@article{wilkins_rapciak_goller_weintraub_mikaelyan_2024, title={Scaling the wall: overcoming barriers to STEM knowledge mobilization}, volume={9}, ISSN={["2297-900X"]}, DOI={10.3389/fcomm.2024.1366207}, abstractNote={Improving science literacy is crucial amidst global challenges like climate change, emerging diseases, AI, and rampant disinformation. This is vital not only for future STEM generations but for all, to make informed decisions. Informal science communication efforts such as podcasts, popular science articles, and museum events are an essential part of the infrastructure for mobilizing knowledge and nurturing science literacy. However, in this Perspective, we emphasize the need to grow our capacity for STEM outreach in the formal K-12 classroom. While the majority of informal outreach mechanisms require audience members to seek out content, classrooms include those hard-to-reach target audiences that are not already STEM-engaged. We contrast the multitude of resources that have been developed to support informal outreach in recent decades with a relative paucity of such efforts in the K-12 formal classroom realm. We advocate for a more balanced deployment of resources and efforts between these two vital components of our knowledge mobilization and STEM engagement infrastructure. In particular, we highlight the key role of K-12 teachers as conduits for knowledge dissemination and the need for greater collaboration between scientists and teachers at individual and organizational levels. We also advocate for greater collaboration across programs in both the informal and formal outreach space, and dedicated effort to construct dissemination networks to share outreach materials at scale across disparate programs. The aim of our piece is to generate discussion about how we might refocus goals, funding mechanisms, and policies to grow the science-engaged society necessary to confront future challenges.}, journal={FRONTIERS IN COMMUNICATION}, author={Wilkins, Matthew R. and Rapciak, Stephanie E. and Goller, Carlos C. and Weintraub, Jory and Mikaelyan, Aram}, year={2024}, month={Mar} }
 @article{sjogren_comstock_goller_2023, title={Connecting Ethical Reasoning to Global Challenges through Analysis of Argumentation}, volume={3}, ISSN={["1935-7885"]}, url={https://doi.org/10.1128/jmbe.00166-22}, DOI={10.1128/jmbe.00166-22}, abstractNote={Scientific literacy is built on critical thinking. The postbaccalaureate workforce enhances our economies and societies by contributing a wealth of knowledge and skill sets to local communities, respective industries, and beyond as our world becomes increasingly interconnected.}, journal={JOURNAL OF MICROBIOLOGY & BIOLOGY EDUCATION}, author={Sjogren, Caroline A. and Comstock, Gary and Goller, Carlos C.}, editor={Shaffer, JustinEditor}, year={2023}, month={Mar} }
 @article{goller_2023, title={Encontrando Soluciones en su Fregadero (Versión en Español del Video de Carlos Goller)}, url={https://doi.org/10.52750/856164}, DOI={10.52750/856164}, abstractNote={¡Las comunidades microbianas que nos rodean tienen un gran potencial y podemos descubrir sus secuencias genéticas y poderes!}, author={Goller, Carlos}, year={2023}, month={Aug} }
 @article{goller_2023, title={Finding Health Solutions In Your Sink}, url={https://doi.org/10.52750/730184}, DOI={10.52750/730184}, abstractNote={The microbial communities around us hold great potential, and we can now uncover their genetic sequences and powers!}, author={Goller, Carlos}, year={2023}, month={Aug} }
 @article{srougi_corbett_garcia_sabaoun_santisteban_sivaraman_chen_goller_kelly_2023, title={Innovating Life Sciences Laboratory Training: Molecular Biology Laboratory Education Modules (MBLEMs) as a Model for Advanced Training at Diverse Institutions}, volume={299}, ISSN={["1083-351X"]}, DOI={10.1016/j.jbc.2023.103522}, number={3}, journal={JOURNAL OF BIOLOGICAL CHEMISTRY}, author={Srougi, Melissa and Corbett, Anita and Garcia, Christina and Sabaoun, Michelle and Santisteban, Maria and Sivaraman, Vijay and Chen, Stefanie and Goller, Carlos and Kelly, Robert}, year={2023}, pages={S260–S260} }
 @article{cangialosi_goller_grewe_tang_taylor_tyler_ortiz_zenon_2023, title={Reimaging Leadership in Open Education: Networking to Promote Social Justice and Systemic Change}, url={https://doi.org/10.13001/joerhe.v2i1.7865}, DOI={10.13001/joerhe.v2i1.7865}, abstractNote={Challenging traditional notions of leadership, and leveraging non-hierarchical learning structures, the Regional Leaders of Open Education Network (RLOE) was created to bring together leaders from a broad diversity of institutions in the U.S. and Canada to build strategic plans for open education that especially support underserved and underrepresented students. All members of the network, including an advisory team, collaborators, student mentors and cohort participants were engaged in a multi-directional learning program over two years (2021-2022) that included a variety of synchronous and asynchronous online engagement opportunities, as well as the opportunity to attend an in-person summit. Analyses of surveys and reports completed by network participants indicated that RLOE was successful in building community and in providing vital networking opportunities that supported them to design and begin to implement open education strategic plans that included initiatives in professional development, forming partnerships, integrating DEI as well as many other goals and accomplishments. Cohort participants indicated statistically significant gains in 1) developing and leveraging their leadership skills to serve marginalized and underrepresented students, 2) understanding how OE practices can empower all students, especially marginalized students, and 3) how OER can be used to specifically support underrepresented and underserved groups. In addition, 90% of cohort participants indicated that the RLOE Network helped them to center principles of diversity, equity and inclusion into their open educational work.}, journal={Journal of Open Educational Resources in Higher Education}, author={Cangialosi, Karen and Goller, Carlos and Grewe, Kim and Tang, Tiffany and Taylor, Robin and Tyler, Deidre and Ortiz, Rebecca Vasquez and Zenon, Esperanza}, year={2023}, month={Oct} }
 @inproceedings{sjogren_goller_2022, title={Developing Interdisciplinary and Inclusive Experiences Beyond the Classroom by Starting with a New CURE}, author={Sjogren, C. and Goller, C.C}, year={2022} }
 @article{goller_johnson_casimo_2022, title={Does organelle shape matter?: Exploring patterns in cell shape and structure with high-throughput (HT) imaging}, url={https://doi.org/10.24918/cs.2022.3}, DOI={10.24918/cs.2022.3}, abstractNote={Organelle structure has been studied and visualized for decades; however, publicly available databases that use improved high-throughput microscopy of gene-edited cell lines have recently revolutionized the amount and quality of information now available for use in undergraduate classes. This lesson demonstrates how the use of high-throughput (HT) microscopy has generated data describing organelle structure and variability. Students access, analyze, and evaluate cell structure images using the Allen Institute for Cell Science’s Allen Cell Explorer. Students synthesize the information to make recommendations and propose a future experiment. Using web-based tools and a realistic scenario that merges antimicrobial drug screens with eukaryotic cell perturbations and structure, this case study provides a guided tour of the powerful applications of high-throughput microscopy.}, journal={CourseSource}, author={Goller, C.C. and Johnson, G.T. and Casimo, K.}, year={2022} }
 @inproceedings{goller_2022, title={Evaluating How Learners Navigate Bioinformatics Narratives and Workflows}, author={Goller, C.C}, year={2022} }
 @article{harris_sikes_bergman_goller_hasley_sjogren_ramirez_gordy_2022, title={Hands-on immunology: Engaging learners of all ages through tactile teaching tools}, volume={13}, ISSN={["1664-302X"]}, url={http://dx.doi.org/10.3389/fmicb.2022.966282}, DOI={10.3389/fmicb.2022.966282}, abstractNote={Ensuring the public has a fundamental understanding of human–microbe interactions, immune responses, and vaccines is a critical challenge in the midst of a pandemic. These topics are commonly taught in undergraduate- and graduate-level microbiology and immunology courses; however, creating engaging methods of teaching these complex concepts to students of all ages is necessary to keep younger students interested when science seems hard. Building on the Tactile Teaching Tools with Guided Inquiry Learning (TTT-GIL) method we used to create an interactive lac operon molecular puzzle, we report here two TTT-GIL activities designed to engage diverse learners from middle schoolers to masters students in exploring molecular interactions within the immune system. By pairing physical models with structured activities built on the constructivist framework of Process-Oriented Guided Inquiry Learning (POGIL), TTT-GIL activities guide learners through their interaction with the model, using the Learning Cycle to facilitate construction of new concepts. Moreover, TTT-GIL activities are designed utilizing Universal Design for Learning (UDL) principles to include all learners through multiple means of engagement, representation, and action. The TTT-GIL activities reported here include a web-enhanced activity designed to teach concepts related to antibody–epitope binding and specificity to deaf and hard-of-hearing middle and high school students in a remote setting and a team-based activity that simulates the evolution of the Major Histocompatibility Complex (MHC) haplotype of a population exposed to pathogens. These activities incorporate TTT-GIL to engage learners in the exploration of fundamental immunology concepts and can be adapted for use with learners of different levels and educational backgrounds.}, journal={FRONTIERS IN MICROBIOLOGY}, publisher={Frontiers Media SA}, author={Harris, Felix R. and Sikes, Michael L. and Bergman, Michael and Goller, Carlos C. and Hasley, Andrew O. and Sjogren, Caroline A. and Ramirez, Melissa V. and Gordy, Claire L.}, year={2022}, month={Aug} }
 @misc{goller_2022, title={Learning Outcomes for CURE's, Assessments for Research-based Courses/Evidence of Student Learning. What are they/we learning?}, author={Goller, C.C.}, year={2022} }
