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Ralph Jimenez

TitleProfessor Adjoint
InstitutionUniversity of Colorado Boulder
DepartmentChemistry
Phone303/492-8439

    Collapse Research 
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    R01GM083849     (PALMER, AMY E)Jul 1, 2008 - Jun 30, 2013
    NIH
    Microfluidics-based Selections for the Optimization of Red Flourescent Proteins
    Role: Co-Principal Investigator

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Mukherjee S, Manna P, Douglas N, Chapagain PP, Jimenez R. Conformational Dynamics of mCherry Variants: A Link between Side-Chain Motions and Fluorescence Brightness. J Phys Chem B. 2023 01 12; 127(1):52-61. PMID: 36574626.
      View in: PubMed
    2. Mukherjee S, Manna P, Hung ST, Vietmeyer F, Friis P, Palmer AE, Jimenez R. Directed Evolution of a Bright Variant of mCherry: Suppression of Nonradiative Decay by Fluorescence Lifetime Selections. J Phys Chem B. 2022 06 30; 126(25):4659-4668. PMID: 35709514.
      View in: PubMed
    3. Mukherjee S, Thomas C, Wilson R, Simmerman E, Hung ST, Jimenez R. Characterizing dark state kinetics and single molecule fluorescence of FusionRed and FusionRed-MQ at low irradiances. Phys Chem Chem Phys. 2022 Jun 15; 24(23):14310-14323. PMID: 35642612.
      View in: PubMed
    4. Lyu T, Sohn SH, Jimenez R, Joo T. Temperature-Dependent Fluorescence of mPlum Fluorescent Protein from 295 to 20 K. J Phys Chem B. 2022 03 31; 126(12):2337-2344. PMID: 35296137.
      View in: PubMed
    5. Mikhaylov A, Wilson RN, Parzuchowski KM, Mazurek MD, Camp CH, Stevens MJ, Jimenez R. Hot-Band Absorption Can Mimic Entangled Two-Photon Absorption. J Phys Chem Lett. 2022 Feb 17; 13(6):1489-1493. PMID: 35129354.
      View in: PubMed
    6. Mukherjee S, Jimenez R. Photophysical Engineering of Fluorescent Proteins: Accomplishments and Challenges of Physical Chemistry Strategies. J Phys Chem B. 2022 02 03; 126(4):735-750. PMID: 35075898.
      View in: PubMed
    7. Lum DJ, Mazurek MD, Mikhaylov A, Parzuchowski KM, Wilson RN, Jimenez R, Gerrits T, Stevens MJ, Cicerone MT, Camp CH. Witnessing the survival of time-energy entanglement through biological tissue and scattering media. Biomed Opt Express. 2021 Jun 01; 12(6):3658-3670. PMID: 34221686.
      View in: PubMed
    8. Mukherjee S, Hung ST, Douglas N, Manna P, Thomas C, Ekrem A, Palmer AE, Jimenez R. Engineering of a Brighter Variant of the FusionRed Fluorescent Protein Using Lifetime Flow Cytometry and Structure-Guided Mutations. Biochemistry. 2020 10 06; 59(39):3669-3682. PMID: 32914619.
      View in: PubMed
    9. Liu Y, Chen Z, Wang X, Cao S, Xu J, Jimenez R, Chen J. Ultrafast spectroscopy of biliverdin dimethyl ester in solution: pathways of excited-state depopulation. Phys Chem Chem Phys. 2020 Sep 21; 22(35):19903-19912. PMID: 32853308.
      View in: PubMed
    10. Hung ST, Mukherjee S, Jimenez R. Enrichment of rare events using a multi-parameter high throughput microfluidic droplet sorter. Lab Chip. 2020 02 21; 20(4):834-843. PMID: 31974539.
      View in: PubMed
    11. Manna P, Hung ST, Mukherjee S, Friis P, Simpson DM, Lo M, Palmer AE, Jimenez R. Erratum: Directed evolution of excited state lifetime and brightness in FusionRed using a microfluidic sorter. Integr Biol (Camb). 2019 12 31; 11(9):372. PMID: 31788687.
      View in: PubMed
    12. Slocum JD, Palmer AE, Jimenez R. Intramolecular Fluorescent Protein Association in a Class of Zinc FRET Sensors Leads to Increased Dynamic Range. J Phys Chem B. 2019 04 11; 123(14):3079-3085. PMID: 30942588.
      View in: PubMed
    13. Cao X, Zhang C, Gao Z, Liu Y, Zhao Y, Yang Y, Chen J, Jimenez R, Xu J. Ultrafast internal conversion dynamics of bilirubin bound to UnaG and its N57A mutant. Phys Chem Chem Phys. 2019 Jan 30; 21(5):2365-2371. PMID: 30666332.
      View in: PubMed
    14. Manna P, Hung ST, Mukherjee S, Friis P, Simpson DM, Lo MN, Palmer AE, Jimenez R. Directed evolution of excited state lifetime and brightness in FusionRed using a microfluidic sorter. Integr Biol (Camb). 2018 09 17; 10(9):516-526. PMID: 30094420.
