2025
Heterogeneous Sox2 transcriptional dynamics mediate pluripotency maintenance in mESCs in response to LIF signaling perturbations
Gaochen Jin, Emilia A. Leyes Porello, Jingchao Zhang, Bomyi Lim
BioRxiv (2025) 10.1101/2025.03.17.643751
3D dynamics of trans enhancer-promoter interactions in living Drosophila embryos reveals spatiotemporal thresholds for transcription activation
Hao Deng, Phillippe Valenti, François Payre, Bomyi Lim
BioRxiv (2025) 10.1101/2025.03.17.643800
2024
Multi-labeling Live Imaging to Quantify Gene Expression Dynamics During Drosophila Embryonic Development
Sahla Syed and Bomyi Lim
Springer Protocols (2024) 10.1007/978-1-0716-3854-5_9
Protocol to quantify the rate of RNA polymerase II elongation with MS2/MCP- and PP7/PCP-based live-imaging systems in early Drosophila embryos
Hao Deng and Bomyi Lim
STAR Protocols (2024) 10.1016/j.xpro.2024.103099
SCO-pH: Microfluidic dynamic phenotyping platform for high-throughput screening of single cell acidification
Hyejoong Jeong, Emilia A. Leyes Porello, Jean Gabriel Rosario, Da Kuang, Syung Hun Han, Jai-Yoon Sul, Bomyi Lim, Daeyeon Lee, and Junhyong Kim
BioRxiv (2024) 2024.05.08.593179
Multifaceted effects on even-skipped transcriptional dynamics upon Krüppel dosage changes
Shufan Lin and Bomyi Lim
Development (2024) 151 (5): dev202132.
2023
Regulation of the Dynamic Pol II Elongation Rate in Drosophila Embryos
Samuel Keller, Hao Deng, and Bomyi Lim
Cell Reports (2023); 42,113225
Transcriptional bursting: stochasticity in deterministic development
Emilia A. Leyes Porello, Robert T. Trudeau, and Bomyi Lim
Development (2023) 150 (12): dev201546.
Modulation of protein-DNA binding reveals mechanisms of spatiotemporal gene control in early Drosophila embryos
Sahla Syed, Yifei Duan, and Bomyi Lim
eLife (2023); 12:e85997
2022
Unveiling dynamic enhancer–promoter interactions in Drosophila melanogaster
Hao Deng, Gaochen Jin, and Bomyi Lim.
Biochem Soc Trans (2022). BST20220325.
Shared Transcriptional Machinery at Homologous Alleles Leads to Reduced Transcription in Early Drosophila Embryos
Hao Deng and Bomyi Lim.
Frontiers in Cell and Developmental Biology (2022). 10:912838
Epigenome editing and gene regulation in disease phenotypes
Gaochen Jin and Bomyi Lim.
Korean Journal of Chemical Engineering (2022). 10.1007/s11814-022-1076-5
Temperature-responsive optogenetic probes of cell signaling
William Benman, Erin E. Berlew, Hao Deng, Caitlyn Parker, ivan A. Kuznetsov, Bomyi Lim, Arndt F. Siekmann, Brian Y. Chow, and Lukasz J. Bugaj.
Nature Chemical Biology (2022). 18(2):152-160
2021
Diverse heterochromatin-associated proteins repress distinct classes of genes and repetitive elements
Ryan L. McCarthy, Kelsey E. Kaeding, Samuel H. Keller, Yu Zhong, Liqin Xu, Antony Hsieh, Yong Hou, Greg Donahue, Justin S. Becker, Oscar Alberto, Bomyi Lim, and Kenneth S. Zaret
Nature Cell Biology (2021). 23,905-914
The nuclear to cytoplasmic ratio directly regulates zygotic transcription in Drosophila through multiple modalities
Sahla Syed, Hentry Wilky, João Raimundo, Bomyi Lim, and Amanda A. Amodeo.
PNAS (2021). 118 (14) e2010210118
Enhancer-promoter communication: hubs or loops?
Bomyi Lim and Michael S Levine.
Current Opinion in Genetics & Development (2021). 67;5-9.
2020
Regulation of spatiotemporal limits of developmental gene expression via enhancer grammar
Samuel H. Keller*, Siddhartha G. Jena*, Yuji Yamazaki, and Bomyi Lim.
PNAS (2020). 117(26):15096-15103
2018
Temporal dynamics of pair-rule stripes in living Drosophila embryos
Bomyi Lim#, Takashi Fukaya, Tyler Heist, and Michael Levine#. (# co-corresponding authors)
PNAS (2018). 115(33):8376-8381
Visualization of transvection in living Drosophila embryos
Bomyi Lim*, Tyler Heist*, Michael Levine, and Takashi Fukaya.
