Paulson Laboratory

Andrew J. Thompson, Ph.D.

The Scripps Research Institute
10550 North Torrey Pines Road, MB-209
La Jolla, CA 92037
858-784-7538 (phone)
858-784-9690 (fax)


2008 to 2012: PhD Chemistry at University of York, United Kingdom

2005 to 2008: BS Biochemistry at Newcastle University, United Kingdom


October 2020 to Present: Senior Staff Scientist, The Scripps Research Institute, La Jolla, CA, USA (Advisor: Prof. James C. Paulson)

August 2018 to September 2020: Staff Scientist, The Scripps Research Institute, La Jolla, CA, USA (Advisor: Prof. James C. Paulson)

March 2018 to July: Senior Research Associate, The Scripps Research Institute, La Jolla, CA, USA (Advisor: Prof. James C. Paulson)

2015 to 2018: Research Associate, The Scripps Research Institute, La Jolla, CA, USA (Advisor: Prof. James C. Paulson)

2012 to 2015: Postdoctoral Research Fellow, Department of Chemistry, University of York, UK (Supervisor: Prof. Gideon Davies)

2008 to 2012: PhD candidate, Department of Chemistry, University of York, UK (Mentor: Prof. Gideon Davies)

2008 to 2011: Laboratory Demonstrator, Department of Chemistry, University of York, UK

2008: Research Assistant, Institute for Cell and Molecular Biosciences, Newcastle University, UK (Supervisor/Mentor: Prof. Chris Dennison)

2007: Summer intern, Institute for Cell and Molecular Biosciences, Newcastle University, UK (Supervisor/Mentor: Prof. Harry Gilbert)


2018 to present: Investigator, Center of Excellence for Influenza Research and Surveillance (CEIRS), St. Jude Children's Research Hospital, USA

2014 to 2017: Long-Term Postdoctoral Fellowship, EMBO excellence in Life Science

2012: Member of the Royal Society of Chemistry (MRSC)

2011: Graduate student representative (elected) on Chemistry Graduate School Board, Department of Chemistry, University of York, UK

2010: Member of the Biochemical Society (UK)

2007: Biochemical Society (UK) summer internship, Institute for Cell and Molecular Biosciences, Newcastle University, UK


Bagdonaite I, Thompson AJ, Wang X, Sogaard M, Fougeroux C, Frank M, Diedrich JK, Yates JR 3rd, Salanti A, Vakhrushev SY, Paulson JC, Wandall HH. Site-Specific O-Glycosylation Analysis of SARS-CoV-2 Spike Protein Produced in Insect and Human Cells. Viruses 2021;13(4):551.

Thompson AJ, Paulson JC. Adaptation of Influenza Viruses to Human Airway Receptors. J Biol Chem. 2021;296:100017.

Lee S, Yang YA, Milano SK, Nguyen T, Ahn C, Sim JH, Thompson AJ, Hillpot EC, Yoo G, Paulson JC, Song J. Salmonella Typhoid Toxin PltB Subunit and Its Non-typhoidal Salmonella Ortholog Confer Differential Host Adaptation and Virulence. Cell Host Microbe. 2020;27(6):937-949.

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. 2020;368(6497):1335-1340. (*Equal contribution)

Wu NC, Otwinowski J, Thompson AJ, Nycholat CM, Nourmohammad A, Wilson IA. Major antigenic site B of human influenza H3N2 viruses has an evolving local fitness landscape. Nat Commun. 2020;11(1):1233.

Thompson AJ, Cao L, Ma Y, Wang X, Diedrich JK, Kikuchi C, Willis S, Worth C, McBride R, Yates JR 3rd, Paulson JC. Human Influenza Virus Hemagglutinins Contain Conserved Oligomannose N-Linked Glycans Allowing Potent Neutralization by Lectins. Cell Host Microbe. 2020;27(5):725-735.

Narimatsu Y, Joshi HJ, Nason R, Van Coillie J, Karlsson R, Sun L, Ye Z, Chen YH, Schjoldager KT, Steentoft C, Furukawa S, Bensing BA, Sullam PM, Thompson AJ, Paulson JC, Büll C, Adema GJ, Mandel U, Hansen L, Bennett EP, Varki A, Vakhrushev SY, Yang Z, Clausen H. An Atlas of Human Glycosylation Pathways Enables Display of the Human Glycome by Gene Engineered Cells. Mol Cell. 2019;75(2):394-407.

Wu NC, Lv H, Thompson AJ, Wu DC, Ng WWS, Kadam RU, Lin CW, Nycholat CM, McBride R, Liang W, Paulson JC, Mok CKP, Wilson IA. Preventing an Antigenically Disruptive Mutation in Egg-Based H3N2 Seasonal Influenza Vaccines by Mutational Incompatibility. Cell Host Microbe. 2019;25(6):836-844.

Thompson AJ, de Vries RP, Paulson JC. Virus recognition of glycan receptors. Curr Opin Virol. 2019,34:117-129.

