{"id":35,"date":"2020-11-25T17:58:31","date_gmt":"2020-11-25T17:58:31","guid":{"rendered":"https:\/\/faculty.engineering.ucdavis.edu\/stevens\/?page_id=35"},"modified":"2026-09-10T14:28:38","modified_gmt":"2026-09-10T21:28:38","slug":"research","status":"publish","type":"page","link":"https:\/\/faculty.engineering.ucdavis.edu\/stevens\/research\/","title":{"rendered":"Research"},"content":{"rendered":"\t\t<div data-elementor-type=\"wp-page\" data-elementor-id=\"35\" class=\"elementor elementor-35\">\n\t\t\t\t\t\t<section class=\"elementor-section elementor-top-section elementor-element elementor-element-662e9a79 elementor-section-boxed elementor-section-height-default elementor-section-height-default\" data-id=\"662e9a79\" data-element_type=\"section\" data-e-type=\"section\" data-settings=\"{&quot;background_background&quot;:&quot;classic&quot;}\">\n\t\t\t\t\t\t<div class=\"elementor-container elementor-column-gap-default\">\n\t\t\t\t\t<div class=\"elementor-column elementor-col-100 elementor-top-column elementor-element elementor-element-5911656b\" data-id=\"5911656b\" data-element_type=\"column\" data-e-type=\"column\" data-settings=\"{&quot;background_background&quot;:&quot;classic&quot;}\">\n\t\t\t<div class=\"elementor-widget-wrap elementor-element-populated\">\n\t\t\t\t\t\t<div class=\"elementor-element elementor-element-7f502f93 elementor-widget elementor-widget-page-title\" data-id=\"7f502f93\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"page-title.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\n\t\t<div class=\"hfe-page-title hfe-page-title-wrapper elementor-widget-heading\">\n\n\t\t\t\t\t\t\t\t<h2 class=\"elementor-heading-title elementor-size-default\">\n\t\t\t\t\t\t\t\t\n\t\t\t\tResearch  \n\t\t\t<\/h2 > \n\t\t\t\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-66cc0bb3 elementor-widget-divider--view-line elementor-widget elementor-widget-divider\" data-id=\"66cc0bb3\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"divider.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t<div class=\"elementor-divider\">\n\t\t\t<span class=\"elementor-divider-separator\">\n\t\t\t\t\t\t<\/span>\n\t\t<\/div>\n\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t<div class=\"elementor-element elementor-element-6a535095 elementor-widget elementor-widget-text-editor\" data-id=\"6a535095\" data-element_type=\"widget\" data-e-type=\"widget\" data-widget_type=\"text-editor.default\">\n\t\t\t\t<div class=\"elementor-widget-container\">\n\t\t\t\t\t\t\t\t\t<div class=\"publication-summary\"><span style=\"color: #002855;font-family: inherit;font-size: var( --e-global-typography-text-font-size )\">Interests<\/span><\/div>\n<h5 class=\"isSelectedEnd\" style=\"color: #000000\">Algorithms<\/h5>\n<p class=\"isSelectedEnd\" style=\"color: #000000\">Design and analysis of algorithms for problems in phylogenetics, genomic sequence analysis, high-throughput sequencing, and computer science education.<\/p>\n\n<h5 class=\"isSelectedEnd\" style=\"color: #000000\">Genomics &amp; Population Genomics<\/h5>\n<p class=\"isSelectedEnd\" style=\"color: #000000\">Reference genome sequencing and population-scale resequencing to identify and characterize genetic variation associated with biological phenotypes.<\/p>\n\n<h5 class=\"isSelectedEnd\" style=\"color: #000000\">Metagenomics &amp; NGS Diagnostics<\/h5>\n<p class=\"isSelectedEnd\" style=\"color: #000000\">Analysis of high-throughput sequencing data for research and diagnostic applications, including the design and validation of NGS diagnostics and bioinformatics workflows for regulatory environments.<\/p>\n\n<h5 class=\"isSelectedEnd\" style=\"color: #000000\">Pedagogy<\/h5>\n<p style=\"color: #000000\">Interdisciplinary computer science education, curriculum development, computational thinking, and algorithmic approaches to problems in teaching and learning.<\/p>\n\n<section class=\"faculty-publications\">\n<div class=\"publication-summary\"><span style=\"color: #002855;font-family: inherit;font-size: var( --e-global-typography-text-font-size )\">Publications<\/span><\/div>\n<!-- Publications list for faculty.engineering.ucdavis.edu\/stevens\/research\/\n     Paste into an Elementor HTML widget (not the Text Editor widget, whose visual mode can rewrite markup).\n     Replaces everything from the stats line through the end of the 2004 list. -->\n\n<div class=\"stevens-publications\">\n\n<p><strong>76 publications<\/strong> \u00b7 <strong>1 preprint<\/strong> \u00b7 <strong>8,347 citations<\/strong> \u00b7 h-index: <strong>30<\/strong> \u00b7 i10-index: <strong>43<\/strong> \u00b7 <a href=\"https:\/\/scholar.google.com\/citations?hl=en&amp;user=xZCizwYAAAAJ\">Google Scholar profile<\/a><\/p>\n<!