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Tapprich WE, Reichart L, Simon DM, Duncan G, McClung W, Grandgenett N, Pauley MA. An instructional definition and assessment rubric for bioinformatics instruction. Biochem Mol Biol Educ 2021; 49:38-45. [PMID: 32744803 DOI: 10.1002/bmb.21361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 02/06/2020] [Accepted: 04/20/2020] [Indexed: 06/11/2023]
Abstract
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 discipline: Bioinformatics is "an interdisciplinary field that is concerned with the development and application of algorithms that analyze biological data to investigate the structure and function of biological polymers and their relationships to living systems." The field is defined in terms of its two primary foundational disciplines, biology and computer science, and its interdisciplinary nature. At the same time, we also created a rubric for assessing open-ended responses to a prompt about what bioinformatics is and how it is used. The rubric has been shown to be reliable in successive rounds of testing using both common percent agreement (89.7%) and intraclass correlation coefficient (0.620) calculations. We offer the definition and rubric to life sciences instructors to help further integrate bioinformatics into biology instruction, as well as for fostering further educational research projects.
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Affiliation(s)
- William E Tapprich
- Department of Biology, University of Nebraska at Omaha, Omaha, Nebraska, USA
| | - Letitia Reichart
- Department of Biology, University of Nebraska at Kearney, Kearney, Nebraska, USA
| | - Dawn M Simon
- Department of Biology, University of Nebraska at Kearney, Kearney, Nebraska, USA
| | - Garry Duncan
- Biology Department, Nebraska Wesleyan University, Lincoln, Nebraska, USA
| | - William McClung
- Mathematics and Computer Science Department, Nebraska Wesleyan University, Lincoln, Nebraska, USA
| | - Neal Grandgenett
- Department of Teacher Education, University of Nebraska at Omaha, Omaha, Nebraska, USA
| | - Mark A Pauley
- School of Interdisciplinary Informatics, University of Nebraska at Omaha, Omaha, Nebraska, USA
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Ryder EF, Morgan WR, Sierk M, Donovan SS, Robertson SD, Orndorf HC, Rosenwald AG, Triplett EW, Dinsdale E, Pauley MA, Tapprich WE. Incubators: Building community networks and developing open educational resources to integrate bioinformatics into life science education. Biochem Mol Biol Educ 2020; 48:381-390. [PMID: 32585745 PMCID: PMC7496352 DOI: 10.1002/bmb.21387] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 05/02/2020] [Accepted: 05/18/2020] [Indexed: 06/11/2023]
Abstract
While it is essential for life science students to be trained in modern techniques and approaches, rapidly developing, interdisciplinary fields such as bioinformatics present distinct challenges to undergraduate educators. In particular, many educators lack training in new fields, and high-quality teaching and learning materials may be sparse. To address this challenge with respect to bioinformatics, the Network for the Integration of Bioinformatics into Life Science Education (NIBLSE), in partnership with Quantitative Undergraduate Biology Education and Synthesis (QUBES), developed incubators, a novel collaborative process for the development of open educational resources (OER). Incubators are short-term, online communities that refine unpublished teaching lessons into more polished and widely usable learning resources. The resulting products are published and made freely available in the NIBLSE Resource Collection, providing recognition of scholarly work by incubator participants. In addition to producing accessible, high-quality resources, incubators also provide opportunities for faculty development. Because participants are intentionally chosen to represent a range of expertise in bioinformatics and pedagogy, incubators also build professional connections among educators with diverse backgrounds and perspectives and promote the discussion of practical issues involved in deploying a resource in the classroom. Here we describe the incubator process and provide examples of beneficial outcomes. Our experience indicates that incubators are a low cost, short-term, flexible method for the development of OERs and professional community that could be adapted to a variety of disciplinary and pedagogical contexts.
