2025
Kothiwal, D.1, Kollasch, A. W., Hollmer, N.1, Ghosh, A.1, Zhang, R.1, Anuganti, M.1, Paul, S. B., Zagar, Y., Abdollahi, M.1, Anderson, Z.1, Belay, F.1, Salotto, M.1, Ulmer, S.1, Abdelalim, Y. A.1, Kumar, S.1, Vangala, M.1, Yang, C.1, Chedotal, A., Jardine, J. G., , , D. J.1, , , , , D. S. & Meijers, R.1. (2025). High-Throughput Machine Learning-Aided Antibody Discovery for Cell Surface Antigens. bioRxiv, 2025.05.15.650607. https://doi.org/10.1101/2025.05.15.650607 2
Zhu, S.1, Jaworski, A. & Meijers, R1. (2025). Expanding ligand-receptor interaction networks for axon guidance: Structural insights into signal crosstalk and specificity. Current Opinion in Neurobiology, 92, 102999. https://doi.org/10.1016/j.conb.2025.102999 2
2024
Erasmus, M. F., Spector, L., Ferrara, F., DiNiro, R., Pohl, T. J., Perea-Schmittle, K., Wang, W., Tessier, P. M., Richardson, C., Turner, L., Kumar, S.1, Bedinger, D., Sormanni, P., Fernández-Quintero, M. L., Ward, A. B., Loeffler, J. R., Swanson, O. M., Deane, C. M., Raybould, M. I. J., . . . . . . Bradbury, A. R. M. (2024). AIntibody: an experimentally validated in silico antibody discovery design challenge. Nature Biotechnology, 42(11), 1637–1642. https://doi.org/10.1038/s41587-024-02469-9
Kahn, R. A., Virk, H., Laflamme, C., Houston, D. W., Polinski, N. K., Meijers, R.1, Levey, A. I., Saper, C. B., Errington, T. M., Turn, R. E., Bandrowski, A., Trimmer, J. S., Rego, M., Freedman, L. P., Ferrara, F., Bradbury, A. R., Cable, H., & Longworth, S. (2024). Antibody characterization is critical to enhance reproducibility in biomedical research. eLife, 13. https://doi.org/10.7554/elife.100211
Colom, M. S.1, Vučinić, J., Adolf‐Bryfogle, J.1, Bowman, J. W.1, Verel, S., Moczygemba, I.1, Schiex, T., Simoncini, D., & Bahl, C. D.1 (2024). Complete combinatorial mutational enumeration of a protein functional site enables sequence‐landscape mapping and identifies highly‐mutated variants that retain activity. Protein Science, 33(8). https://doi.org/10.1002/pro.5109
Hao, Y., Yan, J., Fraser, C., Jiang, A., Anuganti, M.1, Zhang, R.1, Lloyd, K.1, Jardine, J.1, Coppola, J.1, Meijers, R.1, Li, J., & Springer, T. A.1 (2024). Synthetic integrin antibodies discovered by yeast display reveal αV subunit pairing preferences with β subunits. mAbs, 16(1). https://doi.org/10.1080/19420862.2024.2365891 2
Ghosh, A.1, Yang, C.1, Lloyd, K.1, & Meijers, R.1 (2024). High-Throughput protein Expression screening of Cell-Surface protein ectodomains. Methods in Molecular Biology, 301–316. https://doi.org/10.1007/978-1-0716-3878-1_19
Fram, B., Su, Y., Truebridge, I.1, Riesselman, A. J., Ingraham, J. B., Passera, A., Napier, E., Thadani, N. N., Lim, S., Roberts, K., Kaur, G., Stiffler, M. A., Marks, D. S., Bahl, C. D.1, Khan, A. R., Sander, C., & Gauthier, N. P. (2024). Simultaneous enhancement of multiple functional properties using evolution-informed protein design. Nature Communications, 15(1). https://doi.org/10.1038/s41467-024-49119-x
Qin, X., Lam, A., Zhang, X., Sengupta, S., Iorgulescu, J. B., Ni, H., Das, S., Rager, M., Zhou, Z., Zuo, T., Meara, G. K., Floru, A. E., Kemet, C., Veerapaneni, D., Kashy, D., Lin, L., Lloyd, K.1, Kwok, L., Smith, K. S., . . .Meijers, R.1 . . . Feng, H. (2024). CKLF instigates a “cold” microenvironment to promote MYCN-mediated tumor aggressiveness. Science Advances, 10(11). https://doi.org/10.1126/sciadv.adh9547 2
