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cv_KLS.bib
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cv_KLS.bib
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@article{armour_machine_2023,
title = {Machine Learning Classification by Fitting Amplicon Sequences to Existing {{OTUs}}},
author = {Armour, Courtney R. and Sovacool, Kelly L. and Close, William L. and Top{\c c}uo{\u g}lu, Beg{\"u}m D. and Wiens, Jenna and Schloss, Patrick D.},
year = {2023},
month = {aug},
journal = {mSphere},
volume = {0},
number = {0},
pages = {e00336-23},
publisher = {{American Society for Microbiology}},
doi = {10.1128/msphere.00336-23},
url = {https://journals.asm.org/doi/10.1128/msphere.00336-23},
urldate = {2023-08-26}
}
@article{barron_intestinal_2022,
title = {Intestinal {{Inflammation Reversibly Alters}} the {{Microbiota}} to {{Drive Susceptibility}} to {{Clostridioides}} Difficile {{Colonization}} in a {{Mouse Model}} of {{Colitis}}},
author = {Barron, Madeline R. and Sovacool, Kelly L. and {Abernathy-Close}, Lisa and Vendrov, Kimberly C. and Standke, Alexandra K. and Bergin, Ingrid L. and Schloss, Patrick D. and Young, Vincent B.},
year = {2022},
month = {jul},
journal = {mBio},
volume = {0},
number = {0},
pages = {e01904-22},
publisher = {American Society for Microbiology},
doi = {10.1128/mbio.01904-22},
github = {https://github.com/SchlossLab/Barron_IBD-CDI_2022},
}
@article{duda_teaching_2021,
title = {Teaching {{Python}} for {{Data Science}}: {{Collaborative}} Development of a Modular \& Interactive Curriculum},
shorttitle = {Teaching {{Python}} for {{Data Science}}},
author = {*Duda, Marlena and *Sovacool, Kelly L. and Farzaneh, Negar and Nguyen, Vy Kim and Haynes, Sarah E. and Falk, Hayley and Furman, Katherine L. and Walker, Logan A. and Diao, Rucheng and Oneka, Morgan and Drotos, Audrey C. and Woloshin, Alana and Dotson, Gabrielle A. and Kriebel, April and Meng, Lucy and Thiede, Stephanie N. and Lapp, Zena and Wolford, Brooke N.},
year = {2021},
month = {dec},
journal = {JOSE},
volume = {4},
number = {46},
pages = {138},
issn = {2577-3569},
doi = {10.21105/jose.00138},
copyright = {All rights reserved},
github = {https://github.com/GWC-DCMB/curriculum-notebooks},
langid = {english},
file = {/Users/kelly/Documents/Zotero/storage/J25BYSE9/Duda_et_al_2021_Journal_of_Open_Source_Education.pdf}
}
@article{everson_geography_2021,
title = {Geography Is More Important than Life History in the Recent Diversification of the Tiger Salamander Complex},
author = {Everson, Kathryn M. and Gray, Levi N. and Jones, Angela G. and Lawrence, Nicolette M. and Foley, Mary E. and Sovacool, Kelly L. and Kratovil, Justin D. and Hotaling, Scott and Hime, Paul M. and Storfer, Andrew and {Parra-Olea}, Gabriela and {Percino-Daniel}, Ruth and {Aguilar-Miguel}, X. and O'Neill, Eric M. and Zambrano, Luis and Shaffer, H. Bradley and Weisrock, David W.},
year = {2021},
month = {apr},
journal = {PNAS},
volume = {118},
number = {17},
publisher = {{National Academy of Sciences}},
issn = {0027-8424, 1091-6490},
doi = {10.1073/pnas.2014719118},
github = {https://github.com/kelly-sovacool/tiger_salamander_project},
