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Richard Szubin

Title(s)SRA 3, Bioengineering
SchoolVc-academic Affairs
Address9500 Gilman Drive #
La Jolla CA 92093
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Synthetic cross-phyla gene replacement and evolutionary assimilation of major enzymes. Nat Ecol Evol. 2020 Oct; 4(10):1402-1409. Sandberg TE, Szubin R, Phaneuf PV, Palsson BO. PMID: 32778753.
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    2. Revealing 29 sets of independently modulated genes in Staphylococcus aureus, their regulators, and role in key physiological response. Proc Natl Acad Sci U S A. 2020 07 21; 117(29):17228-17239. Poudel S, Tsunemoto H, Seif Y, Sastry AV, Szubin R, Xu S, Machado H, Olson CA, Anand A, Pogliano J, Nizet V, Palsson BO. PMID: 32616573.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    3. Genome Sequence Comparison of Staphylococcus aureus TX0117 and a Beta-Lactamase-Cured Derivative Shows Increased Cationic Peptide Resistance Accompanying Mutations in relA and mnaA. Microbiol Resour Announc. 2020 Apr 30; 9(18). Sales MJ, Sakoulas G, Szubin R, Palsson B, Arias C, Singh KV, Murray BE, Monk JM. PMID: 32354985.
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    4. Genetic Determinants Enabling Medium-Dependent Adaptation to Nafcillin in Methicillin-Resistant Staphylococcus aureus. mSystems. 2020 Mar 31; 5(2). Salazar MJ, Machado H, Dillon NA, Tsunemoto H, Szubin R, Dahesh S, Pogliano J, Sakoulas G, Palsson BO, Nizet V, Feist AM. PMID: 32234776.
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    5. OxyR Is a Convergent Target for Mutations Acquired during Adaptation to Oxidative Stress-Prone Metabolic States. Mol Biol Evol. 2020 03 01; 37(3):660-667. Anand A, Chen K, Catoiu E, Sastry AV, Olson CA, Sandberg TE, Seif Y, Xu S, Szubin R, Yang L, Feist AM, Palsson BO. PMID: 31651953.
      View in: PubMed   Mentions: 2     Fields:    
    6. Distinct Subpopulations of Intravalvular Methicillin-Resistant Staphylococcus aureus with Variable Susceptibility to Daptomycin in Tricuspid Valve Endocarditis. Antimicrob Agents Chemother. 2020 02 21; 64(3). Miller CR, Dey S, Smolenski PD, Kulkarni PS, Monk JM, Szubin R, Sakoulas G, Berti AD. PMID: 31932377.
      View in: PubMed   Mentions: 1     Fields:    
    7. Reduced Production of Bacterial Membrane Vesicles Predicts Mortality in ST45/USA600 Methicillin-Resistant Staphylococcus aureus Bacteremia. Antibiotics (Basel). 2019 Dec 18; 9(1). Dey S, Gudipati S, Giuliano C, Zervos MJ, Monk JM, Szubin R, Jorgensen SCJ, Sakoulas G, Berti AD. PMID: 31861446.
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    8. Profiling the effect of nafcillin on HA-MRSA D712 using bacteriological and physiological media. Sci Data. 2019 12 17; 6(1):322. Rajput A, Poudel S, Tsunemoto H, Meehan M, Szubin R, Olson CA, Lamsa A, Seif Y, Dillon N, Vrbanac A, Sugie J, Dahesh S, Monk JM, Dorrestein PC, Knight R, Nizet V, Palsson BO, Feist AM, Pogliano J. PMID: 31848353.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    9. The Escherichia coli transcriptome mostly consists of independently regulated modules. Nat Commun. 2019 12 04; 10(1):5536. Sastry AV, Gao Y, Szubin R, Hefner Y, Xu S, Kim D, Choudhary KS, Yang L, King ZA, Palsson BO. PMID: 31797920.
      View in: PubMed   Mentions: 9     Fields:    Translation:Cells
    10. Adaptive evolution reveals a tradeoff between growth rate and oxidative stress during naphthoquinone-based aerobic respiration. Proc Natl Acad Sci U S A. 2019 12 10; 116(50):25287-25292. Anand A, Chen K, Yang L, Sastry AV, Olson CA, Poudel S, Seif Y, Hefner Y, Phaneuf PV, Xu S, Szubin R, Feist AM, Palsson BO. PMID: 31767748.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    11. Adaptive laboratory evolution of Escherichia coli under acid stress. Microbiology (Reading). 2020 02; 166(2):141-148. Du B, Olson CA, Sastry AV, Fang X, Phaneuf PV, Chen K, Wu M, Szubin R, Xu S, Gao Y, Hefner Y, Feist AM, Palsson BO. PMID: 31625833.