Priest, J. M., Nichols, E. L., Smock, R. G., Hopkins, J. B., Mendoza, J. L., Meijers, R.1, Shen, K., & Özkan, E. (2024). Structural insights into the formation of repulsive netrin guidance complexes. Science Advances, 10(7). https://doi.org/10.1126/sciadv.adj8083
2023
Kibria, M. G., Lavine, C. L., Tang, W., Wang, S., Gao, H., Shi, W., Zhu, H.1, Voyer, J., Rits‐Volloch, S., Keerti, N., Bi, C., Peng, H., Wesemann, D. R., Lu, J., Xie, H., Seaman, M. S., & Chen, B. (2023). Antibody‐mediated SARS‐CoV‐2 entry in cultured cells. EMBO Reports, 24(12). https://doi.org/10.15252/embr.202357724
Blanchet, C. E., Round, A., Mertens, H. D. T., Ayyer, K., Graewert, M., Awel, S., Franke, D., Dörner, K., Bajt, S., Bean, R., Custódio, T. F., De Wijn, R., Juncheng, E., Henkel, A., Gruzinov, A., Jeffries, C. M., Kim, Y., Kirkwood, H., Kloos, M., . . . Meijers, R.1 . . . Svergun, D. (2023). Form factor determination of biological molecules with X-ray free electron laser small-angle scattering (XFEL-SAS). Communications Biology, 6(1). https://doi.org/10.1038/s42003-023-05416-7
Shi, W., Cai, Y., Zhu, H.1, Peng, H., Voyer, J., Rits-Volloch, S., Cao, H., Mayer, M. L., Song, K., Xu, C., Lu, J., Zhang, J., & Chen, B. (2023). Cryo-EM structure of SARS-CoV-2 postfusion spike in membrane. Nature, 619(7969), 403–409. https://doi.org/10.1038/s41586-023-06273-4
Zhang, J., Tang, W., Gao, H., Lavine, C. L., Shi, W., Peng, H., Zhu, H.1, Anand, K.1, Kosikova, M., Kwon, H. J., Tong, P., Gautam, A., Rits-Volloch, S., Wang, S., Mayer, M. L., Wesemann, D. R., Seaman, M. S., Lu, J., Xiao, T., . . . Chen, B. (2023). Structural and functional characteristics of the SARS-CoV-2 Omicron subvariant BA.2 spike protein. Nature Structural & Molecular Biology, 30(7), 980–990. https://doi.org/10.1038/s41594-023-01023-6
Guédez, G., Loers, G., Jeffries, C. M., Kozak, S., Meijers, R.1, Svergun, D. I., Schachner, M., & Löw, C. (2023). X‐ray structure and function of fibronectin domains two and three of the neural cell adhesion molecule L1. The FASEB Journal, 37(3). https://doi.org/10.1096/fj.202201511r
2022
Jo, M. H., Li, J., Jaumouillé, V., Hao, Y., Coppola, J.1, Yan, J., Waterman, C. M., Springer, T. A.1, & Ha, T. (2022). Single-molecule characterization of subtype-specific β1 integrin mechanics. Nature Communications, 13(1). https://doi.org/10.1038/s41467-022-35173-w 2
Gura, T.1, Acker-Palmer, A., Kolodkin, A., Meijers, R.1, Mizuno, N., Seiradake, E., & Tessier-Lavigne, M. (2022). Molecular neuroscience community shares perspectives. Neuron, 110(22), 3656–3660. https://doi.org/10.1016/j.neuron.2022.10.029
Zhu, S.1, Sridhar, A., Teng, J., Howard, R. J., Lindahl, E., & Hibbs, R. E. (2022). Structural and dynamic mechanisms of GABAA receptor modulators with opposing activities. Nature Communications, 13(1). https://doi.org/10.1038/s41467-022-32212-4
2021
Müller, S., Ackloo, S., Chawaf, A. A., Al-Lazikani, B., Antolin, A., Baell, J. B., Beck, H., Beedie, S., Betz, U. a. K., Bezerra, G. A., Brennan, P. E., Brown, D., Brown, P. J., Bullock, A. N., Carter, A. J., Chaikuad, A., Chaineau, M., Ciulli, A., Collins, I., . . . Fuchs, S. M.1. . . Arrowsmith, C. H. (2021). Target 2035 – update on the quest for a probe for every protein. RSC Medicinal Chemistry, 13(1), 13–21. https://doi.org/10.1039/d1md00228g
Zhang, J., Xiao, T., Cai, Y., Lavine, C. L., Peng, H., Zhu, H.1, Anand, K.1, Tong, P., Gautam, A., Mayer, M. L., Walsh, R. M., Rits-Volloch, S., Wesemann, D. R., Yang, W.1, Seaman, M. S., Lu, J., & Chen, B. (2021). Membrane fusion and immune evasion by the spike protein of SARS-CoV-2 Delta variant. Science, 374(6573), 1353–1360. https://doi.org/10.1126/science.abl9463