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Affiliation(s)
- Elizabeth F. Ryder
- Department of Biology and BiotechnologyWorcester Polytechnic InstituteWorcesterMassachusettsUSA
| | | | - Michael Sierk
- Interdisciplinary Science DepartmentSaint Vincent CollegeLatrobePennsylvaniaUSA
| | - Samuel S. Donovan
- Department of Biological SciencesUniversity of PittsburghPittsburghPennsylvaniaUSA
| | - Sabrina D. Robertson
- Department of Psychology and NeuroscienceUniversity of North CarolinaChapel HillNorth CarolinaUSA
| | - Hayley C. Orndorf
- Department of Biological SciencesUniversity of PittsburghPittsburghPennsylvaniaUSA
| | - Anne G. Rosenwald
- Department of BiologyGeorgetown UniversityWashingtonDistrict of ColumbiaUSA
| | - Eric W. Triplett
- Microbiology and Cell Science DepartmentUniversity of FloridaGainesvilleFloridaUSA
| | | | - Mark A. Pauley
- Division of Undergraduate Education, Directorate for Education and Human ResourcesNational Science FoundationAlexandriaVirginiaUSA
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Williams JJ, Drew JC, Galindo-Gonzalez S, Robic S, Dinsdale E, Morgan WR, Triplett EW, Burnette JM, Donovan SS, Fowlks ER, Goodman AL, Grandgenett NF, Goller CC, Hauser C, Jungck JR, Newman JD, Pearson WR, Ryder EF, Sierk M, Smith TM, Tosado-Acevedo R, Tapprich W, Tobin TC, Toro-Martínez A, Welch LR, Wilson MA, Ebenbach D, McWilliams M, Rosenwald AG, Pauley MA. Barriers to integration of bioinformatics into undergraduate life sciences education: A national study of US life sciences faculty uncover significant barriers to integrating bioinformatics into undergraduate instruction. PLoS One 2019; 14:e0224288. [PMID: 31738797 PMCID: PMC6860448 DOI: 10.1371/journal.pone.0224288] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 10/09/2019] [Indexed: 01/27/2023] Open
Abstract
Bioinformatics, a discipline that combines aspects of biology, statistics, mathematics, and computer science, is becoming increasingly important for biological research. However, bioinformatics instruction is not yet generally integrated into undergraduate life sciences curricula. To understand why we studied how bioinformatics is being included in biology education in the US by conducting a nationwide survey of faculty at two- and four-year institutions. The survey asked several open-ended questions that probed barriers to integration, the answers to which were analyzed using a mixed-methods approach. The barrier most frequently reported by the 1,260 respondents was lack of faculty expertise/training, but other deterrents—lack of student interest, overly-full curricula, and lack of student preparation—were also common. Interestingly, the barriers faculty face depended strongly on whether they are members of an underrepresented group and on the Carnegie Classification of their home institution. We were surprised to discover that the cohort of faculty who were awarded their terminal degree most recently reported the most preparation in bioinformatics but teach it at the lowest rate.
