Publications

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

Zhang Y, Kwok-Shing Ng P, Kucherlapati M, Chen F, Liu Y, Tsang YH, de Velasco G, Jeong KJ, Akbani R, Hadjipanayis A, Pantazi A, Bristow CA, Lee E, Mahadeshwar HS, Tang J, Zhang J, Yang L, Seth S, Lee S, Ren X, Song X, Sun H, Seidman J, Luquette LJ, Xi R, Chin L, Protopopov A, Westbrook TF, Shelley CS, Choueiri TK, Ittmann M, Van Waes C, Weinstein JN, Liang H, Henske EP, Godwin AK, Park PJ,
Kucherlapati R, Scott KL, Mills GB, Kwiatkowski DJ, Creighton CJ. A Pan-Cancer Proteogenomic Atlas of PI3K/AKT/mTOR Pathway Alterations. Cancer cell. 2017; 31(6):820-832.e3. PMID: 28528867.  PMCID: PMC5502825

Kwong LN, Zou L, Chagani S, Pedamallu CS, Liu M, Jiang S, Protopopov A, Zhang J, Getz G, Chin L. Modeling Genomic Instability and Selection Pressure in a Mouse Model of Melanoma. Cell reports. 2017; 19(7):1304-1312. PMID: 28514651. PMCID: PMC5512587

Barthel FP, Wei W, Tang M, Martinez-Ledesma E, Hu X, Amin SB, Akdemir KC, Seth S, Song X, Wang Q, Lichtenberg T, Hu J, Zhang J, Zheng S, Verhaak RG. Systematic analysis of telomere length and somatic alterations in 31 cancer types. Nature genetics. 2017; 49(3):349-357. PMID: 28135248. PMCID: PMC5571729

Cancer Genome Atlas Research Network, … Integrated genomic characterization of oesophageal carcinoma. Nature. 2017;
541(7636):169-175. PMID: 28052061. PMCID: PMC5651175

Reuben A, Spencer CN, Prieto PA, Gopalakrishnan V, Reddy SM, Miller JP, Mao X, DeMacedo MP, Chen J, Song X, Jiang H, Chen PL, Beird HC, Garber HR, Roh W, Wani K, Chen E, Haymaker C, Forget MA, Little LD, Gumbs C, Thornton RL, Hudgens CW, Chen WS, Austin-Breneman J, Sloane RS, Nezi L, Cogdill AP, Bernatchez C, Roszik J, Hwu P, Woodman SE, Chin L, Tawbi H, Davies MA, Gershenwald JE, Amaria RN, Glitza IC, Diab A, Patel SP, Hu J, Lee JE, Grimm EA, Tetzlaff MT, Lazar AJ, Wistuba II, Clise-Dwyer K, Carter BW, Zhang J, Futreal PA, Sharma P, Allison JP, Cooper ZA, Wargo JA. Genomic and immune heterogeneity are
associated with differential responses to therapy in melanoma. NPJ genomic medicine. 2017; 2. PMID: 28819565.

Takahashi K, Wang F, Kantarjian H, Doss D, Khanna K, Thompson E, Zhao L, Patel K, Neelapu S, Gumbs C, Bueso-Ramos C, DiNardo CD, Colla S, Ravandi F, Zhang J, Huang X, Wu X, Samaniego F, Garcia-Manero G, Futreal PA. Preleukaemic clonal haemopoiesis and risk of therapy-related myeloid neoplasms: a case-control study. The Lancet Oncology. 2017; 18(1):100-111. PMCID: PMC5405697.

Integrated genomic characterization of oesophageal carcinoma. Nature. 2017; 541(7636):169-175. PMID: 28052061.

Boutin AT, Liao WT, Wang M, Hwang SS, Karpinets TV, Cheung H, Chu GC, Jiang S, Hu J, Chang K, Vilar E, Song X, Zhang J, Kopetz S, Futreal A, Wang YA, Kwong LN, DePinho RA. Oncogenic Kras drives invasion and maintains metastases in colorectal cancer. Genes & Development. 2017; 31(4):370-382. PMCID: PMC5358757.

Genovese G, Carugo A, Tepper J, Robinson FS, Li L, Svelto M, Nezi L, Corti D, Minelli R, Pettazzoni P, Gutschner T, Wu CC, Seth S, Akdemir KC, Leo E, Amin S, Molin MD, Ying H, Kwong LN, Colla S, Takahashi K, Ghosh P, Giuliani V, Muller F, Dey P, Jiang S, Garvey J, Liu CG, Zhang J, Heffernan TP, Toniatti C, Fleming JB, Goggins MG, Wood LD, Sgambato A, Agaimy A, Maitra A, Roberts CW, Wang H, Viale A, DePinho RA, Draetta GF, Chin L. Synthetic vulnerabilities of mesenchymal subpopulations in pancreatic cancer. Nature. 2017; 542(7641):362-366.  PMID: 28178232

Zhao D, Lu X, Wang G, Lan Z, Liao W, Li J, Liang X, Chen JR, Shah S, Shang X, Tang M, Deng P, Dey P, Chakravarti D, Chen P, Spring DJ, Navone NM, Troncoso P, Zhang J, Wang YA, DePinho RA. Synthetic essentiality of chromatin remodelling factor CHD1 in PTEN-deficient cancer. Nature. 2017; 542(7642):484-488. PMCID: PMC5448706.

