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1,166 results on '"Bolund, Lars"'

1. Mapping the chromothripsis landscape in urothelial carcinoma unravels great intratumoral and intertumoral heterogeneity

Author

Zeng, Yuchen, Lv, Wei, Tao, Huiying, Li, Conghui, Jiang, Shiqi, Liang, Yuan, Chen, Chen, Yu, Tianxi, Li, Yue, Wu, Shuang, Cui, Xin, Liang, Ning, Wang, Ping, Xu, Huixin, Dong, Jingjing, Teng, Huajing, Chen, Ke, Mu, Kai, Fan, Tianda, Cen, Xiaoping, Xu, Zhe, Zhu, Ming, Wang, Wenting, Mi, Jia, Xiang, Xi, Dong, Wei, Yang, Huanming, Bolund, Lars, Lin, Lin, Song, Jinzhao, Song, Xicheng, Luo, Yonglun, Lin, Chunhua, and Han, Peng

Published
2025
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2. Massively targeted evaluation of therapeutic CRISPR off-targets in cells

Author

Pan, Xiaoguang, Qu, Kunli, Yuan, Hao, Xiang, Xi, Anthon, Christian, Pashkova, Liubov, Liang, Xue, Han, Peng, Corsi, Giulia I., Xu, Fengping, Liu, Ping, Zhong, Jiayan, Zhou, Yan, Ma, Tao, Jiang, Hui, Liu, Junnian, Wang, Jian, Jessen, Niels, Bolund, Lars, Yang, Huanming, Xu, Xun, Church, George M., Gorodkin, Jan, Lin, Lin, and Luo, Yonglun

Published
2022
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3. Author Correction: Endothelial cell heterogeneity and microglia regulons revealed by a pig cell landscape at single-cell level

Author

Wang, Fei, Ding, Peiwen, Liang, Xue, Ding, Xiangning, Brandt, Camilla Blunk, Sjöstedt, Evelina, Zhu, Jiacheng, Bolund, Saga, Zhang, Lijing, de Rooij, Laura P. M. H., Luo, Lihua, Wei, Yanan, Zhao, Wandong, Lv, Zhiyuan, Haskó, János, Li, Runchu, Qin, Qiuyu, Jia, Yi, Wu, Wendi, Yuan, Yuting, Pu, Mingyi, Wang, Haoyu, Wu, Aiping, Xie, Lin, Liu, Ping, Chen, Fang, Herold, Jacqueline, Kalucka, Joanna, Karlsson, Max, Zhang, Xiuqing, Helmig, Rikke Bek, Fagerberg, Linn, Lindskog, Cecilia, Pontén, Fredrik, Uhlen, Mathias, Bolund, Lars, Jessen, Niels, Jiang, Hui, Xu, Xun, Yang, Huanming, Carmeliet, Peter, Mulder, Jan, Chen, Dongsheng, Lin, Lin, and Luo, Yonglun

Published
2022
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4. Endothelial cell heterogeneity and microglia regulons revealed by a pig cell landscape at single-cell level

Author

Wang, Fei, Ding, Peiwen, Liang, Xue, Ding, Xiangning, Brandt, Camilla Blunk, Sjöstedt, Evelina, Zhu, Jiacheng, Bolund, Saga, Zhang, Lijing, de Rooij, Laura P. M. H., Luo, Lihua, Wei, Yanan, Zhao, Wandong, Lv, Zhiyuan, Haskó, János, Li, Runchu, Qin, Qiuyu, Jia, Yi, Wu, Wendi, Yuan, Yuting, Pu, Mingyi, Wang, Haoyu, Wu, Aiping, Xie, Lin, Liu, Ping, Chen, Fang, Herold, Jacqueline, Kalucka, Joanna, Karlsson, Max, Zhang, Xiuqing, Helmig, Rikke Bek, Fagerberg, Linn, Lindskog, Cecilia, Pontén, Fredrik, Uhlen, Mathias, Bolund, Lars, Jessen, Niels, Jiang, Hui, Xu, Xun, Yang, Huanming, Carmeliet, Peter, Mulder, Jan, Chen, Dongsheng, Lin, Lin, and Luo, Yonglun

Published
2022
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5. Genome-wide annotation of protein-coding genes in pig

Author

Karlsson, Max, Sjöstedt, Evelina, Oksvold, Per, Sivertsson, Åsa, Huang, Jinrong, Álvez, María Bueno, Arif, Muhammad, Li, Xiangyu, Lin, Lin, Yu, Jiaying, Ma, Tao, Xu, Fengping, Han, Peng, Jiang, Hui, Mardinoglu, Adil, Zhang, Cheng, von Feilitzen, Kalle, Xu, Xun, Wang, Jian, Yang, Huanming, Bolund, Lars, Zhong, Wen, Fagerberg, Linn, Lindskog, Cecilia, Pontén, Fredrik, Mulder, Jan, Luo, Yonglun, and Uhlen, Mathias

Published
2022
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8. Single-Cell RNA Sequencing Maps Endothelial Metabolic Plasticity in Pathological Angiogenesis