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Affiliation(s)
- Jason J. Williams
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States of America
| | - Jennifer C. Drew
- Microbiology and Cell Science Department, University of Florida, Gainesville, FL, United States of America
| | - Sebastian Galindo-Gonzalez
- Department of Agricultural Education and Communication, University of Florida, Gainesville, FL, United States of America
| | - Srebrenka Robic
- Department of Biology, Agnes Scott College, Decatur, GA, United States of America
| | - Elizabeth Dinsdale
- Department of Biology, San Diego State University, San Diego, CA, United States of America
| | - William R. Morgan
- Department of Biology, College of Wooster, Wooster, OH, United States of America
| | - Eric W. Triplett
- Microbiology and Cell Science Department, University of Florida, Gainesville, FL, United States of America
| | - James M. Burnette
- University of California, Riverside, Riverside, CA, United States of America
| | - Samuel S. Donovan
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, United States of America
| | - Edison R. Fowlks
- Department of Biological Sciences, Hampton University, Hampton, VA, United States of America
| | - Anya L. Goodman
- Department of Chemistry and Biochemistry, California Polytechnic State University, San Luis Obispo, CA, United States of America
| | - Nealy F. Grandgenett
- Department of Teacher Education, University of Nebraska at Omaha, Omaha, NE, United States of America
| | - Carlos C. Goller
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States of America
| | - Charles Hauser
- Department of Biological Sciences, Bioinformatics Program, St. Edward’s University, Austin, TX, United States of America
| | - John R. Jungck
- Departments of Biological Sciences and Mathematical Sciences, University of Delaware, Newark, DE, United States of America
| | - Jeffrey D. Newman
- Department of Biology, Lycoming College, Williamsport, PA, United States of America
| | - William R. Pearson
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, United States of America
| | - Elizabeth F. Ryder
- Biology and Biotechnology Department, Worcester Polytechnic Institute, Worcester, MA, United States of America
| | - Michael Sierk
- Bioinformatics Program, Saint Vincent College, Latrobe, PA, United States of America
| | - Todd M. Smith
- Digital World Biology, PMB, Seattle, WA, United States of America
| | - Rafael Tosado-Acevedo
- Department of Natural Sciences, Inter American University of Puerto Rico, Metropolitan Campus, San Juan, PR, United States of America
| | - William Tapprich
- Department of Biology, University of Nebraska at Omaha, Omaha, NE, United States of America
| | - Tammy C. Tobin
- Department of Biology, Susquehanna University, Selinsgrove, PA, United States of America
| | - Arlín Toro-Martínez
- Department of Biology, Chemistry, and Environmental Sciences, Inter American University of Puerto Rico, San Germán Campus, San Germán, PR, United States of America
| | - Lonnie R. Welch
- Department of Computer Science, Ohio University, Athens, OH, United States of America
| | - Melissa A. Wilson
- School of Life Sciences, Arizona State University, Tempe, AZ, United States of America
| | - David Ebenbach
- Center for New Designs in Learning and Scholarship, Georgetown University, Washington, DC, United States of America
| | - Mindy McWilliams
- Center for New Designs in Learning and Scholarship, Georgetown University, Washington, DC, United States of America
| | - Anne G. Rosenwald
- Department of Biology, Georgetown University, Washington, DC, United States of America
| | - Mark A. Pauley
- School of Interdisciplinary Informatics, University of Nebraska at Omaha, Omaha, NE, United States of America
- * E-mail:
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Wilson Sayres MA, Hauser C, Sierk M, Robic S, Rosenwald AG, Smith TM, Triplett EW, Williams JJ, Dinsdale E, Morgan WR, Burnette JM, Donovan SS, Drew JC, Elgin SCR, Fowlks ER, Galindo-Gonzalez S, Goodman AL, Grandgenett NF, Goller CC, Jungck JR, Newman JD, Pearson W, Ryder EF, Tosado-Acevedo R, Tapprich W, Tobin TC, Toro-Martínez A, Welch LR, Wright R, Barone L, Ebenbach D, McWilliams M, Olney KC, Pauley MA. Bioinformatics core competencies for undergraduate life sciences education. PLoS One 2018; 13:e0196878. [PMID: 29870542 PMCID: PMC5988330 DOI: 10.1371/journal.pone.0196878] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 04/21/2018] [Indexed: 11/22/2022] Open
Abstract
Although bioinformatics is becoming increasingly central to research in the life sciences, bioinformatics skills and knowledge are not well integrated into undergraduate biology education. This curricular gap prevents biology students from harnessing the full potential of their education, limiting their career opportunities and slowing research innovation. To advance the integration of bioinformatics into life sciences education, a framework of core bioinformatics competencies is needed. To that end, we here report the results of a survey of biology faculty in the United States about teaching bioinformatics to undergraduate life scientists. Responses were received from 1,260 faculty representing institutions in all fifty states with a combined capacity to educate hundreds of thousands of students every year. Results indicate strong, widespread agreement that bioinformatics knowledge and skills are critical for undergraduate life scientists as well as considerable agreement about which skills are necessary. Perceptions of the importance of some skills varied with the respondent's degree of training, time since degree earned, and/or the Carnegie Classification of the respondent's institution. To assess which skills are currently being taught, we analyzed syllabi of courses with bioinformatics content submitted by survey respondents. Finally, we used the survey results, the analysis of the syllabi, and our collective research and teaching expertise to develop a set of bioinformatics core competencies for undergraduate biology students. These core competencies are intended to serve as a guide for institutions as they work to integrate bioinformatics into their life sciences curricula.