 @article{pike_pandey_goller_herzog_parks_2022, title={Opportunities and Challenges of Online Instruction and Effective Pedagogy That Blurs the Lines between Online and On-Site Teaching and Learning}, volume={4}, ISSN={["1935-7885"]}, url={https://doi.org/10.1128/jmbe.00047-22}, DOI={10.1128/jmbe.00047-22}, abstractNote={There has been an increased focus on online teaching as the COVID-19 pandemic continues. While online teaching is certainly not a new mode of education, it has been further developed and analyzed in current times, as most instructors were required to incorporate novel and effective methods for remote instruction. At the same time, these instructors sought to evaluate the inclusivity and effectiveness of such practices to ensure that students not only learned during their online courses but continued to receive the support needed to overcome systemic biases and stressors. The 2022 themed issue, “Opportunities and Challenges of Online Instruction: Blurring the Lines Between Online and On-Site Teaching and Learning,” focuses on key topics that are most pertinent to online education, the wealth of practices used to facilitate such an approach to teaching, and how these methods can continue to be used as effective pedagogical tools as we strive to improve both remote instruction and the return to in-person teaching. A previous JMBE themed issue on “Teaching in a Time of Crisis,” released during the height of the pandemic in 2021, focused, by necessity, on the rapid switch to online education prompted by the emergence of COVID-19. The articles in that issue reported on the experiences of educators and students during this switch to emergency remote instruction and the challenges brought about by the rapid change. At that point, many faculty members had never taught online before, and for some, the learning curve was very steep, but ultimately successful. As we emerge from the pandemic and look back on the remote instruction that occurred over the past two years, analysis has shown that online education is accessible, flexible, and effective. As educators, we must recognize that now is the time to build on the progress made during the pandemic in fostering a culture of remote instruction in higher education and, where applicable, in K-12 pathways. This issue highlights for all of us the fact that pedagogies incorporating online education, in its many modalities, are the future. As an editorial team, we identified five main themes addressed by the articles included in this themed issue, each of which is discussed below.}, journal={JOURNAL OF MICROBIOLOGY & BIOLOGY EDUCATION}, publisher={American Society for Microbiology}, author={Pike, Andrew and Pandey, Sumali and Goller, Carlos C. and Herzog, Jennifer and Parks, Samantha T.}, year={2022}, month={Apr} }
 @inproceedings{goller_2022, title={Se Hace Camino al Anda}, author={Goller, C.C.}, year={2022} }
 @misc{goller_lenahan_2022, title={Social Annotation with Hypothes.is}, author={Goller, C.C. and Lenahan, M.}, year={2022} }
 @article{goller_2022, title={Some Like it Hot!}, volume={1}, url={https://doi.org/10.52750/924409}, DOI={10.52750/924409}, abstractNote={What are extremophiles?What can we learn from them that is relevant in our warming climate?Carols Goller, Ph.D. introduces you to these resilient microbes, and discusses how we can apply what we learn from them as we face current challenges.(Versión en Español del Video de Carlos Goller)}, publisher={North Carolina State University}, author={Goller, Carlos}, year={2022}, month={Jan} }
 @misc{goller_casimo_metzler_2022, title={The Virtual Science Lab: Does Organelle Shape Matter?}, author={Goller, C.C. and Casimo, K. and Metzler, K.}, year={2022}, month={Apr} }
 @article{goller_2022, title={¡Algunos Prefieren lo Caliente! La Vida en Medio Ambiente Extremo}, volume={1}, url={https://doi.org/10.52750/566490}, DOI={10.52750/566490}, abstractNote={¿Qué son los extremófilos?¿Qué podemos aprender de ellos que que sea relevante al cambio climático?El profesor Goller se presenta estos microbios resilientes y discuten cómo podemos aplicar lo que aprendemos de ellos al enfrentar los retos actuales.}, publisher={North Carolina State University}, author={Goller, Carlos}, year={2022}, month={Jan} }
 @article{dow_wood-charlson_biller_paustian_schirmer_sheik_whitham_krebs_goller_allen_et al._2021, title={Bioinformatic Teaching Resources - For Educators, by Educators - Using KBase, a Free, User-Friendly, Open Source Platform}, volume={6}, ISSN={["2504-284X"]}, DOI={10.3389/feduc.2021.711535}, abstractNote={Over the past year, biology educators and staff at the U.S. Department of Energy Systems Biology Knowledgebase (KBase) initiated a collaborative effort to develop a curriculum for bioinformatics education. KBase is a free web-based platform where anyone can conduct sophisticated and reproducible bioinformatic analyses via a graphical user interface. Here, we demonstrate the utility of KBase as a platform for bioinformatics education, and present a set of modular, adaptable, and customizable instructional units for teaching concepts in Genomics, Metagenomics, Pangenomics, and Phylogenetics. Each module contains teaching resources, publicly available data, analysis tools, and Markdown capability, enabling instructors to modify the lesson as appropriate for their specific course. We present initial student survey data on the effectiveness of using KBase for teaching bioinformatic concepts, provide an example case study, and detail the utility of the platform from an instructor’s perspective. Even as in-person teaching returns, KBase will continue to work with instructors, supporting the development of new active learning curriculum modules. For anyone utilizing the platform, the growing KBase Educators Organization provides an educators network, accompanied by community-sourced guidelines, instructional templates, and peer support, for instructors wishing to use KBase within a classroom at any educational level–whether virtual or in-person.}, journal={FRONTIERS IN EDUCATION}, author={Dow, Ellen G. and Wood-Charlson, Elisha M. and Biller, Steven J. and Paustian, Timothy and Schirmer, Aaron and Sheik, Cody S. and Whitham, Jason M. and Krebs, Rose and Goller, Carlos C. and Allen, Benjamin and et al.}, year={2021}, month={Oct} }
 @inproceedings{goller_frank_zenon_powell_cangialosi_2021, title={Building the Open Education Profession with Regional Leadership}, author={Goller, C. and Frank, E. and Zenon, E. and Powell, R. and Cangialosi, K.}, year={2021}, month={Jul} }
 @inproceedings{tully_cross_mckenney_goller_2021, title={Combining open pedagogy and citizen science to empower learners and educators}, author={Tully, D. and Cross, W. and McKenney, E. and Goller, C.}, year={2021}, month={Apr} }
 @misc{goller_2021, title={Connecting Courses through a Unique Microbe}, author={Goller, C.C}, year={2021} }
 @article{samsa_goller_2021, title={Divide and Conquer: A Simple Modern Technique for Collaborative Small Group Learning with Reciprocal Peer Teaching}, volume={22}, ISSN={["1935-7885"]}, DOI={10.1128/jmbe.v22i1.2153}, abstractNote={Collaborative group learning and peer teaching are robust active learning techniques. Students and instructors interact with technology extensively in their lives and in the classroom.}, number={1}, journal={Journal of Microbiology and Biology Education}, author={Samsa, L.A. and Goller, C.C.}, year={2021}, month={Apr}, pages={ev22i1-2153} }
 @article{gordy_ramirez_vandegrift_goller_2021, title={Editorial: Research Topic Tools, Techniques, and Strategies for Teaching in a Real-World Context With Microbiology}, volume={12}, ISSN={["1664-302X"]}, url={http://dx.doi.org/10.3389/fmicb.2021.755500}, DOI={10.3389/fmicb.2021.755500}, abstractNote={EDITORIAL article Front. Microbiol., 13 October 2021 | https://doi.org/10.3389/fmicb.2021.755500}, journal={FRONTIERS IN MICROBIOLOGY}, publisher={Frontiers Media SA}, author={Gordy, Claire L. and Ramirez, Melissa V. and Vandegrift, Micah and Goller, Carlos C.}, year={2021}, month={Oct} }
 @inproceedings{goller_robertson_2021, title={HITS: A network to create inquiry-based case studies that make high-throughput approaches and discovery accessible}, url={https://qubeshub.org/publications/2467/1}, DOI={10.25334/CPP8-PC40}, publisher={QUBES Educational Resources}, author={Goller, Carlos and Robertson, Sabrina}, year={2021} }
 @article{robertson_bixler_eslinger_gaudier-diaz_kleinschmit_marsteller_o'toole_sankar_goller_2021, title={HITS: Harnessing a Collaborative Training Network to Create Case Studies that Integrate High-Throughput, Complex Datasets into Curricula}, volume={6}, DOI={10.3389/feduc.2021.711512}, abstractNote={As educators and researchers, we often enjoy enlivening classroom discussions by including examples of cutting-edge high-throughput (HT) technologies that propelled scientific discovery and created repositories of new information. We also call for the use of evidence-based teaching practices to engage students in ways that promote equity and learning. The complex datasets produced by HT approaches can open the doors to discovery of novel genes, drugs, and regulatory networks, so students need experience with the effective design, implementation, and analysis of HT research. Nevertheless, we miss opportunities to contextualize, define, and explain the potential and limitations of HT methods. One evidence-based approach is to engage students in realistic HT case studies. HT cases immerse students with messy data, asking them to critically consider data analysis, experimental design, ethical implications, and HT technologies.The NSF HITS (High-throughput Discovery Science and Inquiry-based Case Studies for Today’s Students) Research Coordination Network in Undergraduate Biology Education seeks to improve student quantitative skills and participation in HT discovery. Researchers and instructors in the network learn about case pedagogy, HT technologies, publicly available datasets, and computational tools. Leveraging this training and interdisciplinary teamwork, HITS participants then create and implement HT cases. Our initial case collection has been used in >15 different courses at a variety of institutions engaging >600 students in HT discovery. We share here our rationale for engaging students in HT science, our HT cases, and network model to encourage other life science educators to join us and further develop and integrate HT complex datasets into curricula.}, journal={Frontiers in Education}, author={Robertson, Sabrina D. and Bixler, Andrea and Eslinger, Melissa R. and Gaudier-Diaz, Monica M. and Kleinschmit, Adam J. and Marsteller, Pat and O'Toole, Kate K. and Sankar, Usha and Goller, Carlos C.}, year={2021}, pages={711512} }
 @article{goller_srougi_chen_schenkman_kelly_2021, place={SWITZERLAND}, title={Integrating Bioinformatics Tools into Inquiry-based Molecular Biology Laboratory Education Modules}, volume={6}, ISSN={2504-284X}, DOI={10.3389/feduc.2021.711403}, abstractNote={The accelerating expansion of online bioinformatics tools has profoundly impacted molecular biology, with such tools becoming integral to the modern life sciences. As a result, molecular biology laboratory education must train students to leverage bioinformatics in meaningful ways to be prepared for a spectrum of careers. Institutions of higher learning can benefit from a flexible and dynamic instructional paradigm that blends up-to-date bioinformatics training with best practices in molecular biology laboratory pedagogy. At North Carolina State University, the campus-wide interdisciplinary Biotechnology (BIT) Program has developed cutting-edge, flexible, inquiry-based Molecular Biology Laboratory Education Modules (MBLEMs). MBLEMs incorporate relevant online bioinformatics tools using evidenced-based pedagogical practices and in alignment with national learning frameworks. Students in MBLEMs engage in the most recent experimental developments in modern biology (e.g., CRISPR, metagenomics) through the strategic use of bioinformatics, in combination with wet-lab experiments, to address research questions. MBLEMs are flexible educational units that provide a menu of inquiry-based laboratory exercises that can be used as complete courses or as parts of existing courses. As such, MBLEMs are designed to serve as resources for institutions ranging from community colleges to research-intensive universities, involving a diverse range of learners. Herein, we describe this new paradigm for biology laboratory education that embraces bioinformatics as a critical component of inquiry-based learning for undergraduate and graduate students representing the life sciences, the physical sciences, and engineering.}, number={Article Number: 711403}, journal={Frontiers in Education}, publisher={FRONTIERS MEDIA SA}, author={Goller, C.C. and Srougi, M.C. and Chen, S.H. and Schenkman, L.R. and Kelly, R.M.}, year={2021} }
