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Page 1
Genome-wide repeat landscapes in cancer and cell-free DNA.
Annapragada AV, Niknafs N, White JR, Bruhm DC, Cherry C, Medina JE, Adleff V, Hruban C, Mathios D, Foda ZH, Phallen J, Scharpf RB, Velculescu VE. Annapragada AV, et al. Among authors: niknafs n. Sci Transl Med. 2024 Mar 13;16(738):eadj9283. doi: 10.1126/scitranslmed.adj9283. Epub 2024 Mar 13. Sci Transl Med. 2024. PMID: 38478628
Genome-wide cell-free DNA fragmentation in patients with cancer.
Cristiano S, Leal A, Phallen J, Fiksel J, Adleff V, Bruhm DC, Jensen SØ, Medina JE, Hruban C, White JR, Palsgrove DN, Niknafs N, Anagnostou V, Forde P, Naidoo J, Marrone K, Brahmer J, Woodward BD, Husain H, van Rooijen KL, Ørntoft MW, Madsen AH, van de Velde CJH, Verheij M, Cats A, Punt CJA, Vink GR, van Grieken NCT, Koopman M, Fijneman RJA, Johansen JS, Nielsen HJ, Meijer GA, Andersen CL, Scharpf RB, Velculescu VE. Cristiano S, et al. Among authors: niknafs n. Nature. 2019 Jun;570(7761):385-389. doi: 10.1038/s41586-019-1272-6. Epub 2019 May 29. Nature. 2019. PMID: 31142840 Free PMC article.
Detection and characterization of lung cancer using cell-free DNA fragmentomes.
Mathios D, Johansen JS, Cristiano S, Medina JE, Phallen J, Larsen KR, Bruhm DC, Niknafs N, Ferreira L, Adleff V, Chiao JY, Leal A, Noe M, White JR, Arun AS, Hruban C, Annapragada AV, Jensen SØ, Ørntoft MW, Madsen AH, Carvalho B, de Wit M, Carey J, Dracopoli NC, Maddala T, Fang KC, Hartman AR, Forde PM, Anagnostou V, Brahmer JR, Fijneman RJA, Nielsen HJ, Meijer GA, Andersen CL, Mellemgaard A, Bojesen SE, Scharpf RB, Velculescu VE. Mathios D, et al. Among authors: niknafs n. Nat Commun. 2021 Aug 20;12(1):5060. doi: 10.1038/s41467-021-24994-w. Nat Commun. 2021. PMID: 34417454 Free PMC article.
Detecting Liver Cancer Using Cell-Free DNA Fragmentomes.
Foda ZH, Annapragada AV, Boyapati K, Bruhm DC, Vulpescu NA, Medina JE, Mathios D, Cristiano S, Niknafs N, Luu HT, Goggins MG, Anders RA, Sun J, Meta SH, Thomas DL, Kirk GD, Adleff V, Phallen J, Scharpf RB, Kim AK, Velculescu VE. Foda ZH, et al. Among authors: niknafs n. Cancer Discov. 2023 Mar 1;13(3):616-631. doi: 10.1158/2159-8290.CD-22-0659. Cancer Discov. 2023. PMID: 36399356 Free PMC article.
Dynamics of Sequence and Structural Cell-Free DNA Landscapes in Small-Cell Lung Cancer.
Sivapalan L, Iams WT, Belcaid Z, Scott SC, Niknafs N, Balan A, White JR, Kopparapu P, Cann C, Landon BV, Pereira G, Velculescu VE, Hann CL, Lovly CM, Anagnostou V. Sivapalan L, et al. Among authors: niknafs n. Clin Cancer Res. 2023 Jun 13;29(12):2310-2323. doi: 10.1158/1078-0432.CCR-22-2242. Clin Cancer Res. 2023. PMID: 37071497 Free PMC article.
Evolution of Neoantigen Landscape during Immune Checkpoint Blockade in Non-Small Cell Lung Cancer.
