CSBC Supported Publications

Publications

  • 2019 | ProteinNet: a standardized data set for machine learning of protein structure. AlQuraishi, M BMC Bioinformatics 20 (1): 311. doi: 10.1186/s12859-019-2932-0. PubMed PMID:31185886 PubMed Central PMC6560865
  • 2019 | Using Microarrays to Interrogate Microenvironmental Impact on Cellular Phenotypes in Cancer. Smith, R, Devlin, K, Kilburn, D, Gross, S, Sudar, D, Bucher, E, Nederlof, M, Dane, M, Gray, JW, Heiser, L, Korkola, JE J Vis Exp (147): . doi: 10.3791/58957. PubMed PMID:31180341
  • 2019 | An update on the CNS manifestations of neurofibromatosis type 2. Coy, S, Rashid, R, Stemmer-Rachamimov, A, Santagata, S Acta Neuropathol. : . doi: 10.1007/s00401-019-02029-5. PubMed PMID:31161239
  • 2019 | Identifying Epistasis in Cancer Genomes: A Delicate Affair. van de Haar, J, Canisius, S, Yu, MK, Voest, EE, Wessels, LFA, Ideker, T Cell 177 (6): 1375-1383. doi: 10.1016/j.cell.2019.05.005. PubMed PMID:31150618
  • 2019 | Sparse discriminative latent characteristics for predicting cancer drug sensitivity from genomic features. Knowles, DA, Bouchard, G, Plevritis, S PLoS Comput. Biol. 15 (5): e1006743. doi: 10.1371/journal.pcbi.1006743. PubMed PMID:31136571
  • 2019 | Epithelial-Mesenchymal Plasticity in Organotropism Metastasis and Tumor Immune Escape. Nan, X, Wang, J, Liu, HN, Wong, STC, Zhao, H J Clin Med 8 (5): . doi: 10.3390/jcm8050747. PubMed PMID:31130637
  • 2019 | BRD4 regulates metastatic potential of castration-resistant prostate cancer through AHNAK. Shafran, JS, Andrieu, GP, Gyorffy, B, Denis, GV Mol. Cancer Res. : . doi: 10.1158/1541-7786.MCR-18-1279. PubMed PMID:31110158
  • 2018 | An accessible GenePattern notebook for the copy number variation analysis of Illumina Infinium DNA methylation arrays. Mah, CK, Mesirov, JP, Chavez, L F1000Res 7 : . doi: 10.12688/f1000research.16338.1. PubMed PMID:31105932 PubMed Central PMC6498745
  • 2019 | Characterizing ABC-Transporter Substrate-Likeness Using a Clean-Slate Genetic Background. Sokolov, A, Ashenden, S, Sahin, N, Lewis, R, Erdem, N, Ozaltan, E, Bender, A, Roth, FP, Cokol, M Front Pharmacol 10 : 448. doi: 10.3389/fphar.2019.00448. PubMed PMID:31105571 PubMed Central PMC6494965
  • 2019 | Time-dependent antagonist-agonist switching in receptor tyrosine kinase-mediated signaling. Ghosh, A, Radhakrishnan, R BMC Bioinformatics 20 (1): 242. doi: 10.1186/s12859-019-2816-3. PubMed PMID:31092187 PubMed Central PMC6521356
  • 2019 | Multiplexed, Sequential Secretion Analysis of the Same Single Cells Reveals Distinct Effector Response Dynamics Dependent on the Initial Basal State. Chen, Z, Lu, Y, Zhang, K, Xiao, Y, Lu, J, Fan, R Adv Sci (Weinh) 6 (9): 1801361. doi: 10.1002/advs.201801361. PubMed PMID:31065513 PubMed Central PMC6498135
  • 2019 | Mammalian cell growth dynamics in mitosis. Miettinen, TP, Kang, JH, Yang, LF, Manalis, SR Elife 8 : . doi: 10.7554/eLife.44700. PubMed PMID:31063131 PubMed Central PMC6534395
  • 2019 | Seq-Well: A Sample-Efficient, Portable Picowell Platform for Massively Parallel Single-Cell RNA Sequencing. Aicher, TP, Carroll, S, Raddi, G, Gierahn, T, Wadsworth, MH 2nd, Hughes, TK, Love, C, Shalek, AK Methods Mol. Biol. 1979 : 111-132. doi: 10.1007/978-1-4939-9240-9_8. PubMed PMID:31028635
  • 2019 | Ex vivo Dynamics of Human Glioblastoma Cells in a Microvasculature-on-a-Chip System Correlates with Tumor Heterogeneity and Subtypes. Xiao, Y, Kim, D, Dura, B, Zhang, K, Yan, R, Li, H, Han, E, Ip, J, Zou, P, Liu, J, Chen, AT, Vortmeyer, AO, Zhou, J, Fan, R Adv Sci (Weinh) 6 (8): 1801531. doi: 10.1002/advs.201801531. PubMed PMID:31016107 PubMed Central PMC6468969
  • 2019 | End-to-End Differentiable Learning of Protein Structure. AlQuraishi, M Cell Syst 8 (4): 292-301.e3. doi: 10.1016/j.cels.2019.03.006. PubMed PMID:31005579 PubMed Central PMC6513320
  • 2019 | Resistance to neoadjuvant chemotherapy in triple-negative breast cancer mediated by a reversible drug-tolerant state. Echeverria, GV, Ge, Z, Seth, S, Zhang, X, Jeter-Jones, S, Zhou, X, Cai, S, Tu, Y, McCoy, A, Peoples, M, Sun, Y, Qiu, H, Chang, Q, Bristow, C, Carugo, A, Shao, J, Ma, X, Harris, A, Mundi, P, Lau, R, Ramamoorthy, V, Wu, Y, Alvarez, MJ, Califano, A, Moulder, SL, Symmans, WF, Marszalek, JR, Heffernan, TP, Chang, JT, Piwnica-Worms, H Sci Transl Med 11 (488): . doi: 10.1126/scitranslmed.aav0936. PubMed PMID:30996079 PubMed Central PMC6541393
