David Lopatto

• Grinnell College

The Genomics Education Partnership (GEP; thegep.org) is a collaboration of more than 260 faculty from over 200 colleges and universities across the continental United States and Puerto Rico, all of whom are engaged in bringing Course-based Undergraduate Research Experiences (CUREs) centered in genomics and bioinformatics to their students. The purp...

Previous research has shown that female and Hispanic students who are underrepresented in science, technology, engineering and mathematics (STEM) face more educational barriers than their non-Hispanic, male peers. However, little research has been conducted on the effects of intersectional identities in the STEM space. In an effort to bridge the ga...

The initial phase of the COVID-19 pandemic changed the nature of course delivery from largely in-person to exclusively remote, thus disrupting the well-established pedagogy of the Genomics Education Partnership (GEP; https://www.thegep.org ). However, our web-based research adapted well to the remote learning environment. As usual, students who eng...

The Genomics Education Partnership (GEP), a consortium of diverse colleges and universities, provides support for integrating genomics research into undergraduate curricula. To increase research opportunities for underrepresented students, GEP is expanding to more community colleges (CC). Genomics research, requiring only a computer with Internet a...

The Genomics Education Partnership (GEP), a consortium of diverse colleges/universities, provides support for integrating genomics research into undergraduate curricula. To increase research opportunities for underrepresented students, GEP is expanding to more community colleges (CC). Genomics research, requiring only a computer with internet acces...

The dual mission of the Council of Undergraduate Research, to both stimulate the rigorous assessment of undergraduate research programs and encourage models of undergraduate research programs, presents challenges for assessment. This commentary observes the directions taken by assessment when pursuing either a theoretical model of undergraduate res...

ABSTRACT The Genomics Education Partnership (GEP) engages students in a course-based undergraduate research experience (CURE). To better understand the student attributes that support success in this CURE, we asked students about their attitudes using previously published scales that measure epistemic beliefs about work and science, interest in sci...

The Genomics Education Partnership (GEP) is a community of practice aiming to integrate genomics research into undergraduate curriculum while providing support to faculty in the process. It consists of more than 200 members in over 180 undergraduate institutions across the United States. Following training, faculty can claim annotations from one or...

Few studies have investigated the effects of combining undergraduate research with study abroad. The authors present student self-reported learning gains from two undergraduate courses that embed research within study abroad courses. Students in one course worked in small groups on original research projects; students in the second course collectiv...

A complex research project was translated into a Course‐based Undergraduate Research Experience (CURE), which was implemented in sections of an introductory Cell and Molecular Biology laboratory course. The research laboratory generated an engineered plant line producing a growth‐inhibiting, lipid‐derived plant hormone and mutagenized this line. St...

Undergraduate students participating in the UCLA Undergraduate Research Consortium for Functional Genomics (URCFG) have conducted a two-phased screen using RNA interference (RNAi) in combination with fluorescent reporter proteins to identify genes important for hematopoiesis in Drosophila. This screen disrupted the function of approximately 3500 ge...

Scientists are sequencing new genomes at an increasing rate with the goal of associating genome contents with phenotypic traits. After a new genome is sequenced and assembled, structural gene annotation is often the first step in analysis. Despite advances in computational gene prediction algorithms, most eukaryotic genomes still benefit from manua...

The Genomics Education Partnership (GEP) is a community of practice focused on the integration of genomics research experiences into undergraduate curriculum and supporting faculty in this endeavor. Founded in 2006, GEP has grown to 100+ participating institutions and introduced thousands of students to eukaryotic gene structure, comparative genomi...

A hallmark of the research experience is encountering difficulty and working through those challenges to achieve success. This ability is essential to being a successful scientist, but replicating such challenges in a teaching setting can be difficult. The Genomics Education Partnership (GEP) is a consortium of faculty who engage their students in...

Scientists are sequencing new genomes at an increasing rate with the goal of associating genome contents with phenotypic traits. After a new genome is sequenced and assembled, structural gene annotation is often the first step in analysis. Despite advances in computational gene prediction algorithms, most eukaryotic genomes still benefit from manua...

The CUNY Research Scholars Program (CRSP) provides a yearlong faculty-mentored research experience to associate’s degree students. The program takes place at all 10 associate’s degree–granting colleges within the City University of New York system. We report on a mixed-methods study of 500 students who participated in the program during its initial...

Undergraduate research (UR) is a high-impact practice associated with many positive student outcomes. However, extending UR opportunities to all students is not practical for all psychology programs. Classroom-based UR experiences (CUREs) provide a scalable solution to this problem, but there is a paucity of empirically validated, authentic CUREs a...

A research-based inorganic chemistry laboratory course is described. Using the defined protocol of a course-based undergraduate research experience (CURE), students undertake a self-designed research project to identify new catalysts for the dehydrogenation of ammonia borane. Students select ligands and metals, prepare and characterize catalysts pr...

The Genomics Education Partnership (GEP) is a collaboration between faculty from over 100 diverse institutions with the goal of providing authentic course‐based undergraduate research experiences (CUREs) in bioinformatics and genomics for undergraduate students. The GEP faculty have developed curricula for undergraduates at all levels that allow fa...

