Selected Publications By Affiliated Faculty
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Author
Advances in Experimental Medicine and Biology
- Yan Z, Holmes KV, Hodges RS. (2009) Expression and characterization of recombinant S2 subunit of SARS-coronavirus S fusion protein. Advances in Experimental Medicine and Biology 611:153-154. more details…
American Journal of Respiratory Cell and Molecular Biology
- Qian Z, Travanty EA, Oko L, Edeen K, Berglund A, Wang J, Ito Y, Holmes KV, Mason R. (2013) Innate immune response of human alveolar type II cells infected with SARS-coronavirus. American Journal of Respiratory Cell and Molecular Biology more details…
American Journal of Tropical Medicine and Hygiene
- Kang HJ, Kosoy MY, Shrestha SK, Shrestha MP, Pavlin JA, Gibbons RV, Yanagihara R. (2011) Genetic diversity of Thottapalayam virus, a hantavirus harbored by the Asian house shrew (Suncus murinus) in Nepal. American Journal of Tropical Medicine and Hygiene 85(3):540-545. more details…
- Arai S, Bennett SN, Sumibcay L, Cook JA, Song JW, Hope A, Parmenter C, Nerurkar VR, Yates TL, Yanagihara R. (2008) Phylogenetically distinct hantaviruses in the masked shrew (Sorex cinereus) and dusky shrew (Sorex monticolus) in the United States. American Journal of Tropical Medicine and Hygiene 78(2):348-351. more details…
- Chen HL, Lin SR, Liu HF, King CC, Hsieh SC, Wang WK. (2008) Evolution of dengue virus type 2 during two consecutive outbreaks with an increase in severity in southern Taiwan in 2001-2002. American Journal of Tropical Medicine and Hygiene 79(4):495-505. more details…
Antimicrobial Agents and Chemotherapy
- Podin Y, Sarovich DS, Price EP, Kaestli M, Mayo M, Hii K, Ngian H, Wong S, Wong I, Wong J, Mohan A, Ooi M, Fam T, Wong J, Tuanyok A, Keim P, Giffard PM, Currie BJ. (2014) Burkholderia pseudomallei isolates from Sarawak, Malaysian Borneo, are predominantly susceptible to aminoglycosides and macrolides. Antimicrobial Agents and Chemotherapy 58(1):162-166. more details…
Antiviral Research
- Liu IJ, Kao CL, Hsieh SC, Wey MT, Kan LS, Wang WK. (2009) Identification of a minimal peptide derived from heptad repeat (HR) 2 of spike protein of SARS-CoV and combination of HR1-derived peptides as fusion inhibitors. Antiviral Research 81(1):82-87. more details…
BMC Bioinformatics
- Li D, Xie Z, Pape ML, Dye T. (2015) An evaluation of statistical methods for DNA methylation microarray data analysis. BMC Bioinformatics 16:217. more details…
- Belcaid M, Bergeron A, Poisson G. (2011) The evolution of the tape measure protein: units, duplications and losses. BMC Bioinformatics 12(Suppl 9):S11 (5 October 2011) more details…
BMC Genomics
- Menor M, Baek K, Poisson G. (2013) Multiclass relevance units machine: benchmark evaluation and application to small ncRNA discovery. BMC Genomics 14 Suppl 2S6. more details…
- Park J, Zhang Y, Buboltz AM, Zhang X, Schuster SC, Ahuja U, Liu M, Miller JF, Sebaihia M, Bentley SD, Parkhill J, Harvill ET. (2012) Comparative genomics of the classical Bordetella subspecies: the evolution and exchange of virulence-associated diversity amongst closely related pathogens. BMC Genomics 13:545. more details…
BMC Microbiology
- Ahuja U, Liu M, Tomida S, Park J, Souda P, Whitelegge J, Li H, Harvill ET, Parkhill J, Miller JF. (2012) Phenotypic and genomic analysis of hypervirulent human-associated Bordetella bronchiseptica. BMC Microbiology 12:167. more details…
Bulletin de l’Academie Veterinaire de France
- Hugot J, Gu SH, Feliu C, Ventur J, Ribas A, Dormion J, Yanagihara R, Nicolas V. (2014) Genetic diversity of Talpa europaea and Nova hantavirus (NVAV) in France. Bulletin de l’Academie Veterinaire de France 167(3):277-284. more details…
Cancer Epidemiology, Biomarkers and Prevention
- Hernandez BY, Park SY, Wilkens LR, Henderson BE, Kolonel LN. (2009) Relationship of body mass, height, and weight gain to prostate cancer risk in the multiethnic cohort. Cancer Epidemiology, Biomarkers and Prevention 18(9):2413-2421. more details…
Cancer Microenvironment
- Steude JS, Maskarinec G, Erber E, Verheus M, Hernandez BY, Killeen J, Cline JM. (2009) Mammographic density and matrix metalloproteinases in breast tissue. Cancer Microenvironment more details…
Cancer Research
- Shvetsov YB, Hernandez BY, Wilkens LR, Thompson PJ, Franke AA, Zhu X, Goodman MT. (2010) Plasma micronutrients and the acquisition and clearance of anal human papillomavirus infection: the Hawaii HPV cohort study. Cancer Research 70(23):9787-9797. more details…
