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Bioinformatics Platform

Foerster, S., Floriddia, E. M., van Bruggen, D., Kukanja, P., Hervé, B., Cheng, S., Kim, E., Phillips, B. U.,Heath, C. J., Tripathi, R. B., Call, C., Bartels, T., Ridley, K., Neumann, B., López-Cruz, L., Crawford, A.H.,Lynch, C. J., Serrano, M., Saksid, L., Rowitch, D. H., Möbius, W., Nave, K-A., Rasband, M. N., Bergles, D. E.,Kessaris, N., Richardson, W. D., Bussey, T. J., Zhao, C., Castelo-Branco, G. & Franklin, R. J. M. (2024). Developmental origin of oligodendrocytes determines their function in the adult brain. Nat Neurosci.

Cheng, S., Brenière-Letuffe, D., Ahola, V., Wong, A. O. T., Keung, H. Y., Gurung, B., Zheng, Z., Costa, K. D., Lieu, D. K., Keung, W., & Li, R. A. (2023). Single-cell RNA sequencing reveals maturation trajectory in human pluripotent stem cell-derived cardiomyocytes in engineered tissues. IScience, 26(4), 106302. 

 

Gonçalo Castelo-Branco

Deng, Y., Bartosovic, M., Kukanja, P., Zhang, D., Liu, Y., Su, G., Enninful, A., Bai, Z., Castelo-Branco, G., & Fan, R. (2022). Spatial-CUT&Tag: Spatially resolved chromatin modification profiling at the cellular level. Science, 375(6581), 681–686.

Meijer, M., Agirre, E., Kabbe, M., van Tuijn, C. A., Heskol, A., Zheng, C., Mendanha Falcão, A., Bartosovic, M., Kirby, L., Calini, D., Johnson, M. R., Corces, M. R., Montine, T. J., Chen, X., Chang, H. Y., Malhotra, D., & Castelo-Branco, G. (2022). Epigenomic priming of immune genes implicates oligodendroglia in multiple sclerosis susceptibility. Neuron.

Bonetti, A., Agostini, F., Suzuki, A. M., Hashimoto, K., Pascarella, G., Gimenez, J., Roos, L., Nash, A. J., Ghilotti, M., Cameron, C. J. F., Valentine, M., Medvedeva, Y. A., Noguchi, S., Agirre, E., Kashi, K., Samudyata, Luginbühl, J., Cazzoli, R., Agrawal, S., … Carninci, P. (2020). RADICL-seq identifies general and cell type–specific principles of genome-wide RNA-chromatin interactions. Nature Communications, 11(1), 1018.

Marisca, R., Hoche, T., Agirre, E., Hoodless, L. J., Barkey, W., Auer, F., Castelo-Branco, G., & Czopka, T. (2020). Functionally distinct subgroups of oligodendrocyte precursor cells integrate neural activity and execute myelin formation. Nature Neuroscience, 23(3), 363–374.

Samudyata, Castelo-Branco, G., & Liu, J. (2020). Epigenetic regulation of oligodendrocyte differentiation: From development to demyelinating disorders. GLIA, 68(8), 1619–1630.

Falcão, A. M., Meijer, M., Scaglione, A., Rinwa, P., Agirre, E., Liang, J., Larsen, S. C., Heskol, A., Frawley, R., Klingener, M., Varas-Godoy, M., Raposo, A. A. S. F., Ernfors, P., Castro, D. S., Nielsen, M. L., Casaccia, P., & Castelo-Branco, G. (2019). PAD2-Mediated Citrullination Contributes to Efficient Oligodendrocyte Differentiation and Myelination. Cell Reports, 27(4), 1090-1102.e10.

Floriddia, E. M., & Castelo-Branco, G. (2019). Ancestry Tracing: Uncovering a Gliomagenesis Master Regulator. Cell Stem Cell, 24(5), 677–679.

Jäkel, S., Agirre, E., Mendanha Falcão, A., van Bruggen, D., Lee, K. W., Knuesel, I., Malhotra, D., Ffrench-Constant, C., Williams, A., & Castelo-Branco, G. (2019). Altered human oligodendrocyte heterogeneity in multiple sclerosis. Nature, 566(7745), 543–547.

Kupari, J., Häring, M., Agirre, E., Castelo-Branco, G., & Ernfors, P. (2019). An Atlas of Vagal Sensory Neurons and Their Molecular Specialization. Cell Reports, 27(8), 2508-2523.e4.

Marques, S., van Bruggen, D., & Castelo-Branco, G. (2019). Single-Cell RNA Sequencing of Oligodendrocyte Lineage Cells from the Mouse Central Nervous System. Methods in Molecular Biology (Clifton, N.J.), 1936, 1–21.

Samudyata, Amaral, P. P., Engström, P. G., Robson, S. C., Nielsen, M. L., Kouzarides, T., & Castelo-Branco, G. (2019). Interaction of Sox2 with RNA binding proteins in mouse embryonic stem cells. Experimental Cell Research, 381(1), 129–138.

Falcão, A. M., van Bruggen, D., Marques, S., Meijer, M., Jäkel, S., Agirre, E., Samudyata, Floriddia, E. M., Vanichkina, D. P., Ffrench-Constant, C., Williams, A., Guerreiro-Cacais, A. O., & Castelo-Branco, G. (2018). Disease-specific oligodendrocyte lineage cells arise in multiple sclerosis. Nature Medicine, 24(12), 1837–1844.

