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1. The RNA binding protein EHD6 recruits the m6A reader YTH07 and sequesters OsCOL4 mRNA into phase-separated ribonucleoprotein condensates to promote rice flowering

Author

Cui, Song, Song, Peizhe, Wang, Chaolong, Chen, Saihua, Hao, Benyuan, Xu, Zhuang, Cai, Liang, Chen, Xu, Zhu, Shanshan, Gan, Xiangchao, Dong, Hui, Hu, Yuan, Zhou, Liang, Hou, Haigang, Tian, Yunlu, Liu, Xi, Chen, Liangming, Liu, Shijia, Jiang, Ling, Wang, Haiyang, Jia, Guifang, Zhou, Shirong, and Wan, Jianmin

Published
2024
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3. Corrigendum

Author

Akiyama, Reiko, Briskine, Roman V., Gan, Xiangchao, Hatakeyama, Masaomi, Kudoh, Hiroshi, Lischer, Heidi E. L., Sese, Jun, Shimizu, Kentaro K., Shimizu-Inatsugi, Rie, and Sun, Jianqiang

Published
2021

11. Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions

Author

Alonso-Blanco, Carlos, Andrade, Jorge, Becker, Claude, Bemm, Felix, Bergelson, Joy, Borgwardt, Karsten, Chae, Eunyoung, Dezwaan, Todd, Ding, Wei, Ecker, Joseph R., Expósito-Alonso, Moisés, Farlow, Ashley, Fitz, Joffrey, Gan, Xiangchao, Grimm, Dominik G., Hancock, Angela, Henz, Stefan R., Holm, Svante, Horton, Matthew, Jarsulic, Mike, Kerstetter, Randall A., Korte, Arthur, Korte, Pamela, Lanz, Christa, Lee, Chen-Ruei, Meng, Dazhe, Michael, Todd P., Mott, Richard, Muliyati, Ni Wayan, Nägele, Thomas, Nagler, Matthias, Nizhynska, Viktoria, Nordborg, Magnus, Novikova, Polina, Picó, F. Xavier, Platzer, Alexander, Rabanal, Fernando A., Rodriguez, Alex, Rowan, Beth A., Salomé, Patrice A., Schmid, Karl, Schmitz, Robert J., Seren, Ümit, Sperone, Felice Gianluca, Sudkamp, Mitchell, Svardal, Hannes, Tanzer, Matt M., Todd, Donald, Volchenboum, Samuel L., Wang, Congmao, Wang, George, Wang, Xi, Weckwerth, Wolfram, Weigel, Detlef, Zhou, Xuefeng, Kawakatsu, Taiji, Huang, Shao-shan Carol, Jupe, Florian, Sasaki, Eriko, Urich, Mark A., Castanon, Rosa, Nery, Joseph R., Barragan, Cesar, He, Yupeng, Chen, Huaming, Dubin, Manu, Lee, Cheng-Ruei, O’Neil, Ryan, O’Malley, Ronan C., Quarless, Danjuma X., and Schork, Nicholas J.

Published
2016
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12. 1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana

Author

Alonso-Blanco, Carlos, Andrade, Jorge, Becker, Claude, Bemm, Felix, Bergelson, Joy, Borgwardt, Karsten M., Cao, Jun, Chae, Eunyoung, Dezwaan, Todd M., Ding, Wei, Ecker, Joseph R., Exposito-Alonso, Moises, Farlow, Ashley, Fitz, Joffrey, Gan, Xiangchao, Grimm, Dominik G., Hancock, Angela M., Henz, Stefan R., Holm, Svante, Horton, Matthew, Jarsulic, Mike, Kerstetter, Randall A., Korte, Arthur, Korte, Pamela, Lanz, Christa, Lee, Cheng-Ruei, Meng, Dazhe, Michael, Todd P., Mott, Richard, Muliyati, Ni Wayan, Nägele, Thomas, Nagler, Matthias, Nizhynska, Viktoria, Nordborg, Magnus, Novikova, Polina Yu., Picó, F. Xavier, Platzer, Alexander, Rabanal, Fernando A., Rodriguez, Alex, Rowan, Beth A., Salomé, Patrice A., Schmid, Karl J., Schmitz, Robert J., Seren, Ümit, Sperone, Felice Gianluca, Sudkamp, Mitchell, Svardal, Hannes, Tanzer, Matt M., Todd, Donald, Volchenboum, Samuel L., Wang, Congmao, Wang, George, Wang, Xi, Weckwerth, Wolfram, Weigel, Detlef, and Zhou, Xuefeng

