Research output per year
Research output per year
- 1 - 50 out of 275 results
Search results
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2024
Computational simulations of bispecific T cell engagers by a multiscale model
Su, Z., Almo, S. C. & Wu, Y., Jan 16 2024, In: Biophysical journal. 123, 2, p. 235-247 13 p.Research output: Contribution to journal › Article › peer-review
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Glutamylation of Npm2 and Nap1 acidic disordered regions increases DNA mimicry and histone chaperone efficiency
Lorton, B. M., Warren, C., Ilyas, H., Nandigrami, P., Hegde, S., Cahill, S., Lehman, S. M., Shabanowitz, J., Hunt, D. F., Fiser, A., Cowburn, D. & Shechter, D., Apr 19 2024, In: iScience. 27, 4, 109458.Research output: Contribution to journal › Article › peer-review
Open Access -
Prediction of interactions between cell surface proteins by machine learning
Su, Z., Griffin, B., Emmons, S. & Wu, Y., Apr 2024, In: Proteins: Structure, Function and Bioinformatics. 92, 4, p. 567-580 14 p.Research output: Contribution to journal › Article › peer-review
Open Access -
Probing the Structure and Functional Properties of the Dropout-Induced Correlated Variability in Convolutional Neural Networks
Pan, X., Coen-Cagli, R. & Schwartz, O., Apr 2024, In: Neural computation. 36, 4, p. 621-644 24 p.Research output: Contribution to journal › Article › peer-review
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Response sub-additivity and variability quenching in visual cortex
Goris, R. L. T., Coen-Cagli, R., Miller, K. D., Priebe, N. J. & Lengyel, M., Apr 2024, In: Nature Reviews Neuroscience. 25, 4, p. 237-252 16 p.Research output: Contribution to journal › Article › peer-review
1 Scopus citations -
2023
Chi3l1 Is a Modulator of Glioma Stem Cell States and a Therapeutic Target in Glioblastoma
Guetta-Terrier, C., Karambizi, D., Akosman, B., Zepecki, J. P., Chen, J. S., Kamle, S., Eduardo Fajardo, J., Fiser, A., Singh, R., Toms, S. A., Lee, C. G., Elias, J. A. & Tapinos, N., Jun 15 2023, In: Cancer research. 83, 12, p. 1984-1999 16 p.Research output: Contribution to journal › Article › peer-review
Open Access7 Scopus citations -
Computational analyses of the interactome between TNF and TNFR superfamilies
Dhusia, K., Su, Z. & Wu, Y., Apr 2023, In: Computational Biology and Chemistry. 103, 107823.Research output: Contribution to journal › Article › peer-review
Open Access -
Dietary iron restriction protects against vaso-occlusion and organ damage in murine sickle cell disease
Li, H., Kazmi, J. S., Lee, S., Zhang, D., Gao, X., Maryanovich, M., Torres, L., Verma, D., Kelly, L., Ginzburg, Y. Z., Frenette, P. S. & Manwani, D., Jan 12 2023, In: Blood. 141, 2, p. 194-199 6 p.Research output: Contribution to journal › Article › peer-review
Open Access4 Scopus citations -
Dissecting the general mechanisms of protein cage self-assembly by coarse-grained simulations
Su, Z. & Wu, Y., Feb 2023, In: Protein Science. 32, 2, e4552.Research output: Contribution to journal › Article › peer-review
Open Access -
How does the same ligand activate signaling of different receptors in TNFR superfamily: a computational study
Su, Z. & Wu, Y., Sep 2023, In: Journal of Cell Communication and Signaling. 17, 3, p. 657-671 15 p.Research output: Contribution to journal › Article › peer-review
Open Access -
Identification and functional validation of an enhancer variant in the 9p21.3 locus associated with glaucoma risk and elevated expression of p16INK4a