Carbohydrate Research
- Stone JK, Heiss C, Wang Z, Black I, Grasso SA, Koppisch AT, Azadi P, Keim P, Tuanyok A. (2014) Structural characterization of polysaccharides expressed by Burkholderia oklahomensis E0147. Carbohydrate Research 386:68-72. more details…
Cell Host Microbe
- Aliyari R, Wu Q, Li HW, Wang XH, Li F, Green LD, Han CS, Li WX, Ding SW. (2008) Mechanism of induction and suppression of antiviral immunity directed by virus-derived small RNAs in Drosophila. Cell Host Microbe 4(4):387-397. more details…
Cell Microbiology
- French CT, Panina EM, Yeh SH, Griffith N, Arambula DG, Miller JF. (2009) The Bordetella type III secretion system effector BteA contains a conserved N-terminal motif that guides bacterial virulence factors to lipid rafts. Cell Microbiology 11(12):1735-1749. more details…
Clinical Infectious Diseases
- Shvetsov YB, Hernandez BY, McDuffie K, Wilkens LR, Zhu X, Ning L, Killeen J, Kamemoto L, Goodman MT. (2009) Duration and clearance of anal human papillomavirus (HPV) infection among women: the Hawaii HPV cohort study. Clinical Infectious Diseases 48(5):536-546. more details…
- Wang WK, Chen HL, Yang CF, Hsieh SC, Juan CC, Chang SM, Yu CC, Lin LH, Huang JH, King CC. (2006) Slower rates of clearance of viral load and virus-containing immune complexes in patients with dengue hemorrhagic fever. Clinical Infectious Diseases 43(8):1023-1030. more details…
Conference Proceedings of IEEE Engineering in Medicine and Biology Society
- Fabel S, Baek K, Berkelman P. (2010) Robotic-surgical instrument wrist pose estimation. Conference Proceedings of IEEE Engineering in Medicine and Biology Society 1:971-974. more details…
Conference Proceedings of IEEE Engineering in Medicine and Biology Society
- Baek K, Kim DH, Sajda P. (2004) Inferring direction of figure using a recurrent integrate-and-fire neural circuit. Conference Proceedings of IEEE Engineering in Medicine and Biology Society 6:4576-4579. more details…
Elife
- Zhang X, Guo H, Jin L, Czornyj E, Hodes A, Hui WH, Nieh AW, Miller JF, Zhou ZH. (2013) A new topology of the HK97-like fold revealed in Bordetella bacteriophage by cryoEM at 3.5 A resolution. Elife 2(0):e01299. more details…
Emerging Infectious Diseases
- Gee JE, Allender CJ, Tuanyok A, Elrod MG, Hoffmaster AR. (2014) Burkholderia pseudomallei type G in Western Hemisphere. Emerging Infectious Diseases 20(4):682-684. more details…
- Arai S, Nguyen ST, Boldgiv B, Fukui D, Araki K, Dang CN, Ohdachi SD, Nguyen NX, Pham TD, Boldbaatar B, Satoh H, Yoshikawa Y, Morikawa S, Tanaka-Taya K, Yanagihara R, Oishi K. (2013) Novel bat-borne hantavirus, Vietnam. Emerging Infectious Diseases 19(7):1159-1161. more details…
- Arai S, Song JW, Sumibcay L, Bennett SN, Nerurkar VR, Parmenter C, Cook JA, Yates TL, Yanagihara R. (2007) Hantavirus in northern short-tailed shrew, United States. Emerging Infectious Diseases 13(9):1420-1423. more details…
- Song JW, Baek LJ, Schmaljohn CS, Yanagihara R. (2007) Thottapalayam virus, a prototype shrewborne hantavirus. Emerging Infectious Diseases 13(7):980-985. more details…
- Song JW, Kang HJ, Song KJ, Truong TT, Bennett SN, Arai S, Truong NU, Yanagihara R. (2007) Newfound hantavirus in Chinese mole shrew, Vietnam. Emerging Infectious Diseases 13(11):1784-1787. more details…
Epidemiology and Infection
- Gu SH, Dormion J, Hugot JP, Yanagihara R. (2014) High prevalence of Nova hantavirus infection in the European mole (Talpa europaea) in France. Epidemiology and Infection 142(6):1167-1171. more details…
FEBS Letters
- Li HW, Ding SW. (2005) Antiviral silencing in animals. FEBS Letters 579(26):5965-5973. more details…
Frontiers in Cellular and Infection Microbiology
- Liphardt SW, Kang HJ, Arai S, Gu SH, Cook JA, Yanagihara R (2020) Reassortment between divergent strains of Camp Ripley virus (Hantaviridae) in the northern short-tailed shrew (Blarina brevicauda) Frontiers in Cellular and Infection Microbiology 10, 460 more details…
Genome
- Gulick PJ, Drouin S, Yu Z, Danyluk J, Poisson G, Monroy AF, Sarhan F. (2006) Transcriptome comparison of winter and spring wheat responding to low temperature. Genome 48(5):913-923. more details…
Genome Announcements
- Gu SH, Hejduk J, Markowski J, Markowski M, Liberski PP, Yanagihara R. (2015) Whole-genome sequence of a novel hantavirus isolated from the European mole (Talpa europaea). Genome Announcements 3(3):pii: e00508-15. more details…
