Publications

Selected Publications:

Single-cell spatial transcriptome reveals cell-type organization in the macaque cortex. Chen A.*; Sun Y.*#; Lei Y.*; Li C.*; Liao S.*; Meng J.*; Bai Y.*; Liu Z.*; Liang Z.*; Zhu Z.*; Yuan N.*; Yang H.*; Wu Z.*; ……; Yao J.#; Wei W.#; Li Y.#; Shen Z.#; Liu L.#; Liu Z.#; Xu X.#; Li C.# Cell (2023) Jul 7. PubMed | DOI

Comprehensive spatiotemporal mapping of single-cell lineages in developing mouse brain by CRISPR-based barcoding. Xie L.*; Liu H.*; You Z.; Wang L.; Li Y.; Zhang X.; Ji X.; He H.; Yuan T.; Zheng W.; Wu Z.; Xiong M.; Wei W.#; Chen Y.# Nature Methods (2023) PubMed | DOI

Mapping of clonal lineages across developmental stages in human neural differentiation. You Z.*; Wang L.*; He H.; Wu Z.; Zhang X.; Xue S.; Xu P.; Hong Y.; Xiong M.; Wei W.#; Chen Y.# Cell Stem Cell (2023) PubMed | DOI

Single-molecule, full-length transcript isoform sequencing reveals disease-associated RNA isoforms in cardiomyocytes. Zhu C.*; Wu J.*; Sun H.; Briganti F.; Meder B.; Wei W.#; Steinmetz LM# Nature communications (2021) Jul 9;12(1):4203. PubMed | DOI

Cytosine base editor generates substantial off-target single-nucleotide variants in mouse embryos. Zuo E.*; Sun Y.*; Wei W.* ; Yuan T.*; Ying W.; Sun H.; Yuan L.; Steinmetz L.M.; Li Y.; Yang H. Science (2019) Apr 19. PubMed | DOI

Widespread co-translational RNA decay reveals in vivo ribosome dynamics.  Pelechano, V.*, Wei, W. *; Steinmetz, L.M. Cell (2015) Jun 4. PubMed | DOI

Extensive transcriptional heterogeneity revealed by isoform profiling. Pelechano, V.*, Wei, W. *; Steinmetz, L.M. Nature (2013) Apr 24. PubMed | DOI

Bidirectional promoters generate pervasive transcription in yeast. Xu, Z.*, Wei, W.*, Gagneur, J., Perocchi, F., Clauder-Muenster, S., Camblong, J., Guffanti, E., Stutz, F., Huber, W., & Steinmetz, L.M.  Nature (2009) 457, 1033–1037. PubMed | DOI

Genome sequencing and comparative analysis of Saccharomyces cerevisiae strain YJM789. Wei, W., McCusker, J.H., Hyman, R.H., Jones, T., Ning, Y., Cao, Z., Gu, Z., Bruno, D., Miranda, M., Nguyen, M., Wilhelmy, J., Komp, C., Tamse, R., Wang, X., Jia, P., Luedi, P., Oefner P.J., David, L., Dietrich, F.S., Li, Y., Davis, R.W., Steinmetz, L.M. Proc. Natl. Acad. Sci. USA (2007) 104, 12825-12830. PubMed | DOI

All Publications:

2023

You*, Zhiwen; Wang*, Luyue; He, Hui; Wu, Ziyan; Zhang, Xinyue; Xue, Shuaixiang; Xu, Peibo; Hong, Yanhong; Xiong, Man; Wei#, Wu; Chen#, Yuejun

Mapping of clonal lineages across developmental stages in human neural differentiation Journal Article

Cell Stem Cell, 2023.

BibTeX

Yan*, Nana; Feng*, Hu; Sun*, Yongsen; Xin*, Ying; Zhang*, Haihang; Lu, Hongjiang; Zheng, Jitan; He, Chenfei; Zuo, Zhenrui; Yuan, Tanglong; Li, Nana; Xie, Long; Wei#, Wu; Sun#, Yidi; Zuo#, Erwei

Cytosine base editors induce off-target mutations and adverse phenotypic effects in transgenic mice Journal Article

Nature Communications, 14 (1), pp. 1784, 2023.