Zhu, Y., Tazearslan, C., Rosenfeld, M. G., Fiser, A. & Suh, Y., Sep 2023, In: Aging cell. 22, 9, e13908.Research output: Contribution to journal › Article › peer-review
Open Access -
MAT Gain of Activity Mutation in Helicobacter pylori Is Associated with Resistance to MTAN Transition State Analogues
Feng, M., Namanja-Magliano, H., Rajagopalan, S., Mishra, T., Ducati, R. G., Hirsch, B. M., Kelly, L., Szymczak, W., Fajardo, J. E., Sidoli, S., Fiser, A., Jacobs, W. R. & Schramm, V. L., Apr 14 2023, In: ACS Infectious Diseases. 9, 4, p. 966-978 13 p.Research output: Contribution to journal › Article › peer-review
Open Access2 Scopus citations -
Measuring uncertainty in human visual segmentation
Vacher, J., Launay, C., Mamassian, P. & Coen-Cagli, R., Sep 2023, In: PLoS Computational Biology. 19, 9 September, e1011483.Research output: Contribution to journal › Article › peer-review
Open Access -
Modeling the diverse effects of divisive normalization on noise correlations
Weiss, O., Bounds, H. A., Adesnik, H. & Coen-Cagli, R., Nov 2023, In: PLoS Computational Biology. 19, 11, e1011667.Research output: Contribution to journal › Article › peer-review
Open Access1 Scopus citations -
Optimal selection of suitable templates in protein interface prediction
Grudman, S., Fajardo, J. E. & Fiser, A., Sep 1 2023, In: Bioinformatics. 39, 9, btad510.Research output: Contribution to journal › Article › peer-review
Open Access -
Phenotypic pliancy and the breakdown of epigenetic polycomb mechanisms
Lambros, M., Sella, Y. & Bergman, A., Feb 2023, In: PLoS Computational Biology. 19, 2, e1010889.Research output: Contribution to journal › Article › peer-review
Open Access -
2022
Bacterial hydrogen sulfide drives cryptic redox chemistry in gut microbial communities
Wolfson, S. J., Hitchings, R., Peregrina, K., Cohen, Z., Khan, S., Yilmaz, T., Malena, M., Goluch, E. D., Augenlicht, L. & Kelly, L., Oct 2022, In: Nature Metabolism. 4, 10, p. 1260-1270 11 p.Research output: Contribution to journal › Article › peer-review
Open Access9 Scopus citations -
Bet-hedging antimicrobial strategies in macrophage phagosome acidification drive the dynamics of Cryptococcus neoformans intracellular escape mechanisms
Dragotakes, Q., Jacobs, E., Ramirez, L. S., Yoon, O. I., Perez-Stable, C., Eden, H., Pagnotta, J., Vij, R., Bergman, A., D'Alessio, F. & Casadevall, A., Jul 2022, In: PLoS pathogens. 18, 7, e1010697.Research output: Contribution to journal › Article › peer-review
Open Access6 Scopus citations -
Calibrating vision: Concepts and questions
Bosten, J. M., Coen-Cagli, R., Franklin, A., Solomon, S. G. & Webster, M. A., Dec 2022, In: Vision Research. 201, 108131.Research output: Contribution to journal › Article › peer-review
Open Access3 Scopus citations -
EXCESP: A Structure-Based Online Database for Extracellular Interactome of Cell Surface Proteins in Humans
Dhusia, K., Madrid, C., Su, Z. & Wu, Y., Feb 4 2022, In: Journal of Proteome Research. 21, 2, p. 349-359 11 p.Research output: Contribution to journal › Article › peer-review
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Flexibly regularized mixture models and application to image segmentation
Vacher, J., Launay, C. & Coen-Cagli, R., May 2022, In: Neural Networks. 149, p. 107-123 17 p.Research output: Contribution to journal › Article › peer-review
Open Access9 Scopus citations -
Genome-wide analysis of mitochondrial DNA copy number reveals loci implicated in nucleotide metabolism, platelet activation, and megakaryocyte proliferation
