Publications

Hou P, Kapoor A, Zhang Q, Li J, Wu CJ, Li J, Lan Z, Tang M, Ma X, Ackroyd JJ, Kalluri R, Zhang J, Jiang S, Spring DJ, Wang YA, DePinho RA. Tumor Microenvironment Remodeling Enables Bypass of Oncogenic KRAS Dependency in Pancreatic Cancer. Cancer Discov. 2020 Jul;10(7):1058-1077. doi: 10.1158/2159-8290.CD-19-0597. Epub 2020 Apr 27. PubMed PMID: 32341020; PubMed Central PMCID: PMC7334087. 

Mitra A, Grossman Biegert GW, Delgado AY, Karpinets TV, Solley TN, Mezzari MP, Yoshida-Court K, Petrosino JF, Mikkelson MD, Lin L, Eifel P, Zhang J, Ramondetta LM, Jhingran A, Sims TT, Schmeler K, Okhuysen P, Colbert LE, Klopp AH. Microbial Diversity and Composition Is Associated with Patient-Reported Toxicity during Chemoradiation Therapy for Cervical Cancer.Int J Radiat Oncol Biol Phys. 2020 May 1;107(1):163-171. doi: 10.1016/j.ijrobp.2019.12.040. Epub 2020 Jan 25. PubMed PMID: 31987960. 

Mitra A, Andrews MC, Roh W, De Macedo MP, Hudgens CW, Carapeto F, Singh S, Reuben A, Wang F, Mao X, Song X, Wani K, Tippen S, Ng KS, Schalck A, Sakellariou-Thompson DA, Chen E, Reddy SM, Spencer CN, Wiesnoski D, Little LD, Gumbs C, Cooper ZA, Burton EM, Hwu P, Davies MA, Zhang J, Bernatchez C, Navin N, Sharma P, Allison JP, Wargo JA, Yee C, Tetzlaff MT, Hwu WJ, Lazar AJ, Futreal PA. Spatially resolved analyses link genomic and immune diversity and reveal unfavorable neutrophil activation in melanoma. Nat Commun. 2020 Apr 15;11(1):1839. doi: 10.1038/s41467-020-15538-9. PubMed PMID: 32296058; PubMed Central PMCID: PMC7160105. 

Lee S, Zhao L, Rojas C, Bateman NW, Yao H, Lara OD, Celestino J, Morgan MB, Nguyen TV, Conrads KA, Rangel KM, Dood RL, Hajek RA, Fawcett GL, Chu RA, Wilson K, Loffredo JL, Viollet C, Jazaeri AA, Dalgard CL, Mao X, Song X, Zhou M, Hood BL, Banskota N, Wilkerson MD, Te J, Soltis AR, Roman K, Dunn A, Cordover D, Eterovic AK, Liu J, Burks JK, Baggerly KA, Fleming ND, Lu KH, Westin SN, Coleman RL, Mills GB, Casablanca Y, Zhang J, Conrads TP, Maxwell GL, Futreal PA, Sood AK. Molecular Analysis of Clinically Defined Subsets of High-Grade Serous Ovarian Cancer.Cell Rep. 2020 Apr 14;31(2):107502. doi: 10.1016/j.celrep.2020.03.066. PubMed PMID: 32294438; PubMed Central PMCID: PMC7234854. 

Subudhi SK, Vence L, Zhao H, Blando J, Yadav SS, Xiong Q, Reuben A, Aparicio A, Corn PG, Chapin BF, Pisters LL, Troncoso P, Tidwell RS, Thall P, Wu CJ, Zhang J, Logothetis CL, Futreal A, Allison JP, Sharma P. Neoantigen responses, immune correlates, and favorable outcomes after ipilimumab treatment of patients with prostate cancer. Sci Transl Med. 2020 Apr 1;12(537). doi: 10.1126/scitranslmed.aaz3577. PubMed PMID: 32238575. 

