CSBC Supported Publications

Publications

  • 2019 | Cyclin E Overexpression in Human Mammary Epithelial Cells Promotes Epithelial Cancer-Specific Copy Number Alterations. Giraldez, S, Tamayo, P, Wineinger, N, Kim, W, Reed, SI iScience 19 : 850-859. doi: 10.1016/j.isci.2019.08.043. PubMed PMID:31513970 PubMed Central PMC6739637
  • 2019 | Reproducible biomedical benchmarking in the cloud: lessons from crowd-sourced data challenges. Ellrott, K, Buchanan, A, Creason, A, Mason, M, Schaffter, T, Hoff, B, Eddy, J, Chilton, JM, Yu, T, Stuart, JM, Saez-Rodriguez, J, Stolovitzky, G, Boutros, PC, Guinney, J Genome Biol. 20 (1): 195. doi: 10.1186/s13059-019-1794-0. PubMed PMID:31506093 PubMed Central PMC6737594
  • 2019 | Pathway activity profiling of growth factor receptor network and stemness pathways differentiates metaplastic breast cancer histological subtypes. McQuerry, JA, Jenkins, DF, Yost, SE, Zhang, Y, Schmolze, D, Johnson, WE, Yuan, Y, Bild, AH BMC Cancer 19 (1): 881. doi: 10.1186/s12885-019-6052-z. PubMed PMID:31488082 PubMed Central PMC6727561
  • 2019 | Systems Biology of Cancer Metastasis. Suhail, Y, Cain, MP, Vanaja, K, Kurywchak, PA, Levchenko, A, Kalluri, R, Kshitiz, Cell Syst 9 (2): 109-127. doi: 10.1016/j.cels.2019.07.003. PubMed PMID:31465728 PubMed Central PMC6716621
  • 2019 | Systematic Immunotherapy Target Discovery Using Genome-Scale In Vivo CRISPR Screens in CD8 T Cells. Dong, MB, Wang, G, Chow, RD, Ye, L, Zhu, L, Dai, X, Park, JJ, Kim, HR, Errami, Y, Guzman, CD, Zhou, X, Chen, KY, Renauer, PA, Du, Y, Shen, J, Lam, SZ, Zhou, JJ, Lannin, DR, Herbst, RS, Chen, S Cell 178 (5): 1189-1204.e23. doi: 10.1016/j.cell.2019.07.044. PubMed PMID:31442407 PubMed Central PMC6719679
  • 2019 | Quantitative Insights into Age-Associated DNA-Repair Inefficiency in Single Cells. Young, TZ, Liu, P, Urbonaite, G, Acar, M Cell Rep 28 (8): 2220-2230.e7. doi: 10.1016/j.celrep.2019.07.082. PubMed PMID:31433994 PubMed Central PMC6744837
  • 2019 | Mitogenic and progenitor gene programmes in single pilocytic astrocytoma cells. Reitman, ZJ, Paolella, BR, Bergthold, G, Pelton, K, Becker, S, Jones, R, Sinai, CE, Malkin, H, Huang, Y, Grimmet, L, Herbert, ZT, Sun, Y, Weatherbee, JL, Alberta, JA, Daley, JF, Rozenblatt-Rosen, O, Condurat, AL, Qian, K, Khadka, P, Segal, RA, Haas-Kogan, D, Filbin, MG, Suva, ML, Regev, A, Stiles, CD, Kieran, MW, Goumnerova, L, Ligon, KL, Shalek, AK, Bandopadhayay, P, Beroukhim, R Nat Commun 10 (1): 3731. doi: 10.1038/s41467-019-11493-2. PubMed PMID:31427603 PubMed Central PMC6700116
  • 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 | Rad5 dysregulation drives hyperactive recombination at replication forks resulting in cisplatin sensitivity and genome instability. Bryant, EE, Šunjevarić, I, Berchowitz, L, Rothstein, R, Reid, RJD Nucleic Acids Res. 47 (17): 9144-9159. doi: 10.1093/nar/gkz631. PubMed PMID:31350889
  • 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 PubMed Central PMC6679065
  • 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 | A Non-canonical Role of YAP/TEAD Is Required for Activation of Estrogen-Regulated Enhancers in Breast Cancer. Zhu, C, Li, L, Zhang, Z, Bi, M, Wang, H, Su, W, Hernandez, K, Liu, P, Chen, J, Chen, M, Huang, TH, Chen, L, Liu, Z Mol. Cell 75 (4): 791-806.e8. doi: 10.1016/j.molcel.2019.06.010. PubMed PMID:31303470 PubMed Central PMC6707877
