• HMMRATAC: a Hidden Markov ModeleR for ATAC-seq.

  Tarbell ED, Liu T.
  Nucleic Acids Res. 2019 Sep 19. 16(47).

• Tumor Infiltrating Lymphocytes and Macrophages Improve Survival in Microsatellite Unstable Colorectal Cancer.

  Narayanan S, Kawaguchi T, Peng X, Qi Q, Liu S, Yan L, Takabe K.
  Sci Rep. 2019 Sep 17. 1(9).

• Integrative Molecular Characterization of Resistance to Neoadjuvant Chemoradiation in Rectal Cancer.

  Kamran SC, Lennerz JK, Margolis CA, Liu D, Reardon B, Wankowicz SA, Van Seventer EE, Tracy A, Wo JY, Carter SL, Willers H, Corcoran RB, Hong TS, Van Allen EM.
  Clin Cancer Res. 2019 Sep 15. 18(25).
  
  Data

• Head and Neck Cancer Immunotherapy beyond the Checkpoint Blockade.

  Heath BR, Michmerhuizen NL, Donnelly CR, Sansanaphongpricha K, Sun D, Brenner JC, Lei YL.
  J Dent Res. 2019 Sep. 10(98).

• Immune microenvironment modulation unmasks therapeutic benefit of radiotherapy and checkpoint inhibition.

  Newton JM, Hanoteau A, Liu HC, Gaspero A, Parikh F, Gartrell-Corrado RD, Hart TD, Laoui D, Van Ginderachter JA, Dharmaraj N, Spanos WC, Saenger Y, Young S, Sikora AG.
  J Immunother Cancer. 2019 Aug 13. 1(7).

• Breaking barriers for T cells by targeting the EPHA2/TGF-β/COX-2 axis in pancreatic cancer.

  Conejo-Garcia JR.
  J Clin Invest. 2019 Jul 29. 9(129).

• Illuminating the Onco-GPCRome: Novel G protein-coupled receptor-driven oncocrine networks and targets for cancer immunotherapy.

  Wu V, Yeerna H, Nohata N, Chiou J, Harismendy O, Raimondi F, Inoue A, Russell RB, Tamayo P, Gutkind JS.
  J Biol Chem. 2019 Jul 19. 29(294).

• Pas de Deux: Control of Anti-tumor Immunity by Cancer-Associated Inflammation.

  Shalapour S, Karin M.
  Immunity. 2019 Jul 16. 1(51).

• Engineering the TGFβ Receptor to Enhance the Therapeutic Potential of Natural Killer Cells as an Immunotherapy for Neuroblastoma.

  Burga RA, Yvon E, Chorvinsky E, Fernandes R, Cruz CRY, Bollard CM.
  Clin Cancer Res. 2019 Jul 15. 14(25).
  
  Model

• Immune Modulation of Head and Neck Squamous Cell Carcinoma and the Tumor Microenvironment by Conventional Therapeutics.

  Miyauchi S, Kim SS, Pang J, Gold KA, Gutkind JS, Califano JA, Mell LK, Cohen EEW, Sharabi AB.
  Clin Cancer Res. 2019 Jul 15. 14(25).

• Efficient identification of neoantigen-specific T-cell responses in advanced human ovarian cancer.

  Liu S, Matsuzaki J, Wei L, Tsuji T, Battaglia S, Hu Q, Cortes E, Wong L, Yan L, Long M, Miliotto A, Bateman NW, Lele SB, Chodon T, Koya RC, Yao S, Zhu Q, Conrads TP, Wang J, Maxwell GL, Lugade AA, Odunsi K.
  J Immunother Cancer. 2019 Jun 20. 1(7).

• TOX and TOX2 transcription factors cooperate with NR4A transcription factors to impose CD8⁺ T cell exhaustion.

