Publications
Below is a list of our recent publications, sorted from latest to oldest.
2024
- Uncovering the dual roles of peripheral immune cells and their connections to brain cells in stroke and post-stroke stages through single-cell sequencing
Zheng Xu, Fan Yang#, Lifang Zheng#, Frontiers in Neuroscience, Nov. 18:e1443438.
- An in silico design of a vaccine against all serotypes of the Dengue virus based on virtual screening of B-Cell and T-Cell epitopes
Hikmat Ullah, Shaukat Ullah, Jinze Li, Fan Yang#, Lei Tan#, Biology, Aug. 13(9): p. 681.
- Fast physic-informed mixer architecture for color Lensfree holographic reconstruction
Jiaqian Wang, Guang Zeng, Wang Zhang, JiaYe He, Fan Yang, Yaoqin Xie, Wenjian Qin, Optics and Lasers in Engineering, 2024, 173: 107897.
2023
- Clonal evolution and stereotyped sequences of human IgE lineages in aeroallergen-specific immunotherapy
Ramona A. Hoh, Linnea Thörnqvist, Fan Yang, Magdalena Godzwon, Jasmine J. King, Ji-Yeun Lee, Lennart Greiff, Scott D. Boyd, Mats Ohlin, Journal of Allergy and Clinical Immunology, Feb 23. DOI: 10.1016/j.jaci.2023.02.009.
- Robust T Cell Responses to the Pfizer/BioNTech Vaccine Compared to Infection and Evidence of Attenuated CD8 T Cell Responses Due to COVID-19
Fei Gao, Vamsee Mallajoysula, Prabhu Arunachalam, Kattria van der Ploeg, Monali Manohar, Katharina Röltgen, Fan Yang, Oliver F. Wirz, Ramona Hoh, Emily Haraguchi, Ji Yeun Lee, Richard Willis, Vasanthi Ramachandiran, Jiefu Li, Karan Raj Kathuria, Chunfeng Li, Alexandra S. Lee, Mihir M. Shah, Sayantani B. Sindher, Joseph Gonzalez, John D. Altman, Taia Wang, Scott D. Boyd, Bali Pulendran, Prasanna Jagannathan, Kari Nadeau, Mark M. Davis, Immunity, 2023, 56 (4), 864-878. e4.
- Constructing metabolism-protein interaction relationship to identify glioma prognosis using deep learning
Qingpei Lai, Xiang Liu, Fan Yang, Jie Li, Yaoqin Xie, Wenjian Qin, Computers in Biology and Medicine, 2023, 158: 106875.
2022
- Immune imprinting, breadth of variant recognition and germinal center response in human SARS-CoV-2 infection and vaccination
Katharina Röltgen*, Sandra C. A. Nielsen*, Oscar Silva*, Sheren F. Younes*, Maxim Zaslavsky, Cristina Costales, Fan Yang, Oliver F. Wirz, Daniel Solis, Ramona A. Hoh, Aihui Wang, Prabhu S. Arunachalam, Deana Colburg, Shuchun Zhao, Emily Haraguchi, Alexandra S. Lee, Mihir M. Shah, Monali Manohar, Iris Chang, Fei Gao, Vamsee Mallajosyula, Chunfeng Li, James Liu, Massa J. Shoura, Sayantani B. Sindher, Ella Parsons, Naranjargal J. Dashdorj, Naranbaatar D. Dashdorj, Robert Monroe, Geidy E. Serrano, Thomas G. Beach, R. Sharon Chinthrajah, Gregory W. Charville, Jim L. Wilbur, Jacob Wohlstadter, Mark M. Davis, Bali Pulendran, Megan L. Troxell, George B. Sigal, Yasodha Natkunam, Benjamin A. Pinsky, Kari C. Nadeau#, Scott D. Boyd#, Cell, 2022, 185 (6), 1025-+.
- Multiple early factors anticipate post-acute COVID-19 sequelae
Yapeng Su#, Dan Yuan, Daniel G Chen, Rachel H Ng, Kai Wang, Jongchan Choi, Sarah Li, Sunga Hong, Rongyu Zhang, Jingyi Xie, Sergey A Kornilov, Kelsey Scherler, Ana Jimena Pavlovitch-Bedzyk, Shen Dong, Christopher Lausted, Inyoul Lee, Shannon Fallen, Chengzhen L Dai, Priyanka Baloni, Brett Smith, Venkata R Duvvuri, Kristin G Anderson, Jing Li, Fan Yang, Caroline J Duncombe, Denise J McCulloch, Clifford Rostomily, Pamela Troisch, Jing Zhou, Sean Mackay, Quinn DeGottardi, Damon H May, Ruth Taniguchi, Rachel M Gittelman, Mark Klinger, Thomas M Snyder, Ryan Roper, Gladys Wojciechowska, Kim Murray, Rick Edmark, Simon Evans, Lesley Jones, Yong Zhou, Lee Rowen, Rachel Liu, William Chour, Heather A Algren, William R Berrington, Julie A Wallick, Rebecca A Cochran, Mary E Micikas, Terri Wrin, Christos J Petropoulos, Hunter R Cole, Trevan D Fischer, Wei Wei, Dave SB Hoon, Nathan D Price, Naeha Subramanian, Joshua A Hill, Jennifer Hadlock, Andrew T Magis, Antoni Ribas, Lewis L Lanier, Scott D Boyd, Jeffrey A Bluestone, Helen Chu, Leroy Hood, Raphael Gottardo, Philip D Greenberg, Mark M Davis, Jason D Goldman#, James R Heath#, Cell, 2022, 185 (5), 881-895. e20.