Anagnostou V, Smith KN, Forde PM, Niknafs N, Bhattacharya R, White J, Zhang T, Adleff V, Phallen J, Wali N, Hruban C, Guthrie VB, Rodgers K, Naidoo J, Kang H, Sharfman W, Georgiades C, Verde F, Illei P, Li QK, Gabrielson E, Brock MV, Zahnow CA, Baylin SB, Scharpf RB, Brahmer JR, Karchin R, Pardoll DM, Velculescu VE. Anagnostou V, et al. Among authors: niknafs n. Cancer Discov. 2017 Mar;7(3):264-276. doi: 10.1158/2159-8290.CD-16-0828. Epub 2016 Dec 28. Cancer Discov. 2017. PMID: 28031159 Free PMC article.
High grade serous ovarian carcinomas originate in the fallopian tube.
Labidi-Galy SI, Papp E, Hallberg D, Niknafs N, Adleff V, Noe M, Bhattacharya R, Novak M, Jones S, Phallen J, Hruban CA, Hirsch MS, Lin DI, Schwartz L, Maire CL, Tille JC, Bowden M, Ayhan A, Wood LD, Scharpf RB, Kurman R, Wang TL, Shih IM, Karchin R, Drapkin R, Velculescu VE. Labidi-Galy SI, et al. Among authors: niknafs n. Nat Commun. 2017 Oct 23;8(1):1093. doi: 10.1038/s41467-017-00962-1. Nat Commun. 2017. PMID: 29061967 Free PMC article.
A machine learning approach for somatic mutation discovery.
Wood DE, White JR, Georgiadis A, Van Emburgh B, Parpart-Li S, Mitchell J, Anagnostou V, Niknafs N, Karchin R, Papp E, McCord C, LoVerso P, Riley D, Diaz LA Jr, Jones S, Sausen M, Velculescu VE, Angiuoli SV. Wood DE, et al. Among authors: niknafs n. Sci Transl Med. 2018 Sep 5;10(457):eaar7939. doi: 10.1126/scitranslmed.aar7939. Sci Transl Med. 2018. PMID: 30185652 Free PMC article.
Dynamics of Tumor and Immune Responses during Immune Checkpoint Blockade in Non-Small Cell Lung Cancer.
Anagnostou V, Forde PM, White JR, Niknafs N, Hruban C, Naidoo J, Marrone K, Sivakumar IKA, Bruhm DC, Rosner S, Phallen J, Leal A, Adleff V, Smith KN, Cottrell TR, Rhymee L, Palsgrove DN, Hann CL, Levy B, Feliciano J, Georgiades C, Verde F, Illei P, Li QK, Gabrielson E, Brock MV, Isbell JM, Sauter JL, Taube J, Scharpf RB, Karchin R, Pardoll DM, Chaft JE, Hellmann MD, Brahmer JR, Velculescu VE. Anagnostou V, et al. Among authors: niknafs n. Cancer Res. 2019 Mar 15;79(6):1214-1225. doi: 10.1158/0008-5472.CAN-18-1127. Epub 2018 Dec 12. Cancer Res. 2019. PMID: 30541742 Free PMC article.
Multimodal genomic features predict outcome of immune checkpoint blockade in non-small-cell lung cancer.
Anagnostou V, Niknafs N, Marrone K, Bruhm DC, White JR, Naidoo J, Hummelink K, Monkhorst K, Lalezari F, Lanis M, Rosner S, Reuss JE, Smith KN, Adleff V, Rodgers K, Belcaid Z, Rhymee L, Levy B, Feliciano J, Hann CL, Ettinger DS, Georgiades C, Verde F, Illei P, Li QK, Baras AS, Gabrielson E, Brock MV, Karchin R, Pardoll DM, Baylin SB, Brahmer JR, Scharpf RB, Forde PM, Velculescu VE. Anagnostou V, et al. Among authors: niknafs n. Nat Cancer. 2020 Jan;1(1):99-111. doi: 10.1038/s43018-019-0008-8. Epub 2020 Jan 13. Nat Cancer. 2020. PMID: 32984843 Free PMC article.
58 results