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    12. Cellular responses to reactive oxygen species are predicted from molecular mechanisms. Proc Natl Acad Sci U S A. 2019 07 09; 116(28):14368-14373. Yang L, Mih N, Anand A, Park JH, Tan J, Yurkovich JT, Monk JM, Lloyd CJ, Sandberg TE, Seo SW, Kim D, Sastry AV, Phaneuf P, Gao Y, Broddrick JT, Chen K, Heckmann D, Szubin R, Hefner Y, Feist AM, Palsson BO. PMID: 31270234.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    13. Comparative Genome-Scale Metabolic Modeling of Metallo-Beta-Lactamase-Producing Multidrug-Resistant Klebsiella pneumoniae Clinical Isolates. Front Cell Infect Microbiol. 2019; 9:161. Norsigian CJ, Attia H, Szubin R, Yassin AS, Palsson BØ, Aziz RK, Monk JM. PMID: 31179245.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    14. Characterization of CA-MRSA TCH1516 exposed to nafcillin in bacteriological and physiological media. Sci Data. 2019 04 26; 6(1):43. Poudel S, Tsunemoto H, Meehan M, Szubin R, Olson CA, Lamsa A, Seif Y, Dillon N, Vrbanac A, Sugie J, Dahesh S, Monk JM, Dorrestein PC, Pogliano J, Knight R, Nizet V, Palsson BO, Feist AM. PMID: 31028276.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    15. Draft Genome Sequences of Four Metallo-Beta-Lactamase-Producing Multidrug-Resistant Klebsiella pneumoniae Clinical Isolates, Including Two Colistin-Resistant Strains, from Cairo, Egypt. Microbiol Resour Announc. 2019 Feb; 8(7). Attia H, Szubin R, Yassin AS, Monk JM, Aziz RK. PMID: 30801061.
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    16. Pseudogene repair driven by selection pressure applied in experimental evolution. Nat Microbiol. 2019 03; 4(3):386-389. Anand A, Olson CA, Yang L, Sastry AV, Catoiu E, Choudhary KS, Phaneuf PV, Sandberg TE, Xu S, Hefner Y, Szubin R, Feist AM, Palsson BO. PMID: 30692668.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    17. Metagenomics-Based, Strain-Level Analysis of Escherichia coli From a Time-Series of Microbiome Samples From a Crohn's Disease Patient. Front Microbiol. 2018; 9:2559. Fang X, Monk JM, Nurk S, Akseshina M, Zhu Q, Gemmell C, Gianetto-Hill C, Leung N, Szubin R, Sanders J, Beck PL, Li W, Sandborn WJ, Gray-Owen SD, Knight R, Allen-Vercoe E, Palsson BO, Smarr L. PMID: 30425690.
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    18. Gapless, Unambiguous Genome Sequence for Escherichia coli C, a Workhorse of Industrial Biology. Microbiol Resour Announc. 2018 Oct; 7(13). Pekar JE, Phaneuf P, Szubin R, Palsson B, Feist A, Monk JM. PMID: 30533692.
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    19. Evolution of gene knockout strains of E. coli reveal regulatory architectures governed by metabolism. Nat Commun. 2018 09 18; 9(1):3796. McCloskey D, Xu S, Sandberg TE, Brunk E, Hefner Y, Szubin R, Feist AM, Palsson BO. PMID: 30228271.
      View in: PubMed   Mentions: 9     Fields:    Translation:Cells
    20. Multiple Optimal Phenotypes Overcome Redox and Glycolytic Intermediate Metabolite Imbalances in Escherichia coli pgi Knockout Evolutions. Appl Environ Microbiol. 2018 10 01; 84(19). McCloskey D, Xu S, Sandberg TE, Brunk E, Hefner Y, Szubin R, Feist AM, Palsson BO. PMID: 30054360.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    21. Growth Adaptation of gnd and sdhCB Escherichia coli Deletion Strains Diverges From a Similar Initial Perturbation of the Transcriptome. Front Microbiol. 2018; 9:1793. McCloskey D, Xu S, Sandberg TE, Brunk E, Hefner Y, Szubin R, Feist AM, Palsson BO. PMID: 30131786.
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    22. Adaptive laboratory evolution resolves energy depletion to maintain high aromatic metabolite phenotypes in Escherichia coli strains lacking the Phosphotransferase System. . 2018 07; 48:233-242. McCloskey D, Xu S, Sandberg TE, Brunk E, Hefner Y, Szubin R, Feist AM, Palsson BO. PMID: 29906504.
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    23. Adaptation to the coupling of glycolysis to toxic methylglyoxal production in tpiA deletion strains of Escherichia coli requires synchronized and counterintuitive genetic changes. . 2018 07; 48:82-93. McCloskey D, Xu S, Sandberg TE, Brunk E, Hefner Y, Szubin R, Feist AM, Palsson BO. PMID: 29842925.
