This list includes all publications that feature Bioinformatics Core members as co-authors, and most of the papers where we are acknowledged for providing assistance and/or software that was developed in the Core.
- [Co-authors] — Perry, L.M., Cruz, S.M., Kleber, K.T., Judge, S.J., Darrow, M.A., Jones, L.B., Basmaci, U.N., Joshi, N., Settles, M.L., Durbin-Johnson, B.P. and Gingrich, A.A., 2023. Human soft tissue sarcomas harbor an intratumoral viral microbiome which is linked with natural killer cell infiltrate and prognosis. Journal for ImmunoTherapy of Cancer, 11(1), p.e004285.
- [Co-authors] — Zafarullah, Marwa, Jie Li, Elizabeth Tseng, and Flora Tassone. "Structure and Alternative Splicing of the Antisense FMR1 (ASFMR1) Gene." Molecular Neurobiology (2023): 1-11.
- [Acknowledged, Data Analysis] — Ronning, K.E., Karlen, S.J. & Burns, M.E. Structural and functional distinctions of co-resident microglia and monocyte-derived macrophages after retinal degeneration. J Neuroinflammation 19, 299 (2022).
- [Acknowledged, Data Analysis] — Curtis, Matthew B., Natalie Kelly, Christopher CW Hughes, and Steven C. George. "Organotypic stromal cells impact endothelial cell transcriptome in 3D microvessel networks." Scientific Reports 12, no. 1 (2022): 1-16.
- [Acknowledged, Software] — Basbas, Carl, Sharif Aly, Emmanuel Okello, Betsy M. Karle, Terry Lehenbauer, Deniece Williams, Erika Ganda, Martin Wiedmann, and Richard V. Pereira. "Effect of Intramammary Dry Cow Antimicrobial Treatment on Fresh Cow’s Milk Microbiota in California Commercial Dairies." Antibiotics 11, no. 7 (2022): 963.
- [Acknowledged, Data Analysis] — Khodasevich, Dennis, Anna R. Smith, Karen Huen, Brenda Eskenazi, Andres Cardenas, and Nina Holland. "Comparison of DNA methylation measurements from EPIC BeadChip and SeqCap targeted bisulphite sequencing in PON1 and nine additional candidate genes." Epigenetics (2022): 1-12.
- [Co-authors] — Mederos, Sabrina L., Rafael C. Duarte, Mira Mastoras, Megan Y. Dennis, Matthew L. Settles, Allison R. Lau, Alexandria Scott et al. "Effects of pairing on color change and central gene expression in lined seahorses." Genes, Brain and Behavior (2022): e12812.
- [Acknowledged, Data Analysis] — Leale, D. M., K. Mitchell, J. H. Yik, and D. R. Haudenschild. "AUTOMATED CELL TYPE IDENTIFICATION FOR SINGLE-CELL RNA SEQUENCING ANALYSIS OF WHOLE MOUSE KNEE JOINTS." Osteoarthritis and Cartilage 30 (2022): S353-S354.
- [Acknowledged, Data Analysis] — Garcia, Luis A., Rocio Zapata-Bustos, Samantha E. Day, Baltazar Campos, Yassin Hamzaoui, Linda Wu, Alma D. Leon et al. "Can Exercise Training Alter Human Skeletal Muscle DNA Methylation?". Metabolites 12, no. 3 (2022): 222.
- [Acknowledged, Data Analysis] — Rixon, Jordan A., Claire E. Depew, and Stephen J. McSorley. "Th1 cells are dispensable for primary clearance of Chlamydia from the female reproductive tract of mice." PLoS pathogens 18, no. 2 (2022): e1010333.
- [Acknowledged, Data Analysis] — Gebiola, Marco, Brandon H. Le, and Kerry E. Mauck. "A reproducible and sensitive method for generating high‐quality transcriptomes from single whitefly salivary glands and other low‐input tissues." Insect Science.
- [Acknowledged, Data Analysis] — Lim, Kahui, Matthew Rolston, Samantha Barnum, Cara Wademan, and Harold Leverenz. "A biogeographic 16S rRNA survey of bacterial communities of ureolytic biomineralization from California public restrooms." PLOS ONE 17, no. 1 (2022): e0262425.
- [Co-authors] — Dahlgren, Anna R., Heather K. Knych, Rick M. Arthur, Blythe P. Durbin-Johnson, and Carrie J. Finno. "Transcriptomic Markers of Recombinant Human Erythropoietin Micro-Dosing in Thoroughbred Horses." Genes 12, no. 12 (2021): 1874.
- [Acknowledged, Data Analysis] — Cook, Sarah L., Evelyn P. Sievert, and Roger Sciammas. "B Cell Intrinsic IRF4 Haploinsufficiency Impairs Affinity Maturation." The Journal of Immunology (2021).
- [Co-authors] — Jacob, Cristián, André C. Velásquez, Nikhil A. Joshi, Matthew Settles, Sheng Yang He, and Maeli Melotto. "Dual Transcriptomic Analysis Reveals Metabolic Changes Associated with Differential Persistence of Human Pathogenic Bacteria in Leaves of Arabidopsis and Lettuce." G3 Genes| Genomes| Genetics (2021).
- [Acknowledged, Data Analysis] — Jeamsripong, Saharuetai, Xunde Li, Sharif S. Aly, Zhengchang Su, Richard V. Pereira, and Edward R. Atwill. "Antibiotic Resistance Genes and Associated Phenotypes in Escherichia coli and Enterococcus from Cattle at Different Production Stages on a Dairy Farm in Central California. " Antibiotics 10, no. 9 (2021): 1042.
- [Co-authors] — Mysore, V., Cullere, X., Settles, M.L., Ji, X., Kattan, M.W., Desjardins, M., Durbin-Johnson, B., Gilboa, T., Baden, L.R., Walt, D.R., Lichtman, A.H., Jehi, L., Mayadas, T.N.. "Protective heterologous T cell immunity in COVID-19 induced by the trivalent Measles-Mumps-Rubella and Tetanus-Diptheria-Pertussis vaccine antigens." Med (2021).
- [Co-authors] — Early life exposure to environmentally relevant levels of endocrine disruptors drive multigenerational and transgenerational epigenetic changes in a fish model. Major, Kaley M., Bethany M. DeCourten, Jie Li, Monica Britton, Matthew L. Settles, Alvine C. Mehinto, Richard E. Connon, and Susanne M. Brander. Frontiers in Marine Science 7 (2020): 471.
