Publications

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2024

#Lei Li, #Jiayi Sun, #Yanbin Fu, Siriruk Changrob, Joshua J.C. McGrath, Patrick Wilson. A hybrid demultiplexing strategy that improves performance and robustness of cell hashing Briefings in Bioinformatics (2024) DOI: https://doi.org/10.1093/bib/bbae254 Oxford Press

Kim, Y., Maltseva, N., Tesar, C., Jedrzejczak, R., Endres, M., Ma, H., Dugan, H.L., Stamper, C.T., Chang, C., Li, L. and Changrob, S. Epitopes recognition of SARS-CoV-2 nucleocapsid RNA binding domain by human monoclonal antibodies. Iscience (2024) DOI:https://doi.org/10.1016/j.isci.2024.108976 CellPress

2023

Meng Hu, Christina Kackos, Balaji Banoth, Chet Raj Ojha, Jeremy C. Jones, Shaohua Lei, Lei Li, Lisa Kercher, Richard J. Webby, Charles J. Russel. Hemagglutinin destabilizationin H3N2 vaccine reference viruses skews antigenicity and prevents airborne transmission in ferrets Science Advances (2023) Science Advances

#Jenna Guthmiller, #Linda Yu-Ling Lan, #Lei Li, Carole Henry, Christopher Stamper, Henry Utset, Alec Freyn, Julianna Han, Olivia Stovicek, Jiaolong Wang, Nai-Ying Zheng, Min Huang, Haley Dugan, Micah Tepora, Xueyong Zhu, Yao-Qing Chen, Anna-Karin Palm, Dustin Shaw, Madhumanthi Loganathan, Benjamin Francis, Mia McNair, Philip Mead, Ian Wilson, Adolfo Garcia-Sastre, Raffael Nachbagauer, Peter Palese, Andrew Ward, Lynda Coughlan, Florian Krammer, Patrick Wilson. B cell convergence to distinct broadly reactive epitopes following vaccination with chimeric influenza virus hemagglutinins Pre-print(2023) Research Square

Siriruk Changrob, Peter J. Halfmann, Hejun Liu, Jonathan L. Torres, Joshua J.C. McGrath, Gabriel Ozorowski, Lei Li, G. Dewey Wilbanks, Makoto Kuroda, Tadashi Maemura, Min Huang, Nai-Ying Zheng, Hannah L. Turner, Steven A. Erickson, Yanbin Fu, Atsuhiro Yasuhara, Gagandeep Singh, Brian Monahan, Jacob Mauldin, Komal Srivastava, Viviana Simon, Florian Krammer, D. Noah Sather, Andrew B Ward, Ian A. Wilson, Yoshihiro Kawaoka, Patrick C. Wilson. Site of vulnerability on SARS-CoV-2 spike induces broadly protective antibody to antigenically distinct Omicron subvariants Journal of Clinical Investigation (2023) DOI: 10.1172/JCI166844 JCI

2022

Lei Li, Yu-Ling Lan, Lei Huang, Congting Ye, Jorge Andrade, and Patrick C Wilson. Selecting representative samples from complex biological datasets using k-medoids clustering. Frontiers in Genetics (2022) p. 1787. DOI: 10.3389/fgene.2022.954024 Frontiers in Genetics

Joshua J.C. McGrath, Lei Li, Patrick C. Wilson. Memory B cell diversity: insights for optimized vaccine design Trends in Immunology (2022) https://doi.org/10.1016/j.it.2022.03.005 Cell Press

#Lei Li, #Siriruk Changrob, #Yanbin Fu,Olivia Stovicek, Jenna J. Guthmiller, Joshua JC McGrath, Haley L. Dugan, Christopher T. Stamper, Nai-Ying Zheng, Min Huang, Patrick C Wilson; Librator: a platform for the optimized analysis, design, and expression of mutable influenza viral antigens Briefings in Bioinformatics (2022) bbac028 Oxford Press