Published
2016
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13. Morphomechanical Innovation Drives Explosive Seed Dispersal

Author

Hofhuis, Hugo, Moulton, Derek, Lessinnes, Thomas, Routier-Kierzkowska, Anne-Lise, Bomphrey, Richard J., Mosca, Gabriella, Reinhardt, Hagen, Sarchet, Penny, Gan, Xiangchao, Tsiantis, Miltos, Ventikos, Yiannis, Walker, Simon, Goriely, Alain, Smith, Richard, and Hay, Angela

Published
2016
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14. Molecular signatures of major depression

Author

Cai, Na, Chang, Simon, Li, Yihan, Li, Qibin, Hu, Jingchu, Liang, Jieqin, Song, Li, Kretzschmar, Warren, Gan, Xiangchao, Nicod, Jerome, Rivera, Margarita, Deng, Hong, Du, Bo, Li, Keqing, Sang, Wenhu, Gao, Jingfang, Gao, Shugui, Ha, Baowei, Ho, Hung-Yao, Hu, Chunmei, Hu, Jian, Hu, Zhenfei, Huang, Guoping, Jiang, Guoqing, Jiang, Tao, Jin, Wei, Li, Gongying, Li, Kan, Li, Yi, Li, Yingrui, Li, Youhui, Lin, Yu-Ting, Liu, Lanfen, Liu, Tiebang, Liu, Ying, Liu, Yuan, Lu, Yao, Lv, Luxian, Meng, Huaqing, Qian, Puyi, Sang, Hong, Shen, Jianhua, Shi, Jianguo, Sun, Jing, Tao, Ming, Wang, Gang, Wang, Guangbiao, Wang, Jian, Wang, Linmao, Wang, Xueyi, Wang, Xumei, Yang, Huanming, Yang, Lijun, Yin, Ye, Zhang, Jinbei, Zhang, Kerang, Sun, Ning, Zhang, Wei, Zhang, Xiuqing, Zhang, Zhen, Zhong, Hui, Breen, Gerome, Wang, Jun, Marchini, Jonathan, Chen, Yiping, Xu, Qi, Mott, Richard, Huang, Guo-Jen, Xu, Xun, Kendler, Kenneth, and Flint, Jonathan

Published
2015
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18. The Cardamine hirsuta genome offers insight into the evolution of morphological diversity

Author

Gan, Xiangchao, Hay, Angela, Kwantes, Michiel, Haberer, Georg, Hallab, Asis, Ioio, Raffaele Dello, Hofhuis, Hugo, Pieper, Bjorn, Cartolano, Maria, Neumann, Ulla, Nikolov, Lachezar A., Song, Baoxing, Hajheidari, Mohsen, Briskine, Roman, Kougioumoutzi, Evangelia, Vlad, Daniela, Broholm, Suvi, Hein, Jotun, Meksem, Khalid, Lightfoot, David, Shimizu, Kentaro K., Shimizu-Inatsugi, Rie, Imprialou, Martha, Kudrna, David, Wing, Rod, Sato, Shusei, Huijser, Peter, Filatov, Dmitry, Mayer, Klaus F. X., Mott, Richard, and Tsiantis, Miltos

Published
2016
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19. Sparse whole-genome sequencing identifies two loci for major depressive disorder

