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Modeling site-specific amino-acid preferences deepens phylogenetic estimates of viral sequence divergence.

Hilton SK, Bloom JD.

Virus Evol. 2018 Nov 6;4(2):vey033. doi: 10.1093/ve/vey033. eCollection 2018 Jul.


Jail-Based Competency Restoration.

Felthous AR, Bloom JD.

J Am Acad Psychiatry Law. 2018 Sep;46(3):364-372. doi: 10.29158/JAAPL.003772-18.


Percutaneous Radiofrequency Lower Face and Neck Tightening Technique.

Locketz GD, Bloom JD.

JAMA Facial Plast Surg. 2018 Sep 13. doi: 10.1001/jamafacial.2018.0917. [Epub ahead of print] No abstract available.


Destabilized adaptive influenza variants critical for innate immune system escape are potentiated by host chaperones.

Phillips AM, Ponomarenko AI, Chen K, Ashenberg O, Miao J, McHugh SM, Butty VL, Whittaker CA, Moore CL, Bloom JD, Lin YS, Shoulders MD.

PLoS Biol. 2018 Sep 17;16(9):e3000008. doi: 10.1371/journal.pbio.3000008. eCollection 2018 Sep.


Estimating the frequency of multiplets in single-cell RNA sequencing from cell-mixing experiments.

Bloom JD.

PeerJ. 2018 Sep 3;6:e5578. doi: 10.7717/peerj.5578. eCollection 2018.


Characterization of Influenza B Virus Variants with Reduced Neuraminidase Inhibitor Susceptibility.

Farrukee R, Zarebski AE, McCaw JM, Bloom JD, Reading PC, Hurt AC.

Antimicrob Agents Chemother. 2018 Oct 24;62(11). pii: e01081-18. doi: 10.1128/AAC.01081-18. Print 2018 Nov.


Enhanced ER proteostasis and temperature differentially impact the mutational tolerance of influenza hemagglutinin.

Phillips AM, Doud MB, Gonzalez LO, Butty VL, Lin YS, Bloom JD, Shoulders MD.

Elife. 2018 Sep 6;7. pii: e38795. doi: 10.7554/eLife.38795.


Deep mutational scanning of hemagglutinin helps predict evolutionary fates of human H3N2 influenza variants.

Lee JM, Huddleston J, Doud MB, Hooper KA, Wu NC, Bedford T, Bloom JD.

Proc Natl Acad Sci U S A. 2018 Aug 28;115(35):E8276-E8285. doi: 10.1073/pnas.1806133115. Epub 2018 Aug 13.


Sera from Individuals with Narrowly Focused Influenza Virus Antibodies Rapidly Select Viral Escape Mutations In Ovo.

Davis AKF, McCormick K, Gumina ME, Petrie JG, Martin ET, Xue KS, Bloom JD, Monto AS, Bushman FD, Hensley SE.

J Virol. 2018 Sep 12;92(19). pii: e00859-18. doi: 10.1128/JVI.00859-18. Print 2018 Oct 1.


Complete functional mapping of infection- and vaccine-elicited antibodies against the fusion peptide of HIV.

Dingens AS, Acharya P, Haddox HK, Rawi R, Xu K, Chuang GY, Wei H, Zhang B, Mascola JR, Carragher B, Potter CS, Overbaugh J, Kwong PD, Bloom JD.

PLoS Pathog. 2018 Jul 5;14(7):e1007159. doi: 10.1371/journal.ppat.1007159. eCollection 2018 Jul.


How single mutations affect viral escape from broad and narrow antibodies to H1 influenza hemagglutinin.

Doud MB, Lee JM, Bloom JD.

Nat Commun. 2018 Apr 11;9(1):1386. doi: 10.1038/s41467-018-03665-3.


Mapping mutational effects along the evolutionary landscape of HIV envelope.

Haddox HK, Dingens AS, Hilton SK, Overbaugh J, Bloom JD.