-- TODO: refresh citations, h-index, and i10-index from Google Scholar before publishing -->\n\n<h3>Preprints<\/h3>\n<ul>\n<li>Zonglin Han, Yichen Chen, Jiawen Jiang, Tongan Shi, <strong>Kristian Stevens<\/strong> (2026). <a href=\"https:\/\/doi.org\/10.48550\/arXiv.2608.05455\">Stochasticity Is Not the Hard Part: Reduction and Complexity in Instructional Sequencing over Prerequisite DAGs<\/a>. <em>arXiv<\/em>:2608.05455.<\/li>\n<\/ul>\n\n<h3>2026<\/h3>\n<ol reversed start=\"76\">\n<li>Raied Abou Kubaa, <strong>Kristian Stevens<\/strong>, Teresa M. Erickson, Maher Al Rwahnih (2026). <a href=\"https:\/\/doi.org\/10.3390\/v18090959\">A New HiPlex Amplicon Sequencing Approach for the Detection of Grapevine Leafroll-Associated Virus 3 and Grapevine Red Blotch Virus in Grapevines<\/a>. <em>Viruses<\/em>, 18(9), 959.<\/li>\n<li>Ana Belen Duarte Cruz, V\u00edctor Manuel Mart\u00edn del Campo Soler, <strong>Kristian Stevens<\/strong>, Alfredo D\u00edaz-Lara (2026). <a href=\"https:\/\/doi.org\/10.18781\/r.mex.fit.2605-3\">First detection of bell pepper endornavirus infecting bell pepper in Guanajuato, Mexico<\/a>. <em>Revista Mexicana de Fitopatolog\u00eda<\/em>, 44(3).<\/li>\n<li>Elizabeth J. Indermaur, Anna O. Wunsch, Heather McLane, <strong>Kristian Stevens<\/strong>, Min Sook Hwang, Maher Al Rwahnih, Christine D. Smart, Marc Fuchs (2026). <a href=\"https:\/\/doi.org\/10.1094\/phyto-07-26-0225-sc\">The Virome of Rhubarb Consists of Diverse Viruses Belonging to at Least Four Families<\/a>. <em>Phytopathology<\/em>. Online ahead of print.<\/li>\n<li>Raied Abou Kubaa, Teresa M. Erickson, Haoran Li, <strong>Kristian Stevens<\/strong>, Maher Al Rwahnih (2026). <a href=\"https:\/\/doi.org\/10.1128\/mra.00529-26\">Coding-complete genome sequence of grapevine leafroll-associated virus 13 from grapevine in California<\/a>. <em>Microbiology Resource Announcements<\/em>, e00529-26.<\/li>\n<li>Ahmed Mohamed, <strong>Kristian Stevens<\/strong>, Islam El-Sharkawy, Maher Al Rwahnih, Violeta M. Tsolova (2026). <a href=\"https:\/\/doi.org\/10.1094\/pdis-05-26-1021-pdn\">First report of grapevine virus B in muscadine grape (<em>Muscadinia rotundifolia<\/em> (Michx.) Small) in Florida<\/a>. <em>Plant Disease<\/em>. Online ahead of print.<\/li>\n<li>Rebecca A. Melanson, Carol Chen, <strong>Kristian Stevens<\/strong>, Laura Jenkins Hladky, Maher Al Rwahnih, William M. Wintermantel (2026). <a href=\"https:\/\/doi.org\/10.1094\/pdis-06-25-1154-sc\">Identification of melon severe mosaic virus in cucurbits in Mississippi highlights the need for routine virus monitoring with assays targeting multiple viruses<\/a>. <em>Plant Disease<\/em>. Online ahead of print.<\/li>\n<li>Juan Pedro L\u00f3pez-C\u00f3rdova, Jose A. Garz\u00f3n-Tiznado, Mar\u00eda Eugenia Renter\u00eda-Mart\u00ednez, Juan Manuel Tovar-Pedraza, <strong>Kristian Stevens<\/strong>, Mar\u00eda de los \u00c1ngeles Mora-Ugalde, Alfredo D\u00edaz-Lara (2026). <a href=\"https:\/\/doi.org\/10.1094\/pdis-10-25-2053-pdn\">First Report of Cucumber Green Mottle Mosaic Virus (CGMMV) Infecting Cucumber in Mexico<\/a>. <em>Plant Disease<\/em>, 110(4), 1496.<\/li>\n<li><strong>Kristian Stevens<\/strong>, Juliana Osse de Souza, Haoran Li, Ashrafou Ouro-Djobo, Olufemi J. Alabi, Maher Al Rwahnih (2026). <a href=\"https:\/\/doi.org\/10.1007\/s00705-026-06580-x\">Agave associated crinivirus A: a novel monopartite crinivirus homolog isolated from agave<\/a>. <em>Archives of Virology<\/em>, 171(4), 138.<\/li>\n<li>Zonglin Han, <strong>Kristian Stevens<\/strong> (2026). <a href=\"https:\/\/doi.org\/10.1109\/southeastcon63549.2026.11476160\">Quantifying Cross-System Curriculum Alignment: A Reproducible and Interpretable Method<\/a>. In <em>SoutheastCon 2026<\/em>, IEEE, 1\u20137.<\/li>\n<!-- TODO: add DOI link once confirmed on Springer's site -->\n<li>Alfredo D\u00edaz-Lara, Aranza Mondrag\u00f3n-Cruz, <strong>Kristian Stevens<\/strong>, Oscar P. Hurtado-Gonzales, Juan Manuel Tovar-Pedraza (2026). Molecular Characterization and Genome Annotation of Emerging Fruit Viruses. In <em>Fruit Crops and Viral Pathogens Volume II: Molecular Insights and Sustainable Control<\/em>, 143\u2013169. Springer Nature Singapore.