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Davi R Ortega - Publications

Affiliations: 
California Institute of Technology, Pasadena, CA 
Area:
bioinformatics, data visualization, computational biology
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34 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
2022 Metskas LA, Ortega D, Oltrogge LM, Blikstad C, Lovejoy DR, Laughlin TG, Savage DF, Jensen GJ. Rubisco forms a lattice inside alpha-carboxysomes. Nature Communications. 13: 4863. PMID 35982043 DOI: 10.1038/s41467-022-32584-7  0.476
2022 Kaplan M, Oikonomou CM, Wood CR, Chreifi G, Subramanian P, Ortega DR, Chang YW, Beeby M, Shaffer CL, Jensen GJ. Novel transient cytoplasmic rings stabilize assembling bacterial flagellar motors. The Embo Journal. e109523. PMID 35301732 DOI: 10.15252/embj.2021109523  0.524
2020 Muok AR, Ortega DR, Kurniyati K, Yang W, Maschmann ZA, Sidi Mabrouk A, Li C, Crane BR, Briegel A. Atypical chemoreceptor arrays accommodate high membrane curvature. Nature Communications. 11: 5763. PMID 33188180 DOI: 10.1038/s41467-020-19628-6  0.621
2020 Weaver SJ, Ortega DR, Sazinsky MH, Dalia TN, Dalia AB, Jensen GJ. Publisher Correction: CryoEM structure of the type IVa pilus secretin required for natural competence in Vibrio cholera. Nature Communications. 11: 5533. PMID 33110082 DOI: 10.1038/s41467-020-19389-2  0.728
2020 Weaver SJ, Ortega DR, Sazinsky MH, Dalia TN, Dalia AB, Jensen GJ. CryoEM structure of the type IVa pilus secretin required for natural competence in Vibrio cholerae. Nature Communications. 11: 5080. PMID 33033258 DOI: 10.1038/s41467-020-18866-y  0.748
2020 Ortega DR, Kjaer A, Briegel A. The chemosensory systems of Vibrio cholerae. Molecular Microbiology. PMID 32347610 DOI: 10.1111/Mmi.14520  0.598
2020 Ortega DR, Yang W, Subramanian P, Mann P, Kjær A, Chen S, Watts KJ, Pirbadian S, Collins DA, Kooger R, Kalyuzhnaya MG, Ringgaard S, Briegel A, Jensen GJ. Repurposing a chemosensory macromolecular machine. Nature Communications. 11: 2041. PMID 32341341 DOI: 10.1038/S41467-020-15736-5  0.676
2020 Kaplan M, Sweredoski MJ, Rodrigues JPGLM, Tocheva EI, Chang YW, Ortega DR, Beeby M, Jensen GJ. Bacterial flagellar motor PL-ring disassembly subcomplexes are widespread and ancient. Proceedings of the National Academy of Sciences of the United States of America. PMID 32241888 DOI: 10.1073/Pnas.1916935117  0.564
2019 Gumerov VM, Ortega DR, Adebali O, Ulrich LE, Zhulin IB. MiST 3.0: an updated microbial signal transduction database with an emphasis on chemosensory systems. Nucleic Acids Research. PMID 31754718 DOI: 10.1093/Nar/Gkz988  0.645
2019 O'Neal L, Gullett JM, Aksenova A, Hubler A, Briegel A, Ortega D, Kjær A, Jensen G, Alexandre G. Distinct Chemotaxis Protein Paralogs Assemble into Chemoreceptor Signaling Arrays To Coordinate Signaling Output. Mbio. 10. PMID 31551333 DOI: 10.1128/Mbio.01757-19  0.716
2019 Kaplan M, Subramanian P, Ghosal D, Oikonomou CM, Pirbadian S, Starwalt-Lee R, Mageswaran SK, Ortega DR, Gralnick JA, El-Naggar MY, Jensen GJ. In situ imaging of the bacterial flagellar motor disassembly and assembly processes. The Embo Journal. 38: e100957. PMID 31304634 DOI: 10.15252/Embj.2018100957  0.571