  • 2019 | BRCA1 mutations attenuate super-enhancer function and chromatin looping in haploinsufficient human breast epithelial cells. Zhang, X, Wang, Y, Chiang, HC, Hsieh, YP, Lu, C, Park, BH, Jatoi, I, Jin, VX, Hu, Y, Li, R Breast Cancer Res. 21 (1): 51. doi: 10.1186/s13058-019-1132-1. PubMed PMID:30995943 PubMed Central PMC6472090
  • 2019 | The 2019 Mathematical Oncology Roadmap. Rockne, RC, Hawkins-Daarud, A, Swanson, KR, Sluka, JP, Glazier, JA, Macklin, P, Hormuth, D, Jarrett, AM, Lima, EABDF, Oden, J, Biros, G, Yankeelov, TE, Curtius, K, Bakir, IA, Wodarz, D, Komarova, N, Aparicio, L, Bordyuh, M, Rabadan, R, Finley, S, Enderling, H, Caudell, JJ, Moros, EG, Anderson, ARA, Gatenby, R, Kaznatcheev, A, Jeavons, P, Krishnan, N, Pelesko, J, Wadhwa, RR, Yoon, N, Nichol, D, Marusyk, A, Hinczewski, M, Scott, JG Phys Biol : . doi: 10.1088/1478-3975/ab1a09. PubMed PMID:30991381
  • 2019 | Leveraging Compound Promiscuity to Identify Targetable Cysteines within the Kinome. Rao, S, Gurbani, D, Du, G, Everley, RA, Browne, CM, Chaikuad, A, Tan, L, Schröder, M, Gondi, S, Ficarro, SB, Sim, T, Kim, ND, Berberich, MJ, Knapp, S, Marto, JA, Westover, KD, Sorger, PK, Gray, NS Cell Chem Biol : . doi: 10.1016/j.chembiol.2019.02.021. PubMed PMID:30982749
  • 2019 | Computational algorithms for in silico profiling of activating mutations in cancer. Jordan, EJ, Patil, K, Suresh, K, Park, JH, Mosse, YP, Lemmon, MA, Radhakrishnan, R Cell. Mol. Life Sci. : . doi: 10.1007/s00018-019-03097-2. PubMed PMID:30982079
  • 2019 | Shallow Sparsely-Connected Autoencoders for Gene Set Projection. Gold, MP, LeNail, A, Fraenkel, E Pac Symp Biocomput 24 : 374-385. . PubMed PMID:30963076 PubMed Central PMC6417803
  • 2019 | In vivo profiling of metastatic double knockouts through CRISPR-Cpf1 screens. Chow, RD, Wang, G, Ye, L, Codina, A, Kim, HR, Shen, L, Dong, MB, Errami, Y, Chen, S Nat. Methods 16 (5): 405-408. doi: 10.1038/s41592-019-0371-5. PubMed PMID:30962622
  • 2019 | Multisite HPV infections in the United States (NHANES 2003-2014): An overview and synthesis. Brouwer, AF, Eisenberg, MC, Carey, TE, Meza, R Prev Med 123 : 288-298. doi: 10.1016/j.ypmed.2019.03.040. PubMed PMID:30959071 PubMed Central PMC6534472
  • 2019 | Tissue-Specific Oncogenic Activity of KRASA146T. Poulin, EJ, Bera, AK, Lu, J, Lin, YJ, Strasser, SD, Paulo, JA, Huang, TQ, Morales, C, Yan, W, Cook, J, Nowak, JA, Brubaker, DK, Joughin, BA, Johnson, CW, DeStefanis, RA, Ghazi, PC, Gondi, S, Wales, TE, Iacob, RE, Bogdanova, L, Gierut, JJ, Li, Y, Engen, JR, Perez-Mancera, PA, Braun, BS, Gygi, SP, Lauffenburger, DA, Westover, KD, Haigis, KM Cancer Discov 9 (6): 738-755. doi: 10.1158/2159-8290.CD-18-1220. PubMed PMID:30952657 PubMed Central PMC6548671
  • 2019 | Progesterone Receptor Attenuates STAT1-Mediated IFN Signaling in Breast Cancer. Goodman, ML, Trinca, GM, Walter, KR, Papachristou, EK, D'Santos, CS, Li, T, Liu, Q, Lai, Z, Chalise, P, Madan, R, Fan, F, Markiewicz, MA, Jin, VX, Carroll, JS, Hagan, CR J. Immunol. 202 (10): 3076-3086. doi: 10.4049/jimmunol.1801152. PubMed PMID:30936295 PubMed Central PMC6504603
  • 2019 | SOX11 hypermethylation as a tumor biomarker in endometrial cancer. Shan, T, Uyar, DS, Wang, LS, Mutch, DG, Huang, TH, Rader, JS, Sheng, X, Huang, YW Biochimie 162 : 8-14. doi: 10.1016/j.biochi.2019.03.019. PubMed PMID:30935961 PubMed Central PMC6561798
  • 2019 | Moving Toward a Consensus DSC-MRI Protocol: Validation of a Low-Flip Angle Single-Dose Option as a Reference Standard for Brain Tumors. Schmainda, KM, Prah, MA, Hu, LS, Quarles, CC, Semmineh, N, Rand, SD, Connelly, JM, Anderies, B, Zhou, Y, Liu, Y, Logan, B, Stokes, A, Baird, G, Boxerman, JL AJNR Am J Neuroradiol 40 (4): 626-633. doi: 10.3174/ajnr.A6015. PubMed PMID:30923088 PubMed Central PMC6461489
