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Problem-based learning in clinical bioinformatics education: Does it help to create communities of practice?

Davies AC, Harris D, Banks-Gatenby A, Brass A.

PLoS Comput Biol. 2019 Jun 27;15(6):e1006746. doi: 10.1371/journal.pcbi.1006746. eCollection 2019 Jun.


OR14I1 is a receptor for the human cytomegalovirus pentameric complex and defines viral epithelial cell tropism.

E X, Meraner P, Lu P, Perreira JM, Aker AM, McDougall WM, Zhuge R, Chan GC, Gerstein RM, Caposio P, Yurochko AD, Brass AL, Kowalik TF.

Proc Natl Acad Sci U S A. 2019 Apr 2;116(14):7043-7052. doi: 10.1073/pnas.1814850116. Epub 2019 Mar 20.


A Disintegrin and Metalloproteinase 9 Domain (ADAM9) Is a Major Susceptibility Factor in the Early Stages of Encephalomyocarditis Virus Infection.

Bazzone LE, King M, MacKay CR, Kyawe PP, Meraner P, Lindstrom D, Rojas-Quintero J, Owen CA, Wang JP, Brass AL, Kurt-Jones EA, Finberg RW.

MBio. 2019 Feb 5;10(1). pii: e02734-18. doi: 10.1128/mBio.02734-18.


Viral Infection or IFN-α Alters Mitotic Spindle Orientation by Modulating Pericentrin Levels.

McDougall WM, Perreira JM, Hung HF, Vertii A, Xiaofei E, Zimmerman W, Kowalik TF, Doxsey S, Brass AL.

iScience. 2019 Feb 22;12:270-279. doi: 10.1016/j.isci.2019.01.025. Epub 2019 Jan 21.


Interferon-induced transmembrane protein 3 blocks fusion of sensitive but not resistant viruses by partitioning into virus-carrying endosomes.

Suddala KC, Lee CC, Meraner P, Marin M, Markosyan RM, Desai TM, Cohen FS, Brass AL, Melikyan GB.

PLoS Pathog. 2019 Jan 14;15(1):e1007532. doi: 10.1371/journal.ppat.1007532. eCollection 2019 Jan.


Functional Mapping of Regions Involved in the Negative Imprinting of Virion Particle Infectivity and in Target Cell Protection by Interferon-Induced Transmembrane Protein 3 against HIV-1.

Appourchaux R, Delpeuch M, Zhong L, Burlaud-Gaillard J, Tartour K, Savidis G, Brass A, Etienne L, Roingeard P, Cimarelli A.

J Virol. 2019 Jan 4;93(2). pii: e01716-18. doi: 10.1128/JVI.01716-18. Print 2019 Jan 15.


Capsid-CPSF6 Interaction Licenses Nuclear HIV-1 Trafficking to Sites of Viral DNA Integration.

Achuthan V, Perreira JM, Sowd GA, Puray-Chavez M, McDougall WM, Paulucci-Holthauzen A, Wu X, Fadel HJ, Poeschla EM, Multani AS, Hughes SH, Sarafianos SG, Brass AL, Engelman AN.

Cell Host Microbe. 2018 Sep 12;24(3):392-404.e8. doi: 10.1016/j.chom.2018.08.002. Epub 2018 Aug 30.


CRISPR genetic screens to discover host-virus interactions.

McDougall WM, Perreira JM, Reynolds EC, Brass AL.

Curr Opin Virol. 2018 Apr;29:87-100. doi: 10.1016/j.coviro.2018.03.007. Review.


Exploiting glycan topography for computational design of Env glycoprotein antigenicity.

Yu WH, Zhao P, Draghi M, Arevalo C, Karsten CB, Suscovich TJ, Gunn B, Streeck H, Brass AL, Tiemeyer M, Seaman M, Mascola JR, Wells L, Lauffenburger DA, Alter G.

PLoS Comput Biol. 2018 Apr 20;14(4):e1006093. doi: 10.1371/journal.pcbi.1006093. eCollection 2018 Apr.


The circadian regulator BMAL1 programmes responses to parasitic worm infection via a dendritic cell clock.

Hopwood TW, Hall S, Begley N, Forman R, Brown S, Vonslow R, Saer B, Little MC, Murphy EA, Hurst RJ, Ray DW, MacDonald AS, Brass A, Bechtold DA, Gibbs JE, Loudon AS, Else KJ.

Sci Rep. 2018 Feb 28;8(1):3782. doi: 10.1038/s41598-018-22021-5.


Britain Breathing: using the experience sampling method to collect the seasonal allergy symptoms of a country.

Vigo M, Hassan L, Vance W, Jay C, Brass A, Cruickshank S.

