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Jeese Bloom - Publications

Affiliations: 
Fred Hutch Cancer Research Center 
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36/203 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Crawford KHD, Eguia R, Dingens AS, Loes AN, Malone KD, Wolf CR, Chu HY, Tortorici MA, Veesler D, Murphy M, Pettie D, King NP, Balazs AB, Bloom JD. Protocol and Reagents for Pseudotyping Lentiviral Particles with SARS-CoV-2 Spike Protein for Neutralization Assays. Viruses. 12. PMID 32384820 DOI: 10.3390/V12050513  0.55
2020 Sourisseau M, Lawrence DJP, Schwarz MC, Storrs CH, Veit EC, Bloom JD, Evans MJ. Deep Mutational Scanning to Map How Zika Envelope Protein Mutations Affect Viral Growth and Antibody Escape Proceedings. 50: 93. DOI: 10.3390/proceedings2020050093  0.38
2019 Huang Q, Chan KY, Tobey IG, Chan YA, Poterba T, Boutros CL, Balazs AB, Daneman R, Bloom JM, Seed C, Deverman BE. Delivering genes across the blood-brain barrier: LY6A, a novel cellular receptor for AAV-PHP.B capsids. Plos One. 14: e0225206. PMID 31725765 DOI: 10.1371/Journal.Pone.0225206  0.543
2019 Sourisseau M, Lawrence DJP, Schwarz MC, Storrs CH, Veit EC, Bloom JD, Evans MJ. Deep mutational scanning comprehensively maps how Zika envelope protein mutations affect viral growth and antibody escape. Journal of Virology. PMID 31511387 DOI: 10.1128/JVI.01291-19  0.371
2019 Soh YS, Moncla LH, Eguia R, Bedford T, Bloom JD. Comprehensive mapping of adaptation of the avian influenza polymerase protein PB2 to humans. Elife. 8. PMID 31038123 DOI: 10.7554/Elife.45079  0.31
2019 Hom N, Gentles L, Bloom JD, Lee KK. Deep mutational scan of the highly conserved influenza A M1 matrix protein reveals substantial intrinsic mutational tolerance. Journal of Virology. PMID 31019050 DOI: 10.1128/Jvi.00161-19  0.346
2019 Drummond DA, Bloom JD. A Nobel Prize for evolution Evolution. 73: 630-631. DOI: 10.1111/Evo.13697  0.489
2018 Phillips AM, Ponomarenko AI, Chen K, Ashenberg O, Miao J, McHugh SM, Butty VL, Whittaker CA, Moore CL, Bloom JD, Lin YS, Shoulders MD. Destabilized adaptive influenza variants critical for innate immune system escape are potentiated by host chaperones. Plos Biology. 16: e3000008. PMID 30222731 DOI: 10.1371/Journal.Pbio.3000008  0.63
2018 Phillips AM, Doud MB, Gonzalez LO, Butty VL, Lin YS, Bloom JD, Shoulders MD. Enhanced ER proteostasis and temperature differentially impact the mutational tolerance of influenza hemagglutinin. Elife. 7. PMID 30188321 DOI: 10.7554/Elife.38795  0.32
2017 Ashenberg O, Padmakumar J, Doud MB, Bloom JD. Deep mutational scanning identifies sites in influenza nucleoprotein that affect viral inhibition by MxA. Plos Pathogens. 13: e1006288. PMID 28346537 DOI: 10.1371/Journal.Ppat.1006288  0.648
2016 Doud MB, Bloom JD. Accurate Measurement of the Effects of All Amino-Acid Mutations on Influenza Hemagglutinin. Viruses. 8. PMID 27271655 DOI: 10.3390/v8060155  0.319
2015 Doud MB, Ashenberg O, Bloom JD. Site-Specific Amino Acid Preferences Are Mostly Conserved in Two Closely Related Protein Homologs. Molecular Biology and Evolution. 32: 2944-60. PMID 26226986 DOI: 10.1093/Molbev/Msv167  0.661
2014 Thyagarajan B, Bloom JD. The inherent mutational tolerance and antigenic evolvability of influenza hemagglutinin. Elife. 3. PMID 25006036 DOI: 10.7554/eLife.03300  0.344
2013 Ashenberg O, Gong LI, Bloom JD. Mutational effects on stability are largely conserved during protein evolution. Proceedings of the National Academy of Sciences of the United States of America. 110: 21071-6. PMID 24324165 DOI: 10.1073/Pnas.1314781111  0.698
2013 Balazs AB, Bloom JD, Hong CM, Rao DS, Baltimore D. Broad protection against influenza infection by vectored immunoprophylaxis in mice. Nature Biotechnology. 31: 647-52. PMID 23728362 DOI: 10.1038/Nbt.2618  0.657
2013 Gong LI, Suchard MA, Bloom JD. Stability-mediated epistasis constrains the evolution of an influenza protein. Elife. 2: e00631. PMID 23682315 DOI: 10.7554/Elife.00631  0.324
2013 Ashenberg O, Gong LI, Bloom JD. Mutational effects on stability are largely conserved during protein evolution Proceedings of the National Academy of Sciences of the United States of America. 110: 21071-21076. DOI: 10.1073/pnas.1314781111  0.683
2012 Liberles DA, Teichmann SA, Bahar I, Bastolla U, Bloom J, Bornberg-Bauer E, Colwell LJ, de Koning AP, Dokholyan NV, Echave J, Elofsson A, Gerloff DL, Goldstein RA, Grahnen JA, Holder MT, et al. The interface of protein structure, protein biophysics, and molecular evolution. Protein Science : a Publication of the Protein Society. 21: 769-85. PMID 22528593 DOI: 10.1002/Pro.2071  0.358
2011 Bloom JD, Nayak JS, Baltimore D. A computational-experimental approach identifies mutations that enhance surface expression of an oseltamivir-resistant influenza neuraminidase. Plos One. 6: e22201. PMID 21799795 DOI: 10.1371/journal.pone.0022201  0.465
2010 Bloom JD, Gong LI, Baltimore D. Permissive secondary mutations enable the evolution of influenza oseltamivir resistance. Science (New York, N.Y.). 328: 1272-5. PMID 20522774 DOI: 10.1126/science.1187816  0.459
2010 Jäckel C, Bloom JD, Kast P, Arnold FH, Hilvert D. Consensus protein design without phylogenetic bias. Journal of Molecular Biology. 399: 541-6. PMID 20433850 DOI: 10.1016/J.Jmb.2010.04.039  0.568
2009 Bloom JD, Arnold FH. In the light of directed evolution: pathways of adaptive protein evolution. Proceedings of the National Academy of Sciences of the United States of America. 106: 9995-10000. PMID 19528653 DOI: 10.1073/Pnas.0901522106  0.571
2007 Li Y, Drummond DA, Sawayama AM, Snow CD, Bloom JD, Arnold FH. A diverse family of thermostable cytochrome P450s created by recombination of stabilizing fragments. Nature Biotechnology. 25: 1051-6. PMID 17721510 DOI: 10.1038/Nbt1333  0.645
2007 Bloom JD, Lu Z, Chen D, Raval A, Venturelli OS, Arnold FH. Evolution favors protein mutational robustness in sufficiently large populations. Bmc Biology. 5: 29. PMID 17640347 DOI: 10.1186/1741-7007-5-29  0.551
2007 Bloom JD, Romero PA, Lu Z, Arnold FH. Neutral genetic drift can alter promiscuous protein functions, potentially aiding functional evolution. Biology Direct. 2: 17. PMID 17598905 DOI: 10.1186/1745-6150-2-17  0.698
2007 Bloom JD, Arnold FH, Wilke CO. Breaking proteins with mutations: threads and thresholds in evolution. Molecular Systems Biology. 3: 76. PMID 17262035 DOI: 10.1038/Msb4100119  0.464
2007 Bloom JD, Raval A, Wilke CO. Thermodynamics of neutral protein evolution. Genetics. 175: 255-66. PMID 17110496 DOI: 10.1534/genetics.106.061754  0.38
2007 Li Y, Drummond DA, Sawayama AM, Snow CD, Bloom JD, Arnold FH. Erratum: Corrigendum: A diverse family of thermostable cytochrome P450s created by recombination of stabilizing fragments Nature Biotechnology. 25: 1488-1488. DOI: 10.1038/Nbt1207-1488D  0.591