La Manno, G., Soldatov, R., Zeisel, A., Braun, E., Hochgerner, H., Petukhov, V., Lidschreiber, K., Kastriti, M. E., Lönnerberg, P., Furlan, A., Fan, J., Borm, L. E., Liu, Z., van Bruggen, D., Guo, J., He, X., Barker, R., Sundström, E., Castelo-Branco, G., … Kharchenko, P. V. (2018). RNA velocity of single cells. Nature, 560(7719), 494–498.

Marques, S., van Bruggen, D., Vanichkina, D. P., Floriddia, E. M., Munguba, H., Väremo, L., Giacomello, S., Falcão, A. M., Meijer, M., Björklund, Å. K., Hjerling-Leffler, J., Taft, R. J., & Castelo-Branco, G. (2018). Transcriptional Convergence of Oligodendrocyte Lineage Progenitors during Development. Developmental Cell, 46(4), 504-517.e7.

Samudyata, Castelo-Branco, G., & Bonetti, A. (2018). Birth, coming of age and death: The intriguing life of long noncoding RNAs. Seminars in Cell & Developmental Biology, 79, 143–152.

Sijie Chen

Ho, P.-Y., Chou, T. Y., Kam, C., Huang, W., He, Z., Ngan, A. H. W., & Chen, S. (2023). A dual organelle-targeting mechanosensitive probe. Science Advances, 9(2), eabn5390. 

Wu, M.-Y., Wong, A. Y. H., Leung, J.-K., Kam, C., Wu, K. L.-K., Chan, Y.-S., Liu, K., Ip, N. Y., & Chen, S. (2021). A near-infrared AIE fluorescent probe for myelin imaging: From sciatic nerve to the optically cleared brain tissue in 3D. Proceedings of the National Academy of Sciences, 118 (45) e2106143118.

Ho, P.-Y., Lee, S.-Y., Kam, C., Zhu, J., Shan, G.-G., Hong, Y., Wong, W.-Y., & Chen, S. (2021). Fluorescence Imaging and Photodynamic Inactivation of Bacteria Based on Cationic Cyclometalated Iridium(III) Complexes with Aggregation‐Induced Emission Properties (Adv. Healthcare Mater. 24/2021). Advanced Healthcare Materials, 10(24), 2170116. 

Song, F., Zhang, C., Dong, H., Fan, Y., Wu, M.-Y., Shan, G., Lai, P., Gao, H., Zhao, Y. S., & Chen, S. (2021). A switchable multimode microlaser based on an AIE microsphere. J. Mater. Chem. C.

Wu, M.-Y., Gu, M., Leung, J.-K., Li, X., Yuan, Y., Shen, C., Wang, L., Zhao, E., & Chen, S. (2021). A Membrane-Targeting Photosensitizer with Aggregation-Induced Emission Characteristics for Highly Efficient Photodynamic Combat of Human Coronaviruses. Small, 17(30), 2101770.

Huang, L., Xu, S., Wang, Z., Xue, K., Su, J., Song, Y., Chen, S., Zhu, C., Tang, B. Z., & Ye, R. (2020). Self-Reporting and Photothermally Enhanced Rapid Bacterial Killing on a  Laser-Induced Graphene Mask. ACS Nano, 14(9), 12045–12053.

OwYong, T. C., Ding, S., Wu, N., Fellowes, T., Chen, S., White, J. M., Wong, W. W. H., & Hong, Y. (2020). Optimising molecular rotors to AIE fluorophores for mitochondria uptake and retention. Chemical Communications, 56(94), 14853–14856.

Liu, C., Wang, X., Liu, J., Yue, Q., Chen, S., Lam, J. W. Y., Luo, L., & Tang, B. Z. (2020). Near-Infrared AIE Dots with Chemiluminescence for Deep-Tissue Imaging. Advanced Materials, 32(43), 2004685.

Xu, W., Zhang, Z., Kang, M., Guo, H., Li, Y., Wen, H., Lee, M. M. S., Wang, Z., Kwok, R. T. K., Lam, J. W. Y., Li, K., Xi, L., Chen, S., Wang, D., & Tang, B. Z. (2020). Making the Best Use of Excited-State Energy: Multimodality Theranostic Systems Based on Second Near-Infrared (NIR-II) Aggregation-Induced Emission Luminogens (AIEgens). ACS Materials Letters, 2(8), 1033–1040. 

Lv, W., Long, K., Yang, Y., Chen, S., Zhan, C., & Wang, W. (2020). A Red Light-Triggered Drug Release System Based on One-Photon Upconversion-Like Photolysis. Advanced Healthcare Materials, 9(21), 2001118. 

Gao, H., Zhao, X., & Chen, S. (2018). AIEgen-Based Fluorescent Nanomaterials: Fabrication and Biological Applications. Molecules, 23(2), 419. 

Hoffecker, I. T., Chen, S., Gådin, A., Bosco, A., Teixeira, A. I., & Högberg, B. (2019). Solution-Controlled Conformational Switching of an Anchored Wireframe DNA Nanostructure. Small, 15(1), 1803628. 

