CSBC Supported Publications

Publications

  • 2019 | Variational Autoencoding Tissue Response to Microenvironment Perturbation. Schau, GF, Thibault, G, Dane, MA, Gray, JW, Heiser, LM, Chang, YH Proc SPIE Int Soc Opt Eng 10949 : . doi: 10.1117/12.2512660. PubMed PMID:31379401 PubMed Central PMC6677277
  • 2019 | Cancer cell evolution through the ages. Maley, CC, Shibata, D Science 365 (6452): 440-441. doi: 10.1126/science.aay2859. PubMed PMID:31371596
  • 2019 | Elevated neoantigen levels in tumors with somatic mutations in the HLA-A, HLA-B, HLA-C and B2M genes. Castro, A, Ozturk, K, Pyke, RM, Xian, S, Zanetti, M, Carter, H BMC Med Genomics 12 (Suppl 6): 107. doi: 10.1186/s12920-019-0544-1. PubMed PMID:31345234 PubMed Central PMC6657029
  • 2019 | xml2jupyter: Mapping parameters between XML and Jupyter widgets. Heiland, R, Mishler, D, Zhang, T, Bower, E, Macklin, P J Open Source Softw 4 (39): . doi: 10.21105/joss.01408. PubMed PMID:31342010 PubMed Central PMC6656392
  • 2019 | Small Cell Lung Cancer Therapeutic Responses Through Fractal Measurements: From Radiology to Mitochondrial Biology. Mambetsariev, I, Mirzapoiazova, T, Lennon, F, Jolly, MK, Li, H, Nasser, MW, Vora, L, Kulkarni, P, Batra, SK, Salgia, R J Clin Med 8 (7): . doi: 10.3390/jcm8071038. PubMed PMID:31315252
  • 2019 | Targeted treatment of papillary craniopharyngiomas harboring BRAF V600E mutations. Juratli, TA, Jones, PS, Wang, N, Subramanian, M, Aylwin, SJB, Odia, Y, Rostami, E, Gudjonsson, O, Shaw, BL, Cahill, DP, Galanis, E, Barker, FG 2nd, Santagata, S, Brastianos, PK Cancer 125 (17): 2910-2914. doi: 10.1002/cncr.32197. PubMed PMID:31314136
  • 2019 | PEAK3/C19orf35 pseudokinase, a new NFK3 kinase family member, inhibits CrkII through dimerization. Lopez, ML, Lo, M, Kung, JE, Dudkiewicz, M, Jang, GM, Von Dollen, J, Johnson, JR, Krogan, NJ, Pawłowski, K, Jura, N Proc. Natl. Acad. Sci. U.S.A. 116 (31): 15495-15504. doi: 10.1073/pnas.1906360116. PubMed PMID:31311869 PubMed Central PMC6681764
  • 2019 | VISAGE Reveals a Targetable Mitotic Spindle Vulnerability in Cancer Cells. Patterson, JC, Joughin, BA, Prota, AE, Mühlethaler, T, Jonas, OH, Whitman, MA, Varmeh, S, Chen, S, Balk, SP, Steinmetz, MO, Lauffenburger, DA, Yaffe, MB Cell Syst 9 (1): 74-92.e8. doi: 10.1016/j.cels.2019.05.009. PubMed PMID:31302152 PubMed Central PMC6688637
  • 2019 | Integration of machine learning and mechanistic models accurately predicts variation in cell density of glioblastoma using multiparametric MRI. Gaw, N, Hawkins-Daarud, A, Hu, LS, Yoon, H, Wang, L, Xu, Y, Jackson, PR, Singleton, KW, Baxter, LC, Eschbacher, J, Gonzales, A, Nespodzany, A, Smith, K, Nakaji, P, Mitchell, JR, Wu, T, Swanson, KR, Li, J Sci Rep 9 (1): 10063. doi: 10.1038/s41598-019-46296-4. PubMed PMID:31296889 PubMed Central PMC6624304
  • 2019 | Mapping the protein-protein and genetic interactions of cancer to guide precision medicine. Bouhaddou, M, Eckhardt, M, Chi Naing, ZZ, Kim, M, Ideker, T, Krogan, NJ Curr. Opin. Genet. Dev. 54 : 110-117. doi: 10.1016/j.gde.2019.04.005. PubMed PMID:31288129