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Huch, Susanne; Nersisyan, Lilit; Ropat, Maria; Barrett, Donal; Wu, Mengjun; Wang, Jing; Valeriano, Valerie D; Vardazaryan, Nelli; Huerta-Cepas, Jaime; Wei, Wu; Du, Juan; Steinmetz, Lars M; Engstrand, Lars; Pelechano, Vicent

Atlas of mRNA translation and decay for bacteria Journal Article

Nature Microbiology, pp. 1–14, 2023.

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Zong*, Chunyan; Zhang*, Zhe; Gao*, Li; He*, Jie; Wang, Yiran; Li, Qian; Liu, Xiaoting; Yang, Jie; Chen, Di; Huang, Rui; Zheng, Guopei; Jin, Xiaoliang; Wei#, Wu; Jia#, Renbing; Shen#, Jianfeng

APOBEC3B coordinates R-loop to promote replication stress and sensitize cancer cells to ATR/Chk1 inhibitors Journal Article

Cell Death & Disease, 14 (6), pp. 348, 2023.

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Chen*, Ao ; Sun*#, Yidi ; Lei*, Ying ; Li*, Chao ; Liao*, Sha ; Meng*, Juan ; Bai*, Yiqin ; Liu*, Zhen ; Liang*, Zhifeng ; Zhu*, Zhiyong ; Yuan*, Nini ; Yang*, Hao ; Wu*, Zihan ; Lin, Feng ; Wang, Kexin ; Li, Mei ; Zhang, Shuzhen ; Yang, Meisong ; Fei, Tianyi ; Zhuang, Zhenkun ; Huang, Yiming ; Zhang, Yong ; Xu, Yuanfang ; Cui, Luman ; Zhang, Ruiyi ; Han, Lei ; Sun, Xing ; Chen, Bichao ; Li, Wenjiao ; Huangfu, Baoqian ; Ma, Kailong ; Ma, Jianyun ; Li, Zhao ; Lin, Yikun ; Wang, He ; Zhong, Yanqing ; Zhang, Huifang ; Yu, Qian ; Wang, Yaqian ; Liu, Xing ; Peng, Jian ; Liu, Chuanyu ; Chen, Wei ; Pan, Wentao ; An, Yingjie ; Xia, Shihui ; Lu, Yanbing ; Wang, Mingli ; Song, Xinxiang ; Liu, Shuai ; Wang, Zhifeng ; Gong, Chun ; Huang, Xin ; Yuan, Yue ; Zhao, Yun ; Chai, Qinwen ; Tan, Xing ; Liu, Jianfeng ; Zheng, Mingyuan ; Li, Shengkang ; Huang, Yaling ; Hong, Yan ; Huang, Zirui ; Li, Min ; Jin, Mengmeng ; ……, ; Poo, Muming ; Wang, Jian ; Yao#, Jianhua ; Wei#, Wu ; Li#, Yuxiang ; Shen#, Zhiming ; Liu#, Longqi ; Liu#, Zhiyong ; Xu#, Xun ; Li#, Chengyu

Single-cell spatial transcriptome reveals cell-type organization in the macaque cortex Journal Article

Cell, 2023.

BibTeX

Xie*, Lianshun; Liu*, Hengxin; You, Zhiwen; Wang, Luyue; Li, Yiwen; Zhang, Xinyue; Ji, Xiaoshan; He, Hui; Yuan, Tingli; Zheng, Wenping; Wu, Ziyan; Xiong, Man; Wei#, Wu; Chen#, Yuejun

Comprehensive spatiotemporal mapping of single-cell lineages in developing mouse brain by CRISPR-based barcoding Journal Article

Nature Methods, pp. 1–12, 2023.

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Zhang*, Mao; Huang*, Yingying; Pan*, Jiaomeng; Sang, Chen; Lin, Youpei; Dong, Liangqing; Shen, Xia; Wu, Yingcheng; Song, Guohe; Ji, Shuyi; Liu, Fen; Wang, Mengcheng; Zheng, Yuyan; Zhang, Sirui; Wang, Zefeng; Ren, Jianke; Gao, Daming; Zhou, Jian; Fan, Jia; Wei#, Wu; Lin#, Jian; Gao#, Qiang

An Inflammatory Checkpoint Generated by IL1RN Splicing Offers Therapeutic Opportunity for KRAS-Mutant Intrahepatic Cholangiocarcinoma Journal Article

Cancer Discovery, pp. OF1–OF22, 2023.