  Seo H, Chen J, González-Avalos E, Samaniego-Castruita D, Das A, Wang YH, López-Moyado IF, Georges RO, Zhang W, Onodera A, Wu CJ, Lu LF, Hogan PG, Bhandoola A, Rao A.
  Proc Natl Acad Sci U S A. 2019 Jun 18. 25(116).
  
  Data

• Illuminating G-Protein-Coupling Selectivity of GPCRs.

  Inoue A, Raimondi F, Kadji FMN, Singh G, Kishi T, Uwamizu A, Ono Y, Shinjo Y, Ishida S, Arang N, Kawakami K, Gutkind JS, Aoki J, Russell RB.
  Cell. 2019 Jun 13. 7(177).

• Protein Kinase N1 control of androgen-responsive serum response factor action provides rationale for novel prostate cancer treatment strategy.

  Venkadakrishnan VB, DePriest AD, Kumari S, Senapati D, Ben-Salem S, Su Y, Mudduluru G, Hu Q, Cortes E, Pop E, Mohler JL, Azabdaftari G, Attwood K, Shah RB, Jamieson C, Dehm SM, Magi-Galluzzi C, Klein E, Sharifi N, Liu S, Heemers HV.
  Oncogene. 2019 Jun. 23(38).
  
  Data

• Accurate Quantification of Residual Cancer Cells in Pelvic Washing Reveals Association with Cancer Recurrence Following Robot-Assisted Radical Cystectomy.

  Wei L, Hussein AA, Ma Y, Azabdaftari G, Ahmed Y, Wong LP, Hu Q, Luo W, Cranwell VN, Bunch BL, Kozlowski JD, Singh PK, Glenn ST, Smith G, Johnson CS, Liu S, Guru KA.
  J Urol. 2019 Jun. 6(201).

• MUC1-C Integrates Chromatin Remodeling and PARP1 Activity in the DNA Damage Response of Triple-Negative Breast Cancer Cells.

  Yamamoto M, Jin C, Hata T, Yasumizu Y, Zhang Y, Hong D, Maeda T, Miyo M, Hiraki M, Suzuki Y, Hinohara K, Rajabi H, Kufe D.
  Cancer Res. 2019 Apr 15. 8(79).

• Cytochrome c Deficiency Confers Apoptosome and Mitochondrial Dysfunction in African-American Men with Prostate Cancer.

  Kumar R, Bhat TA, Walsh EM, Chaudhary AK, O'Malley J, Rhim JS, Wang J, Morrison CD, Attwood K, Bshara W, Mohler JL, Yadav N, Chandra D.
  Cancer Res. 2019 Apr 01. 7(79).

• Deep-learning augmented RNA-seq analysis of transcript splicing.

  Zhang Z, Pan Z, Ying Y, Xie Z, Adhikari S, Phillips J, Carstens RP, Black DL, Wu Y, Xing Y.
  Nat Methods. 2019 Apr. 4(16).
  
  Data

• Early-onset triple-negative breast cancer in multiracial/ethnic populations: Distinct trends of prevalence of truncation mutations.

  Liu Q, Yao S, Zhao H, Hu Q, Kwan ML, Roh JM, Ambrosone CB, Kushi LH, Liu S, Zhu Q.
  Cancer Med. 2019 Apr. 4(8).

• ER stress-induced mediator C/EBP homologous protein thwarts effector T cell activity in tumors through T-bet repression.

  Cao Y, Trillo-Tinoco J, Sierra RA, Anadon C, Dai W, Mohamed E, Cen L, Costich TL, Magliocco A, Marchion D, Klar R, Michel S, Jaschinski F, Reich RR, Mehrotra S, Cubillos-Ruiz JR, Munn DH, Conejo-Garcia JR, Rodriguez PC.
  Nat Commun. 2019 Mar 20. 1(10).
  
  Data

• Impact of chemotherapy for breast cancer on leukocyte DNA methylation landscape and cognitive function: a prospective study.