  • 2019 | Stress-Induced Evolutionary Innovation: A Mechanism for the Origin of Cell Types. Wagner, GP, Erkenbrack, EM, Love, AC Bioessays 41 (4): e1800188. doi: 10.1002/bies.201800188. PubMed PMID:30919472
  • 2019 | Acquisition of a hybrid E/M state is essential for tumorigenicity of basal breast cancer cells. Kröger, C, Afeyan, A, Mraz, J, Eaton, EN, Reinhardt, F, Khodor, YL, Thiru, P, Bierie, B, Ye, X, Burge, CB, Weinberg, RA Proc. Natl. Acad. Sci. U.S.A. 116 (15): 7353-7362. doi: 10.1073/pnas.1812876116. PubMed PMID:30910979 PubMed Central PMC6462070
  • 2019 | In situ 10-cell RNA sequencing in tissue and tumor biopsy samples. Singh, S, Wang, L, Schaff, DL, Sutcliffe, MD, Koeppel, AF, Kim, J, Onengut-Gumuscu, S, Park, KS, Zong, H, Janes, KA Sci Rep 9 (1): 4836. doi: 10.1038/s41598-019-41235-9. PubMed PMID:30894605 PubMed Central PMC6426952
  • 2019 | Therapeutic Clues from an Integrated Omic Assessment of East Asian Triple Negative Breast Cancers. Heiser, LM, Mills, GB, Gray, JW Cancer Cell 35 (3): 341-343. doi: 10.1016/j.ccell.2019.02.012. PubMed PMID:30889376 PubMed Central PMC6499473
  • 2019 | The gut microbiome and response to immune checkpoint inhibitors: preclinical and clinical strategies. Gong, J, Chehrazi-Raffle, A, Placencio-Hickok, V, Guan, M, Hendifar, A, Salgia, R Clin Transl Med 8 (1): 9. doi: 10.1186/s40169-019-0225-x. PubMed PMID:30887236 PubMed Central PMC6423251
  • 2019 | Higher order genomic organization and epigenetic control maintain cellular identity and prevent breast cancer. Fritz, AJ, Gillis, NE, Gerrard, DL, Rodriguez, PD, Hong, D, Rose, JT, Ghule, PN, Bolf, EL, Gordon, JA, Tye, CE, Boyd, JR, Tracy, KM, Nickerson, JA, van Wijnen, AJ, Imbalzano, AN, Heath, JL, Frietze, SE, Zaidi, SK, Carr, FE, Lian, JB, Stein, JL, Stein, GS Genes Chromosomes Cancer 58 (7): 484-499. doi: 10.1002/gcc.22731. PubMed PMID:30873710 PubMed Central PMC6549233
  • 2019 | Computational KIR copy number discovery reveals interaction between inhibitory receptor burden and survival. Pyke, RM, Genolet, R, Harari, A, Coukos, G, Gfeller, D, Carter, H Pac Symp Biocomput 24 : 148-159. . PubMed PMID:30864318 PubMed Central PMC6417817
  • 2019 | A multitargeted probe-based strategy to identify signaling vulnerabilities in cancers. Rao, S, Du, G, Hafner, M, Subramanian, K, Sorger, PK, Gray, NS J. Biol. Chem. 294 (21): 8664-8673. doi: 10.1074/jbc.RA118.006805. PubMed PMID:30858179 PubMed Central PMC6544847
  • 2019 | Modeling differentiation-state transitions linked to therapeutic escape in triple-negative breast cancer. Chapman, MP, Risom, T, Aswani, AJ, Langer, EM, Sears, RC, Tomlin, CJ PLoS Comput. Biol. 15 (3): e1006840. doi: 10.1371/journal.pcbi.1006840. PubMed PMID:30856168 PubMed Central PMC6428348
  • 2019 | Multiparameter MRI Predictors of Long-Term Survival in Glioblastoma Multiforme. Stringfield, O, Arrington, JA, Johnston, SK, Rognin, NG, Peeri, NC, Balagurunathan, Y, Jackson, PR, Clark-Swanson, KR, Swanson, KR, Egan, KM, Gatenby, RA, Raghunand, N Tomography 5 (1): 135-144. doi: 10.18383/j.tom.2018.00052. PubMed PMID:30854451 PubMed Central PMC6403044
  • 2019 | MetaMarker: a de novo pipeline for discovering novel metagenomic biomarkers. Koohi-Moghadam, M, Borad, M, Tran, N, Swanson, K, Boardman, L, Sun, H, Wang, J Bioinformatics : . doi: 10.1093/bioinformatics/btz123. PubMed PMID:30825371
  • 2019 | Accurate Patient-Specific Machine Learning Models of Glioblastoma Invasion Using Transfer Learning. Hu, LS, Yoon, H, Eschbacher, JM, Baxter, LC, Dueck, AC, Nespodzany, A, Smith, KA, Nakaji, P, Xu, Y, Wang, L, Karis, JP, Hawkins-Daarud, AJ, Singleton, KW, Jackson, PR, Anderies, BJ, Bendok, BR, Zimmerman, RS, Quarles, C, Porter-Umphrey, AB, Mrugala, MM, Sharma, A, Hoxworth, JM, Sattur, MG, Sanai, N, Koulemberis, PE, Krishna, C, Mitchell, JR, Wu, T, Tran, NL, Swanson, KR, Li, J AJNR Am J Neuroradiol 40 (3): 418-425. doi: 10.3174/ajnr.A5981. PubMed PMID:30819771 PubMed Central PMC6474354
  • 2019 | Structure of the IFNγ receptor complex guides design of biased agonists. Mendoza, JL, Escalante, NK, Jude, KM, Sotolongo Bellon, J, Su, L, Horton, TM, Tsutsumi, N, Berardinelli, SJ, Haltiwanger, RS, Piehler, J, Engleman, EG, Garcia, KC Nature 567 (7746): 56-60. doi: 10.1038/s41586-019-0988-7. PubMed PMID:30814731 PubMed Central PMC6561087