Author

Cai, Na, Bigdeli, Tim B., Kretzschmar, Warren, Li, Yihan, Liang, Jieqin, Song, Li, Hu, Jingchu, Li, Qibin, Jin, Wei, Hu, Zhenfei, Wang, Guangbiao, Wang, Linmao, Qian, Puyi, Liu, Yuan, Jiang, Tao, Lu, Yao, Zhang, Xiuqing, Yin, Ye, Li, Yingrui, Xu, Xun, Gao, Jingfang, Reimers, Mark, Webb, Todd, Riley, Brien, Bacanu, Silviu, Peterson, Roseann E., Chen, Yiping, Zhong, Hui, Liu, Zhengrong, Wang, Gang, Sun, Jing, Sang, Hong, Jiang, Guoqing, Zhou, Xiaoyan, Li, Yi, Zhang, Wei, Wang, Xueyi, Fang, Xiang, Pan, Runde, Miao, Guodong, Zhang, Qiwen, Hu, Jian, Yu, Fengyu, Du, Bo, Sang, Wenhua, Li, Keqing, Chen, Guibing, Cai, Min, Yang, Lijun, Yang, Donglin, Ha, Baowei, Hong, Xiaohong, Deng, Hong, Li, Gongying, Li, Kan, Song, Yan, Gao, Shugui, Zhang, Jinbei, Gan, Zhaoyu, Meng, Huaqing, Pan, Jiyang, Gao, Chengge, Zhang, Kerang, Sun, Ning, Li, Youhui, Niu, Qihui, Zhang, Yutang, Liu, Tieqiao, Hu, Chunmei, Zhang, Zhen, Lv, Luxian, Dong, Jicheng, Wang, Xiaoping, Tao, Ming, Wang, Xumei, Xia, Jing, Rong, Han, He, Qiang, Liu, Tiebang, Huang, Guoping, Mei, Qiyi, Shen, Zhenming, Liu, Ying, Shen, Jianhua, Tian, Tian, Liu, Xiaojuan, Wu, Wenyuan, Gu, Danhua, Fu, Guangyi, Shi, Jianguo, Chen, Yunchun, Gan, Xiangchao, Liu, Lanfen, Wang, Lina, Yang, Fuzhong, Cong, Enzhao, Marchini, Jonathan, Yang, Huanming, Wang, Jian, Shi, Shenxun, Mott, Richard, Xu, Qi, Wang, Jun, Kendler, Kenneth S., and Flint, Jonathan

Published
2015
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20. Cardamine hirsuta: a versatile genetic system for comparative studies

Author

Hay, Angela S., Pieper, Bjorn, Cooke, Elizabeth, Mandáková, Terezie, Cartolano, Maria, Tattersall, Alexander D., Ioio, Raffaele D., McGowan, Simon J., Barkoulas, Michalis, Galinha, Carla, Rast, Madlen I., Hofhuis, Hugo, Then, Christiane, Plieske, Jörg, Ganal, Martin, Mott, Richard, Martinez-Garcia, Jaime F., Carine, Mark A., Scotland, Robert W., Gan, Xiangchao, Filatov, Dmitry A., Lysak, Martin A., and Tsiantis, Miltos

Published
2014
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22. Multiple reference genomes and transcriptomes for Arabidopsis thaliana

Author

Gan, Xiangchao, Stegle, Oliver, Behr, Jonas, Steffen, Joshua G., Drewe, Philipp, Hildebrand, Katie L., Lyngsoe, Rune, Schultheiss, Sebastian J., Osborne, Edward J., Sreedharan, Vipin T., Kahles, André, Bohnert, Regina, Jean, Géraldine, Derwent, Paul, Kersey, Paul, Belfield, Eric J., Harberd, Nicholas P., Kemen, Eric, Toomajian, Christopher, Kover, Paula X., Clark, Richard M., Rätsch, Gunnar, and Mott, Richard

Published
2011
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24. Mouse genomic variation and its effect on phenotypes and gene regulation