2006 Bloom JD, Drummond DA, Arnold FH, Wilke CO. Structural determinants of the rate of protein evolution in yeast. Molecular Biology and Evolution. 23: 1751-61. PMID 16782762 DOI: 10.1093/Molbev/Msl040  0.647
2006 Otey CR, Landwehr M, Endelman JB, Hiraga K, Bloom JD, Arnold FH. Structure-guided recombination creates an artificial family of cytochromes P450. Plos Biology. 4: e112. PMID 16594730 DOI: 10.1371/Journal.Pbio.0040112  0.715
2006 Bloom JD, Labthavikul ST, Otey CR, Arnold FH. Protein stability promotes evolvability. Proceedings of the National Academy of Sciences of the United States of America. 103: 5869-74. PMID 16581913 DOI: 10.1073/Pnas.0510098103  0.577
2005 Drummond DA, Bloom JD, Adami C, Wilke CO, Arnold FH. Why highly expressed proteins evolve slowly. Proceedings of the National Academy of Sciences of the United States of America. 102: 14338-43. PMID 16176987 DOI: 10.1073/Pnas.0504070102  0.652
2005 Wilke CO, Bloom JD, Drummond DA, Raval A. Predicting the tolerance of proteins to random amino acid substitution. Biophysical Journal. 89: 3714-20. PMID 16150971 DOI: 10.1529/Biophysj.105.062125  0.54
2005 Bloom JD, Meyer MM, Meinhold P, Otey CR, MacMillan D, Arnold FH. Evolving strategies for enzyme engineering. Current Opinion in Structural Biology. 15: 447-52. PMID 16006119 DOI: 10.1016/J.Sbi.2005.06.004  0.733
2005 Bloom JD, Silberg JJ, Wilke CO, Drummond DA, Adami C, Arnold FH. Thermodynamic prediction of protein neutrality. Proceedings of the National Academy of Sciences of the United States of America. 102: 606-11. PMID 15644440 DOI: 10.1073/Pnas.0406744102  0.726
2004 Bloom JD, Wilke CO, Arnold FH, Adami C. Stability and the evolvability of function in a model protein. Biophysical Journal. 86: 2758-64. PMID 15111394 DOI: 10.1016/S0006-3495(04)74329-5  0.502
Low-probability matches (unlikely to be authored by this person)
2018 Lee JM, Huddleston J, Doud MB, Hooper KA, Wu NC, Bedford T, Bloom JD. Deep mutational scanning of hemagglutinin helps predict evolutionary fates of human H3N2 influenza variants. Proceedings of the National Academy of Sciences of the United States of America. PMID 30104379 DOI: 10.1073/Pnas.1806133115  0.298
2019 Lee JM, Eguia R, Zost SJ, Choudhary S, Wilson PC, Bedford T, Stevens-Ayers T, Boeckh M, Hurt AC, Lakdawala SS, Hensley SE, Bloom JD. Mapping person-to-person variation in viral mutations that escape polyclonal serum targeting influenza hemagglutinin. Elife. 8. PMID 31452511 DOI: 10.7554/Elife.49324  0.287
2014 Gong LI, Bloom JD. Epistatically interacting substitutions are enriched during adaptive protein evolution. Plos Genetics. 10: e1004328. PMID 24811236 DOI: 10.1371/journal.pgen.1004328  0.283
2017 Hilton SK, Doud MB, Bloom JD. phydms: software for phylogenetic analyses informed by deep mutational scanning. Peerj. 5: e3657. PMID 28785526 DOI: 10.7717/peerj.3657  0.276
2013 Gong LI, Suchard MA, Bloom JD. Author response: Stability-mediated epistasis constrains the evolution of an influenza protein Elife. DOI: 10.7554/Elife.00631.041  0.275
2017 Doud MB, Hensley SE, Bloom JD. Complete mapping of viral escape from neutralizing antibodies. Plos Pathogens. 13: e1006271. PMID 28288189 DOI: 10.1371/Journal.Ppat.1006271  0.272
2020 Starr TN, Greaney AJ, Hilton SK, Ellis D, Crawford KHD, Dingens AS, Navarro MJ, Bowen JE, Tortorici MA, Walls AC, King NP, Veesler D, Bloom JD. Deep Mutational Scanning of SARS-CoV-2 Receptor Binding Domain Reveals Constraints on Folding and ACE2 Binding. Cell. PMID 32841599 DOI: 10.1016/J.Cell.2020.08.012  0.27
2020 Starr TN, Greaney AJ, Hilton SK, Crawford KHD, Navarro MJ, Bowen JE, Tortorici MA, Walls AC, Veesler D, Bloom JD. Deep mutational scanning of SARS-CoV-2 receptor binding domain reveals constraints on folding and ACE2 binding. Biorxiv : the Preprint Server For Biology. PMID 32587970 DOI: 10.1101/2020.06.17.157982  0.27
2018 Xue KS, Greninger AL, Pérez-Osorio A, Bloom JD. Cooperating H3N2 Influenza Virus Variants Are Not Detectable in Primary Clinical Samples. Msphere. 3. PMID 29299533 DOI: 10.1128/mSphereDirect.00552-17  0.27
2014 Bloom JD. An experimentally informed evolutionary model improves phylogenetic fit to divergent lactamase homologs. Molecular Biology and Evolution. 31: 2753-69. PMID 25063439 DOI: 10.1093/molbev/msu220  0.268
2016 Haddox HK, Dingens AS, Bloom JD. Experimental Estimation of the Effects of All Amino-Acid Mutations to HIV's Envelope Protein on Viral Replication in Cell Culture. Plos Pathogens. 12: e1006114. PMID 27959955 DOI: 10.1371/journal.ppat.1006114  0.267
2017 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, ... ... Bloom JD, et al. A framework for exhaustively mapping functional missense variants. Molecular Systems Biology. 13: 957. PMID 29269382 DOI: 10.15252/Msb.20177908  0.259
2018 Haddox HK, Dingens AS, Hilton SK, Overbaugh J, Bloom JD. Mapping mutational effects along the evolutionary landscape of HIV envelope. Elife. 7. PMID 29590010 DOI: 10.7554/eLife.34420  0.259
2020 Xue KS, Bloom JD. Linking influenza virus evolution within and between human hosts. Virus Evolution. 6: veaa010. PMID 32082616 DOI: 10.1093/ve/veaa010  0.258
2019 Setoh YX, Amarilla AA, Peng NYG, Griffiths RE, Carrera J, Freney ME, Nakayama E, Ogawa S, Watterson D, Modhiran N, Nanyonga FE, Torres FJ, Slonchak A, Periasamy P, Prow NA, ... ... Bloom JD, et al. Determinants of Zika virus host tropism uncovered by deep mutational scanning. Nature Microbiology. PMID 30886357 DOI: 10.1038/S41564-019-0399-4  0.253
2019 Dingens AS, Arenz D, Weight H, Overbaugh J, Bloom JD. An Antigenic Atlas of HIV-1 Escape from Broadly Neutralizing Antibodies Distinguishes Functional and Structural Epitopes. Immunity. PMID 30709739 DOI: 10.1016/J.Immuni.2018.12.017  0.251
2015 Hooper KA, Crowe JE, Bloom JD. Influenza viruses with receptor-binding N1 neuraminidases occur sporadically in several lineages and show no attenuation in cell culture or mice. Journal of Virology. 89: 3737-45. PMID 25609803 DOI: 10.1128/JVI.00012-15  0.249
2021 Greaney AJ, Starr TN, Bloom JD. An antibody-escape calculator for mutations to the SARS-CoV-2 receptor-binding domain. Biorxiv : the Preprint Server For Biology. PMID 34909770 DOI: 10.1101/2021.12.04.471236  0.247
2020 McDonnell MM, Crawford KHD, Dingens AS, Bloom JD, Emerman M. APOBEC3C Tandem Domain Proteins Create Super Restriction Factors against HIV-1. Mbio. 11. PMID 32345636 DOI: 10.1128/mBio.00737-20  0.241
2019 Russell AB, Elshina E, Kowalsky JR, Te Velthuis AJW, Bloom JD. Single-cell virus sequencing of influenza infections that trigger innate immunity. Journal of Virology. PMID 31068418 DOI: 10.1128/JVI.00500-19  0.241
2016 Xue KS, Hooper KA, Ollodart AR, Dingens AS, Bloom JD. Cooperation between distinct viral variants promotes growth of H3N2 influenza in cell culture. Elife. 5. PMID 26978794 DOI: 10.7554/eLife.13974  0.238
2003 Bloom JD, Adami C. Apparent dependence of protein evolutionary rate on number of interactions is linked to biases in protein-protein interactions data sets Bmc Evolutionary Biology. 3. PMID 14525624 DOI: 10.1186/1471-2148-3-21  0.237
