CSBC Supported Publications

Publications

  • 2020 | Evolutionary dynamics of neoantigens in growing tumors. Lakatos, E, Williams, MJ, Schenck, RO, Cross, WCH, Househam, J, Zapata, L, Werner, B, Gatenbee, C, Robertson-Tessi, M, Barnes, CP, Anderson, ARA, Sottoriva, A, Graham, TA Nat. Genet. : . doi: 10.1038/s41588-020-0687-1. PubMed PMID:32929288
  • 2020 | Oncoprotein-specific molecular interaction maps (SigMaps) for cancer network analyses. Broyde, J, Simpson, DR, Murray, D, Paull, EO, Chu, BW, Tagore, S, Jones, SJ, Griffin, AT, Giorgi, FM, Lachmann, A, Jackson, P, Sweet-Cordero, EA, Honig, B, Califano, A Nat. Biotechnol. : . doi: 10.1038/s41587-020-0652-7. PubMed PMID:32929263
  • 2020 | Exercise and immunometabolic regulation in cancer. Koelwyn, GJ, Zhuang, X, Tammela, T, Schietinger, A, Jones, LW Nat Metab : . doi: 10.1038/s42255-020-00277-4. PubMed PMID:32929232
  • 2020 | Learning Equations from Biological Data with Limited Time Samples. Nardini, JT, Lagergren, JH, Hawkins-Daarud, A, Curtin, L, Morris, B, Rutter, EM, Swanson, KR, Flores, KB Bull. Math. Biol. 82 (9): 119. doi: 10.1007/s11538-020-00794-z. PubMed PMID:32909137
  • 2019 | Systems biology approaches to measure and model phenotypic heterogeneity in cancer. Meyer, AS, Heiser, LM Curr Opin Syst Biol 17 : 35-40. doi: 10.1016/j.coisb.2019.09.002. PubMed PMID:32864511 PubMed Central PMC7449235
  • 2020 | Fast and multiplexed superresolution imaging with DNA-PAINT-ERS. Civitci, F, Shangguan, J, Zheng, T, Tao, K, Rames, M, Kenison, J, Zhang, Y, Wu, L, Phelps, C, Esener, S, Nan, X Nat Commun 11 (1): 4339. doi: 10.1038/s41467-020-18181-6. PubMed PMID:32859909 PubMed Central PMC7455722
  • 2020 | Regulatory and Safety Considerations in Deploying a Locally Fabricated, Reusable Face Shield in a Hospital Responding to the COVID-19 Pandemic. Mostaghimi, A, Antonini, MJ, Plana, D, Anderson, PD, Beller, B, Boyer, EW, Fannin, A, Freake, J, Oakley, R, Sinha, MS, Smith, L, Van, C, Yang, H, Sorger, PK, LeBoeuf, NR, Yu, SH Med (N Y) : . doi: 10.1016/j.medj.2020.06.003. PubMed PMID:32838357 PubMed Central PMC7304404
  • 2020 | Agent-based modelling reveals strategies to reduce the fitness and metastatic potential of circulating tumour cell clusters. Campenni, M, May, AN, Boddy, A, Harris, V, Nedelcu, AM Evol Appl 13 (7): 1635-1650. doi: 10.1111/eva.12943. PubMed PMID:32821275 PubMed Central PMC7428819
  • 2020 | When, why and how tumour clonal diversity predicts survival. Noble, R, Burley, JT, Le Sueur, C, Hochberg, ME Evol Appl 13 (7): 1558-1568. doi: 10.1111/eva.13057. PubMed PMID:32821272 PubMed Central PMC7428820
  • 2020 | Transcriptomic and proteomic signatures of stemness and differentiation in the colon crypt. Habowski, AN, Flesher, JL, Bates, JM, Tsai, CF, Martin, K, Zhao, R, Ganesan, AK, Edwards, RA, Shi, T, Wiley, HS, Shi, Y, Hertel, KJ, Waterman, ML Commun Biol 3 (1): 453. doi: 10.1038/s42003-020-01181-z. PubMed PMID:32814826 PubMed Central PMC7438495
  • 2020 | Robust Sequence Determinants of α-Synuclein Toxicity in Yeast Implicate Membrane Binding. Newberry, RW, Arhar, T, Costello, J, Hartoularos, GC, Maxwell, AM, Naing, ZZC, Pittman, M, Reddy, NR, Schwarz, DMC, Wassarman, DR, Wu, TS, Barrero, D, Caggiano, C, Catching, A, Cavazos, TB, Estes, LS, Faust, B, Fink, EA, Goldman, MA, Gomez, YK, Gordon, MG, Gunsalus, LM, Hoppe, N, Jaime-Garza, M, Johnson, MC, Jones, MG, Kung, AF, Lopez, KE, Lumpe, J, Martyn, C, McCarthy, EE, Miller-Vedam, LE, Navarro, EJ, Palar, A, Pellegrino, J, Saylor, W, Stephens, CA, Strickland, J, Torosyan, H, Wankowicz, SA, Wong, DR, Wong, G, Redding, S, Chow, ED, DeGrado, WF, Kampmann, M ACS Chem. Biol. 15 (8): 2137-2153. doi: 10.1021/acschembio.0c00339. PubMed PMID:32786289 PubMed Central PMC7442712