  • 2019 | Switch-like enhancement of epithelial-mesenchymal transition by YAP through feedback regulation of WT1 and Rho-family GTPases. Park, J, Kim, DH, Shah, SR, Kim, HN, Kshitiz,, Kim, P, Quiñones-Hinojosa, A, Levchenko, A Nat Commun 10 (1): 2797. doi: 10.1038/s41467-019-10729-5. PubMed PMID:31243273 PubMed Central PMC6594963
  • 2019 | HPV vaccination has not increased sexual activity or accelerated sexual debut in a college-aged cohort of men and women. Brouwer, AF, Delinger, RL, Eisenberg, MC, Campredon, LP, Walline, HM, Carey, TE, Meza, R BMC Public Health 19 (1): 821. doi: 10.1186/s12889-019-7134-1. PubMed PMID:31238911 PubMed Central PMC6593582
  • 2019 | Single-cell Analysis of CAR-T Cell Activation Reveals A Mixed TH1/TH2 Response Independent of Differentiation. Xhangolli, I, Dura, B, Lee, G, Kim, D, Xiao, Y, Fan, R Genomics Proteomics Bioinformatics 17 (2): 129-139. doi: 10.1016/j.gpb.2019.03.002. PubMed PMID:31229590 PubMed Central PMC6620429
  • 2019 | Cross-Species Single-Cell Analysis of Pancreatic Ductal Adenocarcinoma Reveals Antigen-Presenting Cancer-Associated Fibroblasts. Elyada, E, Bolisetty, M, Laise, P, Flynn, WF, Courtois, ET, Burkhart, RA, Teinor, JA, Belleau, P, Biffi, G, Lucito, MS, Sivajothi, S, Armstrong, TD, Engle, DD, Yu, KH, Hao, Y, Wolfgang, CL, Park, Y, Preall, J, Jaffee, EM, Califano, A, Robson, P, Tuveson, DA Cancer Discov 9 (8): 1102-1123. doi: 10.1158/2159-8290.CD-19-0094. PubMed PMID:31197017
  • 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 | Multiomics Profiling Establishes the Polypharmacology of FDA-Approved CDK4/6 Inhibitors and the Potential for Differential Clinical Activity. Hafner, M, Mills, CE, Subramanian, K, Chen, C, Chung, M, Boswell, SA, Everley, RA, Liu, C, Walmsley, CS, Juric, D, Sorger, PK Cell Chem Biol 26 (8): 1067-1080.e8. doi: 10.1016/j.chembiol.2019.05.005. PubMed PMID:31178407
  • 2019 | 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. 294 (29): 11062-11086. doi: 10.1074/jbc.REV119.005601. PubMed PMID:31171722 PubMed Central PMC6643028
  • 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 | A microphysiological model of the bronchial airways reveals the interplay of mechanical and biochemical signals in bronchospasm. Kilic, O, Yoon, A, Shah, SR, Yong, HM, Ruiz-Valls, A, Chang, H, Panettieri, RA Jr, Liggett, SB, Quiñones-Hinojosa, A, An, SS, Levchenko, A Nat Biomed Eng 3 (7): 532-544. doi: 10.1038/s41551-019-0366-7. PubMed PMID:31150010 PubMed Central PMC6653686
  • 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 PubMed Central PMC6555538
  • 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 PubMed Central PMC6571585
  • 2019 | BRD4 Regulates Metastatic Potential of Castration-Resistant Prostate Cancer through AHNAK. Shafran, JS, Andrieu, GP, Györffy, B, Denis, GV Mol. Cancer Res. 17 (8): 1627-1638. doi: 10.1158/1541-7786.MCR-18-1279. PubMed PMID:31110158 PubMed Central PMC6677600
