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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
KCC2@psu.edu

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
  • Neoplasms
  • Skin Pigmentation
  • Brain
  • Histology
  • Pigmentation
  • DNA
  • Population
  • Larva

Recent Publications

2023

Ang, KC, Canfield, VA, Foster, TC, Harbaugh, TD, Early, KA, Harter, RL, Reid, KP, Leong, SL, Kawasawa, YI, Liu, DJ, Hawley, JW & Cheng, KC 2023, 'Native American genetic ancestry and pigmentation allele contributions to skin color in a Caribbean population', eLife, vol. 12. https://doi.org/10.7554/eLife.77514
Kim, HL, Li, T, Kalsi, N, Nguyen, HTT, Shaw, TA, Ang, KC, Cheng, KC, Ratan, A, Peltier, WR, Samanta, D, Pratapneni, M, Schuster, SC & Horton, BP 2023, 'Prehistoric human migration between Sundaland and South Asia was driven by sea-level rise', Communications Biology, vol. 6, no. 1, 150. https://doi.org/10.1038/s42003-023-04510-0
Subbakrishna Adishesha, A, Vanselow, DJ, La Riviere, P, Cheng, KC & Huang, SX 2023, 'Sinogram domain angular upsampling of sparse-view micro-CT with dense residual hierarchical transformer and attention-weighted loss', Computer Methods and Programs in Biomedicine, vol. 242, 107802. https://doi.org/10.1016/j.cmpb.2023.107802

2022

Yakovlev, MA, Vanselow, DJ, Ngu, MS, Zaino, CR, Katz, SR, Ding, Y, Parkinson, D, Wang, SY, Ang, KC, La Riviere, P & Cheng, KC 2022, 'A wide-field micro-computed tomography detector: micron resolution at half-centimetre scale', Journal of Synchrotron Radiation, vol. 29, pp. 505-514. https://doi.org/10.1107/S160057752101287X
Cheng, KC, Burdine, RD, Dickinson, ME, Ekker, SC, Lin, AY, Lloyd, KCK, Lutz, CM, MacRae, CA, Morrison, JH, O'Connor, DH, Postlethwait, JH, Rogers, CD, Sanchez, S, Simpson, JH, Talbot, WS, Wallace, DC, Weimer, JM & Bellen, HJ 2022, 'Promoting validation and cross-phylogenetic integration in model organism research', DMM Disease Models and Mechanisms, vol. 15, no. 9, dmm049600. https://doi.org/10.1242/dmm.049600
Wu, YT, Bennett, HC, Chon, U, Vanselow, DJ, Zhang, Q, Muñoz-Castañeda, R, Cheng, KC, Osten, P, Drew, PJ & Kim, Y 2022, 'Quantitative relationship between cerebrovascular network and neuronal cell types in mice', Cell Reports, vol. 39, no. 12, 110978. https://doi.org/10.1016/j.celrep.2022.110978
Son, S, Manjila, SB, Newmaster, KT, Wu, YT, Vanselow, DJ, Ciarletta, M, Anthony, TE, Cheng, KC & Kim, Y 2022, 'Whole-Brain Wiring Diagram of Oxytocin System in Adult Mice', Journal of Neuroscience, vol. 42, no. 25, pp. 5021-5033. https://doi.org/10.1523/JNEUROSCI.0307-22.2022

2021

Ye, J, Xue, Y, Liu, P, Zaino, R, Cheng, KC & Huang, X 2021, A Multi-attribute Controllable Generative Model for Histopathology Image Synthesis. in M de Bruijne, PC Cattin, S Cotin, N Padoy, S Speidel, Y Zheng & C Essert (eds), Medical Image Computing and Computer Assisted Intervention – MICCAI 2021 - 24th International Conference, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 12908 LNCS, Springer Science and Business Media Deutschland GmbH, pp. 613-623, 24th International Conference on Medical Image Computing and Computer Assisted Intervention, MICCAI 2021, Virtual, Online, 9/27/21. https://doi.org/10.1007/978-3-030-87237-3_59
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. https://doi.org/10.1021/jasms.0c00300
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. https://doi.org/10.1016/j.media.2020.101816
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. https://doi.org/10.7554/eLife.68920
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. https://doi.org/10.1109/ISBI48211.2021.9433914

2020

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. https://doi.org/10.1038/s41586-020-2962-9
Gupta, S, Xue, Y, Ding, Y, Vanselow, D, Yakovlev, M, van Rossum, DB, Huang, SX & Cheng, KC 2020, Supervised machine learning for region assignment of zebrafish brain nuclei based on computational assessment of cell neighborhoods. in A Krol & BS Gimi (eds), Medical Imaging 2020: Biomedical Applications in Molecular, Structural, and Functional Imaging., 113170T, Progress in Biomedical Optics and Imaging - Proceedings of SPIE, vol. 11317, SPIE, Medical Imaging 2020: Biomedical Applications in Molecular, Structural, and Functional Imaging, Houston, United States, 2/18/20. https://doi.org/10.1117/12.2548896
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. https://doi.org/10.1007/978-3-030-59710-8_6