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Collage of Research subjects

2014

Althaus CL, Joos B, Perelson AS, Guenthard HF. Quantifying the Turnover of Transcriptional Subclasses of HIV-1-Infected Cells. Plos Computational Biology. 2014;10(10). doi: 10.1371/journal.pcbi.1003871. PubMed PMID: WOS:000344547900025.

Canini L, Conway JM, Perelson AS, Carrat F. Impact of Different Oseltamivir Regimens on Treating Influenza A Virus Infection and Resistance Emergence: Insights from a Modelling Study (vol 10, e1003568, 2014). Plos Computational Biology. 2014;10(6). doi: 10.1371/journal.pcbi.1003699. PubMed PMID: WOS:000338848100049.

Canini L, Conway JM, Perelson AS, Carrat F. Impact of Different Oseltamivir Regimens on Treating Influenza A Virus Infection and Resistance Emergence: Insights from a Modelling Study. Plos Computational Biology. 2014;10(4). doi: 10.1371/journal.pcbi.1003568. PubMed PMID: WOS:000336507500033.

Canini L, Koh C, Cotler S, Yurdaydin C, Cooper S, Cory D, et al. Understanding hepatitis delta virus dynamics and antiviral efficacy of the prenylation inhibitor lonafarnib. Hepatology. 2014;60:317A-A. PubMed PMID: WOS:000344483801168.

Canini L, Perelson AS. Viral kinetic modeling: state of the art. Journal of Pharmacokinetics and Pharmacodynamics. 2014;41(5):431-43. doi: 10.1007/s10928-014-9363-3. PubMed PMID: WOS:000344331600004.

Cannell BL, Krasnec KV, Campbell K, Jones HI, Miller RD, Stephens N. The pathology and pathogenicity of a novel Haemoproteus spp. infection in wild Little Penguins (Eudyptula minor) (vol 197, pg 74, 2013). Veterinary Parasitology. 2014;205(1-2):416-. doi: 10.1016/j.vetpar.2014.07.021. PubMed PMID: WOS:000342548000063.

Cannon J, Asperti-Boursin F, Fricke M, Letendre K, Moses M. T cell motility within lymph nodes fits a Levy signature. Journal of Immunology. 2014;192. PubMed PMID: WOS:000209765003093.

Chylek LA, Harris LA, Tung CS, Faeder JR, Lopez CF, Hlavacek WS. Rule-based modeling: a computational approach for studying biomolecular site dynamics in cell signaling systems. Wiley Interdisciplinary Reviews-Systems Biology and Medicine. 2014;6(1):13-36. doi: 10.1002/wsbm.1245. PubMed PMID: WOS:000328558500002.

Ciupe SM, Ribeiro RM, Perelson AS. Antibody Responses during Hepatitis B Viral Infection. Plos Computational Biology. 2014;10(7). doi: 10.1371/journal.pcbi.1003730. PubMed PMID: WOS:000339890900041.

Conway JM, Perelson AS. A Hepatitis C Virus Infection Model with Time-Varying Drug Effectiveness: Solution and Analysis. Plos Computational Biology. 2014;10(8). doi: 10.1371/journal.pcbi.1003769. PubMed PMID: WOS:000341573600019.

Dahari H, Cotler SJ. Individualized Treatment for Patients With Low HCV Load (Genotype 1): A Viral Kinetic Approach. Hepatology. 2014;59(6):2422-3. doi: 10.1002/hep.26772. PubMed PMID: WOS:000337567100044.

DebRoy S, Hiraga N, Imamura M, Canini L, Pohl RT, Persiani S, et al. HCV kinetics in uPA-SCID chimeric mice with humanized livers during intravenous silibinin monotherapy. Hepatology. 2014;60:1171A-2A. PubMed PMID: WOS:000344483805070.

Devkota R, Brant SV, Thapa A, Loker ES. Sharing schistosomes: the elephant schistosome Bivitellobilharzia nairi also infects the greater one- horned rhinoceros ( Rhinoceros unicornis) in Chitwan National Park, Nepal. Journal of Helminthology. 2014;88(1):32-40. doi: 10.1017/s0022149x12000697. PubMed PMID: WOS:000332515400005.

