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Wu Y#, Ma J#, Yang X#, Nan F#, Zhang T#, Ji S, Rao D, Feng H, Gao K, Gu X, Jiang S, Song G, Pan J, Zhang M, Xu Y, Zhang S, Fan Y, Wang X, Zhou J, Yang L*, Fan J*, Zhang X* and Gao Q*. Neutrophil profiling illuminates anti-tumor antigen-presenting potency. Cell, 10.1016/j.cell.2024.02.005
Ma XK#, Gao X#, Cao M and Yang L. Base-Editor-Mediated circRNA Knockout by Targeting Predominantly Back-Splice Sites. Methods Mol Biol, 2024, 2765: 193-208 (Book chapter)
Fujiwara R#, Zhai SN#, Liang D, Shah AP, Tracey M, Ma XK, Fields CJ, Mendoza-Figueroa MS, Meline MC, Tatomer DC, Yang L and Wilusz JE*. IntS6 and the Integrator phosphatase module tune the efficiency of select premature transcription termination events. Mol Cell, 2023, 83(24): 4445-4460
Han W#, Qiu HY#, Sun S#, Fu ZC#, Wang GQ#, Qian X#, Wang L, Zhai X, Wei J, Wang Y, Guo YL, Cao GH, Ji RJ, Zhang YZ, Ma H, Wang H, Zhao M, Wu J, Bi L, Chen QB, Li Z, Yu L, Mou X, Yin H, Yang L*, Chen J*, Yang B* and Zhang Y*. Base editing of the HBG promoter induces potent fetal hemoglobin expression with no detectable off-target mutations in human HSCs. Cell Stem Cell, 2023, 30(12): 1624-1639
Yang L* and Jia Chen*. Expanding genome editing scopes with artificial intelligence. Sci Bull, 2023, 68(23): 2881-2883 (News & Views)
Ma XK*, Zhai SN and Yang L*. Approaches and challenges in genome-wide circular RNA identification and quantification. Trends Genet, 2023, 39(12): 897-907 (Review)
Han W#, Gao BQ#, Zhu J#, He Z#, Li J*, Yang L* and Chen J*. Design and application of the transformer base editor in mammalian cells and mice. Nat Protoc, 2023, 18(11): 3194-3228
Zhao W#, Li J#, Wang X#, Xu W#, Gao BQ#, Xiang J, Hou Y, Liu W, Wu J, Qi Q, Wei J, Yang X, Lu L*, Yang L*, Chen J* and Yang B*. Prime editor-mediated functional reshaping of ACE2 prevents the entry of multiple human coronaviruses, including SARS-CoV-2 variants. MedComm, 2023, 4(5): e356
Vromman M, Anckaert J, Bortoluzzi S, Buratin A, Chen CY, Chu Q, Chuang TJ, Dehghannasiri R, Dieterich C, Dong X, Flicek P, Gaffo E, Gu W, He C, Hoffmann S, Izuogu O, Jackson MS, Jakobi T, Lai EC, Nuytens J, Salzman J, Santibanez-Koref M, Stadler P, Thas O, Vanden Eynde E, Verniers K, Wen G, Westholm J, Yang L, Ye CY, Yigit N, Yuan GH, Zhang J, Zhao F, Vandesompele J* and Volders PJ. Large-scale benchmarking of circRNA detection tools reveals large differences in sensitivity but not in precision. Nat Methods, 2023, 20(8): 1159-1169
Ortiz-Barahona V, Soler M, Davalos V, Garcia-Prieto CA, Janin M, Setien F, Fernandez-Rebollo I, Bech-Serra JJ, De La Torre C, Guil S, Villanueva A, Zhang PH, Yang L, Guarnacci M, Schumann U, Preiss T, Balaseviciute U, Montal R, Llovet JM and Esteller M*. Epigenetic inactivation of the 5-methylcytosine RNA methyltransferase NSUN7 is associated with clinical outcome and therapeutic vulnerability in liver cancer. Mol Cancer, 2023, 22(1): 83
