☰

Cinque S. Soto, Ph.D. - Publications

Affiliations: 
Columbia University, New York, NY 
Area:
computational biophysics and bioinformatics
Tree Info Similar researchers PubMed Report error

36 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Gilchuk P, Bombardi RG, Erasmus JH, Tan Q, Nargi R, Soto C, Abbink P, Suscovich TJ, Durnell LA, Khandhar A, Archer J, Liang J, Fouch ME, Davidson E, Doranz BJ, et al. Integrated pipeline for the accelerated discovery of antiviral antibody therapeutics. Nature Biomedical Engineering. PMID 32747832 DOI: 10.1038/S41551-020-0594-X  0.338
2020 Soto C, Finn JA, Willis JR, Day SB, Sinkovits RS, Jones T, Schmitz S, Meiler J, Branchizio A, Crowe JE. PyIR: a scalable wrapper for processing billions of immunoglobulin and T cell receptor sequences using IgBLAST. Bmc Bioinformatics. 21: 314. PMID 32677886 DOI: 10.1186/S12859-020-03649-5  0.342
2020 Schmitz S, Soto C, Crowe JE, Meiler J. Human-likeness of antibody biologics determined by back-translation and comparison with large antibody variable gene repertoires. Mabs. 12: 1758291. PMID 32397786 DOI: 10.1080/19420862.2020.1758291  0.368
2019 Sevy AM, Soto C, Bombardi RG, Meiler J, Crowe JE. Immune repertoire fingerprinting by principal component analysis reveals shared features in subject groups with common exposures. Bmc Bioinformatics. 20: 629. PMID 31801472 DOI: 10.1186/S12859-019-3281-8  0.32
2019 Bennett MR, Dong J, Bombardi RG, Soto C, Parrington HM, Nargi RS, Schoeder CT, Nagel MB, Schey KL, Meiler J, Skaar EP, Crowe JE. Human Gene-Encoded Human Monoclonal Antibodies against Staphylococcus aureus IsdB Use at Least Three Distinct Modes of Binding To Inhibit Bacterial Growth and Pathogenesis. Mbio. 10. PMID 31641091 DOI: 10.1128/Mbio.02473-19  0.305
2019 Lemmin T, Soto CS. Glycosylator: a Python framework for the rapid modeling of glycans. Bmc Bioinformatics. 20: 1-7. PMID 31640540 DOI: 10.1186/S12859-019-3097-6  0.455
2018 Janus BM, Dyk Nv, Zhao X, Howell KA, Soto C, Aman MJ, Li Y, Fuerst TR, Ofek G. Structural basis for broad neutralization of ebolaviruses by an antibody targeting the glycoprotein fusion loop. Nature Communications. 9: 3934-3934. PMID 30258051 DOI: 10.1038/S41467-018-06113-4  0.361
2017 Lemmin T, Soto C, Stuckey J, Kwong PD. Microsecond Dynamics and Network Analysis of the HIV-1 SOSIP Env Trimer Reveal Collective Behavior and Conserved Microdomains of the Glycan Shield. Structure (London, England : 1993). PMID 28890362 DOI: 10.1016/J.Str.2017.07.018  0.343
2017 Zhou T, Doria-Rose NA, Cheng C, Stewart-Jones GBE, Chuang GY, Chambers M, Druz A, Geng H, McKee K, Kwon YD, O'Dell S, Sastry M, Schmidt SD, Xu K, Chen L, ... ... Soto C, et al. Quantification of the Impact of the HIV-1-Glycan Shield on Antibody Elicitation. Cell Reports. 19: 719-732. PMID 28445724 DOI: 10.1016/J.Celrep.2017.04.013  0.334
2017 Shahzad-Ul-Hussan S, Sastry M, Lemmin T, Soto C, Loesgen S, Scott DA, Davison JR, O'Connor R, Kwong PD, Bewley CA. NMR insights into the conformational properties of Man-9 and its recognition by two HIV binding proteins. Chembiochem : a European Journal of Chemical Biology. PMID 28166380 DOI: 10.1002/Cbic.201600665  0.332
2017 Kwong PD, Chuang GY, DeKosky BJ, Gindin T, Georgiev IS, Lemmin T, Schramm CA, Sheng Z, Soto C, Yang AS, Mascola JR, Shapiro L. Antibodyomics: bioinformatics technologies for understanding B-cell immunity to HIV-1. Immunological Reviews. 275: 108-128. PMID 28133812 DOI: 10.1111/Imr.12480  0.353
2016 Joyce MG, Zhang B, Ou L, Chen M, Chuang GY, Druz A, Kong WP, Lai YT, Rundlet EJ, Tsybovsky Y, Yang Y, Georgiev IS, Guttman M, Lees CR, Pancera M, ... ... Soto C, et al. Iterative structure-based improvement of a fusion-glycoprotein vaccine against RSV. Nature Structural & Molecular Biology. PMID 27478931 DOI: 10.1038/Nsmb.3267  0.34
