Invited Talks and Presentations

Talking to the Public

There's only so many times you can be asked why we care about salamanders before you respond with a full color, full hour rant. This was given within my department as well as by invite at the local zoo.

Salamanders

Advertising Services

Running a support center requires telling people about your services. While working for NCGAS, I gave more than thirty presentations in four years, such as this one talking about our de novo transcriptome analysis support.

Research Support

Sharing Research

Traditional academia still demands research presentations and posters. Below is a poster from a collaboration I presented at a genomics conference.

Chernobyl Birds

Invite talks are indicated with an *. Guest lectures are largely omitted for space. Some links include the abstract, others include PDFs of posters.

Doak, T.G., Sanders, S.A., Ganote, C., Papudeshi, B., Fischer, J., & Hancock, D.Y. (2020). National Center for Genome Analysis Support (NCGAS): Genomics and other science in the NSF-funded Jetstream Cloud [Conference Presentation]. Plant and Animal Genome 2020, San Diego, California. Available at http://hdl.handle.net/2022/25301.

Foran, E., Underwood, T.A., Snapp-Childs, W., & Sanders. S. (2020). Automatic capture and classification of frog calls [Poster]. Supercomputing 2020, online. https://hdl.handle.net/2022/25760

Papudeshi, B., Leffler, H., Ganapaneni, S., Sanders, S., Ganote, C., & Doak, T.G. (2020). Mining Microbial Genomes from Datasets on the Sequence Read Archive [Poster]. Plant and Animal Genome 2020, San Diego, California. Available at http://hdl.handle.net/2022/25300.

Cai, J. X., Weathers, J. G., Leffler, H., Ganapaneni, S., Papudeshi, B., Sanders, S., & Doak, T. G. (2019). Navigating the Sequence Read Archive to identify crAssphage, an ubiquitous inhabitant of the human microbiome [Poster]. Holland Summer Science Research Program Poster Session, Bloomington, IN.

Foran, E., Anderson, J., Slayton, T., Guido, E., Doak, T.G., & Sanders, S. (2019). Developing a workflow for bioacoustic recording devices and frog call analysis within Jetstream [Poster]. Center of Excellence for Women & Technology, Bloomington, IN.

Ganapaneni, S., Leffler, H., Papudeshi, B., Sanders, S., & Doak, T.G. (2019). Coupling metagenomics with high-performance computing to mine the Sequence Read Archive (SRA) to analyze Pseudomonas phage PAK-P1 [Poster]. Jim Holland Summer Science Research Program, Bloomington, IN.

Leffler, H., Ganapaneni, S., Papudeshi, B., Sanders, S., & Doak, T.G. (2019). Mining the Sequence Read Archive to identify crAssphage, a ubiquitous inhabitant of the human microbiome, in dog and pig samples [Poster]. Jim Holland Summer Science Research Program Poster, Bloomington, IN.

Leffler, H., Ganapaneni, S., Papudeshi, B., Ganote, C., Sanders, S., & Doak, T.G. (2019). Mining Microbial Genomes from Datasets on the Sequence Read Archive [Poster]. Organization of Biological Field Stations Annual Meeting 2019, Brussels, Belgium.

Leffler, H., Ganapaneni, S., Papudeshi, B., Sanders, S., & Doak, G. T. (2019). A workflow to identify genomes in the Sequence Read Archive for phylogenomic analysis [Poster], ASM Microbe 2019, San Francisco, CA.

Mansfield, C., Tseng, C., Sanders, S., Custer, T.W., Custer, C.M., & Matson, C.W. (2019). Genetic diversity comparison of tree swallow populations in the Great Lakes region using RNA-sequencing [Poster]. SETAC North America 40th Annual Meeting, Toronto, ON, Canada.

Papudeshi, B., Chafin, T., Sanders, S., Ganote, C., Reshetnikov, A., Sokolov, S., Doak, T., Pummil, J.F., Douglas, M.R., & Douglas, M. (2019). Genome and transcriptome analysis of fish tapeworm Nippotaenia percotti through scientific collaboration between research labs and national cyberinfrastructure [Poster]. American Fisheries Society and The Wildlife Society 2019 Join Annual Conference, Reno, NV. *

Papudeshi, B., Ganote, C., Sanders, S., & Doak, T.G. (2019). National cyberinfrastructure and bioinformatic analysis support available to the cancer research community [Poster], Bioinformatics, Convergence Science, and Systems Biology, American Association for Cancer Research, Atlanta, GA. doi: 10.1158/1538-7445.sabcs18-5109.

Papudeshi, B., Sanders, S., Ganote, C., & Doak, G.T. (2019). Compute Resources Available to the Research Community for Microbiome Analysis [Poster], Plant and Animal Genome Conference XXVII, San Diego, CA.

Papudeshi, B., Sanders, S., Ganote, C., Doak, T., Chafin, T., Reshetnikov, A., Sokolov, S., Pummil, J., Douglas, M., & Douglas, M. (2019). The Genome of Fish Tapeworm Nippotaenia percotti as a Potential Bookmark for Gene Loci that Facilitates Anthropogenic Infection [Poster]. Plant and Animal Genome XXVII, San Diego, CA.

Sanders. S, (2019). Teaching Machine Learning to Domain Scientists: Supporting Newcomers to AI on HPC Systems [Presentation]. SuperComputing 19, Denver, CO.*

Sanders, S., Foran, E., Guido, E., Anderson, J., Slayton, T., & Doak, T.G. (2019). Automatically Survey Frogs Using Raspberry Pis, Jetstream Cloud, and Machine Learning [Poster]. Organization of Biological Field Stations Annual Meeting 2019, Brussels, Belgium.