Elife. 2018 Mar 28;7. pii: e34420. doi: 10.7554/eLife.34420.


Within-Host Evolution of Human Influenza Virus.

Xue KS, Moncla LH, Bedford T, Bloom JD.

Trends Microbiol. 2018 Sep;26(9):781-793. doi: 10.1016/j.tim.2018.02.007. Epub 2018 Mar 10. Review.


Extreme heterogeneity of influenza virus infection in single cells.

Russell AB, Trapnell C, Bloom JD.

Elife. 2018 Feb 16;7. pii: e32303. doi: 10.7554/eLife.32303.


Reduction of Submental Fat Continues Beyond 28 Days After ATX-101 Treatment: Results From a Post hoc Analysis.

Dover JS, Shridharani SM, Bloom JD, Somogyi C, Gallagher CJ.

Dermatol Surg. 2018 Nov;44(11):1477-1479. doi: 10.1097/DSS.0000000000001484. No abstract available.


Cooperating H3N2 Influenza Virus Variants Are Not Detectable in Primary Clinical Samples.

Xue KS, Greninger AL, Pérez-Osorio A, Bloom JD.

mSphere. 2018 Jan 3;3(1). pii: e00552-17. doi: 10.1128/mSphereDirect.00552-17. eCollection 2018 Jan-Feb.


The Forensic Mental Health Services Census of Forensic Populations in State Facilities.

Bloom JD, Novosad D.

J Am Acad Psychiatry Law. 2017 Dec;45(4):447-451.


A framework for exhaustively mapping functional missense variants.

Weile J, Sun S, Cote AG, Knapp J, Verby M, Mellor JC, Wu Y, Pons C, Wong C, van Lieshout N, Yang F, Tasan M, Tan G, Yang S, Fowler DM, Nussbaum R, Bloom JD, Vidal M, Hill DE, Aloy P, Roth FP.

Mol Syst Biol. 2017 Dec 21;13(12):957. doi: 10.15252/msb.20177908.


phydms: software for phylogenetic analyses informed by deep mutational scanning.

Hilton SK, Doud MB, Bloom JD.

PeerJ. 2017 Jul 31;5:e3657. doi: 10.7717/peerj.3657. eCollection 2017.


Parallel evolution of influenza across multiple spatiotemporal scales.

Xue KS, Stevens-Ayers T, Campbell AP, Englund JA, Pergam SA, Boeckh M, Bloom JD.

Elife. 2017 Jun 27;6. pii: e26875. doi: 10.7554/eLife.26875.


Computational design of trimeric influenza-neutralizing proteins targeting the hemagglutinin receptor binding site.

Strauch EM, Bernard SM, La D, Bohn AJ, Lee PS, Anderson CE, Nieusma T, Holstein CA, Garcia NK, Hooper KA, Ravichandran R, Nelson JW, Sheffler W, Bloom JD, Lee KK, Ward AB, Yager P, Fuller DH, Wilson IA, Baker D.

Nat Biotechnol. 2017 Jul;35(7):667-671. doi: 10.1038/nbt.3907. Epub 2017 Jun 12.


Comprehensive Mapping of HIV-1 Escape from a Broadly Neutralizing Antibody.

Dingens AS, Haddox HK, Overbaugh J, Bloom JD.

Cell Host Microbe. 2017 Jun 14;21(6):777-787.e4. doi: 10.1016/j.chom.2017.05.003. Epub 2017 Jun 1.


Feasibility and Efficacy of a Smart Mat Technology to Predict Development of Diabetic Plantar Ulcers.

Frykberg RG, Gordon IL, Reyzelman AM, Cazzell SM, Fitzgerald RH, Rothenberg GM, Bloom JD, Petersen BJ, Linders DR, Nouvong A, Najafi B.

Diabetes Care. 2017 Jul;40(7):973-980. doi: 10.2337/dc16-2294. Epub 2017 May 2.


Safety and Efficacy of Bilateral Submental Cryolipolysis With Quantified 3-Dimensional Imaging of Fat Reduction and Skin Tightening.