  • 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 | Adaptation of Human iPSC-Derived Cardiomyocytes to Tyrosine Kinase Inhibitors Reduces Acute Cardiotoxicity via Metabolic Reprogramming. Wang, H, Sheehan, RP, Palmer, AC, Everley, RA, Boswell, SA, Ron-Harel, N, Ringel, AE, Holton, KM, Jacobson, CA, Erickson, AR, Maliszewski, L, Haigis, MC, Sorger, PK Cell Syst 8 (5): 412-426.e7. doi: 10.1016/j.cels.2019.03.009. PubMed PMID:31078528 PubMed Central PMC6657491
  • 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 | Mechanisms of Lymphoma Clearance Induced by High-Dose Alkylating Agents. Lossos, C, Liu, Y, Kolb, KE, Christie, AL, Van Scoyk, A, Prakadan, SM, Shigemori, K, Stevenson, KE, Morrow, S, Plana, OD, Fraser, C, Jones, KL, Liu, H, Pallasch, CP, Modiste, R, Nguyen, QD, Craig, JW, Morgan, EA, Vega, F, Aster, JC, Sarosiek, KA, Shalek, AK, Hemann, MT, Weinstock, DM Cancer Discov 9 (7): 944-961. doi: 10.1158/2159-8290.CD-18-1393. PubMed PMID:31040105 PubMed Central PMC6606344
  • 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, DA, Jarrett, AM, Lima, EABF, Tinsley Oden, J, Biros, G, Yankeelov, TE, Curtius, K, Al Bakir, I, Wodarz, D, Komarova, N, Aparicio, L, Bordyuh, M, Rabadan, R, Finley, SD, Enderling, H, Caudell, J, Moros, EG, Anderson, ARA, Gatenby, RA, Kaznatcheev, A, Jeavons, P, Krishnan, N, Pelesko, J, Wadhwa, RR, Yoon, N, Nichol, D, Marusyk, A, Hinczewski, M, Scott, JG Phys Biol 16 (4): 041005. doi: 10.1088/1478-3975/ab1a09. PubMed PMID:30991381 PubMed Central PMC6655440
  • 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 26 (6): 818-829.e9. doi: 10.1016/j.chembiol.2019.02.021. PubMed PMID:30982749 PubMed Central PMC6634314
  • 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. 76 (14): 2663-2679. doi: 10.1007/s00018-019-03097-2. PubMed PMID:30982079 PubMed Central PMC6589134
  • 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 PubMed Central PMC6592845
  • 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 PubMed Central PMC6675406
  • 2019 | ROS and Oxidative Stress Are Elevated in Mitosis during Asynchronous Cell Cycle Progression and Are Exacerbated by Mitotic Arrest. Patterson, JC, Joughin, BA, van de Kooij, B, Lim, DC, Lauffenburger, DA, Yaffe, MB Cell Syst 8 (2): 163-167.e2. doi: 10.1016/j.cels.2019.01.005. PubMed PMID:30797774 PubMed Central PMC6688173
  • 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 PubMed Central PMC6592847
  • 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 PubMed Central PMC6633916
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  • 2018 | Multiple Routes to Oncogenesis Are Promoted by the Human Papillomavirus-Host Protein Network. Eckhardt, M, Zhang, W, Gross, AM, Von Dollen, J, Johnson, JR, Franks-Skiba, KE, Swaney, DL, Johnson, TL, Jang, GM, Shah, PS, Brand, TM, Archambault, J, Kreisberg, JF, Grandis, JR, Ideker, T, Krogan, NJ Cancer Discov 8 (11): 1474-1489. doi: 10.1158/2159-8290.CD-17-1018. PubMed PMID:30209081 PubMed Central PMC6375299
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  • 2018 | Extravasation of Brownian Spheroidal Nanoparticles through Vascular Pores. Shah, PN, Lin, TY, Aanei, IL, Klass, SH, Smith, BR, Shaqfeh, ESG Biophys. J. 115 (6): 1103-1115. doi: 10.1016/j.bpj.2018.07.038. PubMed PMID:30201266 PubMed Central PMC6139985