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    24. ChIP-exo interrogation of Crp, DNA, and RNAP holoenzyme interactions. PLoS One. 2018; 13(5):e0197272. Latif H, Federowicz S, Ebrahim A, Tarasova J, Szubin R, Utrilla J, Zengler K, Palsson BO. PMID: 29771928.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    25. Genome-scale analysis of Methicillin-resistant Staphylococcus aureus USA300 reveals a tradeoff between pathogenesis and drug resistance. Sci Rep. 2018 02 02; 8(1):2215. Choe D, Szubin R, Dahesh S, Cho S, Nizet V, Palsson B, Cho BK. PMID: 29396540.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    26. Revealing genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles under osmotic stress in Escherichia coli K-12 MG1655. Sci Rep. 2017 05 19; 7(1):2181. Seo SW, Gao Y, Kim D, Szubin R, Yang J, Cho BK, Palsson BO. PMID: 28526842.
      View in: PubMed   Mentions: 7     Fields:    Translation:Cells
    27. Multi-omic data integration enables discovery of hidden biological regularities. Nat Commun. 2016 10 26; 7:13091. Ebrahim A, Brunk E, Tan J, O'Brien EJ, Kim D, Szubin R, Lerman JA, Lechner A, Sastry A, Bordbar A, Feist AM, Palsson BO. PMID: 27782110.
      View in: PubMed   Mentions: 29     Fields:    Translation:Cells
    28. Genome-wide Reconstruction of OxyR and SoxRS Transcriptional Regulatory Networks under Oxidative Stress in Escherichia coli K-12 MG1655. Cell Rep. 2015 Aug 25; 12(8):1289-99. Seo SW, Kim D, Szubin R, Palsson BO. PMID: 26279566.
      View in: PubMed   Mentions: 34     Fields:    Translation:Cells
    29. Decoding genome-wide GadEWX-transcriptional regulatory networks reveals multifaceted cellular responses to acid stress in Escherichia coli. Nat Commun. 2015 Aug 10; 6:7970. Seo SW, Kim D, O'Brien EJ, Szubin R, Palsson BO. PMID: 26258987.
      View in: PubMed   Mentions: 23     Fields:    Translation:Cells
    30. A streamlined ribosome profiling protocol for the characterization of microorganisms. Biotechniques. 2015 Jun; 58(6):329-32. Latif H, Szubin R, Tan J, Brunk E, Lechner A, Zengler K, Palsson BO. PMID: 26054770.
      View in: PubMed   Mentions: 17     Fields:    Translation:Cells
    31. Use of adaptive laboratory evolution to discover key mutations enabling rapid growth of Escherichia coli K-12 MG1655 on glucose minimal medium. Appl Environ Microbiol. 2015 Jan; 81(1):17-30. LaCroix RA, Sandberg TE, O'Brien EJ, Utrilla J, Ebrahim A, Guzman GI, Szubin R, Palsson BO, Feist AM. PMID: 25304508.
      View in: PubMed   Mentions: 62     Fields:    Translation:Cells
    32. Deciphering Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli. Nat Commun. 2014 Sep 15; 5:4910. Seo SW, Kim D, Latif H, O'Brien EJ, Szubin R, Palsson BO. PMID: 25222563.
      View in: PubMed   Mentions: 66     Fields:    Translation:Cells
    33. The early interferon alpha subtype response in infant macaques infected orally with SIV. . 2010 Sep; 55(1):14-28. Easlick J, Szubin R, Lantz S, Baumgarth N, Abel K. PMID: 20616742.
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    34. Human cytomegalovirus suppresses type I interferon secretion by plasmacytoid dendritic cells through its interleukin 10 homolog. Virology. 2009 Aug 01; 390(2):330-7. Chang WL, Barry PA, Szubin R, Wang D, Baumgarth N. PMID: 19524994.
      View in: PubMed   Mentions: 33     Fields:    Translation:HumansCells
    35. Rigid interferon-alpha subtype responses of human plasmacytoid dendritic cells. J Interferon Cytokine Res. 2008 Dec; 28(12):749-63. Szubin R, Chang WL, Greasby T, Beckett L, Baumgarth N. PMID: 18937549.
      View in: PubMed   Mentions: 16     Fields:    Translation:HumansCells
    36. Highly tissue substructure-specific effects of human papilloma virus in mucosa of HIV-infected patients revealed by laser-dissection microscopy-assisted gene expression profiling. Am J Pathol. 2004 Sep; 165(3):707-18. Baumgarth N, Szubin R, Dolganov GM, Watnik MR, Greenspan D, Da Costa M, Palefsky JM, Jordan R, Roederer M, Greenspan JS. PMID: 15331396.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansCells
    37. A novel method of gene transcript profiling in airway biopsy homogenates reveals increased expression of a Na+-K+-Cl- cotransporter (NKCC1) in asthmatic subjects. Genome Res. 2001 Sep; 11(9):1473-83. Dolganov GM, Woodruff PG, Novikov AA, Zhang Y, Ferrando RE, Szubin R, Fahy JV. PMID: 11544191.
      View in: PubMed   Mentions: 45     Fields:    Translation:HumansCells
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