2021 Soh YQS, Malone KD, Eguia RT, Bloom JD. Comprehensive Profiling of Mutations to Influenza Virus PB2 That Confer Resistance to the Cap-Binding Inhibitor Pimodivir. Viruses. 13. PMID 34206520 DOI: 10.3390/v13071196  0.236
2018 Doud MB, Lee JM, Bloom JD. How single mutations affect viral escape from broad and narrow antibodies to H1 influenza hemagglutinin. Nature Communications. 9: 1386. PMID 29643370 DOI: 10.1038/s41467-018-03665-3  0.234
2007 Dong J, Bloom JD, Goncharov V, Chattopadhyay M, Millhauser GL, Lynn DG, Scheibel T, Lindquist S. Probing the role of PrP repeats in conformational conversion and amyloid assembly of chimeric yeast prions. The Journal of Biological Chemistry. 282: 34204-12. PMID 17893150 DOI: 10.1074/Jbc.M704952200  0.234
2004 Bloom JD, Adami C. Evolutionary rate depends on number of protein-protein interactions independently of gene expression level: Response Bmc Evolutionary Biology. 4. PMID 15171796 DOI: 10.1186/1471-2148-4-14  0.233
2017 Xue KS, Stevens-Ayers T, Campbell AP, Englund JA, Pergam SA, Boeckh M, Bloom JD. Parallel evolution of influenza across multiple spatiotemporal scales. Elife. 6. PMID 28653624 DOI: 10.7554/eLife.26875  0.231
2018 Xue KS, Moncla LH, Bedford T, Bloom JD. Within-Host Evolution of Human Influenza Virus. Trends in Microbiology. PMID 29534854 DOI: 10.1016/J.Tim.2018.02.007  0.229
2019 Machkovech HM, Bloom JD, Subramaniam AR. Comprehensive profiling of translation initiation in influenza virus infected cells. Plos Pathogens. 15: e1007518. PMID 30673779 DOI: 10.1371/Journal.Ppat.1007518  0.222
2014 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, et al. Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses. Plos Pathogens. 10: e1004065. PMID 24699865 DOI: 10.1371/journal.ppat.1004065  0.221
2017 Bloom JD. Identification of positive selection in genes is greatly improved by using experimentally informed site-specific models. Biology Direct. 12: 1. PMID 28095902 DOI: 10.1186/s13062-016-0172-z  0.22
2020 Roop JI, Cassidy NA, Dingens AS, Bloom JD, Overbaugh J. Identification of HIV-1 Envelope Mutations that Enhance Entry Using Macaque CD4 and CCR5. Viruses. 12. PMID 32098152 DOI: 10.3390/v12020241  0.219
2021 Dong J, Zost SJ, Greaney AJ, Starr TN, Dingens AS, Chen EC, Chen RE, Case JB, Sutton RE, Gilchuk P, Rodriguez J, Armstrong E, Gainza C, Nargi RS, Binshtein E, ... ... Bloom JD, et al. Genetic and structural basis for recognition of SARS-CoV-2 spike protein by a two-antibody cocktail. Biorxiv : the Preprint Server For Biology. PMID 33532768 DOI: 10.1101/2021.01.27.428529  0.219
2020 Starr TN, Greaney AJ, Addetia A, Hannon WW, Choudhary MC, Dingens AS, Li JZ, Bloom JD. Prospective mapping of viral mutations that escape antibodies used to treat COVID-19. Biorxiv : the Preprint Server For Biology. PMID 33299993 DOI: 10.1101/2020.11.30.405472  0.213
2018 Hilton SK, Bloom JD. Modeling site-specific amino-acid preferences deepens phylogenetic estimates of viral sequence divergence. Virus Evolution. 4: vey033. PMID 30425841 DOI: 10.1093/ve/vey033  0.213
2021 Starr TN, Greaney AJ, Addetia A, Hannon WW, Choudhary MC, Dingens AS, Li JZ, Bloom JD. Prospective mapping of viral mutations that escape antibodies used to treat COVID-19. Science (New York, N.Y.). PMID 33495308 DOI: 10.1126/science.abf9302  0.213
2017 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, et al. Computational design of trimeric influenza-neutralizing proteins targeting the hemagglutinin receptor binding site. Nature Biotechnology. PMID 28604661 DOI: 10.1038/Nbt.3907  0.213
2021 Bloom JD. Recovery of deleted deep sequencing data sheds more light on the early Wuhan SARS-CoV-2 epidemic. Molecular Biology and Evolution. PMID 34398234 DOI: 10.1093/molbev/msab246  0.211
2021 Ellis D, Brunette N, Crawford KHD, Walls AC, Pham MN, Chen C, Herpoldt KL, Fiala B, Murphy M, Pettie D, Kraft JC, Malone KD, Navarro MJ, Ogohara C, Kepl E, ... ... Bloom JD, et al. Stabilization of the SARS-CoV-2 Spike Receptor-Binding Domain Using Deep Mutational Scanning and Structure-Based Design. Frontiers in Immunology. 12: 710263. PMID 34267764 DOI: 10.3389/fimmu.2021.710263  0.209
2018 Davis AKF, McCormick K, Gumina ME, Petrie JG, Martin ET, Xue KS, Bloom JD, Monto AS, Bushman FD, Hensley SE. Sera from individuals with narrowly focused influenza virus antibodies rapidly select viral escape mutations . Journal of Virology. PMID 30045982 DOI: 10.1128/Jvi.00859-18  0.208
2019 Crawford KHD, Bloom JD. alignparse: A Python package for parsing complex features from high-throughput long-read sequencing. Journal of Open Source Software. 4. PMID 31897449 DOI: 10.21105/joss.01915  0.204
2013 Hooper KA, Bloom JD. A mutant influenza virus that uses an N1 neuraminidase as the receptor-binding protein Journal of Virology. 87: 12531-12540. PMID 24027333 DOI: 10.1128/JVI.01889-13  0.203
2021 Hunt AC, Case JB, Park YJ, Cao L, Wu K, Walls AC, Liu Z, Bowen JE, Yeh HW, Saini S, Helms L, Zhao YT, Hsiang TY, Starr TN, Goreshnik I, ... ... Bloom JD, et al. Multivalent designed proteins protect against SARS-CoV-2 variants of concern. Biorxiv : the Preprint Server For Biology. PMID 34268509 DOI: 10.1101/2021.07.07.451375  0.2
2020 Greaney AJ, Starr TN, Gilchuk P, Zost SJ, Binshtein E, Loes AN, Hilton SK, Huddleston J, Eguia R, Crawford KHD, Dingens AS, Nargi RS, Sutton RE, Suryadevara N, Rothlauf PW, ... ... Bloom JD, et al. Complete mapping of mutations to the SARS-CoV-2 spike receptor-binding domain that escape antibody recognition. Biorxiv : the Preprint Server For Biology. PMID 32935107 DOI: 10.1101/2020.09.10.292078  0.199
2020 Greaney AJ, Starr TN, Gilchuk P, Zost SJ, Binshtein E, Loes AN, Hilton SK, Huddleston J, Eguia R, Crawford KHD, Dingens AS, Nargi RS, Sutton RE, Suryadevara N, Rothlauf PW, ... ... Bloom JD, et al. Complete Mapping of Mutations to the SARS-CoV-2 Spike Receptor-Binding Domain that Escape Antibody Recognition. Cell Host & Microbe. PMID 33259788 DOI: 10.1016/j.chom.2020.11.007  0.198
2019 Zost SJ, Lee J, Gumina ME, Parkhouse K, Henry C, Wu NC, Lee CD, Wilson IA, Wilson PC, Bloom JD, Hensley SE. Identification of Antibodies Targeting the H3N2 Hemagglutinin Receptor Binding Site following Vaccination of Humans. Cell Reports. 29: 4460-4470.e8. PMID 31875553 DOI: 10.1016/J.Celrep.2019.11.084  0.197
2014 Bloom JD. An experimentally determined evolutionary model dramatically improves phylogenetic fit. Molecular Biology and Evolution. 31: 1956-78. PMID 24859245 DOI: 10.1093/molbev/msu173  0.196
2021 Le Sage V, Kormuth KA, Nturibi E, Lee JM, Frizzell SA, Myerburg MM, Bloom JD, Lakdawala SS. Cell-Culture Adaptation of H3N2 Influenza Virus Impacts Acid Stability and Reduces Airborne Transmission in Ferret Model. Viruses. 13. PMID 33919124 DOI: 10.3390/v13050719  0.196