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  • 2018 | Quantitative Yeast Genetic Interaction Profiling of Bacterial Effector Proteins Uncovers a Role for the Human Retromer in Salmonella Infection. Patrick, KL, Wojcechowskyj, JA, Bell, SL, Riba, MN, Jing, T, Talmage, S, Xu, P, Cabello, AL, Xu, J, Shales, M, Jimenez-Morales, D, Ficht, TA, de Figueiredo, P, Samuel, JE, Li, P, Krogan, NJ, Watson, RO Cell Syst 7 (3): 323-338.e6. doi: 10.1016/j.cels.2018.06.010. PubMed PMID:30077634 PubMed Central PMC6160342
  • 2018 | Sno-derived RNAs are prevalent molecular markers of cancer immunity. Chow, RD, Chen, S Oncogene 37 (50): 6442-6462. doi: 10.1038/s41388-018-0420-z. PubMed PMID:30072739 PubMed Central PMC6294694
  • 2018 | Programmable DNA repair with CRISPRa/i enhanced homology-directed repair efficiency with a single Cas9. Ye, L, Wang, C, Hong, L, Sun, N, Chen, D, Chen, S, Han, F Cell Discov 4 : 46. doi: 10.1038/s41421-018-0049-7. PubMed PMID:30062046 PubMed Central PMC6056518
  • 2018 | Transmission of rhinovirus in the Utah BIG-LoVE families: Consequences of age and household structure. Adler, FR, Stockmann, C, Ampofo, K, Pavia, AT, Byington, CL PLoS ONE 13 (7): e0199388. doi: 10.1371/journal.pone.0199388. PubMed PMID:30044794 PubMed Central PMC6059387
  • 2018 | Single-cell transcriptome analysis of lineage diversity in high-grade glioma. Yuan, J, Levitin, HM, Frattini, V, Bush, EC, Boyett, DM, Samanamud, J, Ceccarelli, M, Dovas, A, Zanazzi, G, Canoll, P, Bruce, JN, Lasorella, A, Iavarone, A, Sims, PA Genome Med 10 (1): 57. doi: 10.1186/s13073-018-0567-9. PubMed PMID:30041684 PubMed Central PMC6058390
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  • 2018 | Live-Cell Imaging of Chromatin Condensation Dynamics by CRISPR. Xue, Y, Acar, M iScience 4 : 216-235. doi: 10.1016/j.isci.2018.06.001. PubMed PMID:30027155 PubMed Central PMC6048970
  • 2018 | A simple and robust procedure for preparing graphene-oxide cryo-EM grids. Palovcak, E, Wang, F, Zheng, SQ, Yu, Z, Li, S, Betegon, M, Bulkley, D, Agard, DA, Cheng, Y J. Struct. Biol. 204 (1): 80-84. doi: 10.1016/j.jsb.2018.07.007. PubMed PMID:30017701 PubMed Central PMC6119484
  • 2018 | Immune reprogramming via PD-1 inhibition enhances early-stage lung cancer survival. Markowitz, GJ, Havel, LS, Crowley, MJ, Ban, Y, Lee, SB, Thalappillil, JS, Narula, N, Bhinder, B, Elemento, O, Wong, ST, Gao, D, Altorki, NK, Mittal, V JCI Insight 3 (13): . doi: 10.1172/jci.insight.96836. PubMed PMID:29997286 PubMed Central PMC6101707
  • 2018 | The Cytoscape Automation app article collection. Demchak, B, Otasek, D, Pico, AR, Bader, GD, Ono, K, Settle, B, Sage, E, Morris, JH, Longabaugh, W, Lopes, C, Kucera, M, Treister, A, Schwikowski, B, Molenaar, P, Ideker, T F1000Res 7 : 800. doi: 10.12688/f1000research.15355.1. PubMed PMID:29983926 PubMed Central PMC6013757