- [Acknowledged, Data Analysis] — Baxter, A., J. P. Capitanio, K. L. Bales, and E. L. Kinnally. "Biobehavioral Organization Shapes the Immune Epigenome in Infant Rhesus Macaques (Macaca mulatta)." Brain, Behavior, and Immunity (2021).
- [Co-authors] — Batista, Bruna Durante, Manuella Nóbrega Dourado, Everthon Fernandes Figueredo, Renata Ockner Hortencio, João Paulo Rodrigues Marques, Fernando Angelo Piotto, Maria Letícia Bonatelli, Matthew L. Settles, João Lucio Azevedo, and Maria Carolina Quecine. "The auxin-producing Bacillus thuringiensis RZ2MS9 promotes the growth and modifies the root architecture of tomato (Solanum lycopersicum cv. Micro-Tom)." Archives of Microbiology (2021): 1-14.
- [Acknowledged, Data Analysis] — Lebedev, Maxim, Heather A. McEligot, Victoria N. Mutua, Paul Walsh, Francisco R. Carvallo Chaigneau, and Laurel J. Gershwin. "Analysis of lung transcriptome in calves infected with Bovine Respiratory Syncytial Virus and treated with antiviral and/or cyclooxygenase inhibitor." Plos one 16, no. 2 (2021): e0246695.
[Co-authors] — Kim, Myungsuk, M. Nazmul Huda, Annalouise O'Connor, Jody Albright, Blythe P. Durbin-Johnson, and Brian J. Bennett. "Hepatic transcriptional profile reveals the role of diet and genetic backgrounds on metabolic traits in female progenitor strains of the Collaborative Cross. " Physiological Genomics (2021).
[Co-authors] — Wang VE, Blaser BW, Patel RK, Behbehani GK, Rao AA, Durbin-Johnson B, Jiang T, Logan AC, Settles M, Mannis GN, Olin R, Damon LE, Martin TG, Sayre PH, Gaensler KM, McMahon E, Flanders M, Weinberg V, Ye CJ, Carbone DP, Munster PN, Fragiadakis GK, McCormick F, Andreadis C. "Inhibition of MET Signaling with Ficlatuzumab in Combination with Chemotherapy in Refractory AML: Clinical Outcomes and High-Dimensional Analysis." Blood Cancer Discov. 2021 Sep;2(5):434-449. PMID: 34514432.
[Co-authors] — Sarver BAJ, Herrera ND, Sneddon D, Hunter SS, Settles ML, Kronenberg Z, Demboski JR, Good JM, Sullivan J. "Diversification, Introgression, and Rampant Cytonuclear Discordance in Rocky Mountains Chipmunks (Sciuridae: Tamias)." Syst Biol. 2021 Aug 11;70(5):908-921. PMID: 33410870.
[Co-authors] — Sarode GV, Neier K, Shibata NM, Shen Y, Goncharov DA, Goncharova EA, Mazi TA, Joshi N, Settles ML, LaSalle JM, Medici V. "Wilson Disease: Intersecting DNA Methylation and Histone Acetylation Regulation of Gene Expression in a Mouse Model of Hepatic Copper Accumulation." Cell Mol Gastroenterol Hepatol. 2021 Jun 4;12(4):1457-1477. PMID: 34098115.
- [Co-authors] — Kaur, Sarabjit, Jessica A. Kinkade, Madison T. Green, Rachel E. Martin, Tess E. Willemse, Nathan J. Bivens, A. Katrin Schenk et al. "Disruption of global hypothalamic microRNA (miR) profiles and associated behavioral changes in California mice (Peromyscus californicus) developmentally exposed to endocrine disrupting chemicals." Hormones and Behavior (2020): 104890-104890.
- [Co-authors] — Komoroske, Lisa M., Ken M. Jeffries, Andrew Whitehead, Jennifer Roach, Monica Britton, Richard E. Connon, Christine Verhille, Susanne M. Brander, and Nann A. Fangue. "Transcriptional flexibility during thermal challenge corresponds with expanded thermal tolerance in an invasive compared to native fish." Evolutionary Applications.
- [Co-authors] — Questa, Maria, Maryam Moshref, Robert J. Jimenez, Veronica Lopez‐Cervantes, Charles K. Crawford, Matthew L. Settles, Pablo J. Ross, and Amir Kol. "Chromatin accessibility in canine stromal cells and its implications for canine somatic cell reprogramming." Stem cells translational medicine (2020).
- [Acknowledged, Software] — Coates, Laurynne C., Jaclyn Mahoney, John S. Ramsey, EricaRose Warwick, Richard Johnson, Michael J. MacCoss, Stuart B. Krasnoff et al. "Development on Citrus medica infected with ‘Candidatus Liberibacter asiaticus’ has sex-specific and-nonspecific impacts on adult Diaphorina citri and its endosymbionts." PloS one 15, no. 10 (2020): e0239771.
- [Co-authors] — DeCourten, Bethany M., Joshua P. Forbes, Hunter K. Roark, Nathan P. Burns, Kaley M. Major, J. Wilson White, Jie Li, Alvine C. Mehinto, Richard Edward Connon, and Susanne M. Brander. "Multigenerational and transgenerational effects of environmentally relevant concentrations of endocrine disruptors in an estuarine fish model." Environmental Science & Technology (2020).
- [Co-authors] — Milkereit, Janina, Daniel Geisseler, Patricia Lazicki, Matthew L. Settles, Blythe P. Durbin-Johnson, and Amanda Hodson. "Interactions between nitrogen availability, bacterial communities, and nematode indicators of soil food web function in response to organic amendments." Applied Soil Ecology 157: 103767.
- [Co-authors] — Oldt, Robert F., Kimberly J. Bussey, Matthew L. Settles, Joseph N. Fass, Jeffrey A. Roberts, J. Rachel Reader, Srivathsan Komandoor, Victor A. Abrich, and Sreetharan Kanthaswamy. "MYBPC3 Haplotype Linked to Hypertrophic Cardiomyopathy in Rhesus Macaques (Macaca mulatta)." Comparative Medicine (2020).
- [Co-authors] — Major, Kaley M., Bethany M. Decourten, Jie Li, Monica Britton, Matthew L. Settles, Alvine C. Mehinto, Richard Edward Connon, and Susanne M. Brander. "Early life exposure to environmentally relevant levels of endocrine disruptors drive multigenerational and transgenerational epigenetic changes in a fish model." Frontiers in Marine Science 7 (2020): 471.