  • 2020 | A Probabilistic Approach to Explore Signal Execution Mechanisms With Limited Experimental Data. Kochen, MA, Lopez, CF Front Genet 11 : 686. doi: 10.3389/fgene.2020.00686. PubMed PMID:32754196 PubMed Central PMC7381302
  • 2020 | Immune complement and coagulation dysfunction in adverse outcomes of SARS-CoV-2 infection. Ramlall, V, Thangaraj, PM, Meydan, C, Foox, J, Butler, D, Kim, J, May, B, De Freitas, JK, Glicksberg, BS, Mason, CE, Tatonetti, NP, Shapira, SD Nat. Med. : . doi: 10.1038/s41591-020-1021-2. PubMed PMID:32747830
  • 2020 | Cells of origin of lung cancers: lessons from mouse studies. Ferone, G, Lee, MC, Sage, J, Berns, A Genes Dev. 34 (15-16): 1017-1032. doi: 10.1101/gad.338228.120. PubMed PMID:32747478 PubMed Central PMC7397855
  • 2020 | A proof of concept for biomarker-guided targeted therapy against ovarian cancer based on patient-derived tumor xenografts. Palmer, AC, Plana, D, Gao, H, Korn, JM, Yang, G, Green, J, Zhang, X, Velazquez, R, McLaughlin, ME, Ruddy, DA, Kowal, C, Goldovitz, J, Bullock, C, Rivera, S, Rakiec, DP, Elliott, G, Fordjour, P, Meyer, R, Loo, A, Kurth, E, Engelman, JA, Bitter, H, Sellers, WR, Williams, JA, Sorger, PK Cancer Res. : . doi: 10.1158/0008-5472.CAN-19-3850. PubMed PMID:32747364
  • 2020 | Comparative Oncology: New Insights into an Ancient Disease. Boddy, AM, Harrison, TM, Abegglen, LM iScience 23 (8): 101373. doi: 10.1016/j.isci.2020.101373. PubMed PMID:32738614 PubMed Central PMC7394918
  • 2020 | Memory Sequencing Reveals Heritable Single-Cell Gene Expression Programs Associated with Distinct Cellular Behaviors. Shaffer, SM, Emert, BL, Reyes Hueros, RA, Cote, C, Harmange, G, Schaff, DL, Sizemore, AE, Gupte, R, Torre, E, Singh, A, Bassett, DS, Raj, A Cell 182 (4): 947-959.e17. doi: 10.1016/j.cell.2020.07.003. PubMed PMID:32735851
  • 2020 | A molecular map of murine lymph node blood vascular endothelium at single cell resolution. Brulois, K, Rajaraman, A, Szade, A, Nordling, S, Bogoslowski, A, Dermadi, D, Rahman, M, Kiefel, H, O'Hara, E, Koning, JJ, Kawashima, H, Zhou, B, Vestweber, D, Red-Horse, K, Mebius, RE, Adams, RH, Kubes, P, Pan, J, Butcher, EC Nat Commun 11 (1): 3798. doi: 10.1038/s41467-020-17291-5. PubMed PMID:32732867 PubMed Central PMC7393069
  • 2020 | In vivo microscopy reveals macrophage polarization locally promotes coherent microtubule dynamics in migrating cancer cells. Luthria, G, Li, R, Wang, S, Prytyskach, M, Kohler, RH, Lauffenburger, DA, Mitchison, TJ, Weissleder, R, Miller, MA Nat Commun 11 (1): 3521. doi: 10.1038/s41467-020-17147-y. PubMed PMID:32665556 PubMed Central PMC7360550
  • 2020 | Cancer systems immunology. Reticker-Flynn, NE, Engleman, EG Elife 9 : . doi: 10.7554/eLife.53839. PubMed PMID:32657757 PubMed Central PMC7358011
  • 2020 | L1CAM defines the regenerative origin of metastasis-initiating cells in colorectal cancer. Ganesh, K, Basnet, H, Kaygusuz, Y, Laughney, AM, He, L, Sharma, R, O'Rourke, KP, Reuter, VP, Huang, YH, Turkekul, M, Emrah, E, Masilionis, I, Manova-Todorova, K, Weiser, MR, Saltz, LB, Garcia-Aguilar, J, Koche, R, Lowe, SW, Pe'er, D, Shia, J, Massagué, J Nat Cancer 1 (1): 28-45. doi: 10.1038/s43018-019-0006-x. PubMed PMID:32656539 PubMed Central PMC7351134