Author

Rohlenova, Katerina, Goveia, Jermaine, García-Caballero, Melissa, Subramanian, Abhishek, Kalucka, Joanna, Treps, Lucas, Falkenberg, Kim D., de Rooij, Laura P.M.H., Zheng, Yingfeng, Lin, Lin, Sokol, Liliana, Teuwen, Laure-Anne, Geldhof, Vincent, Taverna, Federico, Pircher, Andreas, Conradi, Lena-Christin, Khan, Shawez, Stegen, Steve, Panovska, Dena, De Smet, Frederik, Staal, Frank J.T., Mclaughlin, Rene J., Vinckier, Stefan, Van Bergen, Tine, Ectors, Nadine, De Haes, Patrik, Wang, Jian, Bolund, Lars, Schoonjans, Luc, Karakach, Tobias K., Yang, Huanming, Carmeliet, Geert, Liu, Yizhi, Thienpont, Bernard, Dewerchin, Mieke, Eelen, Guy, Li, Xuri, Luo, Yonglun, and Carmeliet, Peter

Published
2020
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9. Single-Cell Transcriptome Atlas of Murine Endothelial Cells

Author

Kalucka, Joanna, de Rooij, Laura P.M.H., Goveia, Jermaine, Rohlenova, Katerina, Dumas, Sébastien J., Meta, Elda, Conchinha, Nadine V., Taverna, Federico, Teuwen, Laure-Anne, Veys, Koen, García-Caballero, Melissa, Khan, Shawez, Geldhof, Vincent, Sokol, Liliana, Chen, Rongyuan, Treps, Lucas, Borri, Mila, de Zeeuw, Pauline, Dubois, Charlotte, Karakach, Tobias K., Falkenberg, Kim D., Parys, Magdalena, Yin, Xiangke, Vinckier, Stefan, Du, Yuxiang, Fenton, Robert A., Schoonjans, Luc, Dewerchin, Mieke, Eelen, Guy, Thienpont, Bernard, Lin, Lin, Bolund, Lars, Li, Xuri, Luo, Yonglun, and Carmeliet, Peter

Published
2020
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10. De novo assembly of a haplotype-resolved human genome

Author

Cao, Hongzhi, Wu, Honglong, Luo, Ruibang, Huang, Shujia, Sun, Yuhui, Tong, Xin, Xie, Yinlong, Liu, Binghang, Yang, Hailong, Zheng, Hancheng, Li, Jian, Li, Bo, Wang, Yu, Yang, Fang, Sun, Peng, Liu, Siyang, Gao, Peng, Huang, Haodong, Sun, Jing, Chen, Dan, He, Guangzhu, Huang, Weihua, Huang, Zheng, Li, Yue, Tellier, Laurent CAM, Liu, Xiao, Feng, Qiang, Xu, Xun, Zhang, Xiuqing, Bolund, Lars, Krogh, Anders, Kristiansen, Karsten, Drmanac, Radoje, Drmanac, Snezana, Nielsen, Rasmus, Li, Songgang, Wang, Jian, Yang, Huanming, Li, Yingrui, Wong, Gane Ka-Shu, and Wang, Jun

Subjects
Asian People, Base Sequence, Chromosome Mapping, Diploidy, Genome, Human, Genotype, Haplotypes, High-Throughput Nucleotide Sequencing, Humans, Phenotype, Polymorphism, Single Nucleotide, Precision Medicine, Sequence Analysis, DNA
Abstract

The human genome is diploid, and knowledge of the variants on each chromosome is important for the interpretation of genomic information. Here we report the assembly of a haplotype-resolved diploid genome without using a reference genome. Our pipeline relies on fosmid pooling together with whole-genome shotgun strategies, based solely on next-generation sequencing and hierarchical assembly methods. We applied our sequencing method to the genome of an Asian individual and generated a 5.15-Gb assembled genome with a haplotype N50 of 484 kb. Our analysis identified previously undetected indels and 7.49 Mb of novel coding sequences that could not be aligned to the human reference genome, which include at least six predicted genes. This haplotype-resolved genome represents the most complete de novo human genome assembly to date. Application of our approach to identify individual haplotype differences should aid in translating genotypes to phenotypes for the development of personalized medicine.

Published
2015

11. A porcine brain-wide RNA editing landscape

Author

Huang, Jinrong, Lin, Lin, Dong, Zhanying, Yang, Ling, Zheng, Tianyu, Gu, Weiwang, Zhang, Yan, Yin, Tailang, Sjöstedt, Evelina, Mulder, Jan, Uhlén, Mathias, Kristiansen, Karsten, Bolund, Lars, and Luo, Yonglun

Published
2021
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14. Variation and association to diabetes in 2000 full mtDNA sequences mined from an exome study in a Danish population

Author

Li, Shengting, Besenbacher, Soren, Li, Yingrui, Kristiansen, Karsten, Grarup, Niels, Albrechtsen, Anders, Sparsø, Thomas, Korneliussen, Thorfinn, Hansen, Torben, Wang, Jun, Nielsen, Rasmus, Pedersen, Oluf, Bolund, Lars, and Schierup, Mikkel H