- [Acknowledged, Data Analysis] — Budzik, Jonathan M., Danielle L. Swaney, David Jimenez-Morales, Jeffrey R. Johnson, Nicholas E. Garelis, Teresa Repasy, Allison W. Roberts et al. "Dynamic post-translational modification profiling of Mycobacterium tuberculosis-infected primary macrophages." Elife 9 (2020): e51461.
- [Acknowledged, Software] — Genç, Özgür, Joon Y. An, Richard D. Fetter, Yelena Kulik, Giulia Zunino, Stephan J. Sanders, and Graeme W. Davis. "Homeostatic Plasticity Commonly Fails at the Intersection of Autism-Gene Mutations and a Novel Class of Common Phenotypic Modifier." bioRxiv (2020).
- [Acknowledged, Data Analysis] — Huda, M. Nazmul, Melissa VerHague, Jody Albright, Tangi Smallwood, Timothy A. Bell, Excel Que, Darla R. Miller et al. "Dissecting the Genetic Architecture of Cystatin C in Diversity Outbred Mice." G3: Genes, Genomes, Genetics (2020).
- [Acknowledged, Data Analysis] — Verma, Anil, Brian A. Schmidt, Sonny R. Elizaldi, Nancy K. Nguyen, Korey A. Walter, Zoltan Beck, Hung V. Trinh et al. "Impact of Th1 CD4 Follicular Helper T Cell Skewing on Antibody Responses to an HIV-1 Vaccine in Rhesus Macaques." Journal of Virology 94, no. 6 (2020).
[Co-authors] — Rahman, M. J.; Haller, S. L.; Li, J.; Brennan, G.; Rothenburg, S. "Cascade Evolution in Poxviruses: Retrotransposon-Mediated Host Gene Capture, Complementation and Recombination." bioRxiv 2020, 2020.10.26.355610.
[Co-authors] — Bonatelli, M. L.; Li, J.; Dumaresq, A.; Quecine, M. C.; Settles, M. L.; Baltrus, D. A. "Complete Genome Sequence of Bacillus Sp. Strain RZ2MS9, a Multitrait Plant Growth Promoter." Microbiol. Resour. Announc. 2020, 9 (31), e00623-20.
[Acknowledged, Data Analysis] — Rumachik NG, Malaker SA, Poweleit N, Maynard LH, Adams CM, Leib RD, Cirolia G, Thomas D, Stamnes S, Holt K, Sinn P, May AP, Paulk NK. "Methods Matter: Standard Production Platforms for Recombinant AAV Produce Chemically and Functionally Distinct Vectors." Mol Ther Methods Clin Dev. 2020 May 22;18:98-118. PMID: 32995354; PMCID: PMC7488757.
[Co-authors] — Joslin SEK, Durbin-Johnson BP, Britton M, Settles ML, Korf I, Lemay DG. "Association of the Lactase Persistence Haplotype Block With Disease Risk in Populations of European Descent." Front Genet. 2020;11:558762. PMID: 33193640.
[Co-authors] — Bowen L, von Biela VR, McCormick SD, Regish AM, Waters SC, Durbin-Johnson B, Britton M, Settles ML, Donnelly DS, Laske SM, Carey MP, Brown RJ, Zimmerman CE. "Transcriptomic response to elevated water temperatures in adult migrating Yukon River Chinook salmo (Oncorhynchus tshawytscha)." Conserv Physiol. 2020;8(1):coaa084. eCollection 2020. PMID: 34512988.
[Co-authors] — Dragon JA, Gates C, Sui SH, Hutchinson JN, Karuturi RKM, Kucukural A, Polson S, Riva A, Settles ML, Thimmapuram J, Levine SS. "Bioinformatics Core Survey Highlights the Challenges Facing Data Analysis Facilities." J Biomol Tech. 2020 Jul;31(2):66-73. PMID: 32382253.
- [Acknowledged, Software] — Lordan, Ronan, Aaron Walsh, Fiona Crispie, Laura Finnegan, Martina Demuru, Alexandros Tsoupras, Paul D. Cotter, and Ioannis Zabetakis. "Caprine milk fermentation enhances the antithrombotic properties of cheese polar lipids." Journal of Functional Foods 61 (2019): 103507.
- [Co-authors] — Singer-Berk, Moriel H., Kelly E. Knickelbein, Zachary T. Lounsberry, Margo Crausaz, Savanna Vig, Nikhil Joshi, Monica Britton et al. "Additional Evidence for DDB2 T338M as a Genetic Risk Factor for Ocular Squamous Cell Carcinoma in Horses." International journal of genomics 2019 (2019).
- [Acknowledged, Data Analysis] — Harfmann, Jennifer Lynne. PhD diss., "The Role of Terrestrial Organic Matter in the Lower Aquatic Food Web." University of California, Davis, 2019.
- [Acknowledged, Data Analysis] — Whitfield, Damion L., Gaurav Sharma, Gregory T. Smaldone, and Mitchell Singer. "Peripheral rods: a specialized developmental cell type in Myxococcus xanthus." Genomics (2019).
- [Acknowledged, Data Analysis] — Ramsay, Ashley L., Vivian Alonso-Garcia, Cutter Chaboya, Brian Radut, Bryan Le, Jose Florez, Cameron Schumacher, and Fernando A. Fierro. "Modeling Snyder-Robinson Syndrome in multipotent stromal cells reveals impaired mitochondrial function as a potential cause for deficient osteogenesis." Scientific reports 9, no. 1 (2019): 1-10.
- [Acknowledged, Data Analysis] — Doblas-Ibáñez, Paula, Kaiyue Deng, Miguel F. Vasquez, Laura Giese, Paul A. Cobine, Judith M. Kolkman, Helen King et al. "Dominant, Heritable Resistance to Stewart’s Wilt in Maize Is Associated with an Enhanced Vascular Defense Response to Infection with Pantoea stewartii." Molecular Plant-Microbe Interactions 32, no. 12 (2019): 1581-1597.
- [Acknowledged, Data Analysis] — Verma, Anil, Brian A. Schmidt, Sonny R. Elizaldi, Nancy K. Nguyen, Korey A. Walter, Zoltan Beck, Hung V. Trinh et al. "Impact of Th1 CD4 TFH skewing on Antibody Responses to an HIV-1 Vaccine in Rhesus Macaques." Journal of Virology (2019).