Author

Keane, Thomas M., Goodstadt, Leo, Danecek, Petr, White, Michael A., Wong, Kim, Yalcin, Binnaz, Heger, Andreas, Agam, Avigail, Slater, Guy, Goodson, Martin, Furlotte, Nicholas A., Eskin, Eleazar, Nellåker, Christoffer, Whitley, Helen, Cleak, James, Janowitz, Deborah, Hernandez-Pliego, Polinka, Edwards, Andrew, Belgard, Grant T., Oliver, Peter L., McIntyre, Rebecca E., Bhomra, Amarjit, Nicod, Jérôme, Gan, Xiangchao, Yuan, Wei, van der Weyden, Louise, Steward, Charles A., Bala, Sendu, Stalker, Jim, Mott, Richard, Durbin, Richard, Jackson, Ian J., Czechanski, Anne, Guerra-Assunção, José Afonso, Donahue, Leah Rae, Reinholdt, Laura G., Payseur, Bret A., Ponting, Chris P., Birney, Ewan, Flint, Jonathan, and Adams, David J.

Published
2011
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28. Gene expression evolution in pattern-triggered immunity within Arabidopsis thaliana and across Brassicaceae species.

Author

Winkelmüller, Thomas M, Entila, Frederickson, Anver, Shajahan, Piasecka, Anna, Song, Baoxing, Dahms, Eik, Sakakibara, Hitoshi, Gan, Xiangchao, Kułak, Karolina, Sawikowska, Aneta, Krajewski, Paweł, Tsiantis, Miltos, Garrido-Oter, Ruben, Fukushima, Kenji, Schulze-Lefert, Paul, Laurent, Stefan, Bednarek, Paweł, and Tsuda, Kenichi

Published
2021
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29. Discovering biclusters in gene expression data based on high-dimensional linear geometries

Author

Liew Alan, Gan Xiangchao, and Yan Hong

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract

Abstract Background In DNA microarray experiments, discovering groups of genes that share similar transcriptional characteristics is instrumental in functional annotation, tissue classification and motif identification. However, in many situations a subset of genes only exhibits consistent pattern over a subset of conditions. Conventional clustering algorithms that deal with the entire row or column in an expression matrix would therefore fail to detect these useful patterns in the data. Recently, biclustering has been proposed to detect a subset of genes exhibiting consistent pattern over a subset of conditions. However, most existing biclustering algorithms are based on searching for sub-matrices within a data matrix by optimizing certain heuristically defined merit functions. Moreover, most of these algorithms can only detect a restricted set of bicluster patterns. Results In this paper, we present a novel geometric perspective for the biclustering problem. The biclustering process is interpreted as the detection of linear geometries in a high dimensional data space. Such a new perspective views biclusters with different patterns as hyperplanes in a high dimensional space, and allows us to handle different types of linear patterns simultaneously by matching a specific set of linear geometries. This geometric viewpoint also inspires us to propose a generic bicluster pattern, i.e. the linear coherent model that unifies the seemingly incompatible additive and multiplicative bicluster models. As a particular realization of our framework, we have implemented a Hough transform-based hyperplane detection algorithm. The experimental results on human lymphoma gene expression dataset show that our algorithm can find biologically significant subsets of genes. Conclusion We have proposed a novel geometric interpretation of the biclustering problem. We have shown that many common types of bicluster are just different spatial arrangements of hyperplanes in a high dimensional data space. An implementation of the geometric framework using the Fast Hough transform for hyperplane detection can be used to discover biologically significant subsets of genes under subsets of conditions for microarray data analysis.

Published
2008
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30. Complement Genome Annotation Lift Over Using a Weighted Sequence Alignment Strategy.