  • 2019 | One-step generation of modular CAR-T cells with AAV-Cpf1. Dai, X, Park, JJ, Du, Y, Kim, HR, Wang, G, Errami, Y, Chen, S Nat. Methods 16 (3): 247-254. doi: 10.1038/s41592-019-0329-7. PubMed PMID:30804551 PubMed Central PMC6519746
  • 2018 | Mismatch repair deficiency in high-grade meningioma: a rare but recurrent event associated with dramatic immune activation and clinical response to PD-1 blockade. Dunn, IF, Du, Z, Touat, M, Sisti, MB, Wen, PY, Umeton, R, Dubuc, AM, Ducar, M, Canoll, PD, Severson, E, Elvin, JA, Ramkissoon, SH, Lin, JR, Cabrera, L, Acevedo, B, Sorger, PK, Ligon, KL, Santagata, S, Reardon, DA JCO Precis Oncol 2018 : . doi: 10.1200/PO.18.00190. PubMed PMID:30801050 PubMed Central PMC6383717
  • 2019 | Quantifying Drug Combination Synergy along Potency and Efficacy Axes. Meyer, CT, Wooten, DJ, Paudel, BB, Bauer, J, Hardeman, KN, Westover, D, Lovly, CM, Harris, LA, Tyson, DR, Quaranta, V Cell Syst 8 (2): 97-108.e16. doi: 10.1016/j.cels.2019.01.003. PubMed PMID:30797775
  • 2019 | Convergent Identification and Interrogation of Tumor-Intrinsic Factors that Modulate Cancer Immunity In Vivo. Codina, A, Renauer, PA, Wang, G, Chow, RD, Park, JJ, Ye, H, Zhang, K, Dong, MB, Gassaway, B, Ye, L, Errami, Y, Shen, L, Chang, A, Jain, D, Herbst, RS, Bosenberg, M, Rinehart, J, Fan, R, Chen, S Cell Syst 8 (2): 136-151.e7. doi: 10.1016/j.cels.2019.01.004. PubMed PMID:30797773
  • 2019 | Lesion Dynamics Under Varying Paracrine PDGF Signaling in Brain Tissue. Massey, SC, Hawkins-Daarud, A, Gallaher, J, Anderson, ARA, Canoll, P, Swanson, KR Bull. Math. Biol. 81 (6): 1645-1664. doi: 10.1007/s11538-019-00587-z. PubMed PMID:30796683 PubMed Central PMC6494675
  • 2019 | De novo gene signature identification from single-cell RNA-seq with hierarchical Poisson factorization. Levitin, HM, Yuan, J, Cheng, YL, Ruiz, FJ, Bush, EC, Bruce, JN, Canoll, P, Iavarone, A, Lasorella, A, Blei, DM, Sims, PA Mol. Syst. Biol. 15 (2): e8557. doi: 10.15252/msb.20188557. PubMed PMID:30796088 PubMed Central PMC6386217
  • 2019 | Driver Network as a Biomarker: Systematic integration and network modeling of multi-omics data to derive driver signaling pathways for drug combination prediction. Huang, L, Brunell, D, Stephan, C, Mancuso, J, He, B, Thompson, TC, Zinner, R, Kim, J, Davies, P, Wong, STC Bioinformatics : . doi: 10.1093/bioinformatics/btz109. PubMed PMID:30768150
  • 2019 | Quantifying Uncertainty and Robustness in a Biomathematical Model-Based Patient-Specific Response Metric for Glioblastoma. Hawkins-Daarud, A, Johnston, SK, Swanson, KR JCO Clin Cancer Inform 3 : 1-8. doi: 10.1200/CCI.18.00066. PubMed PMID:30758984
  • 2019 | The Role of the Microbiome in Cancer Initiation and Progression: How Microbes and Cancer Cells Utilize Excess Energy and Promote One Another's Growth. Whisner, CM, Athena Aktipis, C Curr Nutr Rep 8 (1): 42-51. doi: 10.1007/s13668-019-0257-2. PubMed PMID:30758778 PubMed Central PMC6426824
  • 2019 | Ventricular-Subventricular Zone Contact by Glioblastoma is Not Associated with Molecular Signatures in Bulk Tumor Data. Mistry, AM, Wooten, DJ, Davis, LT, Mobley, BC, Quaranta, V, Ihrie, RA Sci Rep 9 (1): 1842. doi: 10.1038/s41598-018-37734-w. PubMed PMID:30755636 PubMed Central PMC6372607
  • 2019 | Acidification of Tumor at Stromal Boundaries Drives Transcriptome Alterations Associated with Aggressive Phenotypes. Rohani, N, Hao, L, Alexis, MS, Joughin, BA, Krismer, K, Moufarrej, MN, Soltis, AR, Lauffenburger, DA, Yaffe, MB, Burge, CB, Bhatia, SN, Gertler, FB Cancer Res. 79 (8): 1952-1966. doi: 10.1158/0008-5472.CAN-18-1604. PubMed PMID:30755444 PubMed Central PMC6467770
  • 2019 | Noninvasive monitoring of single-cell mechanics by acoustic scattering. Kang, JH, Miettinen, TP, Chen, L, Olcum, S, Katsikis, G, Doyle, PS, Manalis, SR Nat. Methods 16 (3): 263-269. doi: 10.1038/s41592-019-0326-x. PubMed PMID:30742041 PubMed Central PMC6420125