J Am Med Inform Assoc. 2018 Jan 1;25(1):88-92. doi: 10.1093/jamia/ocx148. Erratum in: J Am Med Inform Assoc. 2018 Oct 1;25(10):1429.


Data journeys: Identifying social and technical barriers to data movement in large, complex organisations.

Eleftheriou I, Embury SM, Moden R, Dobinson P, Brass A.

J Biomed Inform. 2018 Feb;78:102-122. doi: 10.1016/j.jbi.2017.12.001. Epub 2017 Dec 6.


TIGERi: modeling and visualizing the responses to perturbation of a transcription factor network.

Han N, Noyes HA, Brass A.

BMC Bioinformatics. 2017 May 31;18(Suppl 7):260. doi: 10.1186/s12859-017-1636-6.


Compositional Changes in the Gut Mucus Microbiota Precede the Onset of Colitis-Induced Inflammation.

Glymenaki M, Singh G, Brass A, Warhurst G, McBain AJ, Else KJ, Cruickshank SM.

Inflamm Bowel Dis. 2017 Jun;23(6):912-922. doi: 10.1097/MIB.0000000000001118.


Frizzled proteins are colonic epithelial receptors for C. difficile toxin B.

Tao L, Zhang J, Meraner P, Tovaglieri A, Wu X, Gerhard R, Zhang X, Stallcup WB, Miao J, He X, Hurdle JG, Breault DT, Brass AL, Dong M.

Nature. 2016 Oct 20;538(7625):350-355. doi: 10.1038/nature19799. Epub 2016 Sep 28.


Identification of Zika Virus and Dengue Virus Dependency Factors using Functional Genomics.

Savidis G, McDougall WM, Meraner P, Perreira JM, Portmann JM, Trincucci G, John SP, Aker AM, Renzette N, Robbins DR, Guo Z, Green S, Kowalik TF, Brass AL.

Cell Rep. 2016 Jun 28;16(1):232-246. doi: 10.1016/j.celrep.2016.06.028. Epub 2016 Jun 21.


A Survey of Bioinformatics Database and Software Usage through Mining the Literature.

Duck G, Nenadic G, Filannino M, Brass A, Robertson DL, Stevens R.

PLoS One. 2016 Jun 22;11(6):e0157989. doi: 10.1371/journal.pone.0157989. eCollection 2016.


The IFITMs Inhibit Zika Virus Replication.

Savidis G, Perreira JM, Portmann JM, Meraner P, Guo Z, Green S, Brass AL.

Cell Rep. 2016 Jun 14;15(11):2323-30. doi: 10.1016/j.celrep.2016.05.074. Epub 2016 Jun 3.


Glucocorticoid receptor isoforms direct distinct mitochondrial programs to regulate ATP production.

Morgan DJ, Poolman TM, Williamson AJ, Wang Z, Clark NR, Ma'ayan A, Whetton AD, Brass A, Matthews LC, Ray DW.

Sci Rep. 2016 May 26;6:26419. doi: 10.1038/srep26419.


Functional Genomic Strategies for Elucidating Human-Virus Interactions: Will CRISPR Knockout RNAi and Haploid Cells?

Perreira JM, Meraner P, Brass AL.

Adv Virus Res. 2016;94:1-51. doi: 10.1016/bs.aivir.2015.11.001. Epub 2016 Mar 2. Review.


Bias in the reporting of sex and age in biomedical research on mouse models.

Flórez-Vargas O, Brass A, Karystianis G, Bramhall M, Stevens R, Cruickshank S, Nenadic G.

Elife. 2016 Mar 3;5. pii: e13615. doi: 10.7554/eLife.13615.


Meta- and Orthogonal Integration of Influenza "OMICs" Data Defines a Role for UBR4 in Virus Budding.

Tripathi S, Pohl MO, Zhou Y, Rodriguez-Frandsen A, Wang G, Stein DA, Moulton HM, DeJesus P, Che J, Mulder LC, Yángüez E, Andenmatten D, Pache L, Manicassamy B, Albrecht RA, Gonzalez MG, Nguyen Q, Brass A, Elledge S, White M, Shapira S, Hacohen N, Karlas A, Meyer TF, Shales M, Gatorano A, Johnson JR, Jang G, Johnson T, Verschueren E, Sanders D, Krogan N, Shaw M, König R, Stertz S, García-Sastre A, Chanda SK.

Cell Host Microbe. 2015 Dec 9;18(6):723-35. doi: 10.1016/j.chom.2015.11.002.


Direct Visualization of HIV-1 Replication Intermediates Shows that Capsid and CPSF6 Modulate HIV-1 Intra-nuclear Invasion and Integration.

Chin CR, Perreira JM, Savidis G, Portmann JM, Aker AM, Feeley EM, Smith MC, Brass AL.