<\/li>\n<li>Olufemi J. Alabi, Ashrafou Ouro-Djobo, Audrey A. Rodriguez, John Oladeji Oladokun, Min Sook Hwang, Cecilia Villegas, <strong>Kristian Stevens<\/strong>, Maher Al Rwahnih, Kevin Ong (2026). <a href=\"https:\/\/doi.org\/10.1007\/s00705-026-06589-2\">Plumeria ampelovirus 1, a novel ampelovirus subgroup II member infecting <em>Plumeria<\/em> spp.<\/a> <em>Archives of Virology<\/em>, 171(3), 79.<\/li>\n<\/ol>\n\n<h3>2025<\/h3>\n<ol reversed start=\"65\">\n<li>Peter Abrahamian, Weili Cai, Schyler O. Nunziata, <strong>Kristian Stevens<\/strong>, Xiaojun Hu, Min Sook Hwang, et al. (2025). <a href=\"https:\/\/doi.org\/10.1094\/phytofr-03-25-0025-r\">Interlaboratory Validation of High-Throughput Sequencing for the Detection of Viruses and Viroids in Apple, Grapevine, and Stone Fruits<\/a>. <em>PhytoFrontiers<\/em>, 5(4), 623\u2013634.<\/li>\n<!-- TODO: add DOI link once confirmed on Springer's site -->\n<li>Ashrafou Ouro-Djobo, David N. Appel, Sheila A. McBride, <strong>Kristian Stevens<\/strong>, Frances M. Pontasch, Justin J. Scheiner, Maher Al Rwahnih, Olufemi J. Alabi (2025). Virome associated with interspecific hybrid bunch grapevine cultivars in Texas. <em>Journal of Plant Pathology<\/em>, 107(4), 2055\u20132070.<\/li>\n<li>Raied Abou Kubaa, Ashrafou Ouro-Djobo, <strong>Kristian Stevens<\/strong>, Olufemi J. Alabi, Maher Al Rwahnih (2025). <a href=\"https:\/\/doi.org\/10.1007\/s00705-025-06346-x\">Genome characterization of prunus maculavirus 1 (PrMcV-1), a novel member of the genus <em>Maculavirus<\/em> identified in <em>Prunus<\/em> spp.<\/a> <em>Archives of Virology<\/em>, 170(8), 168.<\/li>\n<li>Maher Al Rwahnih, Vicki Klaassen, Teresa M. Erickson, Olufemi J. Alabi, <strong>Kristian Stevens<\/strong>, Min Sook Hwang, Lauren Port (2025). <a href=\"https:\/\/doi.org\/10.1094\/pdis-10-24-2104-fe\">A New Era in Federal Quarantine and State Certification Diagnostics at Clean Plant Centers in the United States<\/a>. <em>Plant Disease<\/em>, 109(7), 1392\u20131403.<\/li>\n<li>Kellee Britt-Ugartemendia, <strong>Kristian Stevens<\/strong>, Maher Al Rwahnih, Amit Levy, \u00d6zgur Batuman (2025). <a href=\"https:\/\/doi.org\/10.1094\/pbiomes-05-24-0055-fi\">RNA-Sequencing-Based Virome Discovery in Florida Citrus Pests<\/a>. <em>Phytobiomes Journal<\/em>, 9(1), 95\u2013108.<\/li>\n<li>Jeffrey S. Groh, Diane C. Vik, Matthew Davis, J. Grey Monroe, <strong>Kristian Stevens<\/strong>, Patrick J. Brown, Charles H. Langley, Graham Coop (2025). <a href=\"https:\/\/doi.org\/10.1126\/science.ado5578\">Ancient structural variants control sex-specific flowering time morphs in walnuts and hickories<\/a>. <em>Science<\/em>, 387(6729), eado5578.<\/li>\n<\/ol>\n\n<h3>2024<\/h3>\n<ol reversed start=\"59\">\n<li><strong>Kristian Stevens<\/strong>, Maher Al Rwahnih (2024). <a href=\"https:\/\/doi.org\/10.3390\/v16121957\">High-Throughput Sequencing for the Detection of Viruses in Grapevine: Performance Analysis and Best Practices<\/a>. <em>Viruses<\/em>, 16(12), 1957.<\/li>\n<li>Juliana Osse de Souza, Vicki Klaassen, <strong>Kristian Stevens<\/strong>, Teresa M. Erickson, Claire Heinitz, Maher Al Rwahnih (2024). <a href=\"https:\/\/doi.org\/10.3390\/v16091457\">Characterization of Genetic Diversity in the Capsid Protein Gene of Grapevine Fleck Virus and Development of a New Real-Time RT-PCR Assay<\/a>. <em>Viruses<\/em>, 16(9), 1457.<\/li>\n<li>Olufemi J. Alabi, <strong>Kristian Stevens<\/strong>, John Oladeji Oladokun, Cecilia Villegas, Min Sook Hwang, Maher Al Rwahnih, et al. (2024). <a href=\"https:\/\/doi.org\/10.1094\/pdis-02-24-0459-re\">Discovery and Characterization of Two Highly Divergent Variants of a Novel Potyvirus Species Infecting Madagascar Periwinkle (<em>Catharanthus roseus<\/em>)<\/a>. <em>Plant Disease<\/em>, 108(8), 2494\u20132502.<\/li>\n<li>Dianella Iglesias, <strong>Kristian Stevens<\/strong>, Ashutosh Sharma, Alfredo D\u00edaz-Lara (2024). <a href=\"https:\/\/doi.org\/10.3390\/pathogens13060504\">A Novel Cryptic Virus Isolated from <em>Galphimia<\/em> spp. in Mexico<\/a>. <em>Pathogens<\/em>, 13(6), 504.<\/li>\n<\/ol>\n\n<h3>2023<\/h3>\n<ol reversed start=\"55\">\n<li>Alfredo D\u00edaz-Lara, <strong>Kristian Stevens<\/strong>, Vivian Hayde Aguilar-Molina, Jos\u00e9 Miguel Fern\u00e1ndez-Cort\u00e9s, V\u00edctor Manuel Chabacano Le\u00f3n, Marcos De Donato, Ashutosh Sharma, Teresa M. Erickson, Maher Al Rwahnih (2023). <a href=\"https:\/\/doi.org\/10.3390\/v15071561\">High-Throughput Sequencing of Grapevine in Mexico Reveals a High Incidence of Viruses including a New Member of the Genus <em>Enamovirus<\/em><\/a>. <em>Viruses<\/em>, 15(7), 1561.