Vision and Change through the Genome Consortium for Active Teaching Using Next-Generation Sequencing (GCAT-SEEK)

Buonaccorsi, Vincent P.; Peterson, Mark S.; Lamendella, Gina; Newman, Jeff; Trun, Nancy; Tobin, Tammy C; Aguilar, Andres; Hunt, Arthur G.; Praul, Craig A.; Grove, David; Roney, J. N.; Roberts, Wade

doi:10.1187/cbe.13-10-0195

Cited by 28 publications

(24 citation statements)

References 1 publication

(1 reference statement)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Multiple instructors, who have conducted BM&C courses in parallel to augment crowd-training and expedite data processing, have been aided greatly by the use of discussion forums and blogs to share feedback and upload systematic evaluation tools, appropriate brain mapping training, and a unified research protocol. Training workshops, in which instructors are equipped with the appropriate starting materials (e.g., tissue sets) along with sample training materials, are recognized as a means to ensure consistency of performance longitudinally as has been done with next-generation sequencing projects (Buonaccorsi et al, 2011(Buonaccorsi et al, , 2014.…”

Section: 4: Scaling Up Bmandcmentioning

confidence: 99%

Cognitive and non-cognitive outcomes associated with student engagement in a novel brain chemoarchitecture mapping course-based undergraduate research experience

D’Arcy

Martínez

Khan

et al. 2019

Preprint

View full text Add to dashboard Cite

Course-based undergraduate research experiences (CUREs) engage emerging scholars in the authentic process of scientific discovery, and foster their development of content knowledge, motivation, and persistence in the science, technology, engineering, and mathematics (STEM) disciplines. Importantly, authentic research courses simultaneously offer investigators unique access to an extended population of students who receive education and mentoring in conducting scientifically relevant investigations and who are thus able to contribute effort toward big-data projects. While this paradigm benefits fields in neuroscience, such as atlas-based brain mapping of nerve cells at the tissue level, there are few documented cases of such laboratory courses offered in the domain.Here, we describe a curriculum designed to address this deficit, evaluate the scientific merit of novel student-produced brainatlasmapsofimmunohistochemically-identifiednervecellpopulations for the rat brain, and assess shifts in science identity, attitudes, and science communication skills of students engaged in the introductory-level Brain Mapping and Connectomics (BM&C) CURE. BM&C students reported gains in research and science process skills following participation in the course. Furthermore, BM&C students experienced a greater sense of science identity, including a greater likelihood to discuss course activities with non-class members compared to their non-CURE counterparts. Importantly, evaluation of student-generated brain atlas maps indicated that the course enabled students to produce scientifically valid products and make new discoveries to advance the field of neuroanatomy. Together, these findings support the efficacy of the BM&C course in addressing the relatively esoteric demands of chemoarchitectural brain mapping.

show abstract

Section: 4: Scaling Up Bmandcmentioning

confidence: 99%

Cognitive and non-cognitive outcomes associated with student engagement in a novel brain chemoarchitecture mapping course-based undergraduate research experience

D’Arcy

Martínez

Khan

et al. 2019

Preprint

View full text Add to dashboard Cite

show abstract

“…A wide variety of CUREs have been developed and assessed; these range from large multi-institutional CUREs to single-section, single-institution CUREs (Hatfull et al ., 2006; Wu, 2013; Buonaccorsi et al ., 2014; Jordan et al ., 2014; Lopatto et al ., 2014; Brownell et al ., 2015; Corwin et al ., 2015; Russell et al ., 2015; Shapiro et al ., 2015). The target demographics for CUREs also vary across the undergraduate spectrum from introductory major and nonmajors courses to upper-level multisemester courses (Nadelson et al ., 2010; Brownell et al ., 2015; Rowe et al ., 2015).…”

Section: Introductionmentioning

confidence: 99%

Implementation of a Collaborative Series of Classroom-Based Undergraduate Research Experiences Spanning Chemical Biology, Biochemistry, and Neurobiology

Kowalski

Johnson

2016

LSE

View full text Add to dashboard Cite

show abstract

“…Recognizing these advantages, a growing number of faculty groups have emerged over the last decade to organize CUREs that include collaborative genome annotation [8,31,32,33]. Recently, several of these groups have come together to form a Genomics Education Alliance (GEA; https://qubeshub.org/community/groups/gea/), which seeks to support this effort by creating a common, well-maintained platform with common curriculum and tools [34].…”

Section: Resultsmentioning

confidence: 99%

G-OnRamp: Generating genome browsers to facilitate undergraduate-driven collaborative genome annotation

Sargent

Liu

Leung

et al. 2019

Preprint

View full text Add to dashboard Cite

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 manual gene annotation. Undergraduates can become skilled annotators, and in the process learn both about genes/genomes and about how to utilize large datasets. Data visualizations provided by a genome browser are essential for manual gene annotation, enabling annotators to quickly evaluate multiple lines of evidence (e.g., sequence similarity, RNA-Seq, gene predictions, repeats). However, creating genome browsers requires extensive computational skills; lack of the expertise required remains a major barrier for many biomedical researchers and educators.

show abstract

Vision and Change through the Genome Consortium for Active Teaching Using Next-Generation Sequencing (GCAT-SEEK)

Abstract: Development of the Genome Consortium on Active Teaching using Next Generation Sequencing (GCAT-SEEK) is described. Workshops, educational modules, assessment resources, data analysis software and computer hardware available for faculty are described.

Cited by 28 publications

References 1 publication

Cognitive and non-cognitive outcomes associated with student engagement in a novel brain chemoarchitecture mapping course-based undergraduate research experience

Cognitive and non-cognitive outcomes associated with student engagement in a novel brain chemoarchitecture mapping course-based undergraduate research experience

Implementation of a Collaborative Series of Classroom-Based Undergraduate Research Experiences Spanning Chemical Biology, Biochemistry, and Neurobiology

G-OnRamp: Generating genome browsers to facilitate undergraduate-driven collaborative genome annotation

Contact Info

Product

Resources

About