 @inproceedings{whitham_goller_mckenney_2021, title={Leveraging instructor involvement to enhance student engagement via social annotation}, author={Whitham, J. and Goller, C. and McKenney, E.}, year={2021}, month={May} }
 @misc{goller_mckenney_mccartney_2021, title={Liquid Margins 20: Making Sense of Science With Social Annotation}, author={Goller, C. and McKenney, E.A. and McCartney, M.}, year={2021}, month={Mar} }
 @article{goller_chen_srougi_2021, title={New Tricks for Old Drugs: Using High-throughput Screening to Repurpose FDA-Approved Drugs to Combat Zika Virus}, url={https://sciencecases.lib.buffalo.edu/collection/detail.html?case_id=1194&id=1194}, journal={National Center for Case Study Teaching in Science}, author={Goller, C. and Chen, S. and Srougi, M.}, year={2021} }
 @misc{goller_2021, title={Of all the bacteria around us... why Delftia? A BIT of an introduction to Biotechnology}, author={Goller, C.C.}, year={2021}, month={Nov} }
 @inproceedings{goller_2021, title={Promoting a Culture of Co-Creation and Equity through Course WordPress Sites on Advanced Molecular Technologies}, author={Goller, C.}, year={2021}, month={Oct} }
 @inproceedings{goller_vinson_2021, title={Publishing your evidence-based teaching activity in CourseSource: a step-by-step workshop for preparing your lesson manuscript}, author={Goller, C and Vinson, E}, year={2021}, month={Jun} }
 @inproceedings{goller_ortiz_tyler_zenon_grewe_cangialosi_2021, title={Reimagining Open Education Leadership to Center Historically Marginalized Communities and Students}, author={Goller, C. and Ortiz, R. and Tyler, D. and Zenon, E. and Grewe, K. and Cangialosi, K.}, year={2021}, month={Oct} }
 @article{bates_goller_gonzales_kovacs_rea_schalmo_tarun_2021, title={Scientists Offering Solutions through Sprints}, url={https://qubeshub.org/publications/2796/1}, DOI={10.25334/V7C0-XJ78}, journal={QUBES Educational Resources}, publisher={QUBES Educational Resources}, author={Bates, Tonya and Goller, Carlos and Gonzales, Lynda and Kovacs, Jennifer and Rea, Anne and Schalmo, Crystal and Tarun, Alice}, year={2021} }
 @inproceedings{whitham_boland_krebs_goller_2021, title={Searching for Silver and Gold: Teaching students how to analyze microbial communities with KBase narratives}, author={Whitham, W. and Boland, M. and Krebs, R. and Goller, C.}, year={2021}, month={Feb} }
 @inproceedings{whitham_boland_krebs_goller_2021, title={Searching for Silver and Gold: Teaching students how to analyze microbial communities with KBase narratives}, author={Whitham, W. and Boland, M. and Krebs, R. and Goller, C.}, year={2021}, month={Jan} }
 @article{goller_vandegrift_cross_smyth_2021, title={Sharing Notes is Encouraged: Annotating and Co-creating with Hypothes.is and Google Docs}, volume={22}, ISSN={["1935-7885"]}, DOI={10.1128/jmbe.v22i1.2135}, abstractNote={Effectively analyzing literature can be challenging for those unfamiliar with studies from rapidly evolving research fields. Previous studies have shown that incorporating primary literature promotes scientific literacy and critical thinking skills.}, number={1}, journal={Journal of Microbiology & Biology Education}, author={Goller, C. and Vandegrift, M. and Cross, W. and Smyth, D.}, year={2021}, month={Jan} }
 @article{gibson_goller_kring_panvini_pruneski_wisner_2021, title={Sharing Stories: Developing OER around Podcasts}, url={https://qubeshub.org/publications/2797/1}, DOI={10.25334/C0QB-AN62}, journal={QUBES Educational Resources}, publisher={QUBES Educational Resources}, author={Gibson, J. and Goller, Carlos and Kring, Stefanie and Panvini, Darlene and Pruneski, Justin and Wisner, Ellen}, year={2021} }
 @misc{goller_simon_vandegrift_cross_2021, title={Show me the Open Science: Dissecting Publishing Contracts}, author={Goller, C.C. and Simon, M. and Vandegrift, M. and Cross, W.}, year={2021}, month={Oct} }
 @inproceedings{whitham_boland_krebs_goller_2021, title={Silver and Gold: Students Learn to Analyze Metagenomes with Kbase}, author={Whitham, J. and Boland, M. and Krebs, R. and Goller, C.}, year={2021}, month={May} }
 @article{samsa_eslinger_kleinschmit_solem_goller_2021, title={Single Cell Insights Into Cancer Transcriptomes: A Five-Part Single-Cell RNAseq Case Study Lesson}, volume={8}, ISSN={2332-6530}, url={http://dx.doi.org/10.24918/cs.2021.26}, DOI={10.24918/cs.2021.26}, abstractNote={There is a growing need for integration of “Big Data” into undergraduate biology curricula. Transcriptomics is one venue to examine biology from an informatics perspective. RNA sequencing has largely replaced the use of microarrays for whole genome gene expression studies. Recently, single cell RNA sequencing (scRNAseq) has unmasked population heterogeneity, offering unprecedented views into the inner workings of individual cells. scRNAseq is transforming our understanding of development, cellular identity, cell function, and disease. As a ‘Big Data,’ scRNAseq can be intimidating for students to conceptualize and analyze, yet it plays an increasingly important role in modern biology. To address these challenges, we created an engaging case study that guides students through an exploration of scRNAseq technologies. Students work in groups to explore external resources, manipulate authentic data and experience how single cell RNA transcriptomics can be used for personalized cancer treatment. This five-part case study is intended for upper-level life science majors and graduate students in genetics, bioinformatics, molecular biology, cell biology, biochemistry, biology, and medical genomics courses. The case modules can be completed sequentially, or individual parts can be separately adapted. The first module can also be used as a stand-alone exercise in an introductory biology course. Students need an intermediate mastery of Microsoft Excel but do not need programming skills. Assessment includes both students’ self-assessment of their learning as answers to previous questions are used to progress through the case study and instructor assessment of final answers. This case provides a practical exercise in the use of high-throughput data analysis to explore the molecular basis of cancer at the level of single cells. Citation: Samsa LA, Eslinger M, Kleinschmit A, Solem A, Goller CC. 2021. Single cell insights into cancer transcriptomes: A five-part single-cell RNAseq case study lesson. CourseSource. https:// doi.org/10.24918/cs.2021.26 Editor: William Morgan, College of Wooster Received: 10/6/2020; Accepted: 3/25/2021; Published: 9/24/2021 Copyright: © 2021 Samsa, Eslinger, Kleinschmit, Solem, and Goller. This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License, which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original author and source are credited. Conflict of Interest and Funding Statement: This case study is part of other cases created as part of the NSF HITS RCN network (NSF award: 1730317). Our goal is to raise awareness of the use of high-throughput approaches and datasets using case study pedagogies. Carlos C. Goller is also supported by an NIH Innovative Program to Enhance Research Training (IPERT) grant “Molecular Biotechnology Laboratory Education Modules (MBLEMs)” 1R25GM130528-01A1. None of the authors has a financial, personal, or professional conflict of interest related to this work. Supporting Materials: Supporting Files S1. scRNAseq – scRNAseq Case Study Parts 1-5 Student version; S2. scRNAseq – scRNAseq Case Study Parts 1-5 Answer key; S3. scRNAseq – Part 1 The patient and diagnosis Student version; S4. scRNAseq – Part 2 The technician and the samples Student version; S5. scRNAseq – Part 3 Data processing Student version; S6. scRNAseq – Part 4 Data visualization Student version; S7. scRNAseq – Part 5 Treatment Student version; S8. scRNAseq – Part 1 The patient and diagnosis Answer key; S9. scRNAseq – Part 2 The technician and the samples Answer key; S10. scRNAseq – Part 3 Data processing Answer key; S11. scRNAseq – Part 4 Data visualization Answer key; S12. scRNAseq – Part 5 Treatment Answer key; S13. scRNAseq – File for Part 2 Sequencing Metadata Student version; S14. scRNAseq – File for Part 2 Sequencing Metadata Instructor version; S15. scRNAseq – File for Part 2 Processing Datasheet Student version; S16. scRNAseq – File for Part 2 Processing Datasheet Instructor version; S17. scRNAseq – File for Part 3 Expression Student version; S18. scRNAseq – File for Part 3 Expression Instructor version; S19. scRNAseq – File for Part 3 Metadata Student version; S20. scRNAseq – File for Part 3 Metadata Instructor version; S21. scRNAseq – File for Part 3 Processing Notes Student version; S22. scRNAseq – File for Part 3 Processing Notes Instructor version; S23. scRNAseq – File from Part 4 Normalized Expression Instructor version; S24. scRNAseq – File from Part 4 Metadata with Clusters Instructor version; S25. scRNAseq – File from Part 4 DE PDX meta vs PDX primaryInstructor Version; and S26. scRNAseq – File for Part 5 Normalized Expression annotated for instructor. *Correspondence to co-corresponding authors: Leigh Ann Samsa: 123 W. Franklin St, Ste 600 B, Chapel Hill, NC 27516. Carlos Goller: Campus Box 7512, 6104 Jordan Hall, 2800 Faucette Drive Raleigh, NC 27695-7512. ccgoller@ncsu.edu CourseSource | www.coursesource.org 2021 | Volume 08 1 Lesson}, journal={CourseSource}, publisher={CourseSource}, author={Samsa, Leigh Ann and Eslinger, Melissa and Kleinschmit, Adam and Solem, Amanda and Goller, Carlos C.}, year={2021} }
 @inproceedings{mckenney_hamon_goller_2021, title={Social annotation builds classroom community and confidence}, author={McKenney, E.A. and Hamon, L. and Goller, C.}, year={2021}, month={Feb} }
 @inproceedings{canglioso_goller_zenon_2021, title={Supporting Open Education Leadership that Promotes Social Justice and Empowers Underserved Students}, author={Canglioso, K. and Goller, C. and Zenon, E.}, year={2021}, month={Aug} }
 @inproceedings{amburn_goller_towsend_whitehurst_2021, title={The Career Educator: Getting Your Dream Job}, author={Amburn, K. and Goller, C. and Towsend, H. and Whitehurst, M.}, year={2021} }
 @inproceedings{calzini_goller_gordy_2021, title={The Ideal Brew: Student-Created Case Studies for Course Improvement}, author={Calzini, M. and Goller, C. and Gordy, C.}, year={2021}, month={May} }
 @article{bixler_eslinger_kleinschmit_gaudier-diaz_sankar_marsteller_goller_robertson_2021, title={Three steps to adapt case studies for synchronous and asynchronous online learning}, volume={22}, ISSN={["1935-7885"]}, DOI={10.1128/jmbe.v22i1.2337}, abstractNote={Pandemic SARS-CoV-2 has ushered in a renewed interest in science along with rapid changes to educational modalities. While technology provides a variety of ways to convey learning resources, the incorporation of alternate modalities can be intimidating for those designing curricula.}, number={1}, journal={Journal of Microbiology and Biology Education}, author={Bixler, A. and Eslinger, M. and Kleinschmit, A.J. and Gaudier-Diaz, M.M. and Sankar, U. and Marsteller, P. and Goller, C.C. and Robertson, S.}, year={2021}, month={Mar}, pages={ev22i1-2337} }