  • 2019 | Modeling heterogeneous tumor growth dynamics and cell-cell interactions at single-cell and cell-population resolution. Harris, LA, Beik, S, Ozawa, PMM, Jimenez, L, Weaver, AM Curr Opin Syst Biol 17 : 24-34. doi: 10.1016/j.coisb.2019.09.005. PubMed PMID:32642602 PubMed Central PMC7343346
  • 2020 | Navigating the path to distant metastasis. Graham, TA, Shibata, D Nat. Genet. 52 (7): 642-643. doi: 10.1038/s41588-020-0660-z. PubMed PMID:32632324
  • 2020 | Is mammography screening beneficial: An individual-based stochastic model for breast cancer incidence and mortality. Le, TTT, Adler, FR PLoS Comput. Biol. 16 (7): e1008036. doi: 10.1371/journal.pcbi.1008036. PubMed PMID:32628726 PubMed Central PMC7365474
  • 2020 | Dual indexed library design enables compatibility of in-Drop single-cell RNA-sequencing with exAMP chemistry sequencing platforms. Southard-Smith, AN, Simmons, AJ, Chen, B, Jones, AL, Ramirez Solano, MA, Vega, PN, Scurrah, CR, Zhao, Y, Brenan, MJ, Xuan, J, Shrubsole, MJ, Porter, EB, Chen, X, Brenan, CJH, Liu, Q, Quigley, LNM, Lau, KS BMC Genomics 21 (1): 456. doi: 10.1186/s12864-020-06843-0. PubMed PMID:32616006 PubMed Central PMC7331155
  • 2020 | Mesenchymal subtype neuroblastomas are addicted to TGF-βR2/HMGCR-driven protein geranylgeranylation. Stokes, ME, Small, JC, Vasciaveo, A, Shimada, K, Hirschhorn, T, Califano, A, Stockwell, BR Sci Rep 10 (1): 10748. doi: 10.1038/s41598-020-67310-0. PubMed PMID:32612149 PubMed Central PMC7329873
  • 2020 | A Cancer Biologist's Primer on Machine Learning Applications in High-Dimensional Cytometry. Keyes, TJ, Domizi, P, Lo, YC, Nolan, GP, Davis, KL Cytometry A 97 (8): 782-799. doi: 10.1002/cyto.a.24158. PubMed PMID:32602650 PubMed Central PMC7416435
  • 2020 | Decoding of persistent multiscale structures in complex biological networks. Zheng, F, Zhang, S, Churas, C, Pratt, D, Bahar, I, Ideker, T bioRxiv : . doi: 10.1101/2020.06.16.151555. PubMed PMID:32587977 PubMed Central PMC7310637
  • 2020 | Unsupervised machine learning reveals risk stratifying glioblastoma tumor cells. Leelatian, N, Sinnaeve, J, Mistry, AM, Barone, SM, Brockman, AA, Diggins, KE, Greenplate, AR, Weaver, KD, Thompson, RC, Chambless, LB, Mobley, BC, Ihrie, RA, Irish, JM Elife 9 : . doi: 10.7554/eLife.56879. PubMed PMID:32573435 PubMed Central PMC7340505
  • 2020 | A single-cell landscape of high-grade serous ovarian cancer. Izar, B, Tirosh, I, Stover, EH, Wakiro, I, Cuoco, MS, Alter, I, Rodman, C, Leeson, R, Su, MJ, Shah, P, Iwanicki, M, Walker, SR, Kanodia, A, Melms, JC, Mei, S, Lin, JR, Porter, CBM, Slyper, M, Waldman, J, Jerby-Arnon, L, Ashenberg, O, Brinker, TJ, Mills, C, Rogava, M, Vigneau, S, Sorger, PK, Garraway, LA, Konstantinopoulos, PA, Liu, JF, Matulonis, U, Johnson, BE, Rozenblatt-Rosen, O, Rotem, A, Regev, A Nat. Med. 26 (8): 1271-1279. doi: 10.1038/s41591-020-0926-0. PubMed PMID:32572264
  • 2020 | Circulating immune cell phenotype dynamics reflect the strength of tumor-immune cell interactions in patients during immunotherapy. Griffiths, JI, Wallet, P, Pflieger, LT, Stenehjem, D, Liu, X, Cosgrove, PA, Leggett, NA, McQuerry, JA, Shrestha, G, Rossetti, M, Sunga, G, Moos, PJ, Adler, FR, Chang, JT, Sharma, S, Bild, AH Proc. Natl. Acad. Sci. U.S.A. 117 (27): 16072-16082. doi: 10.1073/pnas.1918937117. PubMed PMID:32571915 PubMed Central PMC7355015
  • 2020 | Complex Oncological Decision-Making Utilizing Fast-and-Frugal Trees in a Community Setting-Role of Academic and Hybrid Modeling. Salgia, R, Mambetsariev, I, Tan, T, Schwer, A, Pearlstein, DP, Chehabi, H, Baroz, A, Fricke, J, Pharaon, R, Romo, H, Waddington, T, Babikian, R, Buck, L, Kulkarni, P, Cianfrocca, M, Djulbegovic, B, Pal, SK J Clin Med 9 (6): . doi: 10.3390/jcm9061884. PubMed PMID:32560187 PubMed Central PMC7356888