      View in: PubMed
    15. Braselmann E, Wierzba AJ, Polaski JT, Chrominski M, Holmes ZE, Hung ST, Batan D, Wheeler JR, Parker R, Jimenez R, Gryko D, Batey RT, Palmer AE. A multicolor riboswitch-based platform for imaging of RNA in live mammalian cells. Nat Chem Biol. 2018 10; 14(10):964-971. PMID: 30061719.
      View in: PubMed
    16. Carter KP, Carpenter MC, Fiedler B, Jimenez R, Palmer AE. Critical Comparison of FRET-Sensor Functionality in the Cytosol and Endoplasmic Reticulum and Implications for Quantification of Ions. Anal Chem. 2017 09 05; 89(17):9601-9608. PMID: 28758723.
      View in: PubMed
    17. Mo GC, Ross B, Hertel F, Manna P, Yang X, Greenwald E, Booth C, Plummer AM, Tenner B, Chen Z, Wang Y, Kennedy EJ, Cole PA, Fleming KG, Palmer A, Jimenez R, Xiao J, Dedecker P, Zhang J. Genetically encoded biosensors for visualizing live-cell biochemical activity at super-resolution. Nat Methods. 2017 Apr; 14(4):427-434. PMID: 28288122.
      View in: PubMed
    18. O'Neil GC, Miaja-Avila L, Joe YI, Alpert BK, Balasubramanian M, Sagar DM, Doriese W, Fowler JW, Fullagar WK, Chen N, Hilton GC, Jimenez R, Ravel B, Reintsema CD, Schmidt DR, Silverman KL, Swetz DS, Uhlig J, Ullom JN. Ultrafast Time-Resolved X-ray Absorption Spectroscopy of Ferrioxalate Photolysis with a Laser Plasma X-ray Source and Microcalorimeter Array. J Phys Chem Lett. 2017 Mar 02; 8(5):1099-1104. PMID: 28212035.
      View in: PubMed
    19. Fiedler BL, Van Buskirk S, Carter KP, Qin Y, Carpenter MC, Palmer AE, Jimenez R. Droplet Microfluidic Flow Cytometer For Sorting On Transient Cellular Responses Of Genetically-Encoded Sensors. Anal Chem. 2017 01 03; 89(1):711-719. PMID: 27959493.
      View in: PubMed
    20. Lychagov VV, Shemetov AA, Jimenez R, Verkhusha VV. Microfluidic System for In-Flow Reversible Photoswitching of Near-Infrared Fluorescent Proteins. Anal Chem. 2016 12 06; 88(23):11821-11829. PMID: 27807973.
      View in: PubMed
    21. Konold PE, Yoon E, Lee J, Allen SL, Chapagain PP, Gerstman BS, Regmi CK, Piatkevich KD, Verkhusha VV, Joo T, Jimenez R. Fluorescence from Multiple Chromophore Hydrogen-Bonding States in the Far-Red Protein TagRFP675. J Phys Chem Lett. 2016 Aug 04; 7(15):3046-51. PMID: 27447848.
      View in: PubMed
    22. Yoon E, Konold PE, Lee J, Joo T, Jimenez R. Far-Red Emission of mPlum Fluorescent Protein Results from Excited-State Interconversion between Chromophore Hydrogen-Bonding States. J Phys Chem Lett. 2016 Jun 16; 7(12):2170-4. PMID: 27214167.
      View in: PubMed
    23. Sagar DM, Baddour FG, Konold P, Ullom J, Ruddy DA, Johnson JC, Jimenez R. Femtosecond Measurements Of Size-Dependent Spin Crossover In Fe(II)(pyz)Pt(CN)4 Nanocrystals. J Phys Chem Lett. 2016 Jan 07; 7(1):148-53. PMID: 26652065.
      View in: PubMed
    24. Dean KM, Davis LM, Lubbeck JL, Manna P, Friis P, Palmer AE, Jimenez R. High-speed multiparameter photophysical analyses of fluorophore libraries. Anal Chem. 2015; 87(10):5026-30. PMID: 25898152.
      View in: PubMed
    25. Manna P, Jimenez R. Time and frequency-domain measurement of ground-state recovery times in red fluorescent proteins. J Phys Chem B. 2015 Apr 16; 119(15):4944-54. PMID: 25781915.
      View in: PubMed
    26. Konold PE, Jimenez R. Excited state electronic landscape of mPlum revealed by two-dimensional double quantum coherence spectroscopy. J Phys Chem B. 2015 Feb 26; 119(8):3414-22. PMID: 25635507.
      View in: PubMed
    27. Dean KM, Lubbeck JL, Davis LM, Regmi CK, Chapagain PP, Gerstman BS, Jimenez R, Palmer AE. Microfluidics-based selection of red-fluorescent proteins with decreased rates of photobleaching. Integr Biol (Camb). 2015 Feb; 7(2):263-73. PMID: 25477249.
      View in: PubMed
    28. Konold P, Regmi CK, Chapagain PP, Gerstman BS, Jimenez R. Hydrogen bond flexibility correlates with Stokes shift in mPlum variants. J Phys Chem B. 2014 Mar 20; 118(11):2940-8. PMID: 24611679.