  • 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 PubMed Central PMC6746583
  • 2019 | Inference of Population Structure from Time-Series Genotype Data. Joseph, TA, Pe'er, I Am. J. Hum. Genet. 105 (2): 317-333. doi: 10.1016/j.ajhg.2019.06.002. PubMed PMID:31256878 PubMed Central PMC6698887
  • 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 | 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 PubMed Central PMC6727976
  • 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 PubMed Central PMC6736605
  • 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 | Stromal Microenvironment Shapes the Intratumoral Architecture of Pancreatic Cancer. Ligorio, M, Sil, S, Malagon-Lopez, J, Nieman, LT, Misale, S, Di Pilato, M, Ebright, RY, Karabacak, MN, Kulkarni, AS, Liu, A, Vincent Jordan, N, Franses, JW, Philipp, J, Kreuzer, J, Desai, N, Arora, KS, Rajurkar, M, Horwitz, E, Neyaz, A, Tai, E, Magnus, NKC, Vo, KD, Yashaswini, CN, Marangoni, F, Boukhali, M, Fatherree, JP, Damon, LJ, Xega, K, Desai, R, Choz, M, Bersani, F, Langenbucher, A, Thapar, V, Morris, R, Wellner, UF, Schilling, O, Lawrence, MS, Liss, AS, Rivera, MN, Deshpande, V, Benes, CH, Maheswaran, S, Haber, DA, Fernandez-Del-Castillo, C, Ferrone, CR, Haas, W, Aryee, MJ, Ting, DT Cell 178 (1): 160-175.e27. doi: 10.1016/j.cell.2019.05.012. PubMed PMID:31155233 PubMed Central PMC6697165
  • 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 | 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 | 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 | 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 | Transforming Growth Factor-β Signaling in Immunity and Cancer. Batlle, E, Massagué, J Immunity 50 (4): 924-940. doi: 10.1016/j.immuni.2019.03.024. PubMed PMID:30995507
  • 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 | 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 | 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 | 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 | Molecular subtypes of small cell lung cancer: a synthesis of human and mouse model data. Rudin, CM, Poirier, JT, Byers, LA, Dive, C, Dowlati, A, George, J, Heymach, JV, Johnson, JE, Lehman, JM, MacPherson, D, Massion, PP, Minna, JD, Oliver, TG, Quaranta, V, Sage, J, Thomas, RK, Vakoc, CR, Gazdar, AF Nat. Rev. Cancer 19 (5): 289-297. doi: 10.1038/s41568-019-0133-9. PubMed PMID:30926931 PubMed Central PMC6538259
  • 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 | 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 | 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
  • 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 | A Platform of Synthetic Lethal Gene Interaction Networks Reveals that the GNAQ Uveal Melanoma Oncogene Controls the Hippo Pathway through FAK. Feng, X, Arang, N, Rigiracciolo, DC, Lee, JS, Yeerna, H, Wang, Z, Lubrano, S, Kishore, A, Pachter, JA, König, GM, Maggiolini, M, Kostenis, E, Schlaepfer, DD, Tamayo, P, Chen, Q, Ruppin, E, Gutkind, JS Cancer Cell 35 (3): 457-472.e5. doi: 10.1016/j.ccell.2019.01.009. PubMed PMID:30773340 PubMed Central PMC6737937
  • 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
  • 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 | 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 PubMed Central PMC6584763