  • 2019 | Excessive Cell Growth Causes Cytoplasm Dilution And Contributes to Senescence. Neurohr, GE, Terry, RL, Lengefeld, J, Bonney, M, Brittingham, GP, Moretto, F, Miettinen, TP, Vaites, LP, Soares, LM, Paulo, JA, Harper, JW, Buratowski, S, Manalis, S, van Werven, FJ, Holt, LJ, Amon, A Cell 176 (5): 1083-1097.e18. doi: 10.1016/j.cell.2019.01.018. PubMed PMID:30739799 PubMed Central PMC6386581
  • 2019 | Metabolic plasticity meets gene regulation. Paudel, BB, Quaranta, V Proc. Natl. Acad. Sci. U.S.A. 116 (9): 3370-3372. doi: 10.1073/pnas.1900169116. PubMed PMID:30737291 PubMed Central PMC6397587
  • 2019 | A Review of Cell-Based Computational Modeling in Cancer Biology. Metzcar, J, Wang, Y, Heiland, R, Macklin, P JCO Clin Cancer Inform 3 : 1-13. doi: 10.1200/CCI.18.00069. PubMed PMID:30715927
  • 2019 | Robust Cell Detection and Segmentation for Image Cytometry Reveal Th17 Cell Heterogeneity. Tsujikawa, T, Thibault, G, Azimi, V, Sivagnanam, S, Banik, G, Means, C, Kawashima, R, Clayburgh, DR, Gray, JW, Coussens, LM, Chang, YH Cytometry A 95 (4): 389-398. doi: 10.1002/cyto.a.23726. PubMed PMID:30714674 PubMed Central PMC6461524
  • 2018 | Evolutionary Stem Cell Poker and Cancer Risks: The Paradox of The Large And Small Intestines. Shibata, D Curr Pathobiol Rep 6 (3): 193-198. doi: 10.1007/s40139-018-0176-8. PubMed PMID:30713810 PubMed Central PMC6350825
  • 2019 | Nanoparticle Delivery of miR-708 Mimetic Impairs Breast Cancer Metastasis. Ramchandani, D, Lee, SK, Yomtoubian, S, Han, MS, Tung, CH, Mittal, V Mol. Cancer Ther. 18 (3): 579-591. doi: 10.1158/1535-7163.MCT-18-0702. PubMed PMID:30679387 PubMed Central PMC6532393
  • 2019 | Optofluidic real-time cell sorter for longitudinal CTC studies in mouse models of cancer. Hamza, B, Ng, SR, Prakadan, SM, Delgado, FF, Chin, CR, King, EM, Yang, LF, Davidson, SM, DeGouveia, KL, Cermak, N, Navia, AW, Winter, PS, Drake, RS, Tammela, T, Li, CM, Papagiannakopoulos, T, Gupta, AJ, Shaw Bagnall, J, Knudsen, SM, Vander Heiden, MG, Wasserman, SC, Jacks, T, Shalek, AK, Manalis, SR Proc. Natl. Acad. Sci. U.S.A. 116 (6): 2232-2236. doi: 10.1073/pnas.1814102116. PubMed PMID:30674677 PubMed Central PMC6369805
  • 2019 | Experimental microdissection enables functional harmonisation of pancreatic cancer subtypes. Maurer, C, Holmstrom, SR, He, J, Laise, P, Su, T, Ahmed, A, Hibshoosh, H, Chabot, JA, Oberstein, PE, Sepulveda, AR, Genkinger, JM, Zhang, J, Iuga, AC, Bansal, M, Califano, A, Olive, KP Gut 68 (6): 1034-1043. doi: 10.1136/gutjnl-2018-317706. PubMed PMID:30658994 PubMed Central PMC6509007
  • 2018 | Distinct Phenotypic Clusters of Glioblastoma Growth and Response Kinetics Predict Survival. Rayfield, CA, Grady, F, De Leon, G, Rockne, R, Carrasco, E, Jackson, P, Vora, M, Johnston, SK, Hawkins-Daarud, A, Clark-Swanson, KR, Whitmire, S, Gamez, ME, Porter, A, Hu, L, Gonzalez-Cuyar, L, Bendok, B, Vora, S, Swanson, KR JCO Clin Cancer Inform 2 : 1-14. doi: 10.1200/CCI.17.00080. PubMed PMID:30652553 PubMed Central PMC6358416
  • 2019 | Modeling Tumor Phenotypes In Vitro with Three-Dimensional Bioprinting. Langer, EM, Allen-Petersen, BL, King, SM, Kendsersky, ND, Turnidge, MA, Kuziel, GM, Riggers, R, Samatham, R, Amery, TS, Jacques, SL, Sheppard, BC, Korkola, JE, Muschler, JL, Thibault, G, Chang, YH, Gray, JW, Presnell, SC, Nguyen, DG, Sears, RC Cell Rep 26 (3): 608-623.e6. doi: 10.1016/j.celrep.2018.12.090. PubMed PMID:30650355 PubMed Central PMC6366459
  • 2019 | Microtubule regulators act in the nervous system to modulate fat metabolism and longevity through DAF-16 in C. elegans. Xu, A, Zhang, Z, Ko, SH, Fisher, AL, Liu, Z, Chen, L Aging Cell 18 (2): e12884. doi: 10.1111/acel.12884. PubMed PMID:30638295 PubMed Central PMC6413656
  • 2019 | Single-cell microRNA-mRNA co-sequencing reveals non-genetic heterogeneity and mechanisms of microRNA regulation. Wang, N, Zheng, J, Chen, Z, Liu, Y, Dura, B, Kwak, M, Xavier-Ferrucio, J, Lu, YC, Zhang, M, Roden, C, Cheng, J, Krause, DS, Ding, Y, Fan, R, Lu, J Nat Commun 10 (1): 95. doi: 10.1038/s41467-018-07981-6. PubMed PMID:30626865 PubMed Central PMC6327095
  • 2019 | Prognostic Gene Discovery in Glioblastoma Patients using Deep Learning. Wong, KK, Rostomily, R, Wong, STC Cancers (Basel) 11 (1): . doi: 10.3390/cancers11010053. PubMed PMID:30626092 PubMed Central PMC6356839