2019 Kaplan M, Subramanian P, Ghosal D, Oikonomou CM, Pirbadian S, Starwalt-Lee R, Mageswaran SK, Ortega DR, Gralnick JA, El-Naggar MY, Jensen GJ. imaging of the bacterial flagellar motor disassembly and assembly processes. The Embo Journal. PMID 31109936 DOI: 10.15252/embj.2018100957  0.52
2019 Ortega DR, Oikonomou CM, Ding HJ, Rees-Lee P, Jensen GJ. ETDB-Caltech: A blockchain-based distributed public database for electron tomography. Plos One. 14: e0215531. PMID 30986271 DOI: 10.1371/Journal.Pone.0215531  0.51
2019 Kaplan M, Ghosal D, Subramanian P, Oikonomou CM, Kjaer A, Pirbadian S, Ortega DR, Briegel A, El-Naggar MY, Jensen GJ. The presence and absence of periplasmic rings in bacterial flagellar motors correlates with stator type. Elife. 8. PMID 30648971 DOI: 10.7554/Elife.43487  0.686
2018 Ortega DR, Zhulin IB. Phylogenetic and Protein Sequence Analysis of Bacterial Chemoreceptors. Methods in Molecular Biology (Clifton, N.J.). 1729: 373-385. PMID 29429105 DOI: 10.1007/978-1-4939-7577-8_29  0.616
2018 Swulius MT, Nguyen LT, Ladinsky MS, Ortega DR, Aich S, Mishra M, Jensen GJ. Structure of the fission yeast actomyosin ring during constriction. Proceedings of the National Academy of Sciences of the United States of America. PMID 29348205 DOI: 10.1073/Pnas.1711218115  0.539
2018 Kaplan M, Ghosal D, Subramanian P, Oikonomou CM, Kjaer A, Pirbadian S, Ortega DR, Briegel A, El-Naggar MY, Jensen GJ. Author response: The presence and absence of periplasmic rings in bacterial flagellar motors correlates with stator type Elife. DOI: 10.7554/Elife.43487.024  0.672
2017 Ortega DR, Fleetwood AD, Krell T, Harwood CS, Jensen GJ, Zhulin IB. Assigning chemoreceptors to chemosensory pathways in Pseudomonas aeruginosa. Proceedings of the National Academy of Sciences of the United States of America. PMID 29133402 DOI: 10.1073/Pnas.1708842114  0.695
2017 Chang YW, Rettberg LA, Ortega DR, Jensen GJ. In vivo structures of an intact type VI secretion system revealed by electron cryotomography. Embo Reports. PMID 28487352 DOI: 10.15252/Embr.201744072  0.594
2017 Schulz F, Yutin N, Ivanova NN, Ortega DR, Lee TK, Vierheilig J, Daims H, Horn M, Wagner M, Jensen GJ, Kyrpides NC, Koonin EV, Woyke T. Giant viruses with an expanded complement of translation system components. Science (New York, N.Y.). 356: 82-85. PMID 28386012 DOI: 10.1126/Science.Aal4657  0.521
2017 Chang YW, Kjær A, Ortega DR, Kovacikova G, Sutherland JA, Rettberg LA, Taylor RK, Jensen GJ. Architecture of the Vibrio cholerae toxin-coregulated pilus machine revealed by electron cryotomography. Nature Microbiology. 2: 16269. PMID 28165453 DOI: 10.1038/Nmicrobiol.2016.269  0.577
2017 Petukh M, Ortega D, Zhulin IB. Electrostatics Facilitates the Trimer-of-Dimers Formation of the Chemoreceptor Signaling Domain Biophysical Journal. 112: 89a. DOI: 10.1016/J.Bpj.2016.11.523  0.663
2016 Tocheva EI, Ortega DR, Jensen GJ. Sporulation, bacterial cell envelopes and the origin of life. Nature Reviews. Microbiology. 14: 535-542. PMID 28232669 DOI: 10.1038/Nrmicro.2016.85  0.547
