(^ co-first author, # corresponding author)
Endogenous retroviruses:unveiling new targets for cancer immunotherapy
Shengbao Suo#
Nature Reviews Genetics, 2024, 25(12):827
Tissue-resident memory and circulating T cells are early responders to pre-surgical cancer immunotherapy
Adrienne M. Luoma^; Shengbao Suo^#; Yifan Wang; Lauren Gunasti; Caroline B.M. Porter; Nancy Nabilsi; Jenny Tadros; Andrew P. Ferretti; Sida Liao; Cagan Gurer; Yu-Hui Chen; Shana Criscitiello; Cora A. Ricker; Danielle Dionne; Orit Rozenblatt-Rosen; Ravindra Uppaluri; Robert I. Haddad; Orr Ashenberg; Aviv Regev; Eliezer M. Van Allen; Gavin MacBeath; Jonathan D. Schoenfeld#; Kai W. Wucherpfennig#
Cell, 2022, 185(16):2918-2935
Molecular pathways of colon inflammation induced by cancer immunotherapy
Adrienne M. Luoma^; Shengbao Suo^; Hannah L. Williams; Tatyana Sharova; Keri Sullivan; Michael Manos; Peter Bowling; F. Stephen Hodi; Osama Rahma; Ryan J. Sullivan; Genevieve M. Boland; Jonathan A. Nowak; Stephanie K. Dougan; Michael Dougan#; Guo-Cheng Yuan; Kai W. Wucherpfennig#
Cell, 2020, 182(3):655-671
Molecular architecture of lineage allocation and tissue organization in early mouse embryo
Guangdun Peng^#; Shengbao Suo^; Guizhong Cui^; Fang Yu^; Ran Wang; Jun Chen; Shirui Chen; Zhiwen Liu; Guoyu Chen; Yun Qian; Patrick P.L.Tam; Jing-Dong J.Han#; Naihe Jing#
Nature, 2019, 572(7770):528-532
Revealing the critical regulators of cell identity in the mouse cell atlas
Shengbao Suo; Qian Zhu; Assieh Saadatpour; Lijiang Fei; Guoji Guo; Guo-Cheng Yuan#
Cell Reports, 2018, 6(25):1436-1445
Endogenous retroviruses:unveiling new targets for cancer immunotherapy
Shengbao Suo#
Nature Reviews Genetics, 2024, 25(12):827
Profound cellular defects attribute to muscular pathogenesis in the rhesus monkey model of Duchenne muscular dystrophy
Shuaiwei Ren^; Xin Fu^; Wenting Guo^; Raoxian Bai^; Sheng Li; Ting Zhang; Jie Liu; Zhengbo Wang; Hui Zhao; Shengbao Suo; Weikang Zhang; Minzhi Jia; Weizhi Ji#; Ping Hu#; Yongchang Chen#
Cell, 2024, 187(23):6669-6686.e16
Gli1 marks a sentinel muscle stem cell population for muscle regeneration
Jiayin Peng^; Lili Han^; Biao Liu^; Jiawen Song; Yuang Wang; Kunpeng Wang; Qian Guo; XinYan Liu; Yu Li; Jujin Zhang; Wenqing Wu; Sheng Li; Xin Fu; Cheng-le Zhuang; Weikang Zhang; Shengbao Suo; Ping Hu#; Yun Zhao#
Nature Communications, 2023, 14:6993
Three-dimensional molecular architecture of mouse organogenesis
Fangfang Qu^; Wenjia Li^; Jian Xu^; Ruifang Zhang; Jincan Ke; Xiaodie Ren; Xiaogao Meng; Lexin Qin; Jingna Zhang; Fangru Lu; Xin Zhou; Xi Luo; Zhen Zhang; Minhan Wang; Guangming Wu; Duanqing Pei; Jiekai Chen; Guizhong Cui#; Shengbao Suo#; Guangdun Peng#
Nature Communications, 2023, 14:4599
Construction of a cross-species cell landscape at single-cell level
