Abigail S. Jarosz, Amanda L. Pendleton, Michael J. Lashbrook, Erica Cech, Madison Altieri, Austin Kunch, Jaime F. Modiano, Julia V. Halo. Expression and high levels of insertional polymorphism of an endogenous gammaretrovirus lineage in dogs. PLoS Genetics. Dec 19(12). PMID:38055724

Julia Halo and Jeffrey Kidd (2022). Genome of the Month: Canis familiaris (Great Dane breed dog). Trends in Genetics. 38(5) 514-515. PMID:35232612

Julia V. Halo*, Amanda L. Pendleton*, Feichen Shen*, Aurélien J. Doucet, Thomas Derrien, Christophe Hitte, Laura E. Kirby, Bridget Myers, Elzbieta Sliwerska, Sarah Emery, John V. Moran, Adam R. Boyko, Jeffrey M. Kidd (2021). Long-read assembly of a Great Dane genome highlights the contributions of GC-rich sequence and mobile elements to canine genome architecture. 2021 118 (11). Proceedings of the National Academy of Sciences. PMID:33836575

Julia V. Halo*, Amanda L. Pendleton, Abigail S. Jarosz, Robert J. Gifford, Malika L. Day#, Jeffrey Kidd. (2019). Origin and recent expansion of a gammaretroviral lineage in canids. Retrovirology. Mar 7;16(1):6. doi: 10.1186/s12977-019-0468-z. PMID:30845962 *Corresponding

Ke Q#, Weaver W#, Pore A#, Gorgoglione B, Halo JV, Xiao P, Shepherd B, Spear A, Malathi K, Stepien C, Vakharia V, and Leaman D. (2017). Role of Viral Hemorrhagic Septicemia Virus (VHSV) Matrix (M) Protein in Suppressing Host Transcription. Journal of Virology, July 26. PMID: 28747493

Halo JV and Coffin JM. (2017). Pushing the Envelope. eLife, Apr13;6. PMID: 28406395

Halo JV*, Williams ZH*, Montesian M, Subramanian RP, Kidd JM, Coffin JM. (2016). Discovery of unfixed endogenous retrovirus insertions in diverse human populations. Proceedings of the National Academy of Science. 2016 Mar 21. pii: 201602336. PMID: 27001843.

Chatterjee P#, Davis E#, Yu F#, James S#, Halo JV, Wiegmann D, Sherman D, McKay R, LiPuma J, and Wildschutte H. (2016). Environmental pseudomonads inhibit cystic fibrosis patient-derived Pseudomonas aeruginosa. Applied Environmental Microbiology, Jan 2017; 83(2): e02701-16. PMID: 27881418

Halo JV, Baron A, Diroff NM, Kidd JM. (2015). Discovery and characterization of Alu repeat sequences via precise local read assemblyNucleic Acids Research. Oct 25. pii: gkv1089. PMID: 26503250

Soto-Calderón ID, Clark NJ, Halo JV, DiMattio K, Jensen-Seaman MI, Anthony NM. (2014). Identification of species-specific nuclear insertions of mitochondrial DNA (numts) in gorillas and their potential as population genetic markersMolecular Phylogenetics and Evolution. Dec;81:61-70. doi: 10.1016/j.ympev.2014.08.018. Epub 2014 Sep 4. PMID: 25194325

Halo JV, Ram D, Subramanian R, Stevens VL, Coffin JM. (2014). The distribution of insertionally polymorphic endogenous retroviruses in breast cancer patients and cancer-free controlsRetrovirology. Aug 12;11:62. doi: 10.1186/s12977-014-0062-3. PMID: 25112280

Subramanian RP*, Halo JV*, Russo C, Coffin JM. (2011). Identification, characterization, and comparative genomic distribution of the HERV-K (HML-2) group of human endogenous retrovirusesRetrovirology. Nov 8;8:90. doi: 10.1186/1742-4690-8-90. PMID: 22067224

Jensen-Seaman MI, Halo JV, Soto-Calderón ID, Anthony NM. (2009). A comparative approach shows differences in patterns of numt insertion during hominoid evolutionJournal of Molecular Evolution. Jun;68(6):688-99. doi: 10.1007/s00239-009-9243-4. Epub 2009 May 27. PMID: 19471988