  • 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 | 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 | 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 | Quantitative Proteomic Analysis of Small and Large Extracellular Vesicles (EVs) Reveals Enrichment of Adhesion Proteins in Small EVs. Jimenez, L, Yu, H, McKenzie, AJ, Franklin, JL, Patton, JG, Liu, Q, Weaver, AM J. Proteome Res. 18 (3): 947-959. doi: 10.1021/acs.jproteome.8b00647. PubMed PMID:30608700 PubMed Central PMC6411421
  • 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
  • 2019 | Targeting NAD+ Metabolism to Enhance Radiation Therapy Responses. Lewis, JE, Singh, N, Holmila, RJ, Sumer, BD, Williams, NS, Furdui, CM, Kemp, ML, Boothman, DA Semin Radiat Oncol 29 (1): 6-15. doi: 10.1016/j.semradonc.2018.10.009. PubMed PMID:30573185 PubMed Central PMC6310039
  • 2019 | Phf6 Loss Enhances HSC Self-Renewal Driving Tumor Initiation and Leukemia Stem Cell Activity in T-ALL. Wendorff, AA, Quinn, SA, Rashkovan, M, Madubata, CJ, Ambesi-Impiombato, A, Litzow, MR, Tallman, MS, Paietta, E, Paganin, M, Basso, G, Gastier-Foster, JM, Loh, ML, Rabadan, R, Van Vlierberghe, P, Ferrando, AA Cancer Discov 9 (3): 436-451. doi: 10.1158/2159-8290.CD-18-1005. PubMed PMID:30567843 PubMed Central PMC6425751
  • 2019 | Three-dimensional analysis reveals altered chromatin interaction by enhancer inhibitors harbors TCF7L2-regulated cancer gene signature. Gerrard, DL, Wang, Y, Gaddis, M, Zhou, Y, Wang, J, Witt, H, Lin, S, Farnham, PJ, Jin, VX, Frietze, SE J. Cell. Biochem. 120 (3): 3056-3070. doi: 10.1002/jcb.27449. PubMed PMID:30548288 PubMed Central PMC6476548
  • 2019 | Small Cell Lung Cancer Transformation as a Mechanism of Resistance to PD-1 Therapy in KRAS-Mutant Lung Adenocarcinoma: A Report of Two Cases. Iams, WT, Beckermann, KE, Almodovar, K, Hernandez, J, Vnencak-Jones, C, Lim, LP, Raymond, CK, Horn, L, Lovly, CM J Thorac Oncol 14 (3): e45-e48. doi: 10.1016/j.jtho.2018.11.031. PubMed PMID:30543839 PubMed Central PMC6382512
  • 2019 | Tumor growth and calcification in evolving microenvironmental geometries. Chen, Y, Lowengrub, JS J. Theor. Biol. 463 : 138-154. doi: 10.1016/j.jtbi.2018.12.006. PubMed PMID:30528340 PubMed Central PMC6476430
  • 2018 | NSD2 is a conserved driver of metastatic prostate cancer progression. Aytes, A, Giacobbe, A, Mitrofanova, A, Ruggero, K, Cyrta, J, Arriaga, J, Palomero, L, Farran-Matas, S, Rubin, MA, Shen, MM, Califano, A, Abate-Shen, C Nat Commun 9 (1): 5201. doi: 10.1038/s41467-018-07511-4. PubMed PMID:30518758 PubMed Central PMC6281610
  • 2018 | Spontaneous migration of cellular aggregates from giant keratocytes to running spheroids. Beaune, G, Blanch-Mercader, C, Douezan, S, Dumond, J, Gonzalez-Rodriguez, D, Cuvelier, D, Ondarçuhu, T, Sens, P, Dufour, S, Murrell, MP, Brochard-Wyart, F Proc. Natl. Acad. Sci. U.S.A. 115 (51): 12926-12931. doi: 10.1073/pnas.1811348115. PubMed PMID:30504144 PubMed Central PMC6304987
  • 2018 | Linking single-cell measurements of mass, growth rate, and gene expression. Kimmerling, RJ, Prakadan, SM, Gupta, AJ, Calistri, NL, Stevens, MM, Olcum, S, Cermak, N, Drake, RS, Pelton, K, De Smet, F, Ligon, KL, Shalek, AK, Manalis, SR Genome Biol. 19 (1): 207. doi: 10.1186/s13059-018-1576-0. PubMed PMID:30482222 PubMed Central PMC6260722
