1.  Gouterman, M., Mathies, R.A., Smith, B.E. and Caughey, W.S. Porphyrins XIX:  Tripdoublet and Quartet Luminescence in Cu and VO Complexes.  J. Chem. Phys. 52, 3795-3802 (1970).

 2.  Mathies, R. and Albrecht, A.C.  Electric Field Perturbation of the 1A1g®1B2u Transition in Benzene.  Chem. Phys. Lett. 16, 231-234 (1972).

 3.  Mathies, R. and Albrecht, A.C.  Electric Field Broadening of the 1A1(2) Transition in Azulene.  J. Chem. Phys. 60, 1420-1423 (1974).

 4.  Mathies, R. and Albrecht, A.C.  Experimental and Theoretical Studies on the Excited State Polarizabilities of Benzene, Naphthalene and Anthracene.  J. Chem. Phys. 60, 2500-2508 (1974).

 5.  Friedrich, D.M., Mathies, R. and Albrecht, A.C.  Studies of Excited Electronic States of Anthracene and Some of Its Derivatives by Photoselection and PPP-SCF Calculations.  J. Mol. Spectrosc. 51, 166-188 (1974).

 6.  Veatch, W.R., Mathies, R., Eisenberg, M. and Stryer, L.  Simultaneous Fluorescence and Conductance Studies of Planar Bilayer Membranes Containing a Highly Active and Fluorescent Analog of Gramicidin A.  J. Mol. Biol. 99, 75-92 (1975).

 7.  Mathies, R., Oseroff, A.R. and Stryer, L.  Rapid-flow Resonance Raman Spectroscopy of Photolabile Molecules: Rhodopsin and Isorhodopsin.  Proc. Natl. Acad. Sci. USA 73, 1-5 (1976).

 8.  Mathies, R. and Stryer, L.  Retinal Has a Highly Dipolar Vertically Excited Singlet State:  Implications for Vision. Proc. Natl. Acad. Sci. USA 73, 2169-2173 (1976).

 9.  Mathies, R., Oseroff, A.R., Freedman, T.B. and Stryer, L. Resonance Raman Spectroscopy:  Application of Tunable Lasers to the Study of the Molecular Mechanisms and Dynamics of Visual Excitation, in "Tunable Lasers and Applications" (Mooradian, A., Jaeger, T. and Stokseth, P., eds.), Springer-Verlag, p. 294-302 (1976).

10.   Mathies, R., Freedman, T.B. and Stryer, L.  Resonance Raman Studies of the Conformation of Retinal in Rhodopsin and Isorhodopsin.  J. Mol. Biol. 109, 367-372 (1977).

11.   Mathies, R. and Yu, N.-T.  Raman Spectroscopy with Intensified Vidicon Detectors:  A Study of Intact Bovine Lens Proteins. J. Raman Spectrosc. 7, 349-352 (1978).

12.   Eyring, G. and Mathies, R.  Resonance Raman Studies of Bathorhodopsin:  Evidence for a Protonated Schiff Base Linkage. Proc. Natl. Acad. Sci. USA 76, 33-37 (1979).

13.   Mathies, R.  Biological Applications of Resonance Raman Spectroscopy in the Visible and Ultraviolet:  Visual Pigments, Purple Membrane, and Nucleic Acids, in  "Chemical and Biochemical Applications of Lasers," Vol. 4 (Moore, C.B., ed.), Academic Press, pp. 55-99 (1979).

14.   Eyring, G., Curry, B., Mathies, R., Fransen, R., Palings, I. and Lugtenburg, J.  Interpretation of the Resonance Raman Spectrum of Bathorhodopsin Based on Visual Pigment Analogues.  Biochemistry 19, 2410-2418 (1980).

15.   Braiman, M. and Mathies, R.  Resonance Raman Evidence for an All-trans  to 13-cis  Isomerization in the Proton-Pumping Cycle of Bacteriorhodopsin.  Biochemistry 19, 5421-5428 (1980).

16.   Eyring, G., Curry, B., Mathies, R., Broek, A. and Lugtenburg, J.  Assignment of the Anomalous Resonance Raman Vibrations of Bathorhodopsin.  J. Am. Chem. Soc. 102, 5390-5392 (1980).

17.   Mathies, R., Eyring, G., Curry, B., Broek, A., Palings, I., Fransen, R. and Lugtenburg, J.  Interpretation of the Resonance Raman Spectrum of Bathorhodopsin, in "Proceedings of the VIIth International Conference on Raman Spectroscopy," (Murphy, W.F., ed.), North-Holland, p. 546-547 (1980).

18.   Mathies, R.  Resonance Raman Spectroscopy of Rhodopsin and Bacteriorhodopsin Isotopic Analogs.  Meth. Enzymol. 88, 633-643 (1982).

19.   Eyring, G., Curry, B., Broek, A., Lugtenburg, J. and Mathies, R.  Assignment and Interpretation of Hydrogen Out-of-Plane Vibrations in the Resonance Raman Spectra of Rhodopsin and Bathorhodopsin.  Biochemistry 21, 384-393 (1982).

20.   Braiman, M. and Mathies, R.  Resonance Raman Spectra of Bacteriorhodopsin's Primary Photoproduct:  Evidence for a Distorted 13-cis Retinal Chromophore.  Proc. Natl. Acad. Sci. USA 79, 403-407 (1982).

21.   Braiman, M. and Mathies, R.  Spinning Sample Raman Spectroscopy at 77oK:  Bacteriorhodopsin's Primary Photoproduct. Meth. Enzymol. 88, 648-659 (1982).

22.   Barry, B. and Mathies, R.  Resonance Raman Microscopy of Rod and Cone Photoreceptors.  J. Cell Biol. 94, 479-482 (1982).

23.   Curry, B., Broek, A., Lugtenburg, J. and Mathies, R.  Vibrational Analysis of All-trans Retinal.  J. Am. Chem. Soc. 104, 5274-5286 (1982).

24.   Myers, A.B., Mathies, R.A., Tannor, D.J. and Heller, E.J. Excited State Geometry Changes from Preresonance Raman Intensities:  Isoprene and Hexatriene.  J. Chem. Phys. 77, 3857-3866 (1982).

25.   Mathies, R.  Resonance Raman Investigations of the Primary Photochemistry in Visual Pigments and Bacteriorhodopsin, in  "Frontiers in Biochemical and Biophysical Studies of Proteins and Membranes," (Liu, T.-Y., Sakakibara, S., Schechter, A.N., Yagi, K., Yagima, H. and Yasunobu, K.T., eds.), Elsevier, p. 367-386 (1983).

26.   Smith, S.O., Braiman, M. and Mathies, R.  Time-resolved Resonance Raman Spectroscopy of the K610 and O640 Photointermediates of Bacteriorhodopsin, in  "Time-resolved Vibrational Spectroscopy," (Atkinson, G., ed.), Academic Press, p. 219-230 (1983).

27.   Harris, R.A., Mathies, R. and Myers, A.  A Simple Sum Rule in Raman Theory.  Chem. Phys. Lett. 94, 327-330 (1983).

28.   Myers, A.B., Harris, R.A. and Mathies, R.A.  Resonance Raman Excitation Profiles of Bacteriorhodopsin.  J. Chem. Phys. 79, 603-613 (1983).

29.   Ponder, M. and Mathies, R.  Excited-State Polarizabilities and Dipole Moments of Diphenylpolyenes and Retinal.  J. Phys. Chem. 87, 5090-5098 (1983).

30.   Smith, S.O., Pardoen, J.A., Mulder, P.P.J., Curry, B., Lugtenburg, J. and Mathies, R.  Chromophore Structure in Bacteriorhodopsin's O640 Photointermediate.  Biochemistry 22, 6141-6148 (1983).

31.   Curry, B., Palings, I., Broek, A., Pardoen, J.A., Mulder, P.P.J., Lugtenburg, J. and Mathies, R.  Vibrational Analysis of 13-cis Retinal.  J. Phys. Chem. 88, 688-702 (1984).

32.   Mathies, R.A.  Resonance Raman Determination of Retinal Chromophore Structure in Bacteriorhodopsin,  in  "Spectroscopy of Biological Molecules," NATO ASI Series C, Vol. 139, 303-328 (1984).

33.   Harbison, G.S., Smith, S.O., Pardoen, J.A., Mulder, P.P.J., Lugtenburg, J., Herzfeld, J., Mathies, R. and Griffin, R.G.   Solid-state 13C NMR Studies of Retinal in Bacteriorhodopsin.  Biochemistry 23, 2662-2667 (1984).

34.   Smith, S.O., Myers, A.B., Pardoen, J.A., Winkel, C., Mulder, P.P.J., Lugtenburg, J. and Mathies, R.   Determination of Retinal Schiff Base Configuration in Bacteriorhodopsin.  Proc. Natl. Acad. Sci. USA 81, 2055-2059 (1984).

35.   Harbison, G.S., Smith, S.O., Pardoen, J.A., Winkel, C., Lugtenburg, J., Herzfeld, J., Mathies, R. and Griffin, R.G.  Dark-adapted Bacteriorhodopsin Contains 13-cis,15-syn and all-trans,15-anti Retinal Schiff Bases.  Proc. Natl. Acad. Sci. USA 81, 1706-1709 (1984).

36.   Myers, A.B.  and Mathies, R.A.  Excited-state Torsional Dynamics of Cis-stilbene from Resonance Raman Intensities.  J. Chem. Phys. 81, 1552-1558 (1984).

37.   Rothschild, K.J., Marrero, H., Braiman, M. and Mathies, R.  Primary Photochemistry of Bacteriorhodopsin:  Comparison of Fourier Transform Infrared Difference Spectra with Resonance Raman Spectra.  Photochem. Photobiol. 40, 675-679  (1984).

38.   Smith, S.O., Marvin, M.J., Bogomolni, R.A. and Mathies, R.A.  Structure of the Retinal Chromophore in the hR578 Form of Halorhodopsin.  J. Biol. Chem. 259, 12326-12329 (1984).

39.   Curry, B., Palings, I., Broek, A.D., Pardoen, J.A., Lugtenburg, J. and Mathies, R.  Vibrational Analysis of the Retinal Isomers.  Adv. Infrared Raman Spectrosc. 12, 115-178 (1985).

40.   Smith, S.O., Myers, A.B., Mathies, R.A., Pardoen, J.A., Winkel, C., van den Berg, E.M.M. and Lugtenburg, J.  Vibrational Analysis of the All-trans Retinal Protonated Schiff Base.  Biophys. J. 47, 653-664 (1985).

41.   Smith, S.O. and Mathies, R.A.  Resonance Raman Spectra of the Acidified and Deionized Forms of Bacteriorhodopsin.  Biophys. J., 47, 251-254 (1985).

42.   Smith, S.O., Lugtenburg, J. and Mathies, R.A.  Determination of Retinal Chromophore Structure in Bacteriorhodopsin with Resonance Raman Spectroscopy.  J. Membrane Biol. 85, 95-109 (1985).

43.   Harbison, G.S., Smith, S.O., Pardoen, J.A., Courtin, J.M.L., Lugtenburg, J., Herzfeld, J., Mathies, R.A. and Griffin, R.G.  Solid-State 13C NMR Detection of a Perturbed 6-s-trans Chromophore in Bacteriorhodopsin.  Biochemistry, 24, 6955-6962 (1985).

44.   Myers, A.B., Trulson, M.O. and Mathies, R.A.  Quantitation of Homogeneous and Inhomogeneous Broadening Mechanisms in Trans-stilbene Using Absolute Resonance Raman Intensities.  J. Chem. Phys., 83, 5000-5006 (1985).

45.   Stern, D. and Mathies, R.  Picosecond and Nanosecond Resonance Raman Evidence for Structural Relaxation in Bacteriorhodopsin's Primary Photoproduct, in "Time-resolved Vibrational Spectroscopy,"  (M. Stockburger and A. Laubereau, eds.)  Proceedings in Physics, Vol. 4, Springer-Verlag, p. 250-254 (1985).

46.   Myers, A.B., Trulson, M.O., Pardoen, J.A., Heeremans, C., Lugtenburg, J. and Mathies, R.A.  Absolute Resonance Raman Intensities Demonstrate That the Spectral Broadening Induced by the b-ionone Ring in Retinal is Homogeneous, J. Chem. Phys., 84, 633-640 (1986).

47.   Trulson, M.O. and Mathies, R.A.  Raman Cross Section Measurements in the Visible and Ultraviolet Using an Integrating Cavity:  Application to Benzene, Cyclohexane and Cacodylate.  J. Chem. Phys., 84, 2068-2074 (1986).

48.   Mathies, R.A. and Stryer, L.  Single-Molecule Fluorescence Detection:  A Feasibility Study Using Phycoerythrin, in "Fluorescence in the Biological Sciences"  (D.L. Taylor, A.S. Waggoner, F. Lanni, R.F. Murphy and R. Birge, eds.)  Alan R. Liss, 129-140 (1986).

49.   Smith, S.O., Hornung, I., van der Steen, R., Pardoen, J.A., Braiman, M.S., Lugtenburg, J. and Mathies, R.A.  Are C14-C15 Single Bond Isomerizations of the Retinal Chromophore Involved in the Proton-pumping Mechanism of Bacteriorhodopsin?  Proc. Natl. Acad. Sci. USA 83, 967-971 (1986).