- [Acknowledged, Data Analysis] — Stefanson, Ofir., "Development of CRISPR/Cas9 in vivo bladder cancer models." PhD diss., UC Santa Cruz, 2019.
- [Acknowledged, Data Analysis] — Budzik, Jonathan M., Nick E. Garelis, Teresa Repasy, Allison W. Roberts, Lauren Popov, Trevor J. Parry, David Jiminez-Morales et al. "Global proteomic profiling of primary macrophages during M. tuberculosis infection identifies TAX1BP1 as a mediator of autophagy targeting." bioRxiv (2019): 534917.
- [Acknowledged, Data Analysis] — Raj, Christol James Theoga, Trevor Croft, Padmaja Venkatakrishnan, Benjamin Groth, Gagandeep Dhugga, Timothy Cater, and Su-Ju Lin. "The copper-sensing transcription factor Mac1, the histone deacetylase Hst1, and nicotinic acid regulate de novo NAD+ biosynthesis in budding yeast." Journal of Biological Chemistry (2019): jbc-RA118.
- [Acknowledged, Data Analysis] — Huang, L., S. Tepaamorndech, C. P. Kirschke, Y. Cai, J. Zhao, Xiaohan Cao, and Andrew Rao. "Subcongenic analysis of a quantitative trait locus affecting body weight and glucose metabolism in zinc transporter 7 (znt7)-knockout mice." BMC genetics 20, no. 1 (2019): 19.
- [Acknowledged, Data Analysis] — Ronning, Kaitryn E., Sarah J. Karlen, Eric B. Miller, and Marie E. Burns. "Molecular profiling of resident and infiltrating mononuclear phagocytes during rapid adult retinal degeneration using single-cell RNA sequencing." Scientific reports 9, no. 1 (2019): 4858.
- [Co-authors] — Jeffries, Ken M., Richard E. Connon, Christine E. Verhille, Theresa F. Dabruzzi, Monica T. Britton, Blythe P. Durbin‐Johnson, and Nann A. Fangue. "Divergent transcriptomic signatures in response to salinity exposure in two populations of an estuarine fish."Evolutionary Applications.
[Co-authors] — B. Ley, D. G. Torgerson, J. M. Oldham, A. Adegunsoye, S. Liu, J. Li, B. M. Elicker, T. S. Henry, J. A. Golden, K. D. Jones, A. Dressen, B. L. Yaspan, J. R. Arron, I. Noth, T. J. Hoffmann, P. J. Wolters. "Rare protein-altering telomere-related gene variants in patiens with chronic hypersensitivity pneumonitis." Am J Respir Crit Care Med 200:1154-1163 (2019)
[Co-authors] — Y. Wang, D. Chung, L. R. Monteleone, J. Li, C. M. D. Toney, P. A. Beal, “RNA binding candidates for human ADAR3 from substrates of a gain of function mutant expressed in neuronal cells”, Nucleic Acids Res 47(20):10801-10814 (2019)
[Co-authors] — T. Zhu, L. Wang, F.M. You, J.C. Rodriguez, K.R. Deal, L. Chen, J. Li, S. Chakraborty, B. Balan, C.-Z. Jiang, P.J. Brown, C.A. Leslie, M.K. Aradhya, A.M. Dandekar, P.E. McGuire, D. Kluepfel, J. Dvorak, M.-C. Luo, “Sequencing a Juglans regia × J. microcarpa hybrid yields high-quality genome assemblies of parental species”, Horticulture Research 6(1) (2019) 55.
[Co-authors] — de Oliveira Peixoto J, Savoldi IR, Ibelli AMG, Cantão ME, Jaenisch FRF, Giachetto PF, Settles ML, Zanella R, Marchesi JAP, Pandolfi JR, Coutinho LL, Ledur MC. "Proximal femoral
head transcriptome reveals novel candidate genes related to epiphysiolysis in broiler chickens." BMC Genomics. 2019 Dec 30;20(1):1031. PMID: 31888477.
[Co-authors] — Finno CJ, Peterson J, Kang M, Park S, Bordbari MH, Durbin-Johnson B, Settles M, Perez-Flores MC, Lee JH, Yamoah EN. "Single-Cell RNA-seq Reveals Profound Alterations in Mechanosensitive Dorsal Root Ganglion Neurons with Vitamin E Deficiency." iScience. 2019 Nov 22;21:720-735. PMID: 31733517.
[Co-authors] — Holm JB, Humphrys MS, Robinson CK, Settles ML, Ott S, Fu L, Yang H, Gajer P, He X, McComb E, Gravitt PE, Ghanem KG, Brotman RM, Ravel J. "Ultrahigh-Throughput Multiplexing and Sequencing of >500-Base-Pair Amplicon Regions on the Illumina HiSeq 2500 Platform." mSystems. 2019 Jan-Feb;4(1). PMID: 30801027.
[Co-authors] — Marchesi JAP, Ibelli AMG, Peixoto JO, Cantão ME, Pandolfi JRC, Marciano CMM, Zanella R, Settles ML, Coutinho LL, Ledur MC. "Whole transcriptome analysis of the pectoralis major muscle reveals molecular mechanisms involved with white striping in broiler chickens." Poult Sci. 2019 Feb 1;98(2):590-601. PMID: 30239913.
[Co-authors] — Cadena M, Froenicke L, Britton M, Settles ML, Durbin-Johnson B, Kumimoto E, Gallardo RA, Ferreiro A, Chylkova T, Zhou H, Pitesky M. "Transcriptome Analysis of Salmonella Heidelberg after Exposure to Cetylpyridinium Chloride, Acidified Calcium Hypochlorite, and Peroxyacetic Acid." J Food Prot. 2019 Jan;82(1):109-119. PMID: 30702951.
- [Co-authors] — Sheng L, Jena PK, Liu HX, Hu Y, Nagar N, Bronner DN, Settles ML, Bäumler AJ, Wan YJ. "Obesity treatment by epigallocatechin-3-gallate–regulated bile acid signaling and its enriched Akkermansia muciniphila." The FASEB Journal. 2018 Jun 8:fj-201800370R.