Shan L#, Xu G#, Yao RW, Luan PF, Huang Y, Zhang PH, Pan YH, Zhang L, Gao X, Li Y, Cao SM, Gao SX, Yang ZH, Li S, Yang LZ, Wang Y, Wong CCL, Yu L, Li J, Yang L and Chen LL*. Nucleolar URB1 ensures 3' ETS rRNA removal to prevent exosome surveillance. Nature, 2023, 615(7952): 526-534
Wang Y, Qi T, Liu J, Yang Y, Wang Z, Wang Y, Wang T, Li M, Li M, Lu D, Chang ACY, Yang L, Gao S, Wang Y* and Lan F*. A highly specific CRISPR-Cas12j nuclease enables allele-specific genome editing. Sci Adv, 2023, 9(6): eabo6405
Huang Y, Gao BQ, Meng Q, Yang LZ, Ma XK, Wu H, Pan YH, Yang L, Li D and Chen LL*. CRISPR-dCas13-tracing reveals transcriptional memory and limited mRNA export in developing zebrafish embryos. Genome Biol, 2023, 24(1): 15
Chen LL*, Bindereif A, Bozzoni I, Chang HY, Matera AG, Gorospe M, Hansen TB, Kjems J, Ma XK, Pek JW, Rajewsky N, Salzman J, Wilusz JE*, Yang L* and Zhao F. A guide to naming eukaryotic circular RNAs. Nat Cell Biol, 2023, 25(1): 1-5
Wang B*#, Jiang B#, Li GW#, Dong F, Luo Z, Cai B, Wei M, Huang J, Wang K, Feng X, Tong F, Wang S, Wang Q, Han Q, Li C, Zhang X, Yang L* and Bao L*. Somatosensory neurons express specific sets of lincRNAs, and lincRNA CLAP promotes itch sensation in mice. EMBO Rep, 2023, 24(2): e54313
Yuan GH#, Wang Y#, Wang GZ and Yang L*. RNAlight: a machine learning model to identify nucleotide features determining RNA subcellular localization. Brief Bioinform, 2023, 24(1): bbac509
Huang J, Jiang B, Li GW, Zheng D, Li M, Xie X, Pan Y, Wei M, Liu X, Jiang X, Zhang X, Yang L, Bao L* and Wang B*. m(6)A-modified lincRNA Dubr is required for neuronal development by stabilizing YTHDF1/3 and facilitating mRNA translation. Cell Rep, 2022, 41(8): 111693
Gopalan V, Nilsen T, Gopalan V, Altman AM, Stark BC, Feinstein SI, Koski R, Mickiewicz C, Stark B, Gegenheimer P, Kirsebom LA, Arnez JG, Forster AC, Kazakov SA, Yuan Y, Liu F, Jarrous N, Yang L, Jiang G, Jiang T, Rosenbaum JL, Miller G, DiMaio D, Carlson JR, McClain WH, Mathews MB, Kaempfer R, Deutscher MP, Chen LL, Li Y, Wang E, Patutina O, Zenkova M, Vlassov V, Lucks JB and Gopalan V. Tribute to Sidney Altman. RNA, 2022, 28(11): 1393-1429
Yang LZ#, Gao BQ#, Huang Y, Wang Y, Yang L and Chen LL*. Multi-color RNA imaging with CRISPR-Cas13b systems in living cells. Cell Insight, 2022, 1(4):100044
Yang L*, Wilusz JE* and Chen LL*. Biogenesis and Regulatory Roles of Circular RNAs. Annu Rev Cell Dev Biol, 2022, 38263-289 (Review)
Li X#, Zhou L#, Gao BQ#, Li G, Wang X, Wang Y, Wei J, Han W, Wang Z, Li J, Gao R, Zhu J, Xu W, Wu J, Yang B, Sun X*, Yang L* and Chen J*. Highly efficient prime editing by introducing same-sense mutations in pegRNA or stabilizing its structure. Nat Commun, 2022, 13(1): 1669
Gao R#, Fu ZC#, Li X#, Wang Y#, Wei J, Li G, Wang L, Wu J, Huang X*, Yang L* and Chen J*. Genomic and Transcriptomic Analyses of Prime Editing Guide RNA-Independent Off-Target Effects by Prime Editors. CRISPR J, 2022, 5(2): 276-293
Gao X#, Ma XK#, Li X, Li GW, Liu CX, Zhang J, Wang Y, Wei J, Chen J, Chen LL and Yang L*. Knockout of circRNAs by base editing back-splice sites of circularized exons. Genome Biol, 2022, 23(1): 16