Molecular Cell (2018). 70(2):287-296
Imaging transcriptional dynamics
Bomyi Lim
Current Opinion in Biotechnology (2018). 52;49-55.
Synthesizing developmental trajectories
Paul Villoutreix, Joakim Anden, Bomyi Lim, Hang Lu, Ioannis G. Kevrekidis, Amit Singer, and Stanislav Y. Shvartsman
PLoS Computational Biology (2018). 13(9):e1005742
2017
A novel function for the IkB inhibitor Cactus in promoting Dorsal nuclear localization and activity in the Drosophila embryo
Maira Arruda Cardoso, Marcio Fontenele, Bomyi Lim, Paulo Mascarello Bisch, Stanislav Y. Shvartsman, and Helena Araujo
Development (2017). 144(16):2907-2913
Rapid rates of Pol II elongation in the Drosophila embryo
Takashi Fukaya*, Bomyi Lim*, and Michael Levine
Current Biology (2017). 23;27(9):1387-1391.
Transcriptional pre-patterning of Drosophila gastrulation
Bomyi Lim, Michael Levine, and Yuji Yamazaki
Current Biology (2017). 23;27(2):286-290.
Reconstructing ERK signaling in the Drosophila embryo from fixed images
Bomyi Lim, Carmeline J. Dsilva, Ioannis Y. Kevrekidis, and Stanislav Y. Shvartsman
Methods in Molecular Biology (2017). 2017:1487-337-351.
2016
Mitosis-associated repression in development
Emilia Esposito, Bomyi Lim, Ghita Guessous, Hanieh Falahati, and Michael Levine
Genes and Development (2016). 30(13):1508-8.
Enhancer control of transcriptional bursting
Takashi Fukaya*, Bomyi Lim*, and Michael Levine
Cell (2016). 166(2):358-68.
Microfluidics for high-throughput quantitative studies of early development
Thomas J. Levario, Bomyi Lim, Stanislav Y. Shvartsman, and Hang Lu
Annual Review of Biomedical Engineering (2016). 18:285-309.
2015
A systematic ensemble approach to thermodynamic modeling of gene expression from sequence data
Md. Abul Hassan Samee, Bomyi Lim, Nuria Samper, Hang Lu, Christine Rushlow, Gerardo Jimenez, Stanislav Y. Shvartsman, and Saurabh Sinha
Cell Systems (2015)
Dynamics of inductive ERK signaling in the Drosophila embryo
Bomyi Lim, Carmeline J. Dsilva, Thomas J. Levario, Hang Lu, Trudi Schupbach, Ioannis G. Kevrekidis, and Stanislav Y. Shvartsman
Current Biology (2015)
Temporal ordering and registration of images in studies of developmental dynamics
Carmeline J. Dsilva*, Bomyi Lim*, Hang Lu, Amit Singer, Stanislav Y. Shvartsman, and Ioannis G. Kevrekidis
Development (2015)
2014
Zelda potentiates morphogen activity by increasing chromatin accessibility
Sun M. Foo, Yujia Sun, Bomyi Lim, Ruta Ziukaite, Kevin O’Brien, Chung-Yi Nien, Nikolai Kirov, Stanislav Y. Shvartsman, and Christine Rushlow
Current Biology (2014)
2013
Kinetics of gene derepression by ERK signaling
Bomyi Lim, Nuria Samper, Hang Lu, Christine Rushlow, Gerardo Jimenez, and Stanislav Y. Shvartsman
PNAS (2013)
Calpain A modulates Toll responses by limited Cactus/Ik-B proteolysis
Marcio Fontenele, Bomyi Lim, Danielle Oliveira, David H. Perlman, Trudi Schupbach, and Helen Araujo
Molecular Biology of the Cell (2013)
Microfluidic trap array for massively parallel imaging of Drosophila embryos
Thomas J. Levario, Mei Zhan, Bomyi Lim, Stanislav Y. Shvartsman, and Hang Lu
Nature Protocols (2013)
2012
RTK signaling modulates the Dorsal gradient
Aharon Helman, Bomyi Lim, Maria Jose Andreu, Yoosik Kim, Tatyana Shestkin, Hang Lu, Gerardo Jimenez, Stanislav Y. Shvartsman, and Ze’ev Paroush
Development (2012)
Pattern formation by graded and uniform signals in the early Drosophila embryo
Jitendra S. Kanodia, Hsiao-Lang Liang, Yoosik Kim, Bomyi Lim, Mei Zhan, Hang Lu, Christine Rushlow, and Stanislav Y. Shvartsman
Biophysical Journal (2012)
2011
Gene regulation by MAPK substrate competition
Yoosik Kim, Mari Jose Andreu, Bomyi Lim, Kwanghun Chung, Mark Terayama, Gerardo Jimenez, Celeste A. Berg, Hang Lu, and Stanislav Y. Shvartsman
Developmental Cell (2011)