Amogh Subbakrishna Adishesha, Daniel J Vanselow, Patrick La Riviere, Keith C Cheng, Sharon X Huang
Sinogram Domain Angular Upsampling of Sparse-View Micro-CT with Dense Residual Hierarchical Transformer and Noise-Aware Loss.
Computer Methods and Programs in Medicine 2023 September 12.

Quantitative Geometric Modeling of Blood Cells from X-ray Histotomograms of Whole Zebrafish Larvae
Maksim A. Yakovlev, Ke Liang, Carolyn R. Zaino, Daniel J. Vanselow, Andrew L. Sugarman, Alex Y. Lin, Patrick J. La Riviere, Yuxi Zheng, Justin D. Silverman, John C. Leichty, Sharon X. Huang, Keith C. Cheng
Under Review! eLife 2023 June.
doi: 10.1101/2023.05.23.541939.

Khai C Ang, Victor A Canfield, Tiffany C Foster, Thaddeus D Harbaugh, Kathryn A Early, Rachel L Harter, Katherine P Reid, Shou Ling Leong, Yuka I Kawasawa, Dajiang J Liu, John W Hawley, Keith C Cheng
Native American Ancestry and Pigmentation Allele Contributions to Skin Color in a Caribbean Population.
eLife, 2023 June 09.

Hie Lim Kim, Tanghua Li, Namrata Kalsi, Hung Tran The Nguyen, Timothy A Shaw, Khai C Ang, Keith C Cheng, Aakrosh Ratan, W Richard Peltier, Dhrubajyoti Samanta, Mahesh Pratapneni, Stephan C Schuster, Benjamin P Horton
Prehistoric human migration between Sundaland and South Asia was driven by sea-level rise.
Communications Biology, 2023 Feb 04.
doi: 10.1038/s42003-023-04510-0.


Yakovlev MA, Vanselow DJ, Ngu MS, Zaino CR, Katz SR, Ding Y, Parkinson DY, Wang Y, Ang KC, La Riviere P, Cheng KC.
A wide-field micro-computed tomography detector: micron resolution at half-centimetre scale.
J. Synchrotron Rad. 2022 Jan 19.
doi: 10.1107/S160057752101287X.

Cheng, K. C., Burdine, R. D., Dickinson, M. E., Ekker, S. C., Lin, A. Y., Lloyd, K. C. K., Lutz, C. M., MacRae, C. A., Morrison, J. H., O’Connor, D. H., Postlethwait, J. H., Rogers, C. D., Sanchez, S., Simpson, J. H., Talbot, W. S., Wallace, D. C., Weimer, J. M., and Bellen, H. J. (2022).
Promoting validation and cross-phylogenetic integration in model organism research.
Dis Models Mech. 15(9).
doi: 10.1242/dmm.049600.

Yuan-ting Wu, Hannah C. Bennett, Uree Chon, Daniel J. Vanselow, Qingguang Zhang, Rodrigo Munoz-Castaneda, Keith C. Cheng, Pavel Osten, Patrick J. Drew, Yongsoo Kim.
Quantitative relationship between cerebrovascular network and neuronal cell types in mice
Cell Reports, (2022)

Son S, Manjila S, Newmaster KT, Wu T, Vanselow DJ, Ciarletta M, Todd TE, Cheng KC, Kim Y.
Wiring diagram of the oxytocin system in the mouse brain.
Journal of Neuroscience (2022)

Ngu, M. S., Vanselow, D. J., Zaino, C. R., Lin, A. Y., Copper, J. E., Beaton, M. J., Colbourne, J. K., Cheng, K. C., and Ang, K. C. (2022).
Web-based histology reference Atlas for the freshwater crustacean daphnia magna.
doi: 10.1101/2022.03.09.483544


Lin, A., Thomas, G. K., Ang, K. C., Rossum, D. B. V., Canfield, V. A. and Cheng, K. C. (2021).
Time- and cell-dependent atypia and cell death are caused by progressive deficiency in DNA replication. bioRxiv, 2021
doi: 10.1101/2020.12.31.425001

Madra, A., Lin, A. Y., Vanselow, D. J., and Cheng, K. C. (2021)
An adaptively optimized algorithm for counting nuclei in X-ray micro-CT scans of whole organisms.
arXiv arXiv:2112.10670

Katz, S. R., Yakovlev, M. A., Vanselow, D. J., Ding, Y., Lin, A. Y., Parkinson, D. Y., Wang, Y., Canfield, V. A., Ang, K. C., and Cheng, K. C. (2021). Whole-organism 3D quantitative characterization of zebrafish melanin by silver deposition micro-CT. eLife. eLife
doi: 10.7554/eLife.68920


Samarth Gupta, Yuan Xue, Yifu Ding, Daniel Vanselow, Maksim Yakovlev, Damian B. vam Rossum, Sharon X. Huang, Keith C. Cheng
"Supervised machine learning for region assignment of zebrafish brain nuclei based on computational assessment of cell neighborhoods,"
arXivProc. SPIE 11317, Medical Imaging 2020: Biomedical Applications in Molecular, Structural, and Functional Imaging, 113170T (28 February 2020)