Following the growth of online, higher-education courses, academic institutions are now offering fully online degree programs. Yet it is not clear how students who enroll in fully online degree programs are similar to those students who enroll in in-person (“traditional”) degree programs. Because previous work has shown students’ attitudes toward s...

Effective and accurate communication of scientific findings is essential. Unfortunately, scientists are not always well trained in how to best communicate their results with other scientists nor do all appreciate the importance of speaking with the public. Here, we provide an example of how the development of oral communication skills can be integr...

This two-year study describes the assessment of student learning gains arising from participation in a year-long curriculum consisting of a classroom undergraduate research experience (CURE) embedded into second-year, major core Genetics and Cellular and Molecular Biology (CMB) laboratory courses. For the first course in our CURE, students used mic...

Science plays an important role in most aspects of society, and scientists face ethical decisions as a routine part of their work, but science education frequently omits or segregates content related to ethics and broader impacts of science. Undergraduate research experiences have the potential to bridge traditional divides in education and provide...

Challenges particular to second-year students have been identified that can impact persistence in science, technology, engineering, and mathematics (STEM) fields. We implemented a program to improve student success in intermediate-level science courses by helping students to feel they belonged and could succeed in STEM. We used survey measures of p...

Authentic research experiences are valuable components of effective undergraduate education. Research experiences during the first years of college are especially critical to increase persistence in science, technology, engineering, and mathematics fields. The Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science (SEA...

The Genomics Education Partnership (GEP http://gep.wustl.edu ) started in 2006 with 16 member institutions interested in providing genomics research experiences for their upper division students. Over 10 years, GEP has grown to a consortium of faculty from over 100 colleges and universities that provide a course‐based undergraduate research experie...

Many instructors and institutions offer research experiences and training in computing research methods. However, in a national survey, we find that undergraduate students rate their computing research experiences lower than students in other STEM fields. To address this learning gap, we have offered summer undergraduate research experiences in com...

In their 2012 report, the President's Council of Advisors on Science and Technology advocated "replacing standard science laboratory courses with discovery-based research courses"-a challenging proposition that presents practical and pedagogical difficulties. In this paper, we describe our collective experiences working with the Genomics Education...

The Genomics Education Partnership (GEP) is a consortium of educators with common research and educational goals in genomics, and is comprised of 100+ faculty members instructing 1000+ students annually. Our focus is 1) undergraduate education via research in comparative genomics and 2) assessment of pedagogy within diverse student populations. To...

There is widespread agreement that science, technology, engineering, and mathematics programs should provide undergraduates with research experience. Practical issues and limited resources, however, make this a challenge. We have developed a bioinformatics project that provides a course-based research experience for students at a diverse group of s...

Unlabelled: Engaging large numbers of undergraduates in authentic scientific discovery is desirable but difficult to achieve. We have developed a general model in which faculty and teaching assistants from diverse academic institutions are trained to teach a research course for first-year undergraduate students focused on bacteriophage discovery a...

Classroom research experiences can provide outstanding learning opportunities for undergraduate students while also benefiting faculty research programs. However, these courses often require more work than traditional lecture-based courses, potentially discouraging faculty from taking on the challenge. Here, we propose one solution. We describe a r...

Classroom research experiences can provide outstanding learning opportunities for undergraduate students while also benefiting faculty research programs. However, such courses often require more faculty work than traditional lecture-based courses do, potentially discouraging instructors. Here, we propose one solution. We describe a research-based c...

Six pigeons were exposed to a procedure in which a tone preceded response-dependent grain. Pecks during the tone omitted grain for that trial. The magnitude of reinforcement, as manipulated by feeder duration, had no effect on the frequency of omission responding. The results are interpreted in the context of Scalar Expectancy Theory.

A service-learning project appropriate for a biochemistry or advanced biochemistry course was designed and implemented. The project involved students partnering with a homeless shelter to design informational pamphlets to be displayed at the shelter for the clients’ use. The pamphlet topics were based on diseases studied within the course. Students...

The C.R.E.A.T.E. (Consider, Read, Elucidate hypotheses, Analyze and interpret data, Think of the next Experiment) method uses intensive analysis of primary literature in the undergraduate classroom to demystify and humanize science. We have reported previously that the method improves students' critical thinking and content integration abilities, w...

Our study, focused on classroom-based research at the introductory level and using the Phage Genomics course as the model, shows evidence that first-year students doing research learn the process of science as well as how scientists practice science. A preliminary but notable outcome of our work, which is based on a small sample, is the change in s...

Genomics is not only essential for students to understand biology but also provides unprecedented opportunities for undergraduate research. The goal of the Genomics Education Partnership (GEP), a collaboration between a growing number of colleges and universities around the country and the Department of Biology and Genome Center of Washington Unive...

Undergraduate research has shown that the incorporation of hands-on, inquiry-based activities produces a superior learning environment for all disciplines (Lopatto 2004; Seymour et al. 2004). The majority of undergraduate research takes place outside of the normal classroom laboratory experience, although embedding undergraduate research into cours...