Dey P, Li J, Zhang J, Chaurasiya S, Strom A, Wang H, Liao WT, Cavallaro F, Denz P, Bernard V, Yen EY, Genovese G, Gulhati P, Liu J, Chakravarti D, Deng P, Zhang T, Carbone F, Chang Q, Ying H, Shang X, Spring DJ, Ghosh B, Putluri N, Maitra A, Wang YA, DePinho RA. Oncogenic KRAS-Driven Metabolic Reprogramming in Pancreatic Cancer Cells Utilizes Cytokines from the Tumor Microenvironment. Cancer Discov. 2020 Apr;10(4):608-625. doi: 10.1158/2159-8290.CD-19-0297. Epub 2020 Feb 11. PubMed PMID: 32046984; PubMed Central PMCID: PMC7125035. 

Jain P, Zhang S, Kanagal-Shamanna R, Ok CY, Nomie K, Gonzalez GN, Gonzalez-Pagan O, Hill HA, Lee HJ, Fayad L, Westin J, Nastoupil L, Hagemeister F, Chen W, Oriabure O, Badillo M, Jiang C, Yixin Y, Li S, Tang G, Yin CC, Patel KP, Medeiros LJ, Nair R, Ahmed S, Iyer SP, Thirumurthi S, Champlin R, Xu G, Tinsu P, Santos D, Wang R, Han G, Zhang J, Song X, Neelapu S, Romaguera J, Futreal A, Flowers C, Fowler N, Wang L, Wang ML. Genomic profiles and clinical outcomes of de novo blastoid/pleomorphic MCL are distinct from those of transformed MCL. Blood Adv. 2020 Mar 24;4(6):1038-1050. doi: 10.1182/bloodadvances.2019001396. PubMed PMID: 32191807; PubMed Central PMCID: PMC7094021. 

Jin Y, Bao H, Le X, Fan X, Tang M, Shi X, Zhao J, Yan J, Xu Y, Quek K, Elamin YY, Zhang J, Futreal PA, Wistuba II, Heymach JV, Lou G, Shao L, He Q, Lin C, Wu X, Shao YW, Wang X, He J, Chen Y, Stebbing J, Chen M, Zhang J, Yu X. Correction: Distinct co-acquired alterations and genomic evolution during TKI treatment in non-small-cell lung cancer patients with or without acquired T790M mutation. Oncogene. 2020 Feb;39(9):2027. doi: 10.1038/s41388-019-1143-5. PubMed PMID: 31831835. 

Jin Y, Bao H, Le X, Fan X, Tang M, Shi X, Zhao J, Yan J, Xu Y, Quek K, Elamin YY, Zhang J, Futreal PA, Wistuba II, Heymach JV, Lou G, Shao L, He Q, Lin C, Wu X, Shao YW, Wang X, He J, Chen Y, Stebbing J, Chen M, Zhang J, Yu X. Distinct co-acquired alterations and genomic evolution during TKI treatment in non-small-cell lung cancer patients with or without acquired T790M mutation. Oncogene. 2020 Feb;39(9):1846-1859. doi: 10.1038/s41388-019-1104-z. Epub 2019 Nov 21. PubMed PMID: 31754213. 

Reuben A, Zhang J, Chiou SH, Gittelman RM, Li J, Lee WC, Fujimoto J, Behrens C, Liu X, Wang F, Quek K, Wang C, Kheradmand F, Chen R, Chow CW, Lin H, Bernatchez C, Jalali A, Hu X, Wu CJ, Eterovic AK, Parra ER, Yusko E, Emerson R, Benzeno S, Vignali M, Wu X, Ye Y, Little LD, Gumbs C, Mao X, Song X, Tippen S, Thornton RL, Cascone T, Snyder A, Wargo JA, Herbst R, Swisher S, Kadara H, Moran C, Kalhor N, Zhang J, Scheet P, Vaporciyan AA, Sepesi B, Gibbons DL, Robins H, Hwu P, Heymach JV, Sharma P, Allison JP, Baladandayuthapani V, Lee JJ, Davis MM, Wistuba II, Futreal PA, Zhang J. Comprehensive T cell repertoire characterization of non-small cell lung cancer. Nat Commun. 2020 Jan 30;11(1):603. doi: 10.1038/s41467-019-14273-0. PubMed PMID: 32001676; PubMed Central PMCID: PMC6992630. 