Obadan AO, Santos J, Ferreri L, Thompson AJ, Carnaccini S, Geiger G, Gonzalez Reiche AS, Rajao DS, Paulson JC, Perez DR. Flexibility in vitro of amino acid 226 in the receptor-binding site of an H9 subtype influenza A virus and its effect in vivo on virus replication, tropism, and transmission. J Virol. 2019;93(6):02011-18.

Santos JJS, Abente EJ, Obadan AO, Thompson AJ, Ferreri L, Geiger G, Gonzalez-Reiche AS, Lewis NS, Burke DF, Rajao DS, Paulson JC, Vincent AL, Perez DR. Plasticity of amino acid residue 145 near the receptor binding site of H3 swine influenza A viruses and its impact on receptor binding and antibody recognition. J Virol. 2019;93(2):e01413-18.

Fernandez de Toro B, Peng W, Thompson AJ, Dominguez G, Canada FJ, Perez-Castells J, Paulson JC, Jimenez-Barbero J, Canales A. Avenues to Characterize the Interactions of Extended N-glycans with Proteins: The Influenza Hemagglutinin Case. Angew Chem Int Ed Engl. 2018;57(46):15051-15055.

Gao Z, Thompson AJ, Paulson JC, Withers SG. Proximity Ligation-Based Fluorogenic Imaging Agents for Neuraminidases. Angew Chem Int Ed Engl. 2018;57(41):13538-13541.

Imai H, Dinis JM, Zhong G, Moncla LH, Lopes TJS, McBride R, Thompson AJ, Peng W, Le MTQ, Hanson A, Lauck M, Sakai-Tagawa Y, Yamada S, Eggenberger J, O'Connor DH, Suzuki Y, Hatta M, Paulson JC, Neumann G, Friedrich TC, Kawaoka Y. Diversity of Influenza A(H5N1) Viruses in Infected Humans, Northern Vietnam, 2004-2010. Emerg Infect Dis. 2018;24(7):1128-1238.

Wu NC, Thompson AJ, Xie J, Lin CW, Nycholat CM, Zhu X, Lerner RA, Paulson JC, Wilson IA. A complex epistatic network limits the mutational reversibility in the influenza hemagglutinin receptor-binding site. Nat Commun. 2018;9(1):1264.

Yang YA, Lee S, Zhao J, Thompson AJ, McBride R, Tsogtbaatar B, Paulson JC, Nussinov R, Deng L, Song J. In vivo tropism of Salmonella Typhi toxin to cells expressing a multiantennal glycan receptor. Nat Microbiol. 2018;3(2):155-163.

Hatta M, Zhong G, Gao Y, Nakajima N, Fan S, Chiba S, Deering KM, Ito M, Imai M, Kiso M, Nakatsu S, Lopes TJ, Thompson AJ, McBride R, Suarez DL, Macken CA, Sugita S, Neumann G, Hasegawa H, Paulson JC, Toohey-Kurth KL, Kawaoka Y. Characterization of a Feline Influenza A(H7N2) Virus. Emerg Infect Dis. 2018;24(1):75-86.

Imai M, Watanabe T, Kiso M, Nakajima N, Yamayoshi S, Iwatsuki-Horimoto K, Hatta M, Yamada S, Ito M, Sakai-Tagawa Y, Shirakura M, Takashita E, Fujisaki S, McBride R, Thompson AJ, Takahashi K, Maemura T, Mitake H, Chiba S, Zhong G, Fan S, Oishi K, Yasuhara A, Takada K, Nakao T, Fukuyama S, Yamashita M, Lopes TJS, Neumann G, Odagiri T, Watanabe S, Shu Y, Paulson JC, Hasegawa H, Kawaoka Y. A Highly Pathogenic Avian H7N9 Influenza Virus Isolated from A Human Is Lethal in Some Ferrets Infected via Respiratory Droplets. Cell Host Microbe. 2017;22:615-626.

Wu NC, Zost SJ, Thompson AJ, Oyen D, Nycholat CM, McBride R, Paulson JC, Hensley SE, Wilson IA. A structural explanation for the low effectiveness of the seasonal influenza H3N2 vaccine. PLoS Pathog. 2017;13(10):e1006682.

de Vries RP, Peng W, Grant OC, Thompson AJ, Zhu X, Bouwman KM, de la Pena ATT, van Breemen MJ, Ambepitiya Wickramasinghe IN, de Haan CAM, Yu W, McBride R, Sanders RW, Woods RJ, Verheije MH, Wilson IA, Paulson JC. Three mutations switch H7N9 influenza to human-type receptor specificity. PLoS Pathog. 2017;13(6):e1006390.

Tzarum N, de Vries RP, Peng W, Thompson AJ, Bouwman KM, McBride R, Yu W, Zhu X, Verheije MH, Paulson JC, Wilson IA. The 150-Loop Restricts the Host Specificity of Human H10N8 Influenza Virus. Cell Rep. 2017;19(2):235-245.