Bernstein EF, Bloom JD.

JAMA Facial Plast Surg. 2017 Sep 1;19(5):350-357. doi: 10.1001/jamafacial.2017.0102.


Deep mutational scanning identifies sites in influenza nucleoprotein that affect viral inhibition by MxA.

Ashenberg O, Padmakumar J, Doud MB, Bloom JD.

PLoS Pathog. 2017 Mar 27;13(3):e1006288. doi: 10.1371/journal.ppat.1006288. eCollection 2017 Mar.


Complete mapping of viral escape from neutralizing antibodies.

Doud MB, Hensley SE, Bloom JD.

PLoS Pathog. 2017 Mar 13;13(3):e1006271. doi: 10.1371/journal.ppat.1006271. eCollection 2017 Mar.


The Oregon Court of Appeals and the State Civil Commitment Statute.

Bloom JD, Britton J, Berry W.

J Am Acad Psychiatry Law. 2017 Mar;45(1):52-61. Review.


Neck Contouring and Treatment of Submental Adiposity.

Thomas WW, Bloom JD.

J Drugs Dermatol. 2017 Jan 1;16(1):54-57. Review.


Experimental Estimation of the Effects of All Amino-Acid Mutations to HIV's Envelope Protein on Viral Replication in Cell Culture.

Haddox HK, Dingens AS, Bloom JD.

PLoS Pathog. 2016 Dec 13;12(12):e1006114. doi: 10.1371/journal.ppat.1006114. eCollection 2016 Dec.


Cosmetic Use of AbobotulinumtoxinA in Men: Considerations Regarding Anatomical Differences and Product Characteristics.

Bloom JD, Green JB, Bowe W, von Grote E, Nogueira A.

J Drugs Dermatol. 2016 Sep 1;15(9):1056-62. Review.


Accurate Measurement of the Effects of All Amino-Acid Mutations on Influenza Hemagglutinin.

Doud MB, Bloom JD.

Viruses. 2016 Jun 3;8(6). pii: E155. doi: 10.3390/v8060155.


Cooperation between distinct viral variants promotes growth of H3N2 influenza in cell culture.

Xue KS, Hooper KA, Ollodart AR, Dingens AS, Bloom JD.

Elife. 2016 Mar 15;5:e13974. doi: 10.7554/eLife.13974.


Conditional Release Placements of Insanity Acquittees in Oregon: 2012-2014.

Novosad D, Banfe S, Britton J, Bloom JD.

Behav Sci Law. 2016 Mar;34(2-3):366-77. doi: 10.1002/bsl.2218. Epub 2016 Mar 11.


Cultural leisure activities, recovery and work engagement among hospital employees.

Tuisku K, Virtanen M, Bloom JD, Kinnunen U.

Ind Health. 2016 Jun 10;54(3):254-62. doi: 10.2486/indhealth.2015-0124. Epub 2016 Jan 30.


Positive Selection in CD8+ T-Cell Epitopes of Influenza Virus Nucleoprotein Revealed by a Comparative Analysis of Human and Swine Viral Lineages.

Machkovech HM, Bedford T, Suchard MA, Bloom JD.

J Virol. 2015 Nov;89(22):11275-83. doi: 10.1128/JVI.01571-15. Epub 2015 Aug 26.


Site-Specific Amino Acid Preferences Are Mostly Conserved in Two Closely Related Protein Homologs.

Doud MB, Ashenberg O, Bloom JD.

Mol Biol Evol. 2015 Nov;32(11):2944-60. doi: 10.1093/molbev/msv167. Epub 2015 Jul 29.


Psychiatric Boarding in Washington State and the Inadequacy of Mental Health Resources.

Bloom JD.

J Am Acad Psychiatry Law. 2015 Jun;43(2):218-22.


Software for the analysis and visualization of deep mutational scanning data.

Bloom JD.