- Lee JG, Gu SH, Baek LJ, Shin OS, Kim HC, Klein TA, Yanagihara R, Song JW. (2014) Whole-genome sequence of Muju virus, an arvicolid rodent-borne hantavirus. Genome Announcements 2(1):e00099-14 more details…
- Sahl JW, Stone JK, Gelhaus HC, Warren RL, Cruttwell CJ, Funnell SG, Keim P, Tuanyok A. (2013) Genome sequence of Burkholderia pseudomallei NCTC 13392. Genome Announcements 1(3):e00183-13 more details…
- Stone JK, Johnson SL, Bruce DC, Detter JC, Mayo M, Currie BJ, Gelhaus HC, Keim P, Tuanyok A. (2013) Complete genome sequence of the encephalomyelitic Burkholderia pseudomallei strain MSHR305. Genome Announcements 1(4):e00656-13 more details…
Genomics Proteomics Bioinformatics
- Poisson G, Chauve C, Chen X, Bergeron A. (2007) FragAnchor: a large-scale predictor of glycosylphosphatidylinositol anchors in eukaryote protein sequences by qualitative scoring Genomics Proteomics Bioinformatics 5(2):121-130. more details…
Hawaii Medical Journal
- Hernandez BY, Green MD, Cassel KD, Pobutsky AM, Vu V, Wilkens LR. (2010) Preview of Hawaii Cancer Facts and Figures 2010. Hawaii Medical Journal 69(9):223-224. more details…
Human Vaccine
- Hernandez BY, Wilkens LR, Thompson PJ, Shvetso YB, Goodman MT, Ning L, Kaopua L. (2010) Acceptability of prophylactic human papillomavirus vaccination among adult men. Human Vaccine 6(6):467-475. more details…
Immune Network
- Krause KK, Azouz F, Shin OS, Kumar M. (2017) Understanding the pathogenesis of Zika virus infection using animal models. Immune Network 17(5):287-297. more details…
Immunity
- Chen L, Chen Z, Baker K, Halvorsen EM, da Cunha AP, Flak MB, Gerber G, Huang YH, Hosomi S, Arthur JC, Dery KJ, Nagaishi T, Beauchemin N, Holmes KV, Ho JW, Shively JE, Jobin C, Onderdonk AB, Bry L, Weiner HL, Higgins DE, Blumberg RS. (2012) The short isoform of the CEACAM1 receptor in intestinal T cells regulates mucosal immunity and homeostasis via Tfh cell induction. Immunity 37(5):930-946. more details…
Immunobiology
- Seong RK, Seo SW, Kim JA, Fletcher SJ, Morgan NV, Kumar M, Choi YK, Shin OS. (2017) Schlafen 14 (SLFN14) is a novel antiviral factor involved in the control of viral replication. Immunobiology Jul 11. pii: S0171-2985(17)30115-8. more details…
Infection and Immunity
- Toesca IJ, French CT, Miller JF. (2014) The T6SS-5 VgrG spike protein mediates membrane fusion during intercellular spread by pseudomallei-group Burkholderia species. Infection and Immunity more details…
- Inatsuka CS, Xu Q, Vujkovic-Cvijin I, Wong S, Stibitz S, Miller JF, Cotter PA. (2010) Pertactin is required for Bordetella species to resist neutrophil-mediated clearance. Infection and Immunity 78(7):2901-2909. more details…
Infection Genetics and Evolution
- Arai S, Taniguchi S, Aoki K, Yoshikawa Y, Kyuwa S, Tanaka-Taya K, Masangkay JS, Omatsu T, Puentespina R, Watanabe S, Alviola P, Alvarez J, Eres E, Cosico E, Quibod MN, Morikawa S, Yanagihara R, Oishi K. (2016) Molecular phylogeny of a genetically divergent hantavirus harbored by the Geoffroy’s rousette (Rousettus amplexicaudatus), a frugivorous bat species in the Philippines. Infection Genetics and Evolution 45:26-32. more details…
- Gu SH, Arai S, Yu HT, Lim BK, Kang HJ, Yanagihara R. (2016) Genetic variants of Cao Bang hantavirus in the Chinese mole shrew (Anourosorex squamipes) and Taiwanese mole shrew (Anourosorex yamashinai). Infection Genetics and Evolution 40:113-118. more details…
Infection, Genetics and Evolution
- Gu SH, Kim YS, Baek LJ, Kurata T, Yanagihara R, Song JW. (2015) Lethal disease in infant and juvenile Syrian hamsters experimentally infected with Imjin virus, a newfound crocidurine shrew-borne hantavirus. Infection, Genetics and Evolution 36:231-239. more details…
- Yashina LN, Abramov SA, Dupal TA, Danchinova GA, Malyshev BS, Hay J, Gu SH, Yanagihara R. (2015) Hokkaido genotype of Puumala virus in the grey red-backed vole (Myodes rufocanus) and northern red-backed vole (Myodes rutilus) in Siberia. Infection, Genetics and Evolution 33:304-313. more details…
- Gu SH, Hejduk J, Markowski J, Kang HJ, Markowski M, Polatynska M, Sikorska B, Liberski PP, Yanagihara R. (2014) Co-circulation of soricid- and talpid-borne hantaviruses in Poland. Infection, Genetics and Evolution 28C:296-303. more details…