2016 Davenport TM, Gorman J, Joyce MG, Zhou T, Soto C, Guttman M, Moquin S, Yang Y, Zhang B, Doria-Rose NA, Hu SL, Mascola JR, Kwong PD, Lee KK. Somatic Hypermutation-Induced Changes in the Structure and Dynamics of HIV-1 Broadly Neutralizing Antibodies. Structure (London, England : 1993). PMID 27477385 DOI: 10.1016/J.Str.2016.06.012  0.367
2016 Joyce MG, Wheatley AK, Thomas PV, Chuang GY, Soto C, Bailer RT, Druz A, Georgiev IS, Gillespie RA, Kanekiyo M, Kong WP, Leung K, Narpala SN, Prabhakaran MS, Yang ES, et al. Vaccine-Induced Antibodies that Neutralize Group 1 and Group 2 Influenza A Viruses. Cell. PMID 27453470 DOI: 10.1016/J.Cell.2016.06.043  0.331
2016 Soto C, Ofek G, Joyce MG, Zhang B, McKee K, Longo NS, Yang Y, Huang J, Parks R, Eudailey J, Lloyd KE, Alam SM, Haynes BF, Mullikin JC, et al. Developmental Pathway of the MPER-Directed HIV-1-Neutralizing Antibody 10E8. Plos One. 11: e0157409. PMID 27299673 DOI: 10.1371/Journal.Pone.0157409  0.339
2016 Kong R, Xu K, Zhou T, Acharya P, Lemmin T, Liu K, Ozorowski G, Soto C, Taft JD, Bailer RT, Cale EM, Chen L, Choi CW, Chuang GY, Doria-Rose NA, et al. Fusion peptide of HIV-1 as a site of vulnerability to neutralizing antibody. Science (New York, N.Y.). 352: 828-33. PMID 27174988 DOI: 10.1126/Science.Aae0474  0.302
2016 Stewart-Jones GB, Soto C, Lemmin T, Chuang GY, Druz A, Kong R, Thomas PV, Wagh K, Zhou T, Behrens AJ, Bylund T, Choi CW, Davison JR, Georgiev IS, Joyce MG, et al. Trimeric HIV-1-Env Structures Define Glycan Shields from Clades A, B, and G. Cell. PMID 27114034 DOI: 10.1016/J.Cell.2016.04.010  0.367
2015 Gorman J, Soto C, Yang MM, Davenport TM, Guttman M, Bailer RT, Chambers M, Chuang GY, DeKosky BJ, Doria-Rose NA, Druz A, Ernandes MJ, Georgiev IS, Jarosinski MC, Joyce MG, et al. Structures of HIV-1 Env V1V2 with broadly neutralizing antibodies reveal commonalities that enable vaccine design. Nature Structural & Molecular Biology. PMID 26689967 DOI: 10.1038/Nsmb.3144  0.368
2015 Stewart-Jones GB, Thomas PV, Chen M, Druz A, Joyce MG, Kong WP, Sastry M, Soto C, Yang Y, Zhang B, Chen L, Chuang GY, Georgiev IS, McLellan JS, Srivatsan S, et al. A Cysteine Zipper Stabilizes a Pre-Fusion F Glycoprotein Vaccine for Respiratory Syncytial Virus. Plos One. 10: e0128779. PMID 26098893 DOI: 10.1371/Journal.Pone.0128779  0.323
2015 Do Kwon Y, Pancera M, Acharya P, Georgiev IS, Crooks ET, Gorman J, Joyce MG, Guttman M, Ma X, Narpala S, Soto C, Terry DS, Yang Y, Zhou T, Ahlsen G, et al. Crystal structure, conformational fixation and entry-related interactions of mature ligand-free HIV-1 Env. Nature Structural & Molecular Biology. 22: 522-31. PMID 26098315 DOI: 10.1038/Nsmb.3051  0.39
2015 Zhou T, Lynch RM, Chen L, Acharya P, Wu X, Doria-Rose NA, Joyce MG, Lingwood D, Soto C, Bailer RT, Ernandes MJ, Kong R, Longo NS, Louder MK, McKee K, et al. Structural Repertoire of HIV-1-Neutralizing Antibodies Targeting the CD4 Supersite in 14 Donors. Cell. 161: 1280-92. PMID 26004070 DOI: 10.1016/J.Cell.2015.05.007  0.324
2015 Wu X, Zhang Z, Schramm CA, Joyce MG, Kwon YD, Zhou T, Sheng Z, Zhang B, O'Dell S, McKee K, Georgiev IS, Chuang GY, Longo NS, Lynch RM, Saunders KO, ... Soto C, et al. Maturation and Diversity of the VRC01-Antibody Lineage over 15 Years of Chronic HIV-1 Infection. Cell. 161: 470-85. PMID 25865483 DOI: 10.1016/J.Cell.2015.03.004  0.336
2014 Pancera M, Zhou T, Druz A, Georgiev IS, Soto C, Gorman J, Huang J, Acharya P, Chuang GY, Ofek G, Stewart-Jones GB, Stuckey J, Bailer RT, Joyce MG, Louder MK, et al. Structure and immune recognition of trimeric pre-fusion HIV-1 Env. Nature. 514: 455-61. PMID 25296255 DOI: 10.1038/Nature13808  0.367