Tu, Y., Yu, Y., Zhou, Z., Xie, S., Yao, B., Guan, S., Situ, B., Liu, Y., Kwok, R. T. K., Lam, J. W. Y., Chen, S., Huang, X., Zeng, Z., & Tang, B. Z. (2019). Specific and Quantitative Detection of Albumin in Biological Fluids by Tetrazolate-Functionalized Water-Soluble AIEgens. ACS Applied Materials & Interfaces, 11(33), 29619–29629. 

Li, F., Han, J., Cao, T., Lam, W., Fan, B., Tang, W., Chen, S., Fok, K. L., & Li, L. (2019). Design of self-assembly dipeptide hydrogels and machine learning via their chemical features. Proceedings of the National Academy of Sciences, 116(23), 11259–11264. 

Xie, S., Wong, A. Y. H., Chen, S., & Tang, B. Z. (2019). Fluorogenic Detection and Characterization of Proteins by Aggregation-Induced Emission Methods. Chemistry (Weinheim an Der Bergstrasse, Germany), 25(23), 5824–5847. 

Wong, A. Y. H., Xie, S., Tang, B. Z., & Chen, S. (2019). Fluorescent Silver Staining of Proteins in Polyacrylamide Gels. Journal of Visualized Experiments, 146. 

Chen, S., Liu, J., Zhang, S., Zhao, E., Yu, C. Y. Y., Hushiarian, R., Hong, Y., & Tang, B. Z. (2018). Biochromic silole derivatives: a single dye for differentiation, quantitation and imaging of live/

Liu, L., Zou, Q., Leung, J.-K., Wang, J.-L., Kam, C., Chen, S., Feng, S., & Wu, M.-Y. (2019). Ultrafast labeling and high-fidelity imaging of mitochondria in cancer cells using an aggregation-enhanced emission fluorescent probe. Chemical Communications, 55(97), 14681–14684. 

Zhao, E., Lai, P., Xu, Y., Zhang, G., & Chen, S. (2020). Fluorescent Materials With Aggregation-Induced Emission Characteristics for Array-Based Sensing Assay. Frontiers in Chemistry, 8, 288. 

Gu, M., Zeng, Z., Wu, M., Leung, J., Zhao, E., Wang, S., & Chen, S. (2019). Imaging Macrophage Phagocytosis Using AIE Luminogen‐Labeled E. coli. Chemistry – An Asian Journal, 14(6), 775–780. 

Wu, M., Leung, J., Liu, L., Kam, C., Chan, K. Y. K., Li, R. A., Feng, S., & Chen, S. (2020). A Small‐Molecule AIE Chromosome Periphery Probe for Cytogenetic Studies. Angewandte Chemie International Edition, 59(26), 10327–10331. 

Gao, H., Kam, C., Chou, T. Y., Wu, M.-Y., Zhao, X., & Chen, S. (2020). A simple yet effective AIE-based fluorescent nano-thermometer for temperature mapping in living cells using fluorescence lifetime imaging microscopy. Nanoscale Horizons, 5(3), 488–494. 

Xie, S., Wong, A. Y. H., Kwok, R. T. K., Li, Y., Su, H., Lam, J. W. Y., Chen, S., & Tang, B. Z. (2018). Fluorogenic Ag + -Tetrazolate Aggregation Enables Efficient Fluorescent Biological Silver Staining. Angewandte Chemie International Edition, 57(20), 5750–5753. 

 

Simon Elsässer

Lafranchi, L., Schlesinger, D., Kimler, K. J., & Elsässer, S. J. (2020). Universal Single-Residue Terminal Labels for Fluorescent Live Cell Imaging of Microproteins. Journal of the American Chemical Society, jacs.0c09574.

Meineke, B., Heimgärtner, J., Eirich, J., Landreh, M., & Elsässer, S. J. (2020). Site-Specific Incorporation of Two ncAAs for Two-Color Bioorthogonal Labeling and Crosslinking of Proteins on Live Mammalian Cells. Cell Reports, 31(12), 107811.

Navarro, C., Lyu, J., Katsori, A.-M., Caridha, R., & Elsässer, S. J. (2020). An embryonic stem cell-specific heterochromatin state promotes core histone exchange in the absence of DNA accessibility. Nature Communications, 11(1), 5095.

Pesic, M., Egamberdieva, D., Kolodziejczyk, B., Elsässer, S. J., Neergheen, V. S., & Kagansky, A. (2020). Towards policies that capture the expected value of biomolecular diversity for drug discovery, human health, and well-being. Biologia Futura.

Kumar, B., & Elsässer, S. (2019). Quantitative multiplexed ChIP reveals global alterations that shape promoter bivalency in ground state embryonic stem cells. Cell Reports.

van Husen, L. S., Schedin-Weiss, S., Trung, M. N., Kazmi, M. A., Winblad, B., Sakmar, T. P., Elsässer, S. J., & Tjernberg, L. O. (2019). Dual Bioorthogonal Labeling of the Amyloid-β Protein Precursor Facilitates Simultaneous Visualization of the Protein and Its Cleavage Products. Journal of Alzheimer’s Disease, 72(2), 537–548.

Elsässer, S. J. (2018). Generation of Stable Amber Suppression Cell Lines. In Methods in Molecular Biology (pp. 237–245).

Meineke, B., Heimgärtner, J., Lafranchi, L., & Elsässer, S. J. (2018). Methanomethylophilus alvus Mx1201 Provides Basis for Mutual Orthogonal Pyrrolysyl tRNA/Aminoacyl-tRNA Synthetase Pairs in Mammalian Cells. ACS Chemical Biology, 13(11), 3087–3096.