50.   Lugtenburg, J., Muradin-Szweykowska, M., Harbison, G.S., Smith, S.O., Heeremans, C., Pardoen, J.A., Herzfeld, J., Griffin, R.G. and Mathies, R.A.  Mechanism for the Opsin Shift of Retinal's Absorption in Bacteriorhodopsin.  J. Am. Chem. Soc., 108, 3104-3105 (1986).

51.   Cruz, P., Hall, K., Puglisi, J., Davis, P., Hardin, C.C., Trulson, M.O., Mathies, R.A., Tinoco Jr., I., Johnson, W.C., Jr. and Neilson, T.  The Left-handed Z-form of Double-Stranded RNA, in "Biomolecular Stereodynamics IV" (R.H. Sarma and M.H. Sarma, eds.)  Adenine Press, IV, p. 179-200 (1986).

52.   Harris, R.A., Mathies, R.A. and Pollard, W.T.  Simple Interpretation of Dephasing in Absorption and Resonance Raman Theory.  J. Chem. Phys. 85, 3744-3748 (1986).

53.   van der Steen, R., Biesheuvel, P.L., Mathies, R.A., and Lugtenburg, J.  Retinal Analogues with Locked 6-7 Conformations Show That Bacteriorhodopsin Requires the 6-s-trans Conformation of the Chromophore.  J. Am. Chem. Soc. 108, 6410-6411 (1986).

54.   Myers, A.B. and Mathies, R.A.  Resonance Raman Intensities:  A Probe of Excited State Structure and Dynamics, in "Biological Applications of Raman Spectroscopy:   Vol. 2 - Resonance Raman Spectra of Polyenes and Aromatics"  (ed. T.G. Spiro) John Wiley & Sons, Inc., p. 1-58 (1987).

55.   Mathies, R.A., Smith, S.O. and Palings, I.  Determination of Retinal Chromophore Structure in Rhodopsins, in "Biological Applications of Raman Spectroscopy:  Vol.2 - Resonance Raman Spectra of Polyenes and Aromatics" (ed. T.G. Spiro) John Wiley & Sons, Inc. p. 59-108 (1987).

56.   Mathies, R.A. and Myers, A.B.  Femtosecond Excited State Dynamics from Resonance Raman Intensities. in  "Time-Resolved Vibrational Spectroscopy" (ed., Atkinson, G.H.) Gordon and Breach, p. 41-54 (1987).

57.   Smith, S.O., Braiman, M.S., Myers, A.B., Pardoen, J.A., Courtin, J.M.L., Winkel, C., Lugtenburg, J. and Mathies, R.A.  Vibrational Analysis of the All-trans Retinal Chromophore in Light-Adapted Bacteriorhodopsin.  J. Am. Chem. Soc., 109, 3108-3125 (1987).

58.   Smith, S.O., Pardoen, J.A., Lugtenburg, J. and Mathies, R.A.  Vibrational Analysis of the 13-cis Retinal Chromophore in Dark-Adapted Bacteriorhodopsin.  J. Phys. Chem., 91, 804-819 (1987).

59.    Smith, S.O., Palings, I., Copié, V., Raleigh, D.P., Courtin, J., Pardoen, J.A., Lugtenburg, J., Mathies, R.A., and Griffin, R.G.  Low-Temperature Solid-State 13C-NMR Studies of the Retinal Chromophore in Rhodopsin.  Biochemistry, 26, 1606-1611 (1987).

60.   Smith, S.O., Copie, V., Raleigh, D.P., Griffin, R.G., Palings, I., Mathies, R.A., Courtin, J., Winkel, C. and Lugtenburg, J. NMR Studies of Isotopically Labeled Rhodopsins. in  Biophysical Studies of Retinal Proteins, ed. T.G. Ebrey, H. Frauenfelder, B. Honig and K. Nakanishi, University of Illinois Press, p. 226-232 (1987).

61.   Mathies, R.A., Smith, S.O. and Lugtenburg, J. Determination of Retinal Chromophore Structure and Photochemistry in Bacteriorhodopsin with Resonance Raman Spectroscopy. in Biophysical Studies of Retinal Proteins, ed. T.G. Ebrey, H. Frauenfelder, B. Honig and K. Nakanishi, University of Illinois Press, p. 126-132 (1987).

62.   Mathies, R.A., Smith, S.O., Harbison, G.S., Herzfeld, J., Griffin, R.G. and Lugtenburg, J.  Determination of Chromophore Structure and Photochemistry in Bacteriorhodopsin with Resonance Raman, NMR, and Chemical Analogues. in  Primary Processes in Photobiology, ed. T. Kobayashi, Springer-Verlag Proceedings in Physics, 20, p. 136-143 (1987).

63.   Barry, B. and Mathies, R.A.  Raman Microscope Studies of the Primary Photochemistry of Vertebrate Visual Pigments with Absorption Maxima from 430 to 502 nm.  Biochemistry, 26, 59-64 (1987).

64.   Mathies, R.A., Smith, S.O., Harbison, G.S., Courtin, J.M.L., Herzfeld, J., Griffin, R.G., and Lugtenburg, J.  Determination of Retinal Chromophore Structure and Photochemistry in Rhodopsins with Resonance Raman, NMR and Chemical Analogues. in  Retinal Proteins (ed. U. Ovchinnikov) VNU Press, Utrecht, The Netherlands, p. 231-240 (1987).

65.   Palings, I., Pardoen, J.A., van den Berg, E., Winkel, C., Lugtenburg, J., and Mathies, R.A.  Assignment of Fingerprint Vibrations in the Resonance Raman Spectra of Rhodopsin, Isorhodopsin and Bathorhodopsin:  Implications for Chromophore Structure and Environment.  Biochemistry, 26, 2544-2556 (1987).

66.   Trulson, M.O., Dollinger, G.D., and Mathies, R.A.  Femtosecond Photochemical Excited State Ring Opening Dynamics of 1,3-Cyclohexadiene from Resonance Raman Intensities.  J. Am. Chem. Soc., 109, 586-587 (1987).

67.   Barry, B., Mathies, R.A., Pardoen, J.A., and Lugtenburg, J.  Raman Microscope and Quantum Yield Studies on the Primary Photochemistry of A2-Visual Pigments. Biophys. J.,52, 603-610 (1987).

68.   Fodor, S.P.A., Bogomolni, R.A., and Mathies, R.A.  Structure of the Retinal Chromophore in the hRL Intermediate of Halorhodopsin from Resonance Raman Spectroscopy. Biochemistry, 26, 6775-6778 (1987).

69.   Trulson, M.O., Cruz, P., Puglisi, J.D., Tinoco, I., Jr., and Mathies, R.A. Raman Spectroscopic Study of Left-Handed Z-RNA. Biochemistry, 26, 8624-8630 (1987).

70.   Loppnow, G.R. and Mathies R.A. Excited-State Structure and Isomerization Dynamics of the Retinal Chromophore in Rhodopsin from Resonance Raman Intensities. Biophys. J., 54, 35-43 (1988).

71.   Mathies, R.A., Fodor, S.P.A., Smith, S.O., van den Berg, E.M.M., Gebhard, R. and Lugtenburg, J.  Determination of Retinal Chromophore Structure in Rhodopsins with Resonance Raman Spectroscopy, in  Spectroscopy of Biological Molecules - New Advances, ed. E.D. Schmid, F.W. Schneider and F. Siebert, John Wiley & Sons Inc., England, p. 215-223 (1988).

72.   Fodor, S.P.A., Pollard, W.T., Gebhard, R., van den Berg, E.M.M., Lugtenburg, J. and Mathies, R.A. Bacteriorhodopsin's L550 Intermediate Contains a C14-C15 s-trans Retinal Chromophore, Proc. Natl. Acad. Sci. U.S.A., 85, 2156-2160 (1988).

73.   Mathies, R.A., Brito Cruz, C.H., Pollard, W.T., and Shank, C.V.  Direct Observation of the Femtosecond Excited-State cis-trans Isomerization in Bacteriorhodopsin, Science 240, 777-779 (1988).

74.   Lugtenburg, J., Mathies, R.A., Griffin, R.G. and Herzfeld, J.  Structure and Function of Rhodopsins from Solid-State NMR and Resonance Raman Spectroscopy of Isotopic Retinal Derivatives, Trends in Biochemical Sciences, 13, 388-393 (1988).

75.   Fodor, S.P.A., Ames, J.B., Gebhard, R., van den Berg, E.M.M., Stoeckenius, W., Lugtenburg, J., and Mathies, R.A., Chromophore Structure in Bacteriorhodopsin's N Intermediate: Implications for the Proton-Pumping Mechanism.  Biochemistry 27, 7097-7101 (1988).

76.   Fodor, S.P.A., Lagarias, J.C. and Mathies, R.A.,   Resonance Raman Spectra of the Pr-Form of Phytochrome,  Photochem.  Photobiol. 48, 129-136 (1988).

77.   Mathies, R.A., Pollard, W.T., Brito Cruz, C.H., and Shank, C.V.  Direct Observation of the Femtosecond Excited-State Cis-Trans Isomerization in Bacteriorhodopsin. in  Ultrafast Phenomena VI Springer Series in Chemical Physics, eds., Yajima, T., Yoshihara, K., Harris, C.B., and Shionoya, S., Springer-Verlag, Berlin Heidelberg, Vol. 48, p. 584-589 (1988).

78.   Lee, S.-Y. and Mathies, R.A. Polarizability Theory and Sum Rules, Chem. Phys. Lett. 151, 9-15 (1988).

79.   Baselt, D.R., Fodor, S.P.A., van der Steen, R., Lugtenburg, J., Bogomolni, R.A. and Mathies, R.A.   Halorhodopsin and Sensory Rhodopsin Contain a C6-C7 s-trans Retinal Chromophore, Biophys. J.  55, 193-196 (1989).

80.   Palings, I., van den Berg, E.M.M., Lugtenburg, J., and Mathies, R.A.  Complete Assignment of the Hydrogen Out-of-Plane Wagging Vibrations of Bathorhodpsin:  Chromophore Structure and Energy Storage in the Primary Photoproduct of Vision, Biochemistry  28, 1498-1507 (1989).

81.   van der Steen, R., Biesheuvel, P.L., Erkelens, C., Mathies, R.A., Lugtenburg, J.  8,16- and 8,18-methanobacteriorhodopsin.  Synthesis and Spectroscopy of 8,16- and 8,18-methanoretinal and Their Interaction with Bacteriorhodopsin.  Recl. Trav. Chim. Pays-Bas, 108, 83-93 (1989).

82.   Pollard, W.T., Brito Cruz, C.H., Shank, C.V., and Mathies, R.A.  Direct Observation of the Femtosecond Excited-State Cis-trans Photoisomerization of Bacteriorhodopsin:  Multilevel Line Shape Theory for Femtosecond Dynamic Hole Burning and its Application, J. Chem. Phys. 90, 199-208 (1989).

83.   Loppnow, G.R., Barry, B. A. and Mathies, R.A.  Why Are Blue Visual Pigments Blue? A Resonance Raman Microprobe Study,  Proc. Natl. Acad. Sci. U.S.A. 86, 1515-1518 (1989).
       
84.   Ames, J.B., Fodor, S.P.A., Gebhard, R., Raap, J.,  van den Berg, E.M.M., Lugtenburg, J. and Mathies, R.A.  Bacteriorhodopsin's M412 Intermediate Contains a 13-cis, 14-s-trans, 15-anti-Retinal Schiff Base Chromophore, Biochemistry 28, 3681-3687 (1989).

85.   Trulson, M.O., Dollinger, G.D., and Mathies, R.A.  Excited-State Structure and Femtosecond Ring-Opening Dynamics of 1,3-Cyclohexadiene from Absolute Resonance Raman Intensities, J. Chem. Phys. 90, 4274-4281 (1989).

86.   Reid, P.J., Doig, S.J., and Mathies, R.A.  Direct Measurement of the Photochemical Ring Opening in 1,3-Cyclohexadiene by Picosecond Time-Resolved UV Resonance Raman,  Chem. Phys. Lett. 156, 163-168 (1989).

87.   Mathies, R.A., Lugtenburg, J. and Shank  C.V.  From Femtoseconds to Biology:  Mechanism of the Light-Driven Proton Pump in Bacteriorhodopsin,  Proceedings of the International Society for Optical Engineering - SPIE, Volume 1057  "Biomolecular Spectroscopy", 138-145 (1989).

88.   Lee, S.-Y., Pollard, W.T. and Mathies, R.A.  Classical Theory for Real-Time Femtosecond Probing of the NaI* Photodissociation,  J. Chem. Phys. 90, 6146-6150 (1989).
 
89.   Loppnow, G. R. and Mathies, R. A.  A 77-K Cold Stage for Raman Microprobes and Optical Microscopy,  Rev. Sci. Instrum. 60, 2628-2630 (1989).

90.   Peck, K., Stryer, L., Glazer, A. N., and Mathies, R.A.  Single- Molecule Fluorescence Detection:  Autocorrelation Criterion and Experimental Realization with Phycoerythrin,  Proc. Natl. Acad. Sci. U.S.A. 86, 4087-4091 (1989).

91.   Lin, S. W. and Mathies, R.A.  Orientation of the Protonated Retinal Schiff Base Group in Bacteriorhodopsin from Absorption Linear Dichroism, Biophys. J. 56, 653-660 (1989).

92.   Lee, S.-Y., Pollard, W.T. and Mathies, R.A.  Quasi-Classical Models of Transition State Absorption or Emission, Chem. Phys. Lett. 163, 11-18 (1989).