      View in: PubMed
    29. Erickson RA, Jimenez R. Microfluidic cytometer for high-throughput measurement of photosynthetic characteristics and lipid accumulation in individual algal cells. Lab Chip. 2013 Aug 07; 13(15):2893-901. PMID: 23681282.
      View in: PubMed
    30. Davis LM, Lubbeck JL, Dean KM, Palmer AE, Jimenez R. Microfluidic cell sorter for use in developing red fluorescent proteins with improved photostability. Lab Chip. 2013 Jun 21; 13(12):2320-7. PMID: 23636097.
      View in: PubMed
    31. Pozzi EA, Schwall LR, Jimenez R, Weber JM. Pressure-induced changes in the fluorescence behavior of red fluorescent proteins. J Phys Chem B. 2012 Aug 30; 116(34):10311-6. PMID: 22861177.
      View in: PubMed
    32. Lubbeck JL, Dean KM, Ma H, Palmer AE, Jimenez R. Microfluidic flow cytometer for quantifying photobleaching of fluorescent proteins in cells. Anal Chem. 2012 May 01; 84(9):3929-37. PMID: 22424298.
      View in: PubMed
    33. Ma H, Gibson EA, Dittmer PJ, Jimenez R, Palmer AE. High-throughput examination of fluorescence resonance energy transfer-detected metal-ion response in mammalian cells. J Am Chem Soc. 2012 Feb 08; 134(5):2488-91. PMID: 22260720.
      View in: PubMed
    34. Dean KM, Lubbeck JL, Binder JK, Schwall LR, Jimenez R, Palmer AE. Analysis of red-fluorescent proteins provides insight into dark-state conversion and photodegradation. Biophys J. 2011 Aug 17; 101(4):961-9. PMID: 21843488.
      View in: PubMed
    35. Sraj I, Eggleton CD, Jimenez R, Hoover E, Squier J, Chichester J, Marr DW. Cell deformation cytometry using diode-bar optical stretchers. J Biomed Opt. 2010 Jul-Aug; 15(4):047010. PMID: 20799841.
      View in: PubMed
    36. Bristow AD, Karaiskaj D, Dai X, Zhang T, Carlsson C, Hagen KR, Jimenez R, Cundiff ST. A versatile ultrastable platform for optical multidimensional Fourier-transform spectroscopy. Rev Sci Instrum. 2009 Jul; 80(7):073108. PMID: 19655944.
      View in: PubMed
    37. Schafer D, Gibson EA, Salim EA, Palmer AE, Jimenez R, Squier J. Microfluidic cell counter with embedded optical fibers fabricated by femtosecond laser ablation and anodic bonding. Opt Express. 2009 Apr 13; 17(8):6068-73. PMID: 19365429.
      View in: PubMed
    38. Gibson EA, Shen Z, Jimenez R. Three-pulse photon echo peak shift spectroscopy as a probe of flexibility and conformational heterogeneity in protein folding. Chem Phys Lett. 2009 Jan 01; 473(4-6):330-335. PMID: 21103002.
      View in: PubMed
    39. Satterlee JD, Suquet C, Bidwai AK, Erman JE, Schwall L, Jimenez R. Mass instability in isolated recombinant FixL heme domains of Bradyrhizobium japonicum. Biochemistry. 2008 Feb 12; 47(6):1540-53. PMID: 18201102.
      View in: PubMed
    40. Schafer D, Gibson EA, Amir W, Erikson R, Lawrence J, Vestad T, Squier J, Jimenez R, Marr DW. Three-dimensional chemical concentration maps in a microfluidic device using two-photon absorption fluorescence imaging. Opt Lett. 2007 Sep 01; 32(17):2568-70. PMID: 17767307.
      View in: PubMed
    41. Gibson EA, Gaudiosi DM, Kapteyn HC, Jimenez R, Kane S, Huff R, Durfee C, Squier J. Efficient reflection grisms for pulse compression and dispersion compensation of femtosecond pulses. Opt Lett. 2006 Nov 15; 31(22):3363-5. PMID: 17072424.
      View in: PubMed
    42. Gaudiosi DM, Gagnon E, Lytle AL, Fiore JL, Gibson EA, Kane S, Squier J, Murnane MM, Kapteyn HC, Jimenez R, Backus S. Multi-kilohertz repetition rate Ti:sapphire amplifier based on down-chirped pulse amplification. Opt Express. 2006 Oct 02; 14(20):9277-83. PMID: 19529310.
      View in: PubMed
    43. Cho BM, Carlsson CF, Jimenez R. Photon echo spectroscopy of porphyrins and heme proteins: effects of quasidegenerate electronic structure on the peak shift decay. J Chem Phys. 2006 Apr 14; 124(14):144905. PMID: 16626243.
      View in: PubMed
    44. Jimenez R, Salazar G, Yin J, Joo T, Romesberg FE. Protein dynamics and the immunological evolution of molecular recognition. Proc Natl Acad Sci U S A. 2004 Mar 16; 101(11):3803-8. PMID: 15001706.
      View in: PubMed
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