 @inproceedings{goller_2021, title={Using Open Education to Precipitate Gold Nuggets of Wisdom: An Open Pedagogy Model for Crowdsourcing Notes and Citizen Science Research Using Web-Annotation}, author={Goller, C.}, year={2021}, month={Jul} }
 @inproceedings{goller_2021, title={Using Open Educational Resources and Technology to Empower Communities of Undergraduate Scholars}, author={Goller, C.}, year={2021} }
 @inproceedings{tahir_ramilo_lertjanyarak_norman_goller_2021, title={Using WikiEDU to Promote Open Access Science for Sustainable Microbial Biotechnology}, author={Tahir, R. and Ramilo, L. and Lertjanyarak, T. and Norman, D. and Goller, C.}, year={2021}, month={Apr} }
 @article{samsa_andersen_groth_goller_2020, title={A CRISPR/Cas guide RNA design in silico activity}, volume={7}, ISSN={2332-6530}, url={http://dx.doi.org/10.24918/cs.2020.46}, DOI={10.24918/cs.2020.46}, abstractNote={CRISPR biotechnologies inspired by the Clustered Regularly Interspaced Short Palindromic Repeat RNA-guided nuclease adaptive bacterial immune system have revolutionized biology research and become ubiquitous tools for hypothesis and discovery-driven research. Though properly a collection of technologies, today &quot;CRISPR&quot; is synonymous with CRISPR/Cas9 genome targeting. CRISPR is an important interdisciplinary tool and a modern topic to include in the undergraduate biology curriculum. To achieve gene targeting, Cas9 forms a complex with a guideRNA (gRNA). The complex scans double-stranded DNA for a NGG Protospacer Adjacent Motif (PAM) and interrogates complementarity of the adjacent DNA with the 20-nt spacer of the gRNA. If there is a perfect match, Cas9 cleaves the DNA. Resulting repair can yield genome variants: cells repair the damage erroneously to cause indels, and edits can be introduced by leveraging homology-directed repair. In this <em>in silico </em>lab activity, students synthesize and apply their knowledge of gene expression and CRISPR/Cas9 gene-targeting to design an optimized CRISPR/Cas9 gRNA. Students complete a pre-lab quiz then select one of three authentic research scenarios for their lab. The activity guides students through the process of navigating multiple bioinformatics tools, including a genome browser, DNA sequence annotation software, and a browser-based gRNA prediction tool, to complete a guided note sheet and select a suitable gRNA for their chosen scenario. Students report their design and justify their selection in an experiment summary lab report. This interdisciplinary lesson is developed for a special topics CRISPR course and is suitable for students in biochemistry/molecular biology; bioinformatics; cell, plant, animal and developmental biology; microbiology, and especially genetics. <em>Primary image:&nbsp;</em>Schematic overview of the CRISPR/Cas gRNA design in silico lab activity. Image made in &copy;BioRender - biorender.com.}, journal={CourseSource}, publisher={CourseSource}, author={Samsa, Leigh Ann and Andersen, Linnea and Groth, Adam and Goller, Carlos}, year={2020} }
 @article{zambrano_pawlak_daystar_ankeny_goller_venditti_2020, title={Aerobic biodegradation in freshwater and marine environments of textile microfibers generated in clothes laundering: Effects of cellulose and polyester-based microfibers on the microbiome}, volume={151}, ISSN={0025-326X}, url={http://dx.doi.org/10.1016/j.marpolbul.2019.110826}, DOI={10.1016/j.marpolbul.2019.110826}, abstractNote={The aerobic biodegradation of common textiles that shed microfibers during laundering was evaluated under the action of microbes found in the environment, such as lake and seawater, and activated sludge at a low concentration from a wastewater treatment plant (WWTP). Under these conditions, the biodegradation potential was the same in all the experiments: Microcrystalline Cellulose (MCC) > Cotton > Rayon > Polyester/Cotton ≫ Polyester. Nevertheless, for cotton and rayon yarns, >70% biodegradation was achieved with activated sludge at low concentration and lake water, whereas in seawater, about 50% degradation was reached. Polyester did not appreciably degrade. The biodegradation results herein indicate potential not absolutes in nature. The bacterial diversity analyses in the different biodegradation inoculums show that there are distinct bacterial communities related to the assimilation and mineralization of complex carbohydrates that were promoted with the cellulosic MCC, cotton, and rayon samples different than the polyester sample.}, journal={Marine Pollution Bulletin}, publisher={Elsevier BV}, author={Zambrano, Marielis C. and Pawlak, Joel J. and Daystar, Jesse and Ankeny, Mary and Goller, Carlos C. and Venditti, Richard A.}, year={2020}, month={Feb}, pages={110826} }
 @inproceedings{krebs_goller_2020, title={Analyzing the del Gene Cluster for Gold Biomineralization across Delftia spp}, author={Krebs, R. and Goller, C.}, year={2020} }
 @misc{goller_boland_smyth_2020, title={Beyond the Margins: Annotation and Re-Analysis of a Microbiome Study}, author={Goller, C. and Boland, M. and Smyth, D.}, year={2020} }
 @inproceedings{cross_goller_mckenney_tully_2020, title={Building a Sustainable Open Community with the Open Pedagogy Incubator}, author={Cross, W. and Goller, C. and McKenney, E. and Tully, D.}, year={2020}, month={Nov} }
 @article{chen_goller_srougi_2020, title={COVID-19: Where Did You Come From, Where Did You Go? National Center for Case Study Teaching in Science}, url={https://sciencecases.lib.buffalo.edu/collection/detail.html?case_id=1125&id=1125}, journal={National Center for Case Study Teaching in Science}, author={Chen, S and Goller, C and Srougi, M}, year={2020}, month={May} }
 @article{riley_goller_leggett_lewis_ciccone_dunn_2020, title={Catalyzing rapid discovery of gold-precipitating bacterial lineages with university students}, volume={8}, ISSN={2167-8359}, url={http://dx.doi.org/10.7717/peerj.8925}, DOI={10.7717/peerj.8925}, abstractNote={Intriguing and potentially commercially useful microorganisms are found in our surroundings and new tools allow us to learn about their genetic potential and evolutionary history. Engaging students from different disciplines and courses in the search for microbes requires an exciting project with innovative but straightforward procedures and goals. Here we describe an interdisciplinary program to engage students from different courses in the sampling, identification and analysis of the DNA sequences of a unique yet common microbe, Delftia spp. A campus-wide challenge was created to identify the prevalence of this genus, able to precipitate gold, involving introductory level environmental and life science courses, upper-level advanced laboratory modules taken by undergraduate students (juniors and seniors), graduate students and staff from the campus. The number of participants involved allowed for extensive sampling while undergraduate researchers and students in lab-based courses participated in the sample processing and analyses, helping contextualize and solidify their learning of the molecular biology techniques. The results were shared at each step through publicly accessible websites and workshops. This model allows for the rapid discovery of Delftia presence and prevalence and is adaptable to different campuses and experimental questions.}, number={4}, journal={PeerJ}, publisher={PeerJ}, author={Riley, Noah G. and Goller, Carlos C. and Leggett, Zakiya H. and Lewis, Danica M. and Ciccone, Karen and Dunn, Robert R.}, year={2020}, month={Apr}, pages={e8925} }
 @inproceedings{moore_swamy_goller_misra_naganathan_stieben_johnson_wick_2020, title={Does a personalized and long-term teaching mentoring program actually work?}, author={Moore, M.E. and Swamy, U. and Goller, C.C. and Misra, A. and Naganathan, A. and Stieben, M.S. and Johnson, K. and Wick, S.}, year={2020}, month={Jul} }
 @misc{mckenney_goller_2020, title={Does open annotation enhance student performance and sense of belonging?}, author={McKenney, E and Goller, C}, year={2020}, month={Dec} }
 @article{goller_ott_2020, title={Evolution of an 8‐week upper‐division metagenomics course: Diagramming a learning path from observational to quantitative microbiome analysis}, volume={48}, ISBN={1539-3429}, ISSN={1470-8175 1539-3429}, url={http://dx.doi.org/10.1002/bmb.21349}, DOI={10.1002/bmb.21349}, abstractNote={Abstract}, number={4}, journal={Biochemistry and Molecular Biology Education}, publisher={Wiley}, author={Goller, Carlos C. and Ott, Laura E.}, year={2020}, month={Apr}, pages={391–403} }
 @article{moore_naganathan_blumer_goller_misra_raut_swamy_wick_wolyniak_2020, title={Facilitating Long-Term Mentoring To Effectively Implement Active Learning Instruction: Formation of the Promoting Active Learning and Mentoring (PALM) Network
               
                  †}, volume={21}, ISSN={1935-7877 1935-7885}, url={http://dx.doi.org/10.1128/jmbe.v21i3.2203}, DOI={10.1128/jmbe.v21i3.2203}, abstractNote={A large body of data suggests that implementing active learning practices in a STEM classroom contributes to increased success in both achievement of student learning outcomes and retention of students. Despite these findings, significant barriers exist for instructors implementing active learning strategies in their undergraduate classrooms. These barriers can be effectively addressed by providing sustained support to instructors and postdoctoral trainees interested in implementing active learning strategies in their teaching practice. The Promoting Active Learning and Mentoring (PALM) network attains this objective by connecting instructors interested in learning more about active learning (Fellows) with individuals who have extensive expertise related to this practice (mentors). These facilitated connections occur in the form of active mentorship for a year or more, virtual journal clubs, and biannual gatherings of PALM Fellows and mentors. Here, we describe the foundation on which PALM was built and explain how a successful mentorship program can pave the way for educators to adapt and implement evidence-based practices like active learning in a college classroom.}, number={3}, journal={Journal of Microbiology & Biology Education}, publisher={American Society for Microbiology}, author={Moore, Michael E. and Naganathan, Anusha and Blumer, Stephanie Levi and Goller, Carlos C. and Misra, Anjali and Raut, Samiksha A. and Swamy, Uma and Wick, Sue and Wolyniak, Michael J.}, year={2020}, month={Nov} }
 @article{chen_goller_2020, title={Harnessing single‐stranded DNA binding protein to explore protein–protein and protein–DNA interactions}, volume={48}, ISSN={1470-8175 1539-3429}, url={http://dx.doi.org/10.1002/bmb.21324}, DOI={10.1002/bmb.21324}, abstractNote={Abstract}, number={2}, journal={Biochemistry and Molecular Biology Education}, publisher={Wiley}, author={Chen, Stefanie H. and Goller, Carlos C.}, year={2020}, month={Mar}, pages={181–190} }
 @inproceedings{goller_subramanian_lewis_2020, title={Harnessing the power of Nephele to engage students in microbiome analyses}, author={Goller, C. and Subramanian, P. and Lewis, K.}, year={2020} }