- Gu SH, Nicolas V, Lalis A, Sathirapongsasuti N, Yanagihara R. (2013) Complete genome sequence and molecular phylogeny of a newfound hantavirus harbored by the Doucet’s musk shrew (Crocidura douceti) in Guinea. Infection, Genetics and Evolution 20:118-123. more details…
International Journal of Molecular Science
- Menor MS, Baek K, Poisson G. (2015) Prediction of mature microRNA and Piwi-interacting RNA without a genome reference or precursors. International Journal of Molecular Science 16(1):1466-1481. more details…
International Society for Microbial Ecology Journal
- Steward GF, Culley AI, Mueller JA, Wood-Charlson EM, Belcaid M, Poisson G. (2013) Are we missing half of the viruses in the ocean? International Society for Microbial Ecology Journal 7(3):672-679. more details…
Journal of Biological Chemistry
- Hsieh SC, Wu YC, Zou G, Nerurkar VR, Shi PY, Wang WK. (2014) Highly conserved residues in the helical domain of dengue virus type 1 precursor membrane protein are involved in assembly, prM protein cleavage and entry. Journal of Biological Chemistry 289(48):33149-33160. more details…
- Peng G, Xu L, Lin YL, Chen L, Pasquarella JR, Holmes KV, Li F. (2012) Crystal structure of bovine coronavirus spike protein lectin domain. Journal of Biological Chemistry 287(50):41931-41938. more details…
Journal of Clinical Virology
- Noh JY, Cheong HJ, Song JY, Kim WJ, Song KJ, Klein TA, Lee SH, Yanagihara R, Song JW. (2013) Clinical and molecular epidemiological features of hemorrhagic fever with renal syndrome in Korea over a 10-year period. Journal of Clinical Virology 58(1):11-17. more details…
Journal of Computational Biology
- Belcaid M, Bergeron A, Poisson G. (2010) Mosaic graphs and comparative genomics in phage communities. Journal of Computational Biology 17(9):1315-1326. more details…
Journal of General Virology
- Dominguez SR, Shrisastava S, Berglund A, Qian Z, Goes LG, Halpin RA, Fedorova NB, Ransier A, Weston PA, Durigon EL, Jerez JA, Robinson CC, Town CD, Holmes KV. (2014) Isolation, propagation, genome analysis, and epidemiology of HKU1 Betacoronaviruses from Colorado and Brazil. Journal of General Virology more details…
- Dominguez SR, Sims GE, Wentworth DE, Halpin RA, Robinson CC, Town CD, Holmes KV. (2012) Genomic analysis of 16 Colorado human NL63 coronaviruses identifies a new genotype, high sequence diversity in the N-terminal domain of the spike gene and evidence of recombination. Journal of General Virology 93(Pt 11):2387-2398. more details…
- Funk CJ, Wang J, Ito Y, Travanty EA, Voelker DR, Holmes KV, Mason RJ. (2012) Infection of human alveolar macrophages by human coronavirus strain 229E. Journal of General Virology 93(Pt 3):494-503. more details…
- Funk CJ, Manzer R, Miura TA, Groshong SD, Ito Y, Travanty EA, Leete J, Holmes KV, Mason RJ. (2009) Rat respiratory coronavirus infection: replication in airway and alveolar epithelial cells and the innate immune response. Journal of General Virology 90(Pt 12):2956-2964. more details…
- Song KJ, Baek LJ, Moon S, Ha SJ, Kim SH, Park KS, Klein TA, Sames W, Kim HC, Lee JS, Yanagihara R, Song JW. (2007) Muju virus, a novel hantavirus harboured by the arvicolid rodent Myodes regulus in Korea. Journal of General Virology 88(Pt 11):3121-3129. more details…
Journal of Infectious Diseases
- Goodman MT, McDuffie K, Hernandez BY, Wilkens LR, Zhu X, Thompson PJ, Killeen J, Kamemoto L, Shvetsov YB. (2011) The influence of multiple human papillomavirus types on the risk of genotype-concordant incident infections of the anus and cervix: the Hawaii HPV cohort study. Journal of Infectious Diseases 203(3):335-340. more details…
- Goodman MT, Shvetsov YB, McDuffie K, Wilkens LR, Zhu X, Thompson PJ, Ning L, Killeen J, Kamemoto L, Hernandez BY. (2010) Sequential acquisition of human papillomavirus (HPV) infection of the anus and cervix: the Hawaii HPV Cohort Study. Journal of Infectious Diseases 201(9):1331-1339. more details…
- Hernandez BY, Shvetsov YB, Goodman MT, Wilkens LR, Thompson P, Zhu X, Ning L. (2010) Reduced clearance of penile human papillomavirus infection in uncircumcised men. Journal of Infectious Diseases 201(9):1340-1343. more details…
Journal of Investigative Dermatology
- Fitz-Gibbon S, Tomida S, Chiu BH, Nguyen L, Du C, Liu M, Elashoff D, Erfe MC, Loncaric A, Kim J, Modlin RL, Miller JF, Sodergren E, Craft N, Weinstock GM, Li H. (2013) Propionibacterium acnes strain populations in the human skin microbiome associated with acne. Journal of Investigative Dermatology more details…