2014 Rudicell RS, Kwon YD, Ko SY, Pegu A, Louder MK, Georgiev IS, Wu X, Zhu J, Boyington JC, Chen X, Shi W, Yang ZY, Doria-Rose NA, McKee K, O'Dell S, ... ... Soto C, et al. Enhanced potency of a broadly neutralizing HIV-1 antibody in vitro improves protection against lentiviral infection in vivo. Journal of Virology. 88: 12669-82. PMID 25142607 DOI: 10.1128/Jvi.02213-14  0.339
2014 Zhou T, Zhu J, Yang Y, Gorman J, Ofek G, Srivatsan S, Druz A, Lees CR, Lu G, Soto C, Stuckey J, Burton DR, Koff WC, Connors M, Kwong PD, et al. Transplanting supersites of HIV-1 vulnerability. Plos One. 9: e99881. PMID 24992528 DOI: 10.1371/Journal.Pone.0099881  0.331
2014 Doria-Rose NA, Schramm CA, Gorman J, Moore PL, Bhiman JN, DeKosky BJ, Ernandes MJ, Georgiev IS, Kim HJ, Pancera M, Staupe RP, Altae-Tran HR, Bailer RT, Crooks ET, Cupo A, ... ... Soto C, et al. Developmental pathway for potent V1V2-directed HIV-neutralizing antibodies. Nature. 509: 55-62. PMID 24590074 DOI: 10.1038/Nature13036  0.339
2013 McLellan JS, Chen M, Joyce MG, Sastry M, Stewart-Jones GB, Yang Y, Zhang B, Chen L, Srivatsan S, Zheng A, Zhou T, Graepel KW, Kumar A, Moin S, Boyington JC, ... ... Soto C, et al. Structure-based design of a fusion glycoprotein vaccine for respiratory syncytial virus. Science (New York, N.Y.). 342: 592-8. PMID 24179220 DOI: 10.1126/Science.1243283  0.32
2013 Zhu J, Wu X, Zhang B, McKee K, O'Dell S, Soto C, Zhou T, Casazza JP, Mullikin JC, Kwong PD, Mascola JR, Shapiro L. De novo identification of VRC01 class HIV-1-neutralizing antibodies by next-generation sequencing of B-cell transcripts. Proceedings of the National Academy of Sciences of the United States of America. 110: E4088-97. PMID 24106303 DOI: 10.1073/Pnas.1306262110  0.37
2013 Lemmin T, Soto CS, Clinthorne G, DeGrado WF, Dal Peraro M. Assembly of the transmembrane domain of E. coli PhoQ histidine kinase: implications for signal transduction from molecular simulations. Plos Computational Biology. 9: e1002878. PMID 23359663 DOI: 10.1371/Journal.Pcbi.1002878  0.301
2011 Soto CS, Hannigan BT, DeGrado WF. A photon-free approach to transmembrane protein structure determination. Journal of Molecular Biology. 414: 596-610. PMID 22024595 DOI: 10.1016/J.Jmb.2011.10.016  0.438
2010 Cady SD, Schmidt-Rohr K, Wang J, Soto CS, Degrado WF, Hong M. Structure of the amantadine binding site of influenza M2 proton channels in lipid bilayers. Nature. 463: 689-92. PMID 20130653 DOI: 10.1038/Nature08722  0.335
2008 Goldberg SD, Soto CS, Waldburger CD, Degrado WF. Determination of the physiological dimer interface of the PhoQ sensor domain. Journal of Molecular Biology. 379: 656-65. PMID 18468622 DOI: 10.1016/J.Jmb.2008.04.023  0.347
2008 Stouffer AL, Acharya R, Salom D, Levine AS, Di Costanzo L, Soto CS, Tereshko V, Nanda V, Stayrook S, DeGrado WF. Structural basis for the function and inhibition of an influenza virus proton channel. Nature. 451: 596-9. PMID 18235504 DOI: 10.1038/Nature06528  0.322
2008 Soto CS, Fasnacht M, Zhu J, Forrest L, Honig B. Loop modeling: Sampling, filtering, and scoring. Proteins. 70: 834-43. PMID 17729286 DOI: 10.1002/Prot.21612  0.68
2003 Petrey D, Xiang Z, Tang CL, Xie L, Gimpelev M, Mitros T, Soto CS, Goldsmith-Fischman S, Kernytsky A, Schlessinger A, Koh IY, Alexov E, Honig B. Using multiple structure alignments, fast model building, and energetic analysis in fold recognition and homology modeling. Proteins. 53: 430-5. PMID 14579332 DOI: 10.1002/Prot.10550  0.465
2002 Xiang Z, Soto CS, Honig B. Evaluating conformational free energies: the colony energy and its application to the problem of loop prediction. Proceedings of the National Academy of Sciences of the United States of America. 99: 7432-7. PMID 12032300 DOI: 10.1073/Pnas.102179699  0.641
Show low-probability matches.