abstract = {The North American tiger salamander species complex, including its best-known species, the Mexican axolotl, has long been a source of biological fascination. The complex exhibits a wide range of variation in developmental life history strategies, including populations and individuals that undergo metamorphosis; those able to forego metamorphosis and retain a larval, aquatic lifestyle (i.e., paedomorphosis); and those that do both. The evolution of a paedomorphic life history state is thought to lead to increased population genetic differentiation and ultimately reproductive isolation and speciation, but the degree to which it has shaped population- and species-level divergence is poorly understood. Using a large multilocus dataset from hundreds of samples across North America, we identified genetic clusters across the geographic range of the tiger salamander complex. These clusters often contain a mixture of paedomorphic and metamorphic taxa, indicating that geographic isolation has played a larger role in lineage divergence than paedomorphosis in this system. This conclusion is bolstered by geography-informed analyses indicating no effect of life history strategy on population genetic differentiation and by model-based population genetic analyses demonstrating gene flow between adjacent metamorphic and paedomorphic populations. This fine-scale genetic perspective on life history variation establishes a framework for understanding how plasticity, local adaptation, and gene flow contribute to lineage divergence. Many members of the tiger salamander complex are endangered, and the Mexican axolotl is an important model system in regenerative and biomedical research. Our results chart a course for more informed use of these taxa in experimental, ecological, and conservation research.},
chapter = {Biological Sciences},
copyright = {\textcopyright{} 2021 . https://www.pnas.org/site/aboutpnas/licenses.xhtmlPublished under the PNAS license.},
langid = {english},
pmid = {33888580},
keywords = {Ambystoma,life history,phylogenetics,population genomics,salamanders},
file = {/Users/kelly/Documents/Zotero/storage/EBCITZKY/Everson_et_al_2021_PNAS.pdf}
}
@inproceedings{goodin_processing_2016,
title = {Processing {{RNA-Seq}} Data of Plants Infected with Coffee Ringspot Virus},
booktitle = {Proceedings of the 15th {{Annual UT-KBRIN Bioinformatics Summit}} 2016: {{Cadiz}}, {{KY}}, {{USA}}. 8-10 {{April}} 2016},
author = {Goodin, Michael M. and Farman, Mark and Inocencio, Harrison and Jang, Chanyong and Jaromczyk, Jerzy W. and Moore, Neil and Sovacool, Kelly L.},
year = {2016},
month = {aug},
journal = {BMC Bioinform},
publisher = {{BMC Bioinformatics}},
doi = {10.1186/s12859-016-1154-y},
copyright = {All rights reserved}
}
@article{hagan_ten_2020,
title = {Ten Simple Rules to Increase Computational Skills among Biologists with {{Code Clubs}}},
author = {Hagan, Ada K. and Lesniak, Nicholas A. and Balunas, Marcy J. and Bishop, Lucas and Close, William L. and Doherty, Matthew D. and Elmore, Amanda G. and Flynn, Kaitlin J. and Hannigan, Geoffrey D. and Koumpouras, Charlie C. and Jenior, Matthew L. and Kozik, Ariangela J. and McBride, Kathryn and Rifkin, Samara B. and Stough, Joshua M. A. and Sovacool, Kelly L. and Sze, Marc A. and Tomkovich, Sarah and Topcuoglu, Begum D. and Schloss, Patrick D.},
year = {2020},
month = {aug},
journal = {PLoS Comput Biol},
volume = {16},
number = {8},
pages = {e1008119},
publisher = {{Public Library of Science}},
issn = {1553-7358},
doi = {10.1371/journal.pcbi.1008119},
copyright = {All rights reserved},
github = {https://github.com/SchlossLab/Hagan\_CodeClub\_PLOSComp},
langid = {english},
keywords = {Biologists,Learning,Programming languages,Reproducibility,RNA sequencing,Scientists,Syntax,Workshops},
file = {/Users/kelly/Documents/Zotero/storage/MRMMJ35S/Hagan_et_al_2020_PLOS_Computational_Biology.pdf}
}
@article{lapp_developing_2022,
title = {Developing and Deploying an Integrated Workshop Curriculum Teaching Computational Skills for Reproducible Research},