  • 2020 | Personal Protective Equipment for COVID-19: Distributed Fabrication and Additive Manufacturing. Sinha, MS, Bourgeois, FT, Sorger, PK Am J Public Health 110 (8): 1162-1164. doi: 10.2105/AJPH.2020.305753. PubMed PMID:32552025 PubMed Central PMC7349433
  • 2020 | Non-Small Cell Lung Cancer from Genomics to Therapeutics: A Framework for Community Practice Integration to Arrive at Personalized Therapy Strategies. Rajurkar, S, Mambetsariev, I, Pharaon, R, Leach, B, Tan, T, Kulkarni, P, Salgia, R J Clin Med 9 (6): . doi: 10.3390/jcm9061870. PubMed PMID:32549358 PubMed Central PMC7356243
  • 2020 | Unbiased Proteomic Profiling Uncovers a Targetable GNAS/PKA/PP2A Axis in Small Cell Lung Cancer Stem Cells. Coles, GL, Cristea, S, Webber, JT, Levin, RS, Moss, SM, He, A, Sangodkar, J, Hwang, YC, Arand, J, Drainas, AP, Mooney, NA, Demeter, J, Spradlin, JN, Mauch, B, Le, V, Shue, YT, Ko, JH, Lee, MC, Kong, C, Nomura, DK, Ohlmeyer, M, Swaney, DL, Krogan, NJ, Jackson, PK, Narla, G, Gordan, JD, Shokat, KM, Sage, J Cancer Cell 38 (1): 129-143.e7. doi: 10.1016/j.ccell.2020.05.003. PubMed PMID:32531271 PubMed Central PMC7363571
  • 2020 | Role of ultraviolet mutational signature versus tumor mutation burden in predicting response to immunotherapy. Pham, TV, Boichard, A, Goodman, A, Riviere, P, Yeerna, H, Tamayo, P, Kurzrock, R Mol Oncol 14 (8): 1680-1694. doi: 10.1002/1878-0261.12748. PubMed PMID:32530570 PubMed Central PMC7400787
  • 2020 | Notch3 signaling promotes tumor cell adhesion and progression in a murine epithelial ovarian cancer model. Price, JC, Azizi, E, Naiche, LA, Parvani, JG, Shukla, P, Kim, S, Slack-Davis, JK, Pe'er, D, Kitajewski, JK PLoS ONE 15 (6): e0233962. doi: 10.1371/journal.pone.0233962. PubMed PMID:32525899 PubMed Central PMC7289394
  • 2019 | Filament Nucleation Tunes Mechanical Memory in Active Polymer Networks. Yadav, V, Banerjee, DS, Tabatabai, AP, Kovar, DR, Kim, T, Banerjee, S, Murrell, MP Adv Funct Mater 29 (49): . doi: 10.1002/adfm.201905243. PubMed PMID:32523502 PubMed Central PMC7286550
  • 2019 | Opportunities for improving cancer treatment using systems biology. Griffiths, JI, Cohen, AL, Jones, V, Salgia, R, Chang, JT, Bild, AH Curr Opin Syst Biol 17 : 41-50. doi: 10.1016/j.coisb.2019.10.018. PubMed PMID:32518857 PubMed Central PMC7282416
  • 2020 | G protein-regulated endocytic trafficking of adenylyl cyclase type 9. Lazar, AM, Irannejad, R, Baldwin, TA, Sundaram, AB, Gutkind, JS, Inoue, A, Dessauer, CW, Von Zastrow, M Elife 9 : . doi: 10.7554/eLife.58039. PubMed PMID:32515353 PubMed Central PMC7332294
  • 2020 | Rapid prototyping and clinical testing of a reusable face shield for health care workers responding to the COVID-19 pandemic. Mostaghimi, A, Antonini, MJ, Plana, D, Anderson, PD, Beller, B, Boyer, EW, Fannin, A, Freake, J, Oakley, R, Sinha, MS, Smith, L, Van, C, Yang, H, Sorger, PK, LeBoeuf, NR, Yu, SH medRxiv : . doi: 10.1101/2020.04.11.20061960. PubMed PMID:32511612 PubMed Central PMC7276039
  • 2020 | Analysis of SteraMist ionized hydrogen peroxide technology in the sterilization of N95 respirators and other PPE: a quality improvement study. Cramer, A, Plana, D, Yang, HL, Carmack, M, Tian, E, Sinha, MS, Krikorian, D, Turner, D, Mo, J, Li, J, Gupta, R, Manning, H, Bourgeois, FT, Yu, SH, Sorger, P, LeBoeuf, NR medRxiv : . doi: 10.1101/2020.04.19.20069997. PubMed PMID:32511480 PubMed Central PMC7273248
