qi2lab publications


Bingying Chen, Bo-Jui Chang, Philippe Roudot, Felix Zhou, Etai Sapoznik, Madeleine Marlar-Pavey, James B Hayes, Peter T Brown, Chih-Wei Zeng, Talley Lambert, Jonathan R Friedman, Chun-Li Zhang, Dylan T Burnette, Douglas P Shepherd, Kevin M Dean, Reto P Fiolka, Resolution doubling in light-sheet microscopy via oblique plane structured illumination, Nature Methods 19(11) 1419-1426

Franky Djutanta, Peter T Brown, Bonfilio Nainggolan, Alexis Coullomb, Sritharini Radhakrishnan, Jason Sentosa, Bernard Yurke, Rizal F Hariadi, Douglas P Shepherd, Microscopic motility of isolated E coli flagella, arXiv:2208.13854

Omkar D Supekar, Andrew Sias, Sean R Hansen, Gabriel Martinez, Graham C Peet, Xiaoyu Peng, Victor M Bright, Ethan G Hughes, Diego Restrepo, Douglas P Shepherd, Cristin G Welle, Juliet T Gopinath, Emily A Gibson, Miniature structured illumination microscope for in vivo 3D imaging of brain structures with optical sectioning, Biomedical Optics Express 13(4), 2530-2541

Lisa Sikkema et al, An integrated cell atlas of the human lung in health and disease, bioRxiv 2022.03.10.483747

Sina Jazani, Lance W. Q. Xu, Ioannis Sgouralis, Douglas P. Shepherd, and Steve Pressé, Computational Proposal for Tracking Multiple Molecules in a Multifocus Confocal Setup, ACS Photonics 9(7), 2489-2498


B Dnate’ Baxter, Eric D Larson, Laetitia Merle, Paul Feinstein, Arianna Gentile Polese, Andrew N Bubak, Christy S Niemeyer, James Hassell, Doug Shepherd, Vijay R Ramakrishnan, Maria A Nagel, Diego Restrepo, Transcriptional profiling reveals potential involvement of microvillous TRPM5-expressing cells in viral infection of the olfactory epithelium, BMC Genomics 22(1), 1-20

Kurt Weiss, Fabian Voigt, Douglas Shepherd, Jan Huisken, Tutorial: practical considerations for tissue clearing and imaging, Nature Protocols 16(6) 2732-2748

Henry Pinkard, Nico Stuurman, Ivan E. Ivanov, Nicholas M. Anthony, Wei Ouyang, Bin Li, Bin Yang, Mark A. Tsuchida, Bryant Chhun, Grace Zhang, Ryan Mei, Michael Anderson, Douglas P. Shepherd, Ian Hunt-Isaak, Raymond L. Dunn, Wiebke Jahr, Saul Kato, Loïc A. Royer, Jay R. Thiagarajah, Kevin W. Eliceiri, Emma Lundberg, Shalin B. Mehta & Laura Waller, Pycro-Manager: open-source software for customized and reproducible microscope control, Nature Methods 18, 226–228


Etai Sapoznik, Bo-Jui Chang, Jaewon Huh, Robert J Ju, Evgenia V Azarova, Theresa Pohlkamp, Erik S Welf, David Broadbent, Alexandre F Carisey, Samantha J Stehbens, Kyung-Min Lee, Arnoldo Marin, Ariella B Hanker, Jens C Schmidt, Carlos L Arteaga, Bin Yang, Yoshihiko Kobayashi, Purushothama Rao Tata, Rory Kruithoff, Konstantin Dubrovinski, Douglas P Shepherd, Alfred Millet-Sikking, Andrew G York, Kevin M Dean, Reto P Fiolka, A versatile Oblique Plane Microscope for large-scale and high-resolution imaging of subcellular dynamics eLife 2020;e57681

Peter T. Brown, Rory Kruithoff, Gregory J. Seedorf, Douglas P. Shepherd, Multicolor structured illumination microscopy and quantitative control of coherent light with a digital mirror device, bioRxiv 10.1101/2020.07.27.223941

Carly GK Ziegler, et al. SARS-CoV-2 receptor ACE2 is an interferon-stimulated gene in human airway epithelial cells and is detected in specific cell subsets across tissues Cell 2020 181(5), 1016-1035.e19

Gregory J Seedorf*, Christina Kim*, Bradley Wallace, Erica Mandell, Taylor Nowlin, Douglas P Shepherd, Steven H Abman, rhIGF-1/BP3 Preserves Lung Growth and Prevents Pulmonary Hypertension in Experimental BPD, American Journal of Respiratory and Critical Care Medicine 2020 201 (9), 1120-1134