Peng W, de Vries RP, Grant OC, Thompson AJ, McBride R, Tsogtbaatar B, Lee PS, Razi N, Wilson IA, Woods RJ, Paulson JC. Recent H3N2 Viruses Have Evolved Specificity for Extended, Branched Human-type Receptors, Conferring Potential for Increased Avidity. Cell Host Microbe. 2017;21(1):23-34.

Thompson AJ, Speciale G, Iglesias-Fernandez J, Hakki Z, Belz T, Cartmell A, Spears RJ, Chandler E, Temple MJ, Stepper J, Gilbert HJ, Rovira C, Williams SJ, Davies GJ. Evidence for a Boat Conformation at the Transition State of GH76 alpha-1,6-Mannanases-Key Enzymes in Bacterial and Fungal Mannoprotein Metabolism. Angew Chem Int Ed Engl. 2015;54(18):5378–5382.

Thompson AJ, Cuskin F, Spears RJ, Dabin J, Turkenburg JP, Gilbert HJ, Davies GJ. Structure of the GH76 alpha-mannanase homolog, BT2949, from the gut symbiont Bacteroides thetaiotaomicron. Acta Crystallogr D Biol Crystallogr. 2015;71:408-415.

Cuskin F, Lowe EC, Temple MJ, Zhu Y, Cameron EA, Pudlo NA, Porter NT, Urs K, Thompson AJ, Cartmell A, Rogowski A, Hamilton BS, Chen R, Tolbert TJ, Piens K, Bracke D, Vervecken W, Hakki Z, Speciale G, Munōz-Munōz JL, Day A, Peña MJ, McLean R, Suits MD, Boraston AB, Atherly T, Ziemer CJ, Williams SJ, Davies GJ, Abbott DW, Martens EC, Gilbert HJ.Human gut Bacteroidetes can utilize yeast mannan through a selfish mechanism.Nature. 2015;517(7533):165-9.

Hakki Z, Thompson AJ, Bellmaine S, Speciale G, Davies GJ, Williams SJ. Structural and Kinetic Dissection of the endo-a-1,2-Mannanase Activity of Bacterial GH99 Glycoside Hydrolases from Bacteroides spp. Chemistry. 2015;21:1966-1977.

Larsbrink J, Thompson AJ, Lundqvist M, Gardner JG, Davies GJ, Brumer H. A complex gene locus enables xyloglucan utilization in the model saprophyte Cellvibrio japonicus. Mol Microbiol. 2014;94(2):418-33.

Speciale G, Thompson AJ, Davies GJ, Williams SJ. Dissecting conformational contributions to glycosidase catalysis and inhibition. Curr Opin Struct Biol. 2014;28:1-13

Williams RJ, Iglesias-Fernandez J, Stepper J, Jackson A, Thompson AJ, Lowe EC, White JM, Gilbert HJ, Rovira C, Davies GJ, Williams SJ. Combined inhibitor free-energy landscape and structural analysis reports on the mannosidase conformational coordinate. Angew Chem Int Ed Engl. 2014;53(4):1087-91.

Thompson AJ, Williams RJ, Hakki Z, Alonzi DS, Wennekes T, Gloster TM, Songsrirote K, Thomas-Oates JE, Wrodnigg TM, Spreitz J, Stutz AE, Butters TD, Williams SJ, Davies GJ. Structural and mechanistic insight into N-glycan processing by endo-alpha-mannosidase. Proc Natl Acad Sci U S A. 2012;109(3):781-6.

Thompson AJ, Heu T, Shaghasi T, Benyamino R, Jones A, Friis EP, Wilson KS, Davies GJ. Structure of the catalytic core module of the Chaetomium thermophilum family GH6 cellobiohydrolase Cel6A. Acta Crystallogr D Biol Crystallogr. 2012;68(Pt 8):875-82.

Thompson AJ, Dabin J, Iglesias-Fernandez J, Ardevol A, Dinev Z, Williams SJ, Bande O, Siriwardena A, Moreland C, Hu TC, Smith DK, Gilbert HJ, Rovira C, Davies GJ. The reaction coordinate of a bacterial GH47 alpha-mannosidase: a combined quantum mechanical and structural approach. Angew Chem Int Ed Engl. 2012;51(44):10997-1001.

Quach T, Tsegay S, Thompson AJ, Kukushkin NV, Alonzi DS, Butters TD, Davies GJ, Williams SJ. Fleetamine (3-O-alpha-D-glucopyranosyl-swainsonine): the synthesis of a hypothetical inhibitor of endo-alpha-mannosidase. Tetrahedron Asymmetry. 2012;23(13):992-7.

Zhu Y, Suits MD, Thompson AJ, Chavan S, Dinev Z, Dumon C, Smith N, Moremen KW, Xiang Y, Siriwardena A, Williams SJ, Gilbert HJ, Davies GJ. Mechanistic insights into a Ca2+-dependent family of alpha-mannosidases in a human gut symbiont. Nat Chem Biol. 2010;6(2):125-32.

Sato K, Li C, Salard I, Thompson AJ, Banfield MJ, Dennison C. Metal-binding loop length and not sequence dictates structure. Proc Natl Acad Sci U S A. 2009;106(14):5616-21.