2014 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, ... ... Bloom JD, et al. Potential antigenic explanation for atypical H1N1 infections among middle-aged adults during the 2013-2014 influenza season. Proceedings of the National Academy of Sciences of the United States of America. 111: 15798-803. PMID 25331901 DOI: 10.1073/Pnas.1409171111  0.195
2020 Wu NC, Thompson AJ, Lee JM, Su W, Arlian BM, Xie J, Lerner RA, Yen HL, Bloom JD, Wilson IA. Different genetic barriers for resistance to HA stem antibodies in influenza H3 and H1 viruses. Science (New York, N.Y.). 368: 1335-1340. PMID 32554590 DOI: 10.1126/Science.Aaz5143  0.194
2019 Soh YS, Moncla LH, Eguia R, Bedford T, Bloom JD. Author response: Comprehensive mapping of adaptation of the avian influenza polymerase protein PB2 to humans Elife. DOI: 10.7554/Elife.45079.037  0.193
2020 Loes AN, Gentles LE, Greaney AJ, Crawford KHD, Bloom JD. Attenuated Influenza Virions Expressing the SARS-CoV-2 Receptor-Binding Domain Induce Neutralizing Antibodies in Mice. Viruses. 12. PMID 32899480 DOI: 10.3390/v12090987  0.189
2020 Loes AN, Gentles LE, Greaney AJ, Crawford KHD, Bloom JD. Attenuated influenza virions expressing the SARS-CoV-2 receptor-binding domain induce neutralizing antibodies in mice. Biorxiv : the Preprint Server For Biology. PMID 32817935 DOI: 10.1101/2020.08.12.248823  0.189
2021 Greaney AJ, Loes AN, Crawford KHD, Starr TN, Malone KD, Chu HY, Bloom JD. Comprehensive mapping of mutations in the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human plasma antibodies. Cell Host & Microbe. PMID 33592168 DOI: 10.1016/j.chom.2021.02.003  0.189
2019 Dingens AS, Arenz D, Overbaugh J, Bloom JD. Massively Parallel Profiling of HIV-1 Resistance to the Fusion Inhibitor Enfuvirtide. Viruses. 11. PMID 31096572 DOI: 10.3390/v11050439  0.187
2020 Hodcroft EB, Zuber M, Nadeau S, Crawford KHD, Bloom JD, Veesler D, Vaughan TG, Comas I, Candelas FG, Stadler T, Neher RA. Emergence and spread of a SARS-CoV-2 variant through Europe in the summer of 2020. Medrxiv : the Preprint Server For Health Sciences. PMID 33269368 DOI: 10.1101/2020.10.25.20219063  0.186
2015 Machkovech HM, Bedford T, Suchard MA, Bloom JD. Positive Selection in CD8+ T-Cell Epitopes of Influenza Virus Nucleoprotein Revealed by a Comparative Analysis of Human and Swine Viral Lineages. Journal of Virology. 89: 11275-83. PMID 26311880 DOI: 10.1128/Jvi.01571-15  0.185
2021 Guthmiller JJ, Han J, Utset HA, Li L, Lan LY, Henry C, Stamper CT, McMahon M, O'Dell G, Fernández-Quintero ML, Freyn AW, Amanat F, Stovicek O, Gentles L, Richey ST, ... ... Bloom JD, et al. Broadly neutralizing antibodies target a hemagglutinin anchor epitope. Nature. PMID 34942633 DOI: 10.1038/s41586-021-04356-8  0.184
2018 Phillips AM, Doud MB, Gonzalez LO, Butty VL, Lin Y, Bloom JD, Shoulders MD. Author response: Enhanced ER proteostasis and temperature differentially impact the mutational tolerance of influenza hemagglutinin Elife. DOI: 10.7554/Elife.38795.037  0.184
2016 Bloom J. Mapping Constraints on Protein Evolution Biophysical Journal. 110: 21a. DOI: 10.1016/j.bpj.2015.11.174  0.184
2014 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, ... ... Bloom JD, et al. Improving pandemic influenza risk assessment. Elife. 3: e03883. PMID 25321142 DOI: 10.7554/Elife.03883  0.183
2021 Dong J, Zost SJ, Greaney AJ, Starr TN, Dingens AS, Chen EC, Chen RE, Case JB, Sutton RE, Gilchuk P, Rodriguez J, Armstrong E, Gainza C, Nargi RS, Binshtein E, ... ... Bloom JD, et al. Genetic and structural basis for SARS-CoV-2 variant neutralization by a two-antibody cocktail. Nature Microbiology. PMID 34548634 DOI: 10.1038/s41564-021-00972-2  0.18
2021 Park YJ, De Marco A, Starr TN, Liu Z, Pinto D, Walls AC, Zatta F, Zepeda SK, Bowen J, Sprouse KS, Joshi A, Giurdanella M, Guarino B, Noack J, Abdelnabi R, ... ... Bloom JD, et al. Antibody-mediated broad sarbecovirus neutralization through ACE2 molecular mimicry. Biorxiv : the Preprint Server For Biology. PMID 34671770 DOI: 10.1101/2021.10.13.464254  0.18
2021 Shipley MM, Mangala Prasad V, Doepker LE, Dingens AS, Ralph DK, Harkins E, Dhar A, Arenz D, Chohan V, Weight H, Mandaliya K, Bloom JD, Matsen Iv F, Lee KK, Overbaugh JM. Functional development of a V3/glycan-specific broadly neutralizing antibody isolated from a case of HIV superinfection. Elife. 10. PMID 34263727 DOI: 10.7554/eLife.68110  0.179
2021 Starr TN, Greaney AJ, Dingens AS, Bloom JD. Complete map of SARS-CoV-2 RBD mutations that escape the monoclonal antibody LY-CoV555 and its cocktail with LY-CoV016. Biorxiv : the Preprint Server For Biology. PMID 33655250 DOI: 10.1101/2021.02.17.431683  0.179
2021 Starr TN, Greaney AJ, Dingens AS, Bloom JD. Complete map of SARS-CoV-2 RBD mutations that escape the monoclonal antibody LY-CoV555 and its cocktail with LY-CoV016. Cell Reports. Medicine. 2: 100255. PMID 33842902 DOI: 10.1016/j.xcrm.2021.100255  0.178
2021 Tortorici MA, Czudnochowski N, Starr TN, Marzi R, Walls AC, Zatta F, Bowen JE, Jaconi S, Iulio JD, Wang Z, De Marco A, Zepeda SK, Pinto D, Liu Z, Beltramello M, ... ... Bloom JD, et al. Structural basis for broad sarbecovirus neutralization by a human monoclonal antibody. Biorxiv : the Preprint Server For Biology. PMID 33851169 DOI: 10.1101/2021.04.07.438818  0.176
2017 Dingens AS, Haddox HK, Overbaugh J, Bloom JD. Comprehensive Mapping of HIV-1 Escape from a Broadly Neutralizing Antibody. Cell Host & Microbe. PMID 28579254 DOI: 10.1016/j.chom.2017.05.003  0.176
2020 Einav T, Gentles LE, Bloom JD. SnapShot: Influenza by the Numbers. Cell. 182: 532-532.e1. PMID 32707094 DOI: 10.1016/j.cell.2020.05.004  0.174
2021 Greaney AJ, Starr TN, Eguia RT, Loes AN, Khan K, Karim F, Cele S, Bowen JE, Logue JK, Corti D, Veesler D, Chu HY, Sigal A, Bloom JD. A SARS-CoV-2 variant elicits an antibody response with a shifted immunodominance hierarchy. Biorxiv : the Preprint Server For Biology. PMID 34671768 DOI: 10.1101/2021.10.12.464114  0.174
2021 Tortorici MA, Czudnochowski N, Starr TN, Marzi R, Walls AC, Zatta F, Bowen JE, Jaconi S, Di Iulio J, Wang Z, De Marco A, Zepeda SK, Pinto D, Liu Z, Beltramello M, ... ... Bloom JD, et al. Broad sarbecovirus neutralization by a human monoclonal antibody. Nature. PMID 34280951 DOI: 10.1038/s41586-021-03817-4  0.167
2020 Gentles LE, Wan H, Eichelberger MC, Bloom JD. Antibody Neutralization of an Influenza Virus that Uses Neuraminidase for Receptor Binding. Viruses. 12. PMID 32486222 DOI: 10.3390/v12060597  0.167
2021 Hodcroft EB, Zuber M, Nadeau S, Vaughan TG, Crawford KHD, Althaus CL, Reichmuth ML, Bowen JE, Walls AC, Corti D, Bloom JD, Veesler D, Mateo D, Hernando A, Comas I, et al. Spread of a SARS-CoV-2 variant through Europe in the summer of 2020. Nature. PMID 34098568 DOI: 10.1038/s41586-021-03677-y  0.163
2019 Lee JM, Eguia R, Zost SJ, Choudhary S, Wilson PC, Bedford T, Stevens-Ayers T, Boeckh M, Hurt AC, Lakdawala SS, Hensley SE, Bloom JD. Author response: Mapping person-to-person variation in viral mutations that escape polyclonal serum targeting influenza hemagglutinin Elife. DOI: 10.7554/Elife.49324.049  0.162