Cai, Y., Zhang, J., Xiao, T., Lavine, C. L., Rawson, S., Peng, H., Zhu, H.1, Anand, K.1, Tong, P., Gautam, A., Lu, S., Sterling, S. M., Walsh, R. M., Rits-Volloch, S., Lu, J., Wesemann, D. R., Yang, W.1, Seaman, M. S., & Chen, B. (2021). Structural basis for enhanced infectivity and immune evasion of SARS-CoV-2 variants. Science, 373(6555), 642–648. https://doi.org/10.1126/science.abi9745
Stewart, T., Wolfe, B. E., & Fuchs, S. M.1 (2021). Defining the role of the polyasparagine repeat domain of the S. cerevisiae transcription factor Azf1p. PLoS ONE, 16(5), e0247285. https://doi.org/10.1371/journal.pone.0247285
Zhang, J., Cai, Y., Xiao, T., Lu, J., Peng, H., Sterling, S. M., Walsh, R. M., Rits-Volloch, S., Zhu, H.1, Woosley, A. N.1, Yang, W.1, Sliz, P., & Chen, B. (2021). Structural impact on SARS-CoV-2 spike protein by D614G substitution. Science, 372(6541), 525–530. https://doi.org/10.1126/science.abf2303
Meinen, B. A., & Bahl, C. D.1 (2021). Breakthroughs in computational design methods open up new frontiers for de novo protein engineering. Protein Engineering Design and Selection, 34. https://doi.org/10.1093/protein/gzab007
2020
Adolf-Bryfogle, J.1, Teets, F. D.1, & Bahl, C. D.1 (2020). Toward complete rational control over protein structure and function through computational design. Current Opinion in Structural Biology, 66, 170–177. https://doi.org/10.1016/j.sbi.2020.10.015
Gao, M., Mackley, I. G. P., Mesbahi‐Vasey, S.1, Bamonte, H. A., Struyvenberg, S. A., Landolt, L., Pederson, N. J., Williams, L. I., Bahl, C. D.1, Brooks, L., & Amacher, J. F. (2020). Structural characterization and computational analysis of PDZ domains in Monosiga brevicollis. Protein Science, 29(11), 2226–2244. https://doi.org/10.1002/pro.3947
Stewart, T., Exner, A. E., Patnaik, P., & Fuchs, S. M.1 (2020). Contractions of the C-Terminal domain ofSaccharomyces cerevisiaeRPB1P are mediated by RAD5P. G3 Genes Genomes Genetics, 10(7), 2543–2551. https://doi.org/10.1534/g3.120.401409
Anjanappa, R., Garcia-Alai, M., Kopicki, J., Lockhauserbäumer, J., Aboelmagd, M., Hinrichs, J., Nemtanu, I. M., Uetrecht, C., Zacharias, M., Springer, S., & Meijers, R.1 (2020). Structures of peptide-free and partially loaded MHC class I molecules reveal mechanisms of peptide selection. Nature Communications, 11(1). https://doi.org/10.1038/s41467-020-14862-4
2019
Ford, A. S.1, Weitzner, B. D., & Bahl, C. D.1 (2019). Integration of the Rosetta suite with the python software stack via reproducible packaging and core programming interfaces for distributed simulation. Protein Science, 29(1), 43–51. https://doi.org/10.1002/pro.3721
2018
Buchko, G. W., Pulavarti, S. V., Ovchinnikov, V., Shaw, E. A., Rettie, S. A., Myler, P. J., Karplus, M., Szyperski, T., Baker, D., & Bahl, C. D.1 (2018). Cytosolic expression, solution structures, and molecular dynamics simulation of genetically encodable disulfide‐rich de novo designed peptides. Protein Science, 27(9), 1611–1623. https://doi.org/10.1002/pro.3453
Lau, Y. K., Baytshtok, V., Howard, T. A., Fiala, B. M., Johnson, J. M., Carter, L. P., Baker, D., Lima, C. D., & Bahl, C. D.1 (2018). Discovery and engineering of enhanced SUMO protease enzymes. Journal of Biological Chemistry, 293(34), 13224–13233. https://doi.org/10.1074/jbc.ra118.004146
1IPI-affiliated researcher
2Study uses IPI antibodies