Sanders, S., Papudeshi, B., Ganote, C., & Doak, G.T. (2019). NCGAS Makes Robust Transcriptome Assembly even easier with added features to an accessible de no transcriptome assembly workflow [Presentation], Plant and Animal Genome Conference 2019, San Diego, CA.

Sanders, S., Papudeshi, B., Ganote, C., Doak, G.T. Mansfield, C., Tseng, C. Y., Custer, T., Custer, C., & Matson, C. (2019). Population Genetics of Tree Swallows, in Collaboration with NCGAS [Poster]. Plant and Animal Genome XXVII, San Diego, CA.

Ganote, C., Sanders, S., Wu, L., Doak, T.G., & Mockaitis, K. (2018). Solving the challenges of complex genome analysis collaborations on-line using XSEDE resources [Poster]. Plant and Animal Genomics 2018, San Diego, CA.

Papudeshi, B., Sanders, S., Ganote,C., Fischer, J., & Doak, T.G. (2018). Bioinformatic analysis using Jetstream, a cloud computing environment [Poster]. Plant and Animal Genomics 2018, San Diego, CA.

Sanders, S., Ganote, C., Papudeshi, B., & Doak, T.G. (2018). National Center for Genome Analysis Support (NCGAS) use and development of Tripal Genome Browsers on XSEDE’s Jetstream [Presentation]. Plant and Animal Genomics 2018, San Diego, CA.

Sanders, S., Ganote, C., Papudeshi, B., Mockaitis, K., & Doak, T.G. (2018). NCGAS makes robust transcriptome analysis easier with a readily usable workflow following de novo assembly best practices [Presentation]. Plant and Animal Genomics 2018, San Diego, CA.

Sanders, S., Papdicheti, R., Yang, T., Fang, L., Jayathi, S., Tajan, G., Kumar, T.K.S., Medina-Bolivar, F., & Mockaitis, K. (2018). Stilbenoid prenylation pathway discovery in peanut using targeted transcriptomics [Poster]. Plant and Animal Genomics 2018, San Diego, CA.

Ganote. C, Sanders, S., Blood P., & Doak, T.G. (2017). The National Center for Genome Analysis Support [Presentation]. Great Lakes Bioinformatics Conference 2017, Chicago, IL.

Ganote. C, Sanders, S., & Doak, T.G. (2017). National Center for Genome Analysis Support: Providing National Cyberinfrastructure to Biologists, with a Focus on Genomics [Webinar]. Midwest Data Hub Webinar, online.*

Sanders, S., Ganote, C., & Doak, T.G. (2017). Navigating High Performance Computing (HPC) Resources. Advanced Topics in Bioinformatics, Bethune-Cookman University, Orlando, FL.*

Sanders, S. (2016). Moving away from GUIs [Guest Lecture]. Bioinformatics 2 GO, Indiana University, Bloomington, IN.*

Sanders, S. (2016). Conservation transcriptomics of Ambystomatid salamanders and their polyploid hybrids [Dissertation defense]. University of Notre Dame, South Bend, IN.

Sanders, S., Ganote, C., & Doak, T.G. (2016). Data Management and Movement [Presentation]. Environmental Genomics 2016, Mount Desert Island Biological Laboratory, ME.*

Sanders, S., Ganote, C., & Doak, T.G. (2016). Introduction to Cluster Usage [Presentation]. Environmental Genomics 2016, Mount Desert Island Biological Laboratory, ME.*

Sanders, S. , Ganote, C., & Doak, T.G. (2016). Moving forward in Bioinformatics [Presentation]. Advanced Topics in Bioinformatics, Bethune-Cookman University, Orlando, FL.*

Sanders, S., Ganote, C., & Doak, T.G. (2016). Moving from microscopes to model organisms: Community genomics tools [Presentation]. Supercomputing 2016, Salt Lake City, UT.

Sanders, S., Ganote, C., & Doak, T.G. (2016). The white coats are coming: The growth, success, and future of computing in biology [Presentation]. Supercomputing 2016, Salt Lake City, UT.

Sanders, S. (2015). Why we care about salamanders [Presentation]. Potowatomi Zoo, South Bend, IN.*

Sanders, S., Renshaw, M., & Pfrender, M. (2014). Design and implementation eDNA protocol to efficiently survey salamanders of the genus Ambystoma and their cryptic hybrids [Presentation]. Midwest Partners in Amphibian and Reptile Conservation Annual Meeting. Loretto, MN.

Sanders, S. (2014). Impact of Unisexual Salamanders on Disease Risk [Presentation]. Michigan Partners in Amphibian and Reptile Conservation Annual Meeting. East Lansing, MI.

Sanders, S. & J.S. Placyk. (2011). Re-evaluation of the Pseudogeographica Subgroup of Map Turtles (Genus: Graptemys). Joint Meeting of Ichthyologists and Herpetologists [Presentation]. Minneapolis, MN.

Sanders, S., Hively, C., Koukl, K., & Placyk, J.S. (2009). Niche-partitioning of sympatric map turtles in the Sabine River [Presentation]. 7th Annual Turtle Survival Alliance Symposium on Chelonian Conservation and Biology. St. Louis, MO.

Sanders, S., Hively, C., Koukl, K., & Placyk, J.S. (2009). A Re-evaluation of the Systematics of the Ouachita Map Turtle, Graptemys Ouachitensis, Subspecies: Evidence from Molecular, Morphological, and Behavioral Data [Masters Thesis]. Office of Sponsored Research 2009 Student Research Poster Competition. Tyler, TX.