  Yao S, Hu Q, Kerns S, Yan L, Onitilo AA, Misleh J, Young K, Lei L, Bautista J, Mohamed M, Mohile SG, Ambrosone CB, Liu S, Janelsins MC.
  Clin Epigenetics. 2019 Mar 12. 1(11).

• Differences in microRNA expression in breast cancer between women of African and European ancestry.

  Gong Z, Wang J, Wang D, Buas MF, Ren X, Freudenheim JL, Belinsky SA, Liu S, Ambrosone CB, Higgins MJ.
  Carcinogenesis. 2019 Mar 12. 1(40).

• Discovery of Allele-Specific Protein-RNA Interactions in Human Transcriptomes.

  Bahrami-Samani E, Xing Y.
  Am J Hum Genet. 2019 Mar 07. 3(104).

• NR4A transcription factors limit CAR T cell function in solid tumours.

  Chen J, López-Moyado IF, Seo H, Lio CJ, Hempleman LJ, Sekiya T, Yoshimura A, Scott-Browne JP, Rao A.
  Nature. 2019 Mar. 7749(567).
  
  Data

• Genomic correlates of response to immune checkpoint blockade.

  Keenan TE, Burke KP, Van Allen EM.
  Nat Med. 2019 Mar. 3(25).

• Mitochondrial hypoxic stress induces widespread RNA editing by APOBEC3G in natural killer cells.

  Sharma S, Wang J, Alqassim E, Portwood S, Cortes Gomez E, Maguire O, Basse PH, Wang ES, Segal BH, Baysal BE.
  Genome Biol. 2019 Feb 21. 1(20).
  
  Data

• Clonal Deletion of Tumor-Specific T Cells by Interferon-γ Confers Therapeutic Resistance to Combination Immune Checkpoint Blockade.

  Pai CS, Huang JT, Lu X, Simons DM, Park C, Chang A, Tamaki W, Liu E, Roybal KT, Seagal J, Chen M, Hagihara K, Wei XX, DuPage M, Kwek SS, Oh DY, Daud A, Tsai KK, Wu C, Zhang L, Fasso M, Sachidanandam R, Jayaprakash A, Lin I, Casbon AJ, Kinsbury GA, Fong L.
  Immunity. 2019 Feb 19. 2(50).
  
  Data Model

• Exosomes Produced by Mesenchymal Stem Cells Drive Differentiation of Myeloid Cells into Immunosuppressive M2-Polarized Macrophages in Breast Cancer.

  Biswas S, Mandal G, Roy Chowdhury S, Purohit S, Payne KK, Anadon C, Gupta A, Swanson P, Yu X, Conejo-Garcia JR, Bhattacharyya A.
  J Immunol. 2019 Dec 15. 12(203).

• Combined innate and adaptive immunotherapy overcomes resistance of immunologically cold syngeneic murine neuroblastoma to checkpoint inhibition.

  Voeller J, Erbe AK, Slowinski J, Rasmussen K, Carlson PM, Hoefges A, VandenHeuvel S, Stuckwisch A, Wang X, Gillies SD, Patel RB, Farrel A, Rokita JL, Maris J, Hank JA, Morris ZS, Rakhmilevich AL, Sondel PM.
  J Immunother Cancer. 2019 Dec 06. 1(7).
  
  Clinical Trial

• Syngeneic animal models of tobacco-associated oral cancer reveal the activity of in situ anti-CTLA-4.

  Wang Z, Wu VH, Allevato MM, Gilardi M, He Y, Luis Callejas-Valera J, Vitale-Cross L, Martin D, Amornphimoltham P, Mcdermott J, Yung BS, Goto Y, Molinolo AA, Sharabi AB, Cohen EEW, Chen Q, Lyons JG, Alexandrov LB, Gutkind JS.
  Nat Commun. 2019 Dec 05. 1(10).
  
  Model

• Integrative molecular and clinical modeling of clinical outcomes to PD1 blockade in patients with metastatic melanoma.

