Colorado PROFILES, The Colorado Clinical and Translational Sciences Institute (CCTSI)
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Last Name
Institution

Douglas P Shepherd

TitleAsst Professor Adjoint
InstitutionUniversity of Colorado Denver - Anschutz Medical Campus
DepartmentSOM-PHARM General Operations

    Collapse Research 
    Collapse research activities and funding
    RF1MH128867     (SHEPHERD, DOUGLAS)Sep 15, 2021 - Sep 14, 2024
    NIH
    Scalable 3D molecular imaging and data analysis for cell census generation
    Role: Principal Investigator
    R56HL068702     (ABMAN, STEVEN HERBERT)Sep 20, 2018 - Jul 8, 2019
    NIH
    Role of VEGF in Perinatal Hypertension
    Role: Co-Principal Investigator
    R01HL068702     (ABMAN, STEVEN HERBERT)Jun 20, 2001 - Jun 30, 2022
    NIH
    Role of VEGF in Perinatal Hypertension
    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. Pessoa P, Lu C, Tashev SA, Kruithoff R, Shepherd DP, Press? S. REPOP: bacterial population quantification from plate counts. bioRxiv. 2025 Apr 05. PMID: 40236151.
      View in: PubMed
    2. Wang H, Brown PT, Ullom J, Shepherd DP, Heintzmann R, Diederich B. Fully automated multicolour structured illumination module for super-resolution microscopy with two excitation colours. Commun Eng. 2025 Mar 10; 4(1):42. PMID: 40065157.
      View in: PubMed
    3. Saurabh A, Brown PT, Bryan Iv JS, Fox ZR, Kruithoff R, Thompson C, Kural C, Shepherd DP, Press? S. Approaching maximum resolution in structured illumination microscopy via accurate noise modeling. Npj Imaging. 2025; 3(1):5. PMID: 39897617.
      View in: PubMed
    4. Marin Z, Wang X, Collison DW, McFadden C, Lin J, Borges HM, Chen B, Mehra D, Shen Q, Galecki S, Daetwyler S, Sheppard SJ, Thien P, Porter BA, Conzen SD, Shepherd DP, Fiolka R, Dean KM. Navigate: an open-source platform for smart light-sheet microscopy. Nat Methods. 2024 Nov; 21(11):1967-1969. PMID: 39261640.
      View in: PubMed
    5. Sheppard SJ, Brown PT, Shepherd DP. Model based optimization for refractive index mismatched light sheet imaging. Opt Express. 2024 Oct 07; 32(21):36563-36576. PMID: 39573544.
      View in: PubMed
    6. Saurabh A, Brown PT, Bryan JS, Fox ZR, Kruithoff R, Thompson C, Kural C, Shepherd DP, Press? S. Approaching Maximum Resolution in Structured Illumination Microscopy via Accurate Noise Modeling. bioRxiv. 2024 Jul 02. PMID: 38106139.
      View in: PubMed
    7. Chang BJ, Shepherd D, Fiolka R. Projective oblique plane structured illumination microscopy. bioRxiv. 2023 Aug 09. PMID: 37609312.
      View in: PubMed
    8. Sikkema L, Ram?rez-Su?stegui C, Strobl DC, Gillett TE, Zappia L, Madissoon E, Markov NS, Zaragosi LE, Ji Y, Ansari M, Arguel MJ, Apperloo L, Banchero M, B?cavin C, Berg M, Chichelnitskiy E, Chung MI, Collin A, Gay ACA, Gote-Schniering J, Hooshiar Kashani B, Inecik K, Jain M, Kapellos TS, Kole TM, Leroy S, Mayr CH, Oliver AJ, von Papen M, Peter L, Taylor CJ, Walzthoeni T, Xu C, Bui LT, De Donno C, Dony L, Faiz A, Guo M, Gutierrez AJ, Heumos L, Huang N, Ibarra IL, Jackson ND, Kadur Lakshminarasimha Murthy P, Lotfollahi M, Tabib T, Talavera-L?pez C, Travaglini KJ, Wilbrey-Clark A, Worlock KB, Yoshida M, van den Berge M, Boss? Y, Desai TJ, Eickelberg O, Kaminski N, Krasnow MA, Lafyatis R, Nikolic MZ, Powell JE, Rajagopal J, Rojas M, Rozenblatt-Rosen O, Seibold MA, Sheppard D, Shepherd DP, Sin DD, Timens W, Tsankov AM, Whitsett J, Xu Y, Banovich NE, Barbry P, Duong TE, Falk CS, Meyer KB, Kropski JA, Pe'er D, Schiller HB, Tata PR, Schultze JL, Teichmann SA, Misharin AV, Nawijn MC, Luecken MD, Theis FJ. An integrated cell atlas of the lung in health and disease. Nat Med. 2023 Jun; 29(6):1563-1577. PMID: 37291214.
      View in: PubMed
    9. Djutanta F, Brown PT, Nainggolan B, Coullomb A, Radhakrishnan S, Sentosa J, Yurke B, Hariadi RF, Shepherd DP. Decoding the hydrodynamic properties of microscale helical propellers from Brownian fluctuations. Proc Natl Acad Sci U S A. 2023 May 30; 120(22):e2220033120. PMID: 37235635.
      View in: PubMed
    10. Kilic Z, Schweiger M, Moyer C, Shepherd D, Press? S. Gene expression model inference from snapshot RNA data using Bayesian non-parametrics. Nat Comput Sci. 2023 Feb; 3(2):174-183. PMID: 38125199.
      View in: PubMed
