Jinhua Qin#, Jian Zhang#, Jianan Jiang#, Bowen Zhang, Jisheng Li, Xiaosong Lin, Sihan Wang, Meiqi Zhu, Zeng Fan, Yang Lv, Lijuan He, Lin Chen, Wen Yue, Yanhua Li*, Xuetao Pei*.
Direct chemical reprogramming of human cord blood erythroblasts to induced megakaryocytes that produce platelets[J]. Cell Stem Cell, 2022. [ link ]
Xing X#, Shi J#, Jia Y#, Dou Y#, Li Z#, Dong B, Guo T, Cheng X, Li X, Du H, Hu Y, Jia S*, Zhang J*, Li Z*, Ji J*. Effect of neoadjuvant chemotherapy on the immune microenvironment in gastric cancer as determined by multiplex immunofluorescence and T cell receptor repertoire analysis[J]. Journal for immunotherapy of cancer, 2022, 10(3):e003984.[ link ]
Wang J#, Jiang D#, Zheng X, Li W, Zhao T, Wang D, Yu H, Sun D, Li Z, Zhang J, Zhang Z, Hou L, Jiang G, Fei K, Zhang F*, Yang K*, Zhang P*. Tertiary lymphoid structure and decreased CD8+ T cell infiltration in minimally invasive adenocarcinoma[J]. iScience, 2022, 25(3):103883.[ link ]
2021
Wang H#, Feng C#, Lu M, Zhang B, Xu Y, Zeng Q, Xi J, Zhou J, Ying X, Zhang J*, Yue W*, Pei X*. Integrative single-cell transcriptome analysis reveals a subpopulation of fibroblasts associated with favorable prognosis of liver cancer patients[J]. Translational Oncology, 2021, 14(1): 100981.[ link ]
2020
Chu S H, Chabon J R, Matovina C N, Minehart J C, Chen B-R, Zhang J, Kumar V, Xiong Y, Callen E, Hung P J, Feng Z, Koche R P, Liu X S, Chaudhuri J, Nussenzweig A, Sleckman B P, Armstrong S A. Loss of H3K36 Methyltransferase SETD2 Impairs V(D)J Recombination during Lymphoid Development[J]. iScience, 2020, 23(3): 100941.[ link ]
Zhang H#, Liu L#, Zhang J, Chen J, Ye J, Shukla S, Qiao J, Zhan X, Chen H, Wu C J, Fu Y-X*, Li B*. Investigation of Antigen-Specific T-Cell Receptor Clusters in Human Cancers[J]. Clinical Cancer Research, 2020, 26(6): 1359–1371.[ link ]
2019
Zhang J, Hu X, Wang J, Sahu A D, Cohen D, Song L, Ouyang Z, Fan J, Wang B, Fu J, Gu S, Sade-Feldman M, Hacohen N, Li W, Ying X*, Li B*, Liu X S*. Immune receptor repertoires in pediatric and adult acute myeloid leukemia[J]. Genome Medicine, 2019, 11(1): 73.[ link ]
Zhang J, Qian L, Wu J, Lu D, Yuan H, Li W, Ying X*, Hu S*. Up-regulation of FAM64A promotes epithelial-to-mesenchymal transition and enhances stemness features in breast cancer cells[J]. Biochemical and Biophysical Research Communications, 2019.[ link ]
Hu X#, Zhang J#, Wang J, Fu J, Li T, Zheng X, Wang B, Gu S, Jiang P, Fan J, Ying X, Zhang J, Carroll M C, Wucherpfennig K W, Hacohen N, Zhang F, Zhang P, Liu J S*, Li B*, Liu X S*. Landscape of B cell immunity and related immune evasion in human cancers[J]. Nature Genetics, 2019, 51(3): 560–567.[ link ]
2018
Hu X#, Zhang J#, Liu J S, Li B*, Liu X S*. Evaluation of immune repertoire inference methods from RNA-seq data[J]. Nature Biotechnology, 2018, 36(11): 1034–1034.[ link ]
Cornwell M, Vangala M, Taing L, Herbert Z, Köster J, Li B, Sun H, Li T, Zhang J, Qiu X, Pun M, Jeselsohn R, Brown M, Liu X S, Long H W. VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis[J]. BMC Bioinformatics, 2018, 19: 135.[ link ]
Xing X, Guo J, Ding G, Li B, Dong B, Feng Q, Li S, Zhang J, Ying X, Cheng X, Guo T, Du H, Hu Y, Zhou T, Wang X, Li L, Li Q, Xie M, Li L, Gao X, Shan F, Li Z, Jia S, Wen X, Wang J, Ji J. Analysis of PD1, PDL1, PDL2 expression and T cells infiltration in 1014 gastric cancer patients[J]. OncoImmunology, 2018, 7(3): e1356144.[ link ]
2017
Hu S, Yuan H, Li Z, Zhang J, Wu J, Chen Y, Shi Q, Ren W, Shao N, Ying X. Transcriptional response profiles of paired tumor-normal samples offer novel perspectives in pan-cancer analysis[J]. Oncotarget, 2017, 8(25): 41334–41347.[ link ]
Li B, Li T, Wang B, Dou R, Zhang J, Liu J S, Liu X S. Ultrasensitive detection of TCR hypervariable-region sequences in solid-tissue RNA–seq data[J]. Nature Genetics, 2017, 49(4): 482–483.[ link ]
Wu J, Hu S, Chen Y, Li Z, Zhang J, Yuan H, Shi Q, Shao N, Ying X. BCIP: a gene-centered platform for identifying potential regulatory genes in breast cancer[J]. Scientific Reports, 2017, 7: 45235.[ link ]
Chen Y, Li Z, Hu S, Zhang J, Wu J, Shao N, Bo X, Ni M, Ying X. Gut metagenomes of type 2 diabetic patients have characteristic single-nucleotide polymorphism distribution in Bacteroides coprocola[J]. Microbiome, 2017, 5: 15.[ link ]
2016
Ren W, Zhang J, Li W, Li Z, Hu S, Suo J, Ying X. A Tumor-Specific Prognostic Long Non-Coding RNA Signature in Gastric Cancer[J]. Medical Science Monitor, 2016, 22: 3647–3657.[ link ]
Li T, Chen L, Cheng J, Dai J, Huang Y, Zhang J, Liu Z, Li A, Li N, Wang H, Yin X, He K, Yu M, Zhou T, Zhang X, Xia Q. SUMOylated NKAP is essential for chromosome alignment by anchoring CENP-E to kinetochores[J]. Nature Communications, 2016, 7: 12969.[ link ]
Li Z, Chen Y, Hu S, Zhang J, Wu J, Ren W, Shao N, Ying X. Integrative analysis of protein-coding and non-coding RNAs identifies clinically relevant subtypes of clear cell renal cell carcinoma[J]. Oncotarget, 2016, 7(50): 82671–82685.[ link ]