 @inproceedings{leggett_spence_goller_2020, title={Implementing Citizen Science into the Classroom to Expose Undergraduate STEM and non-STEM Majors}, author={Leggett, K. and Spence, P. and Goller, C.}, year={2020} }
 @inproceedings{ramilo_goller_2020, title={Increasing the Online Presence of Delftia acidovorans through an Interactive, Accessible, and Engaging Web Hub}, author={Ramilo, L. and Goller, C.}, year={2020}, month={Jul} }
 @article{garcia_chapman_chen_lazear_lentz_williams_dums_goller_robertson_2020, title={Integrating research into a molecular cloning course to address the evolving biotechnology landscape}, volume={7}, ISSN={1470-8175 1539-3429}, url={http://dx.doi.org/10.1002/bmb.21402}, DOI={10.1002/bmb.21402}, abstractNote={Abstract}, journal={Biochemistry and Molecular Biology Education}, publisher={Wiley}, author={Garcia, Christina B. and Chapman, Ian F. and Chen, Stefanie H. and Lazear, Eric and Lentz, Thomas B. and Williams, Christina and Dums, Jacob T. and Goller, Carlos C. and Robertson, Sabrina D.}, year={2020}, month={Jul} }
 @inproceedings{basta_goller_horak_waddell_2020, title={The Why and How of Evidence-Based Teaching: Getting Fellowship Support from the PALM Network}, author={Basta, H. and Goller, C. and Horak, R. and Waddell, E.}, year={2020}, month={Oct} }
 @article{gordy_goller_2020, title={Using Metabolic Engineering to Connect Molecular Biology Techniques to Societal Challenges}, volume={11}, ISSN={1664-302X}, url={http://dx.doi.org/10.3389/fmicb.2020.577004}, DOI={10.3389/fmicb.2020.577004}, abstractNote={Genetically modified organisms (GMOs) are a topic of broad interest and are discussed in classes ranging from introductory biology to bioethics to more advanced methods-focused molecular biology courses. In most cases, GMOs are discussed in the context of introducing a single protein-coding gene to produce a single desired trait in a crop. For example, a commercially available kit allows students to test whether food products contain GMOs by detecting the Bacillus thuringiensis delta-endotoxin gene, which confers resistance to European corn borers. We have developed an 8-week laboratory module for upper-division undergraduates and graduate students that builds upon students’ basic understanding of GMOs to introduce them to the techniques used to sustainably produce commercially valuable products in yeast through metabolic engineering. In this course, students use recombination-based methods to assemble genes encoding entire metabolic pathways in Saccharomyces cerevisiae, perform genetic screens to identify yeast genes that impact metabolite yield, and use error-prone PCR to optimize metabolic pathway function. In parallel to these laboratory-based activities, students engage with the societal impact of these approaches through case studies of products made via yeast metabolic engineering, such as opioids, omega-3 fatty acids, and the Impossible Burger. In this report, we focus on these case studies as well as an individual sustainability project assignment created for this course. This assignment, which spans the 8-week module, asks students to find examples of yeast metabolic engineering that could be used to address current sustainability challenges in their communities. By the end of the course, students synthesize this information to create a case study that could be used to teach concepts related to metabolic engineering and sustainability to their peers. Student approaches to this project have varied from literature reviews, to news searches, to directly contacting and interviewing researchers using novel metabolic engineering approaches. These student-produced projects are used as case studies in future semesters, amplifying student voices and contributing to student ownership. While developed in the context of this course, the sustainability project and case studies are broadly applicable and could be adapted for use in biology or bioethics courses at the undergraduate or graduate level. Through this report, we hope to gain collaborators interested in implementing a version of the course at their institutions, allowing for robust assessment of the impact of the course on a larger group of students.}, journal={Frontiers in Microbiology}, publisher={Frontiers Media SA}, author={Gordy, Claire L. and Goller, Carlos C.}, year={2020}, month={Nov} }
 @article{williams_drew_galindo-gonzalez_robic_dinsdale_morgan_triplett_burnette_donovan_fowlks_et al._2019, title={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}, volume={14}, ISSN={1932-6203}, url={http://dx.doi.org/10.1371/journal.pone.0224288}, DOI={10.1371/journal.pone.0224288}, abstractNote={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.}, number={11}, journal={PLOS ONE}, publisher={Public Library of Science (PLoS)}, author={Williams, Jason J. and Drew, Jennifer C. and Galindo-Gonzalez, Sebastian and Robic, Srebrenka and Dinsdale, Elizabeth and Morgan, William R. and Triplett, Eric W. and Burnette, James M. and Donovan, Samuel S. and Fowlks, Edison R. and et al.}, editor={Bianchi, CesarioEditor}, year={2019}, month={Nov}, pages={e0224288} }
 @inproceedings{haynes_goller_2019, title={Digging deeper in the pile... mortality composting}, author={Haynes, M and Goller, C.}, year={2019}, month={Jul} }
 @inproceedings{goller_chen_robertson_2019, title={HITS: A network to promote high-throughput (HT) approaches through inquiry-based case studies}, url={https://qubeshub.org/publications/797/1}, DOI={10.25334/Q4FD8J}, booktitle={QUBES Educational Resources}, publisher={QUBES Educational Resources}, author={Goller, Carlos and Chen, Stefanie and Robertson, Sabrina}, year={2019} }
 @inproceedings{goller_chen_robertson_2019, title={HITS: Una red de educadores para la creación de casos para el estudio de tecnologías de alto rendimiento}, author={Goller, C.C. and Chen, S. and Robertson, S.}, year={2019} }
 @article{kleinschmit_brink_roof_goller_robertson_2019, title={Sequence Similarity: An inquiry based and "under the hood" approach for incorporating molecular sequence alignment in introductory undergraduate biology courses}, volume={6}, ISSN={2332-6530}, url={http://dx.doi.org/10.24918/cs.2019.5}, DOI={10.24918/cs.2019.5}, abstractNote={Introductory bioinformatics exercises often walk students through the use of computational tools, but often provide little understanding of what a computational tool does &quot;under the hood.&quot; A solid understanding of how a bioinformatics computational algorithm functions, including its limitations, is key for interpreting the output in a biologically relevant context. This introductory bioinformatics exercise integrates an introduction to web-based sequence alignment algorithms with models to facilitate student reflection and appreciation for how computational tools provide similarity output data. The exercise concludes with a set of inquiry-based questions in which students may apply computational tools to solve a real biological problem. In the module, students first define sequence similarity and then investigate how similarity can be quantitatively compared between two similar length proteins using a Blocks Substitution Matrix (BLOSUM) scoring matrix. Students then look for local regions of similarity between a sequence query and subjects within a large database using Basic Local Alignment Search Tool (BLAST). Lastly, students access text-based FASTA-formatted sequence information via National Center for Biotechnology Information (NCBI) databases as they collect sequences for a multiple sequence alignment using Clustal Omega to generate a phylogram and evaluate evolutionary relationships. The combination of diverse, inquiry-based questions, paper models, and web-based computational resources provides students with a solid basis for more advanced bioinformatics topics and an appreciation for the importance of bioinformatics tools across the discipline of biology.}, journal={CourseSource}, publisher={CourseSource}, author={Kleinschmit, Adam J. and Brink, Benita and Roof, Steven and Goller, Carlos Christopher and Robertson, Sabrina}, year={2019} }
 @article{chen_goller_2019, title={Shifting Faculty Approaches to Pedagogy through Structured Teaching Postdoc Experiences}, volume={20}, ISSN={1935-7877 1935-7885}, url={http://dx.doi.org/10.1128/jmbe.v20i2.1789}, DOI={10.1128/jmbe.v20i2.1789}, abstractNote={Many studies confirm the benefit of active learning in STEM teaching. However, many faculty have been slow to adopt such practices, perhaps due to limited time to learn and implement new approaches. One way to address this deficit is to offer structured teaching postdoctoral experiences to trained scientists who want to enter academia. We outline the benefits of providing pedagogical training at the postdoctoral level and present a framework for structuring an impactful teaching postdoc program.}, number={2}, journal={Journal of Microbiology & Biology Education}, publisher={American Society for Microbiology}, author={Chen, Stefanie H. and Goller, Carlos C.}, year={2019}, month={Jun} }
 @article{wilson sayres_hauser_sierk_robic_rosenwald_smith_triplett_williams_dinsdale_morgan_et al._2018, title={Bioinformatics core competencies for undergraduate life sciences education}, volume={13}, ISSN={1932-6203}, url={http://dx.doi.org/10.1371/journal.pone.0196878}, DOI={10.1371/journal.pone.0196878}, abstractNote={Bioinformatics is becoming increasingly central to research in the life sciences. However, despite its importance, bioinformatics skills and knowledge are not well integrated in undergraduate biology education. This curricular gap prevents biology students from harnessing the full potential of their education, limiting their career opportunities and slowing genomic 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 life sciences 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 syllabi, and our collective research and teaching expertise to develop a set of bioinformatics core competencies for undergraduate life sciences students. These core competencies are intended to serve as a guide for institutions as they work to integrate bioinformatics into their life sciences curricula. Significance Statement Bioinformatics, an interdisciplinary field that uses techniques from computer science and mathematics to store, manage, and analyze biological data, is becoming increasingly central to modern biology research. Given the widespread use of bioinformatics and its impacts on societal problem-solving (e.g., in healthcare, agriculture, and natural resources management), there is a growing need for the integration of bioinformatics competencies into undergraduate life sciences education. Here, we present a set of bioinformatics core competencies for undergraduate life scientists developed using the results of a large national survey and the expertise of our working group of bioinformaticians and educators. We also present results from the survey on the importance of bioinformatics skills and the current state of integration of bioinformatics into biology education.}, number={6}, journal={PLOS ONE}, publisher={Public Library of Science (PLoS)}, author={Wilson Sayres, Melissa A. and Hauser, Charles and Sierk, Michael and Robic, Srebrenka and Rosenwald, Anne G. and Smith, Todd M. and Triplett, Eric W. and Williams, Jason J. and Dinsdale, Elizabeth and Morgan, William R. and et al.}, editor={Dalby, Andrew R.Editor}, year={2018}, month={Jun}, pages={e0196878} }
