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Kristian Stevens

UC Davis
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Research

Interests
Algorithms

Design and analysis of algorithms for problems in phylogenetics, genomic sequence analysis, high-throughput sequencing, and computer science education.

Genomics & Population Genomics

Reference genome sequencing and population-scale resequencing to identify and characterize genetic variation associated with biological phenotypes.

Metagenomics & NGS Diagnostics

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.

Pedagogy

Interdisciplinary computer science education, curriculum development, computational thinking, and algorithmic approaches to problems in teaching and learning.

Publications
75 peer-reviewed publications · 1 preprint 8,347 citations · h-index: 30 · i10-index: 43 · Google Scholar profile

Just in

  1. Zonglin Han, Yichen Chen, Jiawen Jiang, Tongan Shi, Kristian Stevens (2026). Stochasticity Is Not the Hard Part: Reduction and Complexity in Instructional Sequencing over Prerequisite DAGs. arXiv (Cornell University).

2026

  1. Raied Abou Kubaa, Kristian A. Stevens, Teresa M. Erickson, Maher Al Rwahnih (2026). A New HiPlex Amplicon Sequencing Approach for the Detection of Grapevine Leafroll-Associated Virus 3 and Grapevine Red Blotch Virus in Grapevines. Viruses, 18(9), 959.
  2. Ana Belen Duarte Cruz, Víctor Manuel Martín del Campo Soler, Kristian Stevens, Alfredo Diaz Lara (2026). First detection of bell pepper endornavirus infecting bell pepper in Guanajuato, Mexico. Revista Mexicana de Fitopatología, Mexican Journal of Phytopathology, 44(3).
  3. Elizabeth J. Indermaur, Anna O. Wunsch, Heather McLane, Kristian Stevens, Min Sook Hwang, Maher Al Rwahnih, Christine D. Smart, Marc Fuchs (2026). The Virome of Rhubarb Consists of Diverse Viruses Belonging to at Least Four Families. Phytopathology®, PHYTO–07-26-0225-SC.
  4. Raied Abou Kubaa, Teresa M. Erickson, Haoran Li, Kristian Stevens, Maher Al Rwahnih (2026). Coding-complete genome sequence of grapevine leafroll-associated virus 13 from grapevine in California. Microbiology Resource Announcements, e0052926.
  5. Ahmed Mohamed, Kristian Stevens, Islam El-Sharkawy, Maher Al Rwahnih, Violeta M. Tsolova (2026). First report of grapevine virus B in muscadine grape ( Muscadinia rotundifolia (Michx.) Small) in Florida. Plant Disease, PDIS–05-26-1021-PDN.
  6. R. A. Melanson, Carol Chen, Kristian Stevens, Laura Jenkins Hladky, Maher Al Rwahnih, William M. Wintermantel (2026). Identification of melon severe mosaic virus in cucurbits in Mississippi highlights the need for routine virus monitoring with assays targeting multiple viruses. Plant Disease.
  7. Juan Pedro López-Córdova, Jose A. Garzón-Tiznado, María Eugenia Rentería-Martínez, Juan Manuel Tovar-Pedraza, Kristian Stevens, María de los Ángeles Mora-Ugalde, Alfredo Díaz-Lara (2026). First Report of Cucumber Green Mottle Mosaic Virus (CGMMV) Infecting Cucumber in Mexico. Plant Disease, 110(4), 1496.
  8. Kristian Stevens, Juliana Osse de Souza, Haoran Li, Ashrafou Ouro-Djobo, Olufemi J. Alabi, Maher Al Rwahnih (2026). Agave associated crinivirus A: a novel monopartite crinivirus homolog isolated from agave. Archives of Virology, 171(4).
  9. Zonglin Han, Kristian Stevens (2026). Quantifying Cross-System Curriculum Alignment: A Reproducible and Interpretable Method. 1–7.
  10. Olufemi J. Alabi, Ashrafou Ouro-Djobo, Audrey Rodriguez, John Oladeji Oladokun, Minsook Hwang, Cecilia Villegas, Kristian Stevens, Al Rwahnih M., Kevin Ong (2026). Plumeria ampelovirus 1, a novel ampelovirus subgroup II member infecting Plumeria spp.. Archives of Virology, 171(3), 79.

