CSBC Supported Publications

Publications

  • 2019 | Mapping lung cancer epithelial-mesenchymal transition states and trajectories with single-cell resolution. Karacosta, LG, Anchang, B, Ignatiadis, N, Kimmey, SC, Benson, JA, Shrager, JB, Tibshirani, R, Bendall, SC, Plevritis, SK Nat Commun 10 (1): 5587. doi: 10.1038/s41467-019-13441-6. PubMed PMID:31811131 PubMed Central PMC6898514
  • 2019 | Spatial EGFR Dynamics and Metastatic Phenotypes Modulated by Upregulated EphB2 and Src Pathways in Advanced Prostate Cancer. Liu, YL, Horning, AM, Lieberman, B, Kim, M, Lin, CK, Hung, CN, Chou, CW, Wang, CM, Lin, CL, Kirma, NB, Liss, MA, Vasisht, R, Perillo, EP, Blocher, K, Horng, H, Taverna, JA, Ruan, J, Yankeelov, TE, Dunn, AK, Huang, TH, Yeh, HC, Chen, CL Cancers (Basel) 11 (12): . doi: 10.3390/cancers11121910. PubMed PMID:31805710
  • 2019 | Heterogeneity and dynamics of active Kras-induced dysplastic lineages from mouse corpus stomach. Min, J, Vega, PN, Engevik, AC, Williams, JA, Yang, Q, Patterson, LM, Simmons, AJ, Bliton, RJ, Betts, JW, Lau, KS, Magness, ST, Goldenring, JR, Choi, E Nat Commun 10 (1): 5549. doi: 10.1038/s41467-019-13479-6. PubMed PMID:31804471 PubMed Central PMC6895174
  • 2019 | A cancer rainbow mouse for visualizing the functional genomics of oncogenic clonal expansion. Boone, PG, Rochelle, LK, Ginzel, JD, Lubkov, V, Roberts, WL, Nicholls, PJ, Bock, C, Flowers, ML, von Furstenberg, RJ, Stripp, BR, Agarwal, P, Borowsky, AD, Cardiff, RD, Barak, LS, Caron, MG, Lyerly, HK, Snyder, JC Nat Commun 10 (1): 5490. doi: 10.1038/s41467-019-13330-y. PubMed PMID:31792216 PubMed Central PMC6889384
  • 2019 | Evolution of placental invasion and cancer metastasis are causally linked. Kshitiz,, Afzal, J, Maziarz, JD, Hamidzadeh, A, Liang, C, Erkenbrack, EM, Nam, H, Haeger, JD, Pfarrer, C, Hoang, T, Ott, T, Spencer, T, Pavličev, M, Antczak, DF, Levchenko, A, Wagner, GP Nat Ecol Evol 3 (12): 1743-1753. doi: 10.1038/s41559-019-1046-4. PubMed PMID:31768023
  • 2019 | Deregulating MYC in a model of HER2+ breast cancer mimics human intertumoral heterogeneity. Risom, T, Wang, X, Liang, J, Zhang, X, Pelz, C, Campbell, LG, Eng, J, Chin, K, Farrington, C, Narla, G, Langer, EM, Sun, XX, Su, Y, Daniel, CJ, Dai, MS, Löhr, CV, Sears, RC J. Clin. Invest. : . doi: 10.1172/JCI126390. PubMed PMID:31763993
  • 2019 | Dynamic motions of molecular motors in the actin cytoskeleton. Jung, W, Tabatabai, AP, Thomas, JJ, Tabei, SMA, Murrell, MP, Kim, T Cytoskeleton (Hoboken) : . doi: 10.1002/cm.21582. PubMed PMID:31758841
  • 2019 | TCR sequencing paired with massively parallel 3' RNA-seq reveals clonotypic T cell signatures. Tu, AA, Gierahn, TM, Monian, B, Morgan, DM, Mehta, NK, Ruiter, B, Shreffler, WG, Shalek, AK, Love, JC Nat. Immunol. 20 (12): 1692-1699. doi: 10.1038/s41590-019-0544-5. PubMed PMID:31745340
  • 2019 | Inhibition of phosphatidylinositol 3-kinase by PX-866 suppresses temozolomide-induced autophagy and promotes apoptosis in glioblastoma cells. Harder, BG, Peng, S, Sereduk, CP, Sodoma, AM, Kitange, GJ, Loftus, JC, Sarkaria, JN, Tran, NL Mol. Med. 25 (1): 49. doi: 10.1186/s10020-019-0116-z. PubMed PMID:31726966 PubMed Central PMC6854621
  • 2019 | Nanoparticle transport phenomena in confined flows. Radhakrishnan, R, Farokhirad, S, Eckmann, DM, Ayyaswamy, PS Adv Heat Transf 51 : 55-129. doi: 10.1016/bs.aiht.2019.08.002. PubMed PMID:31692964 PubMed Central PMC6831088