Subjects
Biological Sciences, Genetics, Human Genome, Diabetes, 2.1 Biological and endogenous factors, Aetiology, Metabolic and endocrine, Case-Control Studies, DNA, Mitochondrial, Denmark, Diabetes Mellitus, Exome, Gene Frequency, Genetic Association Studies, Genetic Variation, Genetics, Population, Genotype, Humans, Phylogeny, Polymorphism, Genetic, Quantitative Trait, Heritable, White People, diabetes, mtDNA, population history, Clinical Sciences, Genetics & Heredity, Clinical sciences
Abstract

In this paper, we mine full mtDNA sequences from an exome capture data set of 2000 Danes, showing that it is possible to get high-quality full-genome sequences of the mitochondrion from this resource. The sample includes 1000 individuals with type 2 diabetes and 1000 controls. We characterise the variation found in the mtDNA sequence in Danes and relate the variation to diabetes risk as well as to several blood phenotypes of the controls but find no significant associations. We report 2025 polymorphisms, of which 393 have not been reported previously. These 393 mutations are both very rare and estimated to be caused by very recent mutations but individuals with type 2 diabetes do not possess more of these variants. Population genetics analysis using Bayesian skyline plot shows a recent history of rapid population growth in the Danish population in accordance with the fact that >40% of variable sites are observed as singletons.

Published
2014

18. Patient iPSC-Derived Neurons for Disease Modeling of Frontotemporal Dementia with Mutation in CHMP2B

Author

Zhang, Yu, Schmid, Benjamin, Nikolaisen, Nanett K., Rasmussen, Mikkel A., Aldana, Blanca I., Agger, Mikkel, Calloe, Kirstine, Stummann, Tina C., Larsen, Hjalte M., Nielsen, Troels T., Huang, Jinrong, Xu, Fengping, Liu, Xin, Bolund, Lars, Meyer, Morten, Bak, Lasse K., Waagepetersen, Helle S., Luo, Yonglun, Nielsen, Jørgen E., Holst, Bjørn, Clausen, Christian, Hyttel, Poul, and Freude, Kristine K.

Published
2017
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20. Comparison of In-Frame Deletion, Homology-Directed Repair, and Prime Editing-Based Correction of Duchenne Muscular Dystrophy Mutations

Author

Zhao, Xiaoying, Qu, Kunli, Curci, Benedetta, Yang, Huanming, Bolund, Lars, Lin, Lin, Luo, Yonglun, Zhao, Xiaoying, Qu, Kunli, Curci, Benedetta, Yang, Huanming, Bolund, Lars, Lin, Lin, and Luo, Yonglun

Abstract

Recent progress in CRISPR gene editing tools has substantially increased the opportunities for curing devastating genetic diseases. Here we compare in-frame deletion by CRISPR-based non-homologous blunt end joining (NHBEJ), homology-directed repair (HDR), and prime editing (PE, PE2, and PE3)-based correction of two Duchenne Muscular Dystrophy (DMD) loss-of-function mutations (c.5533G>T and c.7893delC). To enable accurate and rapid evaluation of editing efficiency, we generated a genomically integrated synthetic reporter system (VENUS) carrying the DMD mutations. The VENUS contains a modified enhanced green fluorescence protein (EGFP) gene, in which expression was restored upon the CRISPR-mediated correction of DMD loss-of-function mutations. We observed that the highest editing efficiency was achieved by NHBEJ (74–77%), followed by HDR (21–24%) and PE2 (1.5%) in HEK293T VENUS reporter cells. A similar HDR (23%) and PE2 (1.1%) correction efficiency is achieved in fibroblast VENUS cells. With PE3 (PE2 plus nicking gRNA), the c.7893delC correction efficiency was increased 3-fold. Furthermore, an approximately 31% correction efficiency of the endogenous DMD: c.7893delC is achieved in the FACS-enriched HDR-edited VENUS EGFP+ patient fibroblasts. We demonstrated that a highly efficient correction of DMD loss-of-function mutations in patient cells can be achieved by several means of CRISPR gene editing., Recent progress in CRISPR gene editing tools has substantially increased the opportunities for curing devastating genetic diseases. Here we compare in-frame deletion by CRISPR-based non-homologous blunt end joining (NHBEJ), homology-directed repair (HDR), and prime editing (PE, PE2, and PE3)-based correction of two Duchenne Muscular Dystrophy (DMD) loss-of-function mutations (c.5533G>T and c.7893delC). To enable accurate and rapid evaluation of editing efficiency, we generated a genomically integrated synthetic reporter system (VENUS) carrying the DMD mutations. The VENUS contains a modified enhanced green fluorescence protein (EGFP) gene, in which expression was restored upon the CRISPR-mediated correction of DMD loss-of-function mutations. We observed that the highest editing efficiency was achieved by NHBEJ (74–77%), followed by HDR (21–24%) and PE2 (1.5%) in HEK293T VENUS reporter cells. A similar HDR (23%) and PE2 (1.1%) correction efficiency is achieved in fibroblast VENUS cells. With PE3 (PE2 plus nicking gRNA), the c.7893delC correction efficiency was increased 3-fold. Furthermore, an approximately 31% correction efficiency of the endogenous DMD: c.7893delC is achieved in the FACS-enriched HDR-edited VENUS EGFP+ patient fibroblasts. We demonstrated that a highly efficient correction of DMD loss-of-function mutations in patient cells can be achieved by several means of CRISPR gene editing.