  • 2018 | DNA concentration from self samples for HPV testing. Meza, R, Lau, YK, Thomas, TB, Carey, TE, Walline, HM, Eisenberg, MC Int. J. Cancer 143 (11): 3036-3037. doi: 10.1002/ijc.31666. PubMed PMID:29978468 PubMed Central PMC6235705
  • 2018 | Single-Cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment. Azizi, E, Carr, AJ, Plitas, G, Cornish, AE, Konopacki, C, Prabhakaran, S, Nainys, J, Wu, K, Kiseliovas, V, Setty, M, Choi, K, Fromme, RM, Dao, P, McKenney, PT, Wasti, RC, Kadaveru, K, Mazutis, L, Rudensky, AY, Pe'er, D Cell 174 (5): 1293-1308.e36. doi: 10.1016/j.cell.2018.05.060. PubMed PMID:29961579 PubMed Central PMC6348010
  • 2018 | Recovering Gene Interactions from Single-Cell Data Using Data Diffusion. van Dijk, D, Sharma, R, Nainys, J, Yim, K, Kathail, P, Carr, AJ, Burdziak, C, Moon, KR, Chaffer, CL, Pattabiraman, D, Bierie, B, Mazutis, L, Wolf, G, Krishnaswamy, S, Pe'er, D Cell 174 (3): 716-729.e27. doi: 10.1016/j.cell.2018.05.061. PubMed PMID:29961576
  • 2018 | Classifying tumors by supervised network propagation. Zhang, W, Ma, J, Ideker, T Bioinformatics 34 (13): i484-i493. doi: 10.1093/bioinformatics/bty247. PubMed PMID:29949979 PubMed Central PMC6022559
  • 2018 | Synthetic Lethal Networks for Precision Oncology: Promises and Pitfalls. Shen, JP, Ideker, T J. Mol. Biol. 430 (18 Pt A): 2900-2912. doi: 10.1016/j.jmb.2018.06.026. PubMed PMID:29932943 PubMed Central PMC6097899
  • 2018 | Kinase Substrate Profiling Using a Proteome-wide Serine-Oriented Human Peptide Library. Barber, KW, Miller, CJ, Jun, JW, Lou, HJ, Turk, BE, Rinehart, J Biochemistry 57 (31): 4717-4725. doi: 10.1021/acs.biochem.8b00410. PubMed PMID:29920078 PubMed Central PMC6644682
  • 2018 | A precision oncology approach to the pharmacological targeting of mechanistic dependencies in neuroendocrine tumors. Alvarez, MJ, Subramaniam, PS, Tang, LH, Grunn, A, Aburi, M, Rieckhof, G, Komissarova, EV, Hagan, EA, Bodei, L, Clemons, PA, Dela Cruz, FS, Dhall, D, Diolaiti, D, Fraker, DA, Ghavami, A, Kaemmerer, D, Karan, C, Kidd, M, Kim, KM, Kim, HC, Kunju, LP, Langel, Ü, Li, Z, Lee, J, Li, H, LiVolsi, V, Pfragner, R, Rainey, AR, Realubit, RB, Remotti, H, Regberg, J, Roses, R, Rustgi, A, Sepulveda, AR, Serra, S, Shi, C, Yuan, X, Barberis, M, Bergamaschi, R, Chinnaiyan, AM, Detre, T, Ezzat, S, Frilling, A, Hommann, M, Jaeger, D, Kim, MK, Knudsen, BS, Kung, AL, Leahy, E, Metz, DC, Milsom, JW, Park, YS, Reidy-Lagunes, D, Schreiber, S, Washington, K, Wiedenmann, B, Modlin, I, Califano, A Nat. Genet. 50 (7): 979-989. doi: 10.1038/s41588-018-0138-4. PubMed PMID:29915428 PubMed Central PMC6421579
  • 2018 | The Emerging Potential for Network Analysis to Inform Precision Cancer Medicine. Ozturk, K, Dow, M, Carlin, DE, Bejar, R, Carter, H J. Mol. Biol. 430 (18 Pt A): 2875-2899. doi: 10.1016/j.jmb.2018.06.016. PubMed PMID:29908887 PubMed Central PMC6097914
  • 2018 | Case Studies of Gastric, Lung, and Oral Cancer Connect Etiologic Agent Prevalence to Cancer Incidence. Brouwer, AF, Eisenberg, MC, Meza, R Cancer Res. 78 (12): 3386-3396. doi: 10.1158/0008-5472.CAN-17-3467. PubMed PMID:29907681 PubMed Central PMC6007874
