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3D genome mapping identifies subgroup-specific chromosome conformations and tumor-dependency genes in ependymoma.
Okonechnikov K, Camgöz A, Chapman O, Wani S, Park DE, Hübner JM, Chakraborty A, Pagadala M, Bump R, Chandran S, Kraft K, Acuna-Hidalgo R, Reid D, Sikkink K, Mauermann M, Juarez EF, Jenseit A, Robinson JT, Pajtler KW, Milde T, Jäger N, Fiesel P, Morgan L, Sridhar S, Coufal NG, Levy M, Malicki D, Hobbs C, Kingsmore S, Nahas S, Snuderl M, Crawford J, Wechsler-Reya RJ, Davidson TB, Cotter J, Michaiel G, Fleischhack G, Mundlos S, Schmitt A, Carter H, Michealraj KA, Kumar SA, Taylor MD, Rich J, Buchholz F, Mesirov JP, Pfister SM, Ay F, Dixon JR, Kool M, Chavez L. Okonechnikov K, et al. Nat Commun. 2023 Apr 21;14(1):2300. doi: 10.1038/s41467-023-38044-0. Nat Commun. 2023. PMID: 37085539 Free PMC article.
Qualimap: evaluating next-generation sequencing alignment data.
García-Alcalde F, Okonechnikov K, Carbonell J, Cruz LM, Götz S, Tarazona S, Dopazo J, Meyer TF, Conesa A. García-Alcalde F, et al. Among authors: okonechnikov k. Bioinformatics. 2012 Oct 15;28(20):2678-9. doi: 10.1093/bioinformatics/bts503. Epub 2012 Aug 22. Bioinformatics. 2012. PMID: 22914218
Unipro UGENE: a unified bioinformatics toolkit.
Okonechnikov K, Golosova O, Fursov M; UGENE team. Okonechnikov K, et al. Bioinformatics. 2012 Apr 15;28(8):1166-7. doi: 10.1093/bioinformatics/bts091. Epub 2012 Feb 24. Bioinformatics. 2012. PMID: 22368248
DNA methylation-based classification and grading system for meningioma: a multicentre, retrospective analysis.
Sahm F, Schrimpf D, Stichel D, Jones DTW, Hielscher T, Schefzyk S, Okonechnikov K, Koelsche C, Reuss DE, Capper D, Sturm D, Wirsching HG, Berghoff AS, Baumgarten P, Kratz A, Huang K, Wefers AK, Hovestadt V, Sill M, Ellis HP, Kurian KM, Okuducu AF, Jungk C, Drueschler K, Schick M, Bewerunge-Hudler M, Mawrin C, Seiz-Rosenhagen M, Ketter R, Simon M, Westphal M, Lamszus K, Becker A, Koch A, Schittenhelm J, Rushing EJ, Collins VP, Brehmer S, Chavez L, Platten M, Hänggi D, Unterberg A, Paulus W, Wick W, Pfister SM, Mittelbronn M, Preusser M, Herold-Mende C, Weller M, von Deimling A. Sahm F, et al. Among authors: okonechnikov k. Lancet Oncol. 2017 May;18(5):682-694. doi: 10.1016/S1470-2045(17)30155-9. Epub 2017 Mar 15. Lancet Oncol. 2017. PMID: 28314689 Free article.
Therapeutic targeting of ependymoma as informed by oncogenic enhancer profiling.
Mack SC, Pajtler KW, Chavez L, Okonechnikov K, Bertrand KC, Wang X, Erkek S, Federation A, Song A, Lee C, Wang X, McDonald L, Morrow JJ, Saiakhova A, Sin-Chan P, Wu Q, Michaelraj KA, Miller TE, Hubert CG, Ryzhova M, Garzia L, Donovan L, Dombrowski S, Factor DC, Luu B, Valentim CLL, Gimple RC, Morton A, Kim L, Prager BC, Lee JJY, Wu X, Zuccaro J, Thompson Y, Holgado BL, Reimand J, Ke SQ, Tropper A, Lai S, Vijayarajah S, Doan S, Mahadev V, Miñan AF, Gröbner SN, Lienhard M, Zapatka M, Huang Z, Aldape KD, Carcaboso AM, Houghton PJ, Keir ST, Milde T, Witt H, Li Y, Li CJ, Bian XW, Jones DTW, Scott I, Singh SK, Huang A, Dirks PB, Bouffet E, Bradner JE, Ramaswamy V, Jabado N, Rutka JT, Northcott PA, Lupien M, Lichter P, Korshunov A, Scacheri PC, Pfister SM, Kool M, Taylor MD, Rich JN. Mack SC, et al. Among authors: okonechnikov k. Nature. 2018 Jan 4;553(7686):101-105. doi: 10.1038/nature25169. Epub 2017 Dec 20. Nature. 2018. PMID: 29258295 Free PMC article.
Aberrant ERBB4-SRC Signaling as a Hallmark of Group 4 Medulloblastoma Revealed by Integrative Phosphoproteomic Profiling.
Forget A, Martignetti L, Puget S, Calzone L, Brabetz S, Picard D, Montagud A, Liva S, Sta A, Dingli F, Arras G, Rivera J, Loew D, Besnard A, Lacombe J, Pagès M, Varlet P, Dufour C, Yu H, Mercier AL, Indersie E, Chivet A, Leboucher S, Sieber L, Beccaria K, Gombert M, Meyer FD, Qin N, Bartl J, Chavez L, Okonechnikov K, Sharma T, Thatikonda V, Bourdeaut F, Pouponnot C, Ramaswamy V, Korshunov A, Borkhardt A, Reifenberger G, Poullet P, Taylor MD, Kool M, Pfister SM, Kawauchi D, Barillot E, Remke M, Ayrault O. Forget A, et al. Among authors: okonechnikov k. Cancer Cell. 2018 Sep 10;34(3):379-395.e7. doi: 10.1016/j.ccell.2018.08.002. Cancer Cell. 2018. PMID: 30205043 Free article.
Desmoplastic/nodular medulloblastomas (DNMB) and medulloblastomas with extensive nodularity (MBEN) disclose similar epigenetic signatures but different transcriptional profiles.
Korshunov A, Sahm F, Okonechnikov K, Ryzhova M, Stichel D, Schrimpf D, Casalini B, Sievers P, Meyer J, Zheludkova O, Golanov A, Lichter P, Jones DTW, Pfister SM, Kool M, von Deimling A. Korshunov A, et al. Among authors: okonechnikov k. Acta Neuropathol. 2019 Jun;137(6):1003-1015. doi: 10.1007/s00401-019-01981-6. Epub 2019 Mar 2. Acta Neuropathol. 2019. PMID: 30826918
42 results