Publications
2022
Nonlinear manipulation and analysis of large DNA datasets
Meiying Cui, Xueping Zhao, Francesco V Reddavide, Michelle Patino Gaillez, Stephan Heiden, Luca Mannocci, Michael Thompson, Yixin Zhang
Nucleic Acids Research, DOI: 10.1093/nar/gkac672
A Self-Assembled Matrix System for Cell-Bioengineering Applications in Different Dimensions, Scales, and Geometries
Y. Xu, M. Patino Gaillez, K. Zheng, D. Voigt, M. Cui, T. Kurth, L. Xiao, R. Rothe, S. Hauser, P. Lee, R. Wieduwild, W. Lin, M. Bornhäuser, J. Pietzsch, A. R. Boccaccini, Y. Zhang
Small Journal, accepted. DOI: 10.1002/smll.202104758
2021
Processing of fast-gelling hydrogel precursors in microfluidics by electrocoalescence of reactive species
N. Hauck, T. A. Neuendorf, M. J. Männel, L. Vogel, P. Liu, E. Stündel, Y. Zhang, J. Thiele
Soft Matter 2021, accepted. DOI: 10.1039/d1sm01176f
KYNA/Ahr Signaling Suppresses Neural Stem Cell Plasticity and Neurogenesis in Adult Zebrafish Model of Alzheimer's Disease
T. Siddiqui, P. Bhattarai, S. Popova, M. I. Cosacak, S. Sariya, Y. Zhang, R. Mayeux, G. Tosto, C. Kizil
Cells. 2021 Oct 14;10(10):2748. DOI: 10.3390/cells10102748
Peptide Scanning of SARS-CoV and SARS-CoV-2 Spike Protein Subunit 1 Reveals Potential Additional Receptor Binding Sites
W. Lin*, J. Rafeya, V. Roschewitz, D. Smith, A. Keller, Y. Zhang*
bioRxiv (2021) DOI: 10.1101/2021.08.16.456470
Controlling Surface Wettability for Automated In Situ Array Synthesis and Direct Bioscreening
W. Lin, S. Gandhi, A.R.O. Lara, A.K. Thomas, R. Helbig, and Y. Zhang*
Advanced Materials 2021 (accepted) DOI: 10.1002/adma.202102349
Conductive Hydrogels with Dynamic Reversible Networks for Biomedical Applications.
Y. Xu, M.P. Gaillez, R. Rothe, S. Hauser, D. Voigt, J. Pietzsch, Y. Zhang*
Adv. Healthcare Mater. 2021, 2100012, DOI: 10.1002/adhm.202100012
Convergent Synthesis of Diversified Reversible Network Leads to Liquid Metal-Containing Conductive Hydrogel Adhesives
Y. Xu, R. Rothe, D. Voigt, S. Hauser, M. Cui, T. Miyagawa, M. P. Gaillez, M. Bornhäuser, J. Pietzsch* and Y. Zhang*
Nature Communications 2021, 12, 2407, DOI: 10.1038/s41467-021-22675-2
Displaying Lipid Chains in a Peptide–Polysaccharide-Based Self-Assembled Hydrogel Network
P. Liu, W. Lin, R. Wieduwild, R. Towers, A. K. Thomas, M. Günther, S. Butdayev, M. Wobus, M. Bornhäuser, and Y. Zhang*
Chem. Mater. 2021. doi: 10.1021/acs.chemmater.0c04105
A modular, injectable, non-covalently assembled hydrogel system features widescale tunable degradability for controlled release and tissue integration
R. Rothe#, Y. Xu#, A. K. Thomas, S. Meister, Y. Zhang*, J. Pietzsch*, S. Hauser*
Biomaterials. 2021 Feb;269:120637. doi: 10.1016/j.biomaterials.2020.120637.