93.   Lee, S.-Y., Pollard, W.T. and Mathies, R.A.  Quantum Theory for Transition State Absorption, Chem. Phys. Lett. 160, 531-537 (1989).

94.   Fodor, S.P.A., Gebhard, R., Lugtenburg, J., Bogomolni, R.A. and Mathies, R.A.  Structure of the Retinal Chromophore in Sensory Rhodopsin I from Resonance Raman Spectroscopy, J. Biol. Chem. 264, 18280-18283 (1989).

95.   Mathies, R. A., Peck, K., and Stryer, L.  High-Sensitivity Single-Molecule Fluorescence Detection in Theory and Practice,   Proceedings of the 6th Annual BIOTECH USA Conference, San Francisco CA, Oct. 2-4, 205-213 (1989). 

96.   Pollard, W. T., Lee, S.-Y. and Mathies, R. A.  Wave Packet Theory of Dynamic Absorption Spectra in Femtosecond Pump-Probe Experiments,  J. Chem. Phys. 92, 4012-4029 (1990).
   
97.   Netto, M. M., Fodor, S. P. A. and Mathies, R. A.  Ultraviolet Resonance Raman Spectroscopy of Bacteriorhodopsin, Photochem. Photobiol. 52, 605-607 (1990).

98.   Makino, C. L., Kraft, T. W., Mathies, R. A., Lugtenburg, J., Miley, M. E., van der Steen, R., and Baylor, D. A.   Effects of Modified Chromophores on the Spectral Sensitivity of Salamander, Squirrel and Macaque Cones,  J. Physiol. 424, 545-560 (1990).

99.   Smith, S. O., Palings, I., Miley, M. E., Courtin, J., de Groot, H., Lugtenburg, J., Mathies, R. A., and Griffin, R. G.  Solid-State NMR Studies on the Mechanism of the Opsin Shift in the Visual Pigment Rhodopsin, Biochemistry 29, 8158-8164 (1990)
   
100. Trulson, M. O. and Mathies, R. A.  Excited-State Structure and Dynamics of Isoprene from Absolute Resonance Raman Intensities, J. Phys. Chem. 94, 5741-5747 (1990).

101.  Pollard, W. T., Fragnito, H. L., Bigot, J.-Y., Shank, C. V., and Mathies, R. A.  Quantum-Mechanical Theory for 6 fs Dynamic Absorption Spectroscopy and its Application to Nile Blue, Chem. Phys. Letts. 168, 239-245 (1990).

102.  A. N. Glazer, K. Peck and R. A. Mathies,  A Stable Double-Stranded DNA-Ethidium Homodimer Complex. Application to Picogram Fluorescence Detection of DNA in Agarose Gels, Proc. Natl. Acad. Sci. U.S.A. 87, 3851-3855 (1990).

103.  W. T. Pollard and R. A. Mathies,  Wavepacket Theory of Dynamic Absorption Spectra in Femtosecond Pump-probe Studies, in Picosecond and Femtosecond Spectroscopy from Laboratory to Real World, Proceedings of the International Society for Optical Engineering-SPIE 1209, 147-156 (1990).

104.  R. A. Mathies, K. Peck and L. Stryer,  High-sensitivity Single Molecule Fluorescence Detection,  in  Bioimaging and Two-dimensional Spectroscopy,  Proceedings of the International Society for Optical Engineering-SPIE  1205, 52-59 (1990).

105.  Ames, J. B. and Mathies, R. A.  The Role of Back-Reactions and Proton Uptake During the N Æ O Transition in Bacteriorhodopsin's Photocycle: A Kinetic Resonance Raman Study,  Biochemistry 29, 7181-7190 (1990).

106.  Mathies, R. A., Peck, K. and Stryer, L.  Optimization of High-Sensitivity Fluorescence Detection, Anal. Chem. 62, 1786-1791 (1990).

107.  Loppnow, G. R., Miley, M. E., Mathies, R. A., Liu, R. S. H., Kandori, H., Shichida, Y., Fukada, Y. and Yoshizawa, T.  Structure of the Retinal Chromophore in 7,9-dicis Rhodopsin.  Biochemistry 29, 8985-8991 (1990).

108.  Fodor, S. P. A., Lagarias, J. C. and Mathies, R. A.  Resonance Raman Analysis of the Pr and Pfr Forms of Phytochrome, Biochemistry 29, 11141-11146 (1990).

109.  Ames, J. B., Bolton, S. R., Netto, M. M., and Mathies, R. A.  Ultraviolet Resonance Raman Spectroscopy of Bacteriorhodopsin: Evidence Against Tyrosinate in the Photocycle, J. Am. Chem. Soc. 112, 9007-9009 (1990).

110.  Reid, P. J., Doig, S. J., and Mathies, R. A.  Picosecond Time-Resolved UV Resonance Raman Spectroscopy of the Photochemical Ring-Opening Reaction of 1,3,5-Cyclooctatriene and a-Phellandrene, J. Phys. Chem. 94, 8396-8399 (1990).

111. Kraft, T. W., Makino, C. L., Mathies, R. A., Lugtenburg, J., Schnapf, J. L., and Baylor, D. A.  Cone Excitations and Color Vision,  Cold Spring Harbor Symposia on Quantitative Biology, Vol. LV, 635-641 (1990).

112.  Lin, S. W., Fodor, S. P. A., Miercke, L. J. W., Shand, R. F., Betlach, M. C., Stroud, R. M. and Mathies, R.A.  Resonance Raman Spectra of Bacteriorhodopsin Mutants with Substitutions at Asp-85, Asp-96 and Arg-82,  Photochem. Photobiol. 53, 341-346 (1991).

113.  Mathies, R. A.  From Femtoseconds to Biology: Mechanism of Bacteriorhodopsin's Light-Driven Proton Pump, Proc. Indian Acad. Sci. (Chem. Sci.)  103, 283-293 (1991).

114.  Mathies, R. A., Lin, S. W., Ames, J. B. and Pollard, W. T. From Femtoseconds to Biology: Mechanism of Bacteriorhodopsin's Light-Driven Proton Pump,  Annual Reviews of Biophysics and Biophysical Chemistry 20, 491-518 (1991).

115.  Quesada, M. A., Rye, H. S., Gingrich, J. C., Glazer, A. N., and Mathies, R. A.  High-Sensitivity DNA Detection with a Laser- Excited Confocal Fluorescence Gel Scanner, BioTechniques 10,  616-625 (1991).

116.  Rye, H. S., Quesada, M. A., Peck, K., Mathies, R. A. and  Glazer, A. N.  High-Sensitivity Two-Color Detection of Double-Stranded DNA with a Confocal Fluorescence Gel Scanner Using Ethidium Homodimer and Thiazole Orange, Nucleic Acids Research 19, 327-333 (1991).

117.  Reid, P. J., Doig, S. J. and Mathies, R. A.  Pericyclic Photochemical Ring-Opening Reactions are Complete in Picoseconds:  A Time-Resolved UV Resonance Raman Study, in  Biomolecular Spectroscopy,  Proceedings of the International Society for Optical Engineering-SPIE  1432, 172-183 (1991).

118.  Doig, S. J., Reid, P. J. and Mathies, R. A.  Picosecond Time-resolved Resonance Raman Spectroscopy of Bacteriorhodopsin: Structure and Kinetics of the J, K, and KL Intermediates, in  Biomolecular Spectroscopy,  Proceedings of the International Society for Optical Engineering-SPIE  1432, 184-196 (1991).

119.  Doig, S. J., Reid, P. J. and Mathies, R. A.  Picosecond Time-Resolved Resonance Raman Spectroscopy of Bacteriorhodopsin's J, K and KL Intermediates, J. Phys. Chem. 95, 6372-6379 (1991).

120.  Loppnow, G. R., Mathies, R. A., Middendorf, T. R., Gottfried, D. S. and Boxer, S. G.  Photochemical Hole-burning Spectroscopy of Bovine Rhodopsin and Bacteriorhodopsin, J. Phys. Chem. 96, 737-745 (1991).

121.  Schoenlein, R. W., Peteanu, L. A., Mathies, R. A. and Shank, C. V.  The First Step in Vision:  Femtosecond Isomerization of Rhodopsin, Science 254, 412-415 (1991).

122.  Shreve, A. P., Cherepy, N., Franzen, S., Boxer, S. G., and Mathies, R. A.  Rapid-flow Resonance Raman Spectroscopy of Bacterial Photosynthetic Reaction Centers, Proc. Natl. Acad. Sci. USA  88, 11207-11211 (1991).

123.  Rye, H. S., Yue, S., Quesada, M. A., Haughland, R. P., Mathies, R. A. and Glazer, A. N.,  Picogram Detection of Stable Dye-DNA Intercalation Complexes with a Two-Color Laser-Excited Fluorescence Gel Scanner, Methods in Enzymology, Recombinant DNA Part H, Ed. R. Wu, 217, 414-431 (1993).

124.  Dexheimer, S. L., Wang, Q., Peteanu, L. A., Pollard, W. T., Mathies, R. A. and Shank, C. V.   Femtosecond Impulsive Excitation of Nonstationary Vibrational States in Bacteriorhodopsin,  Chem. Phys. Letts. 188, 61-66 (1992).

125.  Shreve, A. P., Cherepy, N. J. and Mathies, R. A.  Effective Rejection of Fluorescence Interference in Raman Spectroscopy Using a Shifted Excitation Difference Technique,  Applied Spectroscopy 46, 707-711 (1992).

126.  Pollard, W. T., Dexheimer, S. L., Wang, Q., Peteanu, L. A., Shank, C. V. and Mathies, R. A.  Theory of Dynamic Absorption Spectroscopy: 4.  Application to 12-Femtosecond Resonant Impulsive Raman Spectroscopy of Bacteriorhodopsin, J. Phys. Chem. 96, 6147-6158 (1992).

127.  Huang, X. C., Quesada, M. A. and Mathies, R. A.  Capillary Array Electrophoresis Using Laser-Excited Confocal Fluorescence Detection, Analytical Chemistry 64, 967-972 (1992).

128.  Huang, X. C., Quesada, M. A. and Mathies, R. A.   DNA Sequencing Using Capillary Array Electrophoresis, Analytical Chemistry 64, 2149-2154 (1992).

129.  Lin, S. W., Sakmar, T. P., Franke, R. R., Khorana, H. G. and Mathies, R. A.  Resonance Raman Microprobe Spectroscopy of Rhodopsin Mutants:  Effect of Substitutions in the Third Transmembrane Helix,  Biochemistry 31, 5105-5111 (1992).

130.  Lawless, M. K. and Mathies, R. A.   Excited-state Structure and Electronic Dephasing Time of Nile Blue from Absolute Resonance Raman Intensities, Journal of Chemical Physics 96, 8037-8045 (1992).

131.  Ames, J. B., Ros, M., Raap, J., Lugtenburg, J. and Mathies, R. A.  Time-resolved Ultraviolet Resonance Raman Studies of Protein Structure: Application to Bacteriorhodopsin, Biochemistry 31, 5328-5334 (1992).

132.  Pollard, W. T., and Mathies, R. A.   Analysis of Femtosecond Dynamic Absorption Spectra of Nonstationary States,  Annual Reviews of Physical Chemistry 43, 497-523 (1992).

133.  Reid, P. J., Wickham, S. D., and Mathies, R. A.   Picosecond UV Resonance Raman Spectroscopy of the Photochemical Hydrogen Migration in 1,3,5-Cycloheptatriene, J. Phys. Chem. 96, 5720-5724 (1992).

134.  Rye, H. S., Yue, S., Wemmer, D. E., Quesada, M. A., Haughland, R. P., Mathies, R. A. and Glazer, A. N.  Stable Fluorescent Complexes of Double-Stranded DNA with Bis-intercalating Asymmetric Cyanine Dyes: Properties and Applications,  Nucleic Acids Research 20, 2803-2812 (1992).

135.  Peteanu, L. A. and Mathies, R. A.  Resonance Raman Intensity Analysis of the Excited-State Proton Transfer in 2-Hydroxyacetophenone, J. Phys. Chem. 96, 6910-6916 (1992).

136.  Cromwell, M. E. M., Gebhard, R., Li, X.-Y., Batenburg, E. S., Hopman, J. C. P., Lugtenburg, J. and Mathies, R. A.  Synthesis and Vibrational Analysis of a Locked 14-s-cis Conformer of Retinal, J. Amer. Chem. Soc. 114, 10860-10869 (1992).

137.  Peteanu, L. A., Pollard, W. T., Mathies, R. A. Schoenlein, R. A., Dexheimer, S. L., Wang, Q. and Shank, C. V.   Femtosecond Spectroscopy of Retinal Proteins, in  "Time-Dependent Quantum Molecular Dynamics" NATO ASI Series B: Physics Vol. 299, ed.J Broeckhove and L. Lathouwers, p. 219-232 (1992).

138.  Ames, J. B., Raap, J., Lugtenburg, J., and Mathies, R. A.   Resonance Raman Study of Halorhodopsin Photocycle Kinetics, Chromophore Structure, and Chloride-Pumping Mechanism,  Biochemistry 31, 12546-12554 (1992).

139.  Rye, H. S., Dabora, J. M., Quesada, M. A., Mathies, R. A. and Glazer, A. N.  Fluorometric Assay Using Dimeric Dyes for Double- and Single-Stranded DNA and RNA with Picogram Sensitivity, Analytical Biochemistry 208, 144-150 (1993).