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Liu*, Zhen; Zhu*, Chenchen; Steinmetz, Lars M; Wei#, Wu

Identification and quantification of small exon-containing isoforms in long-read RNA sequencing data Journal Article

Nucleic Acids Research, pp. gkad810, 2023.

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2022

Sun*, Yuwei; Wang*, Luyue; Zhu, Tong; Wu, Bailin; Wang, Guangqin; Luo, Zhengnan; Li#, Chao; Wei#, Wu; Liu#, Zhiyong

Single-cell transcriptomic landscapes of the otic neuronal lineage at multiple early embryonic ages Journal Article

Cell Reports, 38 (12), pp. 110542, 2022.

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Wahiduzzaman, Md; Liu, Yuexing; Huang, Tao; Wei, Wu; Li, Yixue

Cell-cell communication analysis for single-cell RNA sequencing and its applications in carcinogenesis and COVID-19 Journal Article

Biosafety and Health, 4 (04), pp. 220–227, 2022.

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He, Hao; Yang, Wu; Su, Nan; Zhang, Chuankai; Dai, Jianing; Han, Feng; Singhal, Mahak; Bai, Wenjuan; Zhu, Xiaolan; Zhu, Jing; others,

Activating NO--sGC crosstalk in the mouse vascular niche promotes vascular integrity and mitigates acute lung injury Journal Article

Journal of Experimental Medicine, 220 (2), pp. e20211422, 2022.

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2021

Rodriguez-Galán, Olga; Garcia-Gómez, Juan J; Rosado, Iván V; Wei, Wu; Méndez-Godoy, Alfonso; Pillet, Benjamin; Alekseenko, Alisa; Steinmetz, Lars M; Pelechano, Vicent; Kressler, Dieter; others,

A functional connection between translation elongation and protein folding at the ribosome exit tunnel in Saccharomyces cerevisiae Journal Article

Nucleic Acids Research, 49 (1), pp. 206–220, 2021.

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Zhu*, Chenchen; Wu*, Jingyan; Sun, Han; Briganti, Francesca; Meder, Benjamin; Wei#, Wu; Steinmetz#, Lars M

Single-molecule, full-length transcript isoform sequencing reveals disease-associated RNA isoforms in cardiomyocytes Journal Article

Nature communications, 12 (1), pp. 1–9, 2021.

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Yang, Wu; He, Hao; Wang, Tongtong; Su, Nan; Zhang, Feng; Jiang, Kai; Zhu, Jing; Zhang, Chonghe; Niu, Kongyan; Wang, Luyue; Yuan, Xiaodong; Liu, Nan; Li, Lingjie; Wei, Wu; Hu, Junhao

Single-Cell Transcriptomic Analysis Reveals a Hepatic Stellate Cell--Activation Roadmap and Myofibroblast Origin During Liver Fibrosis in Mice Journal Article

Hepatology, 74 (5), pp. 2774–2790, 2021.

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2020

Dai, Jialin; Zhang, Chonghe; Guo, Lin; He, Hao; Jiang, Kai; Huang, Yingying; Zhang, Xixi; Zhang, Haibing; Wei, Wu; Zhang, Yaoyang; others,

A necroptotic-independent function of MLKL in regulating endothelial cell adhesion molecule expression Journal Article

Cell Death & Disease, 11 (4), pp. 1–16, 2020.

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Zuo, Erwei; Sun, Yidi; Yuan, Tanglong; He, Bingbing; Zhou, Changyang; Ying, Wenqin; Liu, Jing; Wei, Wu; Zeng, Rong; Li, Yixue; others,

A rationally engineered cytosine base editor retains high on-target activity while reducing both DNA and RNA off-target effects Journal Article

Nature Methods, pp. 1–5, 2020.