Screening Arrays of Laminin Peptides on Modified Cellulose for Promotion of Adhesion of Primary Endothelial and Neural Precursor Cells
R. Wetzel, S. Hauser, W. Lin, P. Berg, C. Werner, J. Pietzsch, G. Kempermann, and Y. Zhang*
Adv. Biology 2021, 1900303. DOI: 10.1002/adbi.201900303
A Single-Chain Variable Fragment Antibody Inhibits Aggregation of Phosphorylated Tau and Ameliorates Tau Toxicity in vitro and in vivo
Sen Li*, Yushan Yi, Ke Cui, Yanqiu Zhang, Yange Chen, Dou Han, Ling Sun, Xiaohui Zhang, Fei Chen, Yixin Zhang and Yufeng Yang*
J Alzheimers Dis. 2021;79(4):1613-1629. doi: 10.3233/JAD-191266.
2020
A Novel Synthetic, Xeno-free Biomimetic Surface for Serum-free Expansion of Human Mesenchymal Stromal Cells
K. Thamm, K. Möbus, R. Towers, S. Segeletz, R. Wetzel, M. Bornhäuser, Y. Zhang, M. Wobus*
Advanced Biosystems
Influence of the Geometry of Fluorescently Labelled DNA Constructs on Fluorescence Anisotropy Assay
T. Brom, F. V. Reddavide, S. Heiden, M. Thompson*, Y. Zhang*
Biochemical and Biophysical Research Communications
Advancing DNA Steganography with Incorporation of Randomness
M. Cui, Y. Zhang
ChemBioChem
Screening a Chemically Defined Extracellular Matrix Mimetic Substrate Library to Identify Substrates That Enhance Substrate-Mediated Transfection
A. Hamann, A. K. Thomas, T. Kozisek, E. Farris, S. Lück, Y. Zhang*, A. K. Pannier*
Exp. Biol. Med., 2020 Apr;245(7):606-619.
Neuron-glia interaction through Serotonin-BDNF-NGFR axis underlies the regenerative neurogenesis after Amyloid toxicity in zebrafish brain
P. Bhattarai, M. I. Cosacak, V. Mashkaryan, S. Demir, S. D. Popova, N. Govindarajan, K. Brandt, Y. Zhang, W. Chang, K. Ampatzis, C. Kizil
PLOS Biology, 2020
2019
DNA-Encoded Fragment Libraries: Dynamic Assembly, Single-Molecule Detection, and High-Throughput Hit Validation
F. V. Reddavide, M. Thompson, L. Mannocci, Y. Zhang
Aldrichimica Acta Vol. 52, No. 3, 2019 p63
Multivalent electrostatic microtubule-interactions of synthetic peptides are sufficient to mimic advanced MAP-like behaviour
H. Drechsler, Y. Xu, V. F. Geyer, Y. Zhang, S. Diez
Mol Biol Cell 30(24), 2953-2968, 2019
Analysis and Modelling of Large and Heterogeneous Populations of DNA Using a PCR-Based Method
H. Andrade, A. K. Thomas, W. Lin, F. V. Reddavide, Y. Zhang
ChemBioChem, 2019
Blockchain of Signature Material Combining Cryptographic Hash Function and DNA Steganography
Y. Zhang
arXiv, 2019
Cytocompatible, Injectable, and Electroconductive Soft Adhesives with Hybrid Covalent/Noncovalent Dynamic Network
Y. Xu, P. A. Patsis, S. Hauser, D. Voigt, R. Rothe, M. Günther, M. Cui, X. Yang, R. Wieduwild, K. Eckert, C. Neinhuis, T. F. Akbar, I. R. Minev, J. Pietzsch*, Y. Zhang*
Advanced Science, 2019
Single-Cell Transcriptomics Analyses of Neural Stem Cell Heterogeneity and Contextual Plasticity in a Zebrafish Brain Model of Amyloid Toxicity
M. I. Cosacak, P. Bhattarai, S. Reinhardt, A. Petzold, A. Dahl, Y. Zhang, C. Kizil*
Cell Reports, 2019, 1307–1318
Engineering Hydrogels beyond a Hydrated Network.
R. Wieduwild, Y. Xu, S. Ostrovidov, A. Khademhosseini, Y. Zhang*, G. Orive*
Adv. Healthc. Mater. 2019 Apr 16:e1900038.