140.  Mathies, R. A. and Huang, X. C.  Capillary Array Electrophoresis: An Approach to High-speed, High-throughput DNA Sequencing, Nature 359, 167-169 (1992).

141.  Doig, S. J., Reid, P. J. and Mathies, R. A.  Picosecond Time-Resolved Resonance Raman Spectroscopy of Bacteriorhodopsin:  Structure and Kinetics of the J, K, and  KL Intermediates.  in "Time-Resolved Vibrational Spectroscopy V" (ed., H. Takahashi) Springer-Verlag Proceedings in Physics 68, 45-48 (1992).

142.  Reid, P. J., Doig, S. J. and Mathies, R. A.  Photochemical Ring Openings are Complete in Picoseconds:  A Time-Resolved UV Resonance Raman Study.   in "Time-Resolved Vibrational Spectroscopy V" (ed., H. Takahashi) Springer-Verlag Proceedings in Physic 68, 125-126 (1992).

143.  Lawless, M.K., Reid, P. J. and Mathies R. A.  Analysis of Condensed Phase Photochemical Reaction Mechanisms with Resonance Raman Spectroscopy, in Ultrafast Dynamics of Chemical Systems , J. D. Simon, ed., Kluwer Academic Publishers, The Netherlands, 267-287 (1994).

144.  Reid, P. J., Doig, S. J., Wickham, S. D. and Mathies, R. A.  Photochemical Ring-Opening Reactions are Complete in Picoseconds:  A Time-Resolved Resonance Raman Study, J. Amer. Chem. Soc. 115, 4754-4763 (1993).

145.  Huang, X. C., Quesada, M. A. and Mathies, R. A.  Capillary Array Electrophoresis: An Approach to High-speed, High-throughput DNA Sequencing, in  Advances in DNA Sequencing Technology,  Proceedings of the International Society for Optical Engineering-SPIE  1891, 12-20 (1993).

146.  Huang, X. C. and Mathies, R. A.  Application of Capillary Array Electrophoresis to DNA Sequencing, in Automated DNA Sequencing and Analysis Techniques,  Eds. M. D. Adams, C. Fields and J. Craig Venter, Academic Press, San Diego CA, pp. 17-28 (1994).

147.  Clark, S. M. and Mathies, R. A.  High-speed Parallel Separation of DNA Restriction Fragments using Capillary Array Electrophoresis, Analytical Biochemistry 215, 163-170 (1993).

148.  Mathies, R. A. and Kakitani, T.  Biophysical Chemistry of Retinal Proteins - Introduction and Dedication, Photochemistry and Photobiology  56, 857-858 (1993).

149.  Mathies, R. A., Schoenlein, R. W., Peteanu, L. A., Wang, Q., and Shank, C. V.  Femtobiology: Mechanism and Dynamics of the First Step in Vision.  in Femtosecond Reaction Dynamics, North-Holland Publishing Co. Amsterdam, Ed. D. A. Wiersma, pp. 229-236 (1994).

150.  Reid, P. J., Shreve, A. P. and Mathies, R. A.   Resonance Raman Intensity Analysis of the Photochemical Hydrogen Migration in 1,3,5-Cycloheptatriene, J. Phys. Chem. 97, 12691-12699 (1993).

151.  Schoenlein, R. W., Peteanu, L. A., Wang, Q., Mathies, R. A. and Shank, C. V.  Femtosecond Dynamics of the cis-trans Isomerization in a Visual Pigment Analog: Isorhodopsin, J. Phys. Chem. 97, 12087-12092 (1993).

152.  Benson, S. C., Mathies, R. A. and Glazer, A. N.  Heterodimeric DNA-binding Dyes Designed for Energy Transfer: Stability and Applications of the DNA Complexes, Nucleic Acids Research 21, 5720-5726 (1993).

153.  Lawless, M. K. and Mathies, R. A.  Excited-state Structure and Photochemical Ring-opening Dynamics of 1,3,5-Cyclooctatriene from Absolute Resonance Raman Intensities,  J. Chem. Phys. 100, 2492-2504 (1994).

154.  Peteanu, L. A., Schoenlein, R. W., Wang, Q., Mathies, R. A. and Shank, C. V.   The First Step in Vision Occurs in Femtoseconds:  Complete Blue and Red Spectral Studies, Proc. Natl. Acad. Sci. USA 90, 11762-11766 (1993).

155.  Lin, S. W., Imamoto, Y., Fukada, Y., Shichida, Y., Yoshizawa, T. and Mathies, R. A.   What Makes Red Visual Pigments Red?  A Resonance Raman Microprobe Study of Retinal Chromophore Structure in Iodopsin, Biochemistry 33, 2151-2160 (1994).

156.  Mathies, R. A., Scherer, J. R., Quesada, M. A., Rye, H. S. and Glazer, A. N.   Laser-excited Confocal Fluorescence Gel Scanner, Rev. Sci. Instruments 65, 807-812 (1994).

157.  Lawless, M. K., Wickham, S. D. and Mathies, R. A.  Direct Investigation of the Photochemical Ring-Opening Dynamics of Cyclobutene with Resonance Raman Intensities, J. Amer. Chem. Soc. 116, 1593-1594 (1994).

158.  Cherepy, N. J., Shreve, A. P., Moore, L. J., Franzen, S., Boxer, S. G. and Mathies, R. A.  Near-Infrared Resonance Raman Spectroscopy of the Special Pair and the Accessory Bacteriochlorophylls in Photosynthetic Reaction Centers, J. Phys. Chem. 98, 6023-6029 (1994).

159.  Reid, P. J., Lawless, M. K., Wickham, S. D., and Mathies, R. A.   Determination of Pericyclic Photochemical Reaction Dynamics with Resonance Raman Spectroscopy, J. Phys. Chem. 98, 5597-5606 (1994).

160.  Thompson, P. A. and Mathies, R. A.  Time-resolved Resonance Raman in the Visible and Ultraviolet:  Techniques and Applications, in   Laser Techniques in Chemistry, eds. A. B. Myers and T. R. Rizzo, Volume XXIII in Techniques of Chemistry,  John Wiley and Sons Inc., pp. 185-210 (1995).

161.  Zhu, H., Clark, S. M., Benson, S. C., Rye, H. S., Glazer, A. N. and Mathies, R. A.  High-Sensitivity Capillary Electrophoresis of Double-Stranded DNA Fragments using Monomeric and Dimeric Fluorescent Intercalation Dyes, Analytical Chemistry, 66, 1941-1948 (1994).

162.  R. A. Mathies,  Biomolecular Vibrational Spectroscopy, in Methods in Enzymology, Volume 246 "Biochemical Spectroscopy", ed. K. Sauer, p. 377-389 (1995).

163.  Mathies, R. A.  The Femtosecond Cis-Trans Isomerization in Vision:  A Classic Barrierless Photochemical Reaction,  in  "Ultrafast Processes in Chemistry and Biology", IUPAC Series on Chemistry for the 21st Century, ed. M. A. El-Sayed, I. Tanaka, Y. Molin, Blackwell, Oxford England, p. 215-224 (1995).

164.  Woolley, A. T. and Mathies, R. A.  Ultra-High-Speed DNA Fragment Separations Using Microfabricated Capillary Array Electrophoresis Chips, Proc. Natl. Acad. Sci. U.S.A., 91, 11348-11352 (1994).

165.  Wang, Q., Schoenlein, R. W., Peteanu, L. A., Mathies, R. A. and Shank, C. V.  Vibrationally Coherent Photochemistry in the Femtosecond Primary Event of Vision, Science 266, 422-424 (1994).

166.  Mathies, R. A. and Li, X. Y.  On Modeling the Vibrational Spectra of 14-s-cis Retinal Conformers in Bacteriorhodopsin, Biophysical Chemistry, 56, 47-55 (1995).

167.  Shreve, A. P. and Mathies, R. A.  Thermal Effects in Resonance Raman Scattering: Analysis of the Raman Intensities of Rhodopsin and of the Time-Resolved Raman Scattering of Bacteriorhodopsin, Journal of Physical Chemistry 99, 7285-7299 (1995).

168.  Cherepy, N. J., Holzwarth, A. R. and Mathies, R. A.  Near-Infrared Resonance Raman Spectra of Chloroflexus aurantiacus Photosynthetic Reaction Centers, Biochemistry 34, 5288-5293 (1995).

169.  Wang, Y., Ju, J., Carpenter, B. A., Atherton, J. M., Sensabaugh, G. F. and Mathies, R. A.  Rapid Sizing of Short Tandem Repeat Alleles Using Capillary Array Electrophoresis and Energy Transfer Fluorescent, Analytical Chemistry 67, 1197-1203 (1995).

170.  Ju, J., Ruan, C., Fuller, C. W., Glazer, A. N. and Mathies, R. A.  Fluorescence Energy Transfer Dye-Labeled Primers for DNA Sequencing and Analysis, Proc. Natl. Acad. Sci. U.S.A. 92, 4347-4351 (1995).

171.  Lawless, M. K., Wickham, S. D. and Mathies, R. A.  Resonance Raman View of Pericyclic Photochemical Ring-Opening Reactions: Beyond the Woodward-Hoffmann Rules, Accounts of Chemical Research  28,  493-502 (1995).

172.  Woolley, A. T. and Mathies, R. A.  Ultra-High-Speed DNA Sequencing Using Capillary Array Electrophoresis Chips, in  Ultrasensitive Instrumentation for DNA Sequencing and Biochemical Diagnostics,  Proceedings of the International Society for Optical Engineering-SPIE,  Volume 2386, 36-44 (1995).

173.  Ju, J., Kheterpal, I., Scherer, J. R., Ruan, C., Fuller, C. W., Glazer, A. N. and Mathies, R. A.  Design and Synthesis of Fluorescence Energy Transfer Dye-Labeled Primers and their Application for DNA Sequencing and Analysis, Analytical Biochemistry   231,  131-140 (1995).

174.  Woolley, A. T. and Mathies, R. A.  Ultra-High-Speed DNA Sequencing Using Capillary Electrophoresis Chips, Analytical Chemistry   67,  3676-3680 (1995).

175.  Haab, B. B. and Mathies, R. A.  Single Molecule Fluorescence Burst Detection of DNA Fragments Separated by Capillary Electrophoresis, Analytical Chemistry   67,  3253-3260 (1995).

176.  Kim, M., Mathies, R. A., Hoff, W. D. and Hellingwerf, K. J.  Resonance Raman Evidence That the Thioester-linked 4-Hydroxycinnamyl Chromophore of Photoactive Yellow Protein is Deprotonated, Biochemistry  34,  12669-12672 (1995).

177.  Kochendoerfer, G. G. and Mathies, R. A.  Ultrafast Spectroscopy of Rhodopsins - Photochemistry at its Best, Israeli Journal of Chemistry,  35,  211-226 (1995).

178.  Cherepy, N. J., Du, M., Holzwarth, A. R. and Mathies, R. A.  Near-Infrared Resonance Raman Spectra of Chlorosomes:  Probing Nuclear Coupling in Electronic Energy Transfer, J. Phys. Chem., 100,  4662-4671 (1996).

179.  Ju, J., Glazer, A. N. and Mathies, R. A.  Cassette Labeling for Facile Construction of Energy Transfer Fluorescent Primers, Nucleic Acids Research  24,  1144-1148 (1996).

180.  Ju, J., Glazer, A. N. and Mathies, R. A.  Energy Transfer Primers:  A New Fluorescence Labeling Paradigm for DNA Sequencing and Analysis, Nature Medicine 2,  246-249 (1996).

181.  Hung, S.-C.,  Ju, J.,  Mathies, R. A. and  Glazer, A. N.  Energy Transfer Primers with 5- or 6-Carboxyrhodamine-6G as Acceptor Chromophores, Analytical Biochemistry  238,  165-170 (1996).

182.  Haab, B. B. and Mathies, R. A.  Single Molecule Fluorescence Burst Detection of DNA Separated by Capillary Electrophoresis,  in   Fluorescence Detection IV,  E. Roland Menzel, ed., Proceedings of the International Society for Optical Engineering-SPIE, Volume 2705, 162-169 (1996).

183.  Kheterpal, I., Ju, J., Radhakrishnan, A., Brandt, G. S., Ginther, C. L., Clark, S. M., Scherer, J. R., Sensabaugh, G. F. and Mathies, R. A.  DNA Sequencing Using Four-Color Capillary Array Electrophoresis and Energy Transfer Primers  in  Ultrasensitive Biochemical Diagnostics,  Proceedings of the International Society for Optical Engineering-SPIE, Volume 2680, pp. 204-213 (1996).

184.  Kochendoerfer, G. G. and Mathies, R. A.  Spontaneous Emission Study of the Femtosecond Isomerization Dynamics of Rhodopsin, Journal of Physical Chemistry 100, 14526-14532 (1996).

185.  Wang, Q., Kochendoerfer, G. G., Schoenlein, R. W., Verdegem, P. J. E., Lugtenburg, J., Mathies, R. A. and Shank, C. V.  Femtosecond Spectroscopy of a 13-Demethyl Rhodopsin Visual Pigment Analog:  The Role of Nonbonded Interactions in the Isomerization Process, Journal of Physical Chemistry 100,  17388-17394 (1996).

186.  Wang, Y., Wallin, J. M., Ju, J., Sensabaugh, G. F. and Mathies, R. A.  High-Resolution Capillary Array Electrophoretic Sizing of Multiplexed Short Tandem Repeat Loci Using Energy-Transfer Fluorescent Primers,  Electrophoresis  17,  1485-1490 (1996).