Liu CX#, Guo SK#, Nan F, Xu YF, Yang L and Chen LL*. RNA circles with minimized immunogenicity as potent PKR inhibitors. Mol Cell, 2022, 82(2): 420-434 e426
Zhang Y, Yang L* and Chen LL*. Characterization of Circular RNAs. Methods Mol Biol, 2021, 2372: 179-192 (Book chapter)
Li X, Zhang JL, Lei YN, Liu XQ, Xue W, Zhang Y, Nan F, Gao X, Zhang J, Wei J, Yang L and Chen LL*. Linking circular intronic RNA degradation and function in transcription by RNase H1. Sci China Life Sci, 2021, 64(11): 1795-1809
Li GW#, Nan F#, Yuan GH, Liu CX, Liu X, Chen LL, Tian B and Yang L*. SCAPTURE: a deep learning-embedded pipeline that captures polyadenylation information from 3' tag-based RNA-seq of single cells. Genome Biol, 2021, 22(1): 221
Wu M#, Xu G#, Han C#, Luan PF, Xing YH, Nan F, Yang LZ, Huang Y, Yang ZH, Shan L, Yang L, Liu J* and Chen LL*. lncRNA SLERT controls phase separation of FC/DFCs to facilitate Pol I transcription. Science, 2021, 373(6554): 547-555
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Wang L#, Xue W#, Zhang H#, Gao R#, Qiu H#, Wei J, Zhou L, Lei YN, Wu X, Li X, Liu C, Wu J, Chen Q, Ma H, Huang X, Cai C, Zhang Y, Yang B*, Yin H*, Yang L* and Chen J*. Eliminating base-editor-induced genome-wide and transcriptome-wide off-target mutations. Nat Cell Biol, 2021, 23(5): 552-563
Wei M#, Huang J#, Li GW, Jiang B, Cheng H, Liu X, Jiang X, Zhang X, Yang L, Bao L* and Wang B*. Axon-enriched lincRNA ALAE is required for axon elongation via regulation of local mRNA translation. Cell Rep, 2021, 35(5): 109053
Ma XK, Xue W, Chen LL and Yang L*. CIRCexplorer pipelines for circRNA annotation and quantification from non-polyadenylated RNA-seq datasets. Methods, 2021, 1963-10
Guo SK#, Nan F#, Liu CX, Yang L and Chen LL*. Mapping circular RNA structures in living cells by SHAPE-MaP. Methods, 2021, 19647-55
Xue W, Ma XK and Yang L*. Fast and Furious: insights of back splicing regulation during nascent RNA synthesis. Sci China Life Sci, 2021, 64(7): 1050-1061 (Review)
Li S#, Li X#, Xue W#, Zhang L#, Yang LZ, Cao SM, Lei YN, Liu CX, Guo SK, Shan L, Wu M, Tao X, Zhang JL, Gao X, Zhang J, Wei J, Li J*, Yang L* and Chen LL*. Screening for functional circular RNAs using the CRISPR-Cas13 system. Nat Methods, 2021, 18(1): 51-59
Highlighted by Nat Rev Genet, 2021, 22: 68
Ma XK#, Guo CJ#, Yang L and Chen LL*. Altered processing of lncRNAs in stem cells contributes to non-conserved functions. Chemistry of Life, 2020, 40(7): 985-991 (Review, in Chinese)
Yang L* and Chen J*. A Tale of Two Moieties: Rapidly Evolving CRISPR/Cas-Based Genome Editing. Trends Biochem Sci, 2020, 45(10): 874-888 (Review)
Wang X#, Ding C#, Yu W#, Wang Y#, He S#, Yang B#, Xiong Y-C, Wei J, Li J, Liang J, Lu Z, Zhu W, Wu J, Zhou Z, Huang X, Liu Z*, Yang L* and Chen J*. Cas12a Base Editors Induce Efficient and Specific Editing with Low DNA Damage Response. Cell Rep, 2020, 31(9):107723
Zhang X#, Zhu B#, Chen L#, Xie L, Yu W, Wang Y, Li L, Yin S, Yang L, Hu H, Han H, Li Y, Wang L, Chen G, Ma X, Geng H, Huang W, Pang X, Yang Z, Wu Y, Siwko S, Kurita R, Nakamura Y, Yang L, Liu M and Li D*. Dual base editor catalyzes both cytosine and adenine base conversions in human cells. Nat Biotechnol, 2020, 38(7): 856-860
