Preprints/In revision
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Publications
Yoseop Yoon, Elodie Bournique, Lindsey Soles, Hong Yin, Hsu-Feng Chu, Christopher Yin, Yinyin Zhuang, Xiangyang Liu, Liang Liu, Joshua Jeong, Clinton Yu, Marielle Valdez, Lusong Tian, Lan Huang, Xiaoyu Shi, Georg Seelig, Fangyuan Ding, Liang Tong, Rémi Buisson, Yongsheng Shi
RBBP6 anchors pre-mRNA 3′ end processing to nuclear speckles for efficient gene expression
Molecular Cell, (2025) 85, 1-16
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Christopher Miles, Scott McKinley, Fangyuan Ding, and Richard Lehoucq
Inferring stochastic rates from heterogeneous snapshots of particle positions
Bulletin of Mathematical Biology, (2024) 86:74
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Ziteng Liu, Thao Thi Thu Nguyen, and Fangyuan Ding
STAR Protocols, (2024) 5 (1), 102862
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Iris Dror*, Tsotne Chitiashvili*, Shawn Y.X. Tan, Clara T. Cano, Anna Sahakyan, Yolanda Markaki, Constantinos Chronis, Amanda Collier, Weixian Deng, Guohao Liang, Yu Sun, Anna Afasizheva , Jarrett Miller, Wen Xiao, Douglas Black, Fangyuan Ding and Kathrin Plath
XIST regulates autosomal chromatin state and gene expression in naïve human pluripotent stem cells
Cell, (2024) 187 (1), 110-129.
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Guohao Liang*, Hong Yin*, and Fangyuan Ding
Technical Advances and Applications of Spatial Transcriptomics
GEN Biotechnology, (2023) 2 (5), 384-398.
*: equally contributed
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Sungyun Cho, Yujin Chun, Long He, Cuauhtemoc Blas Ramirez, Kripa Ganesh, Kyungjo Jeong, Junho Song, Jin Gyu Cheong, Zhongchi Li, Jungmin Choi, Joohwn Kim, Nikos Koundouros, Fangyuan Ding, Noah Dephoure, Cholsoon Jang, John Blenis# and Gina Lee#
FAM120A couples SREBP-dependent transcription and splicing of lipogenesis enzymes downstream of mTORC1
Molecular Cell, (2023) 83 (16), 3010–3026
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Fangyuan Ding#, Simona Cocco, Saurabh Raj, Maria Manosas, Thao Nguyen, Michelle Spiering, David Bensimon, Jean-Francois Allemand, and Vincent Croquette#
Displacement and dissociation of oligonucleotides during DNA hairpin closure under strain
Nucleic Acid Research, (2022) 50 (21), 12082-12093
#: co-corresponding authors
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Guohao Liang*, Hong Yin*, Jun Allard and Fangyuan Ding
PLOS ONE, (2022) 17(10): e0275804
*: equally contributed
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Fangyuan Ding#, Christina Su, Ke-Huan Kuo Chow, Guohao Liang, and Elowitz, Michael B#.
Dynamics and functional roles of splicing factor autoregulation​
Cell Reports, (2022) 39(12):110985
#: co-corresponding authors
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Selected Before UCI (2020)
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Ding F, Elowitz M
Constitutive splicing and economies of scale in gene expression
Nature Structural & Molecular Biology, (2019), 26, 424–432.​
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Ding F, Manosas M, Spiering MM, Benkovic SJ, Bensimon D, Allemand JF, Croquette V
Single-molecule mechanical identification and sequencing
Nature Methods, (2012) 9(4), 367-372.
News and Views: S Linnarsson, Nature Methods
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Manosas M, Spiering MM, Ding F, Bensimon D, Allemand JF, Benkovic SJ, Croquette V
Mechanism of strand displacement synthesis by DNA replicative polymerases
Nucleic Acids Research, (2012) 40 (13), 6174-6186.
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Manosas M, Spiering MM, Ding F, Croquette V, Benkovic SJ
Collaborative coupling between polymerase and helicase for leading-strand synthesis
Nucleic Acids Research, (2012) 40 (13), 6187-6198.
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De Cian A, Praly E, Ding F, Singh V, Pietrement O, Lavelle C, Owen-Hughes T, Croquette V, Le Cam E
ATP-independent cooperative binding of yeast Isw1a to bare and nucleosomal DNA
PloS One, (2012) 7 (2), e31845.
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Manosas M, Meglio A, Spiering MM, Ding F, Benkovic SJ, Barre FX, Saleh OA, Allemand JF, Bensimon D, Croquette V
Magnetic Tweezers for the Study of DNA Tracking Motors
Methods. Enzymol. (2010) 475:297-320.
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Meglio A, Praly E, Ding F, Allemand JF, Bensimon D, Croquette V
Single DNA/protein studies with magnetic traps
Curr. Opin. Struct. Biol. (2009) 19(5):615-22.
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Ferrer J*, Ding F*, Tarsa P, Brau R, Lang M
Interlaced Optical Trapping and Fluorescence Excitation improves fluorophore longevity
Curr. Pharm. Biotechnol. (2009) (5): 502-7. (*: authors contributed equally to publication)
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Patents (Depixus @ has licensed all patents)
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Bensimon D, Croquette V, Allemand JF, Manosas M, Ding F
Method of DNA sequencing by polymerization
EP239 0350A1, CA2800637A1, WO2011147929A1, EP2576822A1, CN103097551A, US20130171636A1, EP2576822B1
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Bensimon D, Allemand JF, Manosas M, Ding F, Croquette V
Method of DNA sequencing by hybridization
EP2390351A1, CA2800639A1, WO2011147931A1, EP2576818A1,CN103052718A,US20130137098A1, et al.
Bensimon D, Allemand JF, Ding F, Croquette V
Method of DNA detection and quantification by single-molecule hybridization and manipulation
CA2859913A1, WO2013093005A1, EP2794915A1, US20150031028A1, et al.
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Bensmion D, Croquette V, Gouet G, Allemand JF, Ding F
Process for detection of DNA modifications and protein binding by single molecule manipulation
CA2898151A1, WO2014114687A1