 @misc{goller_riley_2018, title={Delftia’s secrets: gold, mouthwash, and toxins}, author={Goller, C.C. and Riley, Noah}, year={2018} }
 @inproceedings{burd_littleton_goller_2018, title={High-throughput screening and early drug development of potential antimicrobials against Delftia acidovorans}, author={Burd, A. and Littleton, S. and Goller, C.}, year={2018} }
 @misc{goller_2018, title={Inspiring Young Scientists with Genomics Research Opportunities}, author={Goller, C.C.}, year={2018} }
 @misc{goller_2018, title={Outbreaks, metagenomics, and food science}, author={Goller, C.C.}, year={2018} }
 @inproceedings{goller_2018, title={Using the Allen Cell Explorer to introduce high-throughput approaches & image analysis through interrupted case studies}, author={Goller, C.C.}, year={2018} }
 @misc{goller_riley_2018, title={Where do we go to find fascinating microbes? Not very far...}, author={Goller, C.C. and Riley, Noah}, year={2018}, month={Jan} }
 @article{williams_drew_galindo-gonzalez_robic_dinsdale_morgan_triplett_burnette_donovan_elgin_et al._2017, title={Barriers to Integration of Bioinformatics into Undergraduate Life Sciences Education}, volume={10}, url={https://doi.org/10.1101/204420}, DOI={10.1101/204420}, abstractNote={Abstract}, publisher={Cold Spring Harbor Laboratory}, author={Williams, Jason and Drew, Jennifer and Galindo-Gonzalez, Sebastian and Robic, Srebrenka and Dinsdale, Elizabeth and Morgan, William and Triplett, Eric and Burnette, James and Donovan, Sam and Elgin, Sarah and et al.}, year={2017}, month={Oct} }
 @misc{goller_2017, title={From microscopes to personalized medicine: Microbiomes and Cancer Biology}, author={Goller, C.}, year={2017}, month={Feb} }
 @inproceedings{burd_littleton_goller_2017, title={High-throughput screening of oncology drugs as potential antibiotics against Delftia acidovorans}, publisher={North Carolina State University}, author={Burd, A. and Littleton, S. and Goller, C.}, year={2017} }
 @misc{goller_robertson_2017, title={Inspiring Young Deaf Scientists: NC State Research Opportunities. Next-generation sequencing and BIT SURE}, author={Goller, C.C. and Robertson, S.}, year={2017} }
 @inproceedings{burd_littleton_musante_lentz_goller_2017, title={Metagenomic analyses of gutter and amphibian microbiomes from environmental swab samples using high-throughput 16S amplification and sequencing}, author={Burd, A. and Littleton, S. and Musante, M. and Lentz, T. and Goller, C.}, year={2017} }
 @misc{goller_2017, title={Metagenomics in Food Microbiology}, author={Goller, C.C.}, year={2017} }
 @misc{goller_2017, title={Mi viaje como científico}, author={Goller, C.C.}, year={2017}, month={Nov} }
 @article{lentz_ott_robertson_windsor_kelley_wollenberg_dunn_goller_2017, title={Unique Down to Our Microbes—Assessment of an Inquiry-Based Metagenomics Activity †}, volume={18}, ISSN={1935-7877 1935-7885}, url={http://dx.doi.org/10.1128/jmbe.v18i2.1284}, DOI={10.1128/jmbe.v18i2.1284}, abstractNote={Metagenomics is an important method for studying microbial life. However, undergraduate exposure to metagenomics is hindered by associated software, computing demands, and dataset access. In this inquiry-based activity designed for introductory life science majors and nonmajors, students perform an investigation of the bacterial communities inhabiting the human belly button and associated metagenomics data collected through a citizen science project and visualized using an open-access bioinformatics tool. The activity is designed for attainment of the following student learning outcomes: defining terms associated with metagenomics analyses, describing the biological impact of the microbiota on human health, formulating a hypothesis, analyzing and interpreting metagenomics data to compare microbiota, evaluating a specific hypothesis, and synthesizing a conceptual model as to why bacterial populations vary. This activity was implemented in six introductory biology and biotechnology courses across five institutions. Attainment of student learning outcomes was assessed through completion of a quiz and students’ presentations of their findings. In presentations, students demonstrated their ability to develop novel hypotheses and analyze and interpret metagenomic data to evaluate their hypothesis. In quizzes, students demonstrated their ability to define key terms and describe the biological impact of the microbiota on human health. Student learning gains assessment also revealed that students perceived gains for all student learning outcomes. Collectively, our assessment demonstrates achievement of the learning outcomes and supports the utility of this inquiry-based activity to engage undergraduates in the scientific process via analyses of metagenomics datasets and associated exploration of a microbial community that lives on the human body.}, number={2}, journal={Journal of Microbiology & Biology Education}, publisher={American Society for Microbiology}, author={Lentz, Thomas B. and Ott, Laura E. and Robertson, Sabrina D. and Windsor, Sarah C. and Kelley, Joshua B. and Wollenberg, Michael S. and Dunn, Robert R. and Goller, Carlos C.}, year={2017}, month={Aug} }
 @article{stevens_dehority_goller_2017, title={Using QIIME to Interpret Environmental Microbial Communities in an Upper Level Metagenomics Course}, volume={4}, ISSN={2332-6530}, url={http://dx.doi.org/10.24918/cs.2017.3}, DOI={10.24918/cs.2017.3}, abstractNote={Metagenomics is rapidly evolving due to advances in sequencing technologies and bioinformatics, but without proper training to interpret these datasets, student understanding remains limited. Aimed at undergraduate juniors and seniors and graduate students, our eight-week metagenomics course introduces students to different approaches for producing and analyzing metagenomics data to test hypotheses. Here we present our approach for introducing students to the powerful command-line-based sequence analysis pipeline: Quantitative Insights into Microbial Ecology (QIIME, pronounced “chime”). Used extensively in metagenomics research, QIIME performs quality control analysis of raw data from highthroughput sequencers, clusters the data by taxonomic relatedness, and produces a data table of taxonomy by sample. This data table can be further analyzed with QIIME, or used in statistical analysis programs such as R or Primer. In our lesson, students first familiarize themselves with the format of QIIME commands with a worksheet that deconstructs a command to help students understand the input, output, and arguments. Our students have the most trouble with getting a functional version of QIIME running without error, so we have created instructional videos for the setup and running of basic QIIME commands. During one lab period, we lead the class through processing of a sample subset to identify issues and discuss limitations of this approach. Finally, student pairs analyze their own samples and present their findings to the class. This process builds student confidence in their ability to analyze high-throughput sequencing results of metagenomic datasets with the open-source QIIME pipeline. Citation: Stevens, J.L., DeHority, R., and Goller, C.C. 2017. Using QIIME to Interpret Environmental Microbial Communities in an Upper Level Metagenomics Course. CourseSource. https://doi.org/10.24918/cs.2017.3 Editor: Kristin Fox, Union College, Schenectady, NY Received: 06/15/2016; Accepted: 11/28/2017; Published: 03/28/2017 Copyright: © 2017 Stevens, DeHority, and Goller. This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercialShareAlike 4.0 International License, which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original author and source are credited. This manuscript presents original worksheets, videos and information to which authors own the rights. Conflict of Interest and Funding Statement: The North Carolina State University Biotechnology Program provided the resources to offer the course in which this lesson was utilized. None of the authors have a financial, personal, or professional conflict of interest related to this work. Supporting Materials: S1. QIIME activity: Assignment 1 Worksheet, S2. QIIME activity: Assignment 2 Worksheet and key, S3. QIIME activity: Pair presentation grading rubric, S4. QIIME activity. List of tutorial videos and links, S5. QIIME activity: Compressed file with raw data, long step output files, annotated pipeline (link to files), S6. QIIME activity: Worksheet/handout with Helpful basic commands presentation, and S7. QIIME activity: Glossary of commonly used terms in this lesson. *Correspondence to: Jordan Hall 6102, Campus Box 7512, 2800 Faucette Drive, Raleigh, NC 27695. Fax: 919-513-4231. Phone: 919-513-4135 Email: ccgoller@ncsu.edu CourseSource | www.coursesource.org 2017 | Volume 04 1 Lesson}, journal={CourseSource}, publisher={CourseSource}, author={Stevens, Julia L. and DeHority, Riley and Goller, Carlos C.}, year={2017} }
 @article{resnik_smith_chen_goller_2017, title={What is Recklessness in Scientific Research? The Frank Sauer Case}, volume={24}, ISSN={0898-9621 1545-5815}, url={http://dx.doi.org/10.1080/08989621.2017.1397517}, DOI={10.1080/08989621.2017.1397517}, abstractNote={ABSTRACT On May 22, 2017, administrative law Judge Leslie Rogall of the Department of Health and Human Services’ Departmental Appeals Board, Civil Remedies Division, ruled in favor of the Office of Research Integrity (ORI) concerning its decision to charge former University of California at Riverside biochemistry professor Frank Sauer with research misconduct for fabricating or falsifying digital image data included in three papers and seven grant applications submitted to the National Institutes of Health. More specifically, Sauer was deemed responsible for manipulating, reusing, and falsely labeling images of autoradiograms and gels in his research in epigenetics. One month after this decision, ORI announced its final ruling concerning Sauer, which barred him from serving in any advisory capacity to the Public Health Services and required him to retract affected papers. The case raises some interesting and important questions concerning research integrity because it focused on the legal issue of what constitutes recklessness in scientific research.}, number={8}, journal={Accountability in Research}, publisher={Informa UK Limited}, author={Resnik, David B. and Smith, Elise M. and Chen, Stefanie H. and Goller, Carlos}, year={2017}, month={Nov}, pages={497–502} }
 @inproceedings{goller_2016, title={BITS of Metagenomics}, author={Goller, C.C.}, year={2016} }
 @misc{goller_stevens_2016, title={Exploring the Wildlife of Our Homes through Web-based Visualizations}, author={Goller, C.C. and Stevens, J.}, year={2016} }
 @article{arshad_goller_pilla_schoenen_seed_2016, title={Threading the Needle: Small-Molecule Targeting of a Xenobiotic Receptor to Ablate Escherichia coli Polysaccharide Capsule Expression Without Altering Antibiotic Resistance}, volume={213}, ISSN={0022-1899 1537-6613}, url={http://dx.doi.org/10.1093/infdis/jiv584}, DOI={10.1093/infdis/jiv584}, abstractNote={BACKGROUND
Uropathogenic Escherichia coli (UPEC), a leading cause of urinary tract and invasive infections worldwide, is rapidly acquiring multidrug resistance, hastening the need for selective new anti-infective agents. Here we demonstrate the molecular target of DU011, our previously discovered potent, nontoxic, small-molecule inhibitor of UPEC polysaccharide capsule biogenesis and virulence.


