Researcher Profile

Researcher Profile

Keith Cheng, MD, PhD

Keith Cheng, MD, PhD

Distinguished Professor, Department of Pathology and Laboratory Medicine
Division of Experimental Pathology
Distinguished Professor, Department of Biochemistry and Molecular Biology
Distinguished Professor, Department of Pharmacology
Scientific Program:Next-Generation Therapies
Disease Teams:
Institute for CyberScience (ICS) - Associate

Research Interests

In summary, Dr. Keith Cheng's research interests currently include phage genetics, E. coli genetics, recombination, cancer genetics, model system genetics, human genetics, human population genetics, genomics, phenomics, anatomic pathology, computational phenomics, automated phenotyping, microCT, synchrotron microCT, high-throughput imaging, machine learning, skin pigmentation, race, natural selection, social selection, music and medicine, piano, violin, classical music, chamber music, public media and web-based resources.

The Cheng lab is interested in making fundamental contributions to the understanding of genetic and molecular mechanisms involved in human biology and disease. The lab is interested in genetic aspects of human disease, use of model systems such as the zebrafish, contribution to web-based scientific resources and new, potentially high-throughput forms of 3D imaging.

Some of the Cheng lab's specific work is aimed at increasing understanding of the basis of phenotypic variability, particularly as it may impact cancer; basic mechanisms underlying the relationship between human skin pigmentation and skin cancer; contributing to web-based infrastructures for science, education and public service; and working toward a 3D derivative of histology that also allows the identification and characterization of all cell types but utilizes the computer to define slice angle, thickness, point of view  and definition of tissues of interest. Obvious implications include automation of phenotyping, including diagnostics.

  • Zebrafish
  • Genes
  • Mutation
  • Phenotype
  • Skin Pigmentation
  • Neoplasms
  • Pigmentation
  • Histology
  • DNA
  • Population
  • Brain
  • Microsatellite Repeats

Recent Publications


Van Nuffel, S, Ang, KC, Lin, AY & Cheng, KC 2021, 'Chemical Imaging of Retinal Pigment Epithelium in Frozen Sections of Zebrafish Larvae Using ToF-SIMS', Journal of the American Society for Mass Spectrometry, vol. 32, no. 1, pp. 255-261.
Xue, Y, Ye, J, Zhou, Q, Long, LR, Antani, S, Xue, Z, Cornwell, C, Zaino, R, Cheng, KC & Huang, X 2021, 'Selective synthetic augmentation with HistoGAN for improved histopathology image classification', Medical Image Analysis, vol. 67, 101816.
Katz, SR, Yakovlev, MA, Vanselow, DJ, Ding, Y, Lin, AY, Parkinson, DY, Wang, Y, Canfield, VA, Ang, KC & Cheng, KC 2021, 'Whole-organism 3d quantitative characterization of zebrafish melanin by silver deposition micro-ct', eLife, vol. 10, e68920.
Adishesha, AS, Vanselow, DJ, Riviere, PL, Huang, X & Cheng, KC 2021, Zebrafish histotomography noise removal in projection and reconstruction domains. in 2021 IEEE 18th International Symposium on Biomedical Imaging, ISBI 2021., 9433914, Proceedings - International Symposium on Biomedical Imaging, vol. 2021-April, IEEE Computer Society, pp. 140-144, 18th IEEE International Symposium on Biomedical Imaging, ISBI 2021, Nice, France, 4/13/21.


Yang, H, Luan, Y, Liu, T, Lee, HJ, Fang, L, Wang, Y, Wang, X, Zhang, B, Jin, Q, Ang, KC, Xing, X, Wang, J, Xu, J, Song, F, Sriranga, I, Khunsriraksakul, C, Salameh, T, Li, D, Choudhary, MNK, Topczewski, J, Wang, K, Gerhard, GS, Hardison, RC, Wang, T, Cheng, KC & Yue, F 2020, 'A map of cis-regulatory elements and 3D genome structures in zebrafish', Nature, vol. 588, no. 7837, pp. 337-343.
Ye, J, Xue, Y, Long, LR, Antani, S, Xue, Z, Cheng, KC & Huang, X 2020, Synthetic sample selection via reinforcement learning. in AL Martel, P Abolmaesumi, D Stoyanov, D Mateus, MA Zuluaga, SK Zhou, D Racoceanu & L Joskowicz (eds), Medical Image Computing and Computer Assisted Intervention – MICCAI 2020 - 23rd International Conference, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 12261 LNCS, Springer Science and Business Media Deutschland GmbH, pp. 53-63, 23rd International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI 2020, Lima, Peru, 10/4/20.