Newmaster K, Nolan ZT, Chon U, Vanselow DJ, Weit AR, Tabbaa M, Hidema S, Nishimori K, Hammock EAD, Kim Y. Quantitative Cellular-Resolution Map of the Oxytocin Receptor in Postnatally Developing Mouse Brains.
Nature Communications, (2020)

Lin, A. Y., and Cheng, K. C. (2020).
X-ray histotomography: characterising every cell of a whole organism. Research Outreach.
doi: 10.32907/RO-119-5861

Van Nuffel, S., Ang, K. C., Lin, A. Y., and Cheng, K. C. (2020).
Chemical imaging of retinal pigment epithelium in frozen sections of zebrafish larvae using ToF-SIMS. J Am Soc Mass Spectrum. 
doi: 10.1021/jasms.0c00300


Wall, J.D., Stawiski, E.W., Ratan, A., Kim, H.L., Kim, C.H., Gupta, R., Suryamohan, K., Gusareva, E.S., Purbojati, R.W., Bhangale, T., Stepanov, V., Kharkov, V., Schröder, M.S., Ramprasad, V., Tom, J., Durinck, S., Bei, Q.X., Li, J., Guillory, J., Phalke, S., Basu, A., Stinson, J., Nair, S., Malaichamy, S., Biswas, N.K., Chambers, J.C., Cheng, K.C., George, J.T., Khor, S.S., Kim, J., Cho, B., Menon, R., Sattibabu, T., Bassi, A.,Deshmukh, M., Verma, A., Gopalan, V., Shin, J.Y., Pratapneni, M., Santhosh, S., Tokunaga, K., Md-Zain, B.M., Chan, K.G., Parani, M., Natarajan, P., Hauser, M., Allingham, R.R., Santiago-Turla, C., Ghosh, A., Krishna Gadde, S.G., Fuchsberger, C., Forer, L., Schoenherr, S., Sudoyo, H., Lansing, J.S., Friedlaender, J., Koki, G., Cox, M.P., Hammer, M., Karafet, T., Ang, K.C., Mehdi, S.Q., Radha, V., Mohan, V., Majumder, P.P, Seshagiri, S., Seo, J.S., Schuster, S.C. & Peterson, A.S.
The GenomeAsia 100K Project Enables Genetic Discoveries Across Asia. Nature 2019 (576): 106-116. Cover Article

Chon U, Vanselow DJ, Cheng KC, Kim Y.
Enhanced and Unified Anatomical Labeling for a Common Mouse Brain Atlas
Nature Communications:, 2019

Ding Y, Vanselow DJ, Yakovlev MA, Katz SR, Lin AY, Clark DP, Vargas P, Xin X, Copper JE, Canfield VA, Ang KC, Wang Y, Xiao X, De Carlo F, van Rossum DB, La Riviere P, Cheng KC. Computational 3D Histological Phenotyping of Whole Zebrafish by X-ray Histotomography. Elife. 2019 May 7;8.
pii: e44898. doi: 10.7554/eLife.44898 PMID: 31063133.

Perspective Article for Ding et al. 3D Imaging: Taking a closer look at whole organisms by Noriko Ichino and Stephen C Ekker.


Lin AY, Ding Y, Vanselow DJ, Katz SR, Yakovlev MA, Clark D, Mandrell D, Copper JE, van Rossum DB, Cheng KC. Rigid Embedding of Fixed and Stained Whole Millimeter-Scale Specimens for Section-free Imaging by Micro-CT. J Vis Exp. 2018 Oct 17;(140). doi: 10.3791/58293. PMID: 30394379 PMCID: PMC6235553.


Copper JE, Budgeon LR, Foutz CA, van Rossum DB, Vanselow DJ, Hubley MJ, Clark DP, Mandrell DT, Cheng KC. Comparative analysis of fixation and embedding techniques for optimized histological preparation of zebrafish. Comp Biochem Physiol C Toxicol Pharmacol. 2017 Nov 20. pii: S1532-0456(17)30208-9. doi:10.1016/j.cbpc.2017.11.003. PubMed PMID: 29157956, PMCID: PMC5936644. Web-Based Companion site for Copper et al.

Xin X, Clark D, Ang KC, van Rossum DB, Copper J, Xiao X, La Riviere P, Cheng KC. Synchrotron micro-CT Imaging of Soft Tissue in Juvenile Zebrafish Reveals Retinotectal Projections. Proc of SPIE, 2017. Optical Biopsy XV: Towards Real-Time Spectroscopic Imaging and Diagnosis, edited by Robert R. Alfano, Stavros G. Demos, Proc. Of SPIE Vol. 10060, 100601I. doi: 10.1117/12.2267477


Cheng KC, Katz SR, Lin AY, Xin X, Ding Y. Whole-Organism Cellular Pathology: A Systems Approach to Phenomics. Adv Genet. 2016; 95: 89-115. doi: 10.1016/bs.adgen.2016.05.003. Epub 2016 Jul 29. Review. PMID: 27503355 PMCID: In Progress...