Longchamps, R. J., Yang, S. Y., Castellani, C. A., Shi, W., Lane, J., Grove, M. L., Bartz, T. M., Sarnowski, C., Liu, C., Burrows, K., Guyatt, A. L., Gaunt, T. R., Kacprowski, T., Yang, J., De Jager, P. L., Yu, L., Bergman, A., Xia, R., Fornage, M., Feitosa, M. F., & 32 others, Jan 2022, In: Human Genetics. 141, 1, p. 127-146 20 p.Research output: Contribution to journal › Article › peer-review
Open Access23 Scopus citations -
Genomic surveillance of SARS-CoV-2 during the first year of the pandemic in the Bronx enabled clinical and epidemiological inference
Fels, J. M., Khan, S., Forster, R., Skalina, K. A., Sirichand, S., Fox, A. S., Bergman, A., Mitchell, W. B., Wolgast, L. R., Szymczak, W., Bortz, R. H., Dieterle, M. E., Florez, C., Haslwanter, D., Jangra, R. K., Laudermilch, E., Wirchnianski, A. S., Barnhill, J., Goldman, D. L., Khine, H., & 4 others, Aug 2022, In: Cold Spring Harbor Molecular Case Studies. 8, 5, a006211.Research output: Contribution to journal › Article › peer-review
Open Access -
Integrated structure-based protein interface prediction
Walder, M., Edelstein, E., Carroll, M., Lazarev, S., Fajardo, J. E., Fiser, A. & Viswanathan, R., Dec 2022, In: BMC bioinformatics. 23, 1, 301.Research output: Contribution to journal › Article › peer-review
Open Access1 Scopus citations -
INTERCAAT: identifying interface residues between macromolecules
Grudman, S., Fajardo, J. E. & Fiser, A., Jan 15 2022, In: Bioinformatics. 38, 2, p. 554-555 2 p.Research output: Contribution to journal › Article › peer-review
Open Access2 Scopus citations -
Longitudinally monitored immune biomarkers predict the timing of COVID-19 outcomes
Lasso, G., Khan, S., Allen, S. A., Mariano, M., Florez, C., Orner, E. P., Quiroz, J. A., Quevedo, G., Massimi, A., Hegde, A., Wirchnianski, A. S., Bortz, R. H., Malonis, R. J., Georgiev, G. I., Tong, K., Herrera, N. G., Morano, N. C., Garforth, S. J., Malaviya, A., Khokhar, A., & 12 others, Jan 2022, In: PLoS Computational Biology. 18, 1, e1009778.Research output: Contribution to journal › Article › peer-review
Open Access11 Scopus citations -
Natural and Designed Proteins Inspired by Extremotolerant Organisms Can Form Condensates and Attenuate Apoptosis in Human Cells
Veling, M. T., Nguyen, D. T., Thadani, N. N., Oster, M. E., Rollins, N. J., Brock, K. P., Bethel, N. P., Lim, S., Baker, D., Way, J. C., Marks, D. S., Chang, R. L. & Silver, P. A., Mar 18 2022, In: ACS Synthetic Biology. 11, 3, p. 1292-1302 11 p.Research output: Contribution to journal › Article › peer-review
Open Access8 Scopus citations -
On the formation of ordered protein assemblies in cell–cell interfaces
Boni, N., Shapiro, L., Honig, B., Wu, Y. & Rubinstein, R., Aug 23 2022, In: Proceedings of the National Academy of Sciences of the United States of America. 119, 34, e2206175119.Research output: Contribution to journal › Article › peer-review
Open Access1 Scopus citations -
Resolving the structure of phage–bacteria interactions in the context of natural diversity
Kauffman, K. M., Chang, W. K., Brown, J. M., Hussain, F. A., Yang, J., Polz, M. F. & Kelly, L., Dec 2022, In: Nature communications. 13, 1, 372.Research output: Contribution to journal › Article › peer-review
Open Access37 Scopus citations -
Subventricular zone adult mouse neural stem cells require insulin receptor for self-renewal
Chidambaram, S., Velloso, F. J., Rothbard, D. E., Deshpande, K., Cajuste, Y., Snyder, K. M., Fajardo, E., Fiser, A., Tapinos, N., Levison, S. W. & Wood, T. L., Jun 14 2022, In: Stem Cell Reports. 17, 6, p. 1411-1427 17 p.Research output: Contribution to journal › Article › peer-review