Renying Wang^; Peijing Zhang^#; Jingjing Wang^; Lifeng Ma^; Weigao E^; ShengBao Suo^; Mengmeng Jiang^; Jiaqi Li^; Haide Chen; Huiyu Sun; Lijiang Fei; Ziming Zhou; Yincong Zhou; Yao Chen; Weiqi Zhang; Xinru Wang; Yuqing Mei; Zhongyi Sun; Chengxuan Yu; Jikai Shao; Yuting Fu; Yanyu Xiao; Fang Ye; Xing Fang; Hanyu Wu; Qile Guo; Xiunan Fang; Xia Li; Xianzhi Gao; Dan Wang; Peng-Fei Xu; Rui Zeng; Gang Xu; Lijun Zhu; Lie Wang; Jing Qu; Dan Zhang; Hongwei Ouyang; He Huang; Ming Chen; Shyh-Chang NG#; Guang-Hui Liu#; Guo-Cheng Yuan#; Guoji Guo#; Xiaoping Han#
Nucleic Acids Research, 2023, 51(2):501-516
Tissue-resident memory and circulating T cells are early responders to pre-surgical cancer immunotherapy
Adrienne M. Luoma^; Shengbao Suo^#; Yifan Wang; Lauren Gunasti; Caroline B.M. Porter; Nancy Nabilsi; Jenny Tadros; Andrew P. Ferretti; Sida Liao; Cagan Gurer; Yu-Hui Chen; Shana Criscitiello; Cora A. Ricker; Danielle Dionne; Orit Rozenblatt-Rosen; Ravindra Uppaluri; Robert I. Haddad; Orr Ashenberg; Aviv Regev; Eliezer M. Van Allen; Gavin MacBeath; Jonathan D. Schoenfeld#; Kai W. Wucherpfennig#
Cell, 2022, 185(16):2918-2935
Single-nucleus transcriptome analysis of human brain immune response in patients with severe COVID-19
John F Fullard, Hao-Chih Lee, Georgios Voloudakis, Shengbao Suo, Behnam Javidfar, Zhiping Shao, Cyril Peter, Wen Zhang, Shan Jiang, André Corvelo, Heather Wargnier, Emma Woodoff-Leith, Dushyant P Purohit, Sadhna Ahuja, Nadejda M Tsankova, Nathalie Jette, Gabriel E Hoffman, Schahram Akbarian, Mary Fowkes, John F Crary, Guo-Cheng Yuan, Panos Roussos
Genome Medicine, 2021, 13(1):118
Massively parallel in vivo CRISPR screening identifies RNF20/40 as epigenetic regulators of cardiomyocyte maturation
Nathan J VanDusen, Julianna Y Lee, Weiliang Gu, Catalina E Butler, Isha Sethi, Yanjiang Zheng, Justin S King, Pingzhu Zhou, Shengbao Suo, Yuxuan Guo, Qing Ma, Guo-Cheng Yuan, William William Pu
Nature Communications, 2021, 12(1):4442
Immunosuppressive Myeloid Cells Induce Nitric Oxide–Dependent DNA Damage and p53 Pathway Activation in CD8+ T Cells
Adam NR Cartwright, Shengbao Suo, Soumya Badrinath, Sushil Kumar, Johannes Melms, Adrienne Luoma, Archis Bagati, Assieh Saadatpour, Benjamin Izar, Guo-Cheng Yuan, Kai W Wucherpfennig#
Cancer Immunology Research, 2021, 9(4):470-485
New regulators of Drosophila eye development identified from temporal transcriptome changes
Manon Quiquand, Gerard Rimesso, Nan Qiao, Shengbao Suo, Chunyu Zhao, Matthew Slattery, Kevin P White, Jackie J Han, Nicholas E Baker#
Genetics, 2021, 217(4):iyab007
Inhibition of CDK4/6 promotes CD8 T-cell memory formation
Max Heckler, Lestat R Ali, Eleanor Clancy-Thompson, Li Qiang, Katherine S Ventre, Patrick Lenehan, Kevin Roehle, Adrienne Luoma, Kelly Boelaars, Vera Peters, Julia McCreary, Tamara Boschert, Eric S Wang, Shengbao Suo, Francesco Marangoni, Thorsten R Mempel, Henry W Long, Kai W Wucherpfennig, Michael Dougan, Nathanael S Gray, Guo-Cheng Yuan, Shom Goel, Sara M Tolaney, Stephanie K Dougan#
Cancer Discovery, 2021, candisc.1540.2020
Integrated spatial genomics reveals global architecture of single nuclei
Yodai Takei; Jina Yun; Shiwei Zheng; Noah Ollikainen; Nico Pierson; Jonathan White; Sheel Shah; Julian Thomassie; Shengbao Suo; Chee-Huat Linus Eng; Mitchell Guttman; Guo-Cheng Yuan; Long Cai#