Fountzilas E, Kotoula V, Koliou GA, Giannoulatou E, Gogas H, Papadimitriou C, Tikas I, Zhang J, Papadopoulou K, Zagouri F, Christodoulou C, Koutras A, Makatsoris T, Chrisafi S, Linardou H, Varthalitis I, Papatsibas G, Razis E, Papakostas P, Samantas E, Aravantinos G, Bafaloukos D, Kosmidis P, Koumarianou A, Psyrri A, Pentheroudakis G, Pectasides D, Futreal A, Fountzilas G, Tsimberidou AM. Pathogenic mutations and overall survival in 3,084 patients with cancer: the Hellenic Cooperative Oncology Group Precision Medicine Initiative. Oncotarget. 2020 Jan 7;11(1):1-14. doi: 10.18632/oncotarget.27338. eCollection 2020 Jan 7. PubMed PMID: 32002119; PubMed Central PMCID: PMC6967777. 

Wang R, Song S, Harada K, Ghazanfari Amlashi F, Badgwell B, Pizzi MP, Xu Y, Zhao W, Dong X, Jin J, Wang Y, Scott A, Ma L, Huo L, Vicente D, Blum Murphy M, Shanbhag N, Tatlonghari G, Thomas I, Rogers J, Kobayashi M, Vykoukal J, Estrella JS, Roy-Chowdhuri S, Han G, Zhang S, Mao X, Song X, Zhang J, Gu J, Johnson RL, Calin GA, Peng G, Lee JS, Hanash SM, Futreal A, Wang Z, Wang L, Ajani JA. Multiplex profiling of peritoneal metastases from gastric adenocarcinoma identified novel targets and molecular subtypes that predict treatment response. Gut. 2020 Jan;69(1):18-31. doi: 10.1136/gutjnl-2018-318070. Epub 2019 Jun 6. PubMed PMID: 31171626; PubMed Central PMCID: PMC6943252. 

Kapoor A, Yao W, Ying H, Hua S, Liewen A, Wang Q, Zhong Y, Wu CJ, Sadanandam A, Hu B, Chang Q, Chu GC, Al-Khalil R, Jiang S, Xia H, Fletcher-Sananikone E, Lim C, Horwitz GI, Viale A, Pettazzoni P, Sanchez N, Wang H, Protopopov A, Zhang J, Heffernan T, Johnson RL, Chin L, Wang YA, Draetta G, DePinho RA. Yap1 Activation Enables Bypass of Oncogenic Kras Addiction in Pancreatic Cancer. Cell. 2019 Nov 14;179(5):1239. doi: 10.1016/j.cell.2019.10.037. PubMed PMID: 31730860.

Hou P, Ma X, Zhang Q, Wu CJ, Liao W, Li J, Wang H, Zhao J, Zhou X, Guan C, Ackroyd J, Jiang S, Zhang J, Spring DJ, Wang YA, DePinho RA. USP21 deubiquitinase promotes pancreas cancer cell stemness via Wnt pathway activation. Genes Dev. 2019 Oct 1;33(19-20):1361-1366. doi: 10.1101/gad.326314.119. Epub 2019 Sep 5. PubMed PMID: 31488580; PubMed Central PMCID: PMC6771391.

Manasanch EE, Han G, Mathur R, Qing Y, Zhang Z, Lee H, Weber DM, Amini B, Berkova Z, Eterovic K, Zhang S, Zhang J, Song X, Mao X, Morgan M, Feng L, Baladandayuthapani V, Futreal A, Wang L, Neelapu SS, Orlowski RZ. A pilot study of pembrolizumab in smoldering myeloma: report of the clinical, immune, and genomic analysis. Blood Adv. 2019 Aug 13;3(15):2400-2408. doi: 10.1182/bloodadvances.2019000300. PubMed PMID: 31405950; PubMed Central PMCID: PMC6693011.