Published
2023

22. Supplementary Figure 2 from Temporal Dissection of Tumorigenesis in Primary Cancers

Author

Durinck, Steffen, primary, Ho, Christine, primary, Wang, Nicholas J., primary, Liao, Wilson, primary, Jakkula, Lakshmi R., primary, Collisson, Eric A., primary, Pons, Jennifer, primary, Chan, Sai-Wing, primary, Lam, Ernest T., primary, Chu, Catherine, primary, Park, Kyunghee, primary, Hong, Sung-woo, primary, Hur, Joe S., primary, Huh, Nam, primary, Neuhaus, Isaac M., primary, Yu, Siegrid S., primary, Grekin, Roy C., primary, Mauro, Theodora M., primary, Cleaver, James E., primary, Kwok, Pui-Yan, primary, LeBoit, Philip E., primary, Getz, Gad, primary, Cibulskis, Kristian, primary, Aster, Jon C., primary, Huang, Haiyan, primary, Purdom, Elizabeth, primary, Li, Jian, primary, Bolund, Lars, primary, Arron, Sarah T., primary, Gray, Joe W., primary, Spellman, Paul T., primary, and Cho, Raymond J., primary

Published
2023
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23. Supplementary Figure 4 from Temporal Dissection of Tumorigenesis in Primary Cancers

Author

Durinck, Steffen, primary, Ho, Christine, primary, Wang, Nicholas J., primary, Liao, Wilson, primary, Jakkula, Lakshmi R., primary, Collisson, Eric A., primary, Pons, Jennifer, primary, Chan, Sai-Wing, primary, Lam, Ernest T., primary, Chu, Catherine, primary, Park, Kyunghee, primary, Hong, Sung-woo, primary, Hur, Joe S., primary, Huh, Nam, primary, Neuhaus, Isaac M., primary, Yu, Siegrid S., primary, Grekin, Roy C., primary, Mauro, Theodora M., primary, Cleaver, James E., primary, Kwok, Pui-Yan, primary, LeBoit, Philip E., primary, Getz, Gad, primary, Cibulskis, Kristian, primary, Aster, Jon C., primary, Huang, Haiyan, primary, Purdom, Elizabeth, primary, Li, Jian, primary, Bolund, Lars, primary, Arron, Sarah T., primary, Gray, Joe W., primary, Spellman, Paul T., primary, and Cho, Raymond J., primary

Published
2023
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24. Supplementary Table 2 from Temporal Dissection of Tumorigenesis in Primary Cancers

Author

Durinck, Steffen, primary, Ho, Christine, primary, Wang, Nicholas J., primary, Liao, Wilson, primary, Jakkula, Lakshmi R., primary, Collisson, Eric A., primary, Pons, Jennifer, primary, Chan, Sai-Wing, primary, Lam, Ernest T., primary, Chu, Catherine, primary, Park, Kyunghee, primary, Hong, Sung-woo, primary, Hur, Joe S., primary, Huh, Nam, primary, Neuhaus, Isaac M., primary, Yu, Siegrid S., primary, Grekin, Roy C., primary, Mauro, Theodora M., primary, Cleaver, James E., primary, Kwok, Pui-Yan, primary, LeBoit, Philip E., primary, Getz, Gad, primary, Cibulskis, Kristian, primary, Aster, Jon C., primary, Huang, Haiyan, primary, Purdom, Elizabeth, primary, Li, Jian, primary, Bolund, Lars, primary, Arron, Sarah T., primary, Gray, Joe W., primary, Spellman, Paul T., primary, and Cho, Raymond J., primary

Published
2023
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25. Supplementary Figure 3 from Temporal Dissection of Tumorigenesis in Primary Cancers

Author

Durinck, Steffen, primary, Ho, Christine, primary, Wang, Nicholas J., primary, Liao, Wilson, primary, Jakkula, Lakshmi R., primary, Collisson, Eric A., primary, Pons, Jennifer, primary, Chan, Sai-Wing, primary, Lam, Ernest T., primary, Chu, Catherine, primary, Park, Kyunghee, primary, Hong, Sung-woo, primary, Hur, Joe S., primary, Huh, Nam, primary, Neuhaus, Isaac M., primary, Yu, Siegrid S., primary, Grekin, Roy C., primary, Mauro, Theodora M., primary, Cleaver, James E., primary, Kwok, Pui-Yan, primary, LeBoit, Philip E., primary, Getz, Gad, primary, Cibulskis, Kristian, primary, Aster, Jon C., primary, Huang, Haiyan, primary, Purdom, Elizabeth, primary, Li, Jian, primary, Bolund, Lars, primary, Arron, Sarah T., primary, Gray, Joe W., primary, Spellman, Paul T., primary, and Cho, Raymond J., primary

Published
2023
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26. Supplementary Figure Legends 1-4, Methods from Temporal Dissection of Tumorigenesis in Primary Cancers