Journal of Leukocyte Biology
- Miura TA, Holmes KV. (2009) Host-pathogen interactions during coronavirus infection of primary alveolar epithelial cells. Journal of Leukocyte Biology 86(5):1145-1151. more details…
Journal of Medical Virology
- Dominguez SR, Robinson CC, Holmes KV. (2009) Detection of four human coronaviruses in respiratory infections in children: a one-year study in Colorado. Journal of Medical Virology 81(9):1597-1604. more details…
- Baek LJ, Kariwa H, Lokugamage K, Yoshimatsu K, Arikawa J, Takashima I, Kang JI, Moon SS, Chung SY, Kim EJ, Kang HJ, Song KJ, Klein TA, Yanagihara R, Song JW. (2006) Soochong virus: an antigenically and genetically distinct hantavirus isolated from Apodemus peninsulae in Korea. Journal of Medical Virology 78(2):290-297. more details…
Journal of Virology
- Kang HJ, Stanley WT, Esselstyn JA, Gu SH, Yanagihara R. (2014) Expanded host diversity and geographic distribution of hantaviruses in sub-Saharan Africa. Journal of Virology 88(13):7663-7667. more details…
- Kang HJ, Bennett SN, Hope AG, Cook JA, Yanagihara R. (2011) Shared ancestry between a newfound mole-borne hantavirus and hantaviruses harbored by cricetid rodents. Journal of Virology 85(15):7496-7503. more details…
- Lin SR, Zou G, Hsieh SC, Qing M, Tsai WY, Shi PY, Wang WK. (2011) The helical domains of the stem region of dengue virus envelope protein are involved in both virus assembly and entry. Journal of Virology 85(10):5159-5171. more details…
- Hirai A, Ohtsuka N, Ikeda T, Taniguchi R, Blau D, Nakagaki K, Miura HS, Ami Y, Yamada YK, Itohara S, Holmes KV, Taguchi F. (2010) Role of mouse hepatitis virus (MHV) receptor murine CEACAM1 in the resistance of mice to MHV infection: studies of mice with chimeric mCEACAM1a and mCEACAM1b. Journal of Virology 84(13):6654-6666. more details…
- Song JW, Kang HJ, Gu SH, Moon SS, Bennett SN, Song KJ, Baek LJ, Kim HC, O’Guinn ML, Chong ST, Klein TA, Yanagihara R. (2009) Characterization of Imjin virus, a newly isolated hantavirus from the Ussuri white-toothed shrew (Crocidura lasiura). Journal of Virology 83(12):6184-6191. more details…
MBio
- Culley AI, Mueller JA, Belcaid M, Wood-Charlson EM, Poisson G, Steward GF. (2014) The characterization of RNA viruses in tropical seawater using targeted PCR and metagenomics. MBio 5(3): more details…
- Holmes KV, Dominguez SR. (2013) The new age of virus discovery: genomic analysis of a novel human betacoronavirus isolated from a fatal case of pneumonia. MBio 4(1):e00548-12. more details…
- Price EP, Sarovich DS, Mayo M, Tuanyok A, Drees KP, Kaestli M, Beckstrom-Sternberg SM, Babic-Sternberg JS, Kidd TJ, Bell SC, Keim P, Pearson T, Currie BJ. (2013) Within-host evolution of Burkholderia pseudomallei over a twelve-year chronic carriage infection. MBio 4(4):e00388-13. more details…
- Marinelli LJ, Fitz-Gibbon S, Hayes C, Bowman C, Inkeles M, Loncaric A, Russell DA, Jacobs-Sera D, Cokus S, Pellegrini M, Kim J, Miller JF, Hatfull GF, Modlin RL. (2012) Propionibacterium acnes bacteriophages display limited genetic diversity and broad killing activity against bacterial skin isolates. MBio 3(5): more details…
Methods in Molecular Biology
- Yang B, Li H. (2011) Dicer assay in Drosophila S2 cell extract. Methods in Molecular Biology 721:215-229. more details…
Molecular Biology and Evolution
- Bennett SN, Drummond AJ, Kapan DD, Suchard MA, Munoz-Jordan JL, Pybus OG, Holmes EC, Gubler DJ. (2010) Epidemic dynamics revealed in dengue evolution. Molecular Biology and Evolution 27(4):811-818. more details…
Molecular Microbiology
- Medhekar B, Shrivastava R, Mattoo S, Gingery M, Miller JF. (2009) Bordetella Bsp22 forms a filamentous type III secretion system tip complex and is immunoprotective in vitro and in vivo. Molecular Microbiology 71(2):492-504. more details…
Nature
- Lu R, Maduro M, Li F, Li HW, Broitman-Maduro G, Li WX, Ding SW. (2005) Animal virus replication and RNAi-mediated antiviral silencing in Caenorhabditis elegans. Nature 436(7053):1040-1043. more details…
Nature Reviews Microbiology
- Melvin JA, Scheller EV, Miller JF, Cotter PA. (2014) Bordetella pertussis pathogenesis: current and future challenges. Nature Reviews Microbiology more details…
Nucleic Acids Research
- Barrette I, Poisson G, Gendron P, Major F. (2001) Pseudoknots in prion protein mRNAs confirmed by comparative sequence analysis and pattern searching. Nucleic Acids Research 29(3):753-758. more details…