Devkota R, Brant SV, Thapa S, Loker ES. Two avian schistosome cercariae from Nepal, including a Macrobilharzia-like species from Indoplanorbis exustus. Parasitol Int. 2014;63(2):374-80. doi: 10.1016/j.parint.2013.12.009. PubMed PMID: 24369339.

Devkota R, Brant SV, Thapa S, Loker ES. Two avian schistosome cercariae from Nepal, including a Macrobilharzia-like species from Indoplanorbis exustus. Parasitology International. 2014;63(2):374-80. doi: 10.1016/j.parint.2013.12.009. PubMed PMID: WOS:000333549600018.

Dheilly NM, Adema C, Raftos DA, Gourbal B, Grunau C, Du Pasquier L. No more non-model species: The promise of next generation sequencing for comparative immunology. Dev Comp Immunol. 2014;45(1):56-66. Epub 2014/02/11. doi: 10.1016/j.dci.2014.01.022. PubMed PMID: 24508980.

Dheilly NM, Adema C, Raftos DA, Gourbal B, Grunau C, Du Pasquier L. No more non-model species: The promise of next generation sequencing for comparative immunology. Developmental and Comparative Immunology. 2014;45(1):56-66. doi: 10.1016/j.dci.2014.01.022. PubMed PMID: WOS:000335624800006.

Echevarria D, Gutfraind A, Boodram B, Major ME, Cotler S, Dahari H. Modeling treatment scale up effect on hepatitis C prevalence among persons who inject drugs in metropolitan Chicago. Hepatology. 2014;60:671A-2A. PubMed PMID: WOS:000344483803023.

Graw F, Balagopal A, Kandathil AJ, Ray SC, Thomas DL, Ribeiro RM, et al. Inferring Viral Dynamics in Chronically HCV Infected Patients from the Spatial Distribution of Infected Hepatocytes. Plos Computational Biology. 2014;10(11). doi: 10.1371/journal.pcbi.1003934. PubMed PMID: WOS:000345454400023.

Guedj J, Rotman Y, Cotler SJ, Koh C, Schmid P, Albrecht J, et al. Understanding Early Serum Hepatitis D Virus and Hepatitis B Surface Antigen Kinetics During Pegylated Interferon-alpha Therapy Via Mathematical Modeling. Hepatology. 2014;60(6):1902-10. doi: 10.1002/hep.27357. PubMed PMID: WOS:000345517000055.

Guedj J, Yu J, Levi M, Li B, Kern S, Naoumov NV, et al. Modeling Viral Kinetics and Treatment Outcome During Alisporivir Interferon-Free Treatment in Hepatitis C Virus Genotype 2 and 3 Patients. Hepatology. 2014;59(5):1706-14. doi: 10.1002/hep.26989. PubMed PMID: WOS:000337278400013.

Hernandez-Vargas EA, Wilk E, Canini L, Toapanta FR, Binder SC, Uvarovskii A, et al. Effects of Aging on Influenza Virus Infection Dynamics. Journal of Virology. 2014;88(8):4123-31. doi: 10.1128/jvi.03644-13. PubMed PMID: WOS:000333676400018.

Ishida Y, Chung TL, Imamura M, Hiraga N, Canini L, Uprichard SL, et al. HBV infection in humanized chimeric mice has multiphasic viral kinetics from inoculation to steady state and an HBV half-life of 1 hr. Hepatology. 2014;60:1023A-4A. PubMed PMID: WOS:000344483804277.

Kasinathan RS, Sharma LK, Cunningham C, Webb TR, Greenberg RM. Inhibition or Knockdown of ABC Transporters Enhances Susceptibility of Adult and Juvenile Schistosomes to Praziquantel. Plos Neglected Tropical Diseases. 2014;8(10). doi: 10.1371/journal.pntd.0003265. PubMed PMID: WOS:000344589000069.

