class setting, we developed a one-semester extension to the CB-CURE, called CURE+. In CURE+, students execute individual bioinformatics-driven research projects and obtain additional career development and mentoring. To evaluate CURE+, we measured students’ bioinformatics and research self-efficacy, interest in bioinformatics and research, and emotions toward their project. Additionally, we evaluated student mastery of the CURE+ learning outcomes to determine if the experience successfully enabled students to develop their research skills. Our data show significant increases in (i) student self-efficacy in various bioinformatics and research skills and (ii) student interest in bioinformatics-related activities and in biomedical research. Students had positive emotions toward their research project, and a majority of students mastered the CURE+ learning outcomes. Our data suggest that an intensive CURE extension can provide a potentially transformative research experience that helps fill a void in access to research at institutions with a high student-to-faculty ratio.

INTRODUCTION

Undergraduate research experiences (UREs) strengthen interest, motivation, and retention in research careers (1), although not all students are aware of the benefits they can gain from participating in research (2). In response to the calls to include research opportunities in the undergraduate biology curriculum from Vision and Change in Undergraduate Biology Education (3), course-based UREs (CUREs) emerged as a way to increase student awareness and access to research opportunities and have been shown to increase student persistence in science (4, 5). Traditional UREs are often competitive opportunities that involve a significant unpaid time commitment to the participating student and are not an option for everyone (2). However, since CUREs are integrated into a student’s courseload, these hurdles to participating in research are reduced. Consequently, CUREs have been especially effective for populations that have been historically excluded from the sciences (6–10). Additionally, the enrollment and mentorship structure of CUREs, in which one faculty can mentor multiple students that enroll in a course, rather than selecting a single or few students to mentor, allows more students to be involved in the research endeavor (4).

In parallel, there is an increasing need for bioinformatics skills, such as big data analysis, in the life science workforce (11). However, faculty report various barriers to the integration of bioinformatics content in undergraduate curricula, such as a lack of student interest and a lack of faculty expertise (12). To help overcome these barriers, our group previously developed a standalone, one-credit, one-semester computational biology CURE (CB-CURE, a.k.a. Corona CURE) at our institution. This CURE laboratory course provides a topic of interest to many life science students, and as a lab course, it is taught by graduate student teaching assistants with support from a primary faculty instructor. This allows the course to scale the enrollment of students up and down as needed while simultaneously preparing the next generation of faculty to integrate bioinformatics into their teaching. The CB-CURE has been offered every semester since Summer 2020, first as a remote course and later face-to-face on campus. CB-CURE was designed for upper-level students, requiring either Genetics or Biochemistry as a prerequisite and covers content from across the biology curriculum while integrating bioinformatics skills, such as protein family analysis and protein structure visualization, in a coronavirus research context. While learning bioinformatics, students work in small teams to generate preliminary data during Phase 1, the first half of the class. Phase 1 ends with each team presenting their findings and sharing their data. Thereafter, all teams write a research proposal based on a given objective. As they execute their project during Phase 2, they learn more bioinformatics, practice scientific writing, and present their team projects in a poster presentation (for more information, see Supplemental Material 1). By allowing students to experience the research process in action, the CB-CURE aims for students to (i) learn about SARS-CoV-2, (ii) understand the difference between vaccines and antivirals, (iii) communicate their science, and (iv) practice statistical analysis and data interpretation skills, all while learning fundamental bioinformatics. Additionally, students practice crucial transferable skills, such as collaboration, critical thinking, and scientific writing. Preliminary results suggest that the CB-CURE has positive student outcomes, including (i) providing increased access to research experiences, (ii) increased self-efficacy in bioinformatics skills, (iii) positive attitudes toward bioinformatics, and (iv) gains in bioinformatics knowledge.