#Guthmiller, Jenna J; #Julianna Han, Henry A. Utset, Lei Li, Linda Yu-Ling Lan, Carole Henry, Christopher T. Stamper, Meagan McMahon, George O’Dell, Monica L. Fernández-Quintero, Alec W. Freyn, Fatima Amanat, Olivia Stovicek, Lauren Gentles, Sara T. Richey, Alba Torrents de la Peña, Victoria Rosado, Haley L. Dugan, Nai-Ying Zheng, Micah E. Tepora, Dalia J. Bitar, Siriruk Changrob, Shirin Strohmeier, Min Huang, Adolfo García-Sastre, Klaus R. Liedl, Jesse D. Bloom, Raffael Nachbagauer, Peter Palese, Florian Krammer, Lynda Coughlan, Andrew B. Ward & Patrick C. Wilson. Broadly neutralizing antibodies target a hemagglutinin anchor epitope Nature 602, 314–320 (2022) https://doi.org/10.1038/s41586-021-04356-8 Nature

2021

Siriruk Changrob, Yanbin Fu, Jenna Guthmiller, Peter Halfmann, Lei Li, Christopher Stamper, Haley Dugan, Molly Accola, William Rehrauer, Nai-Ying Zheng, Min Huang, Jiaolong Wang, Steven Erickson, Henry Utset, Hortencia Graves, Fatima Amanat, D Noah Sather, Florian Krammer, Yoshihiro Kawaoka, Patrick Wilson; Cross neutralization of emerging SARS-CoV-2 variants of concern by antibodies targeting distinct epitopes on spike mBio 12, no. 6 (2021): e02975-21. ASM Journals

#Li, Lei; #Dugan, Haley L; #Stamper, Christopher; Lan, Linda Yu-Ling; Asby, Nicholas; Knight, Matthew; Stovicek, Olivia; Zheng, Nai-Ying; Madariaga, Maria Lucia; Shanmugarajah, Kumaran; Improved integration of single-cell transcriptome and surface protein expression by LinQ-View Cell Reports Methods 1 (4), 100056 (2021) Cell Press

Guthmiller, Jenna J; Utset, Henry A; Henry, Carole; Li, Lei; Zheng, Nai-Ying; Sun, Weina; Vieira, Marcos C; Zost, Seth; Huang, Min; Hensley, Scott E; An egg-derived sulfated N-Acetyllactosamine glycan is an antigenic decoy of influenza virus vaccines Mbio 12, no. 3 (2021): e00838-21. ASM Journals

#Dugan, Haley L; #Stamper, Christopher; #Li, Lei; Changrob, Siriruk; Asby, Nicholas; Halfmann, Peter; Zheng, Nai-Ying; Huang, Min; Shaw, Dustin G; Cobb, Mari; Profiling B cell immunodominance after SARS-CoV-2 infection reveals antibody evolution to non-neutralizing viral targets Immunity 54, no. 6 (2021): 1290-1303. ScienceDirect

Guthmiller, Jenna J; Stovicek, Olivia; Wang, Jiaolong; Changrob, Siriruk; Li, Lei; Halfmann, Peter; Zheng, Nai-Ying; Utset, Henry; Stamper, Christopher T; Dugan, Haley L; SARS-CoV-2 infection severity is linked to superior humoral immunity against the spike MBio 12, no. 1 (2021): e02940-20 ASM Journals

#Guthmiller, Jenna J; #Han, Julianna; Li, Lei; Freyn, Alec W; Liu, Sean TH; Stovicek, Olivia; Stamper, Christopher; Dugan, Haley L; Tepora, Micah E; Bitar, Dalia J; First exposure to the pandemic H1N1 virus induced broadly neutralizing antibodies targeting hemagglutinin head epitopes Science Translational Medicine 13, no. 596 (2021). DOI: 10.1126/scitranslmed.abg4535 Science Translational Medicine

Surette, Fionna A; Guthmiller, Jenna J; Li, Lei; Sturtz, Alexandria J; Vijay, Rahul; Pope, Rosemary L; McClellan, Brandon L; Pack, Angela D; Zander, Ryan A; Shao, Peng; Extrafollicular CD4 T cell-derived IL-10 functions rapidly and transiently to support anti-Plasmodium humoral immunity PLoS Pathogens 17, no. 2 (2021): e1009288. PLoS Pathogens