<\/li>\n<li>Annelies Haegeman, Yoika Foucart, Kris De Jonghe, Thomas Goedefroit, Maher Al Rwahnih, \u2026, <strong>Kristian Stevens<\/strong>, et al. (2023). <a href=\"https:\/\/doi.org\/10.3390\/plants12112139\">Looking beyond Virus Detection in RNA Sequencing Data: Lessons Learned from a Community-Based Effort to Detect Cellular Plant Pathogens and Pests<\/a>. <em>Plants<\/em>, 12(11), 2139.<\/li>\n<li>Ashrafou Ouro-Djobo, <strong>Kristian Stevens<\/strong>, Justin J. Scheiner, Violeta M. Tsolova, Frances M. Pontasch, Sheila McBride, David N. Appel, Maher Al Rwahnih, Olufemi J. Alabi (2023). <a href=\"https:\/\/doi.org\/10.1094\/phytofr-10-22-0111-sc\">Molecular Characterization of Divergent Isolates of Grapevine Red Blotch Virus from Blanc du Soleil, an Interspecific Hybrid White Grapevine Cultivar<\/a>. <em>PhytoFrontiers<\/em>, 3(2), 290\u2013295.<\/li>\n<li>Anneliek M. ter Horst, Jane D. Fudyma, Aur\u00e9lie Bak, Min Sook Hwang, Christian Santos-Medell\u00edn, <strong>Kristian Stevens<\/strong>, David M. Rizzo, Maher Al Rwahnih, Joanne B. Emerson (2023). <a href=\"https:\/\/doi.org\/10.1094\/pbiomes-12-21-0080-r\">RNA Viral Communities Are Structured by Host Plant Phylogeny in Oak and Conifer Leaves<\/a>. <em>Phytobiomes Journal<\/em>, 7(2), 288\u2013296.<\/li>\n<\/ol>\n\n<h3>2022<\/h3>\n<ol reversed start=\"51\">\n<li>Jiyeong Choi, Anya Clara Osatuke, Griffin Erich, <strong>Kristian Stevens<\/strong>, Min Sook Hwang, Maher Al Rwahnih, Marc Fuchs (2022). <a href=\"https:\/\/doi.org\/10.3390\/plants11243565\">High-Throughput Sequencing Reveals Tobacco and Tomato Ringspot Viruses in Pawpaw<\/a>. <em>Plants<\/em>, 11(24), 3565.<\/li>\n<li>Martin Jaguni\u0107, Alfredo D\u00edaz-Lara, L\u00f3r\u00e1nt Sz\u0151ke, Maher Al Rwahnih, <strong>Kristian Stevens<\/strong>, Goran Zduni\u0107, Darko Von\u010dina (2022). <a href=\"https:\/\/doi.org\/10.3390\/plants11182341\">Incidence and Genetic Diversity of Grapevine Virus G in Croatian Vineyards<\/a>. <em>Plants<\/em>, 11(18), 2341.<\/li>\n<li>Martin Jaguni\u0107, Alfredo D\u00edaz-Lara, Maher Al Rwahnih, Darko Preiner, <strong>Kristian Stevens<\/strong>, Goran Zduni\u0107, Min Sook Hwang, Darko Von\u010dina (2022). <a href=\"https:\/\/doi.org\/10.3390\/plants11162135\">Grapevine Badnavirus 1: Detection, Genetic Diversity, and Distribution in Croatia<\/a>. <em>Plants<\/em>, 11(16), 2135.<\/li>\n<li>Darko Von\u010dina, Alfredo D\u00edaz-Lara, Darko Preiner, Maher Al Rwahnih, <strong>Kristian Stevens<\/strong>, Snje\u017eana Juri\u0107, et al. (2022). <a href=\"https:\/\/doi.org\/10.3390\/plants11111485\">Virus and Virus-like Pathogens in the Grapevine Virus Collection of Croatian Autochthonous Grapevine Cultivars<\/a>. <em>Plants<\/em>, 11(11), 1485.<\/li>\n<li>Jessica W. Wright, <strong>Kristian Stevens<\/strong>, Paul D. Hodgskiss, Charles H. Langley (2022). <a href=\"https:\/\/doi.org\/10.1094\/pdis-08-21-1608-re\">SNPs in a Large Genomic Scaffold Are Strongly Associated with <em>Cr1R<\/em>, Major Gene for Resistance to White Pine Blister Rust in Range-Wide Samples of Sugar Pine (<em>Pinus lambertiana<\/em>)<\/a>. <em>Plant Disease<\/em>, 106(6), 1639\u20131644.<\/li>\n<li>Kellee Britt, Samantha Gebben, Amit Levy, Diann Achor, Peggy J. Sieburth, <strong>Kristian Stevens<\/strong>, Maher Al Rwahnih, \u00d6zgur Batuman (2022). <a href=\"https:\/\/doi.org\/10.3390\/insects13030275\">Analysis of Citrus Tristeza Virus Incidences within Asian Citrus Psyllid (<em>Diaphorina citri<\/em>) Populations in Florida via High-Throughput Sequencing<\/a>. <em>Insects<\/em>, 13(3), 275.<\/li>\n<li>Pedro J. Mart\u00ednez-Garc\u00eda, Alejandra V\u00e1zquez-Lobo, Pablo Mart\u00ednez-Garc\u00eda, Jorge Mas-G\u00f3mez, Carmen Jurado-Ma\u00f1ogil, <strong>Kristian Stevens<\/strong> (2022). <a href=\"https:\/\/doi.org\/10.1007\/978-3-030-93390-6_2\">Advances in Genetic Mapping in Pines<\/a>. In <em>The Pine Genomes<\/em>, Compendium of Plant Genomes, 9\u201319. Springer.<\/li>\n<\/ol>\n\n<h3>2021<\/h3>\n<ol reversed start=\"44\">\n<li>Lucie Tamisier, Annelies Haegeman, Yoika Foucart, Nicolas Fouillien, Maher Al Rwahnih, \u2026, <strong>Kristian Stevens<\/strong>, et al. (2021). <a href=\"https:\/\/doi.org\/10.24072\/pcjournal.62\">Semi-artificial datasets as a resource for validation of bioinformatics pipelines for plant virus detection<\/a>. <em>Peer Community Journal<\/em>, 1.