IRSC Biology, Computer Science and Digital Media students participate in USDA-NIFA research to deliver solutions for citrus greening. Internship Opportunities Available!
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Year long course where IRSC Biology students isolate novel actinobacteriophages and perform functional and comparative genomics. A Howard Hughes Medical Institute sponsored program.
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Publications:
Spotlight: Asian citrus psyllid community genome annotation
Over 20 IRSC students, IRSC faculty team up in an highly collaborative citrus greening research collaboration.
Students and IRSC faculty in bold:
- 2022: Teresa D. Shippy, Prashant S. Hosmani, Mirella Flores-gonzalez, Lukas A. Mueller, Wayne B. Hunter, Susan J. Brown, Tom D’Elia, Surya Saha, Annotation of Hox cluster and Hox cofactor genes in the Asian citrus psyllid, Diaphorina citri, reveals novel features, Gigabyte, 2022 https://doi.org/10.46471/gigabyte.49
- 2022: Max Reynolds, Lucas De Oliveira, Chad Vosburg, Thomson Paris, Crissy Massimino, Jordan Norus, Yasmin Ortiz, Michelle Espino, Nina Davis, Ron Masse, Alan Neiman, Rachel Holcomb, Kylie Gervais, Melissa Kemp, Maria Hoang, Teresa D. Shippy, Prashant S. Hosmani, Mirella Flores-gonzalez, Kirsten Pelz-stelinski, Jawwad A. Qureshi, Lukas A. Mueller, Wayne B. Hunter, Joshua B. Benoit, Susan J. Brown, Tom D’Elia, Surya Saha, Annotation of putative circadian rhythm-associated genes in Diaphorina citri (Hemiptera: Liviidae), Gigabyte, 2022 https://doi.org/10.46471/gigabyte.48
- 2022: Blessy Tamayo, Kyle Kercher, Chad Vosburg, Crissy Massimino, Margaryta R. Jernigan, Denisse L. Hasan, Douglas Harper, Anuja Mathew, Samuel Adkins, Teresa Shippy, Prashant S. Hosmani, Mirella Flores-gonzalez, Naftali Panitz, Lukas A. Mueller, Wayne B. Hunter, Joshua B. Benoit, Susan J. Brown, Tom D’Elia, Surya Saha, Annotation of glycolysis, gluconeogenesis, and trehaloneogenesis pathways provide insight into carbohydrate metabolism in the Asian citrus psyllid, Gigabyte, 2022 https://doi.org/10.46471/gigabyte.41
- 2022: Teresa D. Shippy, Sherry Miller, Blessy Tamayo, Prashant S. Hosmani, Mirella Flores-gonzalez, Lukas A. Mueller, Wayne B. Hunter, Susan J. Brown, Tom D’Elia, Surya Saha, Manual curation and phylogenetic analysis of chitinase family genes in the Asian citrus psyllid, Diaphorina citri, Gigabyte, 2022 https://doi.org/10.46471/gigabyte.46
- 2022: Will Tank, Teresa Shippy, Amanda Thate, Crissy Massimino, Prashant S. Hosmani, Mirella Flores-gonzalez, Lukas A. Mueller, Wayne B. Hunter, Susan J. Brown, Tom D’Elia, Surya Saha, Ubiquitin-proteasome pathway annotation in Diaphorina citri can reveal potential targets for RNAi-based pest management, Gigabyte, 2022 https://doi.org/10.46471/gigabyte.43
- 2022: Rebecca Grace, Crissy Massimino, Teresa D. Shippy, Will Tank, Prashant S. Hosmani, Mirella Flores-Gonzalez, Lukas A. Mueller, Wayne B. Hunter, Joshua B. Benoit, Susan J. Brown, Tom D’Elia and Surya Saha. Genomic identification, annotation, and comparative analysis of Vacuolar-type ATP synthase subunits in Diaphorina citri. Gigabyte. 2022, DOI: 10.46471/gigabyte.39