  • 2018 | Epigenetic Heterogeneity in Human Colorectal Tumors Reveals Preferential Conservation And Evidence of Immune Surveillance. Ryser, MD, Yu, M, Grady, W, Siegmund, K, Shibata, D Sci Rep 8 (1): 17292. doi: 10.1038/s41598-018-35621-y. PubMed PMID:30470817 PubMed Central PMC6251922
  • 2018 | Entropy production rate is maximized in non-contractile actomyosin. Seara, DS, Yadav, V, Linsmeier, I, Tabatabai, AP, Oakes, PW, Tabei, SMA, Banerjee, S, Murrell, MP Nat Commun 9 (1): 4948. doi: 10.1038/s41467-018-07413-5. PubMed PMID:30470750 PubMed Central PMC6251913
  • 2019 | Single-Cell Mass Cytometry of Archived Human Epithelial Tissue for Decoding Cancer Signaling Pathways. Scurrah, CR, Simmons, AJ, Lau, KS Methods Mol. Biol. 1884 : 215-229. doi: 10.1007/978-1-4939-8885-3_15. PubMed PMID:30465206 PubMed Central PMC6282860
  • 2018 | Microfluidic active loading of single cells enables analysis of complex clinical specimens. Calistri, NL, Kimmerling, RJ, Malinowski, SW, Touat, M, Stevens, MM, Olcum, S, Ligon, KL, Manalis, SR Nat Commun 9 (1): 4784. doi: 10.1038/s41467-018-07283-x. PubMed PMID:30429479 PubMed Central PMC6235965
  • 2018 | Developments in Blood-Brain Barrier Penetrance and Drug Repurposing for Improved Treatment of Glioblastoma. Harder, BG, Blomquist, MR, Wang, J, Kim, AJ, Woodworth, GF, Winkles, JA, Loftus, JC, Tran, NL Front Oncol 8 : 462. doi: 10.3389/fonc.2018.00462. PubMed PMID:30406029 PubMed Central PMC6206841
  • 2018 | Analysis of Single-Cell RNA-Seq Identifies Cell-Cell Communication Associated with Tumor Characteristics. Kumar, MP, Du, J, Lagoudas, G, Jiao, Y, Sawyer, A, Drummond, DC, Lauffenburger, DA, Raue, A Cell Rep 25 (6): 1458-1468.e4. doi: 10.1016/j.celrep.2018.10.047. PubMed PMID:30404002
  • 2019 | Adipokines Deregulate Cellular Communication via Epigenetic Repression of Gap Junction Loci in Obese Endometrial Cancer. Polusani, SR, Huang, YW, Huang, G, Chen, CW, Wang, CM, Lin, LL, Osmulski, P, Lucio, ND, Liu, L, Hsu, YT, Zhou, Y, Lin, CL, Aguilera-Barrantes, I, Valente, PT, Kost, ER, Chen, CL, Shim, EY, Lee, SE, Ruan, J, Gaczynska, ME, Yan, P, Goodfellow, PJ, Mutch, DG, Jin, VX, Nicholson, BJ, Huang, TH, Kirma, NB Cancer Res. 79 (1): 196-208. doi: 10.1158/0008-5472.CAN-18-1615. PubMed PMID:30389702 PubMed Central PMC6705596
  • 2019 | Activation of PP2A and Inhibition of mTOR Synergistically Reduce MYC Signaling and Decrease Tumor Growth in Pancreatic Ductal Adenocarcinoma. Allen-Petersen, BL, Risom, T, Feng, Z, Wang, Z, Jenny, ZP, Thoma, MC, Pelz, KR, Morton, JP, Sansom, OJ, Lopez, CD, Sheppard, B, Christensen, DJ, Ohlmeyer, M, Narla, G, Sears, RC Cancer Res. 79 (1): 209-219. doi: 10.1158/0008-5472.CAN-18-0717. PubMed PMID:30389701 PubMed Central PMC6318036
  • 2019 | SJARACNe: a scalable software tool for gene network reverse engineering from big data. Khatamian, A, Paull, EO, Califano, A, Yu, J Bioinformatics 35 (12): 2165-2166. doi: 10.1093/bioinformatics/bty907. PubMed PMID:30388204 PubMed Central PMC6581437
  • 2018 | Post-translational modification localizes MYC to the nuclear pore basket to regulate a subset of target genes involved in cellular responses to environmental signals. Su, Y, Pelz, C, Huang, T, Torkenczy, K, Wang, X, Cherry, A, Daniel, CJ, Liang, J, Nan, X, Dai, MS, Adey, A, Impey, S, Sears, RC Genes Dev. 32 (21-22): 1398-1419. doi: 10.1101/gad.314377.118. PubMed PMID:30366908 PubMed Central PMC6217735