Schumann U#, Zhang HN#, Sibbritt T, Pan A, Horvath A, Gross S, Clark SJ, Yang L and Preiss T*. Multiple links between 5-methylcytosine content of mRNA and translation. BMC Biol, 2020, 18(1):40
Guo CJ#, Ma XK#, Xing YH, Zheng CC, Xu YF, Shan L, Zhang J, Wang S, Wang Y, Carmichael GG, Yang L and Chen LL*. Distinct Processing of lncRNAs Contributes to Non-conserved Functions in Stem Cells. Cell, 2020, 181(3):621-636.e22
Cai C#, Geng A#, Wang M, Yang L, Yu QC* and Zeng YA*. Amphiregulin mediates the hormonal regulation on Rspondin-1 expression in the mammary gland. Dev Biol, 2020, 458(1):43-51
Ma XK, Wang MR, Liu CX, Dong R, Carmichael GG, Chen LL and Yang L*. CIRCexplorer3: A CLEAR pipeline for direct comparison of circular and linear RNA expression. Genomics Proteomics Bioinformatics, 2019, 17(5):511–521
Wang Y#, Gao R#, Wu J#, Xiong YC, Wei J, Zhang S, Yang B, Chen J* and Yang L*. Comparison of cytosine base editors and development of the BEable-GPS database for targeting pathogenic SNVs. Genome Biol, 2019, 20(1):218
Yang L*, Yang B* and Chen J*. One Prime for All Editing. Cell, 2019, 179(7): 1448-1450 (Preview)
Yao RW#, Xu G#, Wang Y, Shan L, Luan PF, Wang Y, Wu M, Yang LZ, Xing YH, Yang L and Chen LL*. Nascent Pre-rRNA Sorting via Phase Separation Drives the Assembly of Dense Fibrillar Components in the Human Nucleolus. Mol Cell, 2019, 76(5): 1-17
Zhu YJ#, Zheng B#, Luo GJ#, Ma XK#, Lu XY, Lin XM, Yang S, Zhao Q, Wu T, Li ZX, Liu XL, Wu R, Liu JF, Ge Y, Yang L, Wang HY* and Chen L*. Circular RNAs negatively regulate cancer stem cells by physically binding FMRP against CCAR1 complex in hepatocellular carcinoma. Theranostics. 2019, 9(12):3526-3540
Liu CX#, Li X#, Nan F#, Jiang S, Gao X, Guo SK, Xue W, Cui Y, Dong K, Ding H, Qu B, Zhou Z, Shen N*, Yang L* and Chen LL*. Structure and Degradation of Circular RNAs Regulate PKR Activation in Innate Immunity. Cell, 2019, 177(4): 865-880.e21 (Featured Article)
Highlighted by Cell, 2019, 177: 797-799
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Yang B*, Yang L* and Chen J*. Development and Application of Base Editors. CRISPR J, 2019(2), 2: 91-104 (Review)
Chen J*, Yang B* and Yang L*. To BE or not to BE, that is the question. Nat Biotechnol, 2019, 37(5): 520–522 (News & Views)
Wang L#, Wang X#, Yang L and Chen J*. Development and application of base editor. Chemistry of Life, 2019, 39(1):13-20 (Review)
Wang Y#, Xiong Y#, Chen J and Yang L*. Computational analysis in CRISPR/Cas genome editing. Chemistry of Life, 2019, 39(1):28-38 (Review)
Dong R, Ma XK, Chen LL and Yang L. Genome-Wide Annotation of circRNAs and Their Alternative Back-Splicing/Splicing with CIRCexplorer Pipeline. Methods Mol Biol, 2019, 1870: 137-149 (Book chapter)
Wang Y#, Hu SB#, Wang MR#, Yao RW, Wu D, Yang L and Chen LL*. Genome-wide screening of NEAT1 regulators reveals cross-regulation between paraspeckles and mitochondria. Nat Cell Biol, 2018, 20(10):1145-1158
Editorial by: Fox AH. Nat Cell Biol, 2018, 20(10): 1108-1109