Nature, 2021, 590(7845):344-350
Molecular pathways of colon inflammation induced by cancer immunotherapy
Adrienne M. Luoma^; Shengbao Suo^; Hannah L. Williams; Tatyana Sharova; Keri Sullivan; Michael Manos; Peter Bowling; F. Stephen Hodi; Osama Rahma; Ryan J. Sullivan; Genevieve M. Boland; Jonathan A. Nowak; Stephanie K. Dougan; Michael Dougan#; Guo-Cheng Yuan; Kai W. Wucherpfennig#
Cell, 2020, 182(3):655-671
Molecular architecture of lineage allocation and tissue organization in early mouse embryo
Guangdun Peng^#; Shengbao Suo^; Guizhong Cui^; Fang Yu^; Ran Wang; Jun Chen; Shirui Chen; Zhiwen Liu; Guoyu Chen; Yun Qian; Patrick P.L.Tam; Jing-Dong J.Han#; Naihe Jing#
Nature, 2019, 572(7770):528-532
Transcriptional network dynamics during the progression of pluripotency revealed by integrative statistical learning
Hani Jieun Kim; Pierre Osteil; Sean J Humphrey; Senthilkumar Cinghu; Andrew J Oldfield; Ellis Patrick; Emilie E Wilkie; Guangdun Peng; Shengbao Suo; Raja Jothi; Patrick P L Tam; Pengyi Yang#
Nucleic Acids Research, 2019, 48(4):1828-1842
A 3D Atlas of Hematopoietic Stem and Progenitor Cell Expansion by Multi-dimensional RNA-Seq Analysis
Yuanyuan Xue^; Denghui Liu^; Guizhong Cui; Yanyan Ding; Daosheng Ai; Suwei Gao; Yifan Zhang; Shengbao Suo; Xiaohan Wang; Peng Lv; Chunyu Zhou; Yizhou Li; Xingwei Chen; Guangdun Peng; Naihe Jing; Jing-Dong J.Han#; Feng Liu#
Cell Reports, 2019, 27(5):1567-1578
Epithelial endoplasmic reticulum stress orchestrates a protective IgA response
Joep Grootjans^; Niklas Krupka^; Shuhei Hosomi^; Juan D.Matute; Thomas Hanley; Svetlana Saveljeva; Thomas Gensollen; Jarom Heijmans; Hai Li; Julien P.Limenitakis; Stephanie C.Ganal-Vonarburg; Shengbao Suo; Adrienne M. Luoma; Yosuke Shimodaira; Jinzhi Duan; David Q.Shih; Margaret E.Conner; Jonathan N.Glickman; Gwenny M.Fuhler; Noah W.Palm; Marcel R.de Zoete; C. Janneke van der Woude; Guo-Cheng Yuan; Kai W.Wucherpfennig; Stephan R. Targan; Philip Rosenstiel; Richard A.Flavell; Kathy D.McCoy; Andrew J. Macpherson; Arthur Kaser; Richard S.Blumberg#
Science, 2019, 363(6430):993-998
Accurate drug repositioning through non- tissue-specific core signatures from cancer transcriptomes
Chi Xu^; Daosheng Ai^; Dawei Shi; Shengbao Suo; Xingwei Chen; Yizhen Yan; Yaqiang Cao; Na Sun; Weizhong Chen; Joseph McDermott; Shiqiang Zhang; Yingying Zeng; Jing-Dong J. Han#
Cell Reports, 2018 , 25(2):523-535
Single-cell transcriptomic analysis of cardiac differentiation from human PSCs reveals HOPX-dependent cardiomyocyte maturation
Clayton E. Friedman^; Quan Nguyen^; Samuel W. Lukowski^; Abbigail Helfer; Han Sheng Chiu; Jason Miklas; Shiri Levy; Shengbao Suo; Jing-Dong Jackie Han; Pierre Osteil; Guangdun Peng; Naihe Jing; Greg J. Baillie; Anne Senabouth; Angelika N. Christ; Timothy J. Bruxner; Charles E. Murry; Emily S. Wong; Jun Ding; Joseph E. Powell#; Nathan J. Palpant#
Cell Stem Cell, 2018, 23(4):586- 598
Revealing the critical regulators of cell identity in the mouse cell atlas