  • 2018 | A METHOD FOR QUANTIFICATION OF CALPONIN EXPRESSION IN MYOEPITHELIAL CELLS IN IMMUNOHISTOCHEMICAL IMAGES OF DUCTAL CARCINOMA IN SITU. Gray, E, Mitchell, E, Jindal, S, Schedin, P, Chang, YH Proc IEEE Int Symp Biomed Imaging 2018 : 796-799. doi: 10.1109/ISBI.2018.8363692. PubMed PMID:30364524 PubMed Central PMC6196724
  • 2018 | Quantitative assessment of cell population diversity in single-cell landscapes. Liu, Q, Herring, CA, Sheng, Q, Ping, J, Simmons, AJ, Chen, B, Banerjee, A, Li, W, Gu, G, Coffey, RJ, Shyr, Y, Lau, KS PLoS Biol. 16 (10): e2006687. doi: 10.1371/journal.pbio.2006687. PubMed PMID:30346945 PubMed Central PMC6211764
  • 2018 | Insights into Bidirectional Gene Expression Control Using the Canonical GAL1/GAL10 Promoter. Elison, GL, Xue, Y, Song, R, Acar, M Cell Rep 25 (3): 737-748.e4. doi: 10.1016/j.celrep.2018.09.050. PubMed PMID:30332652 PubMed Central PMC6263159
  • 2018 | Optimization of Acquisition and Analysis Methods for Clinical Dynamic Susceptibility Contrast MRI Using a Population-Based Digital Reference Object. Semmineh, NB, Bell, LC, Stokes, AM, Hu, LS, Boxerman, JL, Quarles, CC AJNR Am J Neuroradiol 39 (11): 1981-1988. doi: 10.3174/ajnr.A5827. PubMed PMID:30309842 PubMed Central PMC6239921
  • 2019 | Decidualization of Human Endometrial Stromal Fibroblasts is a Multiphasic Process Involving Distinct Transcriptional Programs. Rytkönen, KT, Erkenbrack, EM, Poutanen, M, Elo, LL, Pavlicev, M, Wagner, GP Reprod Sci 26 (3): 323-336. doi: 10.1177/1933719118802056. PubMed PMID:30309298 PubMed Central PMC6728557
  • 2018 | Cross-talk among writers, readers, and erasers of m6A regulates cancer growth and progression. Panneerdoss, S, Eedunuri, VK, Yadav, P, Timilsina, S, Rajamanickam, S, Viswanadhapalli, S, Abdelfattah, N, Onyeagucha, BC, Cui, X, Lai, Z, Mohammad, TA, Gupta, YK, Huang, TH, Huang, Y, Chen, Y, Rao, MK Sci Adv 4 (10): eaar8263. doi: 10.1126/sciadv.aar8263. PubMed PMID:30306128 PubMed Central PMC6170038
  • 2018 | Typing tumors using pathways selected by somatic evolution. Wang, S, Ma, J, Zhang, W, Shen, JP, Huang, J, Peng, J, Ideker, T Nat Commun 9 (1): 4159. doi: 10.1038/s41467-018-06464-y. PubMed PMID:30297789 PubMed Central PMC6175900
  • 2018 | SHIFT: speedy histopathological-to-immunofluorescent translation of whole slide images using conditional generative adversarial networks. Burlingame, EA, Margolin, AA, Gray, JW, Chang, YH Proc SPIE Int Soc Opt Eng 10581 : . doi: 10.1117/12.2293249. PubMed PMID:30283195 PubMed Central PMC6166432
  • 2019 | Remodeling of the Collagen Matrix in Aging Skin Promotes Melanoma Metastasis and Affects Immune Cell Motility. Kaur, A, Ecker, BL, Douglass, SM, Kugel, CH 3rd, Webster, MR, Almeida, FV, Somasundaram, R, Hayden, J, Ban, E, Ahmadzadeh, H, Franco-Barraza, J, Shah, N, Mellis, IA, Keeney, F, Kossenkov, A, Tang, HY, Yin, X, Liu, Q, Xu, X, Fane, M, Brafford, P, Herlyn, M, Speicher, DW, Wargo, JA, Tetzlaff, MT, Haydu, LE, Raj, A, Shenoy, V, Cukierman, E, Weeraratna, AT Cancer Discov 9 (1): 64-81. doi: 10.1158/2159-8290.CD-18-0193. PubMed PMID:30279173 PubMed Central PMC6328333
  • 2018 | Cooperation of dual modes of cell motility promotes epithelial stress relaxation to accelerate wound healing. Staddon, MF, Bi, D, Tabatabai, AP, Ajeti, V, Murrell, MP, Banerjee, S PLoS Comput. Biol. 14 (10): e1006502. doi: 10.1371/journal.pcbi.1006502. PubMed PMID:30273354 PubMed Central PMC6181425