- [Co-authors] — Zavodovskaya R, Stover SM, Murphy BG, Katzman S, Durbin-Johnson B, Britton M, Finno CJ. "Bone formation transcripts dominate the differential gene expression profile in an equine osteoporotic condition associated with pulmonary silicosis." PLOS ONE. 2018 Jun 1;13(6):e0197459.
- [Acknowledged, Data Analysis] — Mengeling BJ, Goodson ML, Furlow JD. "RXR Ligands Modulate Thyroid Hormone Signaling Competence in Young Xenopus laevis Tadpoles." Endocrinology. 2018 May 11.
- [Co-authors] — Finno CJ, Bordbari MH, Gianino G, Ming-Whitfield B, Burns E, Merkel J, Britton M, Durbin-Johnson B, Sloma EA, McMackin M, Cortopassi G. "An innate immune response and altered nuclear receptor activation defines the spinal cord transcriptome during alpha-tocopherol deficiency in Ttpa-null mice" Free Radical Biology and Medicine. 2018 May 20;120:289-302.
[Acknowledged, Data Analysis] — Eskew EA, Shock BC, LaDouceur EE, Keel K, Miller MR, Foley JE, Todd BD. "Gene expression differs in susceptible and resistant amphibians exposed to Batrachochytrium dendrobatidis." Royal Society open science. 2018 Feb 1;5(2):170910.
[Co-authors] — Sheng H, Duan M, Hunter SS, Minnich SA, Settles ML, New DD, Chase JR, Fagnan MW, Hovde CJ. "High-Quality Complete Genome Sequences of Three Bovine Shiga Toxin-Producing Escherichia coli O177: H-(fliCH25) Isolates Harboring Virulent stx2 and Multiple Plasmids." Genome announcements. 2018 Feb 15;6(7):e01592-17.
[Acknowledged, Data Analysis] — Colquitt BM, Mets DG, Brainard MS. "Draft genome assembly of the Bengalese finch, Lonchura striata domestica, a model for motor skill variability and learning." GigaScience. 2018 Feb 15.
[Co-authors] — S. Kahn, Y. Liao, X. Du, W. Xu, J. Li, B. Lonnerdal, “Exosomal MicroRNAs in Milk from Mothers Delivering Preterm Infants Survive in Vitro Digestion and Are Taken Up by Human Intestinal Cells”, Mol Nutr Food Res., 62(11), 1701050 (2018)
[Co-authors] — Seelke AMH, Bond JM, Simmons TC, Joshi N, Settles ML, Stolzenberg D, Rhemtulla M, Bales KL. "Fatherhood alters gene expression within the MPOA." Environ Epigenet. 2018 Oct;4(4):dvy026. PMID: 30568805.
- [Co-authors] — Pandey P, Chiu C, Miao M, Wang Y, Settles M, Del NR, Castillo A, Souza A, Pereira R, Jeannotte R. "16S rRNA analysis of diversity of manure microbial community in dairy farm environment." PloS one. 2018;13(1):e0190126.
- [Acknowledged, Data Analysis] — Nwugo CC, Sengoda VG, Tian L, Lin H.. "Characterization of physiological and molecular processes associated with potato response to Zebra chip disease." Horticulture Research.;4:17069.
- [Acknowledged, Data Analysis] — Aaron PA, Jamklang M, Uhrig JP, Gelli A. "The Human Blood‐Brain Barrier Internalizes Cryptococcus neoformans via the EphA2‐Tyrosine Kinase Receptor." Cellular Microbiology.
[Co-authors] — George S, Manoharan D, Li J, Britton M, Parida A. "Drought and salt stress in Macrotyloma uniflorum leads to common and specific transcriptomic responses and reveals importance of raffinose family oligosaccharides in stress tolerance." Gene Reports. 2017 Oct 22.
- [Co-authors] — Suja George, Deepeka Manoharan, Jie Li, Monica Britton, and Ajay Parida. "Transcriptomic responses to drought and salt stress in desert tree Prosopis juliflora." Plant Gene (2017).
[Acknowledged, Software] —Buchwaldt, Miles Rimmer. " Methods for Transcriptome Assembly in the Allopolyploid Brassica napus." PhD diss., 2017.
- [Acknowledged, Data Analysis] — Browne, G.T., Ott, N.J., Poret-Peterson, A.T., Gouran, H. and Lampinen, B.D.. "Efficacy of anaerobic soil disinfestation for control of Prunus replant disease." Plant Disease.
- [Acknowledged, Data Analysis] — Yalin Liao, Xiaogu Du, Jie Li, and Bo Lönnerdal. "Human milk exosomes and their microRNAs survive digestion in vitro and are taken up by human intestinal cells." Molecular Nutrition & Food Research.
- [Acknowledged, Software] — Søren D Nielsen, Robert L Beverly, Yunyao Qu, Davis C Dallas. "Milk Bioactive Peptide Database: A comprehensive database of milk protein-derived bioactive peptides and novel visualization." Food Chemistry 232 (October). Elsevier: 673–82.
- [Co-authors] — S. George, D. Manoharan, J. Li, M. Britton, A. Parida, “Drought and salt stress in Chrysopogon zizanioides leads to common and specific transcriptomic responses and may affect essential oil composition and benzylisoquinoline alkaloids metabolism”, Curr Plant Biol., 11-12:12-22 (2017)
- [Co-authors] — Byrne A, Rothstein A, Poorten T, Erens J, Settles M, Rosenblum EB. "Unlocking the story in the swab: A new genotyping assay for the amphibian chytrid fungus Batrachochytrium dendrobatidis." Mol Ecol Resour. 2017 Nov;17(6):1283-1292. PMID: 28371384.
- [Co-authors] — Williams JE, Carrothers JM, Lackey KA, Beatty NF, York MA, Brooker SL, Shafii B, Price WJ, Settles ML, McGuire MA, McGuire MK. "Human Milk Microbial Community Structure Is Relatively Stable and Related to Variations in Macronutrient and Micronutrient Intakes in Healthy Lactating Women." J Nutr. 2017 Sep;147(9):1739-1748. PMID: 28724659.
- [Co-authors] — Tighe S, Afshinnekoo E, Rock TM, McGrath K, Alexander N, McIntyre A, Ahsanuddin S, Bezdan D, Green SJ, Joye S, Stewart Johnson S, Baldwin DA, Bivens N, Ajami N, Carmical JR, Herriott IC, Colwell R, Donia M, Foox J, Greenfield N, Hunter T, Hoffman J, Hyman J, Jorgensen E, Krawczyk D, Lee J, Levy S, Garcia-Reyero N, Settles M, Thomas K, Gomez F, Schriml L, Kyrpides N, Zaikova E, Penterman J, Mason CE. "Genomic Methods and Microbiological Technologies for Profiling Novel and Extreme Environments for the Extreme Microbiome Project (XMP)." J Biomol Tech. 2017 Apr;28(1):31-39. PMID: 28337070.
