Dr. Rob Scharpf

Publications

• Lai J, Yang Y, Liu Y, Scharpf RB, Karchin R. Assessing the merits: an opinion on the effectiveness of simulation techniques in tumor subclonal reconstruction. Bioinformatics Advances, 2024 June. doi: 10.1093/bioadv/vbae094. PMID: 38948008; PMCID: PMC11213631.
• Braxton AM, Kiemen AL, Grahn MP, Forjaz A, Parksong J, Mahesh Babu J, Lai J, Zheng L, Niknafs N, Jiang L, Cheng H, Song Q, Reichel R, Graham S, Damanakis AI, Fischer CG, Mou S, Metz C, Granger J, Liu XD, Bachmann N, Zhu Y, Liu Y, Almagro-Pérez C, Jiang AC, Yoo J, Kim B, Du S, Foster E, Hsu JY, Rivera PA, Chu LC, Liu F, Fishman EK, Yuille A, Roberts NJ, Thompson ED, Scharpf RB, Cornish TC, Jiao Y, Karchin R, Hruban RH, Wu PH, Wirtz D, Wood LD. 3D genomic mapping reveals multifocality of human pancreatic precancers. Nature. 2024 May 1. doi: 10.1038/s41586-024-07359-3. Epub ahead of print. PMID: 38693266.
• Zheng L, Niknafs N, Wood LD, Karchin R, Scharpf RB. Estimation of cancer cell fractions and clone trees from multi-region sequencing of tumors. Bioinformatics. 2022 Aug 2;38(15):3677-3683. doi: 10.1093/bioinformatics/btac367. PMID: 35642899; PMCID: PMC9344857.
• Anagnostou V, Bruhm DC, Niknafs N, White JR, Shao XM, Sidhom JW, Stein J, Tsai HL, Wang H, Belcaid Z, Murray J, Balan A, Ferreira L, Ross-Macdonald P, Wind-Rotolo M, Baras AS, Taube J, Karchin R, Scharpf RB, Grasso C, Ribas A, Pardoll DM, Topalian SL, Velculescu VE.. (2020) Integrative tumor and immune cell multi-omic analyses predict response to immune checkpoint blockade in melanoma Cell Rep Med. Nov 17;1(8):100139
• Noë M, Niknafs N, Fischer CG, Hackeng WM, Beleva Guthrie V, Hosoda W, Debeljak M, Papp E, Adleff V, White JR, Luchini C, Pea A, Scarpa A, Butturini G, Zamboni G, Castelli P, Hong SM, Yachida S, Hiraoka N, Gill AJ, Samra JS, Offerhaus GJA, Hoorens A, Verheij J, Jansen C, Adsay NV, Jiang W, Winter J, Albores-Saavedra J, Terris B, Thompson ED, Roberts NJ, Hruban RH, Karchin R, Scharpf RB, Brosens LAA, Velculescu VE, Wood LD. (2020) Genomic characterization of malignant progression in neoplastic pancreatic cysts. Nat. Comm. Aug 14;11(1):4085. doi: 10.1038/s41467-020-17917-8.
• 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 MB, Karchin R, Pardoll DM, Baylin SB, Brahmer JR, Scharpf RB, Forde PM, Velculescu VE. (2020) Multimodal genomic features predict outcome of immune checkpoint blockade in non-small-cell lung cancer Nature Cancer 1 (1), 99-111
• Fischer CG, Guthrie VB, Braxton AM, Zheng L, Wang P, Song Q, Griffin JF, Chianchiano PE, Hosoda W, Niknafs N, Springer S, Molin MD, Masica D, Scharpf RB, Thompson ED, He J, Wolfgang CL, Hruban RH, Roberts NJ, Lennon AM, Jiao Y, Karchin R, Wood LD. Intraductal Papillary Mucinous Neoplasms Arise from Multiple Independent Clones, Each With Distinct Mutations. Gastroenterology. Jun 5. pii: S0016-5085(19)40987-6. doi: 10.1053/j.gastro.2019.06.001.
• Anagnostou V, Forde PM, White JR, Niknafs N, Hruban C, Naidoo J, Marrone KA, 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. (2019). Dynamics of tumor and immune responses during immune checkpoint blockade in non-small cell lung cancer. Cancer Research. Dec 12. pii: canres.1127.2018. doi: 10.1158/0008-5472.CAN-18-1127. [Epub ahead of print]
• 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. High grade serous ovarian carcinomas originate in the fallopian tube. Nat Commun. 2017 Oct 23;8(1):1093. doi: 10.1038/s41467-017-00962-1. PMID: 29061967; PMCID: PMC5653668.
• 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. Evolution of Neoantigen Landscape during Immune Checkpoint Blockade in Non-Small Cell Lung Cancer. Cancer Discov. 2017 Mar;7(3):264-276. doi: 10.1158/2159-8290.CD-16-0828. Epub 2016 Dec 28. PMID: 28031159; PMCID: PMC5733805.
• Bertotti A, Papp E, Jones S, Adleff V, Anagnostou V, Sausen M, Phallen J, Tokheim C, Niknafs N, Nesselbush M, Lytle K, Cottino F, Migliardi G, Zanella ER, Ribero D, Russolillo N, Mellano A, Muratore A, Paraluppi G, Salizzoni M, Marsoni S, Kragh M, Lantto J, Cassingena A, Li QK, Karchin R, Scharpf R, Sartore-Bianchi A, Siena S, Diaz LA, Trusolino L, Velculescu VE (2015) The Genomic Landscape of Response to EGFR Blockade in Colorectal Cancer. Nature. 526(7572):263-7