Lee, Dong-Hun, Mary Lea Killian, Thomas J. Deliberto, Xiu-Feng Wan, Li Lei, David E. Swayne, and Mia Kim Torchetti. H7N1 Low Pathogenicity Avian Influenza Viruses in Poultry in the United States During 2018. Avian Diseases 65, no. 1 (2021): 59-62. Avian Diseases

Vijay, Rahul; Guthmiller, Jenna J; Sturtz, Alexandria J; Crooks, Sequoia; Johnson, Jordan T; Li, Lei; Lan, Linda Yu-Ling; Pope, Rosemary L; Chen, Yani; Rogers, Kai J; Hemolysis-associated phosphatidylserine exposure promotes polyclonal plasmablast differentiation Journal of Experimental Medicine 218, no. 6 (2021): e20202359. JEM

2020

Li, Lei; Chang, Deborah; Han, Lei; Zhang, Xiaojian; Zaia, Joseph; Wan, Xiu-Feng; Multi-task learning sparse group lasso: a method for quantifying antigenicity of influenza A (H1N1) virus using mutations and variations in glycosylation of Hemagglutinin BMC bioinformatics 21 (2020): 1-22. BMC

Hu, Meng; Yang, Guohua; DeBeauchamp, Jennifer; Crumpton, Jeri Carol; Kim, Hyunsuh; Li, Lei; Wan, Xiu-Feng; Kercher, Lisa; Bowman, Andrew S; Webster, Robert G; HA stabilization promotes replication and transmission of swine H1N1 gamma influenza viruses in ferrets Elife 9 (2020): e56236. eLife

#Knight, Matthew; #Changrob, Siriruk; Li, Lei; Wilson, Patrick C; Imprinting, immunodominance, and other impediments to generating broad influenza immunity Immunological Reviews 296, no. 1 (2020): 191-204. Wiley

Zhang, Xiaojian; Cunningham, Fred L; Li, Lei; Hanson-Dorr, Katie; Liu, Liyuan; Waters, Kaitlyn; Guan, Minhui; Olivier, Alicia K; Schmit, Brandon S; Nolting, Jacqueline M; Tissue tropisms of avian influenza A viruses affect their spillovers from wild birds to pigs Journal of Virology 94, no. 24 (2020): e00847-20. JVI

Guthmiller, Jenna J; Lan, Linda Yu-Ling; Fernández-Quintero, Monica L; Han, Julianna; Utset, Henry A; Bitar, Dalia J; Hamel, Natalie J; Stovicek, Olivia; Li, Lei; Tepora, Micah; Polyreactive Broadly Neutralizing B cells Are Selected to Provide Defense against Pandemic Threat Influenza Viruses Immunity 53, no. 6 (2020): 1230-1244. Pubmed

2019

Han, Lei; Li, Lei; Wen, Feng; Zhong, Lei; Zhang, Tong; Wan, Xiu-Feng; Graph-guided multi-task sparse learning model: a method for identifying antigenic variants of influenza A (H3N2) virus Bioinformatics 35, no. 1 (2019): 77-87. PMC

Guan, Minhui; Hall, Jeffrey S; Zhang, Xiaojian; Dusek, Robert J; Olivier, Alicia K; Liu, Liyuan; Li, Lei; Krauss, Scott; Danner, Angela; Li, Tao; Aerosol transmission of gull-origin Iceland subtype H10N7 influenza A virus in ferrets Journal of virology 93, no. 13 (2019): e00282-19. ResearchGate

Krammer, Florian; Li, Lei; Wilson, Patrick C; Emerging from the shadow of hemagglutinin: neuraminidase is an important target for influenza vaccination Cell host & microbe 26, no. 6 (2019): 712-713. Pubmed

2018

#Kosikova, Martina; #Li, Lei; Radvak, Peter; Ye, Zhiping; Wan, Xiu-Feng; Xie, Hang; Imprinting of repeated influenza A/H3 exposures on antibody quantity and antibody quality: implications for seasonal vaccine strain selection and vaccine performance Clinical infectious diseases 67, no. 10 (2018): 1523-1532. Pubmed