  • 2019 | Elucidating synergistic dependencies in lung adenocarcinoma by proteome-wide signaling-network analysis. Bansal, M, He, J, Peyton, M, Kustagi, M, Iyer, A, Comb, M, White, M, Minna, JD, Califano, A PLoS ONE 14 (1): e0208646. doi: 10.1371/journal.pone.0208646. PubMed PMID:30615629 PubMed Central PMC6322741
  • 2019 | Peroxiredoxins in Cancer and Response to Radiation Therapies. Forshaw, TE, Holmila, R, Nelson, KJ, Lewis, JE, Kemp, ML, Tsang, AW, Poole, LB, Lowther, WT, Furdui, CM Antioxidants (Basel) 8 (1): . doi: 10.3390/antiox8010011. PubMed PMID:30609657 PubMed Central PMC6356878
  • 2019 | GRB7 dependent proliferation of basal-like, HER-2 positive human breast cancer cell lines is mediated in part by HER-1 signaling. Luoh, SW, Wagoner, W, Wang, X, Hu, Z, Lai, X, Chin, K, Sears, R, Ramsey, E Mol. Carcinog. 58 (5): 699-707. doi: 10.1002/mc.22963. PubMed PMID:30604896 PubMed Central PMC6561472
  • 2018 | Life History Trade-Offs in Tumors. Boddy, AM, Huang, W, Aktipis, A Curr Pathobiol Rep 6 (4): 201-207. doi: 10.1007/s40139-018-0188-4. PubMed PMID:30595969 PubMed Central PMC6290708
  • 2019 | Arrestin-3 scaffolding of the JNK3 cascade suggests a mechanism for signal amplification. Perry, NA, Kaoud, TS, Ortega, OO, Kaya, AI, Marcus, DJ, Pleinis, JM, Berndt, S, Chen, Q, Zhan, X, Dalby, KN, Lopez, CF, Iverson, TM, Gurevich, VV Proc. Natl. Acad. Sci. U.S.A. 116 (3): 810-815. doi: 10.1073/pnas.1819230116. PubMed PMID:30591558 PubMed Central PMC6338856
  • 2018 | SCOPE-Seq: a scalable technology for linking live cell imaging and single-cell RNA sequencing. Yuan, J, Sheng, J, Sims, PA Genome Biol. 19 (1): 227. doi: 10.1186/s13059-018-1607-x. PubMed PMID:30583733 PubMed Central PMC6305572
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  • 2018 | Spectrum and prevalence of genetic predisposition in medulloblastoma: a retrospective genetic study and prospective validation in a clinical trial cohort. Waszak, SM, Northcott, PA, Buchhalter, I, Robinson, GW, Sutter, C, Groebner, S, Grund, KB, Brugières, L, Jones, DTW, Pajtler, KW, Morrissy, AS, Kool, M, Sturm, D, Chavez, L, Ernst, A, Brabetz, S, Hain, M, Zichner, T, Segura-Wang, M, Weischenfeldt, J, Rausch, T, Mardin, BR, Zhou, X, Baciu, C, Lawerenz, C, Chan, JA, Varlet, P, Guerrini-Rousseau, L, Fults, DW, Grajkowska, W, Hauser, P, Jabado, N, Ra, YS, Zitterbart, K, Shringarpure, SS, De La Vega, FM, Bustamante, CD, Ng, HK, Perry, A, MacDonald, TJ, Hernáiz Driever, P, Bendel, AE, Bowers, DC, McCowage, G, Chintagumpala, MM, Cohn, R, Hassall, T, Fleischhack, G, Eggen, T, Wesenberg, F, Feychting, M, Lannering, B, Schüz, J, Johansen, C, Andersen, TV, Röösli, M, Kuehni, CE, Grotzer, M, Kjaerheim, K, Monoranu, CM, Archer, TC, Duke, E, Pomeroy, SL, Shelagh, R, Frank, S, Sumerauer, D, Scheurlen, W, Ryzhova, MV, Milde, T, Kratz, CP, Samuel, D, Zhang, J, Solomon, DA, Marra, M, Eils, R, Bartram, CR, von Hoff, K, Rutkowski, S, Ramaswamy, V, Gilbertson, RJ, Korshunov, A, Taylor, MD, Lichter, P, Malkin, D, Gajjar, A, Korbel, JO, Pfister, SM Lancet Oncol. 19 (6): 785-798. doi: 10.1016/S1470-2045(18)30242-0. PubMed PMID:29753700 PubMed Central PMC5984248
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  • 2018 | Quantitative assessment of protein activity in orphan tissues and single cells using the metaVIPER algorithm. Ding, H, Douglass, EF Jr, Sonabend, AM, Mela, A, Bose, S, Gonzalez, C, Canoll, PD, Sims, PA, Alvarez, MJ, Califano, A Nat Commun 9 (1): 1471. doi: 10.1038/s41467-018-03843-3. PubMed PMID:29662057 PubMed Central PMC5902599
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  • 2018 | Disruption of NSD1 in Head and Neck Cancer Promotes Favorable Chemotherapeutic Responses Linked to Hypomethylation. Bui, N, Huang, JK, Bojorquez-Gomez, A, Licon, K, Sanchez, KS, Tang, SN, Beckett, AN, Wang, T, Zhang, W, Shen, JP, Kreisberg, JF, Ideker, T Mol. Cancer Ther. 17 (7): 1585-1594. doi: 10.1158/1535-7163.MCT-17-0937. PubMed PMID:29636367 PubMed Central PMC6030464