- 2022: Instructional Models for Course-Based Research Experience (CRE) Teaching. David I. Hanauer, Mark J. Graham, Rachel J. Arnold, Mary A. Ayuk, Mitchell F. Balish, Andrea R. Beyer, Kristen A. Butela, Christine A. Byrum, Catherine P. Chia, Hui-Min Chung, Kari L. Clase, Stephanie Conant, Roy J. Coomans, Tom D’Elia, Jason Diaz, Arturo Diaz, Jean A. Doty, Nicholas P. Edgington, Dustin C. Edwards, Elvira Eivazova, Christine B. Emmons, Kayla M. Fast, Emily J. Fisher, Christine L. Fleischacker, Gregory D. Frederick, Amanda C. Freise, Maria D. Gainey, Chris R. Gissendanner, Urszula P. Golebiewska, Nancy A. Guild, Heather L. Hendrickson, Christopher D. Herren, Margaret S. Hopson-Fernandes, Lee E. Hughes, Deborah Jacobs-Sera, Allison A. Johnson, Bridgette L. Kirkpatrick, Karen K. Klyczek, Ann P. Koga, Hari Kotturi, Janine LeBlanc-Straceski, Julia Y. Lee-Soety, Justin E. Leonard, Matthew D. Mastropaolo, Evan C. Merkhofer, Scott F. Michael, Jon C. Mitchell, Swarna Mohan, Denise L. Monti, Christos Noutsos, Imade Y. Nsa, Nick T. Peters, Ruth Plymale, Richard S. Pollenz, Megan L. Porter, Claire A. Rinehart, German Rosas-Acosta, Joseph F. Ross, Michael R. Rubin, Anne E. Scherer, Stephanie C. Schroeder, Christopher D. Shaffer, Amy B. Sprenkle, C. Nicole Sunnen, Sarah J. Swerdlow, Deborah Tobiason, Sara S. Tolsma, Philippos K. Tsourkas, Robert E. Ward, Vassie C. Ware, Marcie H. Warner, Jacqueline M. Washington, Kristi M. Westover, Simon J. White, JoAnn L. Whitefleet-Smith, Daniel C. Williams, Michael J. Wolyniak, Jill H. Zeilstra-Ryalls, David J. Asai, Graham F. Hatfull, and Viknesh Sivanathan. CBE—Life Sciences Education 2022 21:1
- 2021: Undergraduate virtual engagement in community genome annotation provides flexibility to overcome course disruptions. 2020. Surya Saha, Teresa D Shippy, Susan J Brown, Joshua B Benoit and Tom D’Elia. Journal of Microbiology and Biology Education. Special edition: TEACHING IN A TIME OF CRISIS. January/February, 2021. 22:1. ev22i1.2395. https://doi.org/10.1128/jmbe.v22i1.2395.
- 2021: Crissy Massimino, Chad Vosburg, Teresa Shippy, Prashant S. Hosmani, Mirella Flores-Gonzalez, Lukas A. Mueller, Wayne B. Hunter, Joshua B. Benoit, Susan J. Brown, Tom D’Elia, Surya Saha. Annotation of yellow genes in Diaphorina citri, the vector for Huanglongbing disease. Gigabyte.1:2021 https://doi.org/10.46471/gigabyte.20.
- 2021: Chad Vosburg, Max Reynolds, Rita Noel, Teresa Shippy, Prashant S. Hosmani, Mirella Flores-Gonzalez, Lukas A. Mueller, Wayne B. Hunter, Susan J. Brown, Tom D’Elia, Surya Saha. Utilizing a chromosomal-length genome assembly to annotate the Wnt signaling pathway in the Asian citrus psyllid, Diaphorina citri. Gigabyte.1:2021 https://doi.org/10.46471/gigabyte.21.
- 2021: Sherry Miller, Teresa D. Shippy, Blessy Tamayo, Prashant S. Hosmani, Mirella Flores-Gonzalez, Lukas A. Mueller, Wayne B. Hunter, Susan J. Brown, Tom D’Elia, Surya Saha. Annotation of chitin biosynthesis genes in Diaphorina citri, the Asian citrus psyllid. Gigabyte. 1:2021 https://doi.org/10.46471/gigabyte.23.
- 2021: Sherry Miller, Teresa D. Shippy, Blessy Tamayo, Prashant S. Hosmani, Mirella Flores-Gonzalez, Lukas A. Mueller, Wayne B. Hunter, Susan J. Brown, Tom D’Elia, Surya Saha. In silico characterization of chitin deacetylase genes in the Diaphorina citri genome. Gigabyte. 1:2021 https://doi.org/10.46471/gigabyte.25.
- 2021: Sherry Miller, Teresa D. Shippy, Prashant S. Hosmani, Mirella Flores-Gonzalez, Lukas A. Mueller, Wayne B. Hunter, Susan J. Brown, Tom D’Elia, Surya Saha. Annotation of segmentation pathway genes in the Asian citrus psyllid, Diaphorina citri. Gigabyte. 1:2021. https://doi.org/10.46471/gigabyte.26.