Li, Lei; Bowman, Andrew S; DeLiberto, Thomas J; Killian, Mary L; Krauss, Scott; Nolting, Jacqueline M; Torchetti, Mia Kim; Ramey, Andrew M; Reeves, Andrew B; Stallknecht, David E; Genetic evidence supports sporadic and independent introductions of subtype H5 low-pathogenic avian influenza A viruses from wild birds to domestic poultry in North America Journal of virology 92, no. 19 (2018): e00913-18. JVI

Li, Lei; DeLiberto, Thomas J; Killian, Mary L; Torchetti, Mia K; Wan, Xiu-Feng; Evolutionary pathway for the 2017 emergence of a novel highly pathogenic avian influenza A (H7N9) virus among domestic poultry in Tennessee, United States Virology 525 (2018): 32-39. Pubmed

#Zhang, Xiaojian; #Sun, Hailiang; #Cunningham, Fred L; #Li, Lei; Hanson-Dorr, Katie; Hopken, Matthew W; Cooley, Jim; Long, Li-Ping; Baroch, John A; Li, Tao; Tissue tropisms opt for transmissible reassortants during avian and swine influenza A virus co-infection in swine PLoS Pathogens 14, no. 12 (2018): e1007417. PLoS Pathogen

2017

Martin, Brigitte E; Bowman, Andrew S; Li, Lei; Nolting, Jacqueline M; Smith, David R; Hanson, Larry A; Wan, Xiu-Feng; Detection of antigenic variants of subtype H3 swine influenza A viruses from clinical samples Journal of clinical microbiology 55, no. 4 (2017): 1037-1045. Pubmed

Xie, Hang; Li, Lei; Ye, Zhiping; Li, Xing; Plant, Ewan P; Zoueva, Olga; Zhao, Yangqing; Jing, Xianghong; Lin, Zhengshi; Kawano, Toshiaki; Differential effects of prior influenza exposures on H3N2 cross-reactivity of human postvaccination sera Clinical Infectious Diseases 65, no. 2 (2017): 259-267. Pubmed

Huang, Guangzao; Yuan, Mingshun; Chen, Moliang; Li, Lei; You, Wenjie; Li, Hanjie; Cai, James J; Ji, Guoli; Integrating multiple fitting regression and Bayes decision for cancer diagnosis with transcriptomic data from tumor-educated blood platelets Analyst 142, no. 19 (2017): 3588-3597. Pubmed

2016

Li, Lei; Han, Lei; Wan, Xiu-feng; Identification of glycosylation sites and mutations determining antigenic drift events for influenza A viruses using sparse group lasso regression GLYCOBIOLOGY vol. 26, no. 12, pp. 1393-1394.

2015

Li, Lei; Ji, Guoli; Ye, Congting; Shu, Changlong; Zhang, Jie; Liang, Chun; PlantOrDB: A genome-wide ortholog database for land plants and green algae BMC plant biology 15, no. 1 (2015): 1-11. Pubmed

Ji, Guoli; Li, Lei; Li, Qingshun Q; Wu, Xiangdong; Fu, Jingyi; Chen, Gong; Wu, Xiaohui; PASPA: a web server for mRNA poly (A) site predictions in plants and algae Bioinformatics 31, no. 10 (2015): 1671-1673. Oxford Press

Shi, Jieming; Dong, Min; Li, Lei; Liu, Lin; Luz-Madrigal, Agustin; Tsonis, Panagiotis A; Del Rio-Tsonis, Katia; Liang, Chun; mirPRo–a novel standalone program for differential expression and variation analysis of miRNAs Scientific reports 5, no. 1 (2015): 1-12. Scientific Reports

2014

Ye, Congting; Ji, Guoli; Li, Lei; Liang, Chun; detectIR: a novel program for detecting perfect and imperfect inverted repeats using complex numbers and vector calculation PloS one 9, no. 11 (2014): e113349. PLoS One