Although CUREs address some of the limitations of traditional UREs regarding student access to research, they have some disadvantages to their format, such as being limited to a short experience (usually one semester or less) or requiring strong faculty buy-in (2). Short duration and group projects in a typical CURE can lead to a lack of direct research mentorship and limited career development (4). Additionally, although student interest is piqued during CUREs, they may not have enough time to critically evaluate their role in the research process. Longitudinal data analysis has shown that the time spent on a research experience matters; at least ten hours of research across two semesters can lead to positive outcomes that impact students’ likelihood to join the scientific workforce (13). To increase the time of the bioinformatics CURE research experiences, we developed a CURE sequence in which students could enroll in a second course following the CB-CURE that would provide an internship-like opportunity to expand on their previous research in individual projects. This one-semester CURE extension (called CURE+) bridges the gap between traditional UREs and CUREs, building on the CB-CURE to provide a more comprehensive research experience, including research, writing, career development, and mentoring-like activities that can solidify student interest in research. Additionally, CURE+ addresses current barriers in bioinformatics education by providing students with an opportunity to deepen their knowledge and interest in bioinformatics and biological data science. Here, we discuss the development, implementation, and assessment of CURE+ as a potential new addition to the CURE model that provides an extended research experience, professional development, and mentoring while maintaining the benefit of increased access provided by a course-based research experience.

METHODS

Instructional team and institutional setting

CURE+ was developed in a large, doctoral university with very high research activity (R1), that is designated as a Hispanic-serving institution (HSI) in the United States. The Department of Biological Sciences at this institution, which currently houses almost 50 faculty members that actively perform research, had approximately 4,000 enrolled undergraduate students in Fall 2024, highlighting the need to increase institutional capacity for undergraduate research. We offered two sections of CURE+ in Spring 2024 (n = 29 students), and each section met for 2 h and 50 min twice per week. The instructional team consisted of a faculty lead, a postdoctoral course coordinator, and two graduate student teaching assistants, one for each section of CURE+.

Learning outcomes and curriculum

CURE+ has 13 broad learning outcomes: (i) apply bioinformatics for biomedical research; (ii) communicate scientific concepts and research orally, visually, and in writing; (iii) demonstrate adaptability; (iv) demonstrate awareness of biomedical research career paths; (v) demonstrate technical writing and related skills; (vi) demonstrate work ethic; (vii) discuss and integrate biomedical concepts related to their research; (viii) effectively communicate their research to varying audiences; (ix) execute critical thinking in research; (x) perform data science tasks; (xi) practice effective teamwork; (xii) show proficiency in time management; and (xiii) understand and apply the principles of RCR.

A total of 68 skills and 26 milestones were aligned with the learning outcomes as a guide for student assessment (Table S1). Milestones indicate specific assignments or activities that students must complete to master skills. Students’ skill level was evaluated on a 4-point “Mastery” scale: “No mastery,” “Progressing toward mastery,” “Mastery,” and “Mastery+,” which recognized effort that went above expectations of a mastered skill. To ensure that the learning outcomes are relevant to biological and biomedical careers, we aligned the skills with the Vision and Change core competencies (3), as detailed in the BioSkills Guide tool (14) (Fig. 1A). Skills developed in CURE+ aligned with all Vision and Change core competencies. Additionally, since our focus is on bioinformatics-based research, we repeated this process with the Bioinformatics Core Competencies described by the Network for Integrating Bioinformatics in Life Sciences Education (NIBLSE) (15) (Fig. 1B) and the Data Science Skills Curriculum Map developed by the Biological and Environmental Data Education Network (15) (Fig. 1C). The CURE+ curriculum aims to develop students in all nine Bioinformatics Core Competencies and various important Data Skills, such as data analysis and visualization.

Fig 1.

Alignment of CURE+ Skills with three competency frameworks: (A) Vision and Change (as described in the BioSkills guide), (B) the Bioinformatics Core Competencies, and (C) the BEDE Data Skills Curriculum Map. Full descriptions of competency frameworks and skills are available in Table S1.

Course overview

CURE+ expanded on CB-CURE content and research, focusing specifically on bioinformatics-based evolutionary analyses of coronavirus protein structure in order to identify potential broadly neutralizing antiviral targets with the grand aim to contribute to preventing the next coronavirus pandemic. Each student individually performed research on a specific protein family for 10 h a week (4 h of individual work in addition to the two in-person research sessions). Most of the research project was completed over the first 2 months of the course, while the following 2 months focused on learning to communicate project results and activities to develop readiness for biomedical careers (Fig. 2). As part of the biomedical research activities, students (i) performed guided bioinformatics research on their independent project but progressed as a cohort, (ii) kept an individual electronic lab notebook, (iii) presented weekly research updates, and (iv) participated in five journal clubs. Further, CURE+ students engaged in multiple writing assignments that concluded with writing a paper of their research and participated in career development workshops focused on developing writing strategies, developing career documents (e.g., resumés and personal statements), and learning about potential career paths in biomedical sciences. Additionally, students prepared and presented a research poster at either an institutional research conference or an end-of-course poster session. Additional details of the course structure can be found in the CURE+ syllabus (Supplemental Material 2).