Christina Kim, Gregory J Seedorf, Steven H Abman, Douglas P Shepherd, Heterogeneous response of endothelial cells to insulin like growth factor 1 treatment is explained by spatially clustered sub-populations, Biology Open 2019 8: bio045906

Justin B. Sambur, Douglas P Shepherd, Mahdi Hesari, Michael Van Erdewy, Eric Choudhary, Peng Chen, Correlated Single-Molecule Reaction Imaging and Photocurrent Measurements Reveal Underlying Rate Processes in Photoelectrochemical Water Splitting, Journal of the Electrochemical Society 166 (5), H3286-H3293


Brian Munsky, Guoliang Li, Zachary Fox, Douglas P Shepherd, Gregor Neuert, Distribution shapes govern the discovery of predictive models for gene regulation, Proceedings of the National Academy of Sciences of the United States of America 115 (29) 7533-7538

Elizabeth Gould, Nicolas Busquet, Douglas P Shepherd, Robert Dietz, Paco Herson, Fabio Simoes de Souza, Anan Li, Nicolas George, Diego Restrepo, Wendy Macklin, Mild Myelin Disruption Elicits Early Alteration in Behavior and Proliferation in the Subventricular Zone, eLife e43783


Duncan P Ryan, Elizabeth A Gould, Gregory J Seedorf, Omid Masihzadeh, Steven H Abman, Sukumar Vijayaraghavan, Wendy B Macklin, Diego Restrepo, Douglas P Shepherd, Automatic and adaptive refractive index compensation for light-sheet microscopy, Nature Communications 612

Jasmine N Singh, Taylor M Nowlin, Gregory J Seedorf, Steven H Abman, Douglas P Shepherd, Quantifying three-dimensional rodent retina vascular development using optical tissue clearing and light-sheet microscopy, Journal of Biomedical Optics 22(7) 076011

Megan A Ahern, Claudine P Black, Gregory J Seedorf, Christopher D Baker, Douglas P Shepherd, Hyperoxia impairs pro-angiogenic RNA production in preterm endothelial colony-forming cells, AIMS Biophysics 4(2): 284-297


Koushik Ghosh, Eva Rose M Balog, Jennifer L Kahn, Douglas P Shepherd, Jennifer S Martinez, Reginaldo C Rocha, Multicolor Luminescence from Conjugates of Genetically Encoded Elastin‐like Polymers and Terpyridine‐Lanthanides, Macromolecular Chemistry and Physics 216(18): 1856-1861

Douglas Shepherd, 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 SK Sarkar Physics of Life Reviews 13: 144-145


Christa Brelsford, Douglas Shepherd, Using mixture-tuned match filtering to measure changes in subpixel vegetation area in Las Vegas, Nevada, Journal of Applied Remote Sensing 8(1): 083660

Evan P Perillo, Leyma De Haro, Mary E Phipps, Jennifer S Martinez, Hsin-Chih Yeh, Andrew K Dunn, Douglas P Shepherd, James H Werner, Enhanced 3D localization of individual RNA transcripts via astigmatic imaging, Proceedings Volume 8950, Single Molecule Spectroscopy and Superresolution Imaging VII 895003


Douglas P Shepherd, Nan Li, Sofiya N Micheva-Viteva, Brian Munsky, Elizabeth Hong-Geller, James H Werner, Counting small RNA in pathogenic bacteria, Analytical Chemistry 85(10): 4938-4943 *Featured on journal cover*


Douglas P Shepherd, Nan Li, Elizabeth Hong-Geller, Brian Munsky, James H Werner, New tools for discovering the role sRNA plays in cellular regulation, Proceedings Volume 8228, Single Molecule Spectroscopy and Superresolution Imaging V 822808

Douglas P Shepherd, Justin B Sambur, Yong-Qi Liang, Bruce A Parkinson, Alan Van Orden, In Situ Studies of Photoluminescence Quenching and Photocurrent Yield in Quantum Dot Sensitized Single Crystal TiO2 and ZnO Electrodes, The Journal of Physical Chemistry C 116(39): 21069-21076


Douglas P Shepherd, Kevin J Whitcomb, Kenneth K Milligan, Peter M Goodwin, Martin P Gelfand, Alan Van Orden, Fluorescence intermittency and energy transfer in small clusters of semiconductor quantum dots, The Journal of Physical Chemistry C 114(35): 14831-14837