Neergheen-Bhujun, V., Awan, A. T., Baran, Y., Bunnefeld, N., Chan, K., dela Cruz, T. E., Egamberdieva, D., Elsässer, S., Johnson, M. V., Komai, S., Konevega, A. L., Malone, J. H., Mason, P., Nguon, R., Piper, R., Shrestha, U. B., Pešić, M., & Kagansky, A. (2017). Biodiversity, drug discovery, and the future of global health: Introducing the biodiversity to biomedicine consortium, a call to action. Journal of Global Health, 7(2).

Christian Göritz

Dias, D. O., Kalkitsas, J., Kelahmetoglu, Y., Estrada, C. P., Tatarishvili, J., Holl, D., Jansson, L., Banitalebi, S., Amiry-Moghaddam, M., Ernst, A., Huttner, H. B., Kokaia, Z., Lindvall, O., Brundin, L., Frisén, J., & Göritz, C. (2021). Pericyte-derived fibrotic scarring is conserved across diverse central nervous system lesions. Nature Communications, 12(1), 5501.

Dorst, M. C., Díaz-Moreno, M., Dias, D. O., Guimarães, E. L., Holl, D., Kalkitsas, J., Silberberg, G., & Göritz, C. (2021). Astrocyte-derived neurons provide excitatory input to the adult striatal circuitry. Proceedings of the National Academy of Sciences, 118(33), e2104119118. 

Dias, D. O., & Göritz, C. (2018). Fibrotic scarring following lesions to the central nervous system. Matrix Biology, 68–69, 561–570.

Dias, D. O., Kim, H., Holl, D., Werne Solnestam, B., Lundeberg, J., Carlén, M., Göritz, C., & Frisén, J. (2018). Reducing Pericyte-Derived Scarring Promotes Recovery after Spinal Cord Injury. Cell, 173(1), 153-165.e22.

Reichenbach, B., Classon, J., Aida, T., Tanaka, K., Genander, M., & Göritz, C. (2018). Glutamate transporter Slc1a3 mediates inter‐niche stem cell activation during skin growth. The EMBO Journal, 37(9).

 

Francois Lallemend

Faure, L., Wang, Y., Kastriti, M. E., Fontanet, P., Cheung, K. K. Y., Petitpré, C., Wu, H., Sun, L. L., Runge, K., Croci, L., Landy, M. A., Lai, H. C., Consalez, G. G., de Chevigny, A., Lallemend, F., Adameyko, I., & Hadjab, S. (2020). Single cell RNA sequencing identifies early diversity of sensory neurons forming via bi-potential intermediates. Nature Communications, 11(1), 4175.

Romanov, R. A., Tretiakov, E. O., Kastriti, M. E., Zupancic, M., Häring, M., Korchynska, S., Popadin, K., Benevento, M., Rebernik, P., Lallemend, F., Nishimori, K., Clotman, F., Andrews, W. D., Parnavelas, J. G., Farlik, M., Bock, C., Adameyko, I., Hökfelt, T., Keimpema, E., & Harkany, T. (2020). Molecular design of hypothalamus development. Nature, 582(7811), 246–252.

Bartesaghi, L., Wang, Y., Fontanet, P., Wanderoy, S., Berger, F., Wu, H., Akkuratova, N., Bouçanova, F., Médard, J. J., Petitpré, C., Landy, M. A., Zhang, M. D., Harrer, P., Stendel, C., Stucka, R., Dusl, M., Kastriti, M. E., Croci, L., Lai, H. C., … Chrast, R. (2019). PRDM12 Is Required for Initiation of the Nociceptive Neuron Lineage during Neurogenesis. Cell Reports, 26(13), 3484-3492.e4.

Wang, Y., Wu, H., Fontanet, P., Codeluppi, S., Akkuratova, N., Petitpré, C., Xue-Franzén, Y., Niederreither, K., Sharma, A., Da Silva, F., Comai, G., Agirman, G., Palumberi, D., Linnarsson, S., Adameyko, I., Moqrich, A., Schedl, A., La Manno, G., Hadjab, S., & Lallemend, F. (2019). A cell fitness selection model for neuronal survival during development. Nature Communications, 10(1), 4137.

Wang, Y., Wu, H., Zelenin, P., Fontanet, P., Wanderoy, S., Petitpré, C., Comai, G., Bellardita, C., Xue-Franzén, Y., Huettl, R. E., Huber, A. B., Tajbakhsh, S., Kiehn, O., Ernfors, P., Deliagina, T. G., Lallemend, F., & Hadjab, S. (2019). Muscle-selective RUNX3 dependence of sensorimotor circuit development. Development (Cambridge), 146(20).

Petitpré, C., Wu, H., Sharma, A., Tokarska, A., Fontanet, P., Wang, Y., Helmbacher, F., Yackle, K., Silberberg, G., Hadjab, S., & Lallemend, F. (2018). Neuronal heterogeneity and stereotyped connectivity in the auditory afferent system. Nature Communications, 9(1), 3691.