Cell Rep. 2015 Nov 24;13(8):1717-31. doi: 10.1016/j.celrep.2015.10.036. Epub 2015 Nov 12.


RNASEK Is a V-ATPase-Associated Factor Required for Endocytosis and the Replication of Rhinovirus, Influenza A Virus, and Dengue Virus.

Perreira JM, Aker AM, Savidis G, Chin CR, McDougall WM, Portmann JM, Meraner P, Smith MC, Rahman M, Baker RE, Gauthier A, Franti M, Brass AL.

Cell Rep. 2015 Aug 4;12(5):850-63. doi: 10.1016/j.celrep.2015.06.076. Epub 2015 Jul 23.


Quality of methods reporting in animal models of colitis.

Bramhall M, Flórez-Vargas O, Stevens R, Brass A, Cruickshank S.

Inflamm Bowel Dis. 2015 Jun;21(6):1248-59. doi: 10.1097/MIB.0000000000000369. Review.


Long-term follow-up of successful hepatitis C virus therapy: waning immune responses and disappearance of liver disease are consistent with cure.

Hedenstierna M, Weiland O, Brass A, Bankwitz D, Behrendt P, Uhnoo I, Aleman S, Cardell K, Fryden A, Norkrans G, Eilard A, Glaumann H, Pietschmann T, Sällberg M, Brenndörfer ED.

Aliment Pharmacol Ther. 2015 Mar;41(6):532-43. doi: 10.1111/apt.13096. Epub 2015 Jan 28.


Dysfunctional HIV-specific CD8+ T cell proliferation is associated with increased caspase-8 activity and mediated by necroptosis.

Gaiha GD, McKim KJ, Woods M, Pertel T, Rohrbach J, Barteneva N, Chin CR, Liu D, Soghoian DZ, Cesa K, Wilton S, Waring MT, Chicoine A, Doering T, Wherry EJ, Kaufmann DE, Lichterfeld M, Brass AL, Walker BD.

Immunity. 2014 Dec 18;41(6):1001-12. doi: 10.1016/j.immuni.2014.12.011. Epub 2014 Dec 8.


Functional aspects of intrahepatic hepatitis B virus-specific T cells induced by therapeutic DNA vaccination.

Brass A, Frelin L, Milich DR, Sällberg M, Ahlén G.

Mol Ther. 2015 Mar;23(3):578-90. doi: 10.1038/mt.2014.233. Epub 2014 Dec 10.


Comprehensive identification of host modulators of HIV-1 replication using multiple orthologous RNAi reagents.

Zhu J, Davoli T, Perriera JM, Chin CR, Gaiha GD, John SP, Sigiollot FD, Gao G, Xu Q, Qu H, Pertel T, Sims JS, Smith JA, Baker RE, Maranda L, Ng A, Elledge SJ, Brass AL.

Cell Rep. 2014 Oct 23;9(2):752-66. doi: 10.1016/j.celrep.2014.09.031. Epub 2014 Oct 16.


Extracting patterns of database and software usage from the bioinformatics literature.

Duck G, Nenadic G, Brass A, Robertson DL, Stevens R.

Bioinformatics. 2014 Sep 1;30(17):i601-8. doi: 10.1093/bioinformatics/btu471.


The quality of methods reporting in parasitology experiments.

Flórez-Vargas O, Bramhall M, Noyes H, Cruickshank S, Stevens R, Brass A.

PLoS One. 2014 Jul 30;9(7):e101131. doi: 10.1371/journal.pone.0101131. eCollection 2014.


Into the second 70 years. 1983.

Brass A.

Med J Aust. 2014 May 19;200(9):549. No abstract available.


IFITM3 restricts influenza A virus entry by blocking the formation of fusion pores following virus-endosome hemifusion.

Desai TM, Marin M, Chin CR, Savidis G, Brass AL, Melikyan GB.

PLoS Pathog. 2014 Apr 3;10(4):e1004048. doi: 10.1371/journal.ppat.1004048. eCollection 2014 Apr.


The role of chemokines in hepatitis C virus-mediated liver disease.

Brass A, Brenndörfer ED.

Int J Mol Sci. 2014 Mar 18;15(3):4747-79. doi: 10.3390/ijms15034747. Review.


A statistical analysis of murine incisional and excisional acute wound models.

Ansell DM, Campbell L, Thomason HA, Brass A, Hardman MJ.

Wound Repair Regen. 2014 Mar-Apr;22(2):281-7. doi: 10.1111/wrr.12148.


Immunology. The fiery side of HIV-induced T cell death.

Gaiha GD, Brass AL.

Science. 2014 Jan 24;343(6169):383-4. doi: 10.1126/science.1250175. No abstract available.