  • 2018 | Cooperation of loss of NKX3.1 and inflammation in prostate cancer initiation. Le Magnen, C, Virk, RK, Dutta, A, Kim, JY, Panja, S, Lopez-Bujanda, ZA, Califano, A, Drake, CG, Mitrofanova, A, Abate-Shen, C Dis Model Mech 11 (11): . doi: 10.1242/dmm.035139. PubMed PMID:30266798 PubMed Central PMC6262819
  • 2018 | Multi-component gene network design as a survival strategy in diverse environments. Luo, X, Song, R, Acar, M BMC Syst Biol 12 (1): 85. doi: 10.1186/s12918-018-0609-3. PubMed PMID:30257679 PubMed Central PMC6158886
  • 2018 | Bidirectional Adaptive Signaling between cancer and stromal cells: mechanisms and therapeutics. Boutchueng-Djidjou, M, Rix, U, Haura, EB Expert Rev Proteomics 15 (9): 697-699. doi: 10.1080/14789450.2018.1521276. PubMed PMID:30251554 PubMed Central PMC6435031
  • 2019 | Somatic cell evolution: how to improve with age. Shibata, D J. Pathol. 247 (1): 3-5. doi: 10.1002/path.5173. PubMed PMID:30246391 PubMed Central PMC6428591
  • 2018 | A Loss of Epigenetic Control Can Promote Cell Death through Reversing the Balance of Pathways in a Signaling Network. Vanaja, KG, Timp, W, Feinberg, AP, Levchenko, A Mol. Cell 72 (1): 60-70.e3. doi: 10.1016/j.molcel.2018.08.025. PubMed PMID:30244832 PubMed Central PMC6219618
  • 2018 | Biomechanical interplay between anisotropic re-organization of cells and the surrounding matrix underlies transition to invasive cancer spread. Kim, DH, Ewald, AJ, Park, J, Kshitiz,, Kwak, M, Gray, RS, Su, CY, Seo, J, An, SS, Levchenko, A Sci Rep 8 (1): 14210. doi: 10.1038/s41598-018-32010-3. PubMed PMID:30242256 PubMed Central PMC6155084
  • 2018 | Differentiation-state plasticity is a targetable resistance mechanism in basal-like breast cancer. Risom, T, Langer, EM, Chapman, MP, Rantala, J, Fields, AJ, Boniface, C, Alvarez, MJ, Kendsersky, ND, Pelz, CR, Johnson-Camacho, K, Dobrolecki, LE, Chin, K, Aswani, AJ, Wang, NJ, Califano, A, Lewis, MT, Tomlin, CJ, Spellman, PT, Adey, A, Gray, JW, Sears, RC Nat Commun 9 (1): 3815. doi: 10.1038/s41467-018-05729-w. PubMed PMID:30232459 PubMed Central PMC6145927
  • 2018 | A Human Adult Stem Cell Signature Marks Aggressive Variants across Epithelial Cancers. Smith, BA, Balanis, NG, Nanjundiah, A, Sheu, KM, Tsai, BL, Zhang, Q, Park, JW, Thompson, M, Huang, J, Witte, ON, Graeber, TG Cell Rep 24 (12): 3353-3366.e5. doi: 10.1016/j.celrep.2018.08.062. PubMed PMID:30232014 PubMed Central PMC6382070
  • 2018 | The effect of cellular context on miR-155-mediated gene regulation in four major immune cell types. Hsin, JP, Lu, Y, Loeb, GB, Leslie, CS, Rudensky, AY Nat. Immunol. 19 (10): 1137-1145. doi: 10.1038/s41590-018-0208-x. PubMed PMID:30224821 PubMed Central PMC6158091
  • 2018 | Computational measurement of tumor immune microenvironment in gastric adenocarcinomas. Chang, YH, Heo, YJ, Cho, J, Song, SY, Lee, J, Kim, KM Sci Rep 8 (1): 13887. doi: 10.1038/s41598-018-32299-0. PubMed PMID:30224753 PubMed Central PMC6141531
  • 2018 | PDZ-RhoGEF Is a Signaling Effector for TROY-Induced Glioblastoma Cell Invasion and Survival. Ding, Z, Dhruv, H, Kwiatkowska-Piwowarczyk, A, Ruggieri, R, Kloss, J, Symons, M, Pirrotte, P, Eschbacher, JM, Tran, NL, Loftus, JC Neoplasia 20 (10): 1045-1058. doi: 10.1016/j.neo.2018.08.008. PubMed PMID:30219706 PubMed Central PMC6140379
  • 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