Author

Song, Baoxing, Sang, Qing, Wang, Hai, Pei, Huimin, Gan, XiangChao, and Wang, Fen

Subjects
GENOMES, POPULATION genetics, GENE expression, SEQUENCE alignment, HAPLOTYPES, ANNOTATIONS, DYNAMIC programming
Abstract

With the broad application of high-throughput sequencing, more whole-genome resequencing data and de novo assemblies of natural populations are becoming available. For a particular species, in general, only the reference genome is well established and annotated. Computational tools based on sequence alignment have been developed to investigate the gene models of individuals belonging to the same or closely related species. During this process, inconsistent alignment often obscures genome annotation lift over and leads to improper functional impact prediction for a genomic variant, especially in plant species. Here, we proposed the zebraic striped dynamic programming algorithm, which provides different weights to genetic features to refine genome annotation lift over. Testing of our zebraic striped dynamic programming algorithm on both plant and animal genomic data showed complementation to standard sequence approach for highly diverse individuals. Using the lift over genome annotation as anchors, a base-pair resolution genome-wide sequence alignment and variant calling pipeline for de novo assembly has been implemented in the GEAN software. GEAN could be used to compare haplotype diversity, refine the genetic variant functional annotation, annotate de novo assembly genome sequence, detect homologous syntenic blocks, improve the quantification of gene expression levels using RNA-seq data, and unify genomic variants for population genetic analysis. We expect that GEAN will be a standard tool for the coming of age of de novo assembly population genetics. [ABSTRACT FROM AUTHOR]

Published
2019
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31. Recovery of novel association loci in Arabidopsis thaliana and Drosophila melanogaster through leveraging INDELs association and integrated burden test.

Author

Song, Baoxing, Mott, Richard, and Gan, Xiangchao

Subjects
DROSOPHILA melanogaster, INSERTION mutation, GENETIC testing, ARABIDOPSIS thaliana, SINGLE nucleotide polymorphisms
Abstract

Short insertions, deletions (INDELs) and larger structural variants have been increasingly employed in genetic association studies, but few improvements over SNP-based association have been reported. In order to understand why this might be the case, we analysed two publicly available datasets and observed that 63% of INDELs called in A. thaliana and 64% in D. melanogaster populations are misrepresented as multiple alleles with different functional annotations, i.e. where the same underlying variant is represented by inconsistent alignments leading to different variant calls. To address this issue, we have developed the software Irisas to reclassify and re-annotate these variants, which we then used for single-locus tests of association. We also integrated them to predict the functional impact of SNPs, INDELs, and structural variants for burden testing. Using both approaches, we re-analysed the genetic architecture of complex traits in A. thaliana and D. melanogaster. Heritability analysis using SNPs alone explained on average 27% and 19% of phenotypic variance for A. thaliana and D. melanogaster respectively. Our method explained an additional 11% and 3%, respectively. We also identified novel trait loci that previous SNP-based association studies failed to map, and which contain established candidate genes. Our study shows the value of the association test with INDELs and integrating multiple types of variants in association studies in plants and animals. [ABSTRACT FROM AUTHOR]

Published
2018
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32. Microarray-based ultra-high resolution discovery of genomic deletion mutations.

Author

Belfield, Eric J., Brown, Carly, Gan, Xiangchao, Jiang, Caifu, Baban, Dilair, Mithani, Aziz, Mott, Richard, Ragoussis, Jiannis, and Harberd, Nicholas P.

Abstract

Background: Oligonucleotide microarray-based comparative genomic hybridization (CGH) offers an attractive possible route for the rapid and cost-effective genome-wide discovery of deletion mutations. CGH typically involves comparison of the hybridization intensities of genomic DNA samples with microarray chip representations of entire genomes, and has widespread potential application in experimental research and medical diagnostics. However, the power to detect small deletions is low. Results: Here we use a graduated series of Arabidopsis thaliana genomic deletion mutations (of sizes ranging from 4 bp to ~5 kb) to optimize CGH-based genomic deletion detection. We show that the power to detect smaller deletions (4, 28 and 104 bp) depends upon oligonucleotide density (essentially the number of genomerepresentative oligonucleotides on the microarray chip), and determine the oligonucleotide spacings necessary to guarantee detection of deletions of specified size. Conclusions: Our findings will enhance a wide range of research and clinical applications, and in particular will aid in the discovery of genomic deletions in the absence of a priori knowledge of their existence. [ABSTRACT FROM AUTHOR]