<\/li>\n<li>Kellee Britt, <strong>Kristian Stevens<\/strong>, Samantha Gebben, Amit Levy, Maher Al Rwahnih, \u00d6zgur Batuman (2021). <a href=\"https:\/\/doi.org\/10.1128\/mra.00563-21\">Partial Genome Sequence of a Novel Reo-Like Virus Detected in Asian Citrus Psyllid (<em>Diaphorina citri<\/em>) Populations from Florida Citrus Groves<\/a>. <em>Microbiology Resource Announcements<\/em>, 10(34), e00563-21.<\/li>\n<li>Alfredo D\u00edaz-Lara, <strong>Kristian Stevens<\/strong>, Vicki Klaassen, Min Sook Hwang, Maher Al Rwahnih (2021). <a href=\"https:\/\/doi.org\/10.3390\/v13081442\">Sequencing a Strawberry Germplasm Collection Reveals New Viral Genetic Diversity and the Basis for New RT-qPCR Assays<\/a>. <em>Viruses<\/em>, 13(8), 1442.<\/li>\n<li>Larissa Carvalho Costa, <strong>Kristian Stevens<\/strong>, Xiaojun Hu, Marc Fuchs, Maher Al Rwahnih, Alfredo D\u00edaz-Lara, Clint McFarland, Joseph A. Foster, Oscar P. Hurtado-Gonzales (2021). <a href=\"https:\/\/doi.org\/10.1007\/s00705-021-05174-z\">Identification and characterization of a novel virus associated with an eriophyid mite in extracts of fruit trees leaves<\/a>. <em>Archives of Virology<\/em>, 166(10), 2869\u20132873.<\/li>\n<li>Nourolah Soltani, <strong>Kristian Stevens<\/strong>, Vicki Klaassen, Min Sook Hwang, Deborah A. Golino, Maher Al Rwahnih (2021). <a href=\"https:\/\/doi.org\/10.3390\/v13061130\">Quality Assessment and Validation of High-Throughput Sequencing for Grapevine Virus Diagnostics<\/a>. <em>Viruses<\/em>, 13(6), 1130.<\/li>\n<\/ol>\n\n<h3>2020<\/h3>\n<ol reversed start=\"39\">\n<li>Matthew J. Weiss, Richard A. Sniezko, Daniela Puiu, Marc W. Crepeau, <strong>Kristian Stevens<\/strong>, Steven L. Salzberg, Charles H. Langley, David B. Neale, Amanda R. De La Torre (2020). <a href=\"https:\/\/doi.org\/10.1111\/tpj.14928\">Genomic basis of white pine blister rust quantitative disease resistance and its relationship with qualitative resistance<\/a>. <em>The Plant Journal<\/em>, 104(2), 365\u2013376.<\/li>\n<li>Alfredo D\u00edaz-Lara, Nola J. Mosier, <strong>Kristian Stevens<\/strong>, Karen E. Keller, Robert R. Martin (2020). <a href=\"https:\/\/doi.org\/10.1159\/000509845\">Evidence of Rubus Yellow Net Virus Integration into the Red Raspberry Genome<\/a>. <em>Cytogenetic and Genome Research<\/em>, 160(6), 329\u2013334.<\/li>\n<li>Alexander J. Trouern-Trend, Taylor Falk, Sumaira Zaman, Madison Caballero, David B. Neale, Charles H. Langley, Abhaya M. Dandekar, <strong>Kristian Stevens<\/strong>, Jill L. Wegrzyn (2020). <a href=\"https:\/\/doi.org\/10.1111\/tpj.14630\">Comparative genomics of six <em>Juglans<\/em> species reveals disease-associated gene family contractions<\/a>. <em>The Plant Journal<\/em>, 102(2), 410\u2013423.<\/li>\n<li>Alfredo D\u00edaz-Lara, <strong>Kristian Stevens<\/strong>, Vicki Klaassen, Deborah A. Golino, Maher Al Rwahnih (2020). <a href=\"https:\/\/doi.org\/10.3390\/plants9020273\">Comprehensive Real-Time RT-PCR Assays for the Detection of Fifteen Viruses Infecting <em>Prunus<\/em> spp.<\/a> <em>Plants<\/em>, 9(2), 273.<\/li>\n<\/ol>\n\n<h3>2019<\/h3>\n<ol reversed start=\"35\">\n<li>Maher Al Rwahnih, Olufemi J. Alabi, Min Sook Hwang, <strong>Kristian Stevens<\/strong>, Deborah A. Golino (2019). <a href=\"https:\/\/doi.org\/10.1007\/s00705-019-04434-3\">Identification and genomic characterization of grapevine Kizil Sapak virus, a novel grapevine-infecting member of the family <em>Betaflexiviridae<\/em><\/a>. <em>Archives of Virology<\/em>, 164(12), 3145\u20133149.<\/li>\n<li>Alfredo D\u00edaz-Lara, Beatriz Navarro, Francesco Di Serio, <strong>Kristian Stevens<\/strong>, Min Sook Hwang, Joshua B. Kohl, Sandra Thuy Vu, Bryce W. Falk, Deborah A. Golino, Maher Al Rwahnih (2019). <a href=\"https:\/\/doi.org\/10.3390\/v11080685\">Two Novel Negative-Sense RNA Viruses Infecting Grapevine Are Members of a Newly Proposed Genus within the Family <em>Phenuiviridae<\/em><\/a>. <em>Viruses<\/em>, 11(8), 685.<\/li>\n<li>Annarita Marrano, Pedro J. Mart\u00ednez-Garc\u00eda, Luca Bianco, Gina M. Sideli, Erica A. Di Pierro, \u2026, <strong>Kristian Stevens<\/strong>, et al. (2019). <a href=\"https:\/\/doi.org\/10.1111\/pbi.13034\">A new genomic tool for walnut (<em>Juglans regia<\/em> L.): development and validation of the high-density Axiom\u2122 <em>J. regia<\/em> 700K SNP genotyping array<\/a>. <em>Plant Biotechnology Journal<\/em>, 17(6), 1027\u20131036.<\/li>\n<li>Amanda R. De La Torre, Daniela Puiu, Marc W. Crepeau, <strong>Kristian Stevens<\/strong>, Steven L. Salzberg, Charles H. Langley, David B. Neale (2019). <a href=\"https:\/\/doi.org\/10.1111\/nph.15535\">Genomic architecture of complex traits in loblolly pine<\/a>. <em>New Phytologist<\/em>, 221(4), 1789\u20131801.