Oncotarget
- Kim JA, Park SK, Kumar M, Lee CH, Shin OS. (2015) Insights into the role of immunosenescence during varicella zoster virus infection (shingles) in the aging cell model. Oncotarget more details…
PLoS Genetics
- Guo H, Tse LV, Nieh AW, Czornyj E, Williams S, Oukil S, Liu VB, Miller JF. (2011) Target site recognition by a diversity-generating retroelement. PLoS Genetics 7(12):e1002414. more details…
PLoS Neglected Tropical Diseases
- Limmathurotsakul D, Dance DA, Wuthiekanun V, Kaestli M, Mayo M, Warner J, Wagner DM, Tuanyok A, Wertheim H, Yoke Cheng T, Mukhopadhyay C, Puthucheary S, Day NP, Steinmetz I, Currie BJ, Peacock SJ. (2013) Systematic review and consensus guidelines for environmental sampling of Burkholderia pseudomallei. PLoS Neglected Tropical Diseases 7(3):e2105. more details…
- Thongsripong P, Green A, Kittayapong P, Kapan D, Wilcox B, Bennett S. (2013) Mosquito vector diversity across habitats in central Thailand endemic for dengue and other arthropod-borne diseases. PLoS Neglected Tropical Diseases 7(10):e2507. more details…
PLoS One
- Sarovich DS, Price EP, Webb JR, Ward LM, Voutsinos MY, Tuanyok A, Mayo M, Kaestli M, Currie BJ. (2014) Variable virulence factors in Burkholderia pseudomallei (melioidosis) associated with human disease. PLoS One 9(3):e91682. more details…
- Guttman C, Davidov G, Shaked H, Kolusheva S, Bitton R, Ganguly A, Miller JF, Chill JH, Zarivach R. (2013) Characterization of the N-terminal domain of BteA: a Bordetella type III secreted cytotoxic effector. PLoS One 8(1):e55650. more details…
- Li D, Le Pape MA, Parikh NI, Chen WX, Dye TD. (2013) Assessing differential expression in two-color microarrays: a resampling-based empirical Bayes approach. PLoS One 8(11):e80099. more details…
- Li Y, Kakinami C, Li Q, Yang B, Li H. (2013) Human apolipoprotein A-I is associated with dengue virus and enhances virus infection through SR-BI. PLoS One 8(7):e70390. more details…
- Price EP, Sarovich DS, Webb JR, Ginther JL, Mayo M, Cook JM, Seymour ML, Kaestli M, Theobald V, Hall CM, Busch JD, Foster JT, Keim P, Wagner DM, Tuanyok A, Pearson T, Currie BJ. (2013) Accurate and rapid identification of the Burkholderia pseudomallei near-neighbour, Burkholderia ubonensis, using real-time PCR. PLoS One 8(8):e71647. more details…
- Qian Z, Dominguez SR, Holmes KV. (2013) Role of the spike glycoprotein of human Middle East respiratory syndrome coronavirus (MERS-CoV) in virus entry and syncytia formation. PLoS One 8(10):e76469. more details…
- Lu SX, Kappel LW, Charbonneau-Allard AM, Atallah R, Holland AM, Turbide C, Hubbard VM, Rotolo JA, Smith M, Suh D, King C, Rao UK, Yim N, Bautista JL, Jenq RR, Penack O, Na IK, Liu C, Murphy G, Alpdogan O, Blumberg RS, Macian F, Holmes KV, Beauchemin N, van den Brink MR. (2011) Ceacam1 separates graft-versus-host-disease from graft-versus-tumor activity after experimental allogeneic bone marrow transplantation. PLoS One 6(7):e21611. more details…
- Osborne C, Cryan PM, O’Shea TJ, Oko LM, Ndaluka C, Calisher CH, Berglund AD, Klavetter ML, Bowen RA, Holmes KV, Dominguez SR. (2011) Alphacoronaviruses in New World bats: prevalence, persistence, phylogeny, and potential for interaction with humans. PLoS One 6(5):e19156. more details…
- Kang HJ, Bennett SN, Sumibcay L, Arai S, Hope AG, Mocz G, Song JW, Cook JA, Yanagihara R. (2009) Evolutionary insights from a genetically divergent hantavirus harbored by the European common mole (Talpa europaea). PLoS One 4(7):e6149. more details…
- Bergeron A, Belcaid M, Steward GF, Poisson G. (2007) Divide and conquer: enriching environmental sequencing data. PLoS One 2(9):e830. more details…
Proceedings of the 2010 ACM Symposium on Applied Computing
- Menor M, Baek K, Belcaid M, Gingras Y, Poisson G. (2010) Virus DNA-fragment classification using taxonomic hidden Markov model profile. Proceedings of the 2010 ACM Symposium on Applied Computing 1567-1571. more details…
Proceedings of the 2011 ACM Symposium on Applied Computing
- Belcaid M, Baek K, Haymer D, Poisson G. (2011) Efficient clustering of populations using a minimal SNP panel. Proceedings of the 2011 ACM Symposium on Applied Computing 83-88 more details…
Proceedings of the 2012 ACM Symposium on Applied Computing BIO track
- Menor M, Poisson G, Baek K. (2012) Probabilistic prediction of protein phosphorylation sites using kernel machines. Proceedings of the 2012 ACM Symposium on Applied Computing BIO track 1393-1398 more details…