Donaldson, K, Buchanich, JM, Grigson, PS, Deneke, E, Vrana, KE, Sacks, DB, Kuehn, GJ, Cardamone, D, Pesce, A, Smiley, S, Nickley, J, Krock, K, Thomas, R, Wilkerson, ML, Farag, HA, Challa, SR, Tice, AM, Wolk, DM, Prichard, J, Grant, ML, Regmi, S, Kerbacher, B, Quinton, LE, Tice, AM, Olson, J, Haynes, A, Yu, E, McCully, KS, Assi, J, Wong, M, Zarrin-Khameh, N, Nifong, TP, Hawker, CD, Carlton, GT, Rivera, JM, Foulis, PR, Zuraw, A, Morlote, D, Peker, D, Reddy, V, Harada, S, Crutchfield, C, Zander, D, Barbhuiya, MA, Pederson, EC, Straub, ML, Scott, SC, Neibauer, TL, Salter, WF, Creer, MH, Zhu, Y, Bornhorst, JA, Theobald, JP, Algeciras-Schimnich, A, Cao, L, Knox, J, Hardy, R, Texas, HJ, McGuire, MF, Hunter, RL, Brown, RE, Hicks, J, Cai, Z, Brown, RE, Ali, Y, Cheng, KC, Katz, SR, Ding, Y, Vanselow, DJ, Yakovlev, MA, 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 Rivière, PJ, Newell, J, Hossler, C, Roche, M, Warrick, J, Phaeton, R, Kesterson, J, Myers, C, Barrios, R, Mintz, P, Robyak, K, Hamilton, C, McGhee, P, Pederson, C, Straub, M, Scott, S, Neibauer, T, Salter, W, Robyak, K, Singh, N, Morlote, D, Vnencak-Jones, C, Yemelyanova, A, Harada, S, Shah, M, Moghadamtousi, SZ, Lan, C, Duose, D, Hu, P, Esquenazi, Y, Luthra, R, Ballester, LY, Koenig, AN, Liu, CG, Zhang, J, Kalia, A, Al-Habib, A, Van Arsdall, M, Dhingra, S, Patel, K & Tatevian, N 2019, 'Abstracts of Presentations at the Association of Clinical Scientists 139th Meeting Hershey, PA, May 15-18, 2019', Annals of clinical and laboratory science, vol. 49, no. 3, pp. 403-416.
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, Carlo, FD, Rossum, DBV, Riviere, PL & Cheng, KC 2019, 'Computational 3d histological phenotyping of whole zebrafish by x-ray histotomography', eLife, vol. 8, e44898.
Chon, U, Vanselow, DJ, Cheng, KC & Kim, Y 2019, 'Enhanced and unified anatomical labeling for a common mouse brain atlas', Nature communications, vol. 10, no. 1, 5067.
the GenomeAsia 100K Consortium 2019, 'Identification of African-Specific Admixture between Modern and Archaic Humans', American Journal of Human Genetics, vol. 105, no. 6, pp. 1254-1261.
GenomeAsia100K Consortium 2019, 'The GenomeAsia 100K Project enables genetic discoveries across Asia', Nature, vol. 576, no. 7785, pp. 106-111.


Copper, JE, Budgeon, LR, Foutz, CA, van Rossum, DB, Vanselow, DJ, Hubley, MJ, Clark, DP, Mandrell, DT & Cheng, KC 2018, 'Comparative analysis of fixation and embedding techniques for optimized histological preparation of zebrafish', Comparative Biochemistry and Physiology Part - C: Toxicology and Pharmacology, vol. 208, pp. 38-46.
Peters, DG, Pollack, AN, Cheng, KC, Sun, D, Saido, T, Haaf, MP, Yang, QX, Connor, JR & Meadowcroft, MD 2018, 'Dietary lipophilic iron alters amyloidogenesis and microglial morphology in Alzheimer's disease knock-in APP mice', Metallomics, vol. 10, no. 3, pp. 426-443.
Lin, AY, Ding, Y, Vanselow, DJ, Katz, SR, Yakovlev, MA, Clark, DP, Mandrell, D, Copper, JE, van Rossum, DB & Cheng, KC 2018, 'Rigid Embedding of Fixed and Stained, Whole, Millimeter-Scale Specimens for Section-free 3D Histology by Micro-Computed Tomography', Journal of visualized experiments : JoVE, no. 140.


Xin, X, Clark, D, Ang, KC, Van Rossum, DB, Copper, J, Xiao, X, La Riviere, PJ & Cheng, KC 2017, Synchrotron microCT imaging of soft tissue in juvenile zebrafish reveals retinotectal projections. in RR Alfano & SG Demos (eds), Optical Biopsy XV: Toward Real-Time Spectroscopic Imaging and Diagnosis., 100601I, Progress in Biomedical Optics and Imaging - Proceedings of SPIE, vol. 10060, SPIE, Optical Biopsy XV: Toward Real-Time Spectroscopic Imaging and Diagnosis, San Francisco, United States, 1/31/17.

Clinical Trials Search

Children (age < 18 years)
Adults (age >= 18 years)