<\/li>\n<\/ol>\n\n<h3>2018<\/h3>\n<ol reversed start=\"31\">\n<li>Alfredo D\u00edaz-Lara, Vicki Klaassen, <strong>Kristian Stevens<\/strong>, Mysore R. Sudarshana, Adib Rowhani, Hans J. Maree, et al. (2018). <a href=\"https:\/\/doi.org\/10.1371\/journal.pone.0208862\">Characterization of grapevine leafroll-associated virus 3 genetic variants and application towards RT-qPCR assay design<\/a>. <em>PLOS ONE<\/em>, 13(12), e0208862.<\/li>\n<li><strong>Kristian Stevens<\/strong>, Keith Woeste, Sandeep Chakraborty, Marc W. Crepeau, Charles A. Leslie, Pedro J. Mart\u00ednez-Garc\u00eda, et al. (2018). <a href=\"https:\/\/doi.org\/10.1534\/g3.118.200030\">Genomic Variation Among and Within Six <em>Juglans<\/em> Species<\/a>. <em>G3: Genes|Genomes|Genetics<\/em>, 8(7), 2153\u20132165.<\/li>\n<li>Maher Al Rwahnih, Adib Rowhani, Nathaniel Westrick, <strong>Kristian Stevens<\/strong>, Alfredo D\u00edaz-Lara, Florent P. Trouillas, John E. Preece, Craig E. Kallsen, Kristen Farrar, Deborah A. Golino (2018). <a href=\"https:\/\/doi.org\/10.1094\/pdis-12-17-1988-re\">Discovery of Viruses and Virus-Like Pathogens in Pistachio using High-Throughput Sequencing<\/a>. <em>Plant Disease<\/em>, 102(7), 1419\u20131425.<\/li>\n<\/ol>\n\n<h3>2017<\/h3>\n<ol reversed start=\"28\">\n<li>David B. Neale, Patrick E. McGuire, Nicholas C. Wheeler, <strong>Kristian Stevens<\/strong>, Marc W. Crepeau, Charis M. Cardeno, et al. (2017). <a href=\"https:\/\/doi.org\/10.1534\/g3.117.300078\">The Douglas-Fir Genome Sequence Reveals Specialization of the Photosynthetic Apparatus in Pinaceae<\/a>. <em>G3: Genes|Genomes|Genetics<\/em>, 7(9), 3157\u20133167.<\/li>\n<li>Marc W. Crepeau, Charles H. Langley, <strong>Kristian Stevens<\/strong> (2017). <a href=\"https:\/\/doi.org\/10.1534\/g3.117.040055\">From Pine Cones to Read Clouds: Rescaffolding the Megagenome of Sugar Pine (<em>Pinus lambertiana<\/em>)<\/a>. <em>G3: Genes|Genomes|Genetics<\/em>, 7(5), 1563\u20131568.<\/li>\n<li>Aleksey V. Zimin, <strong>Kristian Stevens<\/strong>, Marc W. Crepeau, Daniela Puiu, Jill L. Wegrzyn, James A. Yorke, Charles H. Langley, David B. Neale, Steven L. Salzberg (2017). <a href=\"https:\/\/doi.org\/10.1093\/gigascience\/giw016\">An improved assembly of the loblolly pine mega-genome using long-read single-molecule sequencing<\/a>. <em>GigaScience<\/em>, 6(1), 1\u20134.<\/li>\n<\/ol>\n\n<h3>2016<\/h3>\n<ol reversed start=\"25\">\n<li>Daniel Gonz\u00e1lez-Ibeas, Pedro J. Mart\u00ednez-Garc\u00eda, Randi A. Famula, Annette Delfino-Mix, <strong>Kristian Stevens<\/strong>, Carol A. Loopstra, Charles H. Langley, David B. Neale, Jill L. Wegrzyn (2016). <a href=\"https:\/\/doi.org\/10.1534\/g3.116.032805\">Assessing the Gene Content of the Megagenome: Sugar Pine (<em>Pinus lambertiana<\/em>)<\/a>. <em>G3: Genes|Genomes|Genetics<\/em>, 6(12), 3787\u20133802.<\/li>\n<li><strong>Kristian Stevens<\/strong>, Jill L. Wegrzyn, Aleksey V. Zimin, Daniela Puiu, Marc W. Crepeau, Charis M. Cardeno, et al. (2016). <a href=\"https:\/\/doi.org\/10.1534\/genetics.116.193227\">Sequence of the Sugar Pine Megagenome<\/a>. <em>Genetics<\/em>, 204(4), 1613\u20131626.<\/li>\n<li>Victoria L. Sork, Sorel T. Fitz-Gibbon, Daniela Puiu, Marc W. Crepeau, Paul F. Gugger, Rachel M. Sherman, <strong>Kristian Stevens<\/strong>, Charles H. Langley, Matteo Pellegrini, Steven L. Salzberg (2016). <a href=\"https:\/\/doi.org\/10.1534\/g3.116.030411\">First Draft Assembly and Annotation of the Genome of a California Endemic Oak <em>Quercus lobata<\/em> N\u00e9e (Fagaceae)<\/a>. <em>G3: Genes|Genomes|Genetics<\/em>, 6(11), 3485\u20133495.<\/li>\n<li>Pedro J. Mart\u00ednez-Garc\u00eda, Marc W. Crepeau, Daniela Puiu, Daniel Gonz\u00e1lez-Ibeas, Jeanne Whalen, <strong>Kristian Stevens<\/strong>, et al. (2016). <a href=\"https:\/\/doi.org\/10.1111\/tpj.13207\">The walnut (<em>Juglans regia<\/em>) genome sequence reveals diversity in genes coding for the biosynthesis of non-structural polyphenols<\/a>. <em>The Plant Journal<\/em>, 87(5), 507\u2013532.<\/li>\n<\/ol>\n\n<h3>2015<\/h3>\n<ol reversed start=\"21\">\n<li>Michael Coulombe, <strong>Kristian Stevens<\/strong>, Dan Gusfield (2015). <a href=\"https:\/\/doi.org\/10.1109\/iccabs.2015.7344709\">Construction, enumeration, and optimization of perfect phylogenies on multi-state data<\/a>. In <em>2015 IEEE 5th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS)<\/em>, 1\u20136.