Hu X, Fujimoto J, Ying L, Fukuoka J, Ashizawa K, Sun W, Reuben A, Chow CW, McGranahan N, Chen R, Hu J, Godoy MC, Tabata K, Kuroda K, Shi L, Li J, Behrens C, Parra ER, Little LD, Gumbs C, Mao X, Song X, Tippen S, Thornton RL, Kadara H, Scheet P, Roarty E, Ostrin EJ, Wang X, Carter BW, Antonoff MB, Zhang J, Vaporciyan AA, Pass H, Swisher SG, Heymach JV, Lee JJ, Wistuba II, Hong WK, Futreal PA, Su D, Zhang J. Multi-region exome sequencing reveals genomic evolution from preneoplasia to lung adenocarcinoma. Nat Commun. 2019 Jul 5;10(1):2978. doi: 10.1038/s41467-019-10877-8. PubMed PMID: 31278276; PubMed Central PMCID: PMC6611767.

Wang R, Song S, Harada K, Ghazanfari Amlashi F, Badgwell B, Pizzi MP, Xu Y, Zhao W, Dong X, Jin J, Wang Y, Scott A, Ma L, Huo L, Vicente D, Blum Murphy M, Shanbhag N, Tatlonghari G, Thomas I, Rogers J, Kobayashi M, Vykoukal J, Estrella JS, Roy-Chowdhuri S, Han G, Zhang S, Mao X, Song X, Zhang J, Gu J, Johnson RL, Calin GA, Peng G, Lee JS, Hanash SM, Futreal A, Wang Z, Wang L, Ajani JA. Multiplex profiling of peritoneal metastases from gastric adenocarcinoma identified novel targets and molecular subtypes that predict treatment response. Gut. 2019 Jun 6;. doi: 10.1136/gutjnl-2018-318070. [Epub ahead of print] PubMed PMID: 31171626.

Zhang L, Yao Y, Zhang S, Liu Y, Guo H, Ahmed M, Bell T, Zhang H, Han G, Lorence E, Badillo M, Zhou S, Sun Y, Di Francesco ME, Feng N, Haun R, Lan R, Mackintosh SG, Mao X, Song X, Zhang J, Pham LV, Lorenzi PL, Marszalek J, Heffernan T, Draetta G, Jones P, Futreal A, Nomie K, Wang L, Wang M. Metabolic reprogramming toward oxidative phosphorylation identifies a therapeutic target for mantle cell lymphoma. Sci Transl Med. 2019 May 8;11(491). doi: 10.1126/scitranslmed.aau1167. PubMed PMID: 31068440.

Liao W, Overman MJ, Boutin AT, Shang X, Zhao D, Dey P, Li J, Wang G, Lan Z, Li J, Tang M, Jiang S, Ma X, Chen P, Katkhuda R, Korphaisarn K, Chakravarti D, Chang A, Spring DJ, Chang Q, Zhang J, Maru DM, Maeda DY, Zebala JA, Kopetz S, Wang YA, DePinho RA. KRAS-IRF2 Axis Drives Immune Suppression and Immune Therapy Resistance in Colorectal Cancer. Cancer Cell.2019 Apr 15;35(4):559-572.e7. doi: 10.1016/j.ccell.2019.02.008. Epub 2019 Mar 21. PubMed PMID: 30905761; PubMed Central PMCID: PMC6467776.

Seth S, Li CY, Ho IL, Corti D, Loponte S, Sapio L, Del Poggetto E, Yen EY, Robinson FS, Peoples M, Karpinets T, Deem AK, Kumar T, Song X, Jiang S, Kang Y, Fleming J, Kim M, Zhang J, Maitra A, Heffernan TP, Giuliani V, Genovese G, Futreal A, Draetta GF, Carugo A, Viale A. Pre-existing Functional Heterogeneity of Tumorigenic Compartment as the Origin of Chemoresistance in Pancreatic Tumors. Cell Rep. 2019 Feb 5;26(6):1518-1532.e9. doi: 10.1016/j.celrep.2019.01.048. PubMed PMID: 30726735.