Dong R#, Ma XK#, Li GW and Yang L*. CIRCpedia v2: An Updated Database for Comprehensive Circular RNA Annotation and Expression Comparison. Genomics Proteomics Bioinformatics, 2018, 16(4):226-233
Wang X#, Li J#, Wang Y#, Yang B#, Wei J#, Wu J, Wang R, Huang X*, Chen J* and Yang L*. Efficient base editing in methylated regions with a human APOBEC3A-Cas9 fusion. Nat Biotechnol, 2018, 36(10):946-949
Zhang R#, Gao Y#, Zhao X#, Gao M#, Wu Y, Han Y, Qiao Y, Luo Z, Yang L, Chen J and Ge G*. FSP1-positive fibroblasts are adipogenic niche and regulate adipose homeostasis. PLoS Biol, 2018, 16(8): e2001493
Li X, Yang L* and Chen LL*. The Biogenesis, Functions, and Challenges of Circular RNAs. Mol Cell, 2018, 71(3):428-442 (Review)
Li X#, Wang Y#, Liu Y#, Yang B#, Wang X, Wei J, Lu Z, Zhang Y, Wu J, Huang X*, Yang L* and Chen J*. Base editing with a cpf1-cytidine deaminase fusion. Nat Biotechnol, 2018, 36(4):324-327
Xiang JF#, Yang Q#, Liu CX#, Wu M, Chen LL* and Yang L*. N6-Methyladenosines Modulate A-to-I RNA Editing. Mol Cell, 2018, 69(1):126-135
Lei L#, Chen H#, Xue W#, Yang B#, Hu B#, Wei J, Wang L, Cui Y, Li W, Wang J, Yan L, Shang W, Gao J, Sha J, Zhuang M, Huang X, Shen B*, Yang L* and Chen J*. APOBEC3 induces mutations during repair of CRISPR–Cas9-generated DNA breaks. Nat Struct Mol Biol, 2018, 25(1):45–52
Liang D, Tatomer DC, Luo Z, Wu H, Yang L, Chen LL, Cherry S, and Wilusz JE*. The Output of Protein-Coding Genes Shifts to Circular RNAs When the Pre-mRNA Processing Machinery Is Limiting. Mol Cell, 2017, 68(5):940–954
Yang L* and Chen LL*. Enhancing the RNA engineering toolkit. Science, 2017, 358(6366):996-997 (Perspectives)
Wang L#, Xue W#, Yan L#, Li X, Wei J, Chen M, Wu J, Yang B*, Yang L* and Chen J*. Enhanced base editing by co-expression of free uracil DNA glycosylase inhibitor. Cell Res, 2017, 27(10):1289-1292
Yang Q, Wang Y and Yang L*. Multifaceted roles of complementary sequences on circRNA formation. Quantitative Biology, 2017, 5(3): 205-209 (Review)
Wu H, Yang L* and Chen LL*. The Diversity of Long Noncoding RNAs and Their Generation. Trends Genet, 2017, 33(8): 540-552 (Review)
Li X#, Liu CX#, Xue W#, Zhang Y, Jiang S, Yin QF, Wei J, Yao RW, Yang L* and Chen LL*.Coordinated circRNA Biogenesis and Function with NF90/NF110 in Viral Infection. Mol Cell, 2017, 67(2): 214-227
Editorial by: Cadena C and Hur S. Mol Cell, 2017, 67: 163-164
Xing YH#, Yao RW#, Zhang Y#, Guo CJ, Jiang S, Xu G, Dong R, Yang L and Chen LL*. SLERT Regulates DDX21 Rings Associated with Pol I Transcription. Cell, 2017, 169(4): 664-678.e16
Chen LL* and Yang L*. ALUternative Regulation for Gene Expression. Trends Cell Biol, 2017, 27(7): 480-490 (Review)
Niu N, Xiang JF, Yang Q, Wang L, Wei Z, Chen LL, Yang L and Zou W*. RNA-binding protein SAMD4 regulates skeleton development through translational inhibition of Mig6 expression. Cell Disc, 2017, 3: 16050
Dong R#, Ma XK#, Chen LL* and Yang L*. Increased complexity of circRNA expression during species evolution. RNA Biol, 2017, 14(8): 1064-1074
