2022
Fangyuan Ding#, Simona Cocco, Saurabh Raj, Maria Manosas, Michelle Spiering, David Bensimon, Jean-Francois Allemand, and Vincent Croquette#
Displacement and dissociation of oligonucleotides during DNA hairpin closure under strain
Nature Chemistry (submitted) (BioRxiv copy)
#: co-corresponding authors
Guohao Liang*, Hong Yin* and Fangyuan Ding
Cost-efficient boundary-free surface patterning achieves high effective-throughput of time-lapse microscopy experiments
PLOS ONE (under review) (BioRxiv copy)
*: equally contributed
2021
Iris Dror*, Tsotne Chitiashvili*, Anna Sahakyan*, Shawn Y.X. Tan, Guohao Liang, Fangyuan Ding, Jarrett Miller and Kathrin Plath
XIST controls X chromosome dampening and autosomal genes in early human development
Cell (in revision)
Ding, Fangyuan# and Su, Christina and Chow, Ke-Huan Kuo and Liang, Guohao and Elowitz, Michael B#.
Dynamics and functional roles of splicing factor autoregulation
Cell Reports (in press) (BioRxiv copy)
#: 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