2025

  1. Raied Abou Kubaa, Ashrafou Ouro-Djobo, Kristian Stevens, Olufemi J. Alabi, Maher Al Rwahnih (2025). Genome characterization of prunus maculavirus 1 (PrMcV-1), a novel member of the genus maculavirus identified in prunus spp.. Archives of Virology, 170(8), 168.
  2. Peter Abrahamian, Weili Cai, Schyler O. Nunziata, Kristian Stevens, Xiaojun Hu, Min Sook Hwang, et al. (2025). Interlaboratory Validation of High-Throughput Sequencing for the Detection of Viruses and Viroids in Apple, Grapevine, and Stone Fruits. PhytoFrontiers™, 5(4), 623–634.
  3. Jeffrey S. Groh, Diane C. Vik, Matthew Davis, J. Grey Monroe, Kristian Stevens, Patrick J. Brown, Charles H. Langley, Graham Coop (2025). Ancient structural variants control sex-specific flowering time morphs in walnuts and hickories. Science, 387(6729), eado5578.

2024

  1. Kristian Stevens, Maher Al Rwahnih (2024). High-Throughput Sequencing for the Detection of Viruses in Grapevine: Performance Analysis and Best Practices. Viruses, 16(12), 1957.
  2. Maher Al Rwahnih, Vicki Klaassen, Teresa M. Erickson, Olufemi J. Alabi, Kristian Stevens, Min Sook Hwang, Lauren Port (2024). A New Era in Federal Quarantine and State Certification Diagnostics at Clean Plant Centers in the United States. Plant Disease, 109(7), 1392–1403.
  3. Kellee Britt-Ugartemendia, Kristian Stevens, Maher Al Rwahnih, Amit Levy, Özgur Batuman (2024). RNA-Sequencing-Based Virome Discovery in Florida Citrus Pests. Phytobiomes Journal, 9(1), 95–108.
  4. Juliana Osse de Souza, Vicki Klaassen, Kristian Stevens, Teresa M. Erickson, Claire Heinitz, Maher Al Rwahnih (2024). Characterization of Genetic Diversity in the Capsid Protein Gene of Grapevine Fleck Virus and Development of a New Real-Time RT-PCR Assay. Viruses, 16(9), 1457.
  5. Dianella Iglesias, Kristian Stevens, Ashutosh Sharma, Alfredo Díaz-Lara (2024). A Novel Cryptic Virus Isolated from Galphimia spp. in Mexico. Pathogens, 13(6), 504.
  6. Olufemi J. Alabi, Kristian Stevens, John Oladeji Oladokun, Cecilia Villegas, Min Sook Hwang, Maher Al Rwahnih, et al. (2024). Discovery and Characterization of Two Highly Divergent Variants of a Novel Potyvirus Species Infecting Madagascar Periwinkle (Catharanthus roseus). Plant Disease, 108(8), 2494–2502.

2023

  1. Annelies Haegeman, Yoika Foucart, Kris de Jonghe, Thomas Goedefroit, Maher Al Rwahnih, …, Kristian Stevens, et al. (2023). Revisiting high throughput sequencing data used for plant virus detection in order to find evidence of nonviralplant pathogens and pests. HAL (Le Centre pour la Communication Scientifique Directe).
  2. Alfredo Díaz-Lara, Kristian Stevens, Vivian Hayde Aguilar-Molina, José Miguel Fernández-Cortés, Víctor Manuel Chabacano León, Marcos De Donato, Ashutosh Sharma, Teresa M. Erickson, Maher Al Rwahnih (2023). High-Throughput Sequencing of Grapevine in Mexico Reveals a High Incidence of Viruses including a New Member of the Genus Enamovirus. Viruses, 15(7), 1561.
  3. Annelies Haegeman, Yoika Foucart, Kris De Jonghe, Thomas Goedefroit, Maher Al Rwahnih, …, Kristian Stevens, et al. (2023). Looking beyond Virus Detection in RNA Sequencing Data: Lessons Learned from a Community-Based Effort to Detect Cellular Plant Pathogens and Pests. Plants, 12(11), 2139.