Proceedings of the National Academy of Sciences USA
- French CT, Toesca IJ, Wu TH, Teslaa T, Beaty SM, Wong W, Liu M, Schroder I, Chiou PY, Teitell MA, Miller JF. (2011) Dissection of the Burkholderia intracellular life cycle using a photothermal nanoblade. Proceedings of the National Academy of Sciences USA 108(29):12095-12100. more details…
- Peng G, Sun D, Rajashankar KR, Qian Z, Holmes KV, Li F. (2011) Crystal structure of mouse coronavirus receptor-binding domain complexed with its murine receptor. Proceedings of the National Academy of Sciences USA 108(26):10696-10701. more details…
- Dai W, Hodes A, Hui WH, Gingery M, Miller JF, Zhou ZH. (2010) Three-dimensional structure of tropism-switching Bordetella bacteriophage. Proceedings of the National Academy of Sciences USA 107(9):4347-4352. more details…
- Arai S, Ohdachi SD, Asakawa M, Kang HJ, Mocz G, Arikawa J, Okabe N, Yanagihara R. (2008) Molecular phylogeny of a newfound hantavirus in the Japanese shrew mole (Urotrichus talpoides). Proceedings of the National Academy of Sciences USA 105(42):16296-16301. more details…
Science
- Wang XH, Aliyari R, Li WX, Li HW, Kim K, Carthew R, Atkinson P, Ding SW. (2006) RNA interference directs innate immunity against viruses in adult Drosophila. Science 312(5772):452-454. more details…
Scientific Reports
- Arai S, Aoki K, Nguyen ST, Vuong TV, Kikuchi F, Kinoshita G, Fukui D, Hoang TT, Gu SH, Yoshikawa Y, Tanaka-Taya K, Morikawa S, Yanagihara R, Oishi K. (2019) Dakrong virus, a novel mobatvirus (Hantaviridae) harbored by the Stoliczka’s Asian trident bat (Aselliscus stoliczkanus) in Vietnam. Scientific Reports 9(1):10239. more details…
- Gu SH, Kumar M, Sikorska B, Hejduk J, Markowski J, Markowski M, Liberski PP, Yanagihara R. (2016) Isolation and partial characterization of a highly divergent lineage of hantavirus from the European mole (Talpa europaea). Scientific Reports 6:21119. more details…
Trends in Microbiology
- Bennett SN, Gu SH, Kang HJ, Arai S, Yanagihara R. (2014) Reconstructing the evolutionary origins and phylogeography of hantaviruses. Trends in Microbiology 22(8):473-482. more details…
Tropical Medicine and Health
- Kang HJ, Gu SH, Cook JA, Yanagihara R. (2016) Dahonggou Creek virus, a divergent lineage of hantavirus harbored by the long-tailed mole (Scaptonyx fusicaudus). Tropical Medicine and Health 44:16. more details…
Tropical Medicine and International Health
- Vanwambeke SO, Bennett SN, Kapan DD. (2011) Spatially disaggregated disease transmission risk: land cover, land use and risk of dengue transmission on the island of Oahu. Tropical Medicine and International Health 16(2):174-185. more details…
Vector Borne and Zoonotic Diseases
- Arai S, Kang HJ, Gu SH, Ohdachi SD, Cook JA, Yashina LN, Tanaka-Taya K, Abramov SA, Morikawa S, Okabe N, Oishi K, Yanagihara R. (2016) Genetic diversity of Artybash virus in the Laxmann’s shrew (Sorex caecutiens). Vector Borne and Zoonotic Diseases 16:468-475. more details…
- Kang HJ, Arai S, Hope AG, Cook JA, Yanagihara R. (2010) Novel hantavirus in the flat-skulled shrew (Sorex roboratus). Vector Borne and Zoonotic Diseases 10(6):593-597. more details…
- Yashina LN, Abramov SA, Gutorov VV, Dupal TA, Krivopalov AV, Panov VV, Danchinova GA, Vinogradov VV, Luchnikova EM, Hay J, Kang HJ, Yanagihara R. (2010) Seewis virus: phylogeography of a shrew-borne hantavirus in Siberia, Russia. Vector Borne and Zoonotic Diseases 10(6):585-591. more details…
Viral Immunology
- Shin OS, Song GS, Kumar M, Yanagihara R, Lee HW, Song JW. (2014) Hantaviruses induce antiviral and pro-inflammatory innate immune responses in astrocytic cells and the brain. Viral Immunology 27(6):256-266. more details…
Virology
- Shin OS, Kumar M, Yanagihara R, Song JW. (2013) Hantaviruses induce cell type- and viral species-specific host microRNA expression signatures. Virology 446(1-2):217-224. more details…
- Arai S, Gu SH, Baek LJ, Tabara K, Bennett SN, Oh HS, Takada N, Kang HJ, Tanaka-Taya K, Morikawa S, Okabe N, Yanagihara R, Song JW. (2012) Divergent ancestral lineages of newfound hantaviruses harbored by phylogenetically related crocidurine shrew species in Korea. Virology 424(2):99-105 more details…
- Shin OS, Yanagihara R, Song J-W. (2012) Distinct innate immune responses in human macrophages and endothelial cells infected with shrew-borne hantaviruses. Virology 434(1):43-49. more details…