- [Co-authors] — Madison-Villar, M. J., Cheng Sun, Nelson C. Lau, Matthew L. Settles, and Rachel Lockridge Mueller. "Small RNAs from a Big Genome: The piRNA Pathway and Transposable Elements in the Salamander Species Desmognathus fuscus." Journal of molecular evolution 83, no. 3-4 (2016): 126-136.
- [Acknowledged] — Shore, Sabrina, et al. "Small RNA Library Preparation Method for Next-Generation Sequencing Using Chemical Modifications to Prevent Adapter Dimer Formation." PloS one 11.11 (2016): e0167009.
- [Acknowledged] — Jimenez, Robyn, and Martin L. Privalsky. "A resistance to thyroid hormone syndrome mutant operates through the target gene repertoire of the wild-type thyroid hormone receptor." Molecular and Cellular Endocrinology (2017).
- [Co-authors] — Schjaerff, Mette, Stefan M. Keller, Joseph Fass, Lutz Froenicke, Robert A. Grahn, Leslie Lyons, Verena K. Affolter, Annemarie T. Kristensen, and Peter F. Moore. "Refinement of the canine CD1 locus topology and investigation of antibody binding to recombinant canine CD1 isoforms." Immunogenetics 68, no. 3 (2016): 191-204.
- [Acknowledged] — Henry, Peter M., and Johan HJ Leveau. "Finished genome sequences of Xanthomonas fragariae, the cause of bacterial angular leaf spot of strawberry." Genome announcements 4.6 (2016): e01271-16.
- [Acknowledged] — Gouran H, Gillespie H, Nascimento R, Chakraborty S, Zaini PA, Jacobson A, Phinney BS, Dolan D, Durbin-Johnson BP, Antonova ES, Lindow SE. "The Secreted Protease PrtA Controls Cell Growth, Biofilm Formation and Pathogenicity in Xylella fastidiosa." Scientific Reports. 2016 Aug 5;6:31098.
- [Co-authors] — Ken M. Jeffries, Richard E. Connon, Brittany E. Davis, Lisa M. Komoroske, Monica T. Britton, Ted Sommer, Anne E. Todgham, Nann A. Fangue. "Effects of high temperatures on threatened estuarine fishes during periods of extreme drought." Journal of Experimental Biology 2016 219: 1705-1716; doi: 10.1242/jeb.134528
- [Co-authors] — Peter J. Dickinson, BVSc, PhD, Dan York, BA, PhD, Robert J. Higgins, BVSc, PhD, Richard A. LeCouteur, BVSc, PhD, Nikhil Joshi, MS, and Danika Bannasch, DVM, PhD. "Chromosomal Aberrations in Canine Gliomas Define Candidate Genes and Common Pathways in Dogs and Humans." 2016 May 31. Journal of Neuropathology and Experimental Neurology. Vol. 0, No. 0, 2016, pp. 1–11.
[Software] — Schirmer, Melanie, et al. "Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform." Nucleic acids research (2015): gku1341.
[Co-authors] — Miller CR, Nagel AC, Scott L, Settles M, Joyce P, Wichman HA. "Love the one you’re with: replicate viral adaptations converge on the same phenotypic change." PeerJ. 2016;4:e2227. PMID: 27547540.
- [Acknowledged] — Ashrafi et al. "De novo assembly of the pepper transcriptome (Capsicum annuum): a benchmark for in silico discovery of SNPs, SSRs and candidate genes." BMC Genomics. 2012, 13, October 30
- [Acknowledged] — Bowen et al. "Enhanced biological processes associated with alopecia in polar bears (Ursus maritimus)." Science of The Total Environment. 2015, 5(29), October 1
- [Software] — Bleed et al. "Genome sequence of Anoxybacillus ayderensis AB04T isolated from the Ayder hot spring in Turkey." Standards in Genomic Science. 2015, 10&(70), September 26
- [Co-authors] — Mariangela Bonizzoni, Eric Ochomo, William Dunn et al. "RNA-seq analyses of changes in the Anopheles gambiae transcriptome associated with resistance to pyrethroids in Kenya: identification of candidate-resistance genes and candidate-resistance SNPs." Parasites & Vectors. 2015, 8(474), September 17
- [Co-authors] — Jillian Ng, Joseph N. Fass, Blythe Durbin-Johnson, David Glenn Smith,, Sree Kanthaswamy. "Identifying rhesus macaque gene orthologs using heterospecific human CNV probes." Genomics Data. 2015, 6, September 16
- [Software] — Wang et al. "Self-renewing diploid Axin2+ cells fuel homeostatic renewal of the liver." Nature. 2015, 524(7564), August 5
- [Co-authors] — Sandeep Chakraborty, Monica Britton, Jill Wegrzyn et al. "YeATS – a tool suite for analyzing RNA-seq derived transcriptome identifies a highly transcribed putative extensin in heartwood/sapwood transition zone in black walnut." F1000 Research. 2015, 4(155), June 17
- [Software] — Genome Sequence of Anoxybacillus thermarum AF/04T, Isolated from the Euganean Hot Springs in Abano Terme, Italy. Genome Announcement. 2015, 3 (3), May 21
- [Co-authors] — Jennifer Luff, Michelle Mader, Monica Britton, Joseph Fass et al. "Complete genome sequence of canine papillomavirus type 16." Genome Announcements. 2015, 3 (3), May 7
- [Software] — Klomp et al. "A cysteine-clamp gene drives embryo polarity in the midge Chironomus." Science. 2015, 348(6238), May 7
- [Co-authors] — Carrie J. Finno, Carlynn Stevens, Amy Young, Verena Affolter, Nikhil A. Joshi et al. "SERPINB11 Frameshift Variant Associated with Novel Hoof Specific Phenotype in Connemara Ponies." PLOS Genetics. 2015, 11 (4), April 13
- [Software] — Keller at al. "Fine-mapping of a major QTL controlling angular leaf spot resistance in common bean (Phaseolus vulgaris L.)." Theoretical and Applied Genetics. 2015, 128 (5), Mar 5