Koh C, Yurdaydin C, Cooper S, Cory D, Dahari H, Haynes-Williams V, et al. Prenylation inhibition with lonafarnib decreases hepatitis D levels in humans. Hepatology. 2014;60:1092A-3A. PubMed PMID: WOS:000344483804422.

Kraus TJ, Brant SV, Adema CM. Characterization of Trematode Cercariae from Physella acuta in the Middle Rio Grande. Comparative Parasitology. 2014;81(1):105-9. PubMed PMID: WOS:000331675100015.

Lelo AE, Mburu DN, Magoma GN, Mungai BN, Kihara JH, Mwangi IN, et al. No Apparent Reduction in Schistosome Burden or Genetic Diversity Following Four Years of School-Based Mass Drug Administration in Mwea, Central Kenya, a Heavy Transmission Area. Plos Neglected Tropical Diseases. 2014;8(10). doi: 10.1371/journal.pntd.0003221. PubMed PMID: WOS:000344589000039.

Liu D, Zuo T, Hora B, Song H, Kong W, Yu X, et al. Preexisting compensatory amino acids compromise fitness costs of a HIV-1 T cell escape mutation. Retrovirology. 2014;11. doi: 10.1186/s12977-014-0101-0. PubMed PMID: WOS:000346678200001.

Miao H, Sangster MY, Livingstone AM, Hilchey SP, Zhang L, Topham DJ, et al. Modeling the Dynamics and Migratory Pathways of Virus-Specific Antibody-Secreting Cell Populations in Primary Influenza Infection. Plos One. 2014;9(8). doi: 10.1371/journal.pone.0104781. PubMed PMID: WOS:000341127500022.

Miller RD, Hansen VL. MARSUPIAL AND MONOTREME IMMUNOGLOBULIN GENETICS. Comparative Immunoglobulin Genetics. 2014:85-105. PubMed PMID: WOS:000361608300005.

Musharrafieh R, Tacchi L, Trujeque J, LaPatra S, Salinas I. Staphylococcus warneri, a resident skin commensal of rainbow trout (Oncorhynchus mykiss) with pathobiont characteristics. Veterinary Microbiology. 2014;169(1-2):80-8. doi: 10.1016/j.vetmic.2013.12.012. PubMed PMID: WOS:000331676100010.

Mutuku MW, Dweni CK, Mwangi M, Kinuthia JM, Mwangi IN, Maina GM, et al. Field-derived Schistosoma mansoni and Biomphalaria pfeifferi in Kenya: a compatible association characterized by lack of strong local adaptation, and presence of some snails able to persistently produce cercariae for over a year. Parasites & Vectors. 2014;7. doi: 10.1186/s13071-014-0533-3. PubMed PMID: WOS:000345896700001.

Mwangi IN, Sanchez MC, Mkoji GM, Agola LE, Runo SM, Cupit PM, et al. Praziquantel sensitivity of Kenyan Schistosoma mansoni isolates and the generation of a laboratory strain with reduced susceptibility to the drug. International Journal for Parasitology-Drugs and Drug Resistance. 2014;4(3):296-300. doi: 10.1016/j.ijpddr.2014.09.006. PubMed PMID: WOS:000347618400017.

Nolan JR, Bergthorsson U, Adema CM. Physella acuta: atypical mitochondrial gene order among panpulmonates (Gastropoda). Journal of Molluscan Studies. 2014;80:388-99. doi: 10.1093/mollus/eyu025. PubMed PMID: WOS:000344623400005.

Rong L, Guedj J, Dahari H, Perelson AS. Treatment of hepatitis C with an interferon-based lead-in phase: a perspective from mathematical modelling. Antiviral Therapy. 2014;19(5):469-77. doi: 10.3851/imp2725. PubMed PMID: WOS:000348602500005.

Rotman Y, Noureddin M, Feld JJ, Guedj J, Witthaus M, Han H, et al. Effect of ribavirin on viral kinetics and liver gene expression in chronic hepatitis C. Gut. 2014;63(1):161-9. Epub 2013/02/12. doi: 10.1136/gutjnl-2012-303852. PubMed PMID: 23396509; PubMed Central PMCID: PMCPmc3778097.