Furlan, A., Dyachuk, V., Kastriti, M. E., Calvo-Enrique, L., Abdo, H., Hadjab, S., Chontorotzea, T., Akkuratova, N., Usoskin, D., Kamenev, D., Petersen, J., Sunadome, K., Memic, F., Marklund, U., Fried, K., Topilko, P., Lallemend, F., Kharchenko, P. V., Ernfors, P., & Adameyko, I. (2017). Multipotent peripheral glial cells generate neuroendocrine cells of the adrenal medulla. Science, 357, 6346.

Peng, C., Li, L., Zhang, M. D., Gonzales, C. B., Parisien, M., Belfer, I., Usoskin, D., Abdo, H., Furlan, A., Häring, M., Lallemend, F., Harkany, T., Diatchenko, L., Hökfelt, T., Hjerling-Leffler, J., & Ernfors, P. (2017). MIR-183 cluster scales mechanical pain sensitivity by regulating basal and neuropathic pain genes. Science, 356(6343), 1168–1171.

Ning Xu Landén

Li D, Peng H, Qu L, Sommar P, Wang A, Chu T, Li X, Bi X, Liu Q, Sérézal IG, Rollman O, Lohcharoenkal W, Zheng X, Angelstig SE, Grünler J, Pivarcsi A, Sonkoly E, Catrina S-B, Xiao C, Ståhle M, Mi Q-S, Zhou L&Landén, N. X. (2020). miR-19a/b and miR-20a promote wound healing by regulating the inflammatory response of keratinocytes. Journal of Investigative Dermatology.

Wang, A., Toma, M. A., Ma, J., Li, D., Vij, M., Chu, T., Wang, J., Li, X., & Xu Landén, N. (2020). Circular RNA hsa_circ_0084443 Is Upregulated in Diabetic Foot Ulcer and Modulates Keratinocyte Migration and Proliferation. Advances in Wound Care, 9(4), 145–160.

Wu, J., & Landén, N. X. (2020). Investigation of Skin Using a Mouse Model. In Methods in molecular biology (Clifton, N.J.) (Vol. 2154, pp. 239–247).

Wu, J., Li, X., Li, D., Ren, X., Li, Y., Herter, E. K., Qian, M., Toma, M.-A., Wintler, A.-M., Sérézal, I. G., Rollman, O., Ståhle, M., Wikstrom, J. D., Ye, X., & Landén, N. X. (2020). MicroRNA-34 Family Enhances Wound Inflammation by Targeting LGR4. Journal of Investigative Dermatology, 140(2), 465-476.e11.

Herter, E. K., Li, D., Toma, M. A., Vij, M., Li, X., Visscher, D., Wang, A., Chu, T., Sommar, P., Blomqvist, L., Berglund, D., Ståhle, M., Wikstrom, J. D., & Xu Landén, N. (2019). WAKMAR2, a Long Noncoding RNA Downregulated in Human Chronic Wounds, Modulates Keratinocyte Motility and Production of Inflammatory Chemokines. Journal of Investigative Dermatology, 139(6), 1373–1384.

Li, D., Kular, L., Vij, M., Herter, E. K., Li, X., Wang, A., Chu, T., Toma, M.-A., Zhang, L., Liapi, E., Mota, A., Blomqvist, L., Sérézal, I. G., Rollman, O., Wikstrom, J. D., Bienko, M., Berglund, D., Ståhle, M., Sommar, P., … Landén, N. X. (2019). Human skin long noncoding RNA WAKMAR1 regulates wound healing by enhancing keratinocyte migration. Proceedings of the National Academy of Sciences, 116(19), 9443–9452.

Herter, E. K., & Xu Landén, N. (2017). Non-Coding RNAs: New Players in Skin Wound Healing. Advances in Wound Care, 6(3), 93–107.

Li, D., & Landén, N. X. (2017). MicroRNAs in skin wound healing. European Journal of Dermatology : EJD, 27(S1), 12–14.

Li, X., Li, D., Wang, A., Chu, T., Lohcharoenkal, W., Zheng, X., Grünler, J., Narayanan, S., Eliasson, S., Herter, E. K., Wang, Y., Ma, Y., Ehrström, M., Eidsmo, L., Kasper, M., Pivarcsi, A., Sonkoly, E., Catrina, S.-B., Ståhle, M., & Xu Landén, N. (2017). MicroRNA-132 with Therapeutic Potential in Chronic Wounds. Journal of Investigative Dermatology, 137(12), 2630–2638.

Li, X., Li, D., Wikstrom, J. D., Pivarcsi, A., Sonkoly, E., Ståhle, M., & Landén, N. X. (2017). MicroRNA-132 promotes fibroblast migration via regulating RAS p21 protein activator 1 in skin wound healing. Scientific Reports, 7(1), 7797.

Fredrik Lanner

Yang, R., Goedel, A., Kang, Y., Si, C., Chu, C., Zheng, Y., Chen, Z., Gruber, P. J., Xiao, Y., Zhou, C., Witman, N., Eroglu, E., Leung, C.-Y., Chen, Y., Fu, J., Ji, W., Lanner, F., Niu, Y., & Chien, K. R. (2021). Amnion signals are essential for mesoderm formation in primates. Nature Communications, 12(1), 5126.

Petrus-Reurer, S., Kumar, P., Padrell Sánchez, S., Aronsson, M., André, H., Bartuma, H., Plaza Reyes, A., Nandrot, E. F., Kvanta, A., & Lanner, F. (2020). Preclinical safety studies of human embryonic stem cell-derived retinal pigment epithelial cells for the treatment of age-related macular degeneration. Stem Cells Translational Medicine, 9(8), 936–953.