  Liu D, Schilling B, Liu D, Sucker A, Livingstone E, Jerby-Arnon L, Zimmer L, Gutzmer R, Satzger I, Loquai C, Grabbe S, Vokes N, Margolis CA, Conway J, He MX, Elmarakeby H, Dietlein F, Miao D, Tracy A, Gogas H, Goldinger SM, Utikal J, Blank CU, Rauschenberg R, von Bubnoff D, Krackhardt A, Weide B, Haferkamp S, Kiecker F, Izar B, Garraway L, Regev A, Flaherty K, Paschen A, Van Allen EM, Schadendorf D.
  Nat Med. 2019 Dec. 12(25).
  
  Data

• Upfront Therapies and Downstream Effects: Navigating Late Effects in Childhood Cancer Survivors in the Current Era.

  Phelan R, Eissa H, Becktell K, Bhatt N, Kudek M, Nuechterlein B, Pommert L, Tanaka R, Baker KS.
  Curr Oncol Rep. 2019 Nov 25. 12(21).

• MUC1-C Activates the NuRD Complex to Drive Dedifferentiation of Triple-Negative Breast Cancer Cells.

  Hata T, Rajabi H, Takahashi H, Yasumizu Y, Li W, Jin C, Long MD, Hu Q, Liu S, Fushimi A, Yamashita N, Kui L, Hong D, Yamamoto M, Miyo M, Hiraki M, Maeda T, Suzuki Y, Samur MK, Kufe D.
  Cancer Res. 2019 Nov 15. 22(79).
  
  Data

• Immunity to commensal papillomaviruses protects against skin cancer.

  Strickley JD, Messerschmidt JL, Awad ME, Li T, Hasegawa T, Ha DT, Nabeta HW, Bevins PA, Ngo KH, Asgari MM, Nazarian RM, Neel VA, Jenson AB, Joh J, Demehri S.
  Nature. 2019 Nov. 7783(575).
  
  Data Model

• MUC1-C represses the RASSF1A tumor suppressor in human carcinoma cells.

  Rajabi H, Hata T, Li W, Long MD, Hu Q, Liu S, Raina D, Kui L, Yasumizu Y, Hong D, Samur M, Kufe D.
  Oncogene. 2019 Nov. 47(38).
  
  Data

• Preclinical Characterization of ^86/90Y-NM600 in a Variety of Murine and Human Cancer Tumor Models.

  Grudzinski JJ, Hernandez R, Marsh I, Patel RB, Aluicio-Sarduy E, Engle J, Morris Z, Bednarz B, Weichert J.
  J Nucl Med. 2019 Nov. 11(60).

• Defining 'T cell exhaustion'.

  Blank CU, Haining WN, Held W, Hogan PG, Kallies A, Lugli E, Lynn RC, Philip M, Rao A, Restifo NP, Schietinger A, Schumacher TN, Schwartzberg PL, Sharpe AH, Speiser DE, Wherry EJ, Youngblood BA, Zehn D.
  Nat Rev Immunol. 2019 Nov. 11(19).

• AMPK Alpha-1 Intrinsically Regulates the Function and Differentiation of Tumor Myeloid-Derived Suppressor Cells.

  Trillo-Tinoco J, Sierra RA, Mohamed E, Cao Y, de Mingo-Pulido Á, Gilvary DL, Anadon CM, Costich TL, Wei S, Flores ER, Ruffell B, Conejo-Garcia JR, Rodriguez PC.
  Cancer Res. 2019 Oct 01. 19(79).

• Identification of candidate neoantigens produced by fusion transcripts in human osteosarcomas.

  Rathe SK, Popescu FE, Johnson JE, Watson AL, Marko TA, Moriarity BS, Ohlfest JR, Largaespada DA.
  Sci Rep. 2019 Jan 23. 1(9).

• Tumor microenvironment modulation enhances immunologic benefit of chemoradiotherapy.