2022

  1. Jiyeong Choi, Anya Clara Osatuke, Griffin Erich, Kristian Stevens, Min Sook Hwang, Maher Al Rwahnih, Marc Fuchs (2022). High-Throughput Sequencing Reveals Tobacco and Tomato Ringspot Viruses in Pawpaw. Plants, 11(24), 3565.
  2. Ashrafou Ouro-Djobo, Kristian Stevens, Justin J. Scheiner, Violeta Tsolova, Frances M. Pontasch, Sheila McBride, David N. Appel, Maher Al Rwahnih, Olufemi J. Alabi (2022). Molecular Characterization of Divergent Isolates of Grapevine Red Blotch Virus from Blanc du Soleil, an Interspecific Hybrid White Grapevine Cultivar. PhytoFrontiers™, 3(2), 290–295.
  3. Martin Jagunić, Alfredo Díaz-Lara, Lóránt Szőke, Maher Al Rwahnih, Kristian Stevens, Goran Zdunić, Darko Vončina (2022). Incidence and Genetic Diversity of Grapevine Virus G in Croatian Vineyards. Plants, 11(18), 2341.
  4. Martin Jagunić, Alfredo Díaz-Lara, Maher Al Rwahnih, Darko Preiner, Kristian Stevens, Goran Zdunić, Minsook Hwang, Darko Vončina (2022). Grapevine Badnavirus 1: Detection, Genetic Diversity, and Distribution in Croatia. Plants, 11(16), 2135.
  5. Darko Vončina, Alfredo Díaz-Lara, Darko Preiner, Maher Al Rwahnih, Kristian Stevens, Snježana Jurić, et al. (2022). Virus and Virus-like Pathogens in the Grapevine Virus Collection of Croatian Autochthonous Grapevine Cultivars. Plants, 11(11), 1485.
  6. Jessica W. Wright, Kristian Stevens, Paul D. Hodgskiss, Charles H. Langley (2022). SNPs in a Large Genomic Scaffold Are Strongly Associated withCr1R, Major Gene for Resistance to White Pine Blister Rust in Range-Wide Samples of Sugar Pine (Pinus lambertiana). Plant Disease, 106(6), 1639–1644.
  7. Anneliek M. ter Horst, Jane Fudyma, Aurélie Bak, Min Sook Hwang, Christian Santos‐Medellín, Kristian Stevens, David M. Rizzo, Maher Al Rwahnih, Joanne Emerson (2022). RNA Viral Communities Are Structured by Host Plant Phylogeny in Oak and Conifer Leaves. Phytobiomes Journal, 7(2), 288–296.
  8. Kellee Britt, Samantha Gebben, Amit Levy, Diann Achor, Peggy J. Sieburth, Kristian Stevens, Maher Al Rwahnih, Özgur Batuman (2022). Analysis of Citrus Tristeza Virus Incidences within Asian Citrus Psyllid (Diaphorina citri) Populations in Florida via High-Throughput Sequencing. Insects, 13(3), 275.
  9. Pedro J. Martínez‐García, Alejandra Vázquez‐Lobo, Pablo Martínez-García, Jorge Mas-Gómez, Carmen Jurado‐Mañogil, Kristian Stevens (2022). Advances in Genetic Mapping in Pines. Compendium of plant genomes, 9–19.

2021

  1. Lucie Tamisier, Annelies Haegeman, Yoika Foucart, Nicolas Fouillien, Maher Al Rwahnih, …, Kristian Stevens, et al. (2021). Semi-artificial datasets as a resource for validation of bioinformatics pipelines for plant virus detection. Peer Community Journal, 1.
  2. Kellee Britt, Kristian Stevens, Samantha Gebben, Amit Levy, Maher Al Rwahnih, Özgur Batuman (2021). Partial Genome Sequence of a Novel Reo-Like Virus Detected in Asian Citrus Psyllid (Diaphorina citri) Populations from Florida Citrus Groves. Microbiology Resource Announcements, 10(34), e0056321.
  3. Alfredo Díaz-Lara, Kristian Stevens, Vicki Klaassen, Min Sook Hwang, Maher Al Rwahnih (2021). Sequencing a Strawberry Germplasm Collection Reveals New Viral Genetic Diversity and the Basis for New RT-qPCR Assays. Viruses, 13(8), 1442.
  4. Larissa Carvalho Costa, Kristian Stevens, Xiaojun Hu, Marc Fuchs, Maher Al Rwahnih, Alfredo Díaz-Lara, Clint McFarland, Joseph A. Foster, Oscar P. Hurtado‐Gonzales (2021). Identification and characterization of a novel virus associated with an eriophyid mite in extracts of fruit trees leaves. Archives of Virology, 166(10), 2869–2873.
  5. Nourolah Soltani, Kristian Stevens, Vicki Klaassen, Minsook Hwang, Deborah Golino, Maher Al Rwahnih (2021). Quality Assessment and Validation of High-Throughput Sequencing for Grapevine Virus Diagnostics. Viruses, 13(6), 1130.