187.  Hage, W., Kim, M., Frei, H. and Mathies, R. A.  Protein Dynamics in the Bacteriorhodopsin Photocycle:  A Nanosecond Step-Scan FTIR Investigation of the KL to L Transition, J. Phys. Chem.  100, 16026-16033 (1996).

188.  Kheterpal, I., Scherer, J. R., Clark, S. M., Radhakrishnan, A., Ju, J., Ginther, C. L., Sensabaugh, G. F. and Mathies, R. A.  DNA Sequencing Using a Four-Color Confocal Fluorescence Capillary Array Scanner, Electrophoresis 17,  1852-1859 (1996).

189.  Woolley, A. T., Hadley, D., Landre, P., deMello, A. J., Mathies, R. A. and Northrup, M A.  Functional Integration of PCR Amplification and Capillary Electrophoresis in a Microfabricated DNA Analysis Device, Analytical Chemistry  68,  4081-4086 (1996).

190.  Hung, S.-C., Ju, J., Mathies, R. A. and Glazer, A. N.  Cyanine Dyes with High Absorption Cross-Section as Donor Chromophores in Energy Transfer Primers, Analytical Biochemistry  243, 15-27 (1996).

191.  Kochendoerfer, G. G., Verdegem, P. J. E., van der Hoef, I., Lugtenburg, J., Mathies, R. A.  Retinal Analog Study of the Role of Steric Interactions in the Excited-State Isomerization Dynamics of Rhodopsin, Biochemistry  35,  16230-16240 (1996).

192.  Andel, F., Lagarias, J. C. and Mathies, R. A.  Resonance Raman Analysis of Chromophore Structure in the Lumi-R Photoproduct of Phytochrome, Biochemistry  35,  15997-16008 (1996).

193.  Clark, S. M. and Mathies, R. A.  Multiplex dsDNA Fragment Sizing Using Dimeric Intercalation Dyes and Capillary Array Electrophoresis:   Ionic Effects on the Stability and Electrophoretic Mobility of DNA:Dye Complexes,  Analytical Chemistry  69, 1355-1363 (1997).

194.  Haab, B. B. and Mathies, R. A.   Optimization of Single Molecule Fluorescence Burst Detection of ds-DNA:  Application to Capillary Electrophoresis Separations of 100-2000 bp Fragments,    Applied Spectroscopy, 51,  1579-1584 (1997).

195.  Cherepy, N. J., Shreve, A. P., Moore, L. J., Boxer, S. G. and Mathies, R. A.   Electronic and Nuclear Dynamics of the Accessory Bacteriochlorophylls in Bacterial Photosynthetic Reaction Centers from Resonance Raman Intensities,  J. Phys. Chem. 101, 3250-3260 (1997).

196.  Glazer, A. N. and Mathies, R. A.    Energy-transfer Fluorescent Reagents for DNA Analyses,  Current Opinion in Biotechnology  8,  94-102 (1997).

197.  Kauffmann, E., Frei, H. and Mathies, R. A.  Nanosecond Time-Resolved Step-Scan FT-IR Spectroscopy of the Photochemical Ring-Opening of 1,3-Cyclohexadiene, Chemical Physics Letters, 266,  554-559 (1997).

198.  Woolley, A. T., Sensabaugh, G. F. and Mathies, R. A.   High-Speed DNA Genotyping Using Microfabricated Capillary Array Electrophoresis Chips,  Analytical Chemistry 69,  2181-2186 (1997).

199.  Cherepy, N. J., Shreve, A. P., Moore, L. J., Boxer, S. G. and Mathies, R. A.  Temperature Dependence of the Qy Resonance Raman Spectra of Bacteriochlorophylls, the Primary Electron Donor, and Bacteriopheophytins in the Bacterial Photosynthetic Reaction Center, Biochemistry  36,  8559-8566 (1997).

200.  Kochendoerfer, G. G., Wang, Z., Oprian, D. D. and Mathies, R. A.   Resonance Raman Examination of the Wavelength Regulation Mechanism in Human Visual Pigments, Biochemistry 36,  6577-6587 (1997).

201.  Wang, Y., Hung, S. -H., Linn, J. F., Steiner, G., Glazer, A. N., Sidransky, D. and Mathies, R. A.   Microsatellite-Based Cancer Detection using Capillary Array Electrophoresis and Energy-Transfer Fluorescent Primers,  Electrophoresis 18,  1742-1749 (1997).

202.  Hung, S. -C., Mathies, R. A. and Glazer, A. N.  Optimization of Spectroscopic and Electrophoretic Properties of Energy Transfer Primers,  Analytical Biochemistry 252,  78-88 (1997).

203.  Ju, J., Glazer, A. N. and Mathies, R. A.  Energy Transfer Fluorescent Primers:  State of the Art in High-Throughput DNA Sequencing, HUGO Newsletter, July 1997 Genome Digest, pp. 8-9 (1997).

204.  Andel, F., Hasson, K. C., Gai, F., Anfinrud, P. and Mathies, R. A.  Femtosecond Time-Resolved Spectroscopy of the Primary Photochemistry of Phytochrome,  BioSpectroscopy 3, 421-433 (1997).

205.  Kochendoerfer, G., Kaminaka, S. and Mathies, R. A.  Ultraviolet Resonance Raman Examination of the Light-Induced Protein Structural Changes in Rhodopsin Activation, Biochemistry 36, 13153-13159 (1997).

206.  Zeng, Z., Clark, S. M., Mathies, R. A. and Glazer, A. N.  Improved Stability and Electrophoretic Properties of Preformed Fluorescent Cationic Dye-DNA Complexes in a Taps-Tetrapentylammonium Buffer in Agarose Slab Gels, Analytical Biochemistry  252,  110-114 (1997).

207.  Wexler, D., Kochendoerfer, G. G. and Mathies, R. A.  Multimode Analysis of Excited State Photochemical Dynamics in the Condensed Phase:  Application to Bacteriorhodopsin,  Nobel Symposium Proceedings Volume 101 on "Femtochemistry and Femtobiology: Ultrafast Reaction Dynamics at Atomic Scale Resolution", Imperial College Press, pp. 724-752 (1998).

208.  Hung, S. -H., Mathies, R. A. and  Glazer, A. N.  Comparison of Fluorescence Energy Transfer Primers with Different Donor-Acceptor Dye Combinations,  Analytical Biochemistry, 255, 32-38 (1998).

209.  Simpson, P. C., Woolley, A. T. and Mathies, R. A.  Microfabrication Technology for the Production of Capillary Array Electrophoresis Chips, Biomedical Microdevices  1,  7-25 (1998).

210.  Kheterpal, I., Li, L., Speed, T. P. and Mathies, R. A.   A Three-Color Labeling Approach for DNA Sequencing Using Energy Transfer Primers and Capillary Electrophoresis, Electrophoresis 19, 1403-1414 (1998).

211.  Woolley, A. T., Lao, K., Glazer, A. N. and Mathies, R. A.  Capillary Electrophoresis Chips with Integrated Electrochemical Detection, Analytical Chemistry 70,  684-688 (1998).

212.  Kaminaka, S. and Mathies, R. A.   A High-Throughput Large Aperture Prism Prefilter for Ultraviolet Resonance Raman Spectroscopy, Applied Spectroscopy  52,  469-473 (1998).

213.  Lin, S. W., Groesbeek, M., van der Hoef, I., Verdegem, P., Lugtenburg, J. and Mathies, R. A.  Vibrational Assignment of Torsional Normal Modes of Rhodopsin:  Probing Excited-State Isomerization Dynamics along the Reactive C11=C12 Torsional Coordinate, Journal of Physical Chemistry 102,  2787-2806 (1998).

214.  Simpson, P. C., Roach, D., Woolley, A. T., Thorsen, T., Johnston, R., Sensabaugh, G. F. and Mathies, R. A.  High Throughput Genetic Analysis using Microfabricated 96 Sample Capillary Array Electrophoresis Micro-Plates, Proceedings of the National Academy of Sciences  U.S.A.95,  2256-2261 (1998).

215.  Simpson, P. C. and Mathies, R. A.  High-Performance Microfabricated Capillary Array Electrophoresis Systems for DNA Analysis, Proceedings of the International Society for Optical Engineering-SPIE, Micro- and Nanofabricated Structures and Devices for Biomedical Environmental Applications, Volume 3258, 170-180  (1998).

216.  Haab, B. B. and Mathies, R. A.  Single Molecule DNA Detection in Microfabricated Capillary Electrophoresis chips,  Proceedings of the International Society for Optical Engineering-SPIE, Progress in Biomedical Optics, Volume 3259, 104-111 (1998).

217.  Lin, S. W., Kochendoerfer, G. G., Carroll, K. S., Wang, D., Mathies, R. A. and Sakmar, T. P.  Mechanism of Spectral Tuning in Blue Cone Visual Pigments.  Visible and Raman Spectroscopy of Blue-Shifted Rhodopsin Mutants, J. Biol. Chem. 273,  24583-24591 (1998).

218.  Mathies, R. A., Simpson, P. C. and Woolley, A. T.  DNA Analysis with Capillary Array Electrophoresis Microplates,  Micro Total Analysis Systems '98,  Proceedings of the Micro-TAS '98 Workshop, Banff Canada, October 13-16, 1998, Kluwer Academic Publishers, eds. D. Jed Harrison and A. van den Berg, pp.1-7 (1998).

219.  Collins, F. S., Patrinos, A., Jordan, E., Chakravarti, A., Gesteland, R., Walters, L. and the members of the DOE and NIH Planning Groups,  New Goals for the U.S. Human Genome Project: 1998-2003,  Science 282,  682-689 (1998).

220.  Kochendoerfer, G. G., Lin, S. W., Sakmar, T. P. and Mathies, R. A.  How color visual pigments are tuned, Trends in Biochemical Sciences 24,  300-305 (1999).

221.  Liu, S., Shi, Y., Ja, W. W., and Mathies, R. A.  Optimization of High-Speed DNA Sequencing on Microfabricated Capillary Electrophoresis Channels, Anal. Chem. 71, 566-573 (1999).

222.  Kheterpal, I. and Mathies, R. A.  Capillary Array Electrophoresis DNA Sequencing, Analytical Chemistry, 71, 31A-37A (1999).

223. Kaminaka, S. and Mathies, R. A.  Time-Resolved Ultraviolet Resonance Raman of Protein Structural Changes in the KL-Intermediate of Bacteriorhodopsin,  Laser Chemistry  19,  165-168 (1999).

224.  Scherer, J. R., Kheterpal, I., Radhakrishnan, A., Ja, W. W. and Mathies, R. A.  Ultra-High Throughput Rotary Capillary Array Electrophoresis Scanner for Fluorescent DNA Sequencing and Analysis, Electrophoresis  20, 1508-1517 (1999).

225.  Mathies, R. A.  Photons, Femtoseconds and Dipolar Interactions:  A Molecular Picture of the Primary Events in Vision,  in   Rhodopsins and Phototransduction,  Novartis Foundation Symposium Volume 224, pp. 70-89 (1999).

226.  Hutt, L. D., Glavin, D. P., Bada, J. L. and Mathies, R. A.  Microfabricated Capillary Electrophoresis Amino Acid Chirality Analyzer for Extraterrestrial Exploration, Analytical Chemistry 71, 4000-4006 (1999).

227.  Zhu, L., Kim, J. and Mathies, R. A.  Picosecond Time-Resolved Raman System for Studying Photochemical Reaction Dynamics:  Application to the Primary Events in Vision,  J. Raman Spectroscopy 30,  777-783 (1999).

228.  Shi, Y., Simpson, P., Scherer, J. R., Wexler, D., Skibola, C., Smith, M. T. and Mathies, R. A.  Radial Capillary Array Electrophoresis Microplate and Scanner for High-Performance Nucleic Acid Analysis, Analytical Chemistry 71,  5354-5361 (1999).

229.  Haab, B. B., and Mathies, R. A.  Single Molecule Detection of DNA Separations in Microfabricated Capillary Electrophoresis Chips Employing Focused Molecular Streams, Analytical Chemistry 71,  5137-5145 (1999).

230.  Andel, F., Murphy, J. T., Haas, J. A., McDowell, M. T., van der Hoef, I., Lugtenburg, J., Lagarias, J. C. and Mathies, R. A.  Probing the Photoreaction Mechanism of Phytochrome Through the Vibrational Analysis of Resonance Raman Spectra of Recombinant Analogs, Biochemistry 39,  2667-2676 (2000)

231.  Mathies, R. A. and Lugtenburg, J.  The Primary Photoreaction of Rhodopsin, in  Handbook of Biological Physics, Volume 3: Molecular Mechanisms in Visual Transduction, Eds. D. G. Stavenga, W. J. DeGrip and E. N. Pugh Jr., Elsevier Science Press, pp.55-90 (2000).

232.  Xie, J., Hung, S.-C., Glazer, A. N., and Mathies, R. A.  Energy Transfer Fluorescent Labels for DNA Sequencing and Analysis, in Topics in Fluorescence Spectroscopy, Volume 7: DNA Technology, ed. J. R. Lakowicz (Kluwer Academic/Plenum Publishers, NY), pp. 105-127 (2003).

