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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). 23,905-914The 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) e2010210118Enhancer-promoter communication: hubs or loops? Bomyi Lim and Michael S Levine.Current Opinion in Genetics & Development (2021). 67;5-9.
2020
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):8376-8381Visualization of transvection in living Drosophila embryos Bomyi Lim*, Tyler Heist*, Michael Levine, and Takashi Fukaya.Molecular Cell (2018). 70(2):287-296Imaging transcriptional dynamics Bomyi LimCurrent 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. ShvartsmanPLoS 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 AraujoDevelopment (2017). 144(16):2907-2913Rapid rates of Pol II elongation in the Drosophila embryo Takashi Fukaya*, Bomyi Lim*, and Michael LevineCurrent Biology (2017). 23;27(9):1387-1391.Transcriptional pre-patterning of Drosophila gastrulation Bomyi Lim, Michael Levine, and Yuji YamazakiCurrent 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. ShvartsmanMethods in Molecular Biology (2017). 2017:1487-337-351.
2016
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 SinhaCell 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. ShvartsmanCurrent 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. KevrekidisDevelopment (2015)
2014
2013
Kinetics of gene derepression by ERK signaling Bomyi Lim, Nuria Samper, Hang Lu, Christine Rushlow, Gerardo Jimenez, and Stanislav Y. ShvartsmanPNAS (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 AraujoMolecular 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 LuNature 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 ParoushDevelopment (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. ShvartsmanBiophysical Journal (2012)
2011