2020

  1. Matthew J. Weiss, Richard A. Sniezko, Daniela Puiu, Marc Crepeau, Kristian Stevens, Steven L. Salzberg, Charles H. Langley, David B. Neale, Amanda R. De La Torre (2020). Genomic basis of white pine blister rust quantitative disease resistance and its relationship with qualitative resistance. The Plant Journal, 104(2), 365–376.
  2. Alfredo Díaz-Lara, Kristian Stevens, Vicki Klaassen, Deborah Golino, Maher Al Rwahnih (2020). Comprehensive Real-Time RT-PCR Assays for the Detection of Fifteen Viruses Infecting Prunus spp.. Plants, 9(2), 273.
  3. Alfredo Díaz-Lara, Nola J. Mosier, Kristian Stevens, Karen E. Keller, Robert R. Martín (2020). Evidence of Rubus Yellow Net Virus Integration into the Red Raspberry Genome. Cytogenetic and Genome Research, 160(6), 329–334.

2019

  1. Alexander J. Trouern‐Trend, Taylor Falk, Sumaira Zaman, Madison Caballero, David B. Neale, Charles H. Langley, Abhaya M. Dandekar, Kristian Stevens, Jill Wegrzyn (2019). Comparative genomics of six Juglans species reveals disease‐associated gene family contractions. The Plant Journal, 102(2), 410–423.
  2. Maher Al Rwahnih, Olufemi J. Alabi, Min Sook Hwang, Kristian Stevens, Deborah Golino (2019). Identification and genomic characterization of grapevine Kizil Sapak virus, a novel grapevine-infecting member of the family Betaflexiviridae. Archives of Virology, 164(12), 3145–3149.
  3. Alfredo Díaz-Lara, Beatriz Navarro, Francesco Di Serio, Kristian Stevens, Min Sook Hwang, Joshua B. Kohl, Sandra Thuy Vu, Bryce W. Falk, Deborah Golino, Maher Al Rwahnih (2019). Two Novel Negative-Sense RNA Viruses Infecting Grapevine Are Members of a Newly Proposed Genus within the Family Phenuiviridae. Viruses, 11(8), 685.

2018

  1. Alfredo Díaz-Lara, Vicki Klaassen, Kristian Stevens, Mysore R. Sudarshana, Adib Rowhani, Hans J. Maree, et al. (2018). Characterization of grapevine leafroll-associated virus 3 genetic variants and application towards RT-qPCR assay design. PLoS ONE, 13(12), e0208862.
  2. Annarita Marrano, Pedro J. Martínez‐García, Luca Bianco, Gina M. Sideli, Erica A. Di Pierro, …, Kristian Stevens, et al. (2018). A new genomic tool for walnut ( Juglans regia L.): development and validation of the high‐density Axiom™ J. regia 700K SNP genotyping array. Plant Biotechnology Journal, 17(6), 1027–1036.
  3. Amanda R. De La Torre, Daniela Puiu, Marc Crepeau, Kristian Stevens, Steven L. Salzberg, Charles H. Langley, David B. Neale (2018). Genomic architecture of complex traits in loblolly pine. New Phytologist, 221(4), 1789–1801.
  4. Kristian Stevens, Keith Woeste, Sandeep Chakraborty, Marc Crepeau, Charles A. Leslie, Pedro J. Martínez‐García, et al. (2018). Genomic Variation Among and Within SixJuglansSpecies. G3 Genes Genomes Genetics, 8(7), 2153–2165.
  5. Maher Al Rwahnih, Adib Rowhani, Nathaniel Westrick, Kristian Stevens, Alfredo Díaz-Lara, Florent P. Trouillas, John E. Preece, Craig E. Kallsen, K. Farrar, Deborah Golino (2018). Discovery of Viruses and Virus-Like Pathogens in Pistachio using High-Throughput Sequencing. Plant Disease, 102(7), 1419–1425.