Highly Conductive, Stretchable and Cell Adhesive Hydrogel by Nanoclay Doping
C. Tondera, T. F. Akbar, A. K. Thomas, C. Werner, V. Busskamp, Y. Zhang and I. R. Minev*
Small. 2019 Apr 26:e1901406.
Second Generation DNA-Encoded Dynamic Combinatorial Chemical Libraries
F. V. Reddavide, M. Cui, W. Lin, N. Fu, S. Heiden, H. Andrade, M. Thompson, Y. Zhang
Chem Commun (Camb). 2019 Mar 26;55(26):3753-3756.
Specificity from Non-Specific Interaction: Regulation of TNF-alpha Activity by DNA
H. Andrade, W. Lin, Y. Zhang
J Biol Chem. 2019 Apr 19;294(16):6397-6404.
Reversibly Assembled Electroconductive Hydrogel via a Host-Guest Interaction for 3D Cell Culture.
Y. Xu, M. Cui, P. A. Patsis, M. Günther, X. Yang, K. Eckert, Y. Zhang
ACS Appl Mater Interfaces. 2019 Feb 15. doi: 10.1021/acsami.8b19482.
Peptidyl prolyl cis/trans isomerase activity on the cell surface correlates with extracellular matrix development.
W. Lin, M. Bonin, A. Boden, R. Wieduwild, P. Murawala, M. Wermke, H. Andrade, M. Bornhäuser, Y. Zhang
Commun Biol. 2019 Feb 11;2:58. doi: 10.1038/s42003-019-0315-8.
The Effect of Terminal Modifications on the Adsorption and Assembly of hIAPP(20-29)
R. Hajiraissi, M. Hanke,O. A. Gonzalez, B. Duderija, U. Hofmann, Y. Zhang, G. Grundmeier, A. Keller
ACS Omega, 2019, 42, 2649-2660
2018
Pharmacophore Nanoarrays on DNA Origami Substrates as a Single-Molecule Assay for Fragment-based Drug Discovery.
C. Kielar, F. Reddavide, S. Tubbenhauer, M. Cui, X. Xu, G. Grundmeier, Y. Zhang*, A. Keller*
Angew Chem Int Ed Engl. 2018 Sep 14. doi: 10.1002/anie.201806778.
Donor-acceptor Stenhouse adduct-grafted polycarbonate surfaces: selectivity of the reaction for secondary amine on surface.
S. Singh*, P. Mai, J. Borowiec, Y. Zhang, Y. Lei, A. Schober
R. Soc. Open. Sci. 2018 Jul 25;5(7):180207. doi: 10.1098/rsos.180207.
3D Culture Method for Alzheimer's Disease Modeling Reveals Interleukin-4 Rescues A?42-Induced Loss of Human Neural Stem Cell Plasticity.
C. Papadimitriou, H. Celikkaya, M. I. Cosacak, V. Mashkaryan, L. Bray, P. Bhattarai, K. Brandt, H. Hollak, X. Chen, S. He, C. L. Antos, W. Lin, A. K. Thomas, A. Dahl, T. Kurth, J. Friedrichs,Y. Zhang, U. Freudenberg, C. Werner, C. Kizil*
Dev. Cell. 2018 Jul 2;46(1):85-101.e8. doi: 10.1016/j.devcel.2018.06.005.
Layer-by-Layer assembly of heparin and peptide-polyethylene glycol conjugates to form hybrid nanothin films of biomatrices
A. K. Thomas, R. Wieduwild, R. Zimmermann, W. Lin, J. Friedrichs, M. Bickle, K. Fahmy, C. Werner, Y. Zhang*
ACS Applied Materials & Interfaces, 2018 May 2;10(17):14264-14270.
Non-covalently Assembled Electroconductive Hydrogel
Y. Xu, X. Yang, A. K. Thomas, P. Patsis, T. Kurth, M. Kräter, K. Eckert, M. Bornhäuser, Y. Zhang*
ACS Applied Materials & Interfaces, 2018 May 2;10(17):14418-14425.