Author

Durinck, Steffen, primary, Ho, Christine, primary, Wang, Nicholas J., primary, Liao, Wilson, primary, Jakkula, Lakshmi R., primary, Collisson, Eric A., primary, Pons, Jennifer, primary, Chan, Sai-Wing, primary, Lam, Ernest T., primary, Chu, Catherine, primary, Park, Kyunghee, primary, Hong, Sung-woo, primary, Hur, Joe S., primary, Huh, Nam, primary, Neuhaus, Isaac M., primary, Yu, Siegrid S., primary, Grekin, Roy C., primary, Mauro, Theodora M., primary, Cleaver, James E., primary, Kwok, Pui-Yan, primary, LeBoit, Philip E., primary, Getz, Gad, primary, Cibulskis, Kristian, primary, Aster, Jon C., primary, Huang, Haiyan, primary, Purdom, Elizabeth, primary, Li, Jian, primary, Bolund, Lars, primary, Arron, Sarah T., primary, Gray, Joe W., primary, Spellman, Paul T., primary, and Cho, Raymond J., primary

Published
2023
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27. Data from Temporal Dissection of Tumorigenesis in Primary Cancers

Author

Durinck, Steffen, primary, Ho, Christine, primary, Wang, Nicholas J., primary, Liao, Wilson, primary, Jakkula, Lakshmi R., primary, Collisson, Eric A., primary, Pons, Jennifer, primary, Chan, Sai-Wing, primary, Lam, Ernest T., primary, Chu, Catherine, primary, Park, Kyunghee, primary, Hong, Sung-woo, primary, Hur, Joe S., primary, Huh, Nam, primary, Neuhaus, Isaac M., primary, Yu, Siegrid S., primary, Grekin, Roy C., primary, Mauro, Theodora M., primary, Cleaver, James E., primary, Kwok, Pui-Yan, primary, LeBoit, Philip E., primary, Getz, Gad, primary, Cibulskis, Kristian, primary, Aster, Jon C., primary, Huang, Haiyan, primary, Purdom, Elizabeth, primary, Li, Jian, primary, Bolund, Lars, primary, Arron, Sarah T., primary, Gray, Joe W., primary, Spellman, Paul T., primary, and Cho, Raymond J., primary

Published
2023
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28. Supplementary Table 1 from Temporal Dissection of Tumorigenesis in Primary Cancers

Author

Durinck, Steffen, primary, Ho, Christine, primary, Wang, Nicholas J., primary, Liao, Wilson, primary, Jakkula, Lakshmi R., primary, Collisson, Eric A., primary, Pons, Jennifer, primary, Chan, Sai-Wing, primary, Lam, Ernest T., primary, Chu, Catherine, primary, Park, Kyunghee, primary, Hong, Sung-woo, primary, Hur, Joe S., primary, Huh, Nam, primary, Neuhaus, Isaac M., primary, Yu, Siegrid S., primary, Grekin, Roy C., primary, Mauro, Theodora M., primary, Cleaver, James E., primary, Kwok, Pui-Yan, primary, LeBoit, Philip E., primary, Getz, Gad, primary, Cibulskis, Kristian, primary, Aster, Jon C., primary, Huang, Haiyan, primary, Purdom, Elizabeth, primary, Li, Jian, primary, Bolund, Lars, primary, Arron, Sarah T., primary, Gray, Joe W., primary, Spellman, Paul T., primary, and Cho, Raymond J., primary

Published
2023
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29. Supplementary Figure 1 from Temporal Dissection of Tumorigenesis in Primary Cancers

Author

Durinck, Steffen, primary, Ho, Christine, primary, Wang, Nicholas J., primary, Liao, Wilson, primary, Jakkula, Lakshmi R., primary, Collisson, Eric A., primary, Pons, Jennifer, primary, Chan, Sai-Wing, primary, Lam, Ernest T., primary, Chu, Catherine, primary, Park, Kyunghee, primary, Hong, Sung-woo, primary, Hur, Joe S., primary, Huh, Nam, primary, Neuhaus, Isaac M., primary, Yu, Siegrid S., primary, Grekin, Roy C., primary, Mauro, Theodora M., primary, Cleaver, James E., primary, Kwok, Pui-Yan, primary, LeBoit, Philip E., primary, Getz, Gad, primary, Cibulskis, Kristian, primary, Aster, Jon C., primary, Huang, Haiyan, primary, Purdom, Elizabeth, primary, Li, Jian, primary, Bolund, Lars, primary, Arron, Sarah T., primary, Gray, Joe W., primary, Spellman, Paul T., primary, and Cho, Raymond J., primary

Published
2023
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31. Extrachromosomal Circular DNA Orchestrates Genome Heterogeneity and Outcome in Urothelial Bladder Carcinoma

Author

Lv, Wei, primary, Pan, Xiaoguang, additional, Han, Peng, additional, Wu, Shuang, additional, Zeng, Yuchen, additional, Wang, Qingqing, additional, Guo, Lidong, additional, Xu, Mengyang, additional, Wang, Fei, additional, Xu, Zhe, additional, Li, Yi, additional, Teng, Huajing, additional, Li, Conghui, additional, Qi, Kairu, additional, Gao, Shang, additional, Yu, Tianxi, additional, Cui, Xin, additional, Xiang, Chongjun, additional, Li, Yue, additional, Tan, Haotian, additional, Liang, Ning, additional, Tao, Huiying, additional, Yu, Guohua, additional, Mi, Jia, additional, Xu, Fuyi, additional, Gong, Benjiao, additional, Shi, Lei, additional, Wang, Tao, additional, Bolund, Lars, additional, Yang, Huan-Ming, additional, Wang, Wenting, additional, Li, Hanbo, additional, Huang, Jinrong, additional, Lin, Chunhua, additional, and Luo, Yonglun, additional