  • 2018 | Proteomics, Post-translational Modifications, and Integrative Analyses Reveal Molecular Heterogeneity within Medulloblastoma Subgroups. Archer, TC, Ehrenberger, T, Mundt, F, Gold, MP, Krug, K, Mah, CK, Mahoney, EL, Daniel, CJ, LeNail, A, Ramamoorthy, D, Mertins, P, Mani, DR, Zhang, H, Gillette, MA, Clauser, K, Noble, M, Tang, LC, Pierre-François, J, Silterra, J, Jensen, J, Tamayo, P, Korshunov, A, Pfister, SM, Kool, M, Northcott, PA, Sears, RC, Lipton, JO, Carr, SA, Mesirov, JP, Pomeroy, SL, Fraenkel, E Cancer Cell 34 (3): 396-410.e8. doi: 10.1016/j.ccell.2018.08.004. PubMed PMID:30205044 PubMed Central PMC6372116
  • 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
  • 2018 | A threonine zipper that mediates protein-protein interactions: Structure and prediction. Oi, C, Treado, JD, Levine, ZA, Lim, CS, Knecht, KM, Xiong, Y, O'Hern, CS, Regan, L Protein Sci. 27 (11): 1969-1977. doi: 10.1002/pro.3505. PubMed PMID:30198622 PubMed Central PMC6201716
  • 2019 | Somatostatin receptor 2 signaling promotes growth and tumor survival in small-cell lung cancer. Lehman, JM, Hoeksema, MD, Staub, J, Qian, J, Harris, B, Callison, JC, Miao, J, Shi, C, Eisenberg, R, Chen, H, Chen, SC, Massion, PP Int. J. Cancer 144 (5): 1104-1114. doi: 10.1002/ijc.31771. PubMed PMID:30152518 PubMed Central PMC6448409
  • 2018 | The mammalian decidual cell evolved from a cellular stress response. Erkenbrack, EM, Maziarz, JD, Griffith, OW, Liang, C, Chavan, AR, Nnamani, MC, Wagner, GP PLoS Biol. 16 (8): e2005594. doi: 10.1371/journal.pbio.2005594. PubMed PMID:30142145 PubMed Central PMC6108454
  • 2018 | Allergic inflammatory memory in human respiratory epithelial progenitor cells. Ordovas-Montanes, J, Dwyer, DF, Nyquist, SK, Buchheit, KM, Vukovic, M, Deb, C, Wadsworth, MH 2nd, Hughes, TK, Kazer, SW, Yoshimoto, E, Cahill, KN, Bhattacharyya, N, Katz, HR, Berger, B, Laidlaw, TM, Boyce, JA, Barrett, NA, Shalek, AK Nature 560 (7720): 649-654. doi: 10.1038/s41586-018-0449-8. PubMed PMID:30135581 PubMed Central PMC6133715
  • 2018 | Homeobox oncogene activation by pan-cancer DNA hypermethylation. Su, J, Huang, YH, Cui, X, Wang, X, Zhang, X, Lei, Y, Xu, J, Lin, X, Chen, K, Lv, J, Goodell, MA, Li, W Genome Biol. 19 (1): 108. doi: 10.1186/s13059-018-1492-3. PubMed PMID:30097071 PubMed Central PMC6085761
  • 2018 | Deep Profiling of Mouse Splenic Architecture with CODEX Multiplexed Imaging. Goltsev, Y, Samusik, N, Kennedy-Darling, J, Bhate, S, Hale, M, Vazquez, G, Black, S, Nolan, GP Cell 174 (4): 968-981.e15. doi: 10.1016/j.cell.2018.07.010. PubMed PMID:30078711 PubMed Central PMC6086938
  • 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
  • 2019 | CIRCOAST: a statistical hypothesis test for cellular colocalization with network structures. Corliss, BA, Ray, HC, Patrie, JT, Mansour, J, Kesting, S, Park, JH, Rohde, G, Yates, PA, Janes, KA, Peirce, SM Bioinformatics 35 (3): 506-514. doi: 10.1093/bioinformatics/bty638. PubMed PMID:30032263 PubMed Central PMC6361237
  • 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 | 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 | Directed migration: Cells navigate by extracellular vesicles. Sung, BH, Weaver, AM J. Cell Biol. 217 (8): 2613-2614. doi: 10.1083/jcb.201806018. PubMed PMID:29976599 PubMed Central PMC6080936