  Hanoteau A, Newton JM, Krupar R, Huang C, Liu HC, Gaspero A, Gartrell RD, Saenger YM, Hart TD, Santegoets SJ, Laoui D, Spanos C, Parikh F, Jayaraman P, Zhang B, Van der Burg SH, Van Ginderachter JA, Melief CJM, Sikora AG.
  J Immunother Cancer. 2019 Jan 15. 1(7).

• Preclinical Models for Studying NASH-Driven HCC: How Useful Are They?

  Febbraio MA, Reibe S, Shalapour S, Ooi GJ, Watt MJ, Karin M.
  Cell Metab. 2019 Jan 08. 1(29).
  
  Model

• Leveraging TCR Affinity in Adoptive Immunotherapy against Shared Tumor/Self-Antigens.

  Miller AM, Bahmanof M, Zehn D, Cohen EEW, Schoenberger SP.
  Cancer Immunol Res. 2019 Jan. 1(7).

• ⁹⁰Y-NM600 targeted radionuclide therapy induces immunologic memory in syngeneic models of T-cell Non-Hodgkin's Lymphoma.

  Hernandez R, Walker KL, Grudzinski JJ, Aluicio-Sarduy E, Patel R, Zahm CD, Pinchuk AN, Massey CF, Bitton AN, Brown RJ, Sondel PM, Morris ZS, Engle JW, Capitini CM, Weichert JP.
  Commun Biol. 2019. (2).

• A Threshold Model for T-Cell Activation in the Era of Checkpoint Blockade Immunotherapy.

  Guram K, Kim SS, Wu V, Sanders PD, Patel S, Schoenberger SP, Cohen EEW, Chen SY, Sharabi AB.
  Front Immunol. 2019. (10).

• TCR Convergence in Individuals Treated With Immune Checkpoint Inhibition for Cancer.

  Looney TJ, Topacio-Hall D, Lowman G, Conroy J, Morrison C, Oh D, Fong L, Zhang L.
  Front Immunol. 2019. (10).

• An Alternative Skew Exponential Power Distribution Formulation.

  Hutson AD.
  Commun Stat Theory Methods. 2019. 12(48).

• A robust Pearson correlation test for a general point null using a surrogate bootstrap distribution.

  Hutson AD.
  PLoS One. 2019. 5(14).

• High MYC mRNA Expression Is More Clinically Relevant than MYC DNA Amplification in Triple-Negative Breast Cancer.

  Katsuta E, Yan L, Takeshita T, McDonald KA, Dasgupta S, Opyrchal M, Takabe K.
  Int J Mol Sci. 2019 Dec 28. 1(21).

• Randomized controlled trial of cryotherapy to prevent paclitaxel-induced peripheral neuropathy (RU221511I); an ACCRU trial.

  Ruddy KJ, Le-Rademacher J, Lacouture ME, Wilkinson M, Onitilo AA, Vander Woude AC, Grosse-Perdekamp MT, Dockter T, Tan AD, Beutler A, Loprinzi CL.
  Breast. 2019 Dec. (48).

• The multikinase inhibitor RXDX-105 is effective against neuroblastoma in vitro and in vivo.

  Flynn SM, Lesperance J, Macias A, Phanhthilath N, Paul MR, Kim JW, Tamayo P, Zage PE.
  Oncotarget. 2019 Oct 29. 59(10).

• Development of an In Situ Cancer Vaccine via Combinational Radiation and Bacterial-Membrane-Coated Nanoparticles.

  Patel RB, Ye M, Carlson PM, Jaquish A, Zangl L, Ma B, Wang Y, Arthur I, Xie R, Brown RJ, Wang X, Sriramaneni R, Kim K, Gong S, Morris ZS.
  Adv Mater. 2019 Oct. 43(31).

• The empirical likelihood prior applied to bias reduction of general estimating equations.

  Vexler A, Zou L, Hutson AD.
  Comput Stat Data Anal. 2019 Oct. (138).