Coacervation-Mediated Combinatorial Synthesis of Biomatrices for Stem Cell Culture and Directed Differentiation
R. Wieduwild, R. Wetzel, D. Husman, S. Bauer, I. El-Sayed, S. Duin, P. Murawala, A. K. Thomas, M. Wobus, M. Bornhäuser, Y. Zhang*
Advanced Materials, 2018 May;30(22):e1706100
Modelling Large, Dynamic, and Heterogeneous Populations Using DNA Libraries
H. Andrade, A. K. Thomas, W. Lin, F. Reddavide, Y. Zhang*
bioRxiv 276873; doi: https://doi.org/10.1101/276873
2017
From malaria to cancer: Computational drug repositioning of amodiaquine using PLIP interaction patterns.
S. Salentin, M. F. Adasme, J. C, Heinrich, V. J. Haup, S. Daminelli, Y. Zhang, M. Schroeder*
Sci Rep. 2017 Sep 12;7(1):11401. doi: 10.1038/s41598-017-11924-4.
Modeling Amyloid-beta42 Toxicity and Neurodegeneration in Adult Zebrafish Brain
P. Bhattarai, A. K. Thomas, M. I. Cosacak, C. Papadimitriou, V. Mashkaryan, Y. Zhang, C. Kizil*
Journal of Visualized Experiments, 2017
The effects of aging on Amyloid-beta42-induced neurodegeneration and regeneration in adult zebrafish brain.
P. Bhattarai, A. K. Thomas, Y. Zhang, C. Kizil*
Neurogenesis. 2017 May 2;4(1):e1322666.
In Vivo Examination of an Injectable Hydrogel System Crosslinked by Peptide–Oligosaccharide Interaction in Immunocompetent Nude Mice.
C. Tondera, R. Wieduwild, E. Röder, C. Werner, Y. Zhang*, J. Pietzsch*
Advanced Functional Materials, 2017 DOI: 10.1002/adfm.201605189
Lab-on-a-chip platform for high throughput drug discovery with DNA-encoded chemical libraries.
S. Grünzner, F. V. Reddavide, C. Steinfelder, M. Cui, M. Busek, U. Klotzbach, Y. Zhang, F. Sonntag
Proc. SPIE 10061, Microfluidics, BioMEMS, and Medical Microsystems XV, 1006111 (28 February 2017); doi: 10.1117/12.2253840
2016
Augmented Reversible Photoswitching of Drug-Target Interaction through “Surface Borrowing”
F. Erdmann, W. Lin, C. Platzer, M. Schmidt, W. Sippl, G. Fischer, Y. Zhang
Biochemical Pharmacology, 2016, 125, 84-92
Thioxylated cyclosporin A for studying protein-drug interactions.
W. Lin, F. Erdmann, A. Quintero, G. Fischer, Y. Zhang
Bioorg Med Chem Lett. 2016, 26(23), 5754-5756
IL4/STAT6 Signaling Activates Neural Stem Cell Proliferation and Neurogenesis upon Amyloid-?42 Aggregation in Adult Zebrafish Brain.
P. Bhattarai, A.K. Thomas, M.I. Cosacak, C. Papadimitriou, V. Mashkaryan, C. Froc, S. Reinhardt, T. Kurth, A. Dahl, Y. Zhang, C. Kizil
Cell Rep. 2016 Oct 18;17(4):941-948. doi: 10.1016/j.celrep.2016.09.075.
New HSP27 inhibitors efficiently suppress drug resistance development in cancer cells
J. Heinrich, S. Donakonda, J. Haupt, P. Lennig, Y. Zhang, M. Schroeder*
Oncotarget, 2016, 7(42):68156-68169.