Fig 2.

Overview of CURE+ Curriculum. The course was offered in Spring 2024, spanning 4 months with 1 week of Spring Break. Students were surveyed at three separate times throughout the semester, indicated by the colored rectangles (yellow for pre-term, green for mid-term, and blue for post-term).

Participant recruitment

All students who had applied to CURE+ and who met the prerequisite (CB-CURE) were provided more information on CURE+, including course expectations for student researchers and what they could expect from the teaching team. Upon agreeing to fulfill the expectations for the course, students were invited to enroll in CURE+. A total of 29 students enrolled in and completed CURE+. All students provided consent to participate in this study. Two students were excluded from the study due to not responding to the post-survey and failing to respond to a straight-lining check (Supplemental Material 3). Enrollment and completion of CURE+ research activities, regardless of study participation, were compensated at $1,000 for the semester.

Development of assessment tools

To evaluate CURE+, we developed quantitative pre-, mid-, and post-term questionnaires focusing on students’ bioinformatics and research self-efficacy, attitudes toward bioinformatics, career intentions and values, and emotions toward research (Supplemental Material 3). The pre-term and post-term questionnaires were divided into three primary sections:

1. The Future Career Reflection section included questions on career interest for specific biology careers (e.g., “physician” or “researcher in a biology field”) and work environment (e.g., “academic lab” or “biotech industry”), which was gauged with a 5-point Likert-type scale ranging from “No, definitely not an option for me” to “Yes, this is a primary option for me.” Additionally, students were asked to determine the level of importance for various career values based on the Science Careers myIDP “Values Assessment” (16).

2. The Self-Assessment of Bioinformatics and Research Skills section measured student self-efficacy in research skills and bioinformatics skills. Research skill items were adapted from the CURE undergraduate research experience survey (17). Additional items specific to the research performed in CURE+ were added as well. Bioinformatics skill items were developed by our team based on the NIBLSE Bioinformatics Core Competencies (18). All self-efficacy questions were measured using a 5-point Likert scale ranging from “Strongly disagree” to “Strongly agree.”

3. The Reflection on Bioinformatics and Biology Topics section measured students’ interest in bioinformatics-related activities, their agreement with various attitude statements about their perceptions of the bioinformatics field, and emotions toward their research. To measure agreement with statements reflecting attitudes toward bioinformatics, we adapted questions from Madlung that use a 5-point Likert scale ranging from “Strongly disagree” to “Strongly agree” (19). The same scale was also used to measure interest in bioinformatics-related activities before and after CURE+, partially based on Bio-ITEST, through post-term questionnaire items (20). To measure students’ emotions toward their research, they were given a list of 12 emotions and asked to select any emotion that applied toward their research (21). Since we were interested in how emotions might differ for students when they are performing research compared to after they have completed their projects, these questions were only asked in the mid-term and post-term questionnaires. The mid-term and post-term questionnaires also contained questions about the pace and content of the research experience.

Statistical analysis

Responses for each Likert-type item in both the pre-term and post-term questionnaires were compared using the Wilcoxon matched-pairs signed-rank test, due to their ordinal nature. Correction for multiple comparisons was done using the Benjamini-Hochberg procedure to control the false discovery rate. For the emotion items in the mid-term and post-term questionnaires, the counts of all times an emotion was selected in a questionnaire were added and grouped as “positive” (“eager,” “excited,” “important,” “optimistic,” “proud,” and “supported”) or “negative” (“anxious,” “confused,” “frustrated,” “not supported,” “overwhelmed,” and “stressed”). McNemar’s test was used to compare mid-term and post-term responses. All statistical analyses were performed using the SciPy v1.13.1 module in Python v3.11.4 (22).