Petrus-Reurer, S., Winblad, N., Kumar, P., Gorchs, L., Chrobok, M., Wagner, A. K., Bartuma, H., Lardner, E., Aronsson, M., Plaza Reyes, Á., André, H., Alici, E., Kaipe, H., Kvanta, A., & Lanner, F. (2020). Generation of Retinal Pigment Epithelial Cells Derived from Human Embryonic Stem Cells Lacking Human Leukocyte Antigen Class I and II. Stem Cell Reports, 14(4), 648–662.

Plaza Reyes, A., Petrus-Reurer, S., Padrell Sánchez, S., Kumar, P., Douagi, I., Bartuma, H., Aronsson, M., Westman, S., Lardner, E., André, H., Falk, A., Nandrot, E. F., Kvanta, A., & Lanner, F. (2020). Identification of cell surface markers and establishment of monolayer differentiation to retinal pigment epithelial cells. Nature Communications, 11, 1609.

Wagner, M., Yoshihara, M., Douagi, I., Damdimopoulos, A., Panula, S., Petropoulos, S., Lu, H., Pettersson, K., Palm, K., Katayama, S., Hovatta, O., Kere, J., Lanner, F., & Damdimopoulou, P. (2020). Single-cell analysis of human ovarian cortex identifies distinct cell populations but no oogonial stem cells. Nature Communications, 11(1), 1147.

Gelali, E., Girelli, G., Matsumoto, M., Wernersson, E., Custodio, J., Mota, A., Schweitzer, M., Ferenc, K., Li, X., Mirzazadeh, R., Agostini, F., Schell, J. P., Lanner, F., Crosetto, N., & Bienko, M. (2019). iFISH is a publically available resource enabling versatile DNA FISH to study genome architecture. Nature Communications, 10(1), 1636.

Wagner, M., Yoshihara, M., Douagi, I., Damdimopoulos, A., Panula, S., Petropoulos, S., Lu, H., Pettersson, K., Palm, K., Katayama, S., Hovatta, O., Kere, J., Lanner, F., & Damdimopoulou, P. (2019). Single cell map of the human ovarian cortex. BioRxiv.

Ortega, N. M., Winblad, N., Plaza Reyes, A., & Lanner, F. (2018). Functional genetics of early human development. Current Opinion in Genetics and Development, 52, 1–6.

Petrus-Reurer, S., Bartuma, H., Aronsson, M., Westman, S., Lanner, F., & Kvanta, A. (2018). Subretinal transplantation of human embryonic stem cell derived-retinal pigment epithelial cells into a large-eyed model of geographic atrophy. Journal of Visualized Experiments, 131.

Plaza Reyes, A., & Lanner, F. (2018). Time Matters: Gene Editing at the Mouse 2-Cell Embryo Stage Boosts Knockin Efficiency. Cell Stem Cell, 23(2), 155–157.

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Hildebrand, S., Hultin, S., Subramani, A., Petropoulos, S., Zhang, Y., Cao, X., Mpindi, J., Kalloniemi, O., Johansson, S., Majumdar, A., Lanner, F., & Holmgren, L. (2017). The E-cadherin/AmotL2 complex organizes actin filaments required for epithelial hexagonal packing and blastocyst hatching. Scientific Reports, 7(1), 9540.

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Petrus-Reurer, S., Bartuma, H., Aronsson, M., Westman, S., Lanner, F., André, H., & Kvanta, A. (2017). Integration of subretinal suspension transplants of human embryonic stem cell-derived retinal pigment epithelial cells in a large-eyed model of geographic atrophy. Investigative Ophthalmology and Visual Science, 58(2), 1314–1322.

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Linxian Li

Miao, L., Lin, J., Huang, Y., Li, L., Delcassian, D., Ge, Y., Shi, Y., & Anderson, D. G. (2020). Synergistic lipid compositions for albumin receptor mediated delivery of mRNA to the liver. Nature Communications, 11(1), 2424.

Wu, Y., Wang, L., Xiong, Y., Zhou, Q., Li, L., Chen, G., Ping, Y., Davidson, G., Levkin, P. A., Gao, L., & Deng, W. (2020). Cell-based high-throughput screening of cationic polymers for efficient DNA and siRNA delivery. Acta Biomaterialia, 115, 410–417.

Wu, Y., Xiong, Y., Wang, L., Zhou, Q., Li, L., Levkin, P. A., Davidson, G., Gao, L., & Deng, W. (2020). Development of new self-assembled cationic amino liposomes for efficient gene delivery. Biomaterials Science, 8(11), 3021–3025.

Guo, J., Wang, D., Sun, Q., Li, L., Zhao, H., Wang, D., Cui, J., Chen, L., & Deng, X. (2019). Omni‐Liquid Droplet Manipulation Platform. Advanced Materials Interfaces, 1900653.

Li, F., Han, J., Cao, T., Lam, W., Fan, B., Tang, W., Chen, S., Fok, K. L., & Li, L. (2019). Design of self-assembly dipeptide hydrogels and machine learning via their chemical features. Proceedings of the National Academy of Sciences, 116(23), 11259–11264.