- 2020: Undergraduate virtual engagement in community genome annotation provides flexibility to overcome course disruptions. 2020. Surya Saha, Teresa D Shippy, Susan J Brown, Joshua B Benoit and Tom D’Elia. Journal of Microbiology and Biology Education.
- 2020: Complete genome sequence of Xanthomonas phage RiverRider, a novel N4‑like bacteriophage that infects the strawberry pathogen Xanthomonas fragariae. Morgan Miller, Alex Deiulio, Chris Holland, Cayce Douthitt, Jessica McMahon, Helen Wiersma‑Koch, William W. Turechek, Tom D’Elia. Archives of Virology. 165:1481–1484
- 2020: Shippy, T.D.; Miller, S; C Massimino, C Vosburg, Hosmani, PS; Flores-Gonzalez, M; Mueller, LA; Hunter, WB; Brown, SJ; D’Elia, T; Saha S. Annotating genes in Diaphorina citri genome version 3. protocols.io. 2020
- 2020: Conant, S., D'Elia, T., Diaz, A., Monti, D. L., Pollenz, R., Ware, V., Takayama, K., Sivanathan, V. (2020). 5Qs: An Activity to Support Students Develop Skills to Interpret Research Observations. Science Education Alliance (SEA) Faculty Group, QUBES Educational Resources. doi:10.25334/YGQ4-5977
- 2020: Conant, S., D'Elia, T., Diaz, A., Monti, D. L., Pollenz, R., Ware, V., Takayama, K., Sivanathan, V. (2020). A Letter to a Young Scientist: Prompting Students To Reflect On And Recognize Their Own Growth As Scientists. Science Education Alliance (SEA) Faculty Group, QUBES Educational Resources. doi:10.25334/CBP1-T733
- 2020: Conant, S., D'Elia, T., Diaz, A., Monti, D. L., Pollenz, R., Ware, V., Takayama, K., Sivanathan, V. (2020). Elevator Pitch: An Activity to Help Students Communicate Their Research. Science Education Alliance (SEA) Faculty Group, QUBES Educational Resources. doi:10.25334/T9X4-SQ93
- 2020: Scott-Brown, A., D’Elia, T., Devey, D.S., Funderburk, J.E., Adkins. S. 2020. Genome characterization of Brugmansia latent virus, a novel tobamovirus. Archives of Virology 165:2389–2392 https://doi.org/10.1007/s00705-020-04718-z
- 2020: Deborah Jacobs-Sera, Lawrence A. Abad, Richard M. Alvey, Kirk R. Anders, Haley G. Aull, Suparna S. Bhalla, Lawrence S. Blumer, David W. Bollivar, J. Alfred Bonilla, Kristen A.Butela, Roy J. Coomans, Steven G. Cresawn, Tom D'Elia, Arturo Diaz, Ashley M. Divens, Nicholas P. Edgington, Gregory D. Frederick, Maria D. Gainey, Rebecca A. Garlena, Kenneth W. Grant, Susan M. R. Gurney, Heather L. Hendrickson, Lee E. Hughes, Margaret A. Kenna, Karen K. Klyczek, Hari Kotturi, Travis N. Mavrich, Angela L. McKinney, Evan C. Merkhofer, Jordan Moberg Parker, Sally D. Molloy, Denise L. Monti, Dana A. Pape-Zambito, Richard S. Pollenz, Welkin H. Pope, Nathan S. Reyna, Claire A. Rinehart, Daniel A. Russell, Christopher D. Shaffer, Viknesh Sivanathan, Ty H. Stoner, Joseph Stukey, C. Nicole Sunnen, Sara S. Tolsma, Philippos K. Tsourkas, Jamie R. Wallen, Vassie C. Ware, Marcie H. Warner, Jacqueline M. Washington, Kristi M. Westover, JoAnn L. Whitefleet-Smith, Helen I. Wiersma-Koch, Daniel C. Williams, Kira M. Zack, Graham F. Hatfull. (2020) Genomic diversity of bacteriophages infecting Microbacterium spp. PLOS ONE 15(6): e0234636. https://doi.org/10.1371/journal.pone.0234636
- 2019. Chromosomal length reference assembly for Diaphorina citri using single-molecule sequencing and Hi-C proximity ligation with manually curated genes in developmental, structural and immune pathways. Prashant S. Hosmani, Mirella Flores-Gonzalez, Teresa Shippy, Chad Vosburg, Crissy Massimino, Will Tank, Max Reynolds, Blessy Tamayo, Sherry Miller, Jordan Norus, Kyle Kercher, Bec Grace, Margaryta Jernigan, Doug Harper, Sam Adkins, Yesmarie DeLaFlor, Thomson Paris, Sara Vandervoort, Rebekah Adams, Seantel Norman, Jessica Ventura, Michael Perry, Matthew Weirauch, Josh Benoit, Wayne B. Hunter, Helen Wiersma-Koch, Tom D’Elia, Susan Brown, Lukas A. Mueller, Surya Saha. bioRxiv 869685; doi: https://doi.org/10.1101/869685
- 2019. Prashant S. Hosmani, Teresa Shippy, Sherry Miller, Joshua B. Benoit, Monica Munoz-Torres, Mirella Flores, Lukas A. Mueller, Helen Wiersma-Koch, Tom D'Elia, Susan J. Brown, Surya Saha. 2018. A quick guide for student-driven community genome annotation. PLoS Computational Biology.