RESULTS

Participant socio-demographics and career interests

Since CURE+ was developed with the intention of increasing access to research experiences, we were interested in the previous research experiences of CURE+ students (aside from participating in CB-CURE). Less than half of the CURE+ students (12 out of 27, 44.4%) had any research experience aside from CB-CURE (Table 1). As CURE+ was designed for upper-level students, most students were in their third year or above, with almost a third of the students (8 out of 27, 29.6%) having recently graduated from their programs (Table 1). Student gender and ethnicity were comparable to statistics for the Department of Biological Sciences at this HSI. However, a majority of CURE+ students (21 out of 27, 77.8%) identified as first-generation college students (Table 1), defined here as a student whose parent or guardian has not completed postsecondary education in the United States, which differs from institutional statistics of 38% of the student population. We also asked students to identify how likely they were to pursue a variety of biomedical and biological sciences careers (Fig. S1). The careers that students were more likely to pursue were “Physician” and “Researcher in a biology field.” Interest in these careers did not change after participation in CURE+ (Table S2).

TABLE 1.

Socio-demographic characteristics of CURE+ students

Characteristic	Category	Count (n = 27)	Percent (%)
Research experience	No research	15	55.6
	Research in a FIU lab	7	25.9
	Research outside of FIU	2	7.4
	Other research	3	11.1
Year in college	2nd year	1	3.7
	3rd year	4	14.8
	4th year or above	14	51.9
	Already graduated	8	29.6
Gender	Male	8	29.6
	Female	19	70.4
Ethnicity	Hispanic or Latine	22	81.5
	Not Hispanic or Latine	4	14.8
	Unspecified	1	3.7
First-generation status	First-generation	21	77.8
	Not first-generation	5	18.5
	Unspecified	1	3.7

Increase in self-efficacy and interest toward research and bioinformatics, and positive emotions toward research projects after participation in CURE+

Comparing pre-term and post-term results for research skill items shows an overall increase in research self-efficacy after CURE+ (Fig. 3). There is a significant increase in self-efficacy for skills relating to data analysis (e.g., “Analyze data”) and scientific communication (e.g., “Present my research results orally”). Interestingly, there were no significant differences between pre-term and post-term results in self-efficacy for the three skills related to primary scientific literature. We observe an overall increase in bioinformatics self-efficacy after participating in CURE+ (Fig. 4). Specifically, self-efficacy in skills relating to database usage and use of bioinformatics tools for research (e.g., “Retrieve data from protein and genome databases”), content knowledge regarding bioinformatics (e.g., “Explain how a mutation in a gene may lead to functional divergence”), and the ability to reproduce CURE+ research methods (e.g., “Perform a BLAST search, extract sequences of interest, make an MSA, and build a phylogenetic tree”) were all significantly increased after CURE+. To gauge the impact of CURE+ on student interest toward bioinformatics and research, we asked students to reflect on how they viewed their interest in five specific activities before participating in CURE+ and after (Fig. 5). Interest was rated significantly higher after CURE+ in all five activities assessed. We were also interested in what emotions CURE+ students felt toward their research project while performing the research and after their project was completed. Students reported feeling significantly more positive emotions than negative emotions at both time points (Fig. 6, P = 1.19 × 10⁻⁵). The positive emotion most selected in both surveys was “Proud.” Although students did not report feeling as many negative emotions, “Stressed” was the most selected negative emotion. In addition to their emotions toward the research, almost all students, 89%, mentioned they would “Definitely recommend” CURE+ to their peers, suggesting that the experience was well-received by the students (Table S2).

Fig 3.

CURE+ student responses for research self-efficacy items. Pre-survey results are indicated in the top bar for each item, while post-survey results are indicated in the bottom bar. Responses are indicated as follows: “Strongly disagree” in purple, “Somewhat disagree” in red, “Neither agree nor disagree” in yellow, “Somewhat agree” in blue, and “Strongly agree” in green. Green arrows next to each item indicate a significant increase in self-efficacy for a skill with a P value < 0.05 in a Wilcoxon signed-rank test with Benjamini-Hochberg correction. Equal signs (=) indicate no significant differences between pre-term and post-term results.