2020 Addetia A, Crawford KHD, Dingens A, Zhu H, Roychoudhury P, Huang ML, Jerome KR, Bloom JD, Greninger AL. Neutralizing antibodies correlate with protection from SARS-CoV-2 in humans during a fishery vessel outbreak with high attack rate. Journal of Clinical Microbiology. PMID 32826322 DOI: 10.1128/Jcm.02107-20  0.16
2020 Addetia A, Crawford KH, Dingens A, Zhu H, Roychoudhury P, Huang M, Jerome KR, Bloom JD, Greninger A. Neutralizing antibodies correlate with protection from SARS-CoV-2 in humans during a fishery vessel outbreak with high attack rate. Medrxiv : the Preprint Server For Health Sciences. PMID 32817980 DOI: 10.1101/2020.08.13.20173161  0.16
2021 Greaney AJ, Loes AN, Gentles LE, Crawford KHD, Starr TN, Malone KD, Chu HY, Bloom JD. Antibodies elicited by mRNA-1273 vaccination bind more broadly to the receptor binding domain than do those from SARS-CoV-2 infection. Science Translational Medicine. PMID 34103407 DOI: 10.1126/scitranslmed.abi9915  0.159
2021 Dingens AS, Pratap P, Malone KD, Hilton SK, Ketas T, Cottrell CA, Overbaugh JM, Moore JP, Klasse PJ, Ward AB, Bloom JD. High-resolution mapping of the neutralizing and binding specificities of polyclonal sera post HIV Env trimer vaccination. Elife. 10. PMID 33438580 DOI: 10.7554/eLife.64281  0.159
2012 Chao DL, Bloom JD, Kochin BF, Antia R, Longini IM. The global spread of drug-resistant influenza. Journal of the Royal Society, Interface / the Royal Society. 9: 648-56. PMID 21865253 DOI: 10.1098/Rsif.2011.0427  0.158
2021 Greaney AJ, Welsh FC, Bloom JD. Co-dominant neutralizing epitopes make anti-measles immunity resistant to viral evolution. Cell Reports. Medicine. 2: 100257. PMID 33948584 DOI: 10.1016/j.xcrm.2021.100257  0.157
2021 Starr TN, Czudnochowski N, Liu Z, Zatta F, Park YJ, Addetia A, Pinto D, Beltramello M, Hernandez P, Greaney AJ, Marzi R, Glass WG, Zhang I, Dingens AS, Bowen JE, ... ... Bloom JD, et al. SARS-CoV-2 RBD antibodies that maximize breadth and resistance to escape. Nature. PMID 34261126 DOI: 10.1038/s41586-021-03807-6  0.156
2018 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. Complete functional mapping of infection- and vaccine-elicited antibodies against the fusion peptide of HIV. Plos Pathogens. 14: e1007159. PMID 29975771 DOI: 10.1371/Journal.Ppat.1007159  0.154
2021 Eguia RT, Crawford KHD, Stevens-Ayers T, Kelnhofer-Millevolte L, Greninger AL, Englund JA, Boeckh MJ, Bloom JD. A human coronavirus evolves antigenically to escape antibody immunity. Plos Pathogens. 17: e1009453. PMID 33831132 DOI: 10.1371/journal.ppat.1009453  0.146
2021 Greaney AJ, Loes AN, Gentles LE, Crawford KHD, Starr TN, Malone KD, Chu HY, Bloom JD. The SARS-CoV-2 mRNA-1273 vaccine elicits more RBD-focused neutralization, but with broader antibody binding within the RBD. Biorxiv : the Preprint Server For Biology. PMID 33880474 DOI: 10.1101/2021.04.14.439844  0.145
2021 Su W, Sia SF, Schmitz AJ, Bricker TL, Starr TN, Greaney AJ, Turner JS, Mohammed BM, Liu Z, Choy KT, Darling TL, Joshi A, Cheng KM, Wong AYL, Harastani HH, ... ... Bloom JD, et al. Neutralizing Monoclonal Antibodies That Target the Spike Receptor Binding Domain Confer Fc Receptor-Independent Protection against SARS-CoV-2 Infection in Syrian Hamsters. Mbio. e0239521. PMID 34517754 DOI: 10.1128/mBio.02395-21  0.145
2021 Starr TN, Czudnochowski N, Zatta F, Park YJ, Liu Z, Addetia A, Pinto D, Beltramello M, Hernandez P, Greaney AJ, Marzi R, Glass WG, Zhang I, Dingens AS, Bowen JE, ... ... Bloom JD, et al. Antibodies to the SARS-CoV-2 receptor-binding domain that maximize breadth and resistance to viral escape. Biorxiv : the Preprint Server For Biology. PMID 33851154 DOI: 10.1101/2021.04.06.438709  0.144
2021 Walls AC, Miranda MC, Pham MN, Schäfer A, Greaney A, Arunachalam PS, Navarro MJ, Tortorici MA, Rogers K, O'Connor MA, Shireff L, Ferrell DE, Brunette N, Kepl E, Bowen J, ... ... Bloom J, et al. Elicitation of broadly protective sarbecovirus immunity by receptor-binding domain nanoparticle vaccines. Biorxiv : the Preprint Server For Biology. PMID 33758839 DOI: 10.1101/2021.03.15.435528  0.14
2020 Garrett ME, Itell HL, Crawford KHD, Basom R, Bloom JD, Overbaugh J. Phage-DMS: A Comprehensive Method for Fine Mapping of Antibody Epitopes. Iscience. 23: 101622. PMID 33089110 DOI: 10.1016/j.isci.2020.101622  0.139
2021 Greaney AJ, Starr TN, Barnes CO, Weisblum Y, Schmidt F, Caskey M, Gaebler C, Cho A, Agudelo M, Finkin S, Wang Z, Poston D, Muecksch F, Hatziioannou T, Bieniasz PD, ... ... Bloom JD, et al. Mapping mutations to the SARS-CoV-2 RBD that escape binding by different classes of antibodies. Nature Communications. 12: 4196. PMID 34234131 DOI: 10.1038/s41467-021-24435-8  0.137
2019 Kong R, Duan H, Sheng Z, Xu K, Acharya P, Chen X, Cheng C, Dingens AS, Gorman J, Sastry M, Shen CH, Zhang B, Zhou T, Chuang GY, Chao CW, ... ... Bloom JD, et al. Antibody Lineages with Vaccine-Induced Antigen-Binding Hotspots Develop Broad HIV Neutralization. Cell. 178: 567-584.e19. PMID 31348886 DOI: 10.1016/j.cell.2019.06.030  0.137
2021 Xie C, Su W, Sia SF, Choy KT, Morrell S, Zhou J, Peiris M, Bloom J, Yen HL. A(H1N1)pdm09 influenza viruses replicating in ferret upper or lower respiratory tract differed in onward transmission potential by air. The Journal of Infectious Diseases. PMID 34036370 DOI: 10.1093/infdis/jiab286  0.135
2004 Scheibel T, Bloom J, Lindquist SL. The elongation of yeast prion fibers involves separable steps of association and conversion. Proceedings of the National Academy of Sciences of the United States of America. 101: 2287-92. PMID 14983002 DOI: 10.1073/Pnas.0308754101  0.134
2021 Walls AC, Miranda MC, Schäfer A, Pham MN, Greaney A, Arunachalam PS, Navarro MJ, Tortorici MA, Rogers K, O'Connor MA, Shirreff L, Ferrell DE, Bowen J, Brunette N, Kepl E, ... ... Bloom J, et al. Elicitation of broadly protective sarbecovirus immunity by receptor-binding domain nanoparticle vaccines. Cell. PMID 34619077 DOI: 10.1016/j.cell.2021.09.015  0.131
2019 Xue KS, Bloom JD. Reconciling disparate estimates of viral genetic diversity during human influenza infections. Nature Genetics. PMID 30804564 DOI: 10.1038/s41588-019-0349-3  0.131
2021 Greaney AJ, Starr TN, Barnes CO, Weisblum Y, Schmidt F, Caskey M, Gaebler C, Cho A, Agudelo M, Finkin S, Wang Z, Poston D, Muecksch F, Hatziioannou T, Bieniasz PD, ... ... Bloom JD, et al. Mutational escape from the polyclonal antibody response to SARS-CoV-2 infection is largely shaped by a single class of antibodies. Biorxiv : the Preprint Server For Biology. PMID 33758856 DOI: 10.1101/2021.03.17.435863  0.131
2019 Bloom JS, Boocock J, Treusch S, Sadhu MJ, Day L, Oates-Barker H, Kruglyak L. Rare variants contribute disproportionately to quantitative trait variation in yeast. Elife. 8. PMID 31647408 DOI: 10.7554/Elife.49212  0.13
2021 Greaney AJ, Welsh FC, Bloom JD. Co-dominant neutralizing epitopes make anti-measles immunity resistant to viral evolution Cell Reports Medicine. 2: 100257. DOI: 10.1016/j.xcrm.2021.100257  0.128