Published
2023
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33. Extrachromosomal Circular DNA Orchestrates Genome Heterogeneity In Urothelial Bladder Carcinoma

Author

Lv, Wei, primary, Pan, Xiaoguang, additional, Han, Peng, additional, Wu, Shuang, additional, Zeng, Yuchen, additional, Wang, Qingqing, additional, Guo, Lidong, additional, Xu, Mengyang, additional, Wang, Fei, additional, Qi, Yanwei, additional, Deng, Li, additional, Xu, Zhe, additional, Li, Yi, additional, Teng, Huajing, additional, Li, Conghui, additional, Gao, Shang, additional, Yu, Tianxi, additional, Cui, Xin, additional, Xiang, Chongjun, additional, Tan, Haotian, additional, Li, Yue, additional, Liang, Ning, additional, Tao, Huiying, additional, Yu, Guohua, additional, Mi, Jia, additional, Xu, Fuyi, additional, Gong, Benjiao, additional, Shi, Lei, additional, Wang, Tao, additional, Yang, Huanming, additional, Dong, Wei, additional, Liu, Siqi, additional, Wu, Kui, additional, Bolund, Lars, additional, Lin, Lin, additional, Wang, Wenting, additional, Li, Hanbo, additional, Huang, Jinrong, additional, Lin, Chunhua, additional, and Luo, Yonglun, additional

Published
2023
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34. Author Correction:Endothelial cell heterogeneity and microglia regulons revealed by a pig cell landscape at single-cell level (Nature Communications, (2022), 13, 1, (3620), 10.1038/s41467-022-31388-z)

Author

Wang, Fei, Ding, Peiwen, Liang, Xue, Ding, Xiangning, Brandt, Camilla Blunk, Sjöstedt, Evelina, Zhu, Jiacheng, Bolund, Saga, Zhang, Lijing, de Rooij, Laura P.M.H., Luo, Lihua, Wei, Yanan, Zhao, Wandong, Lv, Zhiyuan, Haskó, János, Li, Runchu, Qin, Qiuyu, Jia, Yi, Wu, Wendi, Yuan, Yuting, Pu, Mingyi, Wang, Haoyu, Wu, Aiping, Xie, Lin, Liu, Ping, Chen, Fang, Herold, Jacqueline, Kalucka, Joanna, Karlsson, Max, Zhang, Xiuqing, Helmig, Rikke Bek, Fagerberg, Linn, Lindskog, Cecilia, Pontén, Fredrik, Uhlen, Mathias, Bolund, Lars, Jessen, Niels, Jiang, Hui, Xu, Xun, Yang, Huanming, Carmeliet, Peter, Mulder, Jan, Chen, Dongsheng, Lin, Lin, and Luo, Yonglun

Published
2022
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39. A genetically modified minipig model for Alzheimer’s disease with SORL1 haploinsufficiency

Author

Andersen, Olav M., primary, Bøgh, Nikolaj, additional, Landau, Anne M., additional, Pløen, Gro G., additional, Jensen, Anne Mette G., additional, Monti, Giulia, additional, Ulhøi, Benedicte P., additional, Nyengaard, Jens R., additional, Jacobsen, Kirsten R., additional, Jørgensen, Margarita M., additional, Holm, Ida E., additional, Kristensen, Marianne L., additional, Alstrup, Aage Kristian O., additional, Hansen, Esben S.S., additional, Teunissen, Charlotte E., additional, Breidenbach, Laura, additional, Droescher, Mathias, additional, Liu, Ying, additional, Pedersen, Hanne S., additional, Callesen, Henrik, additional, Luo, Yonglun, additional, Bolund, Lars, additional, Brooks, David J., additional, Laustsen, Christoffer, additional, Small, Scott A., additional, Mikkelsen, Lars F., additional, and Sørensen, Charlotte B., additional

Published
2022
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40. In vivo evidence that SORL1, encoding the endosomal recycling receptor SORLA, can function as a causal gene in Alzheimer’s Disease

Author

Andersen, Olav Michael, Bøgh, Nikolaj Hvidt, Landau, Anne, Pløen, Gro Grunnet, Jensen, Anne Mette Gissel, Monti, Giulia, Ulhøi, Benedicte Parm, Nyengaard, Jens Randel, Jacobsen, Kirsten Rosenmay, Jørgensen, Margarita Melnikova, Holm, Ida Elisabeth, Kristensen, Marianne Lundsgaard, Alstrup, Aage Kristian Olsen, Søvsø Szocska Hansen, Esben, Teunissen, Charlotte E, Breidenbach, Laura, Droescher, Mathias, Liu, Ying, Pedersen, Hanne Skovsgaard, Callesen, Henrik, Luo, Yonglun, Bolund, Lars, Brooks, David J, Laustsen, Christoffer, Small, Scott A, Mikkelsen, Lars F., and Sørensen, Charlotte Brandt