Cleavage of the T cell protein tyrosine phosphatase by the hepatitis C virus nonstructural 3/4A protease induces a Th1 to Th2 shift reversible by ribavirin therapy.

Brenndörfer ED, Brass A, Karthe J, Ahlén G, Bode JG, Sällberg M.

J Immunol. 2014 Feb 15;192(4):1671-80. doi: 10.4049/jimmunol.1301077. Epub 2014 Jan 17.


The languages of health in general practice electronic patient records: a Zipf's law analysis.

Kalankesh LR, New JP, Baker PG, Brass A.

J Biomed Semantics. 2014 Jan 10;5(1):2. doi: 10.1186/2041-1480-5-2.


Evaluating the Emotion Ontology through use in the self-reporting of emotional responses at an academic conference.

Hastings J, Brass A, Caine C, Jay C, Stevens R.

J Biomed Semantics. 2014 Sep 3;5:38. doi: 10.1186/2041-1480-5-38. eCollection 2014.


A novel DDB2-ATM feedback loop regulates human cytomegalovirus replication.

E X, Savidis G, Chin CR, Wang S, Lu S, Brass AL, Kowalik TF.

J Virol. 2014 Feb;88(4):2279-90. doi: 10.1128/JVI.03423-13. Epub 2013 Dec 11.


Amphotericin B increases influenza A virus infection by preventing IFITM3-mediated restriction.

Lin TY, Chin CR, Everitt AR, Clare S, Perreira JM, Savidis G, Aker AM, John SP, Sarlah D, Carreira EM, Elledge SJ, Kellam P, Brass AL.

Cell Rep. 2013 Nov 27;5(4):895-908. doi: 10.1016/j.celrep.2013.10.033. Epub 2013 Nov 21.


Educating international students about tuberculosis and infections associated with travel to visit friends and relatives (VFR-travel).

Gibney KB, Brass A, Hume SC, Leder K.

Travel Med Infect Dis. 2014 May-Jun;12(3):274-82. doi: 10.1016/j.tmaid.2013.08.002. Epub 2013 Sep 15.


IFITMs restrict the replication of multiple pathogenic viruses.

Perreira JM, Chin CR, Feeley EM, Brass AL.

J Mol Biol. 2013 Dec 13;425(24):4937-55. doi: 10.1016/j.jmb.2013.09.024. Epub 2013 Sep 25. Review.


Host genetic determinants of influenza pathogenicity.

Lin TY, Brass AL.

Curr Opin Virol. 2013 Oct;3(5):531-6. doi: 10.1016/j.coviro.2013.07.005. Epub 2013 Aug 8. Review.


Taming EHR data: using semantic similarity to reduce dimensionality.

Kalankesh L, Weatherall J, Ba-Dhfari T, Buchan I, Brass A.

Stud Health Technol Inform. 2013;192:52-6.


Containing "The Great Houdini" of viruses: combining direct acting antivirals with the host immune response for the treatment of chronic hepatitis C.

Ahlén G, Frelin L, Brenndörfer ED, Brass A, Weiland O, Chen M, Sällberg M.

Drug Resist Updat. 2013 Jul-Nov;16(3-5):60-7. doi: 10.1016/j.drup.2013.06.001. Epub 2013 Aug 2. Review.


A heterologous prime/boost vaccination strategy enhances the immunogenicity of therapeutic vaccines for hepatitis C virus.

Fournillier A, Frelin L, Jacquier E, Ahlén G, Brass A, Gerossier E, Holmström F, Broderick KE, Sardesai NY, Bonnefoy JY, Inchauspé G, Sällberg M.

J Infect Dis. 2013 Sep;208(6):1008-19. doi: 10.1093/infdis/jit267. Epub 2013 Jun 17.


bioNerDS: exploring bioinformatics' database and software use through literature mining.

Duck G, Nenadic G, Brass A, Robertson DL, Stevens R.

BMC Bioinformatics. 2013 Jun 15;14:194. doi: 10.1186/1471-2105-14-194.


The CD225 domain of IFITM3 is required for both IFITM protein association and inhibition of influenza A virus and dengue virus replication.

John SP, Chin CR, Perreira JM, Feeley EM, Aker AM, Savidis G, Smith SE, Elia AE, Everitt AR, Vora M, Pertel T, Elledge SJ, Kellam P, Brass AL.

J Virol. 2013 Jul;87(14):7837-52. doi: 10.1128/JVI.00481-13. Epub 2013 May 8.


Interferon-inducible transmembrane protein 3 (IFITM3) restricts reovirus cell entry.

Anafu AA, Bowen CH, Chin CR, Brass AL, Holm GH.

J Biol Chem. 2013 Jun 14;288(24):17261-71. doi: 10.1074/jbc.M112.438515. Epub 2013 May 6.

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