Roh W, Chen PL, Reuben A, Spencer CN, Prieto PA, Miller JP, Gopalakrishnan V, Wang F, Cooper ZA, Reddy SM, Gumbs C, Little L, Chang Q, Chen WS, Wani K, De Macedo MP, Chen E, Austin-Breneman JL, Jiang H, Roszik J, Tetzlaff MT, Davies MA, Gershenwald JE, Tawbi H, Lazar AJ, Hwu P, Hwu WJ, Diab A, Glitza IC, Patel SP, Woodman SE, Amaria RN, Prieto VG, Hu J, Sharma P, Allison JP, Chin L, Zhang J, Wargo JA, Futreal PA. Integrated molecular analysis of tumor biopsies on sequential CTLA-4 and PD-1 blockade reveals markers of response and resistance. Science translational medicine. Science Translational Medicine. 2017; 9(379). PMID: 28251903.

Integrated genomic and molecular characterization of cervical cancer. Nature. 2017; 543(7645):378-384. PMCID: PMC5354998.

Quek K, Li J, Estecio M, Zhang J, Fujimoto J, Roarty E, Little L, Chow CW, Song X, Behrens C, Chen T, William WN, Swisher S, Heymach J, Wistuba I, Zhang J, Futreal A, Zhang J. DNA methylation intratumor heterogeneity in localized lung adenocarcinomas. Oncotarget. 2017; 8(13):21994-22002. PMCID: PMC5400640

Marchesini M, Ogoti Y, Fiorini E, Aktas Samur A, Nezi L, D'Anca M, Storti P, Samur MK, Ganan-Gomez I, Fulciniti MT, Mistry N, Jiang S, Bao N, Marchica V, Neri A, Bueso-Ramos C, Wu CJ, Zhang L, Liang H, Peng X, Giuliani N, Draetta G, Clise-Dwyer K, Kantarjian H, Munshi N, Orlowski R, Garcia-Manero G, DePinho RA, Colla S. ILF2 Is a Regulator of RNA Splicing and DNA Damage Response in 1q21-Amplified Multiple Myeloma. Cancer Cell. 2017; 32(1):88-100.e6. PMID: 28669490.

Reuben A, Gittelman RM, Gao J, Zhang J, Yusko E, Wu CJ, Emerson R, Zhang J, Tipton CM, Li J, Quek K, Gopalakrishnan V, Chen R, Vence L, Cascone T, Vignali M, Fujimoto J, Rodriguez-Canales J, Parra ER, Little LD, Gumbs C, Forget MA, Federico L, Haymaker C, Behrens C, Benzeno S, Bernatchez C, Sepesi B, Gibbons DL, Wargo JA, William WN, Swisher SG, Heymach J, Robins H, Lee JJ, Sharma P, Allison JP, Futreal PA, Wistuba II, Zhang J. TCR Repertoire Intratumor Heterogeneity in Localized Lung Adenocarcinomas: an Association with Predicted Neoantigen Heterogeneity and Postsurgical Recurrence. Cancer Discovery. 2017; PMID: 28733428.

Wang G, Lu X, Dey P, Deng P, Wu CC, Jiang S, Fang Z, Zhao K, Konaparthi R, Hua S, Zhang J, Li-Ning-Tapia EM, Kapoor A, Wu CJ, Patel NB, Guo Z, Ramamoorthy V, Tieu TN, Heffernan T, Zhao D, Shang X, Khadka S, Hou P, Hu B, Jin EJ, Yao W, Pan X, Ding Z, Shi Y, Li L, Chang Q, Troncoso P, Logothetis CJ, McArthur MJ, Chin L, Wang YA, DePinho RA. Targeting YAP-Dependent MDSC Infiltration Impairs Tumor Progression. Cancer Discovery. 2016; 6(1):80-95. PMCID: PMC4707102.

Takahashi K, Patel K, Bueso-Ramos C, Zhang J, Gumbs C, Jabbour E, Kadia T, Andreff M, Konopleva M, DiNardo C, Daver N, Cortes J, Estrov Z, Futreal A, Kantarjian H, Garcia-Manero G. Clinical implications of TP53 mutations in myelodysplastic syndromes treated with hypomethylating agents. Oncotarget. 2016; 7(12):14172-87. PMCID: PMC4924706.

Fan Y, Xi L, Hughes DS, Zhang J, Zhang J, Futreal PA, Wheeler DA, Wang W. MuSE: accounting for tumor heterogeneity using a sample-specific error model improves sensitivity and specificity in mutation calling from sequencing data. Genome Biology. 2016; 17(1):178. PMCID: PMC4995747.

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