  • 2020 | Rapid community-driven development of a SARS-CoV-2 tissue simulator. Wang, Y, An, G, Becker, A, Cockrell, C, Collier, N, Craig, M, Davis, CL, Faeder, J, Versypt, ANF, Gianlupi, JF, Glazier, JA, Heiland, R, Hillen, T, Islam, MA, Jenner, A, Liu, B, Morel, PA, Narayanan, A, Ozik, J, Rangamani, P, Shoemaker, JE, Smith, AM, Macklin, P bioRxiv : . doi: 10.1101/2020.04.02.019075. PubMed PMID:32511322 PubMed Central PMC7239052
  • 2020 | Changes in Aged Fibroblast Lipid Metabolism Induce Age-Dependent Melanoma Cell Resistance to Targeted Therapy via the Fatty Acid Transporter FATP2. Alicea, GM, Rebecca, VW, Goldman, AR, Fane, ME, Douglass, SM, Behera, R, Webster, MR, Kugel, CH 3rd, Ecker, BL, Caino, MC, Kossenkov, AV, Tang, HY, Frederick, DT, Flaherty, KT, Xu, X, Liu, Q, Gabrilovich, DI, Herlyn, M, Blair, IA, Schug, ZT, Speicher, DW, Weeraratna, AT Cancer Discov 10 (9): 1282-1295. doi: 10.1158/2159-8290.CD-20-0329. PubMed PMID:32499221 PubMed Central PMC7483379
  • 2020 | The Landscape of Human Cancer Proteins Targeted by SARS-CoV-2. Tutuncuoglu, B, Cakir, M, Batra, J, Bouhaddou, M, Eckhardt, M, Gordon, DE, Krogan, NJ Cancer Discov 10 (7): 916-921. doi: 10.1158/2159-8290.CD-20-0559. PubMed PMID:32444466 PubMed Central PMC7357668
  • 2020 | A multiscale biophysical model for the recruitment of actin nucleating proteins at the membrane interface. Fatunmbi, O, Bradley, RP, Kandy, SK, Bucki, R, Janmey, PA, Radhakrishnan, R Soft Matter 16 (21): 4941-4954. doi: 10.1039/d0sm00267d. PubMed PMID:32436537 PubMed Central PMC7373224
  • 2020 | SARS-CoV-2 infection protects against rechallenge in rhesus macaques. Chandrashekar, A, Liu, J, Martinot, AJ, McMahan, K, Mercado, NB, Peter, L, Tostanoski, LH, Yu, J, Maliga, Z, Nekorchuk, M, Busman-Sahay, K, Terry, M, Wrijil, LM, Ducat, S, Martinez, DR, Atyeo, C, Fischinger, S, Burke, JS, Slein, MD, Pessaint, L, Van Ry, A, Greenhouse, J, Taylor, T, Blade, K, Cook, A, Finneyfrock, B, Brown, R, Teow, E, Velasco, J, Zahn, R, Wegmann, F, Abbink, P, Bondzie, EA, Dagotto, G, Gebre, MS, He, X, Jacob-Dolan, C, Kordana, N, Li, Z, Lifton, MA, Mahrokhian, SH, Maxfield, LF, Nityanandam, R, Nkolola, JP, Schmidt, AG, Miller, AD, Baric, RS, Alter, G, Sorger, PK, Estes, JD, Andersen, H, Lewis, MG, Barouch, DH Science 369 (6505): 812-817. doi: 10.1126/science.abc4776. PubMed PMID:32434946 PubMed Central PMC7243369
  • 2020 | Pathway-Specific Genome Editing of PI3K/mTOR Tumor Suppressor Genes Reveals that PTEN Loss Contributes to Cetuximab Resistance in Head and Neck Cancer. Izumi, H, Wang, Z, Goto, Y, Ando, T, Wu, X, Zhang, X, Li, H, Johnson, DE, Grandis, JR, Gutkind, JS Mol. Cancer Ther. 19 (7): 1562-1571. doi: 10.1158/1535-7163.MCT-19-1036. PubMed PMID:32430488 PubMed Central PMC7357849
  • 2020 | A Single-Cell Transcriptional Roadmap of the Mouse and Human Lymph Node Lymphatic Vasculature. Xiang, M, Grosso, RA, Takeda, A, Pan, J, Bekkhus, T, Brulois, K, Dermadi, D, Nordling, S, Vanlandewijck, M, Jalkanen, S, Ulvmar, MH, Butcher, EC Front Cardiovasc Med 7 : 52. doi: 10.3389/fcvm.2020.00052. PubMed PMID:32426372 PubMed Central PMC7204639
  • 2020 | Enhancer reprogramming driven by high-order assemblies of transcription factors promotes phenotypic plasticity and breast cancer endocrine resistance. Bi, M, Zhang, Z, Jiang, YZ, Xue, P, Wang, H, Lai, Z, Fu, X, De Angelis, C, Gong, Y, Gao, Z, Ruan, J, Jin, VX, Marangoni, E, Montaudon, E, Glass, CK, Li, W, Huang, TH, Shao, ZM, Schiff, R, Chen, L, Liu, Z Nat. Cell Biol. 22 (6): 701-715. doi: 10.1038/s41556-020-0514-z. PubMed PMID:32424275