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Affiliation(s)
| | - Charles Hauser
- Department of Biological Sciences, St. Edward’s University, Austin, Texas, United States of America
| | - Michael Sierk
- Bioinformatics Program, Saint Vincent College, Latrobe, Pennsylvania, United States of America
| | - Srebrenka Robic
- Department of Biology, Agnes Scott College, Decatur, Georgia, United States of America
| | - Anne G. Rosenwald
- Department of Biology, Georgetown University, Washington, D.C., United States of America
| | - Todd M. Smith
- Digital World Biology, Seattle, Washington, United States of America
| | - Eric W. Triplett
- Microbiology and Cell Science Department, University of Florida, Gainesville, Florida, United States of America
| | - Jason J. Williams
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Elizabeth Dinsdale
- Department of Biology, San Diego State University, San Diego, California, United States of America
| | - William R. Morgan
- Department of Biology, College of Wooster, Wooster, Ohio, United States of America
| | - James M. Burnette
- College of Natural & Agricultural Sciences, University of California, Riverside, Riverside, California, United States of America
| | - Samuel S. Donovan
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Jennifer C. Drew
- Microbiology and Cell Science Department, University of Florida, Gainesville, Florida, United States of America
| | - Sarah C. R. Elgin
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Edison R. Fowlks
- Department of Biological Sciences, Hampton University, Hampton, Virginia, United States of America
| | - Sebastian Galindo-Gonzalez
- Department of Agricultural Education and Communication, University of Florida, Gainesville, Florida, United States of America
| | - Anya L. Goodman
- Department of Chemistry and Biochemistry, California Polytechnic State University, San Luis Obispo, California, United States of America
| | - Nealy F. Grandgenett
- Department of Teacher Education, University of Nebraska at Omaha, Omaha, Nebraska, United States of America
| | - Carlos C. Goller
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, United States of America
| | - John R. Jungck
- Department of Biological Sciences, University of Delaware, Newark, Delaware, United States of America
| | - Jeffrey D. Newman
- Department of Biology, Lycoming College, Williamsport, Pennsylvania, United States of America
| | - William Pearson
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia, United States of America
| | - Elizabeth F. Ryder
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, Massachusetts, United States of America
| | - Rafael Tosado-Acevedo
- Department of Natural Sciences, Inter American University of Puerto Rico, Metropolitan Campus, San Juan, Puerto Rico, United States of America
| | - William Tapprich
- Department of Biology, University of Nebraska at Omaha, Omaha, Nebraska, United States of America
| | - Tammy C. Tobin
- Department of Biology, Susquehanna University, Selinsgrove, Pennsylvania, United States of America
| | - Arlín Toro-Martínez
- Department of Biology, Chemistry, and Environmental Sciences, Inter American University of Puerto Rico, San Germán Campus, San Germán, Puerto Rico, United States of America
| | - Lonnie R. Welch
- Department of Computer Science, Ohio University, Athens, Ohio, United States of America
| | - Robin Wright
- Department of Biology Teaching and Learning, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Lindsay Barone
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - David Ebenbach
- Center for New Designs in Learning and Scholarship, Georgetown University, Washington, D.C., United States of America
| | - Mindy McWilliams
- Center for New Designs in Learning and Scholarship, Georgetown University, Washington, D.C., United States of America
| | - Kimberly C. Olney
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | - Mark A. Pauley
- School of Interdisciplinary Informatics, University of Nebraska at Omaha, Omaha, Nebraska, United States of America
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Mulder N, Schwartz R, Brazas MD, Brooksbank C, Gaeta B, Morgan SL, Pauley MA, Rosenwald A, Rustici G, Sierk M, Warnow T, Welch L. The development and application of bioinformatics core competencies to improve bioinformatics training and education. PLoS Comput Biol 2018; 14:e1005772. [PMID: 29390004 PMCID: PMC5794068 DOI: 10.1371/journal.pcbi.1005772] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Bioinformatics is recognized as part of the essential knowledge base of numerous career paths in biomedical research and healthcare. However, there is little agreement in the field over what that knowledge entails or how best to provide it. These disagreements are