The pivotal role of reactivity in the design of novel biotinylation reagents for the chemical-proteomics-based identification of vascular accessible biomarkers
S. Hanke, A. Kerner, W. Nadler, A. Trumpp, Y. Zhang, C. Rösli*
Journal of Proteomics 2016, 141, 57
Conformational Heterogeneity of Cyclosporin A in Cyclophilin 18 Binding
W. Lin, A. Quintero, Y. Zhang*
PLOS ONE 2016 Apr 15;11(4):e0153669
Designing an Antibody-based Chaperoning System through Pro-gramming the Binding and Release of Folding Intermediate
T. Liu, C. Sun, C. Li, J. Lee, Y. Park, Y. Zhang*, S. Li*
ACS Chemical Biology 2016 Apr 15;11(4):1090-7
Automated screening for small organic ligands using DNA-encoded chemical libraries
W. Decurtins, M. Wichert, R. Franzini, F. Buller, M. Stravs, Y. Zhang, D. Neri*, J. Scheuermann*
Nature Protocol 2016 Apr;11(4):764-80.
2015
Rational design of dual peptides targeting ghrelin and Y2 receptors to regulate food intake and body
T. Kilian, N. Klöting, R. Bergmann, S. Els-Heindl, S. Babilon, M. Clément-Ziza, Y. Zhang, A. G. Beck-Sickinger, C. Chollet
J. Med. Chem. 2015, 58(10), 4180-93.
Amphipathic DNA origami nanoparticles can scaffold and deform lipid membrane vesicles
A. Czogalla, D. J. Kauert, H. G. Franquelim, V. Uzunova, Y. Zhang, R. Seidel, P. Schwille
Angew. Chem. Int. Ed. Engl. 2015, 54(22), 6501-5
DNA-Encoded Dynamic Combinatorial Chemical Libraries
F. Reddavide, W. Lin, S. Lehnert, Y. Zhang
Angew. Chem. Int. Ed. Engl. 2015, 54(27), 7924-8
Efficient cargo delivery to parenchymal cells of the brain using a short cell-penetrating peptide.
C. Kizil, A. Iltzsche, A. K. Thomas, P. Bhattarai, Y. Zhang, M. Brand
PLoS one 2015, e0124073
Photopatterning of Multifunctional Hydrogels to Direct Adult Neural Precursor Cells
M. Tsurkan, R. Wetzel, H. Pérez-Hernández, K. Chwalek, A. Kozlova, U. Freudenberg, G. Kempermann, Y. Zhang, A. Lasagni, C. Werner
Advanced Healthcare Materials 2015, 4(4), 516-21.
Noncovalent hydrogel beads as microcarriers for cell culture.
R. Wieduwild, S. Krishnan, K. Chwalek, A. Boden, M. Nowak, D. Drechsel, C. Werner, Y. Zhang
Angew. Chem. Int. Ed. Engl. 2015, 54(13), 3962-6.
Self-Assembling Hydrogels Crosslinked Solely by Receptor-Ligand Interactions: Tunability, Rationalization of Physical Properties and 3D Cell Culture.
M. Thompson, M. Tsurkan, K. Chwalek, M. Bornhauser, M. Schlierf, C. Werner, Y. Zhang
Chem. Eur. J. 2015, 21(8), 3178
Characterization of DNA-conjugated compounds using a regenerable chip.
W. Lin, F. Reddavide, V. Uzunova, F. Gür, Y. Zhang
Analytical Chemistry, 2015, 87(2):864-8
Open-access and Structured Data in Drug Discovery
Y. Zhang
Biomed Data J, Volume 1, Issue 1, p.39-41 (2015)
2014
Encoding Method for Fast Deconvolution of DNA-encoded Chemical Library.
Y. Zhang, J. Herrmann, R. Wieduwild, A. Boden
(German patent 102014200446.2 approved)
Light Induced Inhibition of Protein Phosphatase Calcineurin
A. Quintero, W. Lin, S. Hermanna, Y. Zhang
Chin. J. Chem. 2014, 32, 1011
Chapter 16. Hit Identification and Hit Follow-up
Y. Zhang
A Handbook for DNA-Encoded Chemistry: Theory and Applications for Exploring Chemical Space and Drug Discovery. 2014, p357-376 (Wiley)
A Repertoire of Peptide Tags for Controlled Drug Release from Injectable Non-covalent Hydrogel.