Wu H#, Yin QF#, Luo Z#, Yao RW, Zheng CC, Zhang J, Xiang JF, Yang L and Chen LL*. Unusual Processing Generates SPA LncRNAs that Sequester Multiple RNA Binding Proteins. Mol Cell, 2016, 64(3): 534-548 (Cover Article)
Editorial by: Li R and Fox AH. Mol Cell, 2016, 64: 435-437
Luo Z, Yang Q and Yang L*. RNA Structure Switches RBP Binding. Mol Cell, 2016, 64(2): 219-220 (Previews)
Zhang XO#, Dong R#, Zhang Y#, Zhang JL, Luo Z, Zhang J, Chen LL* and Yang L*. Diverse alternative back-splicing and alternative splicing landscape of circular RNAs. Genome Res, 2016, 26(9): 1277-1287
Zhang Y#, Xue W#, Li X, Zhang J, Chen S, Zhang JL, Yang L* and Chen LL*. The Biogenesis of Nascent Circular RNAs. Cell Rep, 2016, 15(3): 611-624
Dong R, Zhang XO, Zhang Y, Ma XK, Chen LL and Yang L*. CircRNA-derived pseudogenes. Cell Res, 2016, 26(6): 747-750
Zhang Y, Yang L* and Chen LL*. Characterization of Circular RNAs. Methods Mol Biol, 2016, 1402: 215-227 (Book chapter)
Zhong C#, Xie Z#, Yin Q#, Dong R, Yang S, Wu Y, Yang L and Li J*. Parthenogenetic haploid embryonic stem cells efficiently support mouse generation by oocyte injection. Cell Res, 2016, 26(1): 131-134
Yang L. Splicing noncoding RNAs from the inside out. WIREs RNA, 2015, 6(6): 651-660 (Review)
Brooks AN, Duff MO, May G, Yang L, Bolisetty M, Landolin J, Wan K, Sandler J, Celniker SE, Graveley BR* and Brenner SE*. Regulation of alternative splicing in Drosophila by 56 RNA binding proteins. Genome Res, 2015, 25(11): 1771-1780
Xiang JF, Yang L and Chen LL. The long noncoding RNA regulation at the MYC locus. Curr Opin Genet Dev, 2015, 33:41–48 (Review)
Zhong C#, Yin Q#, Xie Z#, Bai M#, Dong R#, Tang W, Xing YH, Zhang H, Yang S, Chen LL, Bartolomei MS, Ferguson-Smith A, Li D, Yang L*, Wu Y* and Li J*. CRISPR-Cas9-Mediated Genetic Screening in Mice with Haploid Embryonic Stem Cells Carrying a Guide RNA Library. Cell Stem Cell, 2015, 17(2): 221-232
Chen LL* and Yang L*. Gear up in circles. Mol Cell, 2015, 58(5): 715-717 (Preview)
Hu SB, Xiang JF, Li X, Xu Y, Xue W, Huang M, Wong CC, Sagum CA, Bedford MT, Yang L, Cheng D, and Chen LL. Protein arginine methyltransferase CARM1 attenuates the paraspeckle-mediated nuclear retention of mRNAs containing IRAlus. Genes & Dev, 2015, 29(6): 630-645
Chen LL* and Yang L*. Regulation of circRNA biogenesis. RNA Biology, 2015, 12(4): 381-388 (Review)
Chen T#, Xiang JF#, Zhu S#, Chen S, Yin QF, Zhang XO, Zhang J, Feng H, Dong R, Li XJ, Yang L* and Chen LL*. 2015. ADAR1 is required for differentiation and neural induction by regulating microRNA processing in a catalytically independent manner. Cell Res, 2015, 25(4): 459-476
Yin QF#, Hu SB#, Xu YF, Yang L, Carmichael GG and Chen LL. SnoVectors for nuclear expression of RNA. Nucleic Acids Res, 2015, 43(1): e5
Wang D#, Cai C#, Dong X, Yu QC, Zhang XO, Yang L and Zeng YA. Identification of multipotent mammary stem cells by protein C receptor expression. Nature, 2015, 517(7532): 81-84
Yin QF, Chen LL* and Yang L*. Fractionation of Non-polyadenylated and Ribosomal-free RNAs from Mammalian Cells. Methods Mol Biol, 2015, 1206: 69-80 (Book chapter)
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