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Wang, Ming; Fu, Aisi; Hu, Ben; Tong, Yongqing; Liu, Ran; Liu, Zhen; Gu, Jiashuang; Xiang, Bin; Liu, Jianghao; Jiang, Wen; Shen, Gaigai; Zhao, Wanxu; Men, Dong; Deng, Zixin; Yu, Lilei; Wei#, Wu; Li#, Yan; Liu#, Tiangang

Nanopore Targeted Sequencing for the Accurate and Comprehensive Detection of SARS-CoV-2 and Other Respiratory Viruses Journal Article

Small, pp. 2002169, 2020.

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Zuo*, Erwei; Sun*, Yidi; Wei*, Wu; Yuan*, Tanglong; Ying, Wenqin; Sun, Hao; Yuan, Liyun; Steinmetz, Lars M; Li, Yixue; Yang, Hui

GOTI, a method to identify genome-wide off-target effects of genome editing in mouse embryos Journal Article

Nature Protocols, pp. 1–21, 2020.

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Wang, Jingwen; Li, Bingnan; Marques, Sueli; Steinmetz, Lars M; Wei, Wu; Pelechano, Vicent

TIF-Seq2 disentangles overlapping isoforms in complex human transcriptomes Journal Article

Nucleic Acids Research, 2020.

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Briganti, Francesca; Sun, Han; Wei, Wu; Wu, Jingyan; Zhu, Chenchen; Liss, Martin; Karakikes, Ioannis; Rego, Shannon; Cipriano, Andrea; Snyder, Michael; others,

iPSC modeling of RBM20-deficient DCM identifies upregulation of RBM20 as a therapeutic strategy Journal Article

Cell Reports, 32 (10), pp. 108117, 2020.

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Wells, Kristen L; Miller, Corey N; Gschwind, Andreas R; Wei, Wu; Phipps, Jonah D; Anderson, Mark S; Steinmetz, Lars M

Combined transient ablation and single-cell RNA-sequencing reveals the development of medullary thymic epithelial cells Journal Article

Elife, 9 , pp. e60188, 2020.

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Schneider, Jay W; Oommen, Saji; Qureshi, Muhammad Y; Goetsch, Sean C; Pease, David R; Sundsbak, Rhianna S; Guo, Wei; Sun, Mingming; Sun, Han; Kuroyanagi, Hidehito; others,

Dysregulated ribonucleoprotein granules promote cardiomyopathy in RBM20 gene-edited pigs Journal Article

Nature Medicine, 26 (11), pp. 1788–1800, 2020.

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2019

Nadal-Ribelles*, Mariona; Islam*, Saiful; Wei*, Wu; Latorre*, Pablo; Nguyen, Michelle; de Nadal, Eulalia; Posas, Francesc; Steinmetz, Lars M

Sensitive high-throughput single-cell RNA-seq reveals within-clonal transcript correlations in yeast populations Journal Article

Nature Microbiology, pp. 1, 2019.

BibTeX

Zuo*, Erwei; Sun*, Yidi; Wei*, Wu; Yuan*, Tanglong; Ying, Wenqin; Sun, Hao; Yuan, Liyun; Steinmetz, Lars M; Li, Yixue; Yang, Hui

Cytosine base editor generates substantial off-target single-nucleotide variants in mouse embryos Journal Article

Science, 364 (6437), pp. 289–292, 2019.

BibTeX

Wei*#, Wu; Hennig, Bianca P; Wang, Jingwen; Zhang, Yujie; Piazza, Ilaria; Sanchez, Yerma Pareja; Chabbert, Christophe D; Adjalley, Sophie H; Steinmetz, Lars M; Pelechano*#, Vicent

Chromatin-sensitive cryptic promoters putatively drive expression of alternative protein isoforms in yeast Journal Article

Genome Research, 29 (12), pp. 1974–1984, 2019.