METHODS
Real-time polymerase chain reaction analysis and a target-overexpression drug-suppressor screen were used to localize the putative inhibitor target. A thermal shift assay quantified interactions between the target protein and the inhibitor, and a novel DNase protection assay measured chemical inhibition of protein-DNA interactions. Virulence of a regulatory target mutant was assessed in a murine sepsis model.


RESULTS
MprA, a MarR family transcriptional repressor, was identified as the putative target of the DU011 inhibitor. Thermal shift measurements indicated the formation of a stable DU011-MprA complex, and DU011 abrogated MprA binding to its DNA promoter site. Knockout of mprA had effects similar to that of DU011 treatment of wild-type bacteria: a loss of encapsulation and complete attenuation in a murine sepsis model, without any negative change in antibiotic resistance.


CONCLUSIONS
MprA regulates UPEC polysaccharide encapsulation, is essential for UPEC virulence, and can be targeted without inducing antibiotic resistance.}, number={8}, journal={Journal of Infectious Diseases}, publisher={Oxford University Press (OUP)}, author={Arshad, Mehreen and Goller, Carlos C. and Pilla, Danielle and Schoenen, Frank J. and Seed, Patrick C.}, year={2016}, month={Apr}, pages={1330–1339} }
 @article{goller_2014, title={A Modern Twist on the Beaumont and St. Martin Case: Encouraging Analysis and Discussion in the Bioethics Classroom with Reflective Writing and Concept Mapping †}, volume={15}, ISSN={1935-7877 1935-7885}, url={http://dx.doi.org/10.1128/jmbe.v15i2.771}, DOI={10.1128/jmbe.v15i2.771}, abstractNote={Historical ethical dilemmas are a valuable tool in bioethics courses. However, garnering student interest in reading and discussing the assigned cases in the classroom can be challenging. In an effort to actively engage undergraduate and graduate students in an Ethical Issues in Biotechnology course, an activity was developed to encourage reflection on a classical ethical dilemma between a patient, St. Martin, and his employer/caretaker, Beaumont. Two different texts were used to analyze the ethical ramifications of this relationship: a chapter in a popular press book and a short perspective in a medical journal. Participants read the book chapter for homework and discussed it in class. This easy read highlights the fundamental ethical issues in the relationship between two men. Students were then provided with a second text focusing on the scientific accomplishments achieved through Beaumont’s experimentation on St. Martin. A structured worksheet prompted participants to reflect on their feelings after reading each text and create a concept map depicting the dilemma. Student-generated concept maps and written reflections indicate participants were able to list the ethical issues, analyze the situation, and evaluate the information provided. This activity not only encouraged higher-level thinking and reflection, it also mirrored the course’s structured approach of using concept mapping and reflection to dissect ethical dilemmas.}, number={2}, journal={Journal of Microbiology & Biology Education}, publisher={American Society for Microbiology}, author={Goller, Carlos C.}, year={2014}, month={Dec}, pages={229–231} }
 @inproceedings{goller_2014, title={Analyzing big data with simple flowcharts and questioning techniques}, author={Goller, C.}, year={2014} }
 @inproceedings{mcneill_defoor_goller_ott_2014, title={Delftia acidovorans induces a proinflammatory response in THP-1 monocyes}, author={McNeill, R. and DeFoor, W. and Goller, C. and Ott, L.}, year={2014} }
 @misc{goller_2014, title={Golden nuggets: Research and discoveries from the teaching lab}, author={Goller, C.C.}, year={2014}, month={Oct} }
 @article{goller_arshad_noah_ananthan_evans_nebane_rasmussen_sosa_tower_white_et al._2014, title={Lifting the Mask: Identification of New Small Molecule Inhibitors of Uropathogenic Escherichia coli Group 2 Capsule Biogenesis}, volume={9}, ISSN={1932-6203}, url={http://dx.doi.org/10.1371/journal.pone.0096054}, DOI={10.1371/journal.pone.0096054}, abstractNote={Uropathogenic Escherichia coli (UPEC) is the leading cause of community-acquired urinary tract infections (UTIs), with over 100 million UTIs occurring annually throughout the world. Increasing antimicrobial resistance among UPEC limits ambulatory care options, delays effective treatment, and may increase overall morbidity and mortality from complications such as urosepsis. The polysaccharide capsules of UPEC are an attractive target a therapeutic, based on their importance in defense against the host immune responses; however, the large number of antigenic types has limited their incorporation into vaccine development. The objective of this study was to identify small-molecule inhibitors of UPEC capsule biogenesis. A large-scale screening effort entailing 338,740 compounds was conducted in a cell-based, phenotypic screen for inhibition of capsule biogenesis in UPEC. The primary and concentration-response assays yielded 29 putative inhibitors of capsule biogenesis, of which 6 were selected for further studies. Secondary confirmatory assays identified two highly active agents, named DU003 and DU011, with 50% inhibitory concentrations of 1.0 µM and 0.69 µM, respectively. Confirmatory assays for capsular antigen and biochemical measurement of capsular sugars verified the inhibitory action of both compounds and demonstrated minimal toxicity and off-target effects. Serum sensitivity assays demonstrated that both compounds produced significant bacterial death upon exposure to active human serum. DU011 administration in mice provided near complete protection against a lethal systemic infection with the prototypic UPEC K1 isolate UTI89. This work has provided a conceptually new class of molecules to combat UPEC infection, and future studies will establish the molecular basis for their action along with efficacy in UTI and other UPEC infections.}, number={7}, journal={PLoS ONE}, publisher={Public Library of Science (PLoS)}, author={Goller, Carlos C. and Arshad, Mehreen and Noah, James W. and Ananthan, Subramaniam and Evans, Carrie W. and Nebane, N. Miranda and Rasmussen, Lynn and Sosa, Melinda and Tower, Nichole A. and White, E. Lucile and et al.}, editor={Skurnik, MikaelEditor}, year={2014}, month={Jul}, pages={e96054} }
 @misc{goller_2014, title={Metagenomics}, author={Goller, C.C.}, year={2014}, month={Feb} }
 @misc{goller_2014, title={Moving DNA around: Introduction to Biotechnology}, author={Goller, C.C.}, year={2014}, month={Apr} }
 @inproceedings{de foor_goller_2014, title={Multiplex PCR as a Tool for the Detection of Delftia acidovorans}, author={De Foor, W and Goller, C}, year={2014} }
 @inproceedings{iyer_goller_2014, title={PCR detection of Delftia acidovorans in Samples from Sinks}, publisher={NCSU}, author={Iyer, A and Goller, C}, year={2014} }
 @misc{goller_2014, title={The wildlife around us and the fascinating questions we can ask using biotechnology techniques}, author={Goller, C.C.}, year={2014}, month={Oct} }
 @misc{goller_2014, title={What scientists and engineers write}, author={Goller, C.C.}, year={2014}, month={Feb} }
 @misc{goller_2014, title={Writing in the sciences and translations}, author={Goller, C.C.}, year={2014}, month={Feb} }
 @article{3-(2,6-difluorobenzamido)-5-(4-ethoxyphenyl) thiophene-2-carboxylic acid inhibits e.coli ut189 bacterial capsule biogenesis_2013, url={https://www.ncbi.nlm.nih.gov/books/NBK143534}, year={2013}, month={Jun} }
 @misc{goller_2013, title={Biofilms and Bioremediation}, author={Goller, C.C.}, year={2013} }
 @article{n-(pyridin-4-yl)benzo[d]thiazole-6-carboxamide inhibits e. coli ut189 bacterial capsule biogenesis_2013, url={https://www.ncbi.nlm.nih.gov/books/NBK148500}, year={2013}, month={Jul} }
 @inproceedings{zinter_goller_2013, title={Uncovering the biodiversity in Lake Raleigh utilizing bioinformatics and deep sequencing}, author={Zinter, M and Goller, C}, year={2013} }
 @misc{goller_2013, title={What I write}, author={Goller, C.C.}, year={2013}, month={Sep} }
 @misc{goller_2013, title={What/how do scientists and engineers write to learn?}, author={Goller, C.}, year={2013} }
 @book{noah_ananthan_evans_nebane_rasmussen_sosa_tower_white_seed_goller_et al._2012, place={Bethesda, MD}, title={3-(2,6-difluorobenzamido)-5-(4-ethoxyphenyl) thiophene-2-carboxylic acid inhibits E.coli UT189 bacterial capsule biogenesis}, url={https://www.ncbi.nlm.nih.gov/books/NBK143534/}, journal={Probe Reports from the NIH Molecular Libraries Program}, institution={National Center for Biotechnology Information}, author={Noah, J.W. and Ananthan, S. and Evans, C.W. and Nebane, N.M. and Rasmussen, L. and Sosa, M. and Tower, N.A. and White, E.L. and Seed, P. and Goller, C. and et al.}, year={2012}, month={Apr} }
 @article{goller_seed_2012, title={Coming of AGE}, volume={3}, ISSN={2150-5594 2150-5608}, url={http://dx.doi.org/10.4161/viru.3.1.19087}, DOI={10.4161/viru.3.1.19087}, abstractNote={Live attenuated vaccine strains for bacterial pathogens are conventionally constructed by inactivating genes important for virulence or metabolism to render the organism less virulent. Ideally, these strains follow a natural route of infection, yet elicit an immune response without causing disease. In particular, live attenuated vaccines often have the advantage of generating cellular immune responses that killed organisms and purified antigens fail to stimulate. Importantly, a fine balance between attenuation and sufficient persistence in the host must be achieved in order to produce a protective and durable immune response. Unfortunately, the reality is that, in most cases, the complete repertoire of factors responsible for virulence is unknown or not well understood, hindering the creation of attenuated vaccine strains. Thus, the generation of live attenuated vaccines would be greatly facilitated by novel, portable approaches for attenuating Gram-negative pathogens.}, number={1}, journal={Virulence}, publisher={Informa UK Limited}, author={Goller, Carlos C. and Seed, Patrick C.}, year={2012}, month={Jan}, pages={12–14} }