Published
2022

41. Isolation and whole genome sequencing of fetal cells from maternal blood towards the ultimate non‐invasive prenatal testing

Author

Chen, Fang, Liu, Ping, Gu, Ying, Zhu, Zhu, Nanisetti, Amulya, Lan, Zhangzhang, Huang, Zhiwei, Liu, Jia Sophie, Kang, Xiongbin, Deng, Yuqing, Luo, Liqiong, Jiang, Dan, Qiu, Yong, Pan, Jianchang, Xia, Jun, Xiong, Ken, Liu, Chao, Xie, Lin, Shi, Qianyu, Li, Jing, Zhang, Xiuqing, Wang, Wei, Drmanac, Snezana, Bolund, Lars, Jiang, Hui, Drmanac, Radoje, and Xu, Xun

Published
2017
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45. Single-Cell Exome Sequencing and Monoclonal Evolution of a JAK2-Negative Myeloproliferative Neoplasm

Author

Hou, Yong, Song, Luting, Zhu, Ping, Zhang, Bo, Tao, Ye, Xu, Xun, Li, Fuqiang, Wu, Kui, Liang, Jie, Shao, Di, Wu, Hanjie, Ye, Xiaofei, Ye, Chen, Wu, Renhua, Jian, Min, Chen, Yan, Xie, Wei, Zhang, Ruren, Chen, Lei, Liu, Xin, Yao, Xiaotian, Zheng, Hancheng, Yu, Chang, Li, Qibin, Gong, Zhuolin, Mao, Mao, Yang, Xu, Yang, Lin, Li, Jingxiang, Wang, Wen, Lu, Zuhong, Gu, Ning, Laurie, Goodman, Bolund, Lars, Kristiansen, Karsten, Wang, Jian, Yang, Huanming, Li, Yingrui, Zhang, Xiuqing, and Wang, Jun

Published
2012
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46. Single-Cell Exome Sequencing Reveals Single-Nucleotide Mutation Characteristics of a Kidney Tumor

Author

Xu, Xun, Hou, Yong, Yin, Xuyang, Bao, Li, Tang, Aifa, Song, Luting, Li, Fuqiang, Tsang, Shirley, Wu, Kui, Wu, Hanjie, He, Weiming, Zeng, Liang, Xing, Manjie, Wu, Renhua, Jiang, Hui, Liu, Xiao, Cao, Dandan, Guo, Guangwu, Hu, Xueda, Gui, Yaoting, Li, Zesong, Xie, Wenyue, Sun, Xiaojuan, Shi, Min, Cai, Zhiming, Wang, Bin, Zhong, Meiming, Li, Jingxiang, Lu, Zuhong, Gu, Ning, Zhang, Xiuqing, Goodman, Laurie, Bolund, Lars, Wang, Jian, Yang, Huanming, Kristiansen, Karsten, Dean, Michael, Li, Yingrui, and Wang, Jun

Published
2012
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47. Archaeology Augments Tibet's Genetic History [Response]

Author

BRANTINGHAM, P. JEFFREY, RHODE, DAVID, MADSEN, DAVID B., YI, XIN, LIANG, YU, HUERTA-SANCHEZ, EMILIA, JIN, XIN, CUO, ZHA XI PING, POOL, JOHN E., XU, XUN, JIANG, HUI, VINCKENBOSCH, NICOLAS, KORNELIUSSEN, THORFINN SAND, ZHENG, HANCHENG, LIU, TAO, HE, WEIMING, LI, KUI, LUO, RUIBANG, NIE, XIFANG, WU, HONGLONG, ZHAO, MEIRU, CAO, HONGZHI, ZOU, JING, SHAN, YING, LI, SHUZHENG, YANG, QI, ASAN, NI, PEIXIANG, TIAN, GENG, XU, JUNMING, LIU, XIAO, JIANG, TAO, WU, RENHUA, ZHOU, GUANGYU, TANG, MEIFANG, QIN, JUNJIE, WANG, TONG, FENG, SHUIJIAN, LI, GUOHONG, LUOSANG, JIANGBAI, WANG, WEI, CHEN, FANG, WANG, YADING, ZHENG, XIAOGUANG, LI, ZHUO, BIANBA, ZHUOMA, YANG, GE, WANG, XINPING, TANG, SHUHUI, GAO, GUOYI, CHEN, YONG, LUO, ZHEN, GUSANG, LAMU, CAO, ZHENG, ZHANG, QINGHUI, OUYANG, WEIHAN, REN, XIAOLI, LIANG, HUIQING, ZHENG, HUISONG, HUANG, YEBO, LI, JINGXIANG, BOLUND, LARS, KRISTIANSEN, KARSTEN, LI, YINGRUI, ZHANG, YONG, ZHANG, XIUQING, LI, RUIQIANG, LI, SONGGANG, YANG, HUANMING, NIELSEN, RASMUS, WANG, JUN, and WANG, JIAN