- Reinfection with SARS-CoV-2 and waning humoral immunity: a case report
Jason D Goldman, Kai Wang, Katharina Röltgen, Sandra CA Nielsen, Jared C Roach#, Samia N Naccache, Fan Yang, Oliver F Wirz, Kathryn E Yost, Ji-Yeun Lee, Kelly Chun, Terri Wrin, Christos J Petropoulos, Inyoul Lee, Shannon Fallen, Paula M Manner, Julie A Wallick, Heather A Algren, Kim M Murray, Jennifer Hadlock, Daniel Chen, Chengzhen L Dai, Dan Yuan, Yapeng Su, Joshua Jeharajah, William R Berrington, George P Pappas, Sonam T Nyatsatsang, Alexander L Greninger, Ansuman T Satpathy, John S Pauk, Scott D Boyd, James R Heath, Vaccines, 2022, 11 (1), 5.
2021
- Shared B cell memory to coronaviruses and other pathogens varies in human age groups and tissues
Fan Yang#, Sandra C. A. Nielsen, Ramona A. Hoh, Katharina Röltgen, Oliver Fabian Wirz, Emily Haraguchi, Grace H Jean, Ji-Yeun Lee, Tho D. Pham, Katherine J.L. Jackson, Krishna M. Roskin, Yi Liu, Khoa Nguyen, Rober S. Ohgami, Kari C. Nadeau, Eleanor L. Marshall, Claus U. Niemann, Julie Parsonnet, Scott D. Boyd#, Science, 2021, 372(6543): p. 738.
- Modeling human adaptive immune responses with tonsil organoids
Lisa E Wagar, Ameen Salahudeen, Christian M Constantz, Ben S Wendel, Michael M Lyons, Vamsee Mallajosyula, Lauren P Jatt, Julia Z Adamska, Lisa K Blum, Neha Gupta, Katherine JL Jackson, Fan Yang, Katharina Röltgen, Krishna M Roskin, Kelly M Blaine, Kara D Meister, Iram N Ahmad, Mario Cortese, Emery G Dora, Sean N Tucker, Anne I Sperling, Aarti Jain, D Huw Davies, Philip L Felgner, Gregory B Hammer, Peter S Kim, William H Robinson, Scott D Boyd, Calvin J Kuo, Mark M Davis, Nature Medicine, 2021, 27 (1), 125-135.
2020
- Human B cell clonal expansion and convergent antibody responses to SARS-CoV-2
Sandra C. A. Nielsen*, Fan Yang*, Katherine J. L. Jackson*, Ramona A. Hoh*, Katharina Röltgen, Bryan Stevens, Ji-Yeun Lee, Arjun Rustagi, Angela J. Rogers, Abigail E. Powell, Javaria Najeeb, Ana R. Otrelo Cardoso, Kathryn E. Yost, Bence Daniel, Howard Y. Chang, Ansuman T. Satpathy, Theodore S. Jardetzky, Peter S. Kim, Taia T. Wang, Benjamin A. Pinsky, Catherine A. Blish#, Scott D. Boyd#, Cell Host & Microbe, 2020, 28 (4), 516-525. e5.
- Pan-cancer analysis of whole genomes
Nature, 578 (7793), 82-93, 2020.
2019 and before
- Quantifying Immune-Based Counterselection of Somatic Mutations
Fan Yang, Dae-Kyum Kim, Hidewaki Nakagawa, Seiya Imoto, Lincoln Stein, Frederick P. Roth, PLoS Genetics, 2019 July, 15(7): e1008227.
- Identifying pathogenicity of human variants via paralog-based yeast complementation
Fan Yang, Song Sun, Guihong Tan, Michael Costanzo, David E. Hill, Marc Vidal, Brenda J. Andrews, Charles Boone, Frederick P. Roth, PLoS Genetics, 2017 May, 13(5), e1006779.