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  • 2018 | A Nonquiescent "Idling" Population State in Drug-Treated, BRAF-Mutated Melanoma. Paudel, BB, Harris, LA, Hardeman, KN, Abugable, AA, Hayford, CE, Tyson, DR, Quaranta, V Biophys. J. 114 (6): 1499-1511. doi: 10.1016/j.bpj.2018.01.016. PubMed PMID:29590606 PubMed Central PMC5883941
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  • 2018 | Targeting Brain-Adaptive Cancer Stem Cells Prohibits Brain Metastatic Colonization of Triple-Negative Breast Cancer. Ren, D, Zhu, X, Kong, R, Zhao, Z, Sheng, J, Wang, J, Xu, X, Liu, J, Cui, K, Zhang, XH, Zhao, H, Wong, STC Cancer Res. 78 (8): 2052-2064. doi: 10.1158/0008-5472.CAN-17-2994. PubMed PMID:29567857 PubMed Central PMC5899649
  • 2018 | Microenvironment-Mediated Mechanisms of Resistance to HER2 Inhibitors Differ between HER2+ Breast Cancer Subtypes. Watson, SS, Dane, M, Chin, K, Tatarova, Z, Liu, M, Liby, T, Thompson, W, Smith, R, Nederlof, M, Bucher, E, Kilburn, D, Whitman, M, Sudar, D, Mills, GB, Heiser, LM, Jonas, O, Gray, JW, Korkola, JE Cell Syst 6 (3): 329-342.e6. doi: 10.1016/j.cels.2018.02.001. PubMed PMID:29550255 PubMed Central PMC5927625
  • 2018 | Single-cell RNA sequencing reveals gene expression signatures of breast cancer-associated endothelial cells. Sun, Z, Wang, CY, Lawson, DA, Kwek, S, Velozo, HG, Owyong, M, Lai, MD, Fong, L, Wilson, M, Su, H, Werb, Z, Cooke, DL Oncotarget 9 (13): 10945-10961. doi: 10.18632/oncotarget.23760. PubMed PMID:29541388 PubMed Central PMC5834272
  • 2018 | Cross-Cohort Analysis Identifies a TEAD4-MYCN Positive Feedback Loop as the Core Regulatory Element of High-Risk Neuroblastoma. Rajbhandari, P, Lopez, G, Capdevila, C, Salvatori, B, Yu, J, Rodriguez-Barrueco, R, Martinez, D, Yarmarkovich, M, Weichert-Leahey, N, Abraham, BJ, Alvarez, MJ, Iyer, A, Harenza, JL, Oldridge, D, De Preter, K, Koster, J, Asgharzadeh, S, Seeger, RC, Wei, JS, Khan, J, Vandesompele, J, Mestdagh, P, Versteeg, R, Look, AT, Young, RA, Iavarone, A, Lasorella, A, Silva, JM, Maris, JM, Califano, A Cancer Discov 8 (5): 582-599. doi: 10.1158/2159-8290.CD-16-0861. PubMed PMID:29510988 PubMed Central PMC5967627
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  • 2018 | Mapping a functional cancer genome atlas of tumor suppressors in mouse liver using AAV-CRISPR-mediated direct in vivo screening. Wang, G, Chow, RD, Ye, L, Guzman, CD, Dai, X, Dong, MB, Zhang, F, Sharp, PA, Platt, RJ, Chen, S Sci Adv 4 (2): eaao5508. doi: 10.1126/sciadv.aao5508. PubMed PMID:29503867 PubMed Central PMC5829971
  • 2018 | In vivo systems biology approaches to chronic immune/inflammatory pathophysiology. Starchenko, A, Lauffenburger, DA Curr. Opin. Biotechnol. 52 : 9-16. doi: 10.1016/j.copbio.2018.02.006. PubMed PMID:29494996
  • 2018 | BET proteins in abnormal metabolism, inflammation, and the breast cancer microenvironment. Andrieu, GP, Shafran, JS, Deeney, JT, Bharadwaj, KR, Rangarajan, A, Denis, GV J. Leukoc. Biol. 104 (2): 265-274. doi: 10.1002/JLB.5RI0917-380RR. PubMed PMID:29493812 PubMed Central PMC6134394
  • 2018 | Brain cancer genomics and epigenomics. Archer, TC, Sengupta, S, Pomeroy, SL Handb Clin Neurol 148 : 785-797. doi: 10.1016/B978-0-444-64076-5.00050-8. PubMed PMID:29478614
  • 2018 | Differential expression of the TWEAK receptor Fn14 in IDH1 wild-type and mutant gliomas. Hersh, DS, Peng, S, Dancy, JG, Galisteo, R, Eschbacher, JM, Castellani, RJ, Heath, JE, Legesse, T, Kim, AJ, Woodworth, GF, Tran, NL, Winkles, JA J. Neurooncol. 138 (2): 241-250. doi: 10.1007/s11060-018-2799-3. PubMed PMID:29453678 PubMed Central PMC6047063
  • 2018 | Combinatorial CRISPR-Cas9 Metabolic Screens Reveal Critical Redox Control Points Dependent on the KEAP1-NRF2 Regulatory Axis. Zhao, D, Badur, MG, Luebeck, J, Magaña, JH, Birmingham, A, Sasik, R, Ahn, CS, Ideker, T, Metallo, CM, Mali, P Mol. Cell 69 (4): 699-708.e7. doi: 10.1016/j.molcel.2018.01.017. PubMed PMID:29452643 PubMed Central PMC5819357
  • 2018 | The ABCs of PTMs. Barber, KW, Rinehart, J Nat. Chem. Biol. 14 (3): 188-192. doi: 10.1038/nchembio.2572. PubMed PMID:29443972 PubMed Central PMC5979263