- 2018. Adkins, S., T. D’Elia, K, Fillmer, K., P. Pongam, and C. Baker. 2018. Biological and genomic characterization of a novel tobamovirus infecting Hoya spp. Plant Disease. https://doi.org/10.1094/PDIS-04-18-0667-RE
- 2018. Fillmer, K., S. Adkins, P. Pongam, and T. D’Elia. 2018. Using tobamoviruses as a model for phylogenetic instruction in undergraduate biology courses. Journal of Microbiology and Biology Education. 19(2):19.2.65. doi:10.1128/jmbe.v19i2.1519.
- 2018. Prashant S. Hosmani, Teresa Shippy, Sherry Miller, Joshua B. Benoit, Monica Munoz-Torres, MirellaFlores, Lukas A. Mueller, Helen Wiersma-Koch, Tom D'Elia, Susan J. Brown, Surya Saha. 2018. A quick guide for student-driven community genome annotation. arXiv. arXiv:1805.03602
- 2017. Chung H-M, D’Elia T, Ross JF, Alvarado SM, Brantley M-C, Bricker LP, Butler CR, Crist C, Dane JM, Farran BW, Hobbs S, Lapak M, Lovell C, Ludergnani N, McMullen A, Mirza SA, Thrift N, Vaughan DP, Worley G, Ejikemeuwa A, ZawM, Albritton CF, Bertrand SC, Chaudhry SS, Cheema VA, Do C, Do ML, Duong HM, El-Desoky DH, Green KM, Lee RN, Thornton LA, Vu JM, Zahra MN, Cresawn SG, Stoner TH, Garlena RA, Jacobs-Sera D, Pope WH, Russell DA, Hatfull GF. 2017. Complete genome sequences of mycobacteriophages Clautastrophe, Kingsolomon, Krypton555, and Nicholas. Genome Announc 5:e01129-17.https://doi.org/10.1128/genomeA.01129-17.
- 2017. Proceedings of the National Academy of Sciences. An Inclusive Research-Education Community (iREC): A model for student engagement in Science. David I Hanauer, Mark Graham, SEA-PHAGES*, Laura Betancur, Aiyana Bobrownicki, Steven G. Cresawn, Rebecca Garlena, Deborah Jacobs-Sera, Nancy Kaufmann, Welkin H Pope, Daniel A Russell, Viknesh Sivanathan, David J. Asai, and Graham F. Hatfull. Dec 2017, 114 (51) 13531-13536; DOI: 10.1073/pnas.1718188115 http://www.pnas.org/content/114/51/13531
- NOTE: *T. D’Elia, is a contributing authors under “SEA-PHAGES” and is listed by name as contributing authors in a searchable, supplementary table of the manuscript
- Surya Saha, Prashant S Hosmani, Krystal Villalobos-Ayala, Sherry Miller, Teresa Shippy, Andrew Rosendale, Chris Cordola, Tracey Bell, Hannah Mann, Gabe DeAvila, Daniel DeAvila, Zachary Moore, Kyle Buller, Kathryn Ciolkevich, Samantha Nandyal, Robert Mahoney, Joshua Von Voorhis, Megan Dunlevy, David Farrow, David Hunter, Taylar Morgan, Kayla Shore, Victoria Guzman, Allison Izsak, Danielle E Dixon, Liliana Cano, Andrew Cridge, Shannon Johnson, Brandi L Cantarel, Stephen Richardson, Adam English, Nan Leng, Xiaolong Cao, Haobo Jiang, Chris Childers, Mei-Ju Chen, Mirella Flores, Wayne Hunter, Michelle Cilia, Lukas A Mueller, Monica Munoz-Torres, David Nelson, Monica F Poelchau, Josh Benoit, Helen Wiersma-Koch, Tom D'Elia, Susan J Brown. Biocuration as an undergraduate training experience: Improving the annotation of the insect vector of Citrus greening disease. Database: The Journal of Biological Databases and Curation. 2017;2017:bax032. doi:10.1093/database/bax032