compounded by the wide range of populations in need of bioinformatics training, with divergent prior backgrounds and intended application areas. The Curriculum Task Force of the International Society of Computational Biology (ISCB) Education Committee has sought to provide a framework for training needs and curricula in terms of a set of bioinformatics core competencies that cut across many user personas and training programs. The initial competencies developed based on surveys of employers and training programs have since been refined through a multiyear process of community engagement. This report describes the current status of the competencies and presents a series of use cases illustrating how they are being applied in diverse training contexts. These use cases are intended to demonstrate how others can make use of the competencies and engage in the process of their continuing refinement and application. The report concludes with a consideration of remaining challenges and future plans. As data size and complexity increase in life science research, so the need for bioinformatics training has increased. This training is required across a wide variety of audiences, but varies in the level of detail and content that needs to be delivered. A scientist wishing to use some bioinformatics tools to analyse their specific dataset will require different competencies than one that provides support in a bioinformatics services environment. The Curriculum Task Force of the International Society of Computational Biology (ISCB) Education Committee has attempted to address this by developing a set of bioinformatics core competencies and mapping these to ten different user profiles across the spectrum of potential trainees. Here we present the final iteration of the competencies and some examples to demonstrate how they have been used to drive bioinformatics curriculum development and training in different settings.
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Affiliation(s)
- Nicola Mulder
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- * E-mail:
| | - Russell Schwartz
- Department of Biological Sciences and Computational Biology Department, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | | | - Cath Brooksbank
- EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Bruno Gaeta
- School of Computer Science and Engineering, University of New South Wales, Sydney, Australia
| | - Sarah L. Morgan
- EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Mark A. Pauley
- School of Interdisciplinary Informatics, University of Nebraska at Omaha, Omaha, Nebraska, United States of America
| | - Anne Rosenwald
- Department of Biology, Georgetown University, Washington, DC, United States of America
| | - Gabriella Rustici
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Michael Sierk
- Saint Vincent College, Latrobe, Pennsylvania, United States of America
| | - Tandy Warnow
- Department of Computer Science and Department of Bioengineering, University of Illinois, Urbana-Champaign, Champaign, United States of America
| | - Lonnie Welch
- School of Electrical Engineering and Computer Science, Ohio University, Athens, Ohio, United States of America
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Affiliation(s)
| | - Mark A. Pauley
- School of Interdisciplinary Informatics, University of Nebraska at Omaha, Omaha, NE 68182
| | - Lonnie Welch
- Interdisciplinary Program in Molecular and Cellular Biology, Ohio University, Athens, OH 45701
| | - Sarah C. R. Elgin
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Robin Wright
- Department of Biology Teaching and Learning, University of Minnesota, St. Paul, MN 55108
| | - Jessamina Blum
- Department of Biology Teaching and Learning, University of Minnesota, St. Paul, MN 55108
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Eaton CD, Allen D, Anderson LJ, Bowser G, Pauley MA, Williams KS, Uno GE. Summit of the Research Coordination Networks for Undergraduate Biology Education. CBE Life Sci Educ 2016; 15:mr1. [PMCID: PMC5132389 DOI: 10.1187/cbe.16-03-0147] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