 @article{noah_ananthan_evans_nebane_rasmussen_sosa_tower_white_seed_goller_et al._2012, place={Bethesda, MD}, title={N-(pyridin-4-yl)benzo[d]thiazole-6-carboxamide inhibits E. coli UT189 bacterial capsule biogenesis}, url={https://www.ncbi.nlm.nih.gov/books/NBK148500/}, journal={Probe Reports from the NIH Molecular Libraries Program}, publisher={National Center for Biotechnology Information}, author={Noah, J.W. and Ananthan, S. and Evans, C.W. and Nebane, N.M. and Rasmussen, L. and Sosa, M. and Tower, N.A. and White, E.L. and Seed, P. and Goller, C. and et al.}, year={2012}, month={Dec} }
 @article{goller_seed_2010, title={High-Throughput Identification of Chemical Inhibitors of E. coli Group 2 Capsule Biogenesis as Anti-Virulence Agents}, volume={5}, ISSN={1932-6203}, url={http://dx.doi.org/10.1371/journal.pone.0011642}, DOI={10.1371/journal.pone.0011642}, abstractNote={Rising antibiotic resistance among Escherichia coli, the leading cause of urinary tract infections (UTIs), has placed a new focus on molecular pathogenesis studies, aiming to identify new therapeutic targets. Anti-virulence agents are attractive as chemotherapeutics to attenuate an organism during disease but not necessarily during benign commensalism, thus decreasing the stress on beneficial microbial communities and lessening the emergence of resistance. We and others have demonstrated that the K antigen capsule of E. coli is a preeminent virulence determinant during UTI and more invasive diseases. Components of assembly and export are highly conserved among the major K antigen capsular types associated with UTI-causing E. coli and are distinct from the capsule biogenesis machinery of many commensal E. coli, making these attractive therapeutic targets. We conducted a screen for anti-capsular small molecules and identified an agent designated “C7” that blocks the production of K1 and K5 capsules, unrelated polysaccharide types among the Group 2–3 capsules. Herein lies proof-of-concept that this screen may be implemented with larger chemical libraries to identify second-generation small-molecule inhibitors of capsule biogenesis. These inhibitors will lead to a better understanding of capsule biogenesis and may represent a new class of therapeutics.}, number={7}, journal={PLoS ONE}, publisher={Public Library of Science (PLoS)}, author={Goller, Carlos C. and Seed, Patrick C.}, editor={Ojcius, David M.Editor}, year={2010}, month={Jul}, pages={e11642} }
 @article{anderson_goller_justice_hultgren_seed_2010, title={Polysaccharide Capsule and Sialic Acid-Mediated Regulation Promote Biofilm-Like Intracellular Bacterial Communities during Cystitis}, volume={78}, ISSN={0019-9567 1098-5522}, url={http://dx.doi.org/10.1128/IAI.00925-09}, DOI={10.1128/IAI.00925-09}, abstractNote={ABSTRACT}, number={3}, journal={Infection and Immunity}, publisher={American Society for Microbiology}, author={Anderson, Gregory G. and Goller, Carlos C. and Justice, Sheryl and Hultgren, Scott J. and Seed, Patrick C.}, year={2010}, month={Jan}, pages={963–975} }
 @article{goller_seed_2010, title={Revisiting the Escherichia coli polysaccharide capsule as a virulence factor during urinary tract infection: Contribution to intracellular biofilm development}, volume={1}, ISSN={2150-5594 2150-5608}, url={http://dx.doi.org/10.4161/viru.1.4.12388}, DOI={10.4161/viru.1.4.12388}, abstractNote={The treatment of urinary tract infections (UTIs) is becoming increasingly challenging as uropathogenic Escherichia coli (UPEC) becomes more resistant to the most widely prescribed oral antibiotics. The treatment of UTIs may also be complicated by the inherent lifestyle of UPEC in the urinary tract, revealed in recent studies demonstrating bacterial invasion into bladder epithelial cells, the formation of intracellular bacterial communities (IBCs; biofilm-like colonies in the host cell cytosol), and chronic intracellular persistence with subversion of normal immune surveillance. Identifying key targets in the pathogenesis of UTIs, including IBC formation, will be crucial to replenish the arsenal of treatments for UTIs. Focused on elucidating bacterial components that underpin the development of IBCs, Anderson et al. recently demonstrated a novel role for the K capsule polysaccharide in IBC formation. Without K capsule, intracellular UPEC failed to undergo normal IBC formation, the intracellular bacteria failed to preclude neutrophil infiltration, and UPEC did not undergo serial cycles of intracellular proliferation, resulting in attenuation of the infection. This study also demonstrated an interconnection between sialic acid homeostasis and IBC formation, demonstrating a unique role for this amino sugar in biofilm formation. This study provides evidence for an expanded role for K capsule in the intracellular and extracellular pathogenesis of UTI, and provides additional rationale for the development of small molecule inhibitors of capsule biogenesis as anti-virulence therapeutics.}, number={4}, journal={Virulence}, publisher={Informa UK Limited}, author={Goller, Carlos C. and Seed, Patrick C.}, year={2010}, month={Jul}, pages={333–337} }
 @inproceedings{goller_prest_seed_2010, title={Role of the sialic acid regulator NanR of Uropathogenic Escherichia coli in urinary tract infections}, author={Goller, C. and Prest, T. and Seed, P.}, year={2010} }
 @inproceedings{goller_seed_2009, title={Inhibitors of Bacterial Capsules as Novel Therapeutic for Urinary Tract Infections}, author={Goller, C and Seed, P}, year={2009} }
 @article{environmental influences on biofilm development._2008, url={https://doi.org/10.1007/978-3-540-75418-3_3}, DOI={10.1007/978-3-540-75418-3_3}, abstractNote={Bacterial biofilms are found under diverse environmental conditions, from sheltered and specialized environments found within mammalian hosts to the extremes of biological survival. The process of forming a biofilm and the eventual return of cells to the planktonic state involve the coordination of vast amounts of genetic information. Nevertheless, the prevailing evidence suggests that the overall progression of this cycle within a given species or strain of bacteria responds to environmental conditions via a finite number of key regulatory factors and pathways, which affect enzymatic and structural elements that are needed for biofilm formation and dispersal. Among the conditions that affect biofilm development are temperature, pH, O 2levels, hydrodynamics, osmolarity, the presence of specific ions, nutrients, and factors derived from the biotic environment. The integration of these influences ultimately determines the pattern of behavior of a given bacterium with respect to biofilm development. This chapter will present examples of how environmental conditions affect biofilm development, most of which come from studies of species that have mammalian hosts.}, journal={Current topics in microbiology and immunology}, year={2008}, month={Jan} }
 @inproceedings{goller_pannuri_romeo_itoh_suzuki_2008, title={PGA Accumulation and Biofilm Formation in Escherichia coli: Modulation by c-di-GMP}, author={Goller, C. and Pannuri, A. and Romeo, T. and Itoh, Y. and Suzuki, K.}, year={2008} }
 @article{itoh_rice_goller_pannuri_taylor_meisner_beveridge_preston_romeo_2008, title={Roles of pgaABCD Genes in Synthesis, Modification, and Export of the Escherichia coli Biofilm Adhesin Poly-β-1,6-N-Acetyl-d-Glucosamine}, volume={190}, ISSN={0021-9193 1098-5530}, url={http://dx.doi.org/10.1128/JB.01920-07}, DOI={10.1128/JB.01920-07}, abstractNote={ABSTRACT}, number={10}, journal={Journal of Bacteriology}, publisher={American Society for Microbiology}, author={Itoh, Yoshikane and Rice, John D. and Goller, Carlos and Pannuri, Archana and Taylor, Jeannette and Meisner, Jeffrey and Beveridge, Terry J. and Preston, James F., III and Romeo, Tony}, year={2008}, month={Mar}, pages={3670–3680} }
 @article{goller_wang_itoh_romeo_2006, title={The Cation-Responsive Protein NhaR of Escherichia coli Activates pgaABCD Transcription, Required for Production of the Biofilm Adhesin Poly-β-1,6-N-Acetyl-d-Glucosamine}, volume={188}, ISSN={0021-9193 1098-5530}, url={http://dx.doi.org/10.1128/JB.01106-06}, DOI={10.1128/JB.01106-06}, abstractNote={ABSTRACT}, number={23}, journal={Journal of Bacteriology}, publisher={American Society for Microbiology}, author={Goller, Carlos and Wang, Xin and Itoh, Yoshikane and Romeo, Tony}, year={2006}, month={Sep}, pages={8022–8032} }
 @article{brown_goller_peters_olean_vernon‐gerstenfeld_gerstenfeld_2002, title={Economics of cage culture in Puerto Rico}, volume={6}, ISSN={1365-7305 1551-8663}, url={http://dx.doi.org/10.1080/13657300209380325}, DOI={10.1080/13657300209380325}, abstractNote={Abstract Puerto Rico has been faced with a decline of fish stocks similar to other parts of the world. Offshore cage aquaculture might be an answer to this problem although there are many unanswered questions. This paper describes a project in Puerto Rico that assessed the economics of offshore cage culture for aquaculture. The first cage was placed in the water in February 2002 with a second one to follow shortly thereafter.}, number={5-6}, journal={Aquaculture Economics & Management}, publisher={Informa UK Limited}, author={Brown, Jason G. and Goller, Carlos C. and Peters, Tara L. and Olean, Adam and Vernon‐Gerstenfeld, Susan and Gerstenfeld, Arthur}, year={2002}, month={Jan}, pages={363–372} }