  • 2020 | Reciprocal fine-tuning of progesterone and prolactin-regulated gene expression in breast cancer cells. Holloran, SM, Nosirov, B, Walter, KR, Trinca, GM, Lai, Z, Jin, VX, Hagan, CR Mol. Cell. Endocrinol. 511 : 110859. doi: 10.1016/j.mce.2020.110859. PubMed PMID:32407979
  • 2020 | A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors. Slyper, M, Porter, CBM, Ashenberg, O, Waldman, J, Drokhlyansky, E, Wakiro, I, Smillie, C, Smith-Rosario, G, Wu, J, Dionne, D, Vigneau, S, Jané-Valbuena, J, Tickle, TL, Napolitano, S, Su, MJ, Patel, AG, Karlstrom, A, Gritsch, S, Nomura, M, Waghray, A, Gohil, SH, Tsankov, AM, Jerby-Arnon, L, Cohen, O, Klughammer, J, Rosen, Y, Gould, J, Nguyen, L, Hofree, M, Tramontozzi, PJ, Li, B, Wu, CJ, Izar, B, Haq, R, Hodi, FS, Yoon, CH, Hata, AN, Baker, SJ, Suvà, ML, Bueno, R, Stover, EH, Clay, MR, Dyer, MA, Collins, NB, Matulonis, UA, Wagle, N, Johnson, BE, Rotem, A, Rozenblatt-Rosen, O, Regev, A Nat. Med. 26 (5): 792-802. doi: 10.1038/s41591-020-0844-1. PubMed PMID:32405060 PubMed Central PMC7220853
  • 2020 | Pooled CRISPR screens with imaging on microraft arrays reveals stress granule-regulatory factors. Wheeler, EC, Vu, AQ, Einstein, JM, DiSalvo, M, Ahmed, N, Van Nostrand, EL, Shishkin, AA, Jin, W, Allbritton, NL, Yeo, GW Nat. Methods 17 (6): 636-642. doi: 10.1038/s41592-020-0826-8. PubMed PMID:32393832 PubMed Central PMC7357298
  • 2020 | Multi-omic single-cell snapshots reveal multiple independent trajectories to drug tolerance in a melanoma cell line. Su, Y, Ko, ME, Cheng, H, Zhu, R, Xue, M, Wang, J, Lee, JW, Frankiw, L, Xu, A, Wong, S, Robert, L, Takata, K, Yuan, D, Lu, Y, Huang, S, Ribas, A, Levine, R, Nolan, GP, Wei, W, Plevritis, SK, Li, G, Baltimore, D, Heath, JR Nat Commun 11 (1): 2345. doi: 10.1038/s41467-020-15956-9. PubMed PMID:32393797 PubMed Central PMC7214418
  • 2020 | A human lung tumor microenvironment interactome identifies clinically relevant cell-type cross-talk. Gentles, AJ, Hui, AB, Feng, W, Azizi, A, Nair, RV, Bouchard, G, Knowles, DA, Yu, A, Jeong, Y, Bejnood, A, Forgó, E, Varma, S, Xu, Y, Kuong, A, Nair, VS, West, R, van de Rijn, M, Hoang, CD, Diehn, M, Plevritis, SK Genome Biol. 21 (1): 107. doi: 10.1186/s13059-020-02019-x. PubMed PMID:32381040 PubMed Central PMC7206807
  • 2020 | A Quantitative Framework for Evaluating Single-Cell Data Structure Preservation by Dimensionality Reduction Techniques. Heiser, CN, Lau, KS Cell Rep 31 (5): 107576. doi: 10.1016/j.celrep.2020.107576. PubMed PMID:32375029 PubMed Central PMC7305633
  • 2020 | Comparison of Cell and Organoid-Level Analysis of Patient-Derived 3D Organoids to Evaluate Tumor Cell Growth Dynamics and Drug Response. Kim, S, Choung, S, Sun, RX, Ung, N, Hashemi, N, Fong, EJ, Lau, R, Spiller, E, Gasho, J, Foo, J, Mumenthaler, SM SLAS Discov 25 (7): 744-754. doi: 10.1177/2472555220915827. PubMed PMID:32349587 PubMed Central PMC7372585
  • 2020 | A comparison of microfluidic methods for high-throughput cell deformability measurements. Urbanska, M, Muñoz, HE, Shaw Bagnall, J, Otto, O, Manalis, SR, Di Carlo, D, Guck, J Nat. Methods 17 (6): 587-593. doi: 10.1038/s41592-020-0818-8. PubMed PMID:32341544 PubMed Central PMC7275893
  • 2020 | Adeft: Acromine-based Disambiguation of Entities from Text with applications to the biomedical literature. Steppi, A, Gyori, BM, Bachman, JA J Open Source Softw 5 (45): . doi: 10.21105/joss.01708. PubMed PMID:32337477 PubMed Central PMC7182313