author = {*Lapp, Zena and *Sovacool, Kelly L. and Lesniak, Nick and King, Dana and Barnier, Catherine and Flickinger, Matthew and Kr{\"u}ger, Jule and Armour, Courtney R. and Lapp, Maya M. and Tallant, Jason and Diao, Rucheng and Oneka, Morgan and Tomkovich, Sarah and Anderson, Jacqueline Moltzau and Lucas, Sarah K. and Schloss, Patrick D.},
year = {2022},
month = {jan},
journal = {JOSE},
doi = {10.21105/jose.00144},
abstract = {Inspired by well-established material and pedagogy provided by The Carpentries (Wilson, 2016), we developed a two-day workshop curriculum that teaches introductory R programming for managing, analyzing, plotting and reporting data using packages from the tidyverse (Wickham et al., 2019), the Unix shell, version control with git, and GitHub. While the official Software Carpentry curriculum is comprehensive, we found that it contains too much content for a two-day workshop. We also felt that the independent nature of the lessons left learners confused about how to integrate the newly acquired programming skills in their own work. Thus, we developed a new curriculum that aims to teach novices how to implement reproducible research principles in their own data analysis. The curriculum integrates live coding lessons with individual-level and group-based practice exercises, and also serves as a succinct resource that learners can reference both during and after the workshop. Moreover, it lowers the entry barrier for new instructors as they do not have to develop their own teaching materials or sift through extensive content. We developed this curriculum during a two-day sprint, successfully used it to host a two-day virtual workshop with almost 40 participants, and updated the material based on instructor and learner feedback. We hope that our new curriculum will prove useful to future instructors interested in teaching workshops with similar learning objectives.},
copyright = {All rights reserved},
github = {https://github.com/UMCarpentries/intro-curriculum-r/},
langid = {english},
file = {/Users/kelly/Documents/Zotero/storage/V6SXU6IH/Lapp et al. - 2022 - Developing and deploying an integrated workshop cu.pdf}
}
@article{sovacool_optifit_2022,
ids = {sovacool_optifit_2021},
title = {{{OptiFit}}: An {{Improved Method}} for {{Fitting Amplicon Sequences}} to {{Existing OTUs}}},
shorttitle = {{{OptiFit}}},
author = {Sovacool, Kelly L. and Westcott, Sarah L. and Mumphrey, M. Brodie and Dotson, Gabrielle A. and Schloss, Patrick D.},
year = {2022},
month = {feb},
journal = {mSphere},
publisher = {{American Society for Microbiology}},
doi = {10.1128/msphere.00916-21},
abstract = {Advancements in DNA sequencing technology have allowed researchers to affordably generate millions of sequence reads from microorganisms in diverse environments. Efficient and robust software tools are needed to assign microbial sequences into taxonomic ...},
copyright = {Copyright \textcopyright{} 2022 Sovacool et al.},
github = {https://github.com/SchlossLab/Sovacool\_OptiFit\_mSphere\_2022},
langid = {english},
annotation = {1752 N St., N.W., Washington, DC},
file = {/Users/kelly/Documents/Zotero/storage/J3QF7UQW/Sovacool_et_al_2022_mSphere.pdf}
}
@article{topcuoglu_mikropml_2021,
title = {Mikropml: {{User-Friendly R Package}} for {{Supervised Machine Learning Pipelines}}},
shorttitle = {Mikropml},
author = {*Top{\c c}uo{\u g}lu, Beg{\"u}m D. and *Lapp, Zena and *Sovacool, Kelly L. and Snitkin, Evan and Wiens, Jenna and Schloss, Patrick D.},
year = {2021},
month = {may},
journal = {JOSS},
volume = {6},
number = {61},
pages = {3073},
issn = {2475-9066},
doi = {10.21105/joss.03073},
copyright = {All rights reserved},
github = {https://github.com/SchlossLab/mikropml},
langid = {english},
file = {/Users/kelly/Documents/Zotero/storage/WZEX2JH3/Topçuoğlu_et_al_2021_JOSS.pdf}
}