Yilmaz M, Wang F, Loghavi S, Bueso-Ramos C, Gumbs C, Little L, Song X, Zhang J, Kadia T, Borthakur G, Jabbour E, Pemmaraju N, Short N, Garcia-Manero G, Estrov Z, Kantarjian H, Futreal A, Takahashi K, Ravandi F. Late relapse in acute myeloid leukemia (AML): clonal evolution or therapy-related leukemia?. Blood Cancer J. 2019 Jan 16;9(2):7. doi: 10.1038/s41408-019-0170-3. PubMed PMID: 30651532; PubMed Central PMCID: PMC6335405.

Ohanian M, Rozovski U, Kanagal-Shamanna R, Abruzzo LV, Loghavi S, Kadia T, Futreal A, Bhalla K, Zuo Z, Huh YO, Post SM, Ruvolo P, Garcia-Manero G, Andreeff M, Kornblau S, Borthakur G, Hu P, Medeiros LJ, Takahashi K, Hornbaker MJ, Zhang J, Nogueras-González GM, Huang X, Verstovsek S, Estrov Z, Pierce S, Ravandi F, Kantarjian HM, Bueso-Ramos CE, Cortes JE. MYC protein expression is an important prognostic factor in acute myeloid leukemia. Leuk Lymphoma. 2019 Jan;60(1):37-48. doi: 10.1080/10428194.2018.1464158. Epub 2018 May 9. PubMed PMID: 29741984; PubMed Central PMCID: PMC6226369.

Gopalakrishnan V, Spencer CN, Nezi L, Reuben A, Andrews MC, Karpinets TV, Prieto PA, Vicente D, Hoffman K, Wei SC, Cogdill AP, Zhao L, Hudgens CW, Hutchinson DS, Manzo T, Petaccia de Macedo M, Cotechini T, Kumar T, Chen WS, Reddy SM, Szczepaniak Sloane R, Galloway-Pena J, Jiang H, Chen PL, Shpall EJ, Rezvani K, Alousi AM, Chemaly RF, Shelburne S, Vence LM, Okhuysen PC, Jensen VB, Swennes AG, McAllister F, Marcelo Riquelme Sanchez E, Zhang Y, Le Chatelier E, Zitvogel L, Pons N, Austin-Breneman JL, Haydu LE, Burton EM, Gardner JM, Sirmans E, Hu J, Lazar AJ, Tsujikawa T, Diab A, Tawbi H, Glitza IC, Hwu WJ, Patel SP, Woodman SE, Amaria RN, Davies MA, Gershenwald JE, Hwu P, Lee JE, Zhang J, Coussens LM, Cooper ZA, Futreal PA, Daniel CR, Ajami NJ, Petrosino JF, Tetzlaff MT, Sharma P, Allison JP, Jenq RR, Wargo JA. Gut microbiome modulates response to anti-PD-1 immunotherapy in melanoma patients. Science. 2018 Jan 5;359(6371):97-103. doi: 10.1126/science.aan4236. Epub 2017 Nov 2. PubMed PMID: 29097493; PubMed Central PMCID: PMC5827966 

Montalban-Bravo G, Takahashi K, Patel K, Wang F, Xingzhi S, Nogueras GM, Huang X, Pierola AA, Jabbour E, Colla S, Gañan-Gomez I, Borthakur G, Daver N, Estrov Z, Kadia T, Pemmaraju N, Ravandi F, Bueso-Ramos C, Chamseddine A, Konopleva M, Zhang J, Kantarjian H, Futreal A, Garcia-Manero G. Impact of the number of mutations in survival and response outcomes to hypomethylating agents in patients with myelodysplastic syndromes or myelodysplastic/myeloproliferative neoplasms. Oncotarget. 2018 Jan 3;9(11):9714-9727. doi: 10.18632/oncotarget.23882. eCollection 2018 Feb 9. PubMed PMID: 29515765; PubMed Central PMCID: PMC5839396.

