Publications

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)