  • 2018 | Visible Machine Learning for Biomedicine. Yu, MK, Ma, J, Fisher, J, Kreisberg, JF, Raphael, BJ, Ideker, T Cell 173 (7): 1562-1565. doi: 10.1016/j.cell.2018.05.056. PubMed PMID:29906441 PubMed Central PMC6483071
  • 2018 | Managing Patients With Relapsed Small-Cell Lung Cancer. Gong, J, Salgia, R J Oncol Pract 14 (6): 359-366. doi: 10.1200/JOP.18.00204. PubMed PMID:29894664 PubMed Central PMC6002253
  • 2018 | Encoding human serine phosphopeptides in bacteria for proteome-wide identification of phosphorylation-dependent interactions. Barber, KW, Muir, P, Szeligowski, RV, Rogulina, S, Gerstein, M, Sampson, JR, Isaacs, FJ, Rinehart, J Nat. Biotechnol. 36 (7): 638-644. doi: 10.1038/nbt.4150. PubMed PMID:29889213 PubMed Central PMC6590076
  • 2018 | Scarless genome editing: progress towards understanding genotype-phenotype relationships. Elison, GL, Acar, M Curr. Genet. 64 (6): 1229-1238. doi: 10.1007/s00294-018-0850-8. PubMed PMID:29872908 PubMed Central PMC6281794
  • 2018 | Harnessing single-cell genomics to improve the physiological fidelity of organoid-derived cell types. Mead, BE, Ordovas-Montanes, J, Braun, AP, Levy, LE, Bhargava, P, Szucs, MJ, Ammendolia, DA, MacMullan, MA, Yin, X, Hughes, TK, Wadsworth, MH 2nd, Ahmad, R, Rakoff-Nahoum, S, Carr, SA, Langer, R, Collins, JJ, Shalek, AK, Karp, JM BMC Biol. 16 (1): 62. doi: 10.1186/s12915-018-0527-2. PubMed PMID:29871632 PubMed Central PMC5989470
  • 2019 | Systematic Identification of Druggable Epithelial-Stromal Crosstalk Signaling Networks in Ovarian Cancer. Yeung, TL, Sheng, J, Leung, CS, Li, F, Kim, J, Ho, SY, Matzuk, MM, Lu, KH, Wong, STC, Mok, SC J. Natl. Cancer Inst. 111 (3): 272-282. doi: 10.1093/jnci/djy097. PubMed PMID:29860390 PubMed Central PMC6410941
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  • 2018 | Diverse AR-V7 cistromes in castration-resistant prostate cancer are governed by HoxB13. Chen, Z, Wu, D, Thomas-Ahner, JM, Lu, C, Zhao, P, Zhang, Q, Geraghty, C, Yan, PS, Hankey, W, Sunkel, B, Cheng, X, Antonarakis, ES, Wang, QE, Liu, Z, Huang, TH, Jin, VX, Clinton, SK, Luo, J, Huang, J, Wang, Q Proc. Natl. Acad. Sci. U.S.A. 115 (26): 6810-6815. doi: 10.1073/pnas.1718811115. PubMed PMID:29844167 PubMed Central PMC6042123
  • 2018 | The complex ecosystem in non small cell lung cancer invasion. Haney, S, Konen, J, Marcus, AI, Bazhenov, M PLoS Comput. Biol. 14 (5): e1006131. doi: 10.1371/journal.pcbi.1006131. PubMed PMID:29795571 PubMed Central PMC5991406
  • 2018 | Profiling human breast epithelial cells using single cell RNA sequencing identifies cell diversity. Nguyen, QH, Pervolarakis, N, Blake, K, Ma, D, Davis, RT, James, N, Phung, AT, Willey, E, Kumar, R, Jabart, E, Driver, I, Rock, J, Goga, A, Khan, SA, Lawson, DA, Werb, Z, Kessenbrock, K Nat Commun 9 (1): 2028. doi: 10.1038/s41467-018-04334-1. PubMed PMID:29795293 PubMed Central PMC5966421