Shengbao Suo; Qian Zhu; Assieh Saadatpour; Lijiang Fei; Guoji Guo; Guo-Cheng Yuan#
Cell Reports, 2018, 6(25):1436-1445
Mouse gastrulation:Attributes of transcription factor regulatory network for epiblast patterning
Guizhong Cui^; Shengbao Suo^; Ran Wang; Yun Qian; Jing-Dong J. Han#; Guangdun Peng#; Patrick P. L. Tam#; Naihe Jing#
Development, Growth & Differentiation, 2018, 60(8):463-472
Spatial transcriptomic analysis of cryosectioned tissue samples with Geo-seq
Jun Chen^; Shengbao Suo^; Patrick PL Tam; Jing-Dong J Han#; Guangdun Peng#; Naihe Jing#
Nature Protocols, 2017, 12(3):566-580
Inference of differentiation time for single cell transcriptomes using cell population reference data
Na Sun^; Xiaoming Yu^; Fang Li^; Denghui Liu; Shengbao Suo; Weiyang Chen; Shirui Chen; Lu Song; Christopher D. Green; Joseph McDermott; Qin Shen; Naihe Jing; Jing-Dong J. Han#
Nature Communications, 2017, 8:1856-1856
Transcriptome analyses of rhesus monkey preimplantation embryos reveal a reduced capacity for DNA double-strand break repair in primate oocytes and early embryos
Xinyi Wang^; Denghui Liu^; Dajian He; Shengbao Suo; Xian Xia; Xiechao He; Jing-Dong J. Han#; Ping Zheng#
Genome Research, 2017, 27( 4):567-579
Nkx2.5 marks angioblasts that contribute to hemogenic endothelium of the endocardium and dorsal aorta
Lyad Zamir^; Reena Singh^; Elisha Nathan; Ralph Patrick; Oren Yifa; Yfat Yahalom-Ronen; Alaa A Arraf; Thomas M Schultheiss; Shengbao Suo; Jing- Dong Jackie Han; Guangdun Peng; Naihe Jing; Yuliang Wang; Nathan Palpant; Patrick PL Tam; Richard P Harvey#; Eldad Tzahor#
eLife, 2017, 6:e20994
A homology-based pipeline for global prediction of post-translational modification sites
Xiang Chen; Shao-Ping Shi; Hao-Dong Xu; Sheng-Bao Suo; Jian-Ding Qiu#
Scientific Reports, 2016, 6:25801
Spatial transcriptome for the molecular annotation of lineage fates and cell identity in mid-gastrula mouse embryo
Guangdun Peng^; Shengbao Suo^; Jun Chen^; Weiyang Chen; Chang Liu; Fang Yu; Ran Wang; Shirui Chen; Na Sun; Guizhong Cui; Lu Song; Patrick P.L. Tam; Jing-Dong J.Han#; Naihe Jing#
Developmental Cell, 2016, 36(6):681-697
Proteomic analysis and prediction of human phosphorylation sites in subcellular level reveal subcellular specificity
Xiang Chen; Shao-Ping Shi; Sheng-Bao Suo; Hao-Dong Xu; Jian-Ding Qiu#
Bioinformatics, 2015, 31(2):194-200
PSEA:Kinase-specific prediction and analysis of human phosphorylation substrates
Sheng-Bao Suo; Jian-Ding Qiu#; Shao-Ping Shi; Xiang Chen; Ru-Ping Liang
Scientific Reports, 2014, 4(4):4524
Proteome-wide analysis of amino acid variations that influences protein lysine acetylation
Sheng-Bao Suo; Jian-Ding Qiu#; Shao-Ping Shi; Xiang Chen; Shu-Yun Huang; Ru-Ping Liang
Journal of Proteome Research, 2013, 12 (2):949-958
Systematic analysis and prediction of pupylation sites in prokaryotic proteins
Xiang Chen; Jian-Ding Qiu#; Shao-Ping Shi; Sheng-Bao Suo; Ru-Ping Liang
PLoS ONE, 2013, 8(9):e74002
Incorporating key position and amino acid residue features to identify general and species-specific Ubiquitin conjugation sites