- [Co-authors] — Jeffries KM, Brander SM, Britton MT, Fangue NA, Connon RE. "Chronic exposures to low and high concentrations of ibuprofen elicit different gene response patterns in a euryhaline fish." Environmental Science and Pollution Resesarch. 2015, March 4
- [Acknowledged], [Software] — Kim et al. "RNA-Seq Analysis of Spatiotemporal Gene Expression Patterns During Fruit Development Revealed Reference Genes for Transcript Normalization in Plums." Plant Molecular Biology Reporter. 2015, February 28
- [Acknowledged] — Yu et al. "Mitochondrial complex I deficiency leads to inflammation and retinal ganglion cell death in the Ndufs4 mouse." Human Molecular Genetics. 2015, 24 (10), February 4
- [Acknowledged] — Lounsberry et al. "Next-generation sequencing workflow for assembly of nonmodel mitogenomes exemplified with North Pacific albatrosses (Phoebastria spp.)." Molecular Ecology. 2015, 15 (4), January 13
- [Software] — Pombert et al. "The Ordospora colligata Genome: Evolution of Extreme Reduction in Microsporidia and Host-To-Parasite Horizontal Gene Transfer." Mbio. 2015, 6(1), January 13
- [Acknowledged, Software] — Elmore et al. "Quantitative Proteomics Reveals Dynamic Changes in the Plasma Membrane During Arabidopsis Immune Signaling." Molecular and Cellular Proteomics. 2012, 11(4), January 3
- [Software] — Bacteroides dorei dominates gut microbiome prior to autoimmunity in Finnish children at high risk for type 1 diabetes. Davis-Richardson et al. Frontiers in Microbiology. 2014, 5, December 10
- [Software] — Biofilm formation by virulent and non-virulent strains of Haemophilus parasuis. Bello-Ortí et al. Veterinary Research. 2014, 45(104), November 27
- [Software] — Genome-wide transcriptional profiling of Botrytis cinerea genes targeting plant cell walls during infections of different hosts. Blanco-Ulate et al. Frontiers in Plant Science. 2014, 5, September 3
- [Software] — A Lack of Parasitic Reduction in the Obligate Parasitic Green Alga Helicosporidium. Pombert et al. PLOS Genetics. 2014, 10(5), May 8
- [Acknowledged] — Analysis of the Salivary Gland Transcriptome of Frankliniella occidentalis. Stafford-Banks et al. PLOS ONE. 2014, April 15
- [Software] — Efficient Genome-Wide Detection and Cataloging of EMS-Induced Mutations Using Exome Capture and Next-Generation Sequencing. Henry et al. Plant Cell. 2014, 26(4), April 11
- [Software] — On Optimal Read Trimming in NGS and Its Complexity. Hedkte et al. Chapter in Algorithms for Computational Biology.
- [Co-authors] — Probing functional polymorphisms in the dengue vector, Aedes aegypti. Mariangela Bonizzoni, Monica Britton, Osvaldo Marinotti, William Augustine Dunn, Joseph Fass and Anthony A James. BMC Genomics. 2013, 14(739), October 29
- [Acknowledged] — RNA-Seq Analysis Identifies a Novel Set of Editing Substrates for Human ADAR2 Present in Saccharomyces cerevisiae. Eifler et al. Biochemistry. 2013, 52(45), October 31
- [Acknowledged] — Gene Regulatory Networks Elucidating Huanglongbing Disease Mechanisms. Martinelli et al. PLOS ONE. 2013, 8(9), September 25
- [Co-authors] — Identifying human-rhesus macaque gene orthologs using heterospecific SNP probes. Kanthaswamy S, Ng J, Ross CT, Trask JS, Smith DG, Buffalo VS, Fass JN, Lin D. Genomics. 2013 Jan;101(1):30-7. doi: 10.1016/j.ygeno.2012.09.001. Epub 2012 Sep 12. PMID:22982528 | PMCID:PMC3534948
- [Acknowledged] — The Influence of Gene Flow on Species Tree Estimation: A Simulation Study. Leaché et al. Systematic Biology. 2013, 63(1), August 13
- [Software] — Replication protein A subunit 3 and the iron efficiency response in soybean. Atwood et al. Plant, Cell, and Environment. 2013, 37(1), July 22
- [Software] — Gene Content and Diversity of the Loci Encoding Biosynthesis of Capsular Polysaccharides of the 15 Serovar Reference Strains of Haemophilus parasuis. Howell et al. Journal of Bacteriology. 2013, 195(18), July 19
- [Acknowledged] — Identification of SNPs in Closely Related Temperate Japonica Rice Cultivars Using Restriction Enzyme-Phased Sequencing. Kim and Tai. PLOS ONE. 2013, 8(3), March 26
- [Software] — High resolution genotyping by restriction enzyme-phased sequencing of advanced backcross lines of rice exhibiting differential cold stress recovery. Kim and Tai. Euphytica. 2013, 192(1), March 6
- [Co-authors] — Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Keith R. Bradnam, Joseph N. Fass, et al. Genome Research 2013, 21 (12) PMID:23870653 | PMCID:PMC3844414
- [Software] — Complete genome sequences from three genetically distinct strains reveal high intraspecies genetic diversity in the microsporidian Encephalitozoon cuniculi. Pombert et al. Eukaryotic Cell. 2015, 12(4), January 4
- [Co-authors] — Differentiating Inbred Mouse Strains from Each Other and Those with Single Gene Mutations Using Hair Proteomics. Robert H. Rice , Katie M. Bradshaw, Blythe P. Durbin-Johnson, David M. Rocke, Richard A. Eigenheer, Brett S. Phinney, John P. Sundberg. PLOS ONE. 2012, December 14
- [Acknowledged] — De novo assembly of the pepper transcriptome (Capsicum annuum): a benchmark for in silico discovery of SNPs, SSRs and candidate genes. Ashrafi et al. BMC Genomics. 2012, 13, October 30