  • 2018 | 3' UTR shortening represses tumor-suppressor genes in trans by disrupting ceRNA crosstalk. Park, HJ, Ji, P, Kim, S, Xia, Z, Rodriguez, B, Li, L, Su, J, Chen, K, Masamha, CP, Baillat, D, Fontes-Garfias, CR, Shyu, AB, Neilson, JR, Wagner, EJ, Li, W Nat. Genet. 50 (6): 783-789. doi: 10.1038/s41588-018-0118-8. PubMed PMID:29785014 PubMed Central PMC6689271
  • 2018 | Microbial Interactions in the Cystic Fibrosis Airway. Granchelli, AM, Adler, FR, Keogh, RH, Kartsonaki, C, Cox, DR, Liou, TG J. Clin. Microbiol. 56 (8): . doi: 10.1128/JCM.00354-18. PubMed PMID:29769279 PubMed Central PMC6062800
  • 2018 | Programmable sequential mutagenesis by inducible Cpf1 crRNA array inversion. Chow, RD, Kim, HR, Chen, S Nat Commun 9 (1): 1903. doi: 10.1038/s41467-018-04158-z. PubMed PMID:29765043 PubMed Central PMC5954137
  • 2018 | GFPT2-Expressing Cancer-Associated Fibroblasts Mediate Metabolic Reprogramming in Human Lung Adenocarcinoma. Zhang, W, Bouchard, G, Yu, A, Shafiq, M, Jamali, M, Shrager, JB, Ayers, K, Bakr, S, Gentles, AJ, Diehn, M, Quon, A, West, RB, Nair, V, van de Rijn, M, Napel, S, Plevritis, SK Cancer Res. 78 (13): 3445-3457. doi: 10.1158/0008-5472.CAN-17-2928. PubMed PMID:29760045 PubMed Central PMC6030462
  • 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
  • 2018 | Inflammatory signatures distinguish metabolic health in African American women with obesity. Denis, GV, Sebastiani, P, Bertrand, KA, Strissel, KJ, Tran, AH, Slama, J, Medina, ND, Andrieu, G, Palmer, JR PLoS ONE 13 (5): e0196755. doi: 10.1371/journal.pone.0196755. PubMed PMID:29738558 PubMed Central PMC5940209
  • 2018 | Pan-cancer transcriptional signatures predictive of oncogenic mutations reveal that Fbw7 regulates cancer cell oxidative metabolism. Davis, RJ, Gönen, M, Margineantu, DH, Handeli, S, Swanger, J, Hoellerbauer, P, Paddison, PJ, Gu, H, Raftery, D, Grim, JE, Hockenbery, DM, Margolin, AA, Clurman, BE Proc. Natl. Acad. Sci. U.S.A. 115 (21): 5462-5467. doi: 10.1073/pnas.1718338115. PubMed PMID:29735700
  • 2018 | Cancer CRISPR Screens In Vivo. Chow, RD, Chen, S Trends Cancer 4 (5): 349-358. doi: 10.1016/j.trecan.2018.03.002. PubMed PMID:29709259 PubMed Central PMC5935117
  • 2018 | The number of titrated microRNA species dictates ceRNA regulation. Chiu, HS, Martínez, MR, Komissarova, EV, Llobet-Navas, D, Bansal, M, Paull, EO, Silva, J, Yang, X, Sumazin, P, Califano, A Nucleic Acids Res. 46 (9): 4354-4369. doi: 10.1093/nar/gky286. PubMed PMID:29684207 PubMed Central PMC5961349
  • 2018 | 3S - Systematic, systemic, and systems biology and toxicology. Smirnova, L, Kleinstreuer, N, Corvi, R, Levchenko, A, Fitzpatrick, SC, Hartung, T ALTEX 35 (2): 139-162. doi: 10.14573/altex.1804051. PubMed PMID:29677694 PubMed Central PMC6696989
  • 2018 | Heritable stress response dynamics revealed by single-cell genealogy. Chatterjee, M, Acar, M Sci Adv 4 (4): e1701775. doi: 10.1126/sciadv.1701775. PubMed PMID:29675464 PubMed Central PMC5906080
  • 2018 | Integrative analysis reveals functional and regulatory roles of H3K79me2 in mediating alternative splicing. Li, T, Liu, Q, Garza, N, Kornblau, S, Jin, VX Genome Med 10 (1): 30. doi: 10.1186/s13073-018-0538-1. PubMed PMID:29665865 PubMed Central PMC5902843