  • 2020 | Gene Networks with Transcriptional Bursting Recapitulate Rare Transient Coordinated High Expression States in Cancer. Schuh, L, Saint-Antoine, M, Sanford, EM, Emert, BL, Singh, A, Marr, C, Raj, A, Goyal, Y Cell Syst 10 (4): 363-378.e12. doi: 10.1016/j.cels.2020.03.004. PubMed PMID:32325034 PubMed Central PMC7293108
  • 2019 | Cancer Ecology and Evolution: Positive interactions and system vulnerability. Adler, FR, Gordon, DM Curr Opin Syst Biol 17 : 1-7. doi: 10.1016/j.coisb.2019.09.001. PubMed PMID:32318644 PubMed Central PMC7172748
  • 2020 | Exploiting evolutionary steering to induce collateral drug sensitivity in cancer. Acar, A, Nichol, D, Fernandez-Mateos, J, Cresswell, GD, Barozzi, I, Hong, SP, Trahearn, N, Spiteri, I, Stubbs, M, Burke, R, Stewart, A, Caravagna, G, Werner, B, Vlachogiannis, G, Maley, CC, Magnani, L, Valeri, N, Banerji, U, Sottoriva, A Nat Commun 11 (1): 1923. doi: 10.1038/s41467-020-15596-z. PubMed PMID:32317663 PubMed Central PMC7174377
  • 2020 | Prognostic significance of an invasive leader cell-derived mutation cluster on chromosome 16q. Pedro, B, Rupji, M, Dwivedi, B, Kowalski, J, Konen, JM, Owonikoko, TK, Ramalingam, SS, Vertino, PM, Marcus, AI Cancer 126 (13): 3140-3150. doi: 10.1002/cncr.32903. PubMed PMID:32315457 PubMed Central PMC7275903
  • 2020 | Measurement and models accounting for cell death capture hidden variation in compound response. Bae, SY, Guan, N, Yan, R, Warner, K, Taylor, SD, Meyer, AS Cell Death Dis 11 (4): 255. doi: 10.1038/s41419-020-2462-8. PubMed PMID:32312951 PubMed Central PMC7171175
  • 2020 | PIN1 Provides Dynamic Control of MYC in Response to Extrinsic Signals. Cohn, GM, Liefwalker, DF, Langer, EM, Sears, RC Front Cell Dev Biol 8 : 224. doi: 10.3389/fcell.2020.00224. PubMed PMID:32300594 PubMed Central PMC7142217
  • 2020 | A Perspective on Expanding Our Understanding of Cancer Treatments by Integrating Approaches from the Biological and Physical Sciences. Fong, EJ, Strelez, C, Mumenthaler, SM SLAS Discov 25 (7): 672-683. doi: 10.1177/2472555220915830. PubMed PMID:32297829 PubMed Central PMC7372587
  • 2020 | Sporadic activation of an oxidative stress-dependent NRF2-p53 signaling network in breast epithelial spheroids and premalignancies. Pereira, EJ, Burns, JS, Lee, CY, Marohl, T, Calderon, D, Wang, L, Atkins, KA, Wang, CC, Janes, KA Sci Signal 13 (627): . doi: 10.1126/scisignal.aba4200. PubMed PMID:32291314 PubMed Central PMC7315801
  • 2019 | Senescent Cells with Augmented Cytokine Production for Microvascular Bioengineering and Tissue Repairs. Xiao, Y, Liu, C, Chen, Z, Blatchley, MR, Kim, D, Zhou, J, Xu, M, Gerecht, S, Fan, R Adv Biosyst 3 (8): . doi: 10.1002/adbi.201900089. PubMed PMID:32270028 PubMed Central PMC7141414
  • 2020 | Integrated single-cell analysis of multicellular immune dynamics during hyperacute HIV-1 infection. Kazer, SW, Aicher, TP, Muema, DM, Carroll, SL, Ordovas-Montanes, J, Miao, VN, Tu, AA, Ziegler, CGK, Nyquist, SK, Wong, EB, Ismail, N, Dong, M, Moodley, A, Berger, B, Love, JC, Dong, KL, Leslie, A, Ndhlovu, ZM, Ndung'u, T, Walker, BD, Shalek, AK Nat. Med. 26 (4): 511-518. doi: 10.1038/s41591-020-0799-2. PubMed PMID:32251406 PubMed Central PMC7237067
  • 2020 | Training Novices in Generation and Analysis of High-Dimensional Human Cell Phospho-Flow Cytometry Data. Roe, CE, Hayes, MJ, Barone, SM, Irish, JM Curr Protoc Cytom 93 (1): e71. doi: 10.1002/cpcy.71. PubMed PMID:32250555
  • 2020 | Network-Based Single-Cell RNA-Seq Data Imputation Enhances Cell Type Identification. Zand, M, Ruan, J Genes (Basel) 11 (4): . doi: 10.3390/genes11040377. PubMed PMID:32244427 PubMed Central PMC7230610