Fig 4.

CURE+ student responses for bioinformatics self-efficacy items. Pre-survey results are indicated in the top bar for each item, while post-survey results are indicated in the bottom bar. Responses are indicated as follows: “Strongly disagree” in purple, “Somewhat disagree” in red, “Neither agree nor disagree” in yellow, “Somewhat agree” in blue, and “Strongly agree” in green. Green arrows next to each item indicate a significant increase in self-efficacy for a skill with a P value < 0.05 in a Wilcoxon signed-rank test with Benjamini-Hochberg correction. ^One data point was missing in the post-term data and imputed using the mean.

Fig 5.

CURE+ student responses for Interest in bioinformatics- and research-related activities. Students self-reported their interest in a topic in two separate sets of questions of the post-survey, one referring to before the internship (top bar) and another for after (bottom bar). Responses are indicated as follows: “Strongly disagree” in purple, “Somewhat disagree” in red, “Neither agree nor disagree” in yellow, “Somewhat agree” in blue, and “Strongly agree” in green. Green arrows next to each item indicate a significant increase in self-efficacy for a skill with a P value < 0.05 in a Wilcoxon signed-rank test with Benjamini-Hochberg correction.

Fig 6.

Emotions toward the research project. Students were asked to choose from a set of emotions how they felt about their research project. These emotions were then grouped into positive or negative emotions, colored as cyan or magenta, respectively. Green indicates results for the mid-term survey, while post-survey results are indicated in blue.

Evaluation of student mastery of CURE+ learning outcomes

When assessing student mastery of CURE+ learning outcomes, we observed that a majority of CURE+ students mastered the learning outcomes, especially those relating to biomedical research, such as “Demonstrate awareness of biomedical research career paths” (27 out of 27, 100%), “Apply bioinformatics for biomedical research” (26 out of 27, 96.3%), and “Discuss and integrate biomedical concepts related to their research” (26 out of 27, 96.3%) (Fig. 7). The outcomes that the least number of students mastered were “Communicate scientific concepts and research orally, visually, and in writing” (17 out of 27, 63%) and “Show proficiency in time management” (14 out of 27, 51.9%). The skills least mastered in these outcomes were: “Describes how their research relates to previous research in the field,” “Discusses potential future directions of research project,” “Identifies and communicates limitations of research project,” and “Meeting deadlines.”

Fig 7.

Evaluation of CURE+ learning outcomes. Each outcome consists of a specific number of skills indicated in parentheses. For a student to master an outcome (indicated in blue), they must have scored “Mastery” or “Mastery+” on every skill related to that learning outcome. The number of students who did not master a skill related to a specific outcome is indicated in orange.

DISCUSSION

Our results show that CURE+, an extension to the CB-CURE, increased student self-efficacy in bioinformatics and research skills. For example, the CURE+ research project includes analyzing 3D models generated with AlphaFold (Supplemental Material 2), and all students strongly agree that they can use PyMOL (Fig. 4), a protein structure visualization software. We observed that self-efficacy for skills related to reading primary scientific literature did not significantly increase after CURE+, indicating an area for improvement in the course. One potential approach to improve the primary scientific literature aspect of the course would be to include annotated articles that emphasize ideas students should consider as they read, a method that has been successful in both introductory and upper-level courses (23, 24). Further, the five journal articles covered in CURE+ may not have provided enough practice in reading primary scientific literature (25).

Students reported a significantly increased interest in bioinformatics and biomedical research after participating in CURE+. Increased interest in bioinformatics promotes student likelihood to participate in additional experiences that build their computational skills (12), while increased interest in biomedical research could lead students to joining the biomedical workforce in the future. These results emphasize the importance of research experiences during their undergraduate tenure. Previous studies have shown that summer research programs positively influence biomedical career outcomes for their participants (26–28). However, to our knowledge, there is a lack of research on career outcomes of students that participate in CUREs or a CURE extension like CURE+. Longitudinal research will be necessary to evaluate if the increase in bioinformatics and biomedical research interest after participation in CURE+ results in students deciding to pursue biomedical research careers.