Open Access3 Scopus citations -
The microbiota regulates hematopoietic stem cell fate decisions by controlling iron availability in bone marrow
Zhang, D., Gao, X., Li, H., Borger, D. K., Wei, Q., Yang, E., Xu, C., Pinho, S. & Frenette, P. S., Feb 3 2022, In: Cell Stem Cell. 29, 2, p. 232-247.e7Research output: Contribution to journal › Article › peer-review
Open Access42 Scopus citations -
Understanding the functional role of membrane confinements in TNF-mediated signaling by multiscale simulations
Su, Z., Dhusia, K. & Wu, Y., Dec 2022, In: Communications Biology. 5, 1, 228.Research output: Contribution to journal › Article › peer-review
Open Access4 Scopus citations -
2021
Access to and safety of COVID-19 convalescent plasma in the United States Expanded Access Program: A national registry study
Senefeld, J. W., Johnson, P. W., Kunze, K. L., Bloch, E. M., Helmond, N. V., Golafshar, M. A., Klassen, S. A., Klompas, A. M., Sexton, M. A., Diaz Soto, J. C., Grossman, B. J., Tobian, A. A. R., Goel, R., Wiggins, C. C., Bruno, K. A., van Buskirk, C. M., Stubbs, J. R., Winters, J. L., Casadevall, A., Paneth, N. S., & 38 others, Dec 2021, In: PLoS Medicine. 18, 12, e1003872.Research output: Contribution to journal › Article › peer-review
Open Access39 Scopus citations -
A computational study of co-inhibitory immune complex assembly at the interface between T cells and antigen presenting cells
Su, Z., Dhusia, K. & Wu, Y., Mar 8 2021, In: PLoS Computational Biology. 17, 3, e1008825.Research output: Contribution to journal › Article › peer-review
Open Access4 Scopus citations -
Allosteric regulation of binding specificity of HVEM for CD160 and BTLA ligands upon G89F mutation
Shrestha, R., Garrett-Thomson, S., Liu, W., Almo, S. C. & Fiser, A., Jan 2021, In: Current Research in Structural Biology. 3, p. 337-345 9 p.Research output: Contribution to journal › Article › peer-review
Open Access -
A multiscale study on the mechanisms of spatial organization in ligand-receptor interactions on cell surfaces
Su, Z., Dhusia, K. & Wu, Y., Jan 2021, In: Computational and Structural Biotechnology Journal. 19, p. 1620-1634 15 p.Research output: Contribution to journal › Article › peer-review
Open Access5 Scopus citations -
A structural-based machine learning method to classify binding affinities between TCR and peptide-MHC complexes
Dhusia, K., Su, Z. & Wu, Y., Nov 2021, In: Molecular Immunology. 139, p. 76-86 11 p.Research output: Contribution to journal › Article › peer-review
Open Access4 Scopus citations -
Bacterial Swarmers Enriched During Intestinal Stress Ameliorate Damage
De, A., Chen, W., Li, H., Wright, J. R., Lamendella, R., Lukin, D. J., Szymczak, W. A., Sun, K., Kelly, L., Ghosh, S., Kearns, D. B., He, Z., Jobin, C., Luo, X., Byju, A., Chatterjee, S., San Yeoh, B., Vijay-Kumar, M., Tang, J. X., Prajapati, M., & 2 others, Jul 2021, In: Gastroenterology. 161, 1, p. 211-224 14 p.Research output: Contribution to journal › Article › peer-review
Open Access14 Scopus citations -
Characterizing the function of domain linkers in regulating the dynamics of multi-domain fusion proteins by microsecond molecular dynamics simulations and artificial intelligence
Wang, B., Su, Z. & Wu, Y., Jul 2021, In: Proteins: Structure, Function and Bioinformatics. 89, 7, p. 884-895 12 p.Research output: Contribution to journal › Article › peer-review
Open Access1 Scopus citations -
Classification of protein–protein association rates based on biophysical informatics