2001 Scheibel T, Kowal AS, Bloom JD, Lindquist SL. Bidirectional amyloid fiber growth for a yeast prion determinant. Current Biology : Cb. 11: 366-9. PMID 11267875 DOI: 10.1016/S0960-9822(01)00099-9  0.128
2018 Russell AB, Trapnell C, Bloom JD. Extreme heterogeneity of influenza virus infection in single cells. Elife. 7. PMID 29451492 DOI: 10.7554/Elife.32303  0.126
2020 Crawford KHD, Dingens AS, Eguia R, Wolf CR, Wilcox N, Logue JK, Shuey K, Casto AM, Fiala B, Wrenn S, Pettie D, King NP, Greninger AL, Chu HY, Bloom JD. Dynamics of neutralizing antibody titers in the months after SARS-CoV-2 infection. The Journal of Infectious Diseases. PMID 33000143 DOI: 10.1093/infdis/jiaa618  0.126
2015 Bloom JD. Software for the analysis and visualization of deep mutational scanning data Bmc Bioinformatics. 16. DOI: 10.1186/s12859-015-0590-4  0.123
2021 Guo L, Bloom J, Sykes S, Huang E, Kashif Z, Pham E, Ho K, Alcaraz A, Xiao XG, Duarte-Vogel S, Kruglyak L. Genetics of white color and iridophoroma in "Lemon Frost" leopard geckos. Plos Genetics. 17: e1009580. PMID 34166378 DOI: 10.1371/journal.pgen.1009580  0.122
2021 Bloom J, Triantafyllidis A, Quaglieri A, Burton Ngov P, Infusini G, Webb A. Mass Dynamics 1.0: A Streamlined, Web-Based Environment for Analyzing, Sharing, and Integrating Label-Free Data. Journal of Proteome Research. PMID 34647461 DOI: 10.1021/acs.jproteome.1c00683  0.122
2020 Hilton SK, Huddleston J, Black A, North K, Dingens AS, Bedford T, Bloom JD. dms-view: Interactive visualization tool for deep mutational scanning data The Journal of Open Source Software. 5: 2353. DOI: 10.21105/Joss.02353  0.118
2018 Haddox HK, Dingens AS, Hilton SK, Overbaugh J, Bloom JD. Author response: Mapping mutational effects along the evolutionary landscape of HIV envelope Elife. DOI: 10.7554/Elife.34420.047  0.116
2020 Schommers P, Gruell H, Abernathy ME, Tran MK, Dingens AS, Gristick HB, Barnes CO, Schoofs T, Schlotz M, Vanshylla K, Kreer C, Weiland D, Holtick U, Scheid C, Valter MM, ... ... Bloom JD, et al. Restriction of HIV-1 Escape by a Highly Broad and Potent Neutralizing Antibody. Cell. PMID 32004464 DOI: 10.1016/J.Cell.2020.01.010  0.115
2020 Einav T, Bloom JD. When two are better than one: Modeling the mechanisms of antibody mixtures. Plos Computational Biology. 16: e1007830. PMID 32365091 DOI: 10.1371/journal.pcbi.1007830  0.104
2021 Bloom JR, Martin EJ, Jones JA. Communication strategies during the COVID-19 pandemic: Unforeseen opportunities and drawbacks. Seminars in Oncology. 48: 292-294. PMID 34736774 DOI: 10.1053/j.seminoncol.2021.10.001  0.104
2021 Bloom JS, Sathe L, Munugala C, Jones EM, Gasperini M, Lubock NB, Yarza F, Thompson EM, Kovary KM, Park J, Marquette D, Kay S, Lucas M, Love T, Sina Booeshaghi A, et al. Massively scaled-up testing for SARS-CoV-2 RNA via next-generation sequencing of pooled and barcoded nasal and saliva samples. Nature Biomedical Engineering. PMID 34211145 DOI: 10.1038/s41551-021-00754-5  0.1
2018 Scott E, Kuypers J, Xue K, Stewart L, Shrestha L, Tielsch J, Steinhoff MC, Katz J, Khatry S, Leclerq SC, Bloom J, Englund J, Chu H. 613. Transmission of Influenza Virus in Mother and Infant Transmission Events in Nepal Open Forum Infectious Diseases. 5: S223-S224. DOI: 10.1093/Ofid/Ofy210.620  0.1
2021 Ben-David E, Boocock J, Guo L, Zdraljevic S, Bloom JS, Kruglyak L. Whole-organism eQTL mapping at cellular resolution with single-cell sequencing. Elife. 10. PMID 33734084 DOI: 10.7554/eLife.65857  0.091
2014 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, ... ... Bloom JD, et al. Author response: Improving pandemic influenza risk assessment Elife. DOI: 10.7554/Elife.03883.006  0.091
2021 Walti CS, Loes AN, Shuey K, Krantz EM, Boonyaratanakornkit J, Keane-Candib J, Loeffelholz T, Wolf CR, Taylor JJ, Gardner RA, Green DJ, Cowan AJ, Maloney DG, Turtle CJ, Pergam SA, ... ... Bloom JD, et al. Humoral immunogenicity of the seasonal influenza vaccine before and after CAR-T-cell therapy. Medrxiv : the Preprint Server For Health Sciences. PMID 34013294 DOI: 10.1101/2021.05.10.21256634  0.086
2021 Walti CS, Loes AN, Shuey K, Krantz EM, Boonyaratanakornkit J, Keane-Candib J, Loeffelholz T, Wolf CR, Taylor JJ, Gardner RA, Green DJ, Cowan AJ, Maloney DG, Turtle CJ, Pergam SA, ... ... Bloom JD, et al. Humoral immunogenicity of the seasonal influenza vaccine before and after CAR-T-cell therapy: a prospective observational study. Journal For Immunotherapy of Cancer. 9. PMID 34702753 DOI: 10.1136/jitc-2021-003428  0.082
2021 Bloom JA, Erlichman Z, Tian T, Doron S, Chen L, Mansur K, Tarnoff ME. The prevalence of asymptomatic carriers of COVID-19 as determined by routine preoperative testing. Journal of Infection Prevention. 22: 7-11. PMID 33841556 DOI: 10.1177/1757177420967096  0.067
2021 Adhikari S, Normand SL, Bloom J, Shahian D, Rose S. Revisiting performance metrics for prediction with rare outcomes. Statistical Methods in Medical Research. 9622802211038754. PMID 34468239 DOI: 10.1177/09622802211038754  0.066
2021 Bloom JD, Chan YA, Baric RS, Bjorkman PJ, Cobey S, Deverman BE, Fisman DN, Gupta R, Iwasaki A, Lipsitch M, Medzhitov R, Neher RA, Nielsen R, Patterson N, Stearns T, et al. Investigate the origins of COVID-19. Science (New York, N.Y.). 372: 694. PMID 33986172 DOI: 10.1126/science.abj0016  0.063
2021 Hilt EE, Boocock J, Trejo M, Le CQ, Guo L, Zhang Y, Sathe L, Arboleda VA, Yin Y, Bloom JS, Wang PC, Elmore JG, Kruglyak L, Shrestha L, Bakhash SAM, et al. Retrospective Detection of SARS-CoV-2 in Symptomatic Patients prior to Widespread Diagnostic Testing in Southern California. Clinical Infectious Diseases : An Official Publication of the Infectious Diseases Society of America. PMID 33939799 DOI: 10.1093/cid/ciab360  0.063
2021 Bloom JD, E Kirkorsky S. Arizona's Insanity Defense, , and the 2007 Legislature. The Journal of the American Academy of Psychiatry and the Law. PMID 34479941 DOI: 10.29158/JAAPL.210033-21  0.062
2021 Wanga V, Gerdes ME, Shi DS, Choudhary R, Dulski TM, Hsu S, Idubor OI, Webber BJ, Wendel AM, Agathis NT, Anderson K, Boyles T, Chiu SK, Click ES, Da Silva J, ... ... Bloom JA, et al. Characteristics and Clinical Outcomes of Children and Adolescents Aged <18 Years Hospitalized with COVID-19 - Six Hospitals, United States, July-August 2021. Mmwr. Morbidity and Mortality Weekly Report. 70: 1766-1772. PMID 34968374 DOI: 10.15585/mmwr.mm705152a3  0.058
2021 Bloom J, Hejrati B. The effects of forearm movements on human gait during walking with various self-selected speeds. Human Movement Science. 79: 102835. PMID 34265508 DOI: 10.1016/j.humov.2021.102835  0.055
2021 Shahian DM, Bowdish ME, Bloom JP, Wyler von Ballmoos MC, Edgerton JR, Antman MS, Kurlansky PA, Lobdell KW, Cleveland JC, Gaudino MFL, Paone G, Vassileva C, Thourani VH, Furnary AP, Badhwar V, et al. The STS CABG composite measure: 2021 methodology update. The Annals of Thoracic Surgery. PMID 34280375 DOI: 10.1016/j.athoracsur.2021.06.036  0.055