Miao, L., Li, L., Huang, Y., Delcassian, D., Chahal, J., Han, J., Shi, Y., Sadtler, K., Gao, W., Lin, J., Doloff, J. C., Langer, R., & Anderson, D. G. (2019). Delivery of mRNA vaccines with heterocyclic lipids increases anti-tumor efficacy by STING-mediated immune cell activation. Nature Biotechnology, 37(10), 1174–1185.

Yang, C., He, G., Zhang, A., Wu, Q., Zhou, L., Hang, T., Liu, D., Xiao, S., Chen, H.-J., Liu, F., Li, L., Wang, J., & Xie, X. (2019). Injectable Slippery Lubricant-Coated Spiky Microparticles with Persistent and Exceptional Biofouling-Resistance. ACS Central Science, 5(2), 250–258.

Yang, J., Wang, D., Liu, H., Li, L., Chen, L., Jiang, H.-R., & Deng, X. (2019). An electric-field-dependent drop selector. Lab on a Chip, 19(7), 1296–1304.

Ronald Li

Chow, M. Z.-Y., Sadrian, S. N., Keung, W., Geng, L., Ren, L., Kong, C.-W., Wong, A. O.-T., Hulot, J.-S., Chen, C. S., Costa, K. D., Hajjar, R. J., & Li, R. A. (2019). Modulation of chromatin remodeling proteins SMYD1 and SMARCD1 promotes contractile function of human pluripotent stem cell-derived ventricular cardiomyocyte in 3D-engineered cardiac tissues. Scientific Reports, 9(1), 7502.

Keung, W., Chan, P. K. W., Backeris, P. C., Lee, E. K., Wong, N., Wong, A. O. T., Wong, G. K. Y., Chan, C. W. Y., Fermini, B., Costa, K. D., & Li, R. A. (2019). Human Cardiac Ventricular‐Like Organoid Chambers and Tissue Strips From Pluripotent Stem Cells as a Two‐Tiered Assay for Inotropic Responses. Clinical Pharmacology & Therapeutics, 106(2), 402–414.

Li, S., Keung, W., Cheng, H., & Li, R. A. (2019). Structural and Mechanistic Bases of Nuclear Calcium Signaling in Human Pluripotent Stem Cell-Derived Ventricular Cardiomyocytes. Stem Cells International, 2019, 1–17.

Ceholski, D. K., Turnbull, I. C., Kong, C.-W., Koplev, S., Mayourian, J., Gorski, P. A., Stillitano, F., Skodras, A. A., Nonnenmacher, M., Cohen, N., Björkegren, J. L. M., Stroik, D. R., Cornea, R. L., Thomas, D. D., Li, R. A., Costa, K. D., & Hajjar, R. J. (2018). Functional and transcriptomic insights into pathogenesis of R9C phospholamban mutation using human induced pluripotent stem cell-derived cardiomyocytes. Journal of Molecular and Cellular Cardiology, 119, 147–154.

Foo, K. S., Lehtinen, M. L., Leung, C. Y., Lian, X., Xu, J., Keung, W., Geng, L., Kolstad, T. R. S., Thams, S., Wong, A. O., Wong, N., Bylund, K., Zhou, C., He, X., Jin, S.-B., Clarke, J., Lendahl, U., Li, R. A., Louch, W. E., & Chien, K. R. (2018). Human ISL1+ Ventricular Progenitors Self-Assemble into an In Vivo Functional Heart Patch and Preserve Cardiac Function Post Infarction. Molecular Therapy, 26(7), 1644–1659.

Geng, L., Kong, C.-W., Wong, A. O. T., Shum, A. M.-Y., Chow, M. Z. Y., Che, H., Zhang, C., Yau, K.-L., Chan, C. W., Keung, W., & Li, R. A. (2018). Probing flecainide block of I using human pluripotent stem cell-derived ventricular cardiomyocytes adapted to automated patch-clamping and 2D monolayers. Toxicology Letters, 294, 61–72.

Kong, C.-W., Geng, L., & Li, R. A. (2018). High-Content Electrophysiological Analysis of Human Pluripotent Stem Cell-Derived Cardiomyocytes (hPSC-CMs). In Methods in molecular biology (Clifton, N.J.) (Vol. 1722, pp. 185–194).

Li, R. A., Keung, W., Cashman, T. J., Backeris, P. C., Johnson, B. V., Bardot, E. S., Wong, A. O. T., Chan, P. K. W., Chan, C. W. Y., & Costa, K. D. (2018). Bioengineering an electro-mechanically functional miniature ventricular heart chamber from human pluripotent stem cells. Biomaterials, 163, 116–127.

Li, Z., Meng, Z., Lu, J., Chen, F. M., Wong, W. T., Tse, G., Zheng, C., Keung, W., Tse, K., Li, R. A., Jiang, L., & Yao, X. (2018). TRPV6 protects ER stress-induced apoptosis via ATF6α-TRPV6-JNK pathway in human embryonic stem cell-derived cardiomyocytes. Journal of Molecular and Cellular Cardiology.

Lu, J., Boheler, K. R., Jiang, L., Chan, C. W., Tse, W. W., Keung, W., Poon, E. N., Li, R. A., & Yao, X. (2018). Polycystin-2 Plays an Essential Role in Glucose Starvation-Induced Autophagy in Human Embryonic Stem Cell-Derived Cardiomyocytes. Stem Cells.

