Li-Fang Chu

Assistant Scientist



(608) 890-4244


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A fascinating feature of embryonic development is the reproducibility of temporal developmental programs (e.g., somite and limb formation) among individuals of the same species. Between different species, however, developmental timing varies drastically; human gestation is roughly 40 weeks, while mice require only 3 weeks. Remarkably, the differentiation rate of human and mouse pluripotent stem cells (PSCs), including embryonic stem cells and induced pluripotent stem cells, recapitulates species-specific timing (mouse PSCs differentiate much faster than human PSCs). This suggests that, without normal developmental cues from an intact embryo, a largely unknown intrinsic timing mechanism exists in PSCs in vitro. My long-term research interest is to understand the developmental timing mechanisms that control cell fate during differentiation and embryonic development.

Areas of Expertise

  • Single-cell RNA-seq analysis on temporal cell state transition.
  • CRISPR/Cas9 mediated knockin or knockout of mouse and human pluripotent stem cells.
  • Derivation of mouse pluripotent stem cells.


Ph.D. Cellular and Molecular Biology, Baylor College of Medicine, Houston, TX, USA.

B.S. Zoology, National Taiwan University, Taipei, Taiwan.


  • Presentation Award, Center of Cell & Gene Therapy Conference, Houston, TX.
  • Claude W. Smith Fellowship Award. Baylor College of Medicine.
  • Dean’s Award at National Taiwan University.
  • Dr. Da-qui Chei & Dr. Song-yen Fong Memorial Scholarship.
  • Undergraduate Research Scholarship. National Taiwan University.

Selected Publications

  • Bacher R*, Chu LF*, Leng N, Gasch A, Newton M, Thomson JA, Stewart R, and Christina Kendziorski. SCnorm: A quantile-regression based approach for robust normalization of single-cell RNA-seq data. Nature Methods. 2017; DOI: 10.1038/NMETH.4263. PMID: 28418000.
    *Co-first author
  • Chu LF*, Leng N*, Zhang J, Hou Z, Mamott D, Vereide DT, Choi J, Kendzrioski C, Stewart RM, Thomson JA. Single-cell RNA-seq reveals novel regulators of human embryonic stem cells differentiation to definitive endoderm. Genome Biology. 2016; 17(1):173. PMID: 27534536.
    †Co-corresponding author, *Co-first author
  • Korthauer KD, Chu LF, Newton MA, Li Y, Thomson JA, Stewart R and Kendziorski C. scDD: A statistical approach for identifying differential distributions in single-cell RNA-seq experiments. Genome Biology. 2016; 17(1):222. PMID: 27782827
  • Leng N, Choi J, Chu LF, Thomson JA, Kendziorski C, Stewart R. OEFinder: A user interface to identify and visualize ordering effects in single-cell RNA-seq data. Bioinformatics. 2016; 32(9):1408-10. PMID: 26743507
  • Leng N*, Chu LF*, Barry C, Li Y, Choi J, Li X, Jiang P, Stewart RM, Thomson JA Kendzrioski C. Oscope identifies oscillatory genes in unsynchronized single cell RNA-seq experiments. Nature Methods. 2015; 12(10):947-50. PMID: 26301841 *Co-first author
  • Vereide DT, Vickerman V, Swanson SA, Chu LF, McIntosh BE, Thomson JA. An expandable, inducible hemangioblast state regulated by fibroblast growth factor. Stem Cell Reports. 2014; 3(6):1043-57. PMID: 25458896
  • Hou Z, Zhang Y, Propson NE, Howden SE, Chu LF, Sontheimer EJ, Thomson JA. Efficient genome engineering in human pluripotent stem cells using Cas9 from Neisseria meningitidis. Proceedings of the National Academy of Sciences. 2013; 110(39):15644-9. PMID: 23940360
  • Stewart R, Rascón CA, Tian S, Nie J, Barry C, Chu LF, Ardalani H, Wagner RJ, Probasco MD, Bolin JM, Leng N, Sengupta S, Volkmer M, Habermann B, Tanaka EM, Thomson JA, Dewey CN. Comparative RNA-seq analysis in the unsequenced axolotl: the oncogene burst highlights early gene expression in the blastema. PLoS Computational Biology. 2013; 9(3): e1002936. PMID: 23505351
  • Chu LF, Surani MA, Jaenisch R, Zwaka TP. Blimp1 expression predicts embryonic stem cell development in vitro. Current Biology. 2011; 21(20): 1759-65. PMID: 22000107. Recommended by Faculty of 1000.
  • Chu LF and Zwaka TP. “Human Pluripotent Cells: The Biology of Pluripotency”. Human Stem Cell Technology and Biology: A Research Guide and Laboratory Manual (2010). Chapter 26. 313-325.
  • Dejosez M, Krumenacker JS, Zitur LJ, Passeri M, Chu LF, Songyang Z, Thomson JA, Zwaka TP.  Ronin is essential for embryogenesis and the pluripotency of mouse embryonic stem cells. Cell. 2008 133(7):1162-74. PMID:18585351