This report highlights the discussions and recommendations featured at the first summit meeting of projects funded by the National Science Foundation’s Research Coordination Networks for Undergraduate Biology Education program, held January 14–16, 2016, in Washington, DC. The first summit of projects funded by the National Science Foundation’s Research Coordination Networks for Undergraduate Biology Education (RCN-UBE) program was held January 14–16, 2016, in Washington, DC. Sixty-five scientists and science educators from 38 of the 41 Incubator and Full RCN-UBE awards discussed the value and contributions of RCNs to the national biology education reform effort. The summit illustrated the progress of this innovative UBE track, first awarded in 2009. Participants shared experiences regarding network development and growth, identified best practices and challenges faced in network management, and discussed work accomplished. We report here on key aspects of network evaluation, characteristics of successful networks, and how to sustain and broaden participation in networks. Evidence from successful networks indicates that 5 years (the length of a Full RCN-UBE) may be insufficient time to produce a cohesive and effective network. While online communication promotes the activities of a network and disseminates effective practices, face-to-face meetings are critical for establishing ties between network participants. Creation of these National Science Foundation–funded networks may be particularly useful for consortia of faculty working to address problems or exchange novel solutions discovered while introducing active-learning methods and/or course-based research into their curricula.
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Affiliation(s)
| | - Deborah Allen
- Department of Biological Sciences, University of Delaware, Newark, DE 19716
| | - Laurel J. Anderson
- Department of Botany & Microbiology, Ohio Wesleyan University, Delaware, OH 43015
| | - Gillian Bowser
- Department of Ecosystem Science and Sustainability, Colorado State University, Fort Collins, CO 80523
| | - Mark A. Pauley
- School of Interdisciplinary Informatics, University of Nebraska at Omaha, Omaha, NE 68182
| | - Kathy S. Williams
- Department of Biology, San Diego State University, San Diego, CA 92182
| | - Gordon E. Uno
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019
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Dinsdale E, Elgin SCR, Grandgenett N, Morgan W, Rosenwald A, Tapprich W, Triplett EW, Pauley MA. NIBLSE: A Network for Integrating Bioinformatics into Life Sciences Education. CBE Life Sci Educ 2015; 14:le3. [PMID: 26466989 PMCID: PMC4710410 DOI: 10.1187/cbe.15-06-0123] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Affiliation(s)
| | - Sarah C R Elgin
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Neal Grandgenett
- Department of Teacher Education, University of Nebraska at Omaha, Omaha, NE 68182
| | - William Morgan
- Department of Biology, College of Wooster, Wooster, OH 44691
| | - Anne Rosenwald
- Department of Biology, Georgetown University, Washington, DC 20057
| | - William Tapprich
- Department of Biology, University of Nebraska at Omaha, Omaha, NE 68182
| | - Eric W Triplett
- Department of Molecular Biology and Cell Science, University of Florida, Gainesville, FL 32611
| | - Mark A Pauley
- School of Interdisciplinary Informatics, University of Nebraska at Omaha, Omaha, NE 68182
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Duan F, Pauley MA, Spindel ER, Zhang L, Norgren RB. Large scale analysis of positional effects of single-base mismatches on microarray gene expression data. BioData Min 2010; 3:2. [PMID: 20429935 PMCID: PMC2877042 DOI: 10.1186/1756-0381-3-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2009] [Accepted: 04/29/2010] [Indexed: 12/02/2022] Open
Abstract
Background Affymetrix GeneChips utilize 25-mer oligonucleotides probes linked to a silica surface to detect targets in solution. Mismatches due to single nucleotide polymorphisms (SNPs) can affect the hybridization between probes and targets. Previous research has indicated that binding between probes and targets strongly depends on the positions of these mismatches. However, there has been substantial variability in the effect of mismatch type across studies. Methods By taking advantage of naturally occurring mismatches between rhesus macaque transcripts and human probes from the Affymetrix U133 Plus 2 GeneChip, we collected the largest 25-mer probes dataset with single-base mismatches at each of the 25 positions on the probe ever used in this type of analysis. Results A mismatch at the center of a probe led to a greater loss in signal intensity than a mismatch at the ends of the probe, regardless of the mismatch type. There was a slight asymmetry between the ends of a probe: effects of mismatches at the 3' end of a probe were greater than those at the 5' end. A cross study comparison of the effect of mismatch types revealed that results were not in good agreement among different reports. However, if the mismatch types were consolidated to purine or pyrimidine mismatches, cross study conclusions could be generated. Conclusion The comprehensive assessment of the effects of single-base mismatches on microarrays provided in this report can be useful for improving future versions of microarray platform design and the corresponding data analysis algorithms.