233.  Lagally, E., Simpson, P. C. and Mathies, R. A.  Monolithic Integrated Microfluidic DNA Amplification and Capillary Electrophoresis System, Sensors and Actuators B 63, 138-146 (2000).

234.  Medintz, I. L., Lee, C.-C. R., Wong, W. W., Pirkola, K., Sidransky, D. and Mathies, R. A.  Loss  of Heterozygosity Assay for Molecular Detection of Cancer using Energy-Transfer Primers and Capillary Array Electrophoresis, Genome Research, 10,  1211-1218 (2000).

235.  Paegel, B. M., Hutt, L. D., Simpson, P. C. and Mathies, R. A.  Turn Geometries for Minimizing Band Broadening in Microfabricated Capillary Electrophoresis Channels,  Analytical Chemistry  72,  3030-3037 (2000).

236.  Lagally, E. T., Paegel, B. M. and Mathies, R. A.  Microfabrication Technology for Chemical and Biochemical Microprocessors, in  Micro Total Analysis Systems 2000, eds. A. van den Berg, W. Olthuis and P. Bergveld, Kluwer Academic Publishers, Dordrecht, The Netherlands, pp. 217-220 (2000).

237.  Medintz, I., Wong, W. W., Sensabaugh, G. and Mathies, R. A.  High Speed Single Nucleotide Polymorphism Typing of a Hereditary Haemochromatosis Mutation with Capillary Array Electrophoresis, Electrophoresis  21, 2352-2358 (2000).

238.  Wedemayer, G., Medintz, I., Wong, W. W., Scherer, J. R. and Mathies, R. A.  Conversion of Capillary Electrophoresis Microchip Data for Analysis with Genetic Profiler Software, BioTechniques  30, 122-128  (2001).

239.  Kim, J. E., McCamant, D. W., Zhu, L. and Mathies, R. A.  Resonance Raman Structural Evidence that the Cis-to-Trans Isomerization in Rhodopsin Occurs in Femtoseconds, Journal of Physical Chemistry  B 105, 1240-1249 (2001).

240.  Lagally, E. T., Medintz, I. and Mathies, R. A.  Single Molecule DNA Amplification and Analysis in an Integrated Microfluidic Device, Anal. Chem.  73, 565-570 (2001).

241.  Medintz, I., Wong, W. W., Berti, L., Shiow, L., Tom, J., Scherer, J. R., Sensabaugh, G. and Mathies, R. A.  High Performance Multiplex SNP Analysis of 3 Haemochromatosis Related Mutations with Capillary Array Electrophoresis Microplates,  Genome Research  11, 413-421 (2001).

242.  Mathies, R. A.  Molecular Mechanism of the Primary Event in Vision, Abstract to the Academy Colloqium on Photoreceptor Proteins: Structure, Photochemistry and Dynamics, Royal Netherlands Academy of Arts and Sciences, Amsterdam, November 24-26, 2000. 

243.  Medintz, I., Wong, W. W. and Mathies, R. A.  Fluorescence Labeling Methods for Microchannel Plate Capillary Electrophoresis DNA Sizing,  Journal of Capillary Electrophoresis and Microchip Technology  007, 40-46 (2002).
 
244.  Berti, L., Xie, J., Medintz, I. L., Glazer, A. N. and Mathies, R. A.  Energy Transfer Cassettes for Facile Labeling of Sequencing and PCR Primers, Analytical Biochemistry  292, 188-197 (2001).

245.  Berti, L., Medintz, I., Tom, J. and Mathies, R. A.  Energy Transfer Cassette Labeling for Capillary Array Electrophoresis Short Tandem Repeat DNA Fragment Sizing,  Bioconjugate Chemistry  12, 493-500 (2001).

246.  Medintz, I. L., Paegel, B. M. and Mathies, R. A.  Microfabricated Capillary Array Electrophoresis DNA Analysis Systems,  J. Chromatography A  924, 265-270 (2001).

247.  Medintz, I. L., Berti, L., Emrich, C. A., Tom, J., Scherer, J. R. and Mathies, R. A.  Genotyping Energy-Transfer Cassette Labeled Short Tandem Repeat Amplicons with Capillary Electrophoresis Microchannel Plates, Clinical Chemistry  47, 1614-1621 (2001).

248.  Scherer, J. R., Paegel, B., Wedemayer, G. J., Medintz, I. L., and Mathies, R. A.  High Pressure Gel-Loader for Capillary Array Electrophoresis Microchannel Plates, BioTechniques 31(5), 1150-1155 (2001).

249.  Pan, D. and Mathies, R. A.  Chromophore Structure in Lumirhodopsin and Metarhodopsin I by Time-Resolved Resonance Raman Microchip Spectroscopy, Biochemistry   40,  7929-7936 (2001).

250.  Kim, J. E., Tauber, M. J. and Mathies, R. A.  Wavelength Dependent Cis-Trans Isomerization in Vision, Biochemistry  40, 13774-13778 (2001).

251.  Medintz, I. L., Paegel, B. M., Blazej, R. G., Emrich, C. A., Berti, L., Scherer, J. R. and Mathies, R. A.  High-Performance Genetic Analysis Using Microfabricated Capillary Array Electrophoresis Microplates, Electrophoresis, 22, 3845-3856 (2001).

252.  Tauber, M. J. and Mathies, R. A.  Fluorescence and Resonance Raman Spectra of the Aqueous Solvated Electron, J. Phys. Chem. A, 105, 10952-10960 (2001).

253.   Mathies, R. A.,  Smaller, Faster and More Sensitive:  Electrophoretic DNA Analysis for the 21st Century,  in Molecular Testing in Laboratory Medicine, eds. D. E. Bruns, Y. M. D. Lo  and C. T. Wittwer (AACC Press, Washington, DC), pp. 127-128 (2002).

254.   Emrich, C. A., Medintz, I. L., Tian, H., Berti, L. and Mathies, R. A.  (Ultra)2-High-throughput Genetic Analysis Using Microfabricated Capillary Array Devices, Micro Total Analysis Systems 2001, eds. J. M. Ramsey and A. van  den Berg, Kluwer Academic (Dordrecht, The Netherlands), pp. 13-15.

255.   Lagally, E. T. and Mathies, R. A.   Integrated PCR-CE System for DNA Analysis to the Single Molecule Limit. Micro Total Analysis Systems 2001, eds. J. M. Ramsey and A. van  den Berg, Kluwer Academic (Dordrecht, The Netherlands), pp. 117-118.

256.   Paegel, B. M., Emrich, C. A., Blazej, R. G., Elkin, C. J., Scherer, J. R.  and Mathies, R. A.  Microfabricated Capillary Array  Electrophoresis:  High-throughput DNA Sequencing and Polymorphism Analysis, Micro Total Analysis Systems 2001, eds. J. M. Ramsey and A. van  den Berg, Kluwer Academic (Dordrecht, The Netherlands), pp. 462-464.

257.  Paegel, B. M., Emrich, C. A., Wedemayer, G. J.,  Scherer, J. R. and Mathies, R. A.  High-Throughput DNA Sequencing with a 96-Lane Capillary Array Electrophoresis Bioprocessor, Proc. Natl. Acad. Sci. U.S.A., 99, 574-579 (2002).
        
258.  Lagally, E. T., Emrich, C. A. and Mathies, R. A.  Fully Integrated PCR-Capillary Electrophoresis Microsystem for DNA Analysis.  Lab-on-A-Chip, 1 (2) 102-107 (2001).

259.  Tauber, M. J. and Mathies, R. A.  Resonance Raman Spectra and Vibronic Analysis of the Aqueous Solvated Electron,  Chem. Phys. Lett., 354, 518-526 (2002).

260.  Pan, D., Ganim, Z., Kim, J. E., Verhoeven, M. A., Lugtenburg, J. and Mathies, R. A.  Time-resolved Resonance Raman Analysis of Chromophore Structural Changes in the Formation and Decay of Rhodopsin’s BSI Intermediate, J. Amer. Chem. Soc., 124, 4857-4864 (2002).

261.  Medintz, I. L., Berti, L. and Mathies, R. A.  Novel Energy Transfer Fluorescence Labeling Cassette, BioTechniques 32, 270 (2002).

262.  Yan, E. C. Y., Kazmi, M. A., De, S., Chang, B. S. W., Seibert, C., Marin, E. P., Mathies, R. A. and Sakmar, T. P.  Function of Extracellular Loop 2 in Rhodopsin.  Glutamic Acid 181 Modulates Stability and Absorption Wavelength of Metarhodopsin II, Biochem.,  41, 3620-3627 (2002).

263.  Emrich, C. A., Tian, H., Medintz, I. and Mathies, R. A.  Microfabricated 384-Lane Capillary Array Electrophoresis Bioanalyzer for Ultra High-Throughput Genetic Analysis, Anal. Chem., 74, 5076-5083 (2002).

264.  McCamant, D. W., Kim, J. E. and Mathies, R. A.  Vibrational Relaxation in b-Carotene Probed by Picosecond Stokes and Anti-Stokes Resonance Raman Spectroscopy, J. Phys. Chem. A, 106, 6030-6038 (2002).

265.  Mathies, R. A., Lagally, E. T., Kamei, T., Grover, W. H., Liu, C. N., Scherer, J. R. and Street, R. A.  Capillary Array Electrophoresis Bioprocessors, Technical Digest of the 2002 Hilton Head Workshop on Solid-State Sensors, Actuators, and Microsystems, Hilton Head Island, SC, Transducers Research Foundation publishers, June 2-6, 2002, pp. 112-117.

266.  Blazej, R. G., Paegel, B. M. and Mathies, R. A. Polymorphism Ratio Sequencing:  A New Approach for Single Nucleotide Polymorphism Discovery and Genotyping, Genome Research, 13, 287-293 (2003).

267.  Kim, J. E. and Mathies, R. A.  Anti-Stokes Raman Study of Vibrational Cooling Dynamics in the Primary Photochemistry of Rhodopsin, J. Phys. Chem. A, 106, 8508-8515 (2002).

268.  Paegel, B. M., Yeung, S. H. I. and Mathies, R. A.  Microchip Bioprocessor for Integrated Nanovolume Sample Purification and DNA Sequencing, Anal. Chem. 74 , 5092-5098 (2002).

269.  Grover, W. H., Skelley, A. M., Liu, C. N., Lagally, E. T., and Mathies, R. A.  Monolithic Membrane Valves and Diaphragm Pumps for Practical Large-Scale Integration into Microfluidic Devices, Sensors & Actuators B, 89,  315-323 (2003).

270.  Skelley, A. M., Grunthaner, F. J., Bada, J. L., and Mathies, R. A. ,Mars Organic Detector III: A Versatile Instrument for Detection of Bio-organic Signatures on Mars, in SPIE Vol. 4878 First Jet Propulsion Laboratory In Situ Instruments Workshop, ed. By G. H. Bearman, P. M. Beauchamp (SPIE. Bellingham, WA 2003), pp. 59-67.

271.  Grover, W. H., Skelley, A. M., Liu, C. N., Lagally, E. T., and Mathies, R. A.  Practical Valves and Pumps for Large-Scale Integration in Microfluidic Devices, Micro Total Analysis Systems 2002, Volume 1, eds. Y. Baba, S. Shoji and A. van den Berg, Kluwer Academic (Dordrecht, The Netherlands), pp 136-138.

272.  Paegel, B. M., Yeung, S. H. I., Scherer, J. R., and Mathies, R. A.  Microfluidic Circuit for Integrated DNA Sequencing Product Purification and Analysis, Micro Total Analysis Systems 2002, Volume 2, eds. Y. Baba, S. Shoji and A. van den Berg, Kluwer Academic (Dordrecht, The Netherlands), pp 940-942.

273.  Kamei, T., Scherer, J. R., Paegel, B.M., Skelley, A. M., Street, R. A., and Mathies, R. A.  Integrated Amorphous Silicon Photodiode Detector for Microfabricated Capillary Electrophoresis Devices, Micro Total Analysis Systems 2002, Volume 1, eds. Y. Baba, S. Shoji and A. van den Berg, Kluwer Academic (Dordrecht, The Netherlands), pp 257-259.
.
274.  Emrich, C. A., and Mathies, R. A.  The Õ-Injector: A new Electrokinetic Dispensing Element for Microdevice Separations, Micro Total Analysis Systems 2002, Volume 2, eds. Y. Baba, S. Shoji and A. van den Berg, Kluwer Academic (Dordrecht, The Netherlands), pp 748-749.

275.  Paegel, B. M., Blazej, R. G., and Mathies, R. A.  Microfabricated DNA Sequencing Devices, in Analytical Techniques in DNA Sequencing, ed. B. K. Nunnally (Taylor and Francis, Boca Raton) pp 61-83 (2005).

276.  Lagally, E. T., and Mathies, R. A.  Monolithic Integrated PCR Reactor-CE System for DNA Amplification and Analysis to the Single Molecule Limit, Proceedings of the 2nd Annual Int. IEEE-EEMBS Special Topic Conference on Microtechnologies in Medicine & Biology, eds. A. Dittmar and D. Beebe, pp. 437-441 (2002).

277.  Tauber, M. J., and Mathies, R. A. Structure of the Aqueous Solvated Electron from Resonance Raman Spectroscopy: Lessons from Isotopic Mixtures, J. Amer. Chem. Soc., 125, 1394-1402 (2003).