Wang JF, Pu X, Zhang X, Chen K, Xi Y, Wang J, Mao X, Zhang J, Heymach JV, Antonoff MB, Hofstetter WL, Mehran RJ, Rice DC, Roth JA, Sepesi B, Swisher SG, Vaporciyan AA, Walsh GL, Meng QH, Shaw KR, Eterovic AK, Fang B. Variants with a low allele frequency detected in genomic DNA affect the accuracy of mutation detection in cell-free DNA by next-generation sequencing.Cancer. 2018 Mar 1;124(5):1061-1069. doi: 10.1002/cncr.31152. Epub 2017 Nov 27. PubMed PMID: 29178133; PubMed Central PMCID: PMC5821585.

Karpinets TV, Gopalakrishnan V, Wargo J, Futreal AP, Schadt CW, Zhang J. Linking Associations of Rare Low-Abundance Species to Their Environments by Association Networks. Front Microbiol. 2018 Mar 7;9:297. doi: 10.3389/fmicb.2018.00297. eCollection 2018. PubMed PMID: 29563898; PubMed Central PMCID: PMC5850922.

Beird HC, Wu CC, Ingram DR, Wang WL, Alimohamed A, Gumbs C, Little L, Song X, Feig BW, Roland CL, Zhang J, Benjamin RS, Hwu P, Lazar AJ, Futreal PA, Somaiah N. Genomic profiling of dedifferentiated liposarcoma compared to matched well-differentiated liposarcoma reveals higher genomic complexity and a common origin. Cold Spring Harb Mol Case Stud. 2018 Apr 2;4(2). pii: a002386. doi: 10.1101/mcs.a002386. Print 2018 Apr. PubMed PMID: 29610390; PubMed Central PMCID: PMC5880260.

Takahashi K, Hu B, Wang F, Yan Y, Kim E, Vitale C, Patel KP, Strati P, Gumbs C, Little L, Tippen S, Song X, Zhang J, Jain N, Thompson P, Garcia-Manero G, Kantarjian H, Estrov Z, Do KA, Keating M, Burger JA, Wierda WG, Futreal PA, Ferrajoli A. Clinical implications of cancer gene mutations in patients with chronic lymphocytic leukemia treated with lenalidomide. Blood. 2018 Apr 19;131(16):1820-1832. doi: 10.1182/blood-2017-11-817296. Epub 2018 Jan 22. PubMed PMID: 29358183; PubMed Central PMCID: PMC5909764.

Romano G, Chen PL, Song P, McQuade JL, Liang RJ, Liu M, Roh W, Duose DY, Carapeto FCL, Li J, Teh JLF, Aplin AE, Chen M, Zhang J, Lazar AJ, Davies MA, Futreal PA, Amaria RN, Zhang DY, Wargo JA, Kwong LN. A Preexisting Rare PIK3CA^E545KSubpopulation Confers Clinical Resistance to MEK plus CDK4/6 Inhibition in NRAS Melanoma and Is Dependent on S6K1 Signaling. Cancer Discov. 2018 May;8(5):556-567. doi: 10.1158/2159-8290.CD-17-0745. Epub 2018 Mar 1. PubMed PMID: 29496665; PubMed Central PMCID: PMC5932238.

Ohanian M, Rozovski U, Kanagal-Shamanna R, Abruzzo LV, Loghavi S, Kadia T, Futreal A, Bhalla K, Zuo Z, Huh YO, Post SM, Ruvolo P, Garcia-Manero G, Andreeff M, Kornblau S, Borthakur G, Hu P, Medeiros LJ, Takahashi K, Hornbaker MJ, Zhang J, Nogueras-González GM, Huang X, Verstovsek S, Estrov Z, Pierce S, Ravandi F, Kantarjian HM, Bueso-Ramos CE, Cortes JE. MYC protein expression is an important prognostic factor in acute myeloid leukemia. Leuk Lymphoma. 2018 May 9:1-12. doi: 10.1080/10428194.2018.1464158. [Epub ahead of print] PubMed PMID: 29741984.