    11. Chen B, Chang BJ, Roudot P, Zhou F, Sapoznik E, Marlar-Pavey M, Hayes JB, Brown PT, Zeng CW, Lambert T, Friedman JR, Zhang CL, Burnette DT, Shepherd DP, Dean KM, Fiolka RP. Resolution doubling in light-sheet microscopy via oblique plane structured illumination. Nat Methods. 2022 11; 19(11):1419-1426. PMID: 36280718.
      View in: PubMed
    12. Jazani S, Xu ??? LWQ, Sgouralis I, Shepherd DP, Press? S. Computational Proposal for Tracking Multiple Molecules in a Multifocus Confocal Setup. ACS Photonics. 2022 Jul 20; 9(7):2489-2498. PMID: 36051355.
      View in: PubMed
    13. Supekar OD, Sias A, Hansen SR, Martinez G, Peet GC, Peng X, Bright VM, Hughes EG, Restrepo D, Shepherd DP, Welle CG, Gopinath JT, Gibson EA. Miniature structured illumination microscope for in vivo 3D imaging of brain structures with optical sectioning. Biomed Opt Express. 2022 Apr 01; 13(4):2530-2541. PMID: 35519247.
      View in: PubMed
    14. Brown PT, Kruithoff R, Seedorf GJ, Shepherd DP. Multicolor structured illumination microscopy and quantitative control of polychromatic light with a digital micromirror device. Biomed Opt Express. 2021 Jun 01; 12(6):3700-3716. PMID: 34221689.
      View in: PubMed
    15. Weiss KR, Voigt FF, Shepherd DP, Huisken J. Tutorial: practical considerations for tissue clearing and imaging. Nat Protoc. 2021 06; 16(6):2732-2748. PMID: 34021294.
      View in: PubMed
    16. Pinkard H, Stuurman N, Ivanov IE, Anthony NM, Ouyang W, Li B, Yang B, Tsuchida MA, Chhun B, Zhang G, Mei R, Anderson M, Shepherd DP, Hunt-Isaak I, Dunn RL, Jahr W, Kato S, Royer LA, Thiagarajah JR, Eliceiri KW, Lundberg E, Mehta SB, Waller L. Pycro-Manager: open-source software for customized and reproducible microscope control. Nat Methods. 2021 03; 18(3):226-228. PMID: 33674797.
      View in: PubMed
    17. Sapoznik E, Chang BJ, Huh J, Ju RJ, Azarova EV, Pohlkamp T, Welf ES, Broadbent D, Carisey AF, Stehbens SJ, Lee KM, Mar?n A, Hanker AB, Schmidt JC, Arteaga CL, Yang B, Kobayashi Y, Tata PR, Kruithoff R, Doubrovinski K, Shepherd DP, Millett-Sikking A, York AG, Dean KM, Fiolka RP. A versatile oblique plane microscope for large-scale and high-resolution imaging of subcellular dynamics. Elife. 2020 11 12; 9. PMID: 33179596.
      View in: PubMed
    18. Seedorf G, Kim C, Wallace B, Mandell EW, Nowlin T, Shepherd D, Abman SH. rhIGF-1/BP3 Preserves Lung Growth and Prevents Pulmonary Hypertension in Experimental Bronchopulmonary Dysplasia. Am J Respir Crit Care Med. 2020 05 01; 201(9):1120-1134. PMID: 32101461.
      View in: PubMed
    19. Kim C, Seedorf GJ, Abman SH, Shepherd DP. Heterogeneous response of endothelial cells to insulin-like growth factor 1 treatment is explained by spatially clustered sub-populations. Biol Open. 2019 Nov 04; 8(11). PMID: 31649121.
      View in: PubMed
    20. Munsky B, Li G, Fox ZR, Shepherd DP, Neuert G. Distribution shapes govern the discovery of predictive models for gene regulation. Proc Natl Acad Sci U S A. 2018 07 17; 115(29):7533-7538. PMID: 29959206.
      View in: PubMed
    21. Gould EA, Busquet N, Shepherd D, Dietz RM, Herson PS, Simoes de Souza FM, Li A, George NM, Restrepo D, Macklin WB. Mild myelin disruption elicits early alteration in behavior and proliferation in the subventricular zone. Elife. 2018 02 13; 7. PMID: 29436368.
      View in: PubMed
    22. Ryan DP, Gould EA, Seedorf GJ, Masihzadeh O, Abman SH, Vijayaraghavan S, Macklin WB, Restrepo D, Shepherd DP. Automatic and adaptive heterogeneous refractive index compensation for light-sheet microscopy. Nat Commun. 2017 09 20; 8(1):612. PMID: 28931809.
      View in: PubMed
    23. Singh JN, Nowlin TM, Seedorf GJ, Abman SH, Shepherd DP. Quantifying three-dimensional rodent retina vascular development using optical tissue clearing and light-sheet microscopy. J Biomed Opt. 2017 07 01; 22(7):76011. PMID: 28717817.
      View in: PubMed
    24. Shepherd D. Life away from the coverslip: Comment on "Extracting physics of life at the molecular level: A review of single-molecule data analyses" by W. Colomb and S.K. Sarkar. Phys Life Rev. 2015 Jun; 13:144-5. PMID: 25936616.
      View in: PubMed
    25. Shepherd DP, Li N, Micheva-Viteva SN, Munsky B, Hong-Geller E, Werner JH. Counting small RNA in pathogenic bacteria. Anal Chem. 2013 May 21; 85(10):4938-43. PMID: 23577771.
      View in: PubMed
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