- A framework for exhaustively mapping functional missense variants
Jochen Weili, Song Sun, Atina G. Cote, Jennifer Knapp, Marta Verby, Joseph Mellor, Yingzhou Wu, Jesse D. Bloom, Carles Pons, Cassandra Wong, Natascha van Lieshout, Fan Yang, Murat Tasan, Guihong Tan, Shan Yang, Robert Nussbaum, Marc Vidal, David E. Hill, Patrick Aloy, Frederick P. Roth, Molecular Systems Biology, 2017 Dec, 13 (12), 957.
- An extended set of yeast-based functional assays accurately identifies human disease mutations
Song Sun, Fan Yang, Guihong Tan, Michael Costanzo, Rose Oughtred, Jodi Hirschman, Chandra Theesfeld, Paul Bansal, Nidhi Sahni, Song Yi, Analyn Yu, Tanya Tyagi, David E. Hill, Marc Vidal, Brenda J. Andrews, Charles Boone, Kara Dolinski, Frederick P. Roth, Genome Research, 2016 May;26(5):670-80. DOI: 10.1101/gr.192526.115
- Widespread expansion of protein interaction capabilities by alternative splicing
Xinping Yang*, Jasmin Coulombe-Huntington*, Shuli Kang*, Gloria M. Sheynkman*, Tong Hao*, Aaron Richardson, Song Sun, Fan Yang, Yun A. Shen, Ryan R. Murray, Kerstin Spirohn, Bridget E. Begg, Miquel Duran-Frigola, Andrew MacWilliams, Samuel J. Pevzner, Quan Zhong, Shelly A. Trigg, Stanley Tam, Lila Ghamsari, Nidhi Sahni, Song Yi, Maria D. Rodriguez, Dawit Balcha, Guihong Tan, Michael Costanzo, Brenda Andrews, Charles Boone, Xianghong J. Zhou, Kourosh Salehi-Ashtiani, Benoit Charloteaux, Alyce A. Chen, Michael A. Calderwood, Patrick Aloy, Frederick P. Roth, David E. Hill, Lilia M. Iakoucheva, Yu Xia and Marc Vidal, Cell, 2016 Feb 11;164(4):805-817. DOI: 10.1016/j.cell.2016.01
- Protein Domain-Level Landscape of Cancer-Type-Specific Somatic Mutations
Fan Yang, Evangelia Petsalaki, Thomas Rolland, David E. Hill, Marc Vidal, Frederick P. Roth, PLoS Computational Biology, 2015 Mar, 11(3): e1004147. DOI: 10.1371/journal.pcbi.1004147
- Widespread macromolecular interaction perturbations in human genetic disorders
Nidhi Sahni*, Song Yi*, Mikko Taipale*, Juan I. Fuxman Bass*, Jasmin Coulombe-Huntington*, Fan Yang, Jian Peng, Jochen Weile, Atanas Kamburov, Irina Krykbaeva, George Tucker, Vikram Khurana, Georgios I. Karras, Amitabh Sharma, Yang-Yu Liu, Nozomu Yachie, Quan Zhong, Yun Shen, Alexandre Palagi, Adriana San-Miguel, Changyu Fan, Dawit Balcha, Amelie Dricot, Daniel M. Jordan, Jennifer M. Walsh, Akash A. Shah, Xinping Yang, Ani Stoyanova, Alex Leighton, Michael A. Calderwood, Yves Jacob, Michael E. Cusick, Luke J. Whitesell, Shamil Sunyaev, Benoit Charloteaux, Bonnie Berger, David E. Hill, Albert-László Barabási, Tong Hao, Frederick P. Roth, Yu Xia, Albertha J.M. Walhout, Susan Lindquist, and Marc Vidal, Cell, 2015 Apr 23;161(3):647-60. DOI: 10.1016/j.cell.2015.04.013
- Impact of the interaction between 3-UTR SNPs and microRNA on the expression of human xenobiotic metabolism enzyme (XMEs) genes
Rongrong Wei, Fan Yang, Thomas J. Urban, Lang Li, Naga Chalasani, David A. Flockhart, Wanqing Liu, Frontiers in Pharmacogenetics and Pharmacogenomics, 2012 Nov, 3(248), DOI: 10.3389/fgene.2012.00248.
- In Situ Demonstration and Quantitative Analysis of the Intrinsic Properties of Glycoside Hydrolases
Xiaomei Zhang, Ning Liu, Fan Yang, Jinghua Li, Lushan Wang, Guanjun Chen, and Peiji Gao, ELECTROPHORESIS, 2012 Jan, 33(2), 280-7. DOI: 10.1002/elps.201100333
- Mechanisms classification for glycoside hydrolases by sequence and structure features using computational methods
Fan Yang, Lin Wang, International Journal of Data Mining and Bioinformatics, 2014 Nov, 9(4): 444-457.