278.  Blazej, R., Paegel, B. M., Emrich, C. A., and Mathies, R. A.  Microfabricated capillary array electrophoresis: implementation and applications, In Lab-on-a-Chip: Miniaturized Systems for (Bio) Chemical Analysis and Synthesis, ed. by A. van den Berg and R. E. Oosterbroek, (Elsevier Science, Amsterdam), pp. 231-248 (2003).

279.  Paegel, B. M., Blazej, R. G., and Mathies, R. A.  Microfluidic Devices for DNA Sequencing Sample Preparation and Electrophoresis Analysis, Current Opinions in Biotechnology, 14, 42-50 (2003).

280.  Bromberg, A, and Mathies, R. A.  Homogeneous Immunoassay for Detection of TNT and its Analogues on a Microfabricated Capillary Electrophoresis Chip, Anal. Chem., 75, 1188-1195 (2003).

281.  Kim, J. E., Tauber, M. J., and Mathies, R. A.  Analysis of the Mode-Specific Excited-State Energy Distribution and Wavelength Dependent Photoreaction Quantum Yield in Rhodopsin, Biophysical Journal, 84, 2492-2501 (2003).

282.  Chan, E.M., Mathies, R.A. and Alivisatos, A. P.  Size-Controlled Growth of CdSe Nanocrystals in Microfluidic Reactors, Nano Letters, 3, 199-201 (2003).

283.  Kim, J. E., Pan, D., and Mathies, R. A., Picosecond Dynamics of GPCR Activation in Rhodopsin from Time-Resolved UV Resonance Raman Spectroscopy, Biochemistry 42, 5169-5175 (2003).

284.  McCamant, D. W., Kukura, P., and Mathies, R. A.  Femtosecond Time-Resolved Stimulated Raman Spectroscopy:  Applications to the Ultrafast Internal Conversion in b-Carotene, J. Phys. Chem A. 107, 8208-8214 (2003).

285.  Yan, E. C. Y., Kazmi, M. A., Ganim, Z., Hou, J. M., Pan, D., Chang, B. S. W., Sakmar, T. P. and Mathies, R. A.  Retinal Counterion  Switch in the Photoactivation of the G-Protein Coupled Receptor Rhodopsin, Proc. Natl. Acad. Sci. U.S.A., 100, 9262-9267 (2003).

286.  Skelley, A. M. and Mathies, R. A. Chiral Separation of Fluorescamine-Labeled Amino Acids using Microfabricated Capillary Electrophoresis Devices Designed for Extraterrestrial Exploration, J. Chromatography A,  1021, 191-199 (2003).

287.  Kamei, T., Paegel, B. M., Scherer, J. R., Skelley, A. M., Street, R. A. and Mathies, R. A.  Integrated Hydrogenated Amorphous Si  Photodiode Detector for Microfluidic Bioanalytical Devices, Anal. Chem., 75, 5300-5305 (2003).

288.  McCamant, D. W., Kukura, P. and Mathies, R. A.  Femtosecond Broadband Stimulated Raman: A New Approach for High-Performance Vibrational Spectroscopy, Appl. Spect., 57, 1317-1323 (2003).

289.  Tauber, M. J., Mathies, R. A., Chen, X. and Bradforth, S. E.  Flowing liquid sample jet for resonance Raman and ultrafast optical spectroscopy, Rev. Sci. Instrum., 74, 4958-4960 (2003).

290.  Lagally, E. T., Scherer, J. R., Blazej, R. G. and Mathies, R. A.  Genetic Analysis Using a Portable PCR-CE Microsystem, in Micro Total Analysis Systems 2003, Vol, 2, eds. M. A. Northrup, K. F. Jensen and D. J. Harrison, pp. 1283-1286.

291.  Bromberg, A. and Mathies, R. A. Homogeneous Immunoassay for Detection of TNT and its Analogues  on a Microfabricated Capillary Array Electrophoresis Chip, , in Micro Total Analysis Systems 2003, Vol. 2, eds. M. A. Northrup, K. F. Jensen and D. J. Harrison, pp. 979-982.

292.   Chan, E. M., Alivisatos, A. P. and Mathies, R. A.  Controlled Growth  of Semiconductor  Nanocrystals in Microfluidic Reactors in Micro Total Analysis Systems 2003 Vol. 1, eds. M. A. Northrup, K. F. Jensen and D. J. Harrison, pp. 425-428.

293.   Pan, D., Philip, A., Hoff, W. D. and Mathies, R. A.  Time-resolved Resonance Raman Structural Studies of the pB’ Intermediate in the Photocycle of Photoactive Yellow Protein, Biophys. J., 86, 2374-2382 (2004).

294.   Bromberg, A. and Mathies, R. A.  Multichannel Homogeneous Immunoassay for Detection of 2,4,6-trinitrotoluene (TNT) using a Microfabricated Capillary Array Electrophoresis Chip, Electrophoresis, 25, 1895-1900 (2004).

295.   Kukura, P., McCamant, D. W., Davis, P. H. and Mathies, R. A.  Vibrational Structure of the S2 (1Bu) Excited State of Diphenyloctatetraene observed by Femtosecond Stimulated Raman Spectroscopy, Chem. Phys. Lett.,  382, 81-86 (2003).

296.   Ertl, P., Emrich, C. A., Singhal, P. and Mathies, R. A., Capillary Electrophoresis Chips with a Sheath-Flow Supported Electrochemical Detection System, Analytical Chemistry, 76, 3749-3755 (2004).

297.   Lagally, E. T., Scherer, J. R.,  Blazej, R. G., Toriello, N. M., Diep, B. A. , Ramchandani, M.,  Sensabaugh, G. F., Riley, L. W. and Mathies, R. A., Integrated Portable Genetic Analysis Microsystem for Pathogen/Infectious Disease Detection, Analytical Chemistry, 76, 3162-3170 (2004).

298.   Tauber, M. J., Stuart, C. M. and Mathies, R. A., Resonance Raman Spectra of Electrons Solvated in Liquid Alcohols, Journal of the American Chemical Society 126, 3414-3415 (2004). 

299.   Yan, E. C. Y., Ganim, Z., Kazmi, M. A., Chang, B. S. W., Sakmar, T. P. and Mathies, R. A.
Resonance Raman Analysis of the Mechanism of Energy-Storage and Chromophore Distortion in the Primary Visual Photoproduct, Biochemistry, 43, 10867-10876 (2004).

300.   Karow, D. S., Pan, D., Pellicena, P., Presley, A., Mathies, R. A. and Marletta, M. A.  Spectroscopic characterization of the sGC-like heme domains from Vibra cholerae and Thermoanaerobacter tengcongensis, Biochemistry, 43, 10203-10211 (2004).

301.   Kukura, P., McCamant, D. W. and Mathies, R. A.  Femtosecond Time-Resolved Stimulated Raman Spectroscopy of the S2 (1Bu+) Excited State of b-Carotene, J. Phys. Chem A., 108, 5921-5925 (2004).

302.   Lee, S. Y., Zhang, D., McCamant, D. W., Kukura, P. and Mathies, R. A.  Theory of femtosecond stimulated Raman spectroscopy, J. Chem. Phys., 121, 3632-3642 (2004).

303.   McCamant, D. W., Kukura, P., Yoon, S. and Mathies, R. A.  Femtosecond Broadband Stimulated Raman Spectroscopy:  Apparatus and Methods.  Review of Scientific Instruments, 75, 4971-4980 (2004).

304.   Doherty, E. A. S., Kan, C-W., Paegel, B. M., Yeung, S. H. I., Cao, S., Mathies, R. A. and Barron,, A. E.  Sparsely Crosslinked “Nanogel” Matrixes as Fluid, Mechanically Stabilized Polymer Networks for High-Throughput Microchannel DNA Sequencing, Analytical Chemistry, 76, 5249-5256 (2004).

305.   Lui, Chang N., Toriello, N. M., Maboudian, R. and Mathies, R. A.  High-Throughput Polymerase Chain Reaction Capillary Array Electrophoresis (PCR-CAE) Microchip, in Micro Total Analysis Systems 2004,  eds. T. Laurell, J. Nilsson, K. Jensen, D. J. Harrison and J. P. Kutter (The Royal Society of Chemistry, Cambridge, UK), pp 297-299.

306.   Emrich, C. A., Ertl, P., Singhal, P. and Mathies, R. A.  Sheath-Flow Support for High-Sensitivity End-Column Electrochemical Detection in Microdevices, in Micro Total Analysis Systems 2004,  eds. T. Laurell, J. Nilsson, K. Jensen, D. J. Harrison and J. P. Kutter (The Royal Society of Chemistry, Cambridge, UK), pp 527-529.

307.    Skelley, A. M., Scherer, J. R., Bada, J. L., Grunthaner, F. J. and Mathies, R. A. Multi-Layer Microfluidic Devices for Amino Acid Analysis:  The Mars Organic Analyzer, Micro Total Analysis Systems 2004,  eds. T. Laurell, J. Nilsson, K. Jensen, D. J. Harrison and J. P. Kutter (The Royal Society of Chemistry, Cambridge, UK), pp 566-568.

308.  Yoon, S., McCamant, D. W., Kukura, P. Mathies, R. A., Zhang, D. and Lee, S. Y. Dependence of Lineshapes in Femtosecond Broadband Stimulated Raman Spectroscopy on Pump-Probe Time Delay, J. Chem. Phys., 122, 024505 (2005).

309.  Kamei, T., Paegel, B. M., Scherer, J. R., Skelley, A. M., Street, R. A. and Mathies, R. A.  Fusion of a-Si:H sensor technology with microfluidic bioanalytical devices, J. Non-Crystalline Solids, 338-340, 715-719 (2004).

310.  Skelley, A. M., Scherer, J. R., Aubrey, A. D., Ivester, R. H. C., Ehrenfreund, P., Grunthaner, F. G., Bada, J. L. and Mathies, R. A.  Sensitive Amino Acid Composition and Chirality Analysis with the Mars Organic Analyzer (MOA), Proceedings of the 55th International Astronautical Congress, 10/4-10/8/04, Vancouver, Canada (2004).

311.  Skelley, A. M., Scherer, J. R., Aubrey, A. D., Grover, W. H., A. D., Ivester, R. H. C., Ehrenfreund, P., Grunthaner, F. G., Bada, J. L. and Mathies, R. A.  Development and Evaluation of a Microdevice for Amino Acid Biomarker Detection and Analysis on Mars, Proc. Natl. Acad. Sci. U.S.A., 102, 1041-1046 (2005).

312.  Tian, H., Emrich, C. A., Scherer, J. R., Mathies, R. A., Andersen, P. S., Larsen, L. A. and Christiansen, M.  High Throughput Single-Strand Conformation Polymorphism Analysis on a Microfabricated Capillary Array Device, Electrophoresis, 26, 1834-1842 (2005).

313.  Drake, I. J., Liu, T. C. N., Gilles, M., Tyliszczak, T., Kilcoyne, A. L. D., Shuh, D. K., Mathies, R. A., Bell, A. T.  An in situ cell for characterization of solids by soft x-ray absorption, Review of Scientific Instruments 75, 3242-3247 (2004).
 314. Lagally, E. T. and Mathies R. A.  Integrated Genetic Analysis Systems, J. Phys. D., 37, R245-R261 (2004).

315.  Kamei, T., Toriello, N. M., Lagally, E. T., Blazej, R. G., Scherer, J. R., Street, R. A. and Mathies, R. A.  Microfluidic Genetic Analysis with an Integrated a-Si:H Detector, Biomedical Microdevices, 7, 147-152 (2005).

316.  McCamant, D. W., Kukura, P. and Mathies, R. A.  Femtosecond Stimulated Raman Study of Excited State Evolution in Bacteriorhodopsin, J. Phys. Chem. B, 105. 10449-10457 (2005).

317.  Grover, W. H. and Mathies, R. A.  An Integrated Microfluidic Processor for Single Nucleotide Polymorphism-Based DNA Computing, Lab-on-a-Chip, 5, 1033-1040 (2005).

318.  Chan, E. M., Alivisatos, A. P. and Mathies, R. A.  High-Temperature Microfluidic Synthesis of CdSe Nanocrystals in Nanoliter Droplets, J. Am. Chem. Soc., 127, 13854-13861 (2005).

319.  Toriello, N. M., Douglas, E. S. and Mathies, R. A.  Microfluidic Device for Electric-Field Driven Single-Cell Capture and Activation, Analytical Chemistry, 77, 6935-6941 (2005).

320.   Yoon, S. Kukura, P., Stuart C. M. and Mathies, R. A.  Direct Observation of the ultrafast intersystem crossing in tris(2,2’-bipyridine)ruthenium(II) using femtosecond stimulated Raman spectroscopy, Molecular Physics, 104, 1275-1282 (2006).

321.   Douglas, E. S., Toriello, N. M. and Mathies, R. A. Microfluidic Device for Electric-Field Driven Single-Cell Capture and Activation, Micro Total Analysis Systems 2005, Vol. 1, Eds. K. F. Jensen, J. Han, D. J. Harrison and J. Voldman, Transducers Research Foundation, pp 391-393.

322.  Chan, E. M., Alivisatos, A. P. and Mathies, R. A.  High-Temperature Microfluidic Synthesis of Semiconductor Nano-crystals in Nanoliter Droplets, Micro Total Analysis Systems 2005, Vol. 2, Eds. K. F. Jensen, J. Han, D. J. Harrison and J. Voldman, Transducers Research Foundation, pp 921-923.