Lee WC, Diao L, Wang J, Zhang J, Roarty EB, Varghese S, Chow CW, Fujimoto J, Behrens C, Cascone T, Peng W, Kalhor N, Moran CA, Weissferdt A, Johnson FM, William WN Jr, Swisher SG, Lee JJ, Hong WK, Heymach JV, Wistuba II, Futreal PA, Zhang J. Multiregion gene expression profiling reveals heterogeneity in molecular subtypes and immunotherapy response signatures in lung cancer. Mod Pathol. 2018 Jun;31(6):947-955. doi: 10.1038/s41379-018-0029-3. Epub 2018 Feb 6. PubMed PMID: 29410488.

Morita K, Kantarjian HM, Wang F, Yan Y, Bueso-Ramos C, Sasaki K, Issa GC, Wang S, Jorgensen J, Song X, Zhang J, Tippen S, Thornton R, Coyle M, Little L, Gumbs C, Pemmaraju N, Daver N, DiNardo CD, Konopleva M, Andreeff M, Ravandi F, Cortes JE, Kadia T, Jabbour E, Garcia-Manero G, Patel KP, Futreal PA, Takahashi K. Clearance of Somatic Mutations at Remission and the Risk of Relapse in Acute Myeloid Leukemia. J Clin Oncol. 2018 Jun 20;36(18):1788-1797. doi: 10.1200/JCO.2017.77.6757. Epub 2018 Apr 27. PubMed PMID: 29702001; PubMed Central PMCID: PMC6008108.

Hillman RT, Celestino J, Terranova C, Beird HC, Gumbs C, Little L, Nguyen T, Thornton R, Tippen S, Zhang J, Lu KH, Gershenson DM, Rai K, Broaddus RR, Futreal PA. KMT2D/MLL2 inactivation is associated with recurrence in adult-type granulosa cell tumors of the ovary. Nat Commun. 2018 Jun 27;9(1):2496. doi: 10.1038/s41467-018-04950-x. PubMed PMID: 29950560; PubMed Central PMCID: PMC6021426.

Nguyen J, Jiao J, Smoot K, Watt GP, Zhao C, Song X, Stevenson HL, McCormick JB, Fisher-Hoch SP, Zhang J, Futreal PA, Beretta L. Toll-like receptor 4: a target for chemoprevention of hepatocellular carcinoma in obesity and steatohepatitis. Oncotarget. 2018 Jun 29;9(50):29495-29507. doi: 10.18632/oncotarget.25685. eCollection 2018 Jun 29. PubMed PMID: 30034633; PubMed Central PMCID: PMC6047684.

Takahashi K, Wang F, Morita K, Yan Y, Hu P, Zhao P, Zhar AA, Wu CJ, Gumbs C, Little L, Tippen S, Thornton R, Coyle M, Mendoza M, Thompson E, Zhang J, DiNardo CD, Jain N, Ravandi F, Cortes JE, Garcia-Manero G, Kornblau S, Andreeff M, Jabbour E, Bueso-Ramos C, Takaori-Kondo A, Konopleva M, Patel K, Kantarjian H, Futreal PA. Integrative genomic analysis of adult mixed phenotype acute leukemia delineates lineage associated molecular subtypes. Nat Commun. 2018 Jul 10;9(1):2670. doi: 10.1038/s41467-018-04924-z. PubMed PMID: 29991687; PubMed Central PMCID: PMC6039465.

Wu CC, Beird HC, Zhang J, Futreal PA. FusionPathway: Prediction of pathways and therapeutic targets associated with gene fusions in cancer. PLoS Comput Biol. 2018 Jul 24;14(7):e1006266. doi: 10.1371/journal.pcbi.1006266. eCollection 2018 Jul. PubMed PMID: 30040819; PubMed Central PMCID: PMC6075785.

