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Preprints/In revision


Christopher Miles, Scott McKinley, Fangyuan Ding, and Richard Lehoucq

Inferring stochastic rates from heterogeneous snapshots of particle positions

Bulletin of Mathematical Biology (in press)

Ziteng Liu, Thao Thi Thu Nguyen, and Fangyuan Ding

A User-Friendly Temperature Control System to Support Microscope, Microfluidic Chambers, and Custom Incubators

STAR Protocols, (2024) 5 (1), 102862

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.

Guohao Liang*, Hong Yin*, and Fangyuan Ding

Technical Advances and Applications of Spatial Transcriptomics

GEN Biotechnology, (2023) 2 (5), 384-398.

*: equally contributed

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

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

Guohao Liang*, Hong Yin*, Jun Allard and Fangyuan Ding

Cost-efficient boundary-free surface patterning achieves high effective-throughput of time-lapse microscopy experiments 

PLOS ONE, (2022) 17(10): e0275804

*: equally contributed

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

Selected Before UCI (2020)

Ding F, Elowitz M 

Constitutive splicing and economies of scale in gene expression

Nature Structural & Molecular Biology, (2019), 26, 424–432.​

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

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.

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.

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.

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.

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.

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)

Patents (Depixus @ has licensed all patents)

Bensimon D, Croquette V, Allemand JF, Manosas M, Ding F

Method of DNA sequencing by polymerization

EP239 0350A1, CA2800637A1, WO2011147929A1, EP2576822A1, CN103097551A, US20130171636A1, EP2576822B1

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.

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

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