- Saha, S.; Hosmani, P; Villalobos-Ayala, K; Miller, S, Shippy, T., Flores, M, Rosendale, A, Cordola, C, Bell, T, Mann, H, DeAvila, G, DeAvila, D, Moore, Z, Buller, K, Ciolkevich , K, Nandyal , S, Mahoney, R, Voorhis, J, Dunlevy, M, Farrow, DW.; Hunter, D, Morgan, T, Shore, K, Guzman, V, Izsak, A, Dixon, D, Cridge, A, Cano, L, Cao, X, Jiang, H, Leng, N, Johnson, S, Cantarel, B, Richards, S, English, A, Shatters, R, Childers, C, Chen, M-J, Hunter, W, Cilia, M, Mueller, LA., Munoz-Torres, M, Nelson, DR, Poelchau, M, Benoit, JB., Wiersma-Koch, H; D'Elia, T, Brown, S, (2017). Diaphorina citri Official Gene Set v1.0. Ag Data Commons. http://dx.doi.org/10.15482/USDA.ADC/1345524.
- Fillmer, K., S. Adkins, P. Pongam, and T. D’Elia. 2016. The Complete Nucleotide Sequence and Genomic Characterization of Tropical Soda Apple Mosaic Virus. Archives of Virology. 161: 2317-2320.
- Graham F. Hatfull, Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES)*, Program, KwaZulu-Natal Research Institute for Tuberculosis and HIV (K-RITH) Mycobacterial Genetics Course, University of California–Los Angeles Research Immersion Laboratory in Virology, Phage Hunters Integrating Research and Education (PHIRE) Program. Complete Genome Sequences of 61 Mycobacteriophages. Genome Announcements. 3(2): e00389-16
- NOTE: *T. D’Elia and IRSC 2015-16 students are contributing authors under “SEA-PHAGES”
- Fillmer, K., S. Adkins, P. Pongam, and T. D’Elia. 2015. Complete Genome Sequence of Tomato Mottle Mosaic Virus Isolate from the United States. Genome Announcements. 3(2): e00167-15
- Fillmer, K., S. Adkins, P. Pongam, and T. D’Elia. 2015. Complete Genome Sequence of Tomato Mosaic Virus Isolate from Jasmine in the United States. Genome Annoncements. 3(4): e00706-15
- Shtarkman, Y.M, Z. A. Koçer, R. Edgar, R. Veerapaneni, T. D’Elia, P. F. Morris and S. O. Rogers. 2013. Subglacial Lake Vostok (Antarctica) accretion ice contains a diverse set of sequences from aquatic and marine Bacteria and Eukarya. PLoS One. 8(7):e67221.
- Note: This article is in the top 25% of cited articles from this journal (See supporting materials): http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0067221&utm_source=plos&utm_medium=email-button&utm_campaign=one-1707-alms
- Rogers SO, Y.M. Shtarkman, Z.A. Koçer, R. Edgar, R. Veerapaneni, and T. D'Elia. 2013. Ecology of Subglacial Lake Vostok (Antarctica), Based on Metagenomic/Metatranscriptomic Analyses of Accretion Ice. Biology. 2(2):629-650.
- Knowlton C., R. Veerapaneni, T. D’Elia and S.O. Rogers. 2013. Microbial analysis of ancient ice core sections from Greenland and Antarctica. Biology. 2(1), 206-232.
- D’Elia, T., R. Veerapaneni, V. Theraisnathan and S. O. Rogers. 2009. Isolation of Fungi from Lake Vostok Accretion ice. Mycologia. 101: 751-763.
- D’Elia, T., R. Veerapaneni and S. O. Rogers. 2008. Isolation of Microbes from Lake Vostok Accretion Ice. Applied and Environmental Microbiology. 74: 4962-4965.
- D’Elia, T., C. Cooper, and C. Johnston. 2007. Source Tracking of Escherichia coli by 16S-23S Intergenic Spacer Region denaturing Gradient Gel Electrophoresis (DGGE) of the rrnB Ribosomal Operon. The Canadian Journal of Microbiology. 53:1174-1184.