- Hsieh SC, Zou G, Tsai WY, Qing M, Chang GJ, Shi PY, Wang WK. (2011) The C-terminal helical domain of dengue virus precursor membrane protein is involved in virus assembly and entry. Virology 410(1):170-180. more details…
- Steel A, Gubler DJ, Bennett SN. (2010) Natural attenuation of dengue virus type-2 after a series of island outbreaks: a retrospective phylogenetic study of events in the South Pacific three decades ago. Virology 405(2):505-512. more details…
- Kang HJ, Bennett SN, Dizney L, Sumibcay L, Arai S, Ruedas LA, Song JW, Yanagihara R. (2009) Host switch during evolution of a genetically distinct hantavirus in the American shrew mole (Neurotrichus gibbsii). Virology 388(1):8-14. more details…
- Hsieh SC, Liu IJ, King CC, Chang GJ, Wang WK. (2008) A strong endoplasmic reticulum retention signal in the stem-anchor region of envelope glycoprotein of dengue virus type 2 affects the production of virus-like particles. Virology 374(2):338-350. more details…
- Hu HP, Hsieh SC, King CC, Wang WK. (2007) Characterization of retrovirus-based reporter viruses pseudotyped with the precursor membrane and envelope glycoproteins of four serotypes of dengue viruses. Virology 368(2):376-387. more details…
Virology Journal
- Gu SH, Markowski J, Kang HJ, Hejduk J, Sikorska B, Liberski PP, Yanagihara R. (2013) Boginia virus, a newfound hantavirus harbored by the Eurasian water shrew (Neomys fodiens) in Poland. Virology Journal 10(1):160. more details…
- Sumibcay L, Kadjo B, Gu SH, Kang HJ, Lim BK, Cook JA, Song JW, Yanagihara R. (2012) Divergent lineage of a novel hantavirus in the banana pipistrelle (Neoromicia nanus) in Cote d’Ivoire. Virology Journal 9(1):34. more details…
- Gu SH, Kang HJ, Baek LJ, Noh JY, Kim HC, Klein TA, Yanagihara R, Song JW. (2011) Genetic diversity of Imjin virus in the Ussuri white-toothed shrew (Crocidura lasiura) in the Republic of Korea, 2004-2010. Virology Journal 8(1):56. more details…
- Kang HJ, Kadjo B, Dubey S, Jacquet F, Yanagihara R. (2011) Molecular evolution of Azagny virus, a newfound hantavirus harbored by the West African pygmy shrew (Crocidura obscurior) in Cote d’Ivoire. Virology Journal 8(1):373. more details…
- Kang HJ, Arai S, Hope AG, Song JW, Cook JA, Yanagihara R. (2009) Genetic diversity and phylogeography of Seewis virus in the Eurasian common shrew in Finland and Hungary. Virology Journal 6:208. more details…
- Song JW, Gu SH, Bennett SN, Arai S, Puorger M, Hilbe M, Yanagihara R. (2007) Seewis virus, a genetically distinct hantavirus in the Eurasian common shrew (Sorex araneus). Virology Journal 4:114. more details…
Virus Genes
- Song JW, Baek LJ, Song KJ, Skrok A, Markowski J, Bratosiewicz-Wasik J, Kordek R, Liberski PP, Yanagihara R. (2004) Characterization of Tula virus from common voles (Microtus arvalis) in Poland: evidence for geographic-specific phylogenetic clustering. Virus Genes 29(2):239-247. more details…
Virus Research
- Yanagihara R, Gu SH, Arai S, Kang HJ, Song JW. (2014) Hantaviruses: rediscovery and new beginnings. Virus Research 187:6-14. more details…
Viruses
- Kang HJ, Gu SH, Yashina LN, Cook JA, Yanagihara R. (2019) Highly divergent genetic variants of soricid-borne Altai virus (Hantaviridae) in Eurasia suggest ancient host-switching events. Viruses 11(9): pii: E857. more details…
- Liphardt SW, Kang HJ, Dizney LJ, Ruedas LA, Cook JA, Yanagihara R. (2019) Complex history of codiversification and host switching of a newfound soricid-borne orthohantavirus in North America. Viruses 1(7). pii: E637. more details…
- Gu SH, Lim BK, Kadjo B, Arai S, Kim JA, Nicolas V, Lalis A, Denys C, Cook JA, Dominguez SR, Holmes KV, Urushadze L, Sidamonidze K, Putkaradze D, Kuzmin IV, Kosoy MY, Song JW, Yanagihara R. (2014) Molecular phylogeny of hantaviruses harbored by insectivorous bats in Cote d’Ivoire and Vietnam. Viruses 6(5):1897-1910. more details…
- Lee JG, Gu SH, Baek LJ, Shin OS, Park KS, Kim HC, Klein TA, Yanagihara R, Song JW. (2014) Muju virus, harbored by Myodes regulus in Korea, might represent a genetic variant of Puumala virus, the prototype arvicolid rodent-borne hantavirus. Viruses 6(4):1701-1714. more details…
Yeast
- Yang X, Talibi D, Weber S, Poisson G, Raymond M. (2001) Functional isolation of the Candida albicans FCR3 gene encoding a bZip transcription factor homologous to Saccharomyces cerevisiae Yap3p. Yeast 18(13):1217-1225. more details…