Publications

2020

Bacher R, Chu LF, Argus C, Bolin JM, Knight P, Thomson JA, Stewart R, Kendziorski C. (2020). Enhancing biological signals and detection rates in single-cell RNA-seq experiments with cDNA library equalization.

bioRxiv: https://www.biorxiv.org/content/10.1101/2020.10.05.326553v1

Seirup M, Sengupta S, Swanson S, McIntosh E, Colins M, Chu LF, Cheng Z, Gorkin DU, Duffin B, Bolin JM, Argus C, Stewart R, Thomson JA. (2020). Rapid changes in chromatin structure during dedifferentiation of primary hepatocytes in vitro.

bioRxiv: https://www.biorxiv.org/content/10.1101/2020.09.21.307363v1

Deshpande A, Chu LF, Stewart R and Gitter A. Network Inference with Granger Causality Ensembles on Single-Cell Transcriptomic Data.

bioRxiv: https://doi.org/10.1101/534834v1

Seirup M, Chu LF, Sengupta S, Leng N, Browder H, Kapadia K, Shafer CM, Duffin B, Elwell AL, Bolin JM, Swanson SA, Stewart R, Kendziorski C, Thomson JA, Bacher R. Reproducibility across single-cell RNA-seq protocols for spatial ordering analysis. PLoS One. 2020; PMID: 32986734.

2019

Chu LF^†, Mamott D, Ni Z, Bacher R, Liu C, Swanson S, Kendziorski C, Stewart R and Thomson JA^†. An in vitro human segmentation clock model derived from embryonic stem cells. Cell Reports. 2019; PMID: 31461642. ^†Co-corresponding author

In the News, Human Developmental Clock Mimicked in a Dish: Morgridge Institute for Research, EurekAlert!, Neuroscience News, Sleep Review, Labroots

Finding a rhythm. Real-time live-cell gene oscillating video selected as one of the best GIFs in science by Scientific America (2019-09-06)

Joseph DB, Chandrashekar AS, Abler LL, Chu LF, Thomson JA and Vezina CM. Epithelial DNA methyltransferase-1 regulates cell survival, growth and maturation in developing prostatic buds. Developmental Biology. 2019. PMID:30659795.

Joseph DB, Chandrashekar AS, Chu LF, Thomson JA and Vezina CM. A folic acid-enriched diet attenuates prostate involution in response to androgen deprivation. Prostate. 2018.PMID:30298636.

2018

Bacher R, Leng N, Chu LF, Thomson JA Kendziorski C Stewart R. Trendy: Segmented regression analysis of expression dynamics for high-throughput ordered profiling experiments. BMC Bioinformatics. 2018. PMID:30326833.

Joseph DB, Chandrashekar AS, Abler LL, Chu LF, Thomson JA, Mendelsohn C, Vezina CM. In vivo replacement of damaged bladder urothelium by Wolffian duct epithelial cells. Proceedings of the National Academy of Sciences. 2018. PMID:30061411.

Vermillion KL, Bacher R, Tannenbaum AP, Swanson S, Jiang P, Chu LF, Stewart R, Thomson JA, and Vereide DT. Novel Spatial Patterns of Gene Expression are Revealed in the Chick Primitive Streak by Ordering Single Cell Transcriptomes. Developmental Biology. 2018. PMID:29678445.

2017

Phillips MJ, Jiang P, Howden S, Barney P, Min J, York NW, Chu LF, Capowski EE, Cash A, Jain S, Barlow K, Tabassum T, Stewart R, Pattnaik BR, Thomson JA, Gamm DM. A novel approach to single cell RNA-seq analysis facilitates in silico gene reporting of human pluripotent stem cell-derived retinal cell types. Stem Cells. 2017, PMID:29230913.

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; PMID: 28418000. *Co-first author.

Recommended by Faculty of 1000

Zhang J, Chu LF, Hou Z, Schwartz MP, Hacker T, Vickerman V, Swanson S, Leng N, Nguyen BK, Elwell A, Bolin J, Brown ME, Stewart R, Burlingham WJ, Murphy WL, Thomson JA. Functional characterization of human pluripotent stem cell-derived arterial endothelial cells. Proceedings of the National Academy of Sciences. 2017; PMID:28696312.

In the News, Stem Cell Advance Brings Bioengineered Arteries Closer to Reality: Bioquicknews, Milwaukee Journal Sentinel, Wisconsin State Journal

2016

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; PMID: 27534536. †Co-corresponding author, *Co-first author

Korthauer K, 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; PMID:27782827.

Lee WH, Higuchi H, Ikeda S, Macke E, Takimoto T, Pattnaik B, Liu C, Chu LF, Siepka SM, Krentz KJ, Rubinstein D, Kalejta RF, Thomson JA, Mullins R, Takahashi JS, Pinto L, Ikeda A. Mouse Tmem135 mutation reveals a mechanism involving mitochondrial dynamics that leads to age-dependent retinal pathologies. eLIFE. 2016; PMID:27863209.

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; PMID:26743507.

2015

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; PMID: 26301841. *Co-first author

In the News, Algorithm helps identify elusive genes that express like clockwork: Morgridge Institute for Research, ScienceDaily

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; PMID: 25458896.

2013

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; 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; PMID: 23505351.

Graduate Works

Chu LF, Surani MA, Jaenisch R, Zwaka TP. Blimp1 expression predicts embryonic stem cell development in vitro. Current Biology. 2011; 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 (2011). 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; PMID:18585351.

Shah R, Medina-Martinez O, Chu LF, Samaco RC, Jamrich M. Expression of FoxP2 during zebrafish development and in the adult brain. International Journal of Developmental Biology. 2006; PMID: 16525940.