2021 Bloom JD, E Hansen T, Blekic A. Competency to Stand Trial, Civil Commitment, and Oregon State Hospital. The Journal of the American Academy of Psychiatry and the Law. PMID 34880078 DOI: 10.29158/JAAPL.210055-21  0.054
2018 Bloom JD. Estimating the frequency of multiplets in single-cell RNA sequencing from cell-mixing experiments. Peerj. 6: e5578. PMID 30202659 DOI: 10.7717/peerj.5578  0.054
2019 Maldonado MDM, Rosado-González G, Bloom J, Duconge J, Ruiz-Calderón JF, Hernández-O'Farrill E, Vlaar C, Rodríguez-Orengo JF, Dharmawardhane S. Pharmacokinetics of the Rac/Cdc42 Inhibitor MBQ-167 in Mice by Supercritical Fluid Chromatography-Tandem Mass Spectrometry. Acs Omega. 4: 17981-17989. PMID 31720502 DOI: 10.1021/acsomega.9b01641  0.049
2020 Dingens AS, Crawford KHD, Adler A, Steele SL, Lacombe K, Eguia R, Amanat F, Walls AC, Wolf CR, Murphy M, Pettie D, Carter L, Qin X, King NP, Veesler D, ... ... Bloom JD, et al. Serological identification of SARS-CoV-2 infections among children visiting a hospital during the initial Seattle outbreak. Nature Communications. 11: 4378. PMID 32873791 DOI: 10.1038/S41467-020-18178-1  0.049
2020 Locketz GD, Lozada KN, Bloom JD. Tranexamic Acid in Aesthetic Facial Plastic Surgery: A Systematic Review of Evidence, Applications, and Outcomes. Aesthetic Surgery Journal. Open Forum. 2: ojaa029. PMID 33791652 DOI: 10.1093/asjof/ojaa029  0.047
2021 Mahfoud F, Townsend RR, Kandzari DE, Kario K, Schmieder RE, Tsioufis K, Pocock S, David S, Patel K, Rao A, Walton A, Bloom JE, Weber T, Suppan M, Lauder L, et al. Changes in Plasma Renin Activity after Renal Artery Sympathetic Denervation. Journal of the American College of Cardiology. PMID 33957242 DOI: 10.1016/j.jacc.2021.04.044  0.046
2021 Bloom JD, Kirkorsky SE. , Competency to Stand Trial, and Guilty but Mentally Ill. The Journal of the American Academy of Psychiatry and the Law. PMID 33627379 DOI: 10.29158/JAAPL.200105-20  0.046
2020 Dingens AS, Crawford KH, Adler A, Steele SL, Lacombe K, Eguia R, Amanat F, Walls AC, Wolf CR, Murphy M, Pettie D, Carter L, Qin X, King NP, Veesler D, ... ... Bloom JD, et al. Seroprevalence of SARS-CoV-2 among children visiting a hospital during the initial Seattle outbreak. Medrxiv : the Preprint Server For Health Sciences. PMID 32511483 DOI: 10.1101/2020.05.26.20114124  0.046
2021 McLennan V, Dorsett P, Bloom J, Goossen T, Porter F. Back2Work: a new model of early vocational rehabilitation for people with spinal cord injury. Australian Health Review : a Publication of the Australian Hospital Association. PMID 34706809 DOI: 10.1071/AH21069  0.044
2021 Fink JJ, Schreiner JD, Bloom JE, James J, Baker DS, Robinson TM, Lieberman R, Loew LM, Chamberlain SJ, Levine ES. Hyperexcitable Phenotypes in Induced Pluripotent Stem Cell-Derived Neurons From Patients With 15q11-q13 Duplication Syndrome, a Genetic Form of Autism. Biological Psychiatry. PMID 34538422 DOI: 10.1016/j.biopsych.2021.07.018  0.044
2021 Cook PF, Hoard VA, Dolui S, Frederick BD, Redfern R, Dennison SE, Halaska B, Bloom J, Kruse-Elliott KT, Whitmer ER, Trumbull EJ, Berns GS, Detre JA, D'Esposito M, Gulland FMD, et al. An MRI protocol for anatomical and functional evaluation of the California sea lion brain. Journal of Neuroscience Methods. 109097. PMID 33581216 DOI: 10.1016/j.jneumeth.2021.109097  0.044
2019 Bloom JP, Moonsamy P, Gartland RM, O'Malley C, Tolis G, Villavicencio-Theoduloz MA, Burkhardt C, Dunn P, Sundt TM, D'Alessandro DA. Impact of staff turnover during cardiac surgical procedures. The Journal of Thoracic and Cardiovascular Surgery. PMID 31928826 DOI: 10.1016/j.jtcvs.2019.11.051  0.042
2020 Alessa D, Bloom JD. Microneedling Options for Skin Rejuvenation, Including Non-temperature-controlled Fractional Microneedle Radiofrequency Treatments. Facial Plastic Surgery Clinics of North America. 28: 1-7. PMID 31779933 DOI: 10.1016/j.fsc.2019.09.001  0.035
2021 Noaman S, Dinh D, Reid CM, Brennan AL, Clark D, Shaw J, Freeman M, Sebastian M, Oqueli E, Ajani A, Walton A, Bloom J, Biswas S, Stub D, Duffy SJ, et al. Comparison of Outcomes of Coronary Artery Disease Treated by Percutaneous Coronary Intervention in 3 Different Age Groups (<45, 46-65, and >65 Years). The American Journal of Cardiology. PMID 34147208 DOI: 10.1016/j.amjcard.2021.05.002  0.034
2021 Reed AK, Cameron DE, Bloom JP. Early failure of a bioprosthetic valve in the pulmonary position causing panic. The Annals of Thoracic Surgery. PMID 34637769 DOI: 10.1016/j.athoracsur.2021.09.013  0.034
2021 Bloom JD, Kirkorsky SE. The Ninth Circuit Court of Appeals and Jail-Based Competency Evaluation and Restoration. The Journal of the American Academy of Psychiatry and the Law. PMID 34001672 DOI: 10.29158/JAAPL.200099-20  0.033
2021 Shehan JN, Agarwal P, O'Neil Danis D, Ghulam-Smith M, Bloom J, Piraquive J, Tracy LF, Levi JR. Effects of COVID-19 on telemedicine practice patterns in outpatient otolaryngology. American Journal of Otolaryngology. 42: 103044. PMID 34091321 DOI: 10.1016/j.amjoto.2021.103044  0.033
2021 Ahdoot M, Lebastchi AH, Long L, Wilbur AR, Gomella PT, Mehralivand S, Daneshvar MA, Yerram NK, O'Connor LP, Wang AZ, Gurram S, Bloom J, Siddiqui MM, Linehan WM, Merino M, et al. Using Prostate Imaging-Reporting and Data System (PI-RADS) Scores to Select an Optimal Prostate Biopsy Method: A Secondary Analysis of the Trio Study. European Urology Oncology. PMID 33846112 DOI: 10.1016/j.euo.2021.03.004  0.032
2020 Petersen BJ, Rothenberg GM, Lakhani PJ, Zhou M, Linders DR, Bloom JD, Wood KA, Armstrong DG. Ulcer metastasis? Anatomical locations of recurrence for patients in diabetic foot remission. Journal of Foot and Ankle Research. 13: 1. PMID 31956341 DOI: 10.1186/s13047-020-0369-3  0.031
2021 Bloom JP, Attia RQ, Sundt TM, Cameron DE, Hedgire SS, Bhatt AB, Isselbacher EM, Srivastava SD, Kwolek CJ, Eagleton MJ, Mohebali J, Jassar AS. Outcomes of open and endovascular repair of Kommerell diverticulum. European Journal of Cardio-Thoracic Surgery : Official Journal of the European Association For Cardio-Thoracic Surgery. PMID 33582760 DOI: 10.1093/ejcts/ezab072  0.03
2021 Bloom JA, Erlichman Z, Foroutanjazi S, Beqiraj Z, Jonczyk MM, Persing SM, Chatterjee A. The Use of Hemostatic Agents to Decrease Bleeding Complications in General Plastic Surgery Procedures. Plastic and Reconstructive Surgery. Global Open. 9: e3744. PMID 34667700 DOI: 10.1097/GOX.0000000000003744  0.029
2021 Bloom JB, Daneshvar MA, Lebastchi AH, Ahdoot M, Gold SA, Hale G, Mehralivand S, Sanford T, Valera V, Wood BJ, Choyke PL, Merino MJ, Turkbey B, Parnes HL, Pinto PA. Risk of adverse pathology at prostatectomy in the era of MRI and targeted biopsies; rethinking active surveillance for intermediate risk prostate cancer patients. Urologic Oncology. PMID 33736975 DOI: 10.1016/j.urolonc.2021.02.018  0.029