  • 2019 | Annot: a Django-based sample, reagent, and experiment metadata tracking system. Bucher, E, Claunch, CJ, Hee, D, Smith, RL, Devlin, K, Thompson, W, Korkola, JE, Heiser, LM BMC Bioinformatics 20 (1): 542. doi: 10.1186/s12859-019-3147-0. PubMed PMID:31675914 PubMed Central PMC6824123
  • 2019 | High-throughput single-particle tracking reveals nested membrane domains that dictate KRasG12D diffusion and trafficking. Lee, Y, Phelps, C, Huang, T, Mostofian, B, Wu, L, Zhang, Y, Tao, K, Chang, YH, Stork, PJ, Gray, JW, Zuckerman, DM, Nan, X Elife 8 : . doi: 10.7554/eLife.46393. PubMed PMID:31674905
  • 2019 | Thermodynamic analysis of multivalent binding of functionalized nanoparticles to membrane surface reveals the importance of membrane entropy and nanoparticle entropy in adhesion of flexible nanoparticles. Farokhirad, S, Bradley, RP, Radhakrishnan, R Soft Matter 15 (45): 9271-9286. doi: 10.1039/c9sm01653h. PubMed PMID:31670338 PubMed Central PMC6868310
  • 2019 | Social feeding behavior of Trichoplax adhaerens. Fortunato, A, Aktipis, A Front Ecol Evol 7 : . doi: 10.3389/fevo.2019.00019. PubMed PMID:31667165 PubMed Central PMC6821444
  • 2019 | A Deep Convolutional Neural Network for Annotation of Magnetic Resonance Imaging Sequence Type. Ranjbar, S, Singleton, KW, Jackson, PR, Rickertsen, CR, Whitmire, SA, Clark-Swanson, KR, Mitchell, JR, Swanson, KR, Hu, LS J Digit Imaging : . doi: 10.1007/s10278-019-00282-4. PubMed PMID:31654174
  • 2019 | Key challenges facing data-driven multicellular systems biology. Macklin, P Gigascience 8 (10): . doi: 10.1093/gigascience/giz127. PubMed PMID:31648301 PubMed Central PMC6812467
  • 2019 | Mapping genetic interactions in cancer: a road to rational combination therapies. Tutuncuoglu, B, Krogan, NJ Genome Med 11 (1): 62. doi: 10.1186/s13073-019-0680-4. PubMed PMID:31640753 PubMed Central PMC6805649
  • 2019 | Phenotypic Switching of Naïve T Cells to Immune-Suppressive Treg-Like Cells by Mutant KRAS. Kalvala, A, Wallet, P, Yang, L, Wang, C, Li, H, Nam, A, Nathan, A, Mambetsariev, I, Poroyko, V, Gao, H, Chu, P, Sattler, M, Bild, A, Manuel, ER, Lee, PP, Jolly, MK, Kulkarni, P, Salgia, R J Clin Med 8 (10): . doi: 10.3390/jcm8101726. PubMed PMID:31635338 PubMed Central PMC6832522
  • 2019 | Monitoring and Determining Mitochondrial Network Parameters in Live Lung Cancer Cells. Mirzapoiazova, T, Li, H, Nathan, A, Srivstava, S, Nasser, MW, Lennon, F, Armstrong, B, Mambetsariev, I, Chu, PG, Achuthan, S, Batra, SK, Kulkarni, P, Salgia, R J Clin Med 8 (10): . doi: 10.3390/jcm8101723. PubMed PMID:31635288 PubMed Central PMC6832496
  • 2019 | Substrate-based kinase activity inference identifies MK2 as driver of colitis. Strasser, SD, Ghazi, PC, Starchenko, A, Boukhali, M, Edwards, A, Suarez-Lopez, L, Lyons, J, Changelian, PS, Monahan, JB, Jacobsen, J, Brubaker, DK, Joughin, BA, Yaffe, MB, Haas, W, Lauffenburger, DA, Haigis, KM Integr Biol (Camb) 11 (7): 301-314. doi: 10.1093/intbio/zyz025. PubMed PMID:31617572
  • 2019 | Multiplexed activation of endogenous genes by CRISPRa elicits potent antitumor immunity. Wang, G, Chow, RD, Bai, Z, Zhu, L, Errami, Y, Dai, X, Dong, MB, Ye, L, Zhang, X, Renauer, PA, Park, JJ, Shen, L, Ye, H, Fuchs, CS, Chen, S Nat. Immunol. 20 (11): 1494-1505. doi: 10.1038/s41590-019-0500-4. PubMed PMID:31611701 PubMed Central PMC6858551
  • 2019 | Germline-Encoded Affinity for Cognate Antigen Enables Vaccine Amplification of a Human Broadly Neutralizing Response against Influenza Virus. Sangesland, M, Ronsard, L, Kazer, SW, Bals, J, Boyoglu-Barnum, S, Yousif, AS, Barnes, R, Feldman, J, Quirindongo-Crespo, M, McTamney, PM, Rohrer, D, Lonberg, N, Chackerian, B, Graham, BS, Kanekiyo, M, Shalek, AK, Lingwood, D Immunity 51 (4): 735-749.e8. doi: 10.1016/j.immuni.2019.09.001. PubMed PMID:31563464 PubMed Central PMC6801110