2016 Briegel A, Ortega DR, Mann P, Kjær A, Ringgaard S, Jensen GJ. Chemotaxis cluster 1 proteins form cytoplasmic arrays in Vibrio cholerae and are stabilized by a double signaling domain receptor DosM. Proceedings of the National Academy of Sciences of the United States of America. PMID 27573843 DOI: 10.1073/Pnas.1604693113  0.729
2016 Tocheva EI, Ortega DR, Jensen GJ. Author's reply. Nature Reviews. Microbiology. PMID 27452232 DOI: 10.1038/nrmicro.2016.114  0.383
2016 Ortega DR, Zhulin IB. Evolutionary Genomics Suggests That CheV Is an Additional Adaptor for Accommodating Specific Chemoreceptors within the Chemotaxis Signaling Complex. Plos Computational Biology. 12: e1004723. PMID 26844549 DOI: 10.1371/Journal.Pcbi.1004723  0.673
2015 Briegel A, Ortega DR, Huang AN, Oikonomou CM, Gunsalus RP, Jensen GJ. Structural conservation of chemotaxis machinery across Archaea and Bacteria. Environmental Microbiology Reports. 7: 414-9. PMID 25581459 DOI: 10.1111/1758-2229.12265  0.741
2015 Adebali O, Ortega DR, Zhulin IB. CDvist: a webserver for identification and visualization of conserved domains in protein sequences. Bioinformatics (Oxford, England). 31: 1475-7. PMID 25527097 DOI: 10.1093/Bioinformatics/Btu836  0.597
2013 Ortega DR, Yang C, Ames P, Baudry J, Parkinson JS, Zhulin IB. A phenylalanine rotameric switch for signal-state control in bacterial chemoreceptors. Nature Communications. 4: 2881. PMID 24335957 DOI: 10.1038/Ncomms3881  0.645
2013 Ortega DR, Mo G, Lee K, Zhou H, Baudry J, Dahlquist FW, Zhulin IB. Conformational coupling between receptor and kinase binding sites through a conserved salt bridge in a signaling complex scaffold protein. Plos Computational Biology. 9: e1003337. PMID 24244143 DOI: 10.1371/Journal.Pcbi.1003337  0.638
2013 Cashman DJ, Ortega DR, Zhulin IB, Baudry J. Homology modeling of the CheW coupling protein of the chemotaxis signaling complex. Plos One. 8: e70705. PMID 23950985 DOI: 10.1371/Journal.Pone.0070705  0.619
2013 Li X, Fleetwood AD, Bayas C, Bilwes AM, Ortega DR, Falke JJ, Zhulin IB, Crane BR. The 3.2 Å resolution structure of a receptor: CheA:CheW signaling complex defines overlapping binding sites and key residue interactions within bacterial chemosensory arrays. Biochemistry. 52: 3852-65. PMID 23668907 DOI: 10.1021/Bi400383E  0.648
2009 Briegel A, Ortega DR, Tocheva EI, Wuichet K, Li Z, Chen S, Müller A, Iancu CV, Murphy GE, Dobro MJ, Zhulin IB, Jensen GJ. Universal architecture of bacterial chemoreceptor arrays. Proceedings of the National Academy of Sciences of the United States of America. 106: 17181-6. PMID 19805102 DOI: 10.1073/Pnas.0905181106  0.72
2008 Bible AN, Stephens BB, Ortega DR, Xie Z, Alexandre G. Function of a chemotaxis-like signal transduction pathway in modulating motility, cell clumping, and cell length in the alphaproteobacterium Azospirillum brasilense. Journal of Bacteriology. 190: 6365-75. PMID 18641130 DOI: 10.1128/Jb.00734-08  0.322
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