Efficient and unique cobarcoding of second-generation sequencing reads from long DNA molecules enabling cost-effective and accurate sequencing, haplotyping, and de novo assembly
Wang, Ou, Chin, Robert, Cheng, Xiaofang, Wu, Michelle Ka Yan, Mao, Qing, Tang, Jingbo, Sun, Yuhui, Anderson, Ellis, Lam, Han K, Chen, Dan, Zhou, Yujun, Wang, Linying, Fan, Fei, Zou, Yan, Xie, Yinlong, Zhang, Rebecca Yu, Drmanac, Snezana, Nguyen, Darlene, Xu, Chongjun, Villarosa, Christian, Gablenz, Scott, Barua, Nina, Nguyen, Staci, Tian, Wenlan, Liu, Jia Sophie, Wang, Jingwan, Liu, Xiao, Qi, Xiaojuan, Chen, Ao, Wang, He, Dong, Yuliang, Zhang, Wenwei, Alexeev, Andrei, Yang, Huanming, Wang, Jian, Kristiansen, Karsten, Xu, Xun, Drmanac, Radoje, Peters, Brock A
Published in Genome research (01.05.2019)
Published in Genome research (01.05.2019)
Get full text
Journal Article
SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler
Luo, Ruibang, Liu, Binghang, Xie, Yinlong, Li, Zhenyu, Huang, Weihua, Yuan, Jianying, He, Guangzhu, Chen, Yanxiang, Pan, Qi, Liu, Yunjie, Tang, Jingbo, Wu, Gengxiong, Zhang, Hao, Shi, Yujian, Liu, Yong, Yu, Chang, Wang, Bo, Lu, Yao, Han, Changlei, Cheung, David W, Yiu, Siu-Ming, Peng, Shaoliang, Xiaoqian, Zhu, Liu, Guangming, Liao, Xiangke, Li, Yingrui, Yang, Huanming, Wang, Jian, Lam, Tak-Wah, Wang, Jun
Published in Gigascience (27.12.2012)
Published in Gigascience (27.12.2012)
Get full text
Journal Article
COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly
BINGHANG LIU, JIANYING YUAN, RUIBANG LUO, YIU, Siu-Ming, ZHENYU LI, YINLONG XIE, YANXIANG CHEN, YUJIAN SHI, HAO ZHANG, YINGRUI LI, LAM, Tak-Wah
Published in Bioinformatics (15.11.2012)
Published in Bioinformatics (15.11.2012)
Get full text
Journal Article
IterCluster: a barcode clustering algorithm for long fragment read analysis
Weng, Jiancong, Chen, Tian, Xie, Yinlong, Xu, Xun, Zhang, Gengyun, Peters, Brock A, Drmanac, Radoje
Published in PeerJ (San Francisco, CA) (24.03.2020)
Published in PeerJ (San Francisco, CA) (24.03.2020)
Get full text
Journal Article
An efficient large‐scale whole‐genome sequencing analyses practice with an average daily analysis of 100Tbp: ZBOLT
Li, Zhichao, Xie, Yinlong, Zeng, Wenjun, Huang, Yushan, Gu, Shengchang, Gao, Ya, Huang, Weihua, Lu, Lihua, Wang, Xiaohong, Wu, Jiasheng, Yin, Xiaoxu, Zhu, Rongyi, Huang, Guodong, Lu, Lin, Tang, Jingbo, Zheng, Yunping, Liu, Quan, Zhou, Xianqiang, Shan, Riqiang, Wang, Bo, Fang, Mingyan, Jin, Xin
Published in Clinical and translational discovery (01.12.2023)
Published in Clinical and translational discovery (01.12.2023)
Get full text
Journal Article
SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads
Xie, Yinlong, Wu, Gengxiong, Tang, Jingbo, Luo, Ruibang, Patterson, Jordan, Liu, Shanlin, Huang, Weihua, He, Guangzhu, Gu, Shengchang, Li, Shengkang, Zhou, Xin, Lam, Tak-Wah, Li, Yingrui, Xu, Xun, Wong, Gane Ka-Shu, Wang, Jun
Published in Bioinformatics (Oxford, England) (15.06.2014)
Published in Bioinformatics (Oxford, England) (15.06.2014)
Get full text
Journal Article
Independent optical excitation of distinct neural populations