Consortia Publications

Lyraki M, Hibbert A, Langley-Hobbs S, Lait P, Buckley RM, Warren WC, Lyons LA; 99 Lives Consortium (2022). CTSK variant implicated in suspected pyknodysostosis in a domestic cat. Journal of Feline Medicine and Surgery Open Reports. 2022 Dec 12;8(2). PMID: 36532681

Lyons LA, Buckley RM, Harvey RJ; 99 Lives Cat Genome Consortium (2021). Mining the 99Lives Cat Genome Sequencing Consortium database implicates genes and variants for the Ticked locus in domestic cats (Felis catus). Anim Genet. 2021 Jun;52(3):321-332. PMID: 33780570

Genova F, Nonnis S, Maffioli E, Tedeschi G, Strillacci MG, Carisetti M, Sironi G, Cupaioli FA, Di Nanni N, Mezzelani A, Mosca E, Helps CR, Leegwater PAJ, Dorso L; 99 Lives Consortium; Longeri M (2021). Multi-omic analyses in Abyssinian cats with primary renal amyloid deposits. Scientific Reports. 2021 Apr 16;11(1):8339. PMID: 33863921

Emily C. Graff, J. Nicholas Cochran, Christopher B. Kaelin, Kenneth Day, Heather L. Gray-Edwards, Rie Watanabe, Jey W. Koehler, Rebecca A. Falgoust, Jeremy W. Prokop, Richard M. Myers, Nancy R. Cox, Gregory S. Barsh, Douglas R. Martin, 99 Lives Consortium. (2020). PEA15 loss of function and defective cerebral development in the domestic cat. PLoS Genetics. 2020 Dec; 16(12).PMCID:PMC7723247

Cogné B, Latypova X, Senaratne LDS, Martin L, Koboldt DC, Kellaris G, Fievet L, Le Meur G, Caldari D, Debray D, Nizon M, Frengen E, Bowne SJ; 99 Lives Consortium, Cadena EL, Daiger SP, Bujakowska KM, Pierce EA, Gorin M, Katsanis N, Bézieau S, Petersen-Jones SM, Occelli LM, Lyons LA, Legeai-Mallet L, Sullivan LS, Davis EE, Isidor B. (2020). Mutation in the Kinesin-2 motor KIF3B cause an autosomal-dominant ciliopathy. American Journal of Human Genetics. Jun 4;106(6). PMID:32386558

Ontiveros ES, Ueda Y, Harris SP, Stern JA, 99 Lives Consortium. (2018). Precision medicine validation: identifying the MYBPC3 A31P variant with whole-genome sequencing in two Maine Coon cats with hypertrophic cardiomyopathyJournal of Feline Medicine and Surgery. Dec 18:1098612X18816460. doi: 10.1177/1098612X18816460. PMID:30558461

Genova F, Longeri M, Lyons LA, Bagnato A; 99Lives Consortium, Strillacci MG, 99 Lives Consortium. (2018). First genome-wide CNV mapping in FELIS CATUS using next generation sequencing data. BMC Genomics. Dec 10;19(1):895. doi: 10.1186/s12864-018-5297-2. PMID: 30526495

Aberdein D, Munday JS, Gandolfi B, Dittmer KE, Malik R, Garrick DJ, Lyons LA; 99 LivesConsortium. (2017). A FAS-ligand variant associated with autoimmune lymphoproliferative syndrome in catsMammalian Genome. Feb;28(1-2):47-55. doi: 10.1007/s00335-016-9668-1. Erratum in: Mamm Genome. 2017 Apr;28(3-4):152-154.

Daniela A. Mauler, Barbara Gandolfi, Carol R. Reinero, Dennis P. O’Brien, Jeanie L. Spooner, Leslie A Lyons, 99 Lives Consortium. (2016). Precision medicine in cats: novel Niemann-Pick Type C1 diagnosed by whole genome sequencing. Journal of Veterinary Internal Medicine. Mar;31(2):539-544. doi: 10.1111/jvim.14599. PMID:28233346

Oh A, Pearce JW, Gandolfi B, Creighton EK, Suedmeyer WK, Selig M, Bosiack AP, Castaner L.J., Whiting REH, Belknap E., Lyons LA, and 99 Lives Consortium. (2016). Early-Onset Progressive Retinal Atrophy Associated with an IQCB1 Variant in African Black-Footed Cats (Felis nigripes). Scientific Reports March 21;7. PMID: 28322220

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