- [Acknowledged] — Induced Pluripotency and Oncogenic Transformation Are Related Processes. Riggs et al. Stem Cells and Development. 2012, 22(1), October 26
- [Co-authors] — Multiple clonal MLL fusions in a patient receiving CHOP-based chemotherapy. Shih SJ, Fass J, Buffalo V, Lin D, Singh SP, Diaz MO, Vaughan AT. Br J Haematol. 2012 Oct;159(1):50-7. doi: 10.1111/j.1365-2141.2012.09248.x. Epub 2012 Jul 30. PMID:22845170 | PMCID:PMC3444640
- [Co-authors] — Genome-wide SNP discovery in walnut with an AGSNP pipeline updated for SNP discovery in allogamous organisms. You FM, Deal KR, Wang J, Britton MT, Fass JN, Lin D, Dandekar AM, Leslie CA, Aradhya M, Luo MC, Dvorak J. BMC Genomics. 2012 Jul 31;13:354. doi: 10.1186/1471-2164-13-354. PMID:22849334 | PMCID:PMC3527177
- [Co-authors] — High density SNP mapping and QTL analysis for fruit quality characteristics in peach (Prunus persica L.). Pedro J. Martínez-García , Dan E. Parfitt, Ebenezer A. Ogundiwin, Joseph Fass, Helen M. Chan, Riaz Ahmad, Susan Lurie, Abhaya Dandekar, Thomas M. Gradziel, Carlos H. Crisosto. Tree Genetics & Genomes. 2012, 9(1), June 24
- [Co-authors] — Reference genome-independent assessment of mutation density using restriction enzyme-phased sequencing. Monson-Miller J, Sanchez-Mendez DC, Fass J, Henry IM, Tai TH, Comai L. BMC Genomics. 2012 February 14;13:72. doi: 10.1186/1471-2164-13-72. PMID:22333298 | PMCID:PMC3305632
- [Co-authors] — Transcriptome profiling of citrus fruit response to huanglongbing disease. Martinelli F, Uratsu SL, Albrecht U, Reagan RL, Phu ML, Britton M, Buffalo V, Fass J, Leicht E, Zhao W, Lin D, D’Souza R, Davis CE, Bowman KD, Dandekar AM. PLoS One. 2012;7(5):e38039. doi: 10.1371/journal.pone.0038039. Epub 2012 May 31. PMID:22675433 | PMCID:PMC3364978
- [Acknowledged] — Case Study of Sequence Capture Enrichment Technology: Identification of Variation Underpinning Developmental Syndromes in an Amniote Model. Robb and Delaney. Genes. 2012, 3(2), March 26
- [Co-authors] — Assemblathon 1: a competitive assessment of de novo short read assembly methods. Earl D, Bradnam K, St John J, Darling A, Lin D, Fass J, Yu HO, Buffalo V, Zerbino DR, Diekhans M, Nguyen N, Ariyaratne PN, Sung WK, Ning Z, Haimel M, Simpson JT, Fonseca NA, Birol İ, Docking TR, Ho IY, Rokhsar DS, Chikhi R, et al. Genome Res. 2011 Dec;21(12):2224-41. doi: 10.1101/gr.126599.111. Epub 2011 Sep 16. PMID:21926179 | PMCID:PMC3227110
- [Co-authors] —Whole genome sequencing of peach (Prunus persica L.) for SNP identification and selection. Ahmad R, Parfitt DE, Fass J, Ogundiwin E, Dhingra A, Gradziel TM, Lin D, Joshi NA, Martinez-Garcia PJ, Crisosto CH. BMC Genomics. 2011 Nov 22;12:569. doi: 10.1186/1471-2164-12-569. PMID:22108025 | PMCID:PMC3253712
- [Co-authors] — Genome-Scale Analysis of Programmed DNA Elimination Sites in Tetrahymena thermophila. Fass JN, Joshi NA, Couvillion MT, Bowen J, Gorovsky MA, Hamilton EP, Orias E, Hong K, Coyne RS, Eisen JA, Chalker DL, Lin D, Collins K. G3 (Bethesda). 2011 Nov;1(6):515-22. doi: 10.1534/g3.111.000927. Epub 2011 Nov 1. PMID:22384362 | PMCID:PMC3276166
- [Co-authors] — Exploring the Transcriptome Landscape of Pomegranate Fruit Peel for Natural Product Biosynthetic Gene and SSR Marker Discovery. Ono NN, Britton MT, Fass JN, Nicolet CM, Lin D, Tian L. J Integr Plant Biol. 2011 Sep 12. doi: 10.1111/j.1744-7909.2011.01073.x. [Epub ahead of print] PMID:21910825
- [Co-authors] — Discovery of rare mutations in populations: TILLING by sequencing. Tsai H, Howell T, Nitcher R, Missirian V, Watson B, Ngo KJ, Lieberman M, Fass J, Uauy C, Tran RK, Khan AA, Filkov V, Tai TH, Dubcovsky J, Comai L. Plant Physiol. 2011 Jul;156(3):1257-68. doi: 10.1104/pp.110.169748. Epub 2011 Apr 29. PMID:21531898 | PMCID:PMC3135940
- [Co-authors] — A label-free differential quantitative mass spectrometry method for the characterization and identification of protein changes during citrus fruit development. Katz E, Fon M, Eigenheer RA, Phinney BS, Fass JN, Lin D, Sadka A, Blumwald E. Proteome Sci. 2010 Dec 16;8:68. doi: 10.1186/1477-5956-8-68. PMID:21162737 | PMCID:PMC3017515
- [Co-authors] — Mitochondrial DNA variant discovery and evaluation in human Cardiomyopathies through next-generation sequencing. Zaragoza MV, Fass J, Diegoli M, Lin D, Arbustini E. PLoS One. 2010 Aug 20;5(8):e12295. doi: 10.1371/journal.pone.0012295. PMID:20808834 | PMCID:PMC2924892
- [Co-authors] — Analysis of early host responses for asymptomatic disease detection and management of specialty crops. Dandekar AM, Martinelli F, Davis CE, Bhushan A, Zhao W, Fiehn O, Skogerson K, Wohlgemuth G, D’Souza R, Roy S, Reagan RL, Lin D, Cary R, Pardington P, Gupta G. Crit Rev Immunol. 2010;30(3):277-89. Review. PMID:20370635
- [Co-authors] — Functional consequences of overexpressing the gap junction Cx43 in the cardiogenic potential of pluripotent human embryonic stem cells. Moore JC, Tsang SY, Rushing SN, Lin D, Tse HF, Chan CW, Li RA. Biochem Biophys Res Commun. 2008 Dec 5;377(1):46-51. doi: 10.1016/j.bbrc.2008.09.076. Epub 2008 Sep 25. PMID: 18823947