Xiang Chen; Jian-Ding Qiu#; Shao-Ping Shi; Sheng-Bao Suo; Shu-Yun Huang; Ru-Ping Liang
Bioinformatics, 2013, 29(13):1614-1622
The prediction of palmitoylation site locations using a multiple feature extraction method
Shao-Ping Shi; Xing-Yu Sun; Jian-Ding Qiu#; Sheng-Bao Suo; Xiang Chen; Shu-Yun Huang; Ru-Ping Liang
Journal of Molecular Graphics & Modelling, 2013, 40:125-130
A method to distinguish between lysine acetylation and lysine methylation from protein sequences
Shao-Ping Shi; Jian-Ding Qiu#; Xing-Yu Sun; Sheng-Bao Suo; Shu-Yun Huang; Ru-Ping Liang
Journal of Theoretical Biology, 2012, 310:223-230
PredSulSite:Prediction of protein tyrosine sulfation sites with multiple features and analysis
Shu-Yun Huang; Shao-Ping Shi; Jian-Ding Qiu#; Xing-Yu Sun; Sheng-Bao Suo; Ru-Ping Liang
Analytical Biochemistry, 2012, 428 (1):16-23
PMeS:Prediction of methylation sites based on enhanced feature encoding scheme
Shao-Ping Shi; Jian-Ding Qiu#; Xing-Yu Sun; Sheng-Bao Suo; Shu-Yun Huang; Ru-Ping Liang
PLoS ONE, 2012, 7(6):e38772
A novel algorithm combining support vector machine with the discrete wavelet transform for the prediction of protein subcellular localization
Ru-Ping Liang; Shu-Yun Huang; Shao-Ping Shi; Xing-Yu Sun; Sheng-Bao Suo; Jian-Ding Qiu#
Computers in Biology and Medicine, 2012, 42(2):180-187
Identifying protein quaternary structural attributes by incorporating physicochemical properties into the general form of Chou’s PseAAC via discrete wavelet transform
Xing-Yu Sun; Shao-Ping Shi; Jian-Ding Qiu#; Sheng-Bao Suo; Shu-Yun Huang; Ru-Ping Liang
Molecular BioSystems, 2012, 8(12):3178-3184
PLMLA:prediction of lysine methylation and lysine acetylation by combining multiple features
Shao-Ping Shi; Jian-Ding Qiu#; Xing-Yu Sun; Sheng-Bao Suo; Shu-Yun Huang; Ru-Ping Liang
Molecular BioSystems, 2012, 8(5):1520-1527
Position-Specific Analysis and Prediction for Protein Lysine Acetylation Based on Multiple Features
Sheng-Bao Suo; Jian-Ding Qiu#; Shao-Ping Shi; Xing-Yu Sun; Shu-Yun Huang; Xiang Chen; Ru-Ping Liang
PLoS ONE, 2012, 7( 11):e49108
OligoPred:A web-server for predicting homo-oligomeric proteins by incorporating discrete wavelet transform into Chou’s pseudo amino acid composition
Jian-Ding Qiu#; Sheng-Bao Suo; Xing-Yu Sun; Shao-Ping Shi; Ru-Ping Liang
Journal of Molecular Graphics & Modelling, 2011, 30:129-134
Predicting homo-oligomers and hetero-oligomers by pseudo-amino acid composition An approach from discrete wavelet transformation
Jian-Ding Qiu#; Xing-Yu Sun; Sheng-Bao Suo; Shao-Ping Shi; Shu-Yun Huang; Ru-Ping Liang; Li Zhang
Biochimie, 2011, 93(7):1132-1138
Identify submitochondria and subchloroplast locations with pseudo amino acid composition Approach from the strategy of discrete wavelet transform feature extraction
Shao-Ping Shi; Jian-Ding Qiu#; Xing-Yu Sun; Jian-Hua Huang; Shu-Yun Huang; Sheng-Bao Suo; Ru-Ping Liang; Li Zhang
Biochimica et Biophysica Acta - Molecular Cell Research, 2011, 1813(3):424-430