Dongan Wang

Dong, Z., Meng, X., Yang, W., Zhang, J., Sun, P., Zhang, H., Fang, X., Wang, D.-A., & Fan, C. (2021). Progress of gelatin-based microspheres (GMSs) as delivery vehicles of drug and cell. Materials Science and Engineering: C, 122, 111949. 


Jin, M., Shi, J., Zhu, W., Yao, H., & Wang, D.-A. (2021). Polysaccharide-Based Biomaterials in Tissue Engineering: A Review. Tissue Engineering Part B: Reviews, ten.teb.2020.0208. 


Ling, Y., Zhang, W., Wang, P., Xie, W., Yang, W., Wang, D.-A., & Fan, C. (2021). Three-dimensional (3D) hydrogel serves as a platform to identify potential markers of chondrocyte dedifferentiation by combining RNA sequencing. Bioactive Materials, 6(9), 2914–2926. 


Tao, C., Jin, M., Yao, H., & Wang, D.-A. (2021). Dopamine based adhesive nano-coatings on extracellular matrix (ECM) based grafts for enhanced host–graft interfacing affinity. Nanoscale. 


Tao, C., & Wang, D.-A. (2021). Tissue Engineering for Mimics and Modulations of Immune Functions. Advanced Healthcare Materials, 10(12), 2100146. 

Zongli Zheng

Lian S., Lu C., Li F., Yu X., Ai L., Wu B., Gong X., Zhou W., Liang X., Zhan J., Yuan Y., Fang F., Liu Z., Ji M., Zheng Z. (2024). Monitoring Hepatocellular Carcinoma Using Tumor Content in Circulating Cell-Free DNA. Clin Cancer Res. Jul 1;30(13):2772-2779.

Thean, D. G. L., Chu, H. Y., Fong, J. H. C., Chan, B. K. C., Zhou, P., Kwok, C. C. S., Chan, Y. M., Mak, S. Y. L., Choi, G. C. G., Ho, J. W. K., Zheng, Z., & Wong, A. S. L. (2022). Machine learning-coupled combinatorial mutagenesis enables resource-efficient engineering of CRISPR-Cas9 genome editor activities. Nature Communications, 13(1), 2219. 

Yuen, C. T. L., Thean, D. G. L., Chan, B. K. C., Zhou, P., Kwok, C. C. S., Chu, H. Y., Cheung, M. S. H., Wang, B., Chan, Y. M., Mak, S. Y. L., Leung, A. Y., Choi, G. C. G., Zheng, Z., & Wong, A. S. L. (2022). High-fidelity KKH variant of Staphylococcus aureus Cas9 nucleases with improved base mismatch discrimination. Nucleic Acids Research, 50(3), 1650–1660. 

Song, Z., Lian, S., Mak, S., Chow, ZY, Xu, C., Wang, W., Keung, HY., Lu, C., Kebede, TF., Gao, Y., Cheuk, W., Cho, CS, Yang, M., & Zheng, Z. (2021). Deep RNA sequencing revealed fusion junctional heterogeneity may predict crizotinib treatment efficacy in ALK-rearranged non-small cell lung cancer. Journal of Thoracic Oncology.

Song, Z., Lu, C., Xu, C.-W., & Zheng, Z. (2021). Noncanonical Gene Fusions Detected at the DNA Level Necessitate Orthogonal Diagnosis Methods Before Targeted Therapy. Journal of Thoracic Oncology, 16(3), 344–348.

Wan, Y. C. E., Leung, T. C. S., Ding, D., Sun, X., Liu, J., Zhu, L., Kang, T. Z. E., Yang, D., Zhang, Y., Zhang, J., Qian, C., Huen, M. S. Y., Li, Q., Chow, M. Z. Y., Zheng, Z., Han, J., Goel, A., Wang, X., Ishibashi, T., & Chan, K. M. (2020). Cancer-associated histone mutation H2BG53D disrupts DNA–histone octamer interaction and promotes oncogenic phenotypes. Signal Transduction and Targeted Therapy, 5(1), 27.

Zhou, P., Chan, B. K. C., Wan, Y. K., Yuen, C. T. L., Choi, G. C. G., Li, X., Tong, C. S. W., Zhong, S. S. W., Sun, J., Bao, Y., Mak, S. Y. L., Chow, M. Z. Y., Khaw, J. V., Leung, S. Y., Zheng, Z., Cheung, L. W. T., Tan, K., Wong, K. H., Chan, H. Y. E., & Wong, A. S. L. (2020). A Three-Way Combinatorial CRISPR Screen for Analyzing Interactions among Druggable Targets. Cell Reports, 32(6), 108020.

Choi, G. C. G., Zhou, P., Yuen, C. T. L., Chan, B. K. C., Xu, F., Bao, S., Chu, H. Y., Thean, D., Tan, K., Wong, K. H., Zheng, Z., & Wong, A. S. L. (2019). Combinatorial mutagenesis en masse optimizes the genome editing activities of SpCas9. Nature Methods, 16(8), 722–730.

Tan, Y., Chu, A. H. Y., Bao, S., Hoang, D. A., Kebede, F. T., Xiong, W., Ji, M., Shi, J., & Zheng, Z. (2019). Rationally engineered Staphylococcus aureus Cas9 nucleases with high genome-wide specificity. Proceedings of the National Academy of Sciences, 116(42), 20969–20976.