Klapoetke, Nathan C, Murata, Yasunobu, Kim, Sung Soo, Pulver, Stefan R, Birdsey-Benson, Amanda, Cho, Yong Ku, Morimoto, Tania K, Chuong, Amy S, Carpenter, Eric J, Tian, Zhijian, Wang, Jun, Xie, Yinlong, Yan, Zhixiang, Zhang, Yong, Chow, Brian Y, Surek, Barbara, Melkonian, Michael, Jayaraman, Vivek, Constantine-Paton, Martha, Wong, Gane Ka-Shu, Boyden, Edward S
Published in Nature methods (01.03.2014)
Published in Nature methods (01.03.2014)
Get full text
Journal Article
Phylogenomics resolves the timing and pattern of insect evolution
Misof, Bernhard, Liu, Shanlin, Meusemann, Karen, Peters, Ralph S., Donath, Alexander, Mayer, Christoph, Frandsen, Paul B., Ware, Jessica, Flouri, Tomáš, Beutel, Rolf G., Niehuis, Oliver, Petersen, Malte, Izquierdo-Carrasco, Fernando, Wappler, Torsten, Rust, Jes, Aberer, Andre J., Aspöck, Ulrike, Aspöck, Horst, Bartel, Daniela, Blanke, Alexander, Berger, Simon, Böhm, Alexander, Buckley, Thomas R., Calcott, Brett, Chen, Junqing, Friedrich, Frank, Fukui, Makiko, Fujita, Mari, Greve, Carola, Grobe, Peter, Gu, Shengchang, Huang, Ying, Jermiin, Lars S., Kawahara, Akito Y., Krogmann, Lars, Kubiak, Martin, Lanfear, Robert, Letsch, Harald, Li, Yiyuan, Li, Zhenyu, Li, Jiguang, Lu, Haorong, Machida, Ryuichiro, Mashimo, Yuta, Kapli, Pashalia, McKenna, Duane D., Meng, Guanliang, Nakagaki, Yasutaka, Navarrete-Heredia, José Luis, Ott, Michael, Ou, Yanxiang, Pass, Günther, Podsiadlowski, Lars, Pohl, Hans, von Reumont, Björn M., Schütte, Kai, Sekiya, Kaoru, Shimizu, Shota, Slipinski, Adam, Stamatakis, Alexandros, Song, Wenhui, Su, Xu, Szucsich, Nikolaus U., Tan, Meihua, Tan, Xuemei, Tang, Min, Tang, Jingbo, Timelthaler, Gerald, Tomizuka, Shigekazu, Trautwein, Michelle, Tong, Xiaoli, Uchifune, Toshiki, Walzl, Manfred G., Wiegmann, Brian M., Wilbrandt, Jeanne, Wipfler, Benjamin, Wong, Thomas K. F., Wu, Gengxiong, Xie, Yinlong, Yang, Shenzhou, Yang, Qing, Yeates, David K., Yoshizawa, Kazunori, Zhang, Qing, Zhang, Rui, Zhang, Wenwei, Zhang, Yunhui, Zhao, Jing, Zhou, Chengran, Zhou, Lili, Ziesmann, Tanja, Zou, Shijie, Li, Yingrui, Xu, Xun, Zhang, Yong, Yang, Huanming, Wang, Jian, Wang, Jun, Kjer, Karl M., Zhou, Xin
Published in Science (American Association for the Advancement of Science) (07.11.2014)
Published in Science (American Association for the Advancement of Science) (07.11.2014)
Get full text
Journal Article
Dissecting Molecular Evolution in the Highly Diverse Plant Clade Caryophyllales Using Transcriptome Sequencing
Yang, Ya, Moore, Michael J, Brockington, Samuel F, Soltis, Douglas E, Wong, Gane Ka-Shu, Carpenter, Eric J, Zhang, Yong, Chen, Li, Yan, Zhixiang, Xie, Yinlong, Sage, Rowan F, Covshoff, Sarah, Hibberd, Julian M, Nelson, Matthew N, Smith, Stephen A
Published in Molecular biology and evolution (01.08.2015)
Published in Molecular biology and evolution (01.08.2015)
Get full text
Journal Article
A human gut microbial gene catalogue established by metagenomic sequencing
Zhu, Hongmei, Li, Shengting, Cao, Jianjun, Mende, Daniel R, Yu, Chang, Xu, Junming, Turner, Keith, Arumugam, Manimozhiyan, Nielsen, Trine, Wang, Jian, Guarner, Francisco, Bertalan, Marcelo, Sicheritz-Ponten, Thomas, Li, Shaochuan, Li, Songgang, Li, Ruiqiang, Qin, Junjie, Tap, Julien, Li, Yingrui, Pedersen, Oluf, Pons, Nicolas, Doré, Joel, Bork, Peer, Burgdorf, Kristoffer Solvsten, Renault, Pierre, Lepage, Patricia, Yamada, Takuji, Weissenbach, Jean, Xie, Yinlong, Zhou, Yan, Raes, Jeroen, Qin, Nan, Brunak, Søren, Liang, Huiqing, Levenez, Florence, Batto, Jean-Michel, Jian, Min, Li, Junhua, Parkhill, Julian, Linneberg, Allan, Nielsen, H. Bjørn, Kristiansen, Karsten, Yang, Huanming, Wang, Bo, Zheng, Huisong, Wang, Jun, Zhang, Xiuqing, Pelletier, Eric, Hansen, Torben, Le Paslier, Denis, Ehrlich, S. Dusko, Li, Dongfang, Manichanh, Chaysavanh