  • 2019 | Delineating the role of MITF isoforms in pigmentation and tissue homeostasis. Flesher, JL, Paterson-Coleman, EK, Vasudeva, P, Ruiz-Vega, R, Marshall, M, Pearlman, E, MacGregor, GR, Neumann, J, Ganesan, AK Pigment Cell Melanoma Res : . doi: 10.1111/pcmr.12828. PubMed PMID:31562697
  • 2019 | Emergent membrane morphologies in relaxed and tense membranes in presence of reversible adhesive pinning interactions. Kandy, SK, Radhakrishnan, R Phys Biol 16 (6): 066011. doi: 10.1088/1478-3975/ab48d5. PubMed PMID:31561242 PubMed Central PMC6830734
  • 2019 | In vivo CRISPR screening in CD8 T cells with AAV-Sleeping Beauty hybrid vectors identifies membrane targets for improving immunotherapy for glioblastoma. Ye, L, Park, JJ, Dong, MB, Yang, Q, Chow, RD, Peng, L, Du, Y, Guo, J, Dai, X, Wang, G, Errami, Y, Chen, S Nat. Biotechnol. 37 (11): 1302-1313. doi: 10.1038/s41587-019-0246-4. PubMed PMID:31548728 PubMed Central PMC6834896
  • 2019 | Postdiagnosis Loss of Skeletal Muscle, but Not Adipose Tissue, Is Associated with Shorter Survival of Patients with Advanced Pancreatic Cancer. Babic, A, Rosenthal, MH, Bamlet, WR, Takahashi, N, Sugimoto, M, Danai, LV, Morales-Oyarvide, V, Khalaf, N, Dunne, RF, Brais, LK, Welch, MW, Zellers, CL, Dennis, C, Rifai, N, Prado, CM, Caan, B, Sundaresan, TK, Meyerhardt, JA, Kulke, MH, Clish, CB, Ng, K, Heiden, MGV, Petersen, GM, Wolpin, BM Cancer Epidemiol. Biomarkers Prev. 28 (12): 2062-2069. doi: 10.1158/1055-9965.EPI-19-0370. PubMed PMID:31533940 PubMed Central PMC6891169
  • 2019 | The eIF2α Kinase GCN2 Modulates Period and Rhythmicity of the Circadian Clock by Translational Control of Atf4. Pathak, SS, Liu, D, Li, T, de Zavalia, N, Zhu, L, Li, J, Karthikeyan, R, Alain, T, Liu, AC, Storch, KF, Kaufman, RJ, Jin, VX, Amir, S, Sonenberg, N, Cao, R Neuron 104 (4): 724-735.e6. doi: 10.1016/j.neuron.2019.08.007. PubMed PMID:31522764 PubMed Central PMC6872934
  • 2019 | Proteogenomic Network Analysis of Context-Specific KRAS Signaling in Mouse-to-Human Cross-Species Translation. Brubaker, DK, Paulo, JA, Sheth, S, Poulin, EJ, Popow, O, Joughin, BA, Strasser, SD, Starchenko, A, Gygi, SP, Lauffenburger, DA, Haigis, KM Cell Syst 9 (3): 258-270.e6. doi: 10.1016/j.cels.2019.07.006. PubMed PMID:31521603 PubMed Central PMC6816257
  • 2019 | GATA3-Controlled Nucleosome Eviction Drives MYC Enhancer Activity in T-cell Development and Leukemia. Belver, L, Yang, AY, Albero, R, Herranz, D, Brundu, FG, Quinn, SA, Pérez-Durán, P, Álvarez, S, Gianni, F, Rashkovan, M, Gurung, D, Rocha, PP, Raviram, R, Reglero, C, Cortés, JR, Cooke, AJ, Wendorff, AA, Cordó, V, Meijerink, JP, Rabadan, R, Ferrando, AA Cancer Discov 9 (12): 1774-1791. doi: 10.1158/2159-8290.CD-19-0471. PubMed PMID:31519704 PubMed Central PMC6891196
  • 2019 | Genetic heterogeneity within collective invasion packs drives leader and follower cell phenotypes. Zoeller, EL, Pedro, B, Konen, J, Dwivedi, B, Rupji, M, Sundararaman, N, Wang, L, Horton, JR, Zhong, C, Barwick, BG, Cheng, X, Martinez, ED, Torres, MP, Kowalski, J, Marcus, AI, Vertino, PM J. Cell. Sci. 132 (19): . doi: 10.1242/jcs.231514. PubMed PMID:31515279 PubMed Central PMC6803364
  • 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
  • 2020 | Cyclic Multiplexed-Immunofluorescence (cmIF), a Highly Multiplexed Method for Single-Cell Analysis. Eng, J, Thibault, G, Luoh, SW, Gray, JW, Chang, YH, Chin, K Methods Mol. Biol. 2055 : 521-562. doi: 10.1007/978-1-4939-9773-2_24. PubMed PMID:31502168