BMC Bioinformatics. 2015 May 20;16:168. doi: 10.1186/s12859-015-0590-4.


Oregon's Gun Relief Program for Adjudicated Mentally Ill Persons: The Psychiatric Security Review Board.

Britton J, Bloom JD.

Behav Sci Law. 2015 Jun;33(2-3):323-33. doi: 10.1002/bsl.2167. Epub 2015 Feb 27.


Influenza viruses with receptor-binding N1 neuraminidases occur sporadically in several lineages and show no attenuation in cell culture or mice.

Hooper KA, Crowe JE Jr, Bloom JD.

J Virol. 2015 Apr;89(7):3737-45. doi: 10.1128/JVI.00012-15. Epub 2015 Jan 21.


Non-invasive fat reduction of the flanks using a new cryolipolysis applicator and overlapping, two-cycle treatments.

Bernstein EF, Bloom JD, Basilavecchio LD, Plugis JM.

Lasers Surg Med. 2014 Dec;46(10):731-5. doi: 10.1002/lsm.22302. Epub 2014 Nov 13.


Potential antigenic explanation for atypical H1N1 infections among middle-aged adults during the 2013-2014 influenza season.

Linderman SL, Chambers BS, Zost SJ, Parkhouse K, Li Y, Herrmann C, Ellebedy AH, Carter DM, Andrews SF, Zheng NY, Huang M, Huang Y, Strauss D, Shaz BH, Hodinka RL, Reyes-Terán G, Ross TM, Wilson PC, Ahmed R, Bloom JD, Hensley SE.

Proc Natl Acad Sci U S A. 2014 Nov 4;111(44):15798-803. doi: 10.1073/pnas.1409171111. Epub 2014 Oct 20.


Statewide survey of living arrangements for conditionally released insanity acquittees.

Novosad D, Follansbee J, Banfe S, Bloom JD.

Behav Sci Law. 2014 Sep;32(5):659-65. doi: 10.1002/bsl.2139.


Improving pandemic influenza risk assessment.

Russell CA, Kasson PM, Donis RO, Riley S, Dunbar J, Rambaut A, Asher J, Burke S, Davis CT, Garten RJ, Gnanakaran S, Hay SI, Herfst S, Lewis NS, Lloyd-Smith JO, Macken CA, Maurer-Stroh S, Neuhaus E, Parrish CR, Pepin KM, Shepard SS, Smith DL, Suarez DL, Trock SC, Widdowson MA, George DB, Lipsitch M, Bloom JD.

Elife. 2014 Oct 16;3:e03883. doi: 10.7554/eLife.03883.


An experimentally informed evolutionary model improves phylogenetic fit to divergent lactamase homologs.

Bloom JD.

Mol Biol Evol. 2014 Oct;31(10):2753-69. doi: 10.1093/molbev/msu220. Epub 2014 Jul 24.


The inherent mutational tolerance and antigenic evolvability of influenza hemagglutinin.

Thyagarajan B, Bloom JD.

Elife. 2014 Jul 8;3. doi: 10.7554/eLife.03300.


An experimentally determined evolutionary model dramatically improves phylogenetic fit.

Bloom JD.

Mol Biol Evol. 2014 Aug;31(8):1956-78. doi: 10.1093/molbev/msu173. Epub 2014 May 24.


Epistatically interacting substitutions are enriched during adaptive protein evolution.

Gong LI, Bloom JD.

PLoS Genet. 2014 May 8;10(5):e1004328. doi: 10.1371/journal.pgen.1004328. eCollection 2014 May.


Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses.

Butler J, Hooper KA, Petrie S, Lee R, Maurer-Stroh S, Reh L, Guarnaccia T, Baas C, Xue L, Vitesnik S, Leang SK, McVernon J, Kelso A, Barr IG, McCaw JM, Bloom JD, Hurt AC.

PLoS Pathog. 2014 Apr 3;10(4):e1004065. doi: 10.1371/journal.ppat.1004065. eCollection 2014 Apr.

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