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Landscape and Dynamics of Single Immune Cells in Hepatocellular Carcinoma.
Zhang Q, He Y, Luo N, Patel SJ, Han Y, Gao R, Modak M, Carotta S, Haslinger C, Kind D, Peet GW, Zhong G, Lu S, Zhu W, Mao Y, Xiao M, Bergmann M, Hu X, Kerkar SP, Vogt AB, Pflanz S, Liu K, Peng J, Ren X, Zhang Z. Zhang Q, et al. Among authors: he y. Cell. 2019 Oct 31;179(4):829-845.e20. doi: 10.1016/j.cell.2019.10.003. Cell. 2019. PMID: 31675496 Free article.
Single-Cell Analyses Inform Mechanisms of Myeloid-Targeted Therapies in Colon Cancer.
Zhang L, Li Z, Skrzypczynska KM, Fang Q, Zhang W, O'Brien SA, He Y, Wang L, Zhang Q, Kim A, Gao R, Orf J, Wang T, Sawant D, Kang J, Bhatt D, Lu D, Li CM, Rapaport AS, Perez K, Ye Y, Wang S, Hu X, Ren X, Ouyang W, Shen Z, Egen JG, Zhang Z, Yu X. Zhang L, et al. Among authors: he y. Cell. 2020 Apr 16;181(2):442-459.e29. doi: 10.1016/j.cell.2020.03.048. Cell. 2020. PMID: 32302573 Free article.
Direct Comparative Analyses of 10X Genomics Chromium and Smart-seq2.
Wang X, He Y, Zhang Q, Ren X, Zhang Z. Wang X, et al. Among authors: he y. Genomics Proteomics Bioinformatics. 2021 Apr;19(2):253-266. doi: 10.1016/j.gpb.2020.02.005. Epub 2021 Mar 2. Genomics Proteomics Bioinformatics. 2021. PMID: 33662621 Free PMC article.
Genomic basis for RNA alterations in cancer.
PCAWG Transcriptome Core Group; Calabrese C, Davidson NR, Demircioğlu D, Fonseca NA, He Y, Kahles A, Lehmann KV, Liu F, Shiraishi Y, Soulette CM, Urban L, Greger L, Li S, Liu D, Perry MD, Xiang Q, Zhang F, Zhang J, Bailey P, Erkek S, Hoadley KA, Hou Y, Huska MR, Kilpinen H, Korbel JO, Marin MG, Markowski J, Nandi T, Pan-Hammarström Q, Pedamallu CS, Siebert R, Stark SG, Su H, Tan P, Waszak SM, Yung C, Zhu S, Awadalla P, Creighton CJ, Meyerson M, Ouellette BFF, Wu K, Yang H; PCAWG Transcriptome Working Group; Brazma A, Brooks AN, Göke J, Rätsch G, Schwarz RF, Stegle O, Zhang Z; PCAWG Consortium. PCAWG Transcriptome Core Group, et al. Among authors: he y. Nature. 2020 Feb;578(7793):129-136. doi: 10.1038/s41586-020-1970-0. Epub 2020 Feb 5. Nature. 2020. PMID: 32025019 Free PMC article.
High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations.
Zhang Y, Chen F, Fonseca NA, He Y, Fujita M, Nakagawa H, Zhang Z, Brazma A; PCAWG Transcriptome Working Group; PCAWG Structural Variation Working Group; Creighton CJ; PCAWG Consortium. Zhang Y, et al. Among authors: he y. Nat Commun. 2020 Feb 5;11(1):736. doi: 10.1038/s41467-019-13885-w. Nat Commun. 2020. PMID: 32024823 Free PMC article.
The landscape of viral associations in human cancers.
Zapatka M, Borozan I, Brewer DS, Iskar M, Grundhoff A, Alawi M, Desai N, Sültmann H, Moch H; PCAWG Pathogens; Cooper CS, Eils R, Ferretti V, Lichter P; PCAWG Consortium. Zapatka M, et al. Nat Genet. 2020 Mar;52(3):320-330. doi: 10.1038/s41588-019-0558-9. Epub 2020 Feb 5. Nat Genet. 2020. PMID: 32025001 Free PMC article.
Pathway and network analysis of more than 2500 whole cancer genomes.
Reyna MA, Haan D, Paczkowska M, Verbeke LPC, Vazquez M, Kahraman A, Pulido-Tamayo S, Barenboim J, Wadi L, Dhingra P, Shrestha R, Getz G, Lawrence MS, Pedersen JS, Rubin MA, Wheeler DA, Brunak S, Izarzugaza JMG, Khurana E, Marchal K, von Mering C, Sahinalp SC, Valencia A; PCAWG Drivers and Functional Interpretation Working Group; Reimand J, Stuart JM, Raphael BJ; PCAWG Consortium. Reyna MA, et al. Nat Commun. 2020 Feb 5;11(1):729. doi: 10.1038/s41467-020-14367-0. Nat Commun. 2020. PMID: 32024854 Free PMC article.
Integrative pathway enrichment analysis of multivariate omics data.
Paczkowska M, Barenboim J, Sintupisut N, Fox NS, Zhu H, Abd-Rabbo D, Mee MW, Boutros PC; PCAWG Drivers and Functional Interpretation Working Group; Reimand J; PCAWG Consortium. Paczkowska M, et al. Nat Commun. 2020 Feb 5;11(1):735. doi: 10.1038/s41467-019-13983-9. Nat Commun. 2020. PMID: 32024846 Free PMC article.
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