Published
2014
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33. Commercially Available Outbred Mice for Genome-Wide Association Studies

Author

Yalcin, Binnaz, Nicod, Jérôme, Bhomra, Amarjit, Davidson, Stuart, Cleak, James, Farinelli, Laurent, Østerås, Magne, Whitley, Adam, Yuan, Wei, Gan, Xiangchao, Goodson, Martin, Klenerman, Paul, Satpathy, Ansu, Mott, Richard, Flint, Jonathan, Mathis, Diane J., Benoist, Christophe O., and Adams, David J.

Abstract

Genome-wide association studies using commercially available outbred mice can detect genes involved in phenotypes of biomedical interest. Useful populations need high-frequency alleles to ensure high power to detect quantitative trait loci (QTLs), low linkage disequilibrium between markers to obtain accurate mapping resolution, and an absence of population structure to prevent false positive associations. We surveyed 66 colonies for inbreeding, genetic diversity, and linkage disequilibrium, and we demonstrate that some have haplotype blocks of less than 100 Kb, enabling gene-level mapping resolution. The same alleles contribute to variation in different colonies, so that when mapping progress stalls in one, another can be used in its stead. Colonies are genetically diverse: 45% of the total genetic variation is attributable to differences between colonies. However, quantitative differences in allele frequencies, rather than the existence of private alleles, are responsible for these population differences. The colonies derive from a limited pool of ancestral haplotypes resembling those found in inbred strains: over 95% of sequence variants segregating in outbred populations are found in inbred strains. Consequently it is possible to impute the sequence of any mouse from a dense SNP map combined with inbred strain sequence data, which opens up the possibility of cataloguing and testing all variants for association, a situation that has so far eluded studies in completely outbred populations. We demonstrate the colonies' potential by identifying a deletion in the promoter of H2-Ea as the molecular change that strongly contributes to setting the ratio of CD4+ and CD8+ lymphocytes.

Published
2010
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34. Regenerant Arabidopsis Lineages Display a Distinct Genome-Wide Spectrum of Mutations Conferring Variant Phenotypes

Author

Jiang, Caifu, Mithani, Aziz, Gan, Xiangchao, Belfield, Eric J., Klingler, John P., Zhu, Jian-Kang, Ragoussis, Jiannis, Mott, Richard, and Harberd, Nicholas P.

Subjects
*ARABIDOPSIS, *GENOMES, *GENETIC mutation, *PHENOTYPES, *REGENERATION (Biology), *SOMATIC cells, *GENE expression, *NUCLEOTIDE sequence
Abstract

Summary: Multicellular organisms can be regenerated from totipotent differentiated somatic cell or nuclear founders []. Organisms regenerated from clonally related isogenic founders might a priori have been expected to be phenotypically invariant. However, clonal regenerant animals display variant phenotypes caused by defective epigenetic reprogramming of gene expression [], and clonal regenerant plants exhibit poorly understood heritable phenotypic (“somaclonal”) variation []. Here we show that somaclonal variation in regenerant Arabidopsis lineages is associated with genome-wide elevation in DNA sequence mutation rate. We also show that regenerant mutations comprise a distinctive molecular spectrum of base substitutions, insertions, and deletions that probably results from decreased DNA repair fidelity. Finally, we show that while regenerant base substitutions are a likely major genetic cause of the somaclonal variation of regenerant Arabidopsis lineages, transposon movement is unlikely to contribute substantially to that variation. We conclude that the phenotypic variation of regenerant plants, unlike that of regenerant animals, is substantially due to DNA sequence mutation. [ABSTRACT FROM AUTHOR]

Published
2011
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