R. Wieduwild, W. Lin, A. Boden, K. Kretschmer, Y. Zhang
Biomacromolecules. 2014, 15(6), 2058-66.
Calcineurin regulates coordinated outgrowth of zebrafish regenerating fins.
S. Kujawski, W. Lin, F. Kitte, M. Börmel, S. Fuchs, G. Arulmozhivarman, S. Vogt, D. Theil, Y. Zhang, C. L. Antos
Developmental Cell. 2014, 28(5), 573-87
2013
Chaperone-like effects of a scFv antibody on the folding of human muscle creatine kinase.
S. Li, C. Sun, N. Teng, W. Yang, L. Zhou, Y. Zhang
Protein Eng. Des. Sel. 2013, 26(8), p523-31
Minimal Peptide Motif for Non-covalent Peptide-Heparin Hydrogels
R. Wieduwild, M. Tsurkan, K. Chwalek, P. Murawala, M. Nowak, U. Freudenberg, C. Neinhuis, C. Werner, Y. Zhang
J. Am. Chem. Soc. 2013 Feb 27;135(8):2919-22.
Switchable domain partitioning and diffusion of DNA origami rods on membranes
A. Czogalla, E. P. Petrov, D. J. Kauert, V. Uzunova, Y. Zhang, R. Seidel and P. Schwille
Faraday Discussion, 2013, 161, 31
2012
Discovery of small-molecule interleukin-2 inhibitors from a DNA-encoded chemical library.
M. Leimbacher, Y. Zhang, L. Mannocci, M. Stravs, T. Geppert, J. Scheuermann, G. Schneider, D. Neri
Chemistry - A European Journal 2012 Jun 18;18(25):7729-37
2010
Reversible photoswitching of protein function.
F. Erdmann, Y. Zhang
Mol. Biosyst. 2010 Nov;6(11):2103-9.
2009
Discovery of TNF inhibitors from a DNA-encoded chemical library based on diels-alder cycloaddition
F. Buller, Y. Zhang, J. Scheuermann, J. Schäfer, P. Bühlmann, D. Neri
Chem Biol. 2009 16(10):1075-86.
Augmented photoswitching modulates immune signaling.
Y. Zhang, F. Erdmann, G. Fischer
Nature Chem. Biol. 2009 5(10):724-6.
2008
High-throughput sequencing allows the identification of binding molecules isolated from DNA-encoded chemical libraries.
L. Mannocci, Y. Zhang, J. Scheuermann, M. Leimbacher, G. De Bellis, E. Rizzi, C. Dumelin, S. Melkko, D. Neri
Proc. Natl. Acad. Sci. 2008 105(46):17670-5.
2007
Isolation of high-affinity trypsin inhibitors from a DNA-encoded chemical library.
S. Melkko, Y. Zhang, C. E. Dumelin, J. Scheuermann, D. Neri
Angew. Chem. Int. Ed. Engl. 2007 46(25):4671-4.
2005
Unexpected side chain effects at residue 8 of cyclosporin a derivatives allow photoswitching of immunosuppression.
Y. Zhang, F. Erdmann, R. Baumgrass, M. Schutkowski, G. Fischer
J. Biol. Chem. 2005 280(6):4842-50
2004
Branches on the alpha-C atom of cyclosporin A residue 3 result in direct calcineurin inhibition and rapid cyclophilin 18 binding.
Y. Zhang, R. Baumgrass, M. Schutkowski, G. Fischer
Chembiochem. 2004 5(7):1006-9
Substitution in position 3 of cyclosporin A abolishes the cyclophilin-mediated gain-of-function mechanism but not immunosuppression.
R. Baumgrass, Y. Zhang, F. Erdmann, A. Thiel, M. Weiwad, A. Radbruch, G. Fischer
J. Biol. Chem. 2004 279(4):2470-9
2002
Substrate-based design of reversible Pin1 inhibitors.
Y. Zhang, S. Füssel, U. Reimer, M. Schutkowski, G. Fischer
Biochemistry. 2002 41(39):11868-77.