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Affiliation(s)
- Fenghai Duan
- Center for Statistical Sciences, Brown University, Providence, RI, USA.
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Spindel ER, Pauley MA, Jia Y, Gravett C, Thompson SL, Boyle NF, Ojeda SR, Norgren RB. Leveraging human genomic information to identify nonhuman primate sequences for expression array development. BMC Genomics 2005; 6:160. [PMID: 16288651 PMCID: PMC1314899 DOI: 10.1186/1471-2164-6-160] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2005] [Accepted: 11/15/2005] [Indexed: 01/16/2023] Open
Abstract
Background Nonhuman primates (NHPs) are essential for biomedical research due to their similarities to humans. The utility of NHPs will be greatly increased by the application of genomics-based approaches such as gene expression profiling. Sequence information from the 3' end of genes is the key resource needed to create oligonucleotide expression arrays. Results We have developed the algorithms and procedures necessary to quickly acquire sequence information from the 3' end of nonhuman primate orthologs of human genes. To accomplish this, we identified terminal exons of over 15,000 human genes by aligning mRNA sequences with genomic sequence. We found the mean length of complete last exons to be approximately 1,400 bp, significantly longer than previous estimates. We designed primers to amplify genomic DNA, which included at least 300 bp of the terminal exon. We cloned and sequenced the PCR products representing over 5,500 Macaca mulatta (rhesus monkey) orthologs of human genes. This sequence information has been used to select probes for rhesus gene expression profiling. We have also tested 10 sets of primers with genomic DNA from Macaca fascicularis (Cynomolgus monkey), Papio hamadryas (Baboon), and Chlorocebus aethiops (African green monkey, vervet). The results indicate that the primers developed for this study will be useful for acquiring sequence from the 3' end of genes for other nonhuman primate species. Conclusion This study demonstrates that human genomic DNA sequence can be leveraged to obtain sequence from the 3' end of NHP orthologs and that this sequence can then be used to generate NHP oligonucleotide microarrays. Affymetrix and Agilent used sequences obtained with this approach in the design of their rhesus macaque oligonucleotide microarrays.
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Affiliation(s)
- Eliot R Spindel
- Division of Neuroscience, Oregon National Primate Research Center, Beaverton, OR 97006, USA
| | - Mark A Pauley
- College of Information Science & Technology, University of Nebraska at Omaha, Omaha, NE, 68182 USA
| | - Yibing Jia
- Division of Neuroscience, Oregon National Primate Research Center, Beaverton, OR 97006, USA
| | - Courtney Gravett
- Division of Neuroscience, Oregon National Primate Research Center, Beaverton, OR 97006, USA
| | - Shaun L Thompson
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Nicholas F Boyle
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Sergio R Ojeda
- Division of Neuroscience, Oregon National Primate Research Center, Beaverton, OR 97006, USA
| | - Robert B Norgren
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, 68198, USA
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