2021 Bloom JL, Frank B, Weinman JP, Galambos C, O'Leary ST, Liptzin DR, Fuhlbrigge RC. Diffuse alveolar hemorrhage in children with trisomy 21. Pediatric Rheumatology Online Journal. 19: 114. PMID 34273981 DOI: 10.1186/s12969-021-00592-4  0.025
2021 Ufere NN, Robinson B, Donlan J, Indriolo T, Bloom J, Scherrer A, Mason NM, Patel A, Lai JC, Chung RT, Volandes A, El-Jawahri A. Pilot Randomized Controlled Trial of an Advance Care Planning Video Decision Tool for Patients with Advanced Liver Disease. Clinical Gastroenterology and Hepatology : the Official Clinical Practice Journal of the American Gastroenterological Association. PMID 34718173 DOI: 10.1016/j.cgh.2021.10.027  0.024
2021 Bloom JP, Vlahakes GJ. To MUF or not to MUF, that is the question. Journal of Cardiac Surgery. PMID 34309907 DOI: 10.1111/jocs.15840  0.023
2021 Saba P, Melnyk R, Holler T, Oppenheimer D, Schuler N, Tabayoyong W, Bloom J, Bandari J, Frye T, Joseph J, Weinberg E, Hollenberg G, Ghazi A. Comparison of Multi-Parametric MRI of the Prostate to 3D Prostate Computer Aided Designs and 3D-Printed Prostate Models for Pre-Operative Planning of Radical Prostatectomies: A Pilot Study. Urology. PMID 34496263 DOI: 10.1016/j.urology.2021.08.031  0.022
2021 Bloom JE, Andrew E, Nehme Z, Dinh DT, Fernando H, Shi WY, Vriesendorp P, Nanayakarra S, Dawson LP, Brennan A, Noaman S, Layland J, William J, Al-Fiadh A, Brooks M, et al. Pre-hospital heparin use for ST-elevation myocardial infarction is safe and improves angiographic outcomes. European Heart Journal. Acute Cardiovascular Care. PMID 34189566 DOI: 10.1093/ehjacc/zuab032  0.021
2021 Bloom JA, Sekigami Y, Young R, Macera L, Russell CA, Cao Y, Buchsbaum RJ, Naber SP, Chatterjee A. Discordance in Oncotype DX Breast Recurrence Score Results for Bilateral Breast Cancer. Annals of Surgical Oncology. PMID 34241750 DOI: 10.1245/s10434-021-10387-2  0.02
2021 Bloom JL, Furniss A, Suresh K, Fuhlbrigge RC, Lamb MM, Rosenberg S, Edwards A, O'Leary ST. The Impact of Altitude at Birth on Perinatal Respiratory Support for Neonates with Trisomy 21. American Journal of Perinatology. PMID 34674211 DOI: 10.1055/s-0041-1736594  0.019
2021 Dawson LP, Chen D, Dagan M, Bloom J, Taylor A, Duffy SJ, Shaw J, Lefkovits J, Stub D. Assessment of Pretreatment With Oral P2Y12 Inhibitors and Cardiovascular and Bleeding Outcomes in Patients With Non-ST Elevation Acute Coronary Syndromes: A Systematic Review and Meta-analysis. Jama Network Open. 4: e2134322. PMID 34797371 DOI: 10.1001/jamanetworkopen.2021.34322  0.019
2021 Jacobs JP, Shahian DM, Grau-Sepulveda M, O'Brien SM, Pruitt EY, Bloom JP, Edgerton JR, Kurlansky PA, Habib RH, Antman MS, Cleveland JC, Fernandez FG, Thourani VH, Badhwar V. Current Penetration, Completeness, and Representativeness of The Society of Thoracic Surgeons Adult Cardiac Surgery Database. The Annals of Thoracic Surgery. PMID 34153294 DOI: 10.1016/j.athoracsur.2021.04.107  0.018
2021 Tong DC, Bloom JE, Quinn S, Nasis A, Hiew C, Roberts-Thomson P, Adams H, Sriamareswaran R, Htun NM, Wilson W, Stub D, van Gaal W, Howes L, Yeap A, Yip B, et al. Colchicine in Patients With Acute Coronary Syndrome: Two-Year Follow-Up of the Australian COPS Randomized Clinical Trial. Circulation. 144: 1584-1586. PMID 34748393 DOI: 10.1161/CIRCULATIONAHA.121.054610  0.018
2021 Bloom JA, Homsy C. Abdominal-based free flaps in head and neck reconstruction. Current Opinion in Otolaryngology & Head and Neck Surgery. 29: 314-319. PMID 34183562 DOI: 10.1097/MOO.0000000000000720  0.017
2021 Bloom JA, Foroutanjazi S, Erlichman Z, Beqiraj Z, Jonczyk MM, Persing SM, Chatterjee A. The Use of Hemostatic Agents to Decrease Bleeding Complications in Breast Cancer Surgery. The American Surgeon. 31348211029866. PMID 34176297 DOI: 10.1177/00031348211029866  0.017
2019 Batchelor R, Liu DH, Bloom J, Noaman S, Chan W. Association of periprocedural intravenous morphine use on clinical outcomes in ST-elevation myocardial infarction (STEMI) treated by primary percutaneous coronary intervention: Systematic review and meta-analysis. Catheterization and Cardiovascular Interventions : Official Journal of the Society For Cardiac Angiography & Interventions. PMID 31654491 DOI: 10.1002/ccd.28561  0.016
2021 Wojcik BM, McKinley SK, Fong ZV, Mansur A, Bloom JP, Amari N, Hamdi I, Chang DC, Petrusa E, Mullen JT, Phitayakorn R. The Resident-Run Minor Surgery Clinic: A Four-Year Analysis of Patient Outcomes, Satisfaction, and Resident Education. Journal of Surgical Education. PMID 34092535 DOI: 10.1016/j.jsurg.2021.04.003  0.016
2021 Char SN, Bloom JA, DeMarco D, Chatterjee A. Evaluating the Quality of Cost-Effectiveness Literature in Breast Surgery: What Do We Do Well and How Can We Do Better? A Systematic Review. The American Surgeon. 31348211011148. PMID 33861654 DOI: 10.1177/00031348211011148  0.016
2021 Tian T, Zaepfel C, Bloom J, Alnahhal K, Chatterjee A, Allison GM, Iafrati M, Salehi P. Reporting of Financial Conflicts of Interest in Studies of Placental Membrane Allografts. Advances in Wound Care. PMID 34235968 DOI: 10.1089/wound.2021.0075  0.016
2021 Shi WY, Bloom JE, Shen R, Levvey BJ, Walton AS, Marasco SF, Zimmet A, Snell G, McGiffin DC. Mitral Valve Regurgitation After Lung Transplantation: Aetiology, Management and Outcome. Heart, Lung & Circulation. PMID 34838453 DOI: 10.1016/j.hlc.2021.10.010  0.012
2021 Passalent L, Sundararajan K, Perruccio AV, Hawke C, Coyte PC, Bombardier C, Bloom JA, Haroon N, Inman RD, Rampersaud YR. Bridging the Gap between Symptom Onset and Diagnosis in Axial Spondyloarthritis. Arthritis Care & Research. PMID 34268914 DOI: 10.1002/acr.24751  0.012
2021 Bloom JA, Sekigami Y, Young R, Macera L, Russell CA, Cao Y, Buchsbaum RJ, Naber SP, Chatterjee A. ASO Visual Abstract: Discordance in Oncotype DX Breast Recurrence Score® Results for Bilateral Breast Cancer. Annals of Surgical Oncology. PMID 34240296 DOI: 10.1245/s10434-021-10429-9  0.01
2021 Osinski T, Bloom JB. Editorial Comment. The Journal of Urology. 101097JU000000000000. PMID 34137275 DOI: 10.1097/JU.0000000000001810.01  0.01
2021 Mehralivand S, George AK, Hoang AN, Rais-Bahrami S, Rastinehad AR, Lebastchi AH, Ahdoot M, Siddiqui MM, Bloom J, Sidana A, Merino MJ, Choyke PL, Shih JH, Turkbey B, Wood BJ, et al. MRI-guided focal laser ablation of prostate cancer: a prospective single-arm, single-center trial with 3 years of follow-up. Diagnostic and Interventional Radiology (Ankara, Turkey). 27: 394-400. PMID 34003127 DOI: 10.5152/dir.2021.20095  0.01
2020 Bloom JP, Shapeton AD, Rasalingam R, Zenati MA. Postoperative Echocardiographic Appearance of the Mitral Valve After Nonresectional Leaflet Remodeling Repair Mimicking Thrombus. Circulation. Cardiovascular Imaging. 13: e009853. PMID 31906701 DOI: 10.1161/CIRCIMAGING.119.009853  0.01
2019 Kirkorsky SE, Shao W, Bloom JD. Letters. The Journal of the American Academy of Psychiatry and the Law. 47: 538. PMID 31811082 DOI: 10.29158/JAAPL.003906-19  0.01
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