Published in Nature (London) (04.03.2010)
Published in Nature (London) (04.03.2010)
Get full text
Journal Article
Assemblathon 1: a competitive assessment of de novo short read assembly methods
Earl, Dent, Bradnam, Keith, St John, John, Darling, Aaron, Lin, Dawei, Fass, Joseph, Yu, Hung On Ken, Buffalo, Vince, Zerbino, Daniel R, Diekhans, Mark, Nguyen, Ngan, Ariyaratne, Pramila Nuwantha, Sung, Wing-Kin, Ning, Zemin, Haimel, Matthias, Simpson, Jared T, Fonseca, Nuno A, Birol, İnanç, Docking, T Roderick, Ho, Isaac Y, Rokhsar, Daniel S, Chikhi, Rayan, Lavenier, Dominique, Chapuis, Guillaume, Naquin, Delphine, Maillet, Nicolas, Schatz, Michael C, Kelley, David R, Phillippy, Adam M, Koren, Sergey, Yang, Shiaw-Pyng, Wu, Wei, Chou, Wen-Chi, Srivastava, Anuj, Shaw, Timothy I, Ruby, J Graham, Skewes-Cox, Peter, Betegon, Miguel, Dimon, Michelle T, Solovyev, Victor, Seledtsov, Igor, Kosarev, Petr, Vorobyev, Denis, Ramirez-Gonzalez, Ricardo, Leggett, Richard, MacLean, Dan, Xia, Fangfang, Luo, Ruibang, Li, Zhenyu, Xie, Yinlong, Liu, Binghang, Gnerre, Sante, MacCallum, Iain, Przybylski, Dariusz, Ribeiro, Filipe J, Yin, Shuangye, Sharpe, Ted, Hall, Giles, Kersey, Paul J, Durbin, Richard, Jackman, Shaun D, Chapman, Jarrod A, Huang, Xiaoqiu, DeRisi, Joseph L, Caccamo, Mario, Li, Yingrui, Jaffe, David B, Green, Richard E, Haussler, David, Korf, Ian, Paten, Benedict
Published in Genome research (01.12.2011)
Published in Genome research (01.12.2011)
Get full text
Journal Article
Microbial-type terpene synthase genes occur widely in nonseed land plants, but not in seed plants
Jia, Qidong, Li, Guanglin, Köllner, Tobias G., Fu, Jianyu, Chen, Xinlu, Xiong, Wangdan, Crandall-Stotler, Barbara J., Bowman, John L., Weston, David J., Zhang, Yong, Chen, Li, Xie, Yinlong, Li, Fay-Wei, Rothfels, Carl J., Larsson, Anders, Graham, Sean W., Stevenson, Dennis W., Wong, Gane Ka-Shu, Gershenzon, Jonathan, Chen, Feng
Published in Proceedings of the National Academy of Sciences - PNAS (25.10.2016)
Published in Proceedings of the National Academy of Sciences - PNAS (25.10.2016)
Get full text
Journal Article
Diversity of ABC transporter genes across the plant kingdom and their potential utility in biotechnology
Lane, Thomas S, Rempe, Caroline S, Davitt, Jack, Staton, Margaret E, Peng, Yanhui, Soltis, Douglas Edward, Melkonian, Michael, Deyholos, Michael, Leebens-Mack, James H, Chase, Mark, Rothfels, Carl J, Stevenson, Dennis, Graham, Sean W, Yu, Jun, Liu, Tao, Pires, J Chris, Edger, Patrick P, Zhang, Yong, Xie, Yinlong, Zhu, Ying, Carpenter, Eric, Wong, Gane Ka-Shu, Stewart, Jr, C Neal
Published in BMC biotechnology (31.05.2016)
Published in BMC biotechnology (31.05.2016)
Get full text
Journal Article
Erratum: SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler
Luo, Ruibang, Liu, Binghang, Xie, Yinlong, Li, Zhenyu, Huang, Weihua, Yuan, Jianying, He, Guangzhu, Chen, Yanxiang, Pan, Qi, Liu, Yunjie, Tang, Jingbo, Wu, Gengxiong, Zhang, Hao, Shi, Yujian, Liu, Yong, Yu, Chang, Wang, Bo, Lu, Yao, Han, Changlei, Cheung, David W, Yiu, Siu-Ming, Peng, Shaoliang, Xiaoqian, Zhu, Liu, Guangming, Liao, Xiangke, Li, Yingrui, Yang, Huanming, Wang, Jian, Lam, Tak-Wah, Wang, Jun
Published in Gigascience (08.07.2015)
Published in Gigascience (08.07.2015)
Get full text
Journal Article
De novo assembly of a haplotype-resolved human genome
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 C A M, 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, Wang, Jun
Published in Nature biotechnology (01.06.2015)
Published in Nature biotechnology (01.06.2015)
Get full text
Journal Article
The oyster genome reveals stress adaptation and complexity of shell formation
GUOFAN ZHANG, XIAODONG FANG, ZHIQIANG XIONG, HUAYONG QUE, YINLONG XIE, HOLLAND, Peter W. H, PAPS, Jordi, YABING ZHU, FUCUN WU, YUANXIN CHEN, JIAFENG WANG, CHUNFANG PENG, XIMING GUO, JIE MENG, LAN YANG, JUN LIU, BO WEN, NA ZHAN, ZHIYONG HUANG, QIHUI ZHU, YUE FENG, MOUNT, Andrew, HEDGECOCK, Dennis, LI LI, ZHE XU, YUNJIE LIU, DOMAZET-LOSO, Tomislav, YISHUAI DU, XIAOQING SUN, SHOUDU ZHANG, BINGHANG LIU, PEIZHOU CHENG, XUANTING JIANG, JUAN LI, RUIBANG LUO, DINGDING FAN, WEI WANG, WENJING FU, TONG WANG, BO WANG, JIBIAO ZHANG, ZHIYU PENG, YINGXIAN LI, NA LI, JINPENG WANG, FEI XU, MAOSHAN CHEN, YAN HE, FENGJI TAN, XIAORUI SONG, QIUMEI ZHENG, RONGLIAN HUANG, HAILONG YANG, XUEDI DU, LI CHEN, MEI YANG, PENGCHENG YANG, LINLIN ZHANG, XIAOTONG WANG, HAIGANG QI
Published in Nature (London) (04.10.2012)
Published in Nature (London) (04.10.2012)
Get full text
Journal Article
Independent optical excitation of distinct neural populations
Klapoetke, Nathan C, Murata, Yasunobu, Kim, Sung Soo, Pulver, Stefan R, Birdsey-Benson, Amanda, Cho, Yong Ku, Morimoto, Tania K, Chuong, Amy S, Carpenter, Eric J, Tian, Zhijian, Wang, Jun, Xie, Yinlong, Yan, Zhixiang, Zhang, Yong, Chow, Brian Y, Surek, Barbara, Melkonian, Michael, Jayaraman, Vivek, Constantine-Paton, Martha, Wong, Gane Ka-Shu, Boyden, Edward S
Published in Nature methods (01.09.2014)
Published in Nature methods (01.09.2014)
Get full text
Journal Article
Corrigendum: Independent optical excitation of distinct neural populations
Klapoetke, Nathan C, Murata, Yasunobu, Kim, Sung Soo, Pulver, Stefan R, Birdsey-benson, Amanda, Cho, Yong Ku, Morimoto, Tania K, Chuong, Amy S, Carpenter, Eric J, Tian, Zhijian, Wang, Jun, Xie, Yinlong, Yan, Zhixiang, Zhang, Yong, Chow, Brian Y, Surek, Barbara, Melkonian, Michael, Jayaraman, Vivek, Constantine-paton, Martha, Wong, Gane Ka-shu, Boyden, Edward S
Published in Nature methods (01.09.2014)
Published in Nature methods (01.09.2014)
Get full text
Journal Article
Addendum: independent optical excitation of distinct neural populations
Klapoetke, Nathan C, Murata, Yasunobu, Kim, Sung Soo, Pulver, Stefan R, Birdsey-Benson, Amanda, Cho, Yong Ku, Morimoto, Tania K, Chuong, Amy S, Carpenter, Eric J, Tian, Zhijian, Wang, Jun, Xie, Yinlong, Yan, Zhixiang, Zhang, Yong, Chow, Brian Y, Surek, Barbara, Melkonian, Michael, Jayaraman, Vivek, Constantine-Paton, Martha, Wong, Gane Ka-Shu, Edward S Boyden, Edward S Boyden
Published in Nature methods (01.09.2014)
Published in Nature methods (01.09.2014)
Get full text
Journal Article