  • 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 | 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
  • 2018 | Mechanisms for the epigenetic inheritance of stress response in single cells. Xue, Y, Acar, M Curr. Genet. 64 (6): 1221-1228. doi: 10.1007/s00294-018-0849-1. PubMed PMID:29846762 PubMed Central PMC6215725
  • 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 | 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 | 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
  • 2018 | Automated brightfield morphometry of 3D organoid populations by OrganoSeg. Borten, MA, Bajikar, SS, Sasaki, N, Clevers, H, Janes, KA Sci Rep 8 (1): 5319. doi: 10.1038/s41598-017-18815-8. PubMed PMID:29593296 PubMed Central PMC5871765
  • 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
  • 2018 | Topotaxis: A New Mechanism of Directed Cell Migration in Topographic ECM Gradients. Park, J, Kim, DH, Levchenko, A Biophys. J. 114 (6): 1257-1263. doi: 10.1016/j.bpj.2017.11.3813. PubMed PMID:29590582 PubMed Central PMC5883610
  • 2018 | iterClust: a statistical framework for iterative clustering analysis. Ding, H, Wang, W, Califano, A Bioinformatics 34 (16): 2865-2866. doi: 10.1093/bioinformatics/bty176. PubMed PMID:29579153 PubMed Central PMC6084607
  • 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
  • 2018 | Using deep learning to model the hierarchical structure and function of a cell. Ma, J, Yu, MK, Fong, S, Ono, K, Sage, E, Demchak, B, Sharan, R, Ideker, T Nat. Methods 15 (4): 290-298. doi: 10.1038/nmeth.4627. PubMed PMID:29505029 PubMed Central PMC5882547
  • 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 | 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 | 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 | 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 | 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
  • 2017 | A new method for post-translationally labeling proteins in live cells for fluorescence imaging and tracking. Hinrichsen, M, Lenz, M, Edwards, JM, Miller, OK, Mochrie, SGJ, Swain, PS, Schwarz-Linek, U, Regan, L Protein Eng. Des. Sel. 30 (12): 771-780. doi: 10.1093/protein/gzx059. PubMed PMID:29228311 PubMed Central PMC6680098
  • 2018 | Tamoxifen Resistance in Breast Cancer Is Regulated by the EZH2-ERα-GREB1 Transcriptional Axis. Wu, Y, Zhang, Z, Cenciarini, ME, Proietti, CJ, Amasino, M, Hong, T, Yang, M, Liao, Y, Chiang, HC, Kaklamani, VG, Jeselsohn, R, Vadlamudi, RK, Huang, TH, Li, R, De Angelis, C, Fu, X, Elizalde, PV, Schiff, R, Brown, M, Xu, K Cancer Res. 78 (3): 671-684. doi: 10.1158/0008-5472.CAN-17-1327. PubMed PMID:29212856 PubMed Central PMC5967248
  • 2018 | Vimentin Is Required for Lung Adenocarcinoma Metastasis via Heterotypic Tumor Cell-Cancer-Associated Fibroblast Interactions during Collective Invasion. Richardson, AM, Havel, LS, Koyen, AE, Konen, JM, Shupe, J, Wiles, WG 4th, Martin, WD, Grossniklaus, HE, Sica, G, Gilbert-Ross, M, Marcus, AI Clin. Cancer Res. 24 (2): 420-432. doi: 10.1158/1078-0432.CCR-17-1776. PubMed PMID:29208669 PubMed Central PMC5771825
  • 2017 | Tumor-Suppressor Inactivation of GDF11 Occurs by Precursor Sequestration in Triple-Negative Breast Cancer. Bajikar, SS, Wang, CC, Borten, MA, Pereira, EJ, Atkins, KA, Janes, KA Dev. Cell 43 (4): 418-435.e13. doi: 10.1016/j.devcel.2017.10.027. PubMed PMID:29161592 PubMed Central PMC5726799
Search PubMed