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2018

Roy, Kevin R; Smith, Justin D; Vonesch, Sibylle C; Lin, Gen; Tu, Chelsea Szu; Lederer, Alex R; Chu, Angela; Suresh, Sundari; Nguyen, Michelle; Tripathi, Ashutosh Horecka Joe; Burnett, Wallace T; Morgan, Maddison A; Schulz, Julia; Orsley, Kevin M; Wei, Wu; Aiyar, Raeka S; Davis, Ronald W; Bankaitis, Vytas A; Haber, James E; Salit, Marc L; Onge, Robert St P; Steinmetz, Lars M

Multiplexed precision genome editing with trackable genomic barcodes in yeast Journal Article

Nature biotechnology, 2018.

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2017

Birey, Fikri; Andersen, Jimena; Makinson, Christopher D; Islam, Saiful; Wei, Wu; Huber, Nina; Fan, Christina H; Metzler, Kimberly Cordes R; Panagiotakos, Georgia; Thom, Nicholas; others,

Assembly of functionally integrated human forebrain spheroids Journal Article

Nature, 545 (7652), pp. 54, 2017.

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2016

Pelechano, Vicent; Wei, Wu; Steinmetz, Lars M

Genome-wide quantification of 5′-phosphorylated mRNA degradation intermediates for analysis of ribosome dynamics Journal Article

Nature protocols, 11 (2), pp. 359, 2016.

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Chlamydas, Sarantis; Holz, Herbert; Samata, Maria; Chelmicki, Tomasz; Georgiev, Plamen; Pelechano, Vicent; Dündar, Friederike; Dasmeh, Pouria; Mittler, Gerhard; Cadete, Filipe Tavares; Ramírez, Fidel; Conrad, Thomas; Wei, Wu; Raja, Sunil; Manke, Thomas; Luscombe, Nicholas M; Steinmetz, Lars M; Akhtar, Asifa

Functional interplay between MSL1 and CDK7 controls RNA polymerase II Ser5 phosphorylation Journal Article

Nature Structural and Molecular Biology, 23 (6), pp. 580, 2016.

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2015

Pelechano*, Vicent; Wei*, Wu; Steinmetz, Lars M

Widespread co-translational RNA decay reveals ribosome dynamics Journal Article

Cell, 161 (6), pp. 1400–1412, 2015.

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2014

Pelechano, Vicent; Wei, Wu; Jakob, Petra; Steinmetz, Lars M

Genome-wide identification of transcript start and end sites by transcript isoform sequencing Journal Article

Nature protocols, 9 (7), pp. 1740, 2014.

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Moore, Lindsay S; Wei, Wu; Stolovicki, Elad; Benbenishty, Tamar; Wilkening, Stefan; Steinmetz, Lars M; Braun, Erez; David, Lior

Induced mutations in yeast cell populations adapting to an unforeseen challenge Journal Article

PloS one, 9 (10), pp. e111133, 2014.

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2013

Wilkening, Stefan; Tekkedil, Manu M; Lin, Gen; Fritsch, Emilie S; Wei, Wu; Gagneur, Julien; Lazinski, David W; Camilli, Andrew; Steinmetz, Lars M

Genotyping 1000 yeast strains by next-generation sequencing Journal Article

BMC Genomics, 14 (1), pp. 90, 2013.

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Pelechano*, Vicent; Wei*, Wu; Steinmetz, Lars M

Extensive transcriptional heterogeneity revealed by isoform profiling Journal Article

Nature, 497 (7447), pp. 127, 2013.

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Fehrmann, Steffen; Bottin-Duplus, Helene; Leonidou, Andri; Mollereau, Esther; Barthelaix, Audrey; Wei, Wu; Steinmetz, Lars M; Yvert, Gael

Natural sequence variants of yeast environmental sensors confer cell-to-cell expression variability Journal Article

Molecular systems biology, 9 (1), pp. 695, 2013.

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2012

Hobson, David J; Wei, Wu; Steinmetz, Lars M; Svejstrup, Jesper Q

RNA Polymerase II Collision Interrupts Convergent Transcription Journal Article

Molecular Cell, 2012.

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2011

Mischo, Hannah E; Gómez-González, Belén; Grzechnik, Pawel; Rondón, Ana G; Wei, Wu; Steinmetz, Lars; Aguilera, Andrés; Proudfoot, Nick J

Yeast Sen1 helicase protects the genome from transcription-associated instability Journal Article

Molecular cell, 41 (1), pp. 21–32, 2011.