Published
2010

48. Sequencing of 50 Human Exomes Reveals Adaptation to High Altitude

Author

Yi, Xin, Liang, Yu, Huerta-Sanchez, Emilia, Jin, Xin, Cuo, Zha Xi Ping, Pool, John E., Xu, Xun, Jiang, Hui, Vinckenbosch, Nicolas, Korneliussen, Thorfinn Sand, Zheng, Hancheng, Liu, Tao, He, Weiming, Li, Kui, Luo, Ruibang, Nie, Xifang, Wu, Honglong, Zhao, Meiru, Cao, Hongzhi, Zou, Jing, Shan, Ying, Li, Shuzheng, Yang, Qi, Asan, Ni, Peixiang, Tian, Geng, Xu, Junming, Liu, Xiao, Jiang, Tao, Wu, Renhua, Zhou, Guangyu, Tang, Meifang, Qin, Junjie, Wang, Tong, Feng, Shuijian, Li, Guohong, Huasang, Luosang, Jiangbai, Wang, Wei, Chen, Fang, Wang, Yading, Zheng, Xiaoguang, Li, Zhuo, Bianba, Zhuoma, Yang, Ge, Wang, Xinping, Tang, Shuhui, Gao, Guoyi, Chen, Yong, Luo, Zhen, Gusang, Lamu, Cao, Zheng, Zhang, Qinghui, Ouyang, Weihan, Ren, Xiaoli, Liang, Huiqing, Zheng, Huisong, Huang, Yebo, Li, Jingxiang, Bolund, Lars, Kristiansen, Karsten, Li, Yingrui, Zhang, Yong, Zhang, Xiuqing, Li, Ruiqiang, Li, Songgang, Yang, Huanming, Nielsen, Rasmus, Wang, Jun, and Wang, Jian

Published
2010

49. Circle-Seq reveals genomic and disease-specific hallmarks in urinary cell-free extrachromosomal circular DNAs

Author

Lv, Wei, Pan, Xiaoguang, Han, Peng, Wang, Ziyu, Feng, Weijia, Xing, Xue, Wang, Qingqing, Qu, Kunli, Zeng, Yuchen, Zhang, Cailin, Xu, Zhe, Li, Yi, Zheng, Tianyu, Lin, Ling, Liu, Chengxun, Liu, Xuemei, Li, Hanbo, Henriksen, Rasmus Amund, Bolund, Lars, Lin, Lin, Jin, Xin, Yang, Huanming, Zhang, Xiuqing, Yin, Tailang, Regenberg, Birgitte, He, Fan, Luo, Yonglun, Lv, Wei, Pan, Xiaoguang, Han, Peng, Wang, Ziyu, Feng, Weijia, Xing, Xue, Wang, Qingqing, Qu, Kunli, Zeng, Yuchen, Zhang, Cailin, Xu, Zhe, Li, Yi, Zheng, Tianyu, Lin, Ling, Liu, Chengxun, Liu, Xuemei, Li, Hanbo, Henriksen, Rasmus Amund, Bolund, Lars, Lin, Lin, Jin, Xin, Yang, Huanming, Zhang, Xiuqing, Yin, Tailang, Regenberg, Birgitte, He, Fan, and Luo, Yonglun

Abstract

BACKGROUND: Extrachromosomal circular deoxyribonucleic acid (eccDNA) is evolving as a valuable biomarker, while little is known about its presence in urine.METHODS: Here, we report the discovery and analysis of urinary cell-free eccDNAs (ucf-eccDNAs) in healthy controls and patients with advanced chronic kidney disease (CKD) by Circle-Seq.RESULTS: Millions of unique ucf-eccDNAs were identified and comprehensively characterised. The ucf-eccDNAs are GC-rich. Most ucf-eccDNAs are less than 1000 bp and are enriched in four pronounced peaks at 207, 358, 553 and 732 bp. Analysis of the genomic distribution of ucf-eccDNAs shows that eccDNAs are found on all chromosomes but enriched on chromosomes 17, 19 and 20 with a high density of protein-coding genes, CpG islands, short interspersed transposable elements (SINEs) and simple repeat elements. Analysis of eccDNA junction sequences further suggests that microhomology and palindromic repeats might be involved in eccDNA formation. The ucf-eccDNAs in CKD patients are significantly higher than those in healthy controls. Moreover, eccDNA with miRNA genes is highly enriched in CKD ucf-eccDNA.CONCLUSIONS: This work discovers and provides the first deep characterisation of ucf-eccDNAs and suggests ucf-eccDNA as a valuable noninnvasive biomarker for urogenital disorder diagnosis and monitoring.

Published
2022

50. State of the art de novo assembly of human genomes from massively parallel sequencing data

Author

Li Yingrui, Hu Yujie, Bolund Lars, and Wang Jun

Subjects
de novo assembly, de Bruijn graph, massively parallel sequencing, Medicine, Genetics, QH426-470
Abstract

Abstract Recent studies in human genomes have demonstrated the use of de novo assemblies to identify genetic variations that are difficult for mapping-based approaches. Construction of multiple human genome assemblies is enabled by massively parallel sequencing, but a conventional bioinformatics solution is costly and slow, creating bottle-necks in the process. This review describes two public short-read de novo assembly applications that can handle human genomes, ABySS and SOAPdenovo. It also discusses the technical aspects and future challenges of human genome de novo assembly by short reads.

Published
2010
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