<\/li>\n<li>Justin B. Lack, Charis M. Cardeno, Marc W. Crepeau, William Taylor, Russell B. Corbett-Detig, <strong>Kristian Stevens<\/strong>, Charles H. Langley, John E. Pool (2015). <a href=\"https:\/\/doi.org\/10.1534\/genetics.115.174664\">The <em>Drosophila<\/em> Genome Nexus: A Population Genomic Resource of 623 <em>Drosophila melanogaster<\/em> Genomes, Including 197 from a Single Ancestral Range Population<\/a>. <em>Genetics<\/em>, 199(4), 1229\u20131241.<\/li>\n<\/ol>\n\n<h3>2014<\/h3>\n<ol reversed start=\"19\">\n<li>Bonnie Kirkpatrick, <strong>Kristian Stevens<\/strong> (2014). <a href=\"https:\/\/doi.org\/10.1109\/tcbb.2014.2316005\">Perfect Phylogeny Problems with Missing Values<\/a>. <em>IEEE\/ACM Transactions on Computational Biology and Bioinformatics<\/em>, 11(5), 928\u2013941.<\/li>\n<li>David B. Neale, Jill L. Wegrzyn, <strong>Kristian Stevens<\/strong>, Aleksey V. Zimin, Daniela Puiu, Marc W. Crepeau, et al. (2014). <a href=\"https:\/\/doi.org\/10.1186\/gb-2014-15-3-r59\">Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies<\/a>. <em>Genome Biology<\/em>, 15(3), R59.<\/li>\n<li>Jill L. Wegrzyn, John D. Liechty, <strong>Kristian Stevens<\/strong>, Le-Shin Wu, Carol A. Loopstra, Hans A. Vasquez-Gross, et al. (2014). <a href=\"https:\/\/doi.org\/10.1534\/genetics.113.159996\">Unique Features of the Loblolly Pine (<em>Pinus taeda<\/em> L.) Megagenome Revealed Through Sequence Annotation<\/a>. <em>Genetics<\/em>, 196(3), 891\u2013909.<\/li>\n<li>Aleksey V. Zimin, <strong>Kristian Stevens<\/strong>, Marc W. Crepeau, Ann Holtz-Morris, Maxim Koriabine, Guillaume Mar\u00e7ais, et al. (2014). <a href=\"https:\/\/doi.org\/10.1534\/genetics.113.159715\">Sequencing and Assembly of the 22-Gb Loblolly Pine Genome<\/a>. <em>Genetics<\/em>, 196(3), 875\u2013890.<\/li>\n<\/ol>\n\n<h3>2013<\/h3>\n<ol reversed start=\"15\">\n<li>Jill L. Wegrzyn, Brian Y. Lin, Jacob J. Zieve, William M. Dougherty, Pedro J. Mart\u00ednez-Garc\u00eda, \u2026, <strong>Kristian Stevens<\/strong>, et al. (2013). <a href=\"https:\/\/doi.org\/10.1371\/journal.pone.0072439\">Insights into the Loblolly Pine Genome: Characterization of BAC and Fosmid Sequences<\/a>. <em>PLOS ONE<\/em>, 8(9), e72439.<\/li>\n<li>Pedro J. Mart\u00ednez-Garc\u00eda, <strong>Kristian Stevens<\/strong>, Jill L. Wegrzyn, John D. Liechty, Marc W. Crepeau, Charles H. Langley, David B. Neale (2013). <a href=\"https:\/\/doi.org\/10.1007\/s11295-013-0646-4\">Combination of multipoint maximum likelihood (MML) and regression mapping algorithms to construct a high-density genetic linkage map for loblolly pine (<em>Pinus taeda<\/em> L.)<\/a>. <em>Tree Genetics &amp; Genomes<\/em>, 9(6), 1529\u20131535.<\/li>\n<li>Rob Gysel, Dan Gusfield, <strong>Kristian Stevens<\/strong> (2013). <a href=\"https:\/\/doi.org\/10.1109\/iccabs.2013.6629217\">Triangulation heuristics for maximum character compatibility<\/a>. In <em>2013 IEEE 3rd International Conference on Computational Advances in Bio and Medical Sciences (ICCABS)<\/em>, 1\u20132.<\/li>\n<\/ol>\n\n<h3>2012<\/h3>\n<ol reversed start=\"12\">\n<li>John E. Pool, Russell B. Corbett-Detig, Ryuichi P. Sugino, <strong>Kristian Stevens<\/strong>, Charis M. Cardeno, Marc W. Crepeau, et al. (2012). <a href=\"https:\/\/doi.org\/10.1371\/journal.pgen.1003080\">Population Genomics of Sub-Saharan <em>Drosophila melanogaster<\/em>: African Diversity and Non-African Admixture<\/a>. <em>PLOS Genetics<\/em>, 8(12), e1003080.<\/li>\n<li>Charles H. Langley, <strong>Kristian Stevens<\/strong>, Charis M. Cardeno, Yuh Chwen G. Lee, Daniel R. Schrider, John E. Pool, et al. (2012). <a href=\"https:\/\/doi.org\/10.1534\/genetics.112.142018\">Genomic Variation in Natural Populations of <em>Drosophila melanogaster<\/em><\/a>. <em>Genetics<\/em>, 192(2), 533\u2013598.<\/li>\n<li>Rob Gysel, <strong>Kristian Stevens<\/strong>, Dan Gusfield (2012). <a href=\"https:\/\/doi.org\/10.1007\/978-3-642-33122-0_8\">Reducing Problems in Unrooted Tree Compatibility to Restricted Triangulations of Intersection Graphs<\/a>. In <em>Algorithms in Bioinformatics (WABI 2012)<\/em>, Lecture Notes in Computer Science 7534, 93\u2013105.<\/li>\n<\/ol>\n\n<h3>2011<\/h3>\n<ol reversed start=\"9\">\n<li>Daniel R. Schrider, <strong>Kristian Stevens<\/strong>, Charis M. Cardeno, Charles H. Langley, Matthew W. Hahn (2011). <a href=\"https:\/\/doi.org\/10.1101\/gr.116434.110\">Genome-wide analysis of retrogene polymorphisms in <em>Drosophila melanogaster<\/em><\/a>. <em>Genome Research<\/em>, 21(12), 2087\u20132095.