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Xu*, Zhenyu; Wei*, Wu; Gagneur, Julien; Clauder-Münster, Sandra; Smolik, Milosz; Huber, Wolfgang; Steinmetz, Lars M

Antisense expression increases gene expression variability and locus interdependency Journal Article

Molecular systems biology, 7 (1), pp. 468, 2011.

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Wei*, Wu; Pelechano*, Vicent; Järvelin*, Aino I; Steinmetz, Lars M

Functional consequences of bidirectional promoters Journal Article

Trends in Genetics, 27 (7), pp. 267–276, 2011.

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Chen, Wei-Hua; Wei, Wu; Lercher, Martin J

Minimal regulatory spaces in yeast genomes Journal Article

BMC genomics, 12 (1), pp. 320, 2011.

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2010

Nishant*, KT; Wei*, Wu; Mancera*, Eugenio; Argueso, Juan Lucas; Schlattl, Andreas; Delhomme, Nicolas; Ma, Xin; Bustamante, Carlos D; Korbel, Jan O; Gu, Zhenglong; others,

The baker's yeast diploid genome is remarkably stable in vegetative growth and meiosis Journal Article

PLoS genetics, 6 (9), pp. e1001109, 2010.

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2009

Xu*, Zhenyu; Wei*, Wu; Gagneur, Julien; Perocchi, Fabiana; Clauder-Münster, Sandra; Camblong, Jurgi; Guffanti, Elisa; ç, Fran; Huber, Wolfgang; Steinmetz, Lars M

Bidirectional promoters generate pervasive transcription in yeast Journal Article

Nature, 457 (7232), pp. 1033, 2009.

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2008

Li, Na; Yang, Xiao-Mei; Cao, Xing-Jun; CAO, Zhi-Wei; WEI, Wu; XU, Hao; LIU, Qing-Ping; JIANG, Juan; JIN, Hong; ZENG, Rong; others,

Proteomic analysis of biofilm related proteins in RP62A Journal Article

Prog Biochem Biophys, 3 , pp. 1–13, 2008.

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2007

Wei, Wu; McCusker, John H; Hyman, Richard W; Jones, Ted; Ning, Ye; Cao, Zhiwei; Gu, Zhenglong; Bruno, Dan; Miranda, Molly; Nguyen, Michelle; others,

Genome sequencing and comparative analysis of Saccharomyces cerevisiae strain YJM789 Journal Article

Proceedings of the National Academy of Sciences, 104 (31), pp. 12825, 2007.

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Wei, Wu; Wang, Weihua; Cao, Zhiwei; Yu, Hong; Wang, Xiaojing; Zhao, Jing; Tan, Hao; Xu, Hao; Jiang, Weihong; Li, Yixue

Comparative Analysis of Two-component Signal Transduction System in Two Streptomycete Genomes Journal Article

Acta biochimica et biophysica Sinica, 39 (5), pp. 317–325, 2007.

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Wang, Xiaojing; Wei, Wu; Zheng, SiYuan; Cao, Z; Li, Yixue

Ab-origin: An Improved Tool of Heavy Chain Rearrangement Analysis for Human Immunoglobulin Journal Article

Computational Science--ICCS 2007, pp. 363–369, 2007.

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2006

Wei, Wu; Cao, ZhiWei; Zhu, Yu-Li; Wang, XiaoJing; Ding, GuoHui; Xu, Hao; Jia, PeiLin; Qu, Di; Danchin, Antoine; Li, YiXue

Conserved genes in a path from commensalism to pathogenicity: comparative phylogenetic profiles of Staphylococcus epidermidis RP62A and ATCC12228 Journal Article

BMC genomics, 7 (1), pp. 112, 2006.

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Wei, Wu; Ding, Guohui; Wang, Xiaojing; Sun, Jingchun; Tu, Kang; HAO, Pei; Wang, Chuan; Cao, Zhiwei; Shi, Tieliu; Li, Yixue

Comparative analysis of whole-genome sequences of Streptococcus suis Journal Article

Chinese Science Bulletin, 51 (10), pp. 1199–1209, 2006.

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