2017

  1. David B Neale, Patrick E. McGuire, Nicholas C. Wheeler, Kristian Stevens, Marc Crepeau, Charis Cardeno, et al. (2017). The Douglas-Fir Genome Sequence Reveals Specialization of the Photosynthetic Apparatus in Pinaceae. G3 Genes Genomes Genetics, 7(9), 3157–3167.
  2. Marc Crepeau, Charles H. Langley, Kristian Stevens (2017). From Pine Cones to Read Clouds: Rescaffolding the Megagenome of Sugar Pine (Pinus lambertiana). G3 Genes Genomes Genetics, 7(5), 1563–1568.
  3. Aleksey V. Zimin, Kristian Stevens, Marc Crepeau, Daniela Puiu, Jill Wegrzyn, James A. Yorke, Charles H. Langley, David B. Neale, Steven L. Salzberg (2017). An improved assembly of the loblolly pine mega-genome using long-read single-molecule sequencing. GigaScience, 6(1), 1–4.

2016

  1. Daniel González‐Ibeas, Pedro J. Martínez‐García, Randi A. Famula, Annette Delfino-Mix, Kristian Stevens, Carol A. Loopstra, Charles H. Langley, David B Neale, Jill Wegrzyn (2016). Assessing the Gene Content of the Megagenome: Sugar Pine (Pinus lambertiana). G3 Genes Genomes Genetics, 6(12), 3787–3802.
  2. Kristian Stevens, Jill Wegrzyn, Aleksey V. Zimin, Daniela Puiu, Marc Crepeau, Charis Cardeno, et al. (2016). Sequence of the Sugar Pine Megagenome. Genetics, 204(4), 1613–1626.
  3. Victoria L. Sork, Sorel Fitz‐Gibbon, Daniela Puiu, Marc Crepeau, Paul F. Gugger, Rachel M. Sherman, Kristian Stevens, Charles H. Langley, Matteo Pellegrini, Steven L. Salzberg (2016). First Draft Assembly and Annotation of the Genome of a California Endemic OakQuercus lobataNée (Fagaceae). G3 Genes Genomes Genetics, 6(11), 3485–3495.
  4. Pedro J. Martínez‐García, Marc Crepeau, Daniela Puiu, Daniel González‐Ibeas, Jeanne Whalen, Kristian Stevens, et al. (2016). The walnut (Juglans regia) genome sequence reveals diversity in genes coding for the biosynthesis of non‐structural polyphenols. The Plant Journal, 87(5), 507–532.

2015

  1. Michael Coulombe, Kristian Stevens, Dan Gusfield (2015). Construction, enumeration, and optimization of perfect phylogenies on multi-state data. 1–6.
  2. Justin Lack, Charis Cardeno, Marc Crepeau, William M. Taylor, Russell Corbett‐Detig, Kristian Stevens, Charles H. Langley, John E. Pool (2015). The Drosophila Genome Nexus: A Population Genomic Resource of 623 Drosophila melanogaster Genomes, Including 197 from a Single Ancestral Range Population. Genetics, 199(4), 1229–1241.

2014

  1. Bonnie Kirkpatrick, Kristian Stevens (2014). Perfect Phylogeny Problems with Missing Values. IEEE Transactions on Computational Biology and Bioinformatics, 11(5), 928–941.
  2. David B Neale, Jill Wegrzyn, Kristian Stevens, Aleksey V. Zimin, Daniela Puiu, Marc Crepeau, et al. (2014). Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies. Genome biology, 15(3), R59.
  3. Jill Wegrzyn, John D Liechty, Kristian Stevens, Le-Shin Wu, Carol A. Loopstra, Hans Vasquez-Gross, et al. (2014). Unique Features of the Loblolly Pine (Pinus taeda L.) Megagenome Revealed Through Sequence Annotation. Genetics, 196(3), 891–909.
  4. Aleksey V. Zimin, Kristian Stevens, Marc Crepeau, Ann Holtz-Morris, Maxim Koriabine, Guillaume Marçais, et al. (2014). Sequencing and Assembly of the 22-Gb Loblolly Pine Genome. Genetics, 196(3), 875–890.