323.  Grover, W. H. and Mathies, R. A.  An Integrated Microfluidic Processor for Single Nucleotide Polymorphism-Based DNA Computing, Micro Total Analysis Systems 2005, Vol. 1, Eds. K. F. Jensen, J. Han, D. J. Harrison and J. Voldman, Transducers Research Foundation, pp 214-216 (2005).

324.  Yeung, S. H. I., Greenspoon, S. A., McGuckian, A., Crouse, C. A., Emrich, C. A.,  Ban, J. and Mathies, R. A.  Rapid and High-Throughput Forensic Short Tandem Repeat Typing Using a 96-Lane Microfabricated Capillary Array Electrophoresis Device, Journal of Forensic Sciences, 51, 740-747 (2006).

325.  Kukura, P., McCamant, D. W., Yoon, S., Wandschneider, D. B. and Mathies, R. A.  Structural Observation of the Primary Isomerization in Vision with Femtosecond Stimulated Raman, Science, 310, 1006-1009 (2005). 

326.  Crouse, C., Yeung, S., Greenspoon, S., McGuckian, A., Sikorsky, J.,  Ban, J., and Mathies, R. A.  Improving Efficiency of a Small Forensic DNA Laboratory: Validation of Robotic Assays and Evaluation of Microcapillary Array Device, Croatian Medical Journal 46, 563-577 (2005).

327.  Karow, D. S., Pan, D., Davis, J. H., Behrends, S., Mathies, R. A. and Marletta, M. A. Characterization of Functional Heme Domains from Soluble Guanylate Cyclase, Biochem. 44, 16266-16274 (2005).

328.  Blazej, R. G., Kumaresan, P. and Mathies, R. A. Microfabricated bioprocessor for integrated nanoliter-scale Sanger DNA sequencing, PNAS 103, 7240-7245 (2006).

329.  Chandra, R. A., Douglas, E. S., Mathies, R. A., Bertozzi, C. R. and Francis, M. B. Programmable Cell Adhesion Encoded by DNA Hybridization, Angew. Chem. Int. Ed., 45, 896-901 (2006).

330.  Derbyshire E. R, Tran R., Mathies, R. A., Marletta, M. A.  Characterization of nitrosoalkane binding and activation of soluble guanylate cyclase, Biochem, 44, 16257-16265 (2005). 

331.  Bada, J. L., Sephton, M. A., Ehrenfreund, P., Mathies, R. A., Skelley, A. M. , Grunthaner,  F.  J., Zent, A. P., Quinn, R. C., Josset,  J. L., Robert, F.,  Botta, O.,  Glavin, D. P.  New strategies to detect life on Mars, Astronomy & Geophysics 46, 26-27 (2005).

332.  Grover, W. H., Ivester, R. H. C., Jensen, E. C. and Mathies, R. A.  Development and multiplexed control of latching pneumatic valves using microfluidic logical structures, Lab on a Chip 6, 623-631 (2006).

333.  Kukura, P., Yoon, S. and Mathies R. A.  Femtosecond Stimulated Raman Spectroscopy: A New Approach for Analytical Vibrtational Spectroscopy and Chemical Reaction Dynamics, Anal. Chem., invited review article in press (2006).

334.  Liu, C. N., Toriello, N. M. and Mathies, R. A.   Multichannel PCR-CE Microdevice for Genetic Analysis, Anal. Chem., 78, 5474-5479 (2006).

335.  Kukura, P., Frontiera, R. and Mathies, R. A.  Direct Observation of anharmonic coupling in the time domain with femtosecond stimulated Raman, Phys. Rev. Lett., 96, 238303 (2006).

336.  Skelley, A. M., Cleaves, H. J., Jayarajah, C. N., Bada, J. L. and Mathies, R. A. Application of the Mars Organic Analyzer to Nucleobase and Amine Biomarker Detection, Astrobiology, 6, 824-837 (2006).

337.  Shim, S. and Mathies, R. A.  Generation of narrow-bandwidth picosecond visible pulses from broadband femtosecond pulses for femtosecond stimulated Raman, App. Phys. Lett., 89 121124 (2006).

338.  Aubrey, A., Cleaves, H. J., Chalmers, J. H., Skelley, A. M., Mathies, R. A., Grunthaner, F. J., Ehrenfreund, P. and Bada, J. L.  Sulfate minerals and organic compounds on Mars, Geology, 34, 357-360 (2006).

339.  Skelley, A. M. and Mathies, R. A. Rapid On-Column Analysis of Glucosamine and its Mutarotation by Microchip Capillary Electrophoresis, J. Chromatography A, 1132, 304-309 (2006).

340.  Boon, E. M., Davis, J. H., Tran, R., Karow, D. S., Huang, S. H., Pan, D., Miazgowicz, M. M., Mathies, R. A., Marletta, M. A.  Nitric oxide binding to prokaryotic homologs of the soluble guanylate cyclase beta 1 H-NOX domain, J. Biol. Chem., 281, 21892-21902 (2006).

341.  Toriello, N. M., Lui, C. N., Mathies, R. A., Multichannel Reverse Transcription-PCR Microdevice for Rapid Gene Expression and Biomarker Analysis, Anal. Chem., 78, 7997-8003 (2006).

342.  Kukura, P., McCamanat, D. W., Mathies, R. A., Femtosecond Stimulated Raman Spectroscopy, Ann. Rev. Phys. Chem. 2007, in press (2007). 

343. Grover, W. H., Jensen, E. C., Ivester, R. H. C. and Mathies, R. A. Programmable Pneumatic Logical Circuits for Microfluidic Device Control, Micro TAS 2006, Vol. I, November 5-9, 2006, Tokyo, Japan, eds. T. Kitamori, H. Fujita, S. Hasebe, pp. 506-508.

344.   Blazej, R. G., Kumaresan, P. and Mathies, R. A.  Microfabricated Bioprocessor for Nanoliter-Scale Sanger DNA Sequencing, MicroTAS 2006, Vol. II,  November 5-9, 2006, Tokyo, Japan, eds. T. Kitamori, H. Fujita, S. Hasebe, pp. 1567-1569.

345.   Toriello, N. M., Liu, C. N. and Mathies, R. A.  Multichannel Reverse Transcription-PCR Microdevice for Rapid Multiplex Gene Expression Analysis, Micro TAS 2006, Vol. II, November 5-9, 2006, Tokyo, Japan, eds. T. Kitamori, H. Fujita, S. Hasebe, pp. 1453-1455.

346.  Skelley, A. M., Aubrey, A. D., Willis, P. A., Amashukeli, X., Ehrenfreund, P., Bada, J. L., Grunthaner, F. J. and Mathies, R. A. Organic amine biomarker detection in the Yungay region of the Atacama Desert with the Urey Instrument, J. Geophys. Res., 112, G04S11, doi:10.1029/2006JG000329 (2007). 

347.  Adesokan, A. A., Pan, D., Fredj, E., Mathies, R. A., and Gerber, R. B. Anharmonic Vibrational Calculations Modeling the Raman Spectra of Intermediates in the Protein (PYP) Photocycle, JACS 129, 4584-4594 (2007).

348.  Liu, P., Seo, T. S., Beyor, N., Shin, K., Scherer, J. R., and Mathies, R. A. Integrated Portable PCR-Capillary Electrophoresis Microsystem for Rapid Forensic Short Tandem Repeat Typing, Anal. Chem., 79, 1881-1889 (2007).

349.  Paegel, B. M., Grover, W. H., Skelley, A. M., Mathies, R. A., and Joyce, G. F. Microfluidic Serial Dilution Circuit, Anal. Chem., 78, 7522-7527 (2006).

350.  Stuart, C. S., Tauber, M. J. and Mathies. R. A.  Structure and Dynamics of the Solvated Electron in Alcohols from Resonance Raman Spectroscopy, J. Phys. Chem. 111, 8390-8400 (2007).

351.  Liu, P., Yeung, S. H. I., Seo, T. S., Shin, K.J., Beyor, N., Scherer, J. R. and Mathies, R. A., Microfabricated Genetic Analyzers for Rapid Forensic Short Tandem Repeat Typing, Proceedings of the Promega Corporation 17th International Symposium on Human ID, 2006.

352.  Jensen, E. C., Grover, W. H. and Mathies, R. A., Micropneutmatic Digital Logic Structures for Integrated Microdevice Computation and Control, Journal of Microelectromechanical Systems, 16, 1378-1385 (2007).

353.  Blazej, R. G., Kumaresan, P., Cronier, S. A. and Mathies, R. A.  In-line Injection Microdevice for Attomole-Scale Sanger DNA Sequencing, Anal. Chem., 79, 4499-4506 (2007).

354.  Emrich, C. A. and Mathies, R. A.  Microfabricated Electrophoresis Devices for High-Throughput Genetic Analysis:  Milestones and Challenges, in Handbook of Capillary and Microchip Electrophoresis and Associated Microtechniques, ed. J. P. Landers,  Third Edition (CRC Press), pp. 1277-1295 (2008).

355.  Emrich, C. A., Medintz, I. L., Chu, W. K. and Mathies, R. A., Microfabricated Two-Dimensional Electrophoresis Device for Differential Protein Expression Profiling, Analytical Chemistry 79, 7360-7366 (2007).

356.  Douglas, E. S., Toriello, N. M., Liu, C. N. and Mathies, R. A.  Advanced Microfluidic Tools for Single Cell Manipulation and Analysis, in Biological Applications of Microfluidics, ed. F. A. Gomez (Wiley-Interscience), in press 2007.

357.  Toriello, N. M., Liu, C. N., Thaitrong, N. and Mathies, R. A.  Integrated Affinity Capture, Purification and Capillary Electrophoresis Microdevice for Quantitative Double-Stranded DNA Analysis, MicroTAS 2007, October 7-11, 2007, Paris, France, Vol. I, eds. J.-L. Viovy, P. Tabeling,S. Descroix and L. Malaquin, pp. 1195-1197.

358.  Kumaresan, P., Blazej, R. G. and Mathies, R. A.  Microfabricated Droplet Generator for Single Molecule PCR in Tunable, Monodisperse Emulsions, MicroTAS 2007, October 7-11, 2007, Paris, France, Vol. I, eds. J.-L. Viovy, P. Tabeling,S. Descroix and L. Malaquin, pp.949-951.

359.  Grunthaner, F. J., Bada, J. L., Skelley, A. M., Mathies R. A., Quinn, R., Zent, A., Willis, P., Amashukeli, X., Farrington, A., Aubrey, A. and Ehrenfreund, P., The Urey Instrument: An Integrated End-to-End in situ Analytical System Designed for the Ultra-Sensitive Chemical Detection of Extant or Extinct Life on Mars, MicroTAS 2007, October 7-11, 2007, Paris, France, Vol. I, eds. J.-L. Viovy, P. Tabeling,S. Descroix and L. Malaquin, pp. 254-257.

360.  Chan, E. M., Marcus, M. A., Fakra, S., Elnaggar, M. S., Mathies, R. A. and Alivisatos, A. P. Millisecond kinetics of nanocrystal cation exchange using microfluidic X-ray absorption spectroscopy, J. Phys. Chem . A, 111, 12210-12215 (2007).

361.  Shim, S., Stuart, C. M. and Mathies, R. A.  Resonance Raman Cross-Sections and Vibronic Analysis of Rhodamine 6G from Broadband Stimulated Raman Spectroscopy, ChemPhysChem submitted 2007.

362.  Toriello, N. M., Liu, C. N., Blazej, R. G., Thaitrong, N. and Mathies, R. A.  Integrated Affinity Capture, Purification and Capillary Electrophoresis Microdevice for Quantitative Double-Stranded DNA Analysis, Anal. Chem., 79, 8549-8556 (2007).

363.  Beyor, N., Seo T. S. and Mathies, R. A.  Immunomagnetic Bead-Based Cell Concentration Microdevice for Dilute Pathogen Detection, Anal. Chem., submitted.

364.  Jayarajah, C. N., Skelley, A. M., Fortner, A. and Mathies, R. A.  Analysis of neuroactive amines in fermented beverages using a portable microchip capillary electrophoresis system, Anal. Chem, 79, 8162-8169 (2007).

365.  Frontiera, R. R. and Mathies, R. A.  Polarization dependence of vibrational coupling signals in femtosecond stimulated raman spectroscopy, J. Chem. Phys. 127, 124501 (2007).

366.  Stuart, C. M., Frontiera, R. R. and Mathies, R. A.  Excited State Structure and Dynamics of Cis-and Trans-Azobenzene from Resonance Raman Intensity Analysis, J. Phys. Chem. A 111 12072-12080 (2007).

367.  Douglas, E. S., Chandra, R. A., Bertozzi, C. R. , Mathies, R. A. and Francis, M. B.  Self-Assembled Cellular Microarrays Patterned Using DNA Barcodes, Lab-on-a-Chip, 7, 1442-1448 (2007).

368.  Greenspoon, S. A., Yeung, S. H. I., Johnson, K. R., Chu, B. S., Rhee, H. N., McGuckian, A. B., Crouse, C. A., Chiesl, T. N., Barron, A. E., Scherer, J. R., Ban, J. D. and Mathies, R. A.  A Forensic Laboratory Tests the Berkeley Microfabricated Capillary Array Electrophoresis Device, Journal of Forensic Sciences, in press.

369.  Greenspoon, S. A., Yeung, S. H. I., Ban, J. D. and Mathies, R. A.  Microchip Capillary Electrophoresis: Progress Toward an Integrated Forensic Analysis System, Profiles in DNA 10, 16-18 (2007).