<\/li>\n<li>Charles H. Langley, Marc W. Crepeau, Charis M. Cardeno, Russell B. Corbett-Detig, <strong>Kristian Stevens<\/strong> (2011). <a href=\"https:\/\/doi.org\/10.1534\/genetics.111.127530\">Circumventing Heterozygosity: Sequencing the Amplified Genome of a Single Haploid <em>Drosophila melanogaster<\/em> Embryo<\/a>. <em>Genetics<\/em>, 188(2), 239\u2013246.<\/li>\n<li><strong>Kristian Stevens<\/strong>, Bonnie Kirkpatrick (2011). <a href=\"https:\/\/doi.org\/10.1007\/978-3-642-23038-7_24\">Efficiently Solvable Perfect Phylogeny Problems on Binary and k-State Data with Missing Values<\/a>. In <em>Algorithms in Bioinformatics (WABI 2011)<\/em>, Lecture Notes in Computer Science 6833, 282\u2013297.<\/li>\n<\/ol>\n\n<h3>2010<\/h3>\n<ol reversed start=\"6\">\n<li><strong>Kristian Stevens<\/strong>, Henry Chen, Terry Filiba, Peter L. McMahon, Yun S. Song (2010). <a href=\"https:\/\/doi.org\/10.1109\/fpl.2010.121\">SeqHive: A Reconfigurable Computer Cluster for Genome Re-sequencing<\/a>. In <em>2010 International Conference on Field Programmable Logic and Applications (FPL)<\/em>, IEEE, 442\u2013447.<\/li>\n<li><strong>Kristian Stevens<\/strong>, Dan Gusfield (2010). <a href=\"https:\/\/doi.org\/10.1007\/978-3-642-15294-8_23\">Reducing Multi-state to Binary Perfect Phylogeny with Applications to Missing, Removable, Inserted, and Deleted Data<\/a>. In <em>Algorithms in Bioinformatics (WABI 2010)<\/em>, Lecture Notes in Computer Science 6293, 274\u2013287.<\/li>\n<\/ol>\n\n<h3>2009<\/h3>\n<ol reversed start=\"4\">\n<li>Wei-Chun Kao, <strong>Kristian Stevens<\/strong>, Yun S. Song (2009). <a href=\"https:\/\/doi.org\/10.1101\/gr.095299.109\">BayesCall: A model-based base-calling algorithm for high-throughput short-read sequencing<\/a>. <em>Genome Research<\/em>, 19(10), 1884\u20131895.<\/li>\n<\/ol>\n\n<h3>2007<\/h3>\n<ol reversed start=\"3\">\n<li>David J. Begun, Alisha K. Holloway, <strong>Kristian Stevens<\/strong>, LaDeana W. Hillier, Yu-Ping Poh, Matthew W. Hahn, et al. (2007). <a href=\"https:\/\/doi.org\/10.1371\/journal.pbio.0050310\">Population Genomics: Whole-Genome Analysis of Polymorphism and Divergence in <em>Drosophila simulans<\/em><\/a>. <em>PLOS Biology<\/em>, 5(11), e310.<\/li>\n<\/ol>\n\n<h3>2004<\/h3>\n<ol reversed start=\"2\">\n<li>Ursula Vitt, Darryl Gietzen, <strong>Kristian Stevens<\/strong>, Jim Wingrove, Shanya Becha, Sean Bulloch, et al. (2004). <a href=\"https:\/\/doi.org\/10.1101\/gr.1932304\">Identification of Candidate Disease Genes by EST Alignments, Synteny, and Expression and Verification of Ensembl Genes on Rat Chromosome 1q43-54<\/a>. <em>Genome Research<\/em>, 14(4), 640\u2013650.<\/li>\n<li>Rat Genome Sequencing Project Consortium, including <strong>Kristian Stevens<\/strong> (2004). <a href=\"https:\/\/doi.org\/10.1038\/nature02426\">Genome sequence of the Brown Norway rat yields insights into mammalian evolution<\/a>. <em>Nature<\/em>, 428(6982), 493\u2013521.<\/li>\n<\/ol>\n\n<\/div>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t<\/div>\n\t\t","protected":false},"excerpt":{"rendered":"<p>Research Interests Algorithms Design and analysis of algorithms for problems in phylogenetics, genomic sequence analysis, high-throughput sequencing, and computer science education. Genomics &amp; Population Genomics Reference genome sequencing and population-scale resequencing to identify and characterize genetic variation associated with biological phenotypes. Metagenomics &amp; NGS Diagnostics Analysis of high-throughput sequencing data for research and diagnostic applications, [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"inline_featured_image":false,"footnotes":""},"class_list":["post-35","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/faculty.engineering.ucdavis.edu\/stevens\/wp-json\/wp\/v2\/pages\/35","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/faculty.engineering.ucdavis.edu\/stevens\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/faculty.engineering.ucdavis.edu\/stevens\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/faculty.engineering.ucdavis.edu\/stevens\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/faculty.engineering.ucdavis.edu\/stevens\/wp-json\/wp\/v2\/comments?post=35"}],"version-history":[{"count":42,"href":"https:\/\/faculty.engineering.ucdavis.edu\/stevens\/wp-json\/wp\/v2\/pages\/35\/revisions"}],"predecessor-version":[{"id":1149,"href":"https:\/\/faculty.engineering.ucdavis.edu\/stevens\/wp-json\/wp\/v2\/pages\/35\/revisions\/1149"}],"wp:attachment":[{"href":"https:\/\/faculty.engineering.ucdavis.edu\/stevens\/wp-json\/wp\/v2\/media?parent=35"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}