2013

  1. Jill Wegrzyn, Brian Y Lin, Jacob J Zieve, W. Dougherty, Pedro J. Martínez‐García, …, Kristian Stevens, et al. (2013). Insights into the Loblolly Pine Genome: Characterization of BAC and Fosmid Sequences. PLoS ONE, 8(9), e72439.
  2. Pedro J. Martínez‐García, Kristian Stevens, Jill Wegrzyn, John D Liechty, Marc Crepeau, Charles H. Langley, David B. Neale (2013). Combination of multipoint maximum likelihood (MML) and regression mapping algorithms to construct a high-density genetic linkage map for loblolly pine (Pinus taeda L.). Tree Genetics & Genomes, 9(6), 1529–1535.
  3. Rob Gysel, Dan Gusfield, Kristian Stevens (2013). Triangulation heuristics for maximum character compatibility. 4, 1–2.

2012

  1. John E. Pool, Russell Corbett‐Detig, Ryuichi P. Sugino, Kristian Stevens, Charis Cardeno, Marc Crepeau, et al. (2012). Population Genomics of Sub-Saharan Drosophila melanogaster: African Diversity and Non-African Admixture. PLoS Genetics, 8(12), e1003080.
  2. Charles H. Langley, Kristian Stevens, Charis Cardeno, Yuh Chwen G. Lee, Daniel R. Schrider, John E. Pool, et al. (2012). Genomic Variation in Natural Populations ofDrosophila melanogaster. Genetics, 192(2), 533–598.
  3. Rob Gysel, Kristian Stevens, Dan Gusfield (2012). Reducing Problems in Unrooted Tree Compatibility to Restricted Triangulations of Intersection Graphs. Lecture notes in computer science, 93–105.

2011

  1. Daniel R. Schrider, Kristian Stevens, Charis Cardeno, Charles H. Langley, Matthew W. Hahn (2011). Genome-wide analysis of retrogene polymorphisms in Drosophila melanogaster. Genome Research, 21(12), 2087–2095.
  2. Charles H. Langley, Marc Crepeau, Charis Cardeno, Russell Corbett‐Detig, Kristian Stevens (2011). Circumventing Heterozygosity: Sequencing the Amplified Genome of a Single HaploidDrosophila melanogasterEmbryo. Genetics, 188(2), 239–246.
  3. Kristian Stevens, Bonnie Kirkpatrick (2011). Efficiently Solvable Perfect Phylogeny Problems on Binary and k-State Data with Missing Values. Lecture notes in computer science, 282–297.

2010

  1. Kristian Stevens, Henry Chen, Terry Filiba, Peter L. McMahon, Yun S. Song (2010). SeqHive: A Reconfigurable Computer Cluster for Genome Re-sequencing. 442–447.
  2. Kristian Stevens, Dan Gusfield (2010). Reducing Multi-state to Binary Perfect Phylogeny with Applications to Missing, Removable, Inserted, and Deleted Data. Lecture notes in computer science, 274–287.

2009

  1. Wei‐Chun Kao, Kristian Stevens, Yun S. Song (2009). BayesCall: A model-based base-calling algorithm for high-throughput short-read sequencing. Genome Research, 19(10), 1884–1895.

2007

  1. David J Begun, Alisha K. Holloway, Kristian Stevens, LaDeana W. Hillier, Yu-Ping Poh, Matthew W. Hahn, et al. (2007). Population Genomics: Whole-Genome Analysis of Polymorphism and Divergence in Drosophila simulans. PLoS Biology, 5(11), e310.

2004

  1. Ursula Vitt, Darryl Gietzen, Kristian Stevens, Jim Wingrove, Shanya Becha, Sean Bulloch, et al. (2004). Identification of Candidate Disease Genes by EST Alignments, Synteny, and Expression and Verification of Ensembl Genes on Rat Chromosome 1q43-54. Genome Research, 14(4), 640–650.
  2. Richard A. Gibbs, George M. Weinstock, Michael L. Metzker, Donna M. Muzny, Erica Sodergren, Steven E. Scherer, et al. (2004). Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature, 428(6982), 493–521.