Kalaora S, Wolf Y, Feferman T, Barnea E, Greenstein E, Reshef D, Tirosh I, Reuben A, Patkar S, Levy R, Quinkhardt J, Omokoko T, Qutob N, Golani O, Zhang J, Mao X, Song X, Bernatchez C, Haymaker C, Forget MA, Creasy C, Greenberg P, Carter BW, Cooper ZA, Rosenberg SA, Lotem M, Sahin U, Shakhar G, Ruppin E, Wargo JA, Friedman N, Admon A, Samuels Y. Combined Analysis of Antigen Presentation and T-cell Recognition Reveals Restricted Immune Responses in Melanoma. Cancer Discov. 2018 Sep 12. doi: 10.1158/2159-8290.CD-17-1418. [Epub ahead of print] PubMed PMID: 30209080.

Sakellariou-Thompson D, Forget MA, Creasy C, Bernard V, Zhao L, Kim YU, Hurd MW, Uraoka N, Parra ER, Kang Y, Bristow CA, Rodriguez-Canales J, Fleming JB, Varadhachary G, Javle M, Overman MJ, Alvarez HA, Heffernan TP, Zhang J, Hwu P, Maitra A, Haymaker C, Bernatchez C. 4-1BB Agonist Focuses CD8 Tumor-Infiltrating T-Cell Growth into a Distinct Repertoire Capable of Tumor Recognition in Pancreatic Cancer. Clinical cancer research: an official journal of the American Association for Cancer Research. 2017; 23(23):7263-7275. PMID: 28947567 

Wang JF, Pu X, Zhang X, Chen K, Xi Y, Wang J, Mao X, Zhang J, Heymach JV, Antonoff MB, Hofstetter WL, Mehran RJ, Rice DC, Roth JA, Sepesi B, Swisher SG, Vaporciyan AA, Walsh GL, Meng QH, Shaw KR, Eterovic AK, Fang B. Variants with a low allele frequency detected in genomic DNA affect the accuracy of mutation detection in cell-free DNA by next-generation sequencing. Cancer. 2017. PMID: 29178133 

Gopalakrishnan V, Spencer CN, Nezi L, Reuben A, Andrews MC, Karpinets TV, Prieto PA, Vicente D, Hoffman K, Wei SC, Cogdill AP, Zhao L, Hudgens CW, Hutchinson DS, Manzo T, Petaccia de Macedo M, Cotechini T, Kumar T, Chen WS, Reddy SM, Sloane RS, Galloway-Pena J, Jiang H, Chen PL, Shpall EJ, Rezvani K, Alousi AM, Chemaly RF, Shelburne S, Vence LM, Okhuysen PC, Jensen VB, Swennes AG, McAllister F, Sanchez EMR, Zhang Y, Le Chatelier E, Zitvogel L, Pons N, Austin-Breneman JL, Haydu LE, Burton EM, Gardner JM, Sirmans E, Hu J, Lazar AJ, Tsujikawa T, Diab A, Tawbi H, Glitza IC, Hwu WJ, Patel SP, Woodman SE, Amaria RN, Davies MA, Gershenwald JE, Hwu P, Lee JE, Zhang J, Coussens LM, Cooper ZA, Futreal PA, Daniel CR, Ajami NJ, Petrosino JF, Tetzlaff MT, Sharma P, Allison JP, Jenq RR, Wargo JA. Gut microbiome modulates response to anti-PD-1 immunotherapy in melanoma patients. Science. 2017. PMID: 29097493 

Liu B, Mitani Y, Rao X, Zafereo M, Zhang J, Zhang J, Futreal PA, Lozano G, El-Naggar AK. Spatio-Temporal Genomic Heterogeneity, Phylogeny, and Metastatic Evolution in Salivary Adenoid Cystic Carcinoma. Journal of the National Cancer Institute. 2017; 109(10). PMID: 29117356

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