  • 2018 | Comprehensive characterisation of compartment-specific long non-coding RNAs associated with pancreatic ductal adenocarcinoma. Arnes, L, Liu, Z, Wang, J, Maurer, C, Sagalovskiy, I, Sanchez-Martin, M, Bommakanti, N, Garofalo, DC, Balderes, DA, Sussel, L, Olive, KP, Rabadan, R Gut : . doi: 10.1136/gutjnl-2017-314353. PubMed PMID:29440233 PubMed Central PMC6086768
  • 2018 | Cross-talk Signaling between HER3 and HPV16 E6 and E7 Mediates Resistance to PI3K Inhibitors in Head and Neck Cancer. Brand, TM, Hartmann, S, Bhola, NE, Li, H, Zeng, Y, O'Keefe, RA, Ranall, MV, Bandyopadhyay, S, Soucheray, M, Krogan, NJ, Kemp, C, Duvvuri, U, LaVallee, T, Johnson, DE, Ozbun, MA, Bauman, JE, Grandis, JR Cancer Res. 78 (9): 2383-2395. doi: 10.1158/0008-5472.CAN-17-1672. PubMed PMID:29440171 PubMed Central PMC6537867
  • 2018 | BET Proteins Exhibit Transcriptional and Functional Opposition in the Epithelial-to-Mesenchymal Transition. Andrieu, GP, Denis, GV Mol. Cancer Res. 16 (4): 580-586. doi: 10.1158/1541-7786.MCR-17-0568. PubMed PMID:29437854 PubMed Central PMC5882530
  • 2018 | A drift-diffusion checkpoint model predicts a highly variable and growth-factor-sensitive portion of the cell cycle G1 phase. Jones, ZW, Leander, R, Quaranta, V, Harris, LA, Tyson, DR PLoS ONE 13 (2): e0192087. doi: 10.1371/journal.pone.0192087. PubMed PMID:29432467 PubMed Central PMC5809023
  • 2018 | Comparing side chain packing in soluble proteins, protein-protein interfaces, and transmembrane proteins. Gaines, JC, Acebes, S, Virrueta, A, Butler, M, Regan, L, O'Hern, CS Proteins 86 (5): 581-591. doi: 10.1002/prot.25479. PubMed PMID:29427530 PubMed Central PMC5912992
  • 2018 | Targeting minimal residual disease: a path to cure?. Luskin, MR, Murakami, MA, Manalis, SR, Weinstock, DM Nat. Rev. Cancer 18 (4): 255-263. doi: 10.1038/nrc.2017.125. PubMed PMID:29376520 PubMed Central PMC6398166
  • 2018 | N-Carboxyanhydride Polymerization of Glycopolypeptides That Activate Antigen-Presenting Cells through Dectin-1 and Dectin-2. Zhou, MN, Delaveris, CS, Kramer, JR, Kenkel, JA, Engleman, EG, Bertozzi, CR Angew. Chem. Int. Ed. Engl. 57 (12): 3137-3142. doi: 10.1002/anie.201713075. PubMed PMID:29370452 PubMed Central PMC5842139
  • 2018 | Discovering Altered Regulation and Signaling Through Network-based Integration of Transcriptomic, Epigenomic, and Proteomic Tumor Data. Kedaigle, AJ, Fraenkel, E Methods Mol. Biol. 1711 : 13-26. doi: 10.1007/978-1-4939-7493-1_2. PubMed PMID:29344883 PubMed Central PMC6309679
  • 2018 | Clonal evolution mechanisms in NT5C2 mutant-relapsed acute lymphoblastic leukaemia. Tzoneva, G, Dieck, CL, Oshima, K, Ambesi-Impiombato, A, Sánchez-Martín, M, Madubata, CJ, Khiabanian, H, Yu, J, Waanders, E, Iacobucci, I, Sulis, ML, Kato, M, Koh, K, Paganin, M, Basso, G, Gastier-Foster, JM, Loh, ML, Kirschner-Schwabe, R, Mullighan, CG, Rabadan, R, Ferrando, AA Nature 553 (7689): 511-514. doi: 10.1038/nature25186. PubMed PMID:29342136 PubMed Central PMC5931372
  • 2018 | HIF signaling in osteoblast-lineage cells promotes systemic breast cancer growth and metastasis in mice. Devignes, CS, Aslan, Y, Brenot, A, Devillers, A, Schepers, K, Fabre, S, Chou, J, Casbon, AJ, Werb, Z, Provot, S Proc. Natl. Acad. Sci. U.S.A. 115 (5): E992-E1001. doi: 10.1073/pnas.1718009115. PubMed PMID:29339479 PubMed Central PMC5798374
  • 2018 | Cancer-associated fibroblasts regulate endothelial adhesion protein LPP to promote ovarian cancer chemoresistance. Leung, CS, Yeung, TL, Yip, KP, Wong, KK, Ho, SY, Mangala, LS, Sood, AK, Lopez-Berestein, G, Sheng, J, Wong, ST, Birrer, MJ, Mok, SC J. Clin. Invest. 128 (2): 589-606. doi: 10.1172/JCI95200. PubMed PMID:29251630 PubMed Central PMC5785271
  • 2018 | Single-Cell RNA-seq Reveals a Subpopulation of Prostate Cancer Cells with Enhanced Cell-Cycle-Related Transcription and Attenuated Androgen Response. Horning, AM, Wang, Y, Lin, CK, Louie, AD, Jadhav, RR, Hung, CN, Wang, CM, Lin, CL, Kirma, NB, Liss, MA, Kumar, AP, Sun, L, Liu, Z, Chao, WT, Wang, Q, Jin, VX, Chen, CL, Huang, TH Cancer Res. 78 (4): 853-864. doi: 10.1158/0008-5472.CAN-17-1924. PubMed PMID:29233929 PubMed Central PMC5983359
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