  • 2019 | Molecular determinants for enzalutamide-induced transcription in prostate cancer. Yuan, F, Hankey, W, Wu, D, Wang, H, Somarelli, J, Armstrong, AJ, Huang, J, Chen, Z, Wang, Q Nucleic Acids Res. 47 (19): 10104-10114. doi: 10.1093/nar/gkz790. PubMed PMID:31501863 PubMed Central PMC6821169
  • 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 | Predicting the broadly neutralizing antibody susceptibility of the HIV reservoir. Yu, WH, Su, D, Torabi, J, Fennessey, CM, Shiakolas, A, Lynch, R, Chun, TW, Doria-Rose, N, Alter, G, Seaman, MS, Keele, BF, Lauffenburger, DA, Julg, B JCI Insight 4 (17): . doi: 10.1172/jci.insight.130153. PubMed PMID:31484826 PubMed Central PMC6777915
  • 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 | Single-Cell Survey of Human Lymphatics Unveils Marked Endothelial Cell Heterogeneity and Mechanisms of Homing for Neutrophils. Takeda, A, Hollmén, M, Dermadi, D, Pan, J, Brulois, KF, Kaukonen, R, Lönnberg, T, Boström, P, Koskivuo, I, Irjala, H, Miyasaka, M, Salmi, M, Butcher, EC, Jalkanen, S Immunity 51 (3): 561-572.e5. doi: 10.1016/j.immuni.2019.06.027. PubMed PMID:31402260
  • 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 | Spatially constrained tumour growth affects the patterns of clonal selection and neutral drift in cancer genomic data. Chkhaidze, K, Heide, T, Werner, B, Williams, MJ, Huang, W, Caravagna, G, Graham, TA, Sottoriva, A PLoS Comput. Biol. 15 (7): e1007243. doi: 10.1371/journal.pcbi.1007243. PubMed PMID:31356595 PubMed Central PMC6687187
  • 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 PubMed Central PMC6753471
  • 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 | Improved Prognosis and Increased Tumor-Infiltrating Lymphocytes in Patients Who Have SCLC With Neurologic Paraneoplastic Syndromes. Iams, WT, Shiuan, E, Meador, CB, Roth, M, Bordeaux, J, Vaupel, C, Boyd, KL, Summitt, IB, Wang, LL, Schneider, JT, Warner, JL, Zhao, Z, Lovly, CM J Thorac Oncol 14 (11): 1970-1981. doi: 10.1016/j.jtho.2019.05.042. PubMed PMID:31201935 PubMed Central PMC6823126
  • 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 | Illuminating G-Protein-Coupling Selectivity of GPCRs. Inoue, A, Raimondi, F, Kadji, FMN, Singh, G, Kishi, T, Uwamizu, A, Ono, Y, Shinjo, Y, Ishida, S, Arang, N, Kawakami, K, Gutkind, JS, Aoki, J, Russell, RB Cell 177 (7): 1933-1947.e25. doi: 10.1016/j.cell.2019.04.044. PubMed PMID:31160049 PubMed Central PMC6773469
  • 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 PubMed Central PMC6816465
  • 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
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  • 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
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  • 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
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  • 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
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  • 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
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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 | 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
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  • 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
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  • 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
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