Rotman Y, Noureddin M, Feld JJ, Guedj J, Witthaus M, Han H, et al. Effect of ribavirin on viral kinetics and liver gene expression in chronic hepatitis C. Gut. 2014;63(1):161-9. doi: 10.1136/gutjnl-2012-303852. PubMed PMID: WOS:000327835000019.

Sansone N, Dahari H, Subramanya G, Perelson AS, Uprichard SL. Modeling HCVcc infection reveals new insights into the dynamics that maintain the in vitro HCV steady state and the mechanisms of action of the NS5A inhibitor daclatasvir. Hepatology. 2014;60:1165A-A. PubMed PMID: WOS:000344483805056.

Saunders NR, Noor NM, Dziegielewska KM, Wheaton BJ, Liddelow SA, Steer DL, et al. Age-Dependent Transcriptome and Proteome Following Transection of Neonatal Spinal Cord of Monodelphis domestica (South American Grey Short-Tailed Opossum). Plos One. 2014;9(6). doi: 10.1371/journal.pone.0099080. PubMed PMID: WOS:000340947700059.

Schulte E, Dorn J, Harding S, Forrest S, Weimer W. Post-compiler Software Optimization for Reducing Energy. Acm Sigplan Notices. 2014;49(4):639-51. doi: 10.1145/2541940.2541980. PubMed PMID: WOS:000360535000044.

Schulte E, Fry ZP, Fast E, Weimer W, Forrest S. Software mutational robustness. Genetic Programming and Evolvable Machines. 2014;15(3):281-312. doi: 10.1007/s10710-013-9195-8. PubMed PMID: WOS:000339383900004.

Sharma LK, Cupit PM, Goronga T, Webb TR, Cunningham C. Design and synthesis of molecular probes for the determination of the target of the anthelmintic drug praziquantel. Bioorganic & Medicinal Chemistry Letters. 2014;24(11):2469-72. doi: 10.1016/j.bmcl.2014.04.014. PubMed PMID: WOS:000335518300017.

Sherman KE, Guedj J, Shata MT, Blackard JT, Rouster SD, Castro M, et al. Modulation of HCV replication after combination antiretroviral therapy in HCV/HIV co-infected patients. Science Translational Medicine. 2014;6(246). doi: 10.1126/scitranslmed.3008195. PubMed PMID: WOS:000339661400005.

Song H, Hora B, Bhattacharya T, Goonetilleke N, Liu MKP, Wiehe K, et al. Reversion and T Cell Escape Mutations Compensate the Fitness Loss of a CD8(+) T Cell Escape Mutant in Their Cognate Transmitted/Founder Virus. Plos One. 2014;9(7). doi: 10.1371/journal.pone.0102734. PubMed PMID: WOS:000341306600096.

Szmygiel C, Schmidt-Rhaesa A, Hanelt B, Bolek MG. Comparative descriptions of non-adult stages of four genera of Gordiids (Phylum: Nematomorpha). Zootaxa. 2014;3768(2):101-18. PubMed PMID: WOS:000331806900001.

Tacchi L, Musharrafieh R, Larragoite ET, Crossey K, Erhardt EB, Martin SAM, et al. Nasal immunity is an ancient arm of the mucosal immune system of vertebrates. Nature Communications. 2014;5. doi: 10.1038/ncomms6205. PubMed PMID: WOS:000343982500004.

Thanhvu N, Kapur D, Weimer W, Forrest S. DIG: A Dynamic Invariant Generator for Polynomial and Array Invariants. Acm Transactions on Software Engineering and Methodology. 2014;23(4). doi: 10.1145/2556782. PubMed PMID: WOS:000341938200004.

Zhang TY, Tacchi L, Wei ZG, Zhao YF, Salinas I. Intraclass diversification of immunoglobulin heavy chain genes in the African lungfish. Immunogenetics. 2014;66(5):335-51. doi: 10.1007/s00251-014-0769-2. PubMed PMID: WOS:000334596800005.