Dhusia, K. & Wu, Y., Dec 2021, In: BMC bioinformatics. 22, 1, 408.Research output: Contribution to journal › Article › peer-review
Open Access1 Scopus citations -
Coarse-grained simulations of phase separation driven by DNA and its sensor protein cGAS
Su, Z., Dhusia, K. & Wu, Y., Oct 15 2021, In: Archives of Biochemistry and Biophysics. 710, 109001.Research output: Contribution to journal › Article › peer-review
4 Scopus citations -
Computational Assessment of Protein–protein Binding Affinity by Reversely Engineering the Energetics in Protein Complexes
Wang, B., Su, Z. & Wu, Y., Dec 2021, In: Genomics, Proteomics and Bioinformatics. 19, 6, p. 1012-1022 11 p.Research output: Contribution to journal › Article › peer-review
Open Access4 Scopus citations -
Computational Simulation of Holin S105 in Membrane Bilayer and Its Dimerization Through a Helix-Turn-Helix Motif
Zhou, B., Wu, Y. & Su, Z., Aug 2021, In: Journal of Membrane Biology. 254, 4, p. 397-407 11 p.Research output: Contribution to journal › Article › peer-review
Open Access1 Scopus citations -
Degradation of host translational machinery drives tRNA acquisition in viruses
Yang, J. Y., Fang, W., Miranda-Sanchez, F., Brown, J. M., Kauffman, K. M., Acevero, C. M., Bartel, D. P., Polz, M. F. & Kelly, L., Aug 18 2021, In: Cell Systems. 12, 8, p. 771-779.e5Research output: Contribution to journal › Article › peer-review
Open Access21 Scopus citations -
Emerging Adaptive Strategies Under Temperature Fluctuations in a Laboratory Evolution Experiment of Escherichia Coli
Lambros, M., Pechuan-Jorge, X., Biro, D., Ye, K. & Bergman, A., Oct 22 2021, In: Frontiers in Microbiology. 12, 724982.Research output: Contribution to journal › Article › peer-review
Open Access5 Scopus citations -
Endotoxin Acts Synergistically with Clostridioides difficile Toxin B to Increase Interleukin 1β Production: A Potential Role for the Intestinal Biome in Modifying the Severity of C. difficile Colitis
Htwe, P., Aung, H., Kywe, B., Niang, P. T., Oo, T. S., Monhandas, S., Kelly, L. & Goldman, D. L., Nov 1 2021, In: Journal of Infectious Diseases. 224, 9, p. 1556-1565 10 p.Research output: Contribution to journal › Article › peer-review
1 Scopus citations -
Estimating the accuracy of pharmacophore-based detection of cognate receptor-ligand pairs in the immunoglobulin superfamily
Gil, N., Shrestha, R. & Fiser, A., Jun 2021, In: Proteins: Structure, Function and Bioinformatics. 89, 6, p. 632-638 7 p.Research output: Contribution to journal › Article › peer-review
Open Access -
Flexible contextual modulation of naturalistic texture perception in peripheral vision
Herrera-Esposito, D., Coen-Cagli, R. & Gomez-Sena, L., 2021, In: Journal of Vision. 21, 1, p. 1-26 26 p.Research output: Contribution to journal › Article › peer-review
Open Access5 Scopus citations -
MAEA is an E3 ubiquitin ligase promoting autophagy and maintenance of haematopoietic stem cells
Wei, Q., Pinho, S., Dong, S., Pierce, H., Li, H., Nakahara, F., Xu, J., Xu, C., Boulais, P. E., Zhang, D., Maryanovich, M., Cuervo, A. M. & Frenette, P. S., Dec 1 2021, In: Nature communications. 12, 1, 2522.Research output: Contribution to journal › Article › peer-review
Open Access22 Scopus citations -
Mechanistic dissection of spatial organization in NF-κB signaling pathways by hybrid simulations
Wu, Y., Dhusia, K. & Su, Z., May 1 2021, In: Integrative Biology. 13, 5, p. 109-120 12 p.Research output: Contribution to journal › Article › peer-review
Open Access1 Scopus citations