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