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Landscape of RNA polyadenylation in E. coli.
Maes A, Gracia C, Innocenti N, Zhang K, Aurell E, Hajnsdorf E. Maes A, et al. Among authors: zhang k. Nucleic Acids Res. 2017 Mar 17;45(5):2746-2756. doi: 10.1093/nar/gkw894. Nucleic Acids Res. 2017. PMID: 28426097 Free PMC article.
Identifying differentially methylated sites in samples with varying tumor purity.
Häkkinen A, Alkodsi A, Facciotto C, Zhang K, Kaipio K, Leppä S, Carpén O, Grénman S, Hynninen J, Hietanen S, Lehtonen R, Hautaniemi S. Häkkinen A, et al. Among authors: zhang k. Bioinformatics. 2018 Sep 15;34(18):3078-3085. doi: 10.1093/bioinformatics/bty310. Bioinformatics. 2018. PMID: 29912358
PRISM: recovering cell-type-specific expression profiles from individual composite RNA-seq samples.
Häkkinen A, Zhang K, Alkodsi A, Andersson N, Erkan EP, Dai J, Kaipio K, Lamminen T, Mansuri N, Huhtinen K, Vähärautio A, Carpén O, Hynninen J, Hietanen S, Lehtonen R, Hautaniemi S. Häkkinen A, et al. Among authors: zhang k. Bioinformatics. 2021 Sep 29;37(18):2882-2888. doi: 10.1093/bioinformatics/btab178. Bioinformatics. 2021. PMID: 33720334 Free PMC article.
Longitudinal single-cell RNA-seq analysis reveals stress-promoted chemoresistance in metastatic ovarian cancer.
Zhang K, Erkan EP, Jamalzadeh S, Dai J, Andersson N, Kaipio K, Lamminen T, Mansuri N, Huhtinen K, Carpén O, Hietanen S, Oikkonen J, Hynninen J, Virtanen A, Häkkinen A, Hautaniemi S, Vähärautio A. Zhang K, et al. Sci Adv. 2022 Feb 25;8(8):eabm1831. doi: 10.1126/sciadv.abm1831. Epub 2022 Feb 23. Sci Adv. 2022. PMID: 35196078 Free PMC article.
Anduril 2: upgraded large-scale data integration framework.
Cervera A, Rantanen V, Ovaska K, Laakso M, Nuñez-Fontarnau J, Alkodsi A, Casado J, Facciotto C, Häkkinen A, Louhimo R, Karinen S, Zhang K, Lavikka K, Lyly L, Pal Singh M, Hautaniemi S. Cervera A, et al. Among authors: zhang k. Bioinformatics. 2019 Oct 1;35(19):3815-3817. doi: 10.1093/bioinformatics/btz133. Bioinformatics. 2019. PMID: 30793160
Co-evolution of matrisome and adaptive adhesion dynamics drives ovarian cancer chemoresistance.
Pietilä EA, Gonzalez-Molina J, Moyano-Galceran L, Jamalzadeh S, Zhang K, Lehtinen L, Turunen SP, Martins TA, Gultekin O, Lamminen T, Kaipio K, Joneborg U, Hynninen J, Hietanen S, Grénman S, Lehtonen R, Hautaniemi S, Carpén O, Carlson JW, Lehti K. Pietilä EA, et al. Among authors: zhang k. Nat Commun. 2021 Jun 23;12(1):3904. doi: 10.1038/s41467-021-24009-8. Nat Commun. 2021. PMID: 34162871 Free PMC article.
Prospective Longitudinal ctDNA Workflow Reveals Clinically Actionable Alterations in Ovarian Cancer.
Oikkonen J, Zhang K, Salminen L, Schulman I, Lavikka K, Andersson N, Ojanperä E, Hietanen S, Grénman S, Lehtonen R, Huhtinen K, Carpén O, Hynninen J, Färkkilä A, Hautaniemi S. Oikkonen J, et al. Among authors: zhang k. JCO Precis Oncol. 2019 May 3;3:PO.18.00343. doi: 10.1200/PO.18.00343. eCollection 2019. JCO Precis Oncol. 2019. PMID: 32914024 Free PMC article.
Human cell transformation by combined lineage conversion and oncogene expression.
Sahu B, Pihlajamaa P, Zhang K, Palin K, Ahonen S, Cervera A, Ristimäki A, Aaltonen LA, Hautaniemi S, Taipale J. Sahu B, et al. Among authors: zhang k. Oncogene. 2021 Sep;40(36):5533-5547. doi: 10.1038/s41388-021-01940-0. Epub 2021 Jul 23. Oncogene. 2021. PMID: 34302118 Free PMC article.
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