CURE+ participants reported largely positive emotions toward their research project, both while they were performing the research and after the research project was completed. Positive emotions are linked to a higher sense of belonging (29), which in turn, is linked to student achievement and motivation (30–32). If students are experiencing positive emotions toward their research, this could affect their sense of belonging to the research community, influencing their career decisions. More than one-third (37%) of students reported feeling “Stressed” during the mid-term survey. Due to the previously reported role of negative emotions, such as frustration, in successful research experiences (33), this might be a normal response to the iterative nature of research, which can produce negative emotions that result in learning gains.

We aimed to determine if CURE+ students were gaining experience in the skills the course was designed to develop. We observed that a majority of students mastered the CURE+ learning outcomes, demonstrating its effectiveness at developing research, career readiness, and transferable skills. However, the outcome that students least mastered was “Show proficiency in time management,” which measured students’ ability to perform their research duties in a timely manner, meet assignment deadlines, and arrive on time. Time management has long been identified as a challenging skill to teach, but necessary for success during undergraduate studies and in the workforce (34–36). A potential way to improve students’ time management skills would be to implement a short intervention at the start of the experience that focuses on effective planning skills (36). The CURE+ curriculum is intense and involves dedicated time for bioinformatics research primarily in the first two months followed by writing and revision (Fig. 1). Slight restructuring of the curriculum could help students manage their time more efficiently, including balancing time dedicated to the research performed in CURE+ and planning ahead to meet deadlines.

CURE+ reached 29 students who were able to complete a research project including writing a paper and presenting a research poster in one semester. However, the pilot CURE+ curriculum presented here was teaching-intensive, which could serve as a potential limitation for its implementation. Even though the pilot CURE+ teaching team consisted of four instructors, efforts to develop a version of CURE+ where one instructor may teach the course alone to 20–24 students are underway. The CURE+ curriculum builds on the CB-CURE and was developed over multiple semesters, highlighting the workload of creating a CURE extension. However, once the course structure is in place, it is versatile and can rather easily be adapted to new research objectives and other topics suitable for bioinformatics investigations. For example, in the Spring 2025 semester, we have implemented the CURE+ curriculum with a new research focus on cancer genomics.

Here, we presented CURE+, a CURE extension aligned to Vision and Change, bioinformatics, and data science competencies, that provides substantial research experience, adding on to that of a single CURE. This model enables more students to benefit from URE-like experiences beyond CUREs to participate more actively in the research endeavor. In addition to the positive outcomes typically associated with CUREs, such as increased self-efficacy, CURE extensions can provide career development and mentoring experiences that allow students to explore and potentially bolster their interest in biomedical research careers. CURE+ also addresses a number of barriers to the integration of bioinformatics content into the undergraduate curriculum by increasing student interest and skill in bioinformatics. Finally, CURE+ demonstrates that bioinformatics-driven CURE extensions can serve as an expansion of the CURE model, increasing access to potentially transformative research experiences centered on developing skills for the biomedical workforce to far more students than a typical faculty can provide in their research labs.

DATA AVAILABILITY

Data are available upon request.

ETHICS APPROVAL

This study was approved by the Florida International University Institutional Review Board as protocol #IRB-24-0003-AM01.

SUPPLEMENTAL MATERIAL

The following material is available online at https://doi.org/10.1128/jmbe.00231-24.

Supplemental Material 1 - CB-CURE overview. jmbe.00231-24-s0001.pdf.

A short overview of the CB-CURE.

Supplemental Material 2 - CURE+ syllabus. jmbe.00231-24-s0002.pdf.

CURE+ syllabus.

Supplemental Material 3 - CURE+ questionnaires. jmbe.00231-24-s0003.pdf.

Questionnaires used in the study.

Fig. S1. jmbe.00231-24-s0004.pdf.

Biomedical and biological career interests of CURE+ students.

Table S1. jmbe.00231-24-s0005.xlsx.

CURE+ learning outcomes.

Table S2. jmbe.00231-24-s0006.xlsx.

CURE+ additional results.

ASM does not own the copyrights to Supplemental Material that may be linked to, or accessed through, an article. The authors have granted ASM a non-exclusive, world-wide license to publish the Supplemental Material files. Please contact the corresponding author directly for reuse.