  • 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
  • 2018 | DRUG-NEM: Optimizing drug combinations using single-cell perturbation response to account for intratumoral heterogeneity. Anchang, B, Davis, KL, Fienberg, HG, Williamson, BD, Bendall, SC, Karacosta, LG, Tibshirani, R, Nolan, GP, Plevritis, SK Proc. Natl. Acad. Sci. U.S.A. 115 (18): E4294-E4303. doi: 10.1073/pnas.1711365115. PubMed PMID:29654148 PubMed Central PMC5939057
  • 2018 | Value-based genomics. Gong, J, Pan, K, Fakih, M, Pal, S, Salgia, R Oncotarget 9 (21): 15792-15815. doi: 10.18632/oncotarget.24353. PubMed PMID:29644010 PubMed Central PMC5884665
  • 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
  • 2018 | The Immune Landscape of Cancer. Thorsson, V, Gibbs, DL, Brown, SD, Wolf, D, Bortone, DS, Ou Yang, TH, Porta-Pardo, E, Gao, GF, Plaisier, CL, Eddy, JA, Ziv, E, Culhane, AC, Paull, EO, Sivakumar, IKA, Gentles, AJ, Malhotra, R, Farshidfar, F, Colaprico, A, Parker, JS, Mose, LE, Vo, NS, Liu, J, Liu, Y, Rader, J, Dhankani, V, Reynolds, SM, Bowlby, R, Califano, A, Cherniack, AD, Anastassiou, D, Bedognetti, D, Mokrab, Y, Newman, AM, Rao, A, Chen, K, Krasnitz, A, Hu, H, Malta, TM, Noushmehr, H, Pedamallu, CS, Bullman, S, Ojesina, AI, Lamb, A, Zhou, W, Shen, H, Choueiri, TK, Weinstein, JN, Guinney, J, Saltz, J, Holt, RA, Rabkin, CS, Cancer Genome Atlas Research Network, Lazar, AJ, Serody, JS, Demicco, EG, Disis, ML, Vincent, BG, Shmulevich, I Immunity 48 (4): 812-830.e14. doi: 10.1016/j.immuni.2018.03.023. PubMed PMID:29628290 PubMed Central PMC5982584
  • 2018 | A CLK3-HMGA2 Alternative Splicing Axis Impacts Human Hematopoietic Stem Cell Molecular Identity throughout Development. Cesana, M, Guo, MH, Cacchiarelli, D, Wahlster, L, Barragan, J, Doulatov, S, Vo, LT, Salvatori, B, Trapnell, C, Clement, K, Cahan, P, Tsanov, KM, Sousa, PM, Tazon-Vega, B, Bolondi, A, Giorgi, FM, Califano, A, Rinn, JL, Meissner, A, Hirschhorn, JN, Daley, GQ Cell Stem Cell 22 (4): 575-588.e7. doi: 10.1016/j.stem.2018.03.012. PubMed PMID:29625070 PubMed Central PMC5957284
  • 2018 | A global transcriptional network connecting noncoding mutations to changes in tumor gene expression. Zhang, W, Bojorquez-Gomez, A, Velez, DO, Xu, G, Sanchez, KS, Shen, JP, Chen, K, Licon, K, Melton, C, Olson, KM, Yu, MK, Huang, JK, Carter, H, Farley, EK, Snyder, M, Fraley, SI, Kreisberg, JF, Ideker, T Nat. Genet. 50 (4): 613-620. doi: 10.1038/s41588-018-0091-2. PubMed PMID:29610481 PubMed Central PMC5893414
  • 2018 | pyNBS: a Python implementation for network-based stratification of tumor mutations. Huang, JK, Jia, T, Carlin, DE, Ideker, T Bioinformatics 34 (16): 2859-2861. doi: 10.1093/bioinformatics/bty186. PubMed PMID:29608663 PubMed Central PMC6084608
  • 2018 | Systematic Evaluation of Molecular Networks for Discovery of Disease Genes. Huang, JK, Carlin, DE, Yu, MK, Zhang, W, Kreisberg, JF, Tamayo, P, Ideker, T Cell Syst 6 (4): 484-495.e5. doi: 10.1016/j.cels.2018.03.001. PubMed PMID:29605183 PubMed Central PMC5920724
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