Comments from invited faculty speakers who participated in the research deconstruction courses, provided as testimonials. (0.03 MB DOC)

Video excerpts of seminar and deconstruction classes. (18.04 MB MOV)

Video excerpts of seminar and deconstruction classes. (17.29 MB MOV)

Sample problem set questions from research deconstruction courses. (0.03 MB DOC)

Video excerpts of seminar and deconstruction classes. (17.11 MB MOV)

Video excerpt of seminar and enhanced deconstruction class. (14.03 MB MOV)

Focused analysis of current research projects provides an effective platform for teaching early-stage undergraduates the logic of scientific inquiry.

University mission statements increasingly emphasize internationalization and employers increasingly seek graduates with experience in the global arena. This focus on international experience has led to the development of a variety of models for study abroad, including research abroad programs. To assess the value of an international research exper...

The advances in genome sequencing technology have led to the generation of massive amounts of publicly available data creating new opportunities for student‐scientist research partnerships. With appropriate training, undergraduate students can provide the labor‐intensive sequence improvement and annotation required for effective use of sequence dat...

The Genomics Education Partnership offers an inclusive model for undergraduate research experiences incorporated into the academic year science curriculum, with students pooling their work to contribute to international data bases.

Explicit networking helps undergraduates get the most out of the diverse curriculum available at a large university.

The present study examined the reliability of student evaluations of summer undergraduate research experiences using the SURE (Survey of Undergraduate Research Experiences) and a follow-up survey disseminated 9 mo later. The survey further examines the hypothesis that undergraduate research enhances the educational experience of science undergradua...

In this study, I examined the hypothesis that undergraduate research enhances the educational experience of science undergraduates, attracts and retains talented students to careers in science, and acts as a pathway for minority students into science careers. Undergraduates from 41 institutions participated in an online survey on the benefits of un...

Older adults and college students were tested with two procedures that measure stereotypy and response variability. In Experiment 1 subjects guided a marker through a 6 by 6 matrix by pressing two computer keys. Points were awarded on either a continuous or variable ratio 3 schedule of reinforcement. Points were exchanged for money. Continuous rein...

A group of 4– and 5–yr.-old children were asked the meaning of the word “handicapped,” while another group were asked the meaning of a nonsense word. Five of 15 children claimed to know the meaning of “handicapped” but none could supply a factual definition. Two of 15 children in the comparison group claimed to know the meaning of the nonsense word...

40 preschool children and 11 college students were asked to move a marker through a computer matrix to accumulate points and hear music. An operant conditioning view suggests that each of the 252 functionally equivalent response sequences has an initially equal likelihood of occurring, but the present data indicated they do not. Most subjects showe...

College students participated in three experiments on operant sequential stereotypy. In Experiment 1, subjects guided a marker through a 6 × 6 matrix by pressing two computer keys in sequence. Subjects were awarded points on seven schedules of reinforcement. Points were exchanged for money. The results showed that the level of stereotypy was greate...

Self-control was analyzed in an operant conditioning experiment using pigeons as subjects. In past experiments, subjects were presented a brief stimulus such that a peck against a response key during the stimulus resulted in a small reinforcer, and not pecking during the stimulus resulted in a large reinforcer, delivered sometime later. Pecking the...

Key pecking in pigeons was studied in a signal-control procedure in which a signal preceded a grain reinforcer. We used two signals: a light on the grain key and a tone. And we used an omission contingency: pecking the grain key during the signal stopped delivery of grain following the signal. To determine if the pigeons were sensitive to the omiss...

Twelve pigeons were exposed to trials in which a signal was followed by peck-dependent grain. If the pigeon pecked a key while the signal was on, grain availability was omitted for that trial. Birds in Group 1 were tested with three types of signal: tone, keylight and diffuse light. The tone produced more omission responding than either visual stim...

Discussions of the ethics of animal experimentation have included attacks on scientific practice, attacks that go beyond the humanitarian issues to question the enterprise of experimental psychology. Charges of pointless experiments, obvious findings, repetitious experiments, and lack of external validity reveal a misunderstanding of the aim and pr...

Pigeons' not pecking or pecking constituted choice between a delayed, large reinforcer and an immediate, small reinforcer (self-control) and at other times between a delayed reinforcer and no reinforcer (omission). Both a tone and a keylight were tested as choice signals, and the delayed reinforcer was either response independent or response depend...

In two experiments, rats were shocked every 30 sec. Before a response, a bar press, shocks were long (2 sec); for 3 min after a response, shocks were short (0.1, 0.5, or 1 sec). When responding reduced shocks from 2 to 0.1 sec, bar pressing was acquired, and the shorter the shocks the more time spent with the short-shock condition in effect. In ano...

The diverse literature on the problem of self-control is reviewed in an attempt to clarify a behavioral definition of the concept. The components and determinants of self-control behavior are analyzed with emphasis given to its trans-situational generalizability. Finally, data from an experiment are described to illustrate the value of conceptualiz...

A three-year research project is proposed whose overall goals are to: • Clarify the nature of authentic undergraduate research experiences—and their variations—in a sample of science disciplines from the viewpoints of participating and non-participating undergraduates (both as seniors and one year from graduation), from faculty, and from their inst...