  • 2020 | How Machine Learning Will Transform Biomedicine. Goecks, J, Jalili, V, Heiser, LM, Gray, JW Cell 181 (1): 92-101. doi: 10.1016/j.cell.2020.03.022. PubMed PMID:32243801 PubMed Central PMC7141410
  • 2020 | Deconstructing Pancreatic Adenocarcinoma by Targeting the Conductor, MYC. English, IA, Sears, RC Cancer Discov 10 (4): 495-497. doi: 10.1158/2159-8290.CD-20-0046. PubMed PMID:32238397
  • 2020 | Measuring the distribution of fitness effects in somatic evolution by combining clonal dynamics with dN/dS ratios. Williams, MJ, Zapata, L, Werner, B, Barnes, CP, Sottoriva, A, Graham, TA Elife 9 : . doi: 10.7554/eLife.48714. PubMed PMID:32223898 PubMed Central PMC7105384
  • 2020 | Mapping the breast cancer metastatic cascade onto ctDNA using genetic and epigenetic clonal tracking. Cresswell, GD, Nichol, D, Spiteri, I, Tari, H, Zapata, L, Heide, T, Maley, CC, Magnani, L, Schiavon, G, Ashworth, A, Barry, P, Sottoriva, A Nat Commun 11 (1): 1446. doi: 10.1038/s41467-020-15047-9. PubMed PMID:32221288 PubMed Central PMC7101390
  • 2020 | Image-based metric of invasiveness predicts response to adjuvant temozolomide for primary glioblastoma. Massey, SC, White, H, Whitmire, P, Doyle, T, Johnston, SK, Singleton, KW, Jackson, PR, Hawkins-Daarud, A, Bendok, BR, Porter, AB, Vora, S, Sarkaria, JN, Hu, LS, Mrugala, MM, Swanson, KR PLoS ONE 15 (3): e0230492. doi: 10.1371/journal.pone.0230492. PubMed PMID:32218600 PubMed Central PMC7100932
  • 2020 | Imaging and quantifying drug delivery in skin - Part 2: Fluorescence andvibrational spectroscopic imaging methods. Pena, AM, Chen, X, Pence, IJ, Bornschlögl, T, Jeong, S, Grégoire, S, Luengo, GS, Hallegot, P, Obeidy, P, Feizpour, A, Chan, KF, Evans, CL Adv. Drug Deliv. Rev. 153 : 147-168. doi: 10.1016/j.addr.2020.03.003. PubMed PMID:32217069 PubMed Central PMC7483684
  • 2020 | Selective USP7 inhibition elicits cancer cell killing through a p53-dependent mechanism. Schauer, NJ, Liu, X, Magin, RS, Doherty, LM, Chan, WC, Ficarro, SB, Hu, W, Roberts, RM, Iacob, RE, Stolte, B, Giacomelli, AO, Perera, S, McKay, K, Boswell, SA, Weisberg, EL, Ray, A, Chauhan, D, Dhe-Paganon, S, Anderson, KC, Griffin, JD, Li, J, Hahn, WC, Sorger, PK, Engen, JR, Stegmaier, K, Marto, JA, Buhrlage, SJ Sci Rep 10 (1): 5324. doi: 10.1038/s41598-020-62076-x. PubMed PMID:32210275 PubMed Central PMC7093416
  • 2020 | Subpopulation targeting of pyruvate dehydrogenase and GLUT1 decouples metabolic heterogeneity during collective cancer cell invasion. Commander, R, Wei, C, Sharma, A, Mouw, JK, Burton, LJ, Summerbell, E, Mahboubi, D, Peterson, RJ, Konen, J, Zhou, W, Du, Y, Fu, H, Shanmugam, M, Marcus, AI Nat Commun 11 (1): 1533. doi: 10.1038/s41467-020-15219-7. PubMed PMID:32210228 PubMed Central PMC7093428
  • 2020 | Immunogenomic profiling determines responses to combined PARP and PD-1 inhibition in ovarian cancer. Färkkilä, A, Gulhan, DC, Casado, J, Jacobson, CA, Nguyen, H, Kochupurakkal, B, Maliga, Z, Yapp, C, Chen, YA, Schapiro, D, Zhou, Y, Graham, JR, Dezube, BJ, Munster, P, Santagata, S, Garcia, E, Rodig, S, Lako, A, Chowdhury, D, Shapiro, GI, Matulonis, UA, Park, PJ, Hautaniemi, S, Sorger, PK, Swisher, EM, D'Andrea, AD, Konstantinopoulos, PA Nat Commun 11 (1): 1459. doi: 10.1038/s41467-020-15315-8. PubMed PMID:32193378 PubMed Central PMC7081234
  • 2020 | Radiomic prediction of mutation status based on MR imaging of lung cancer brain metastases. Chen, BT, Jin, T, Ye, N, Mambetsariev, I, Daniel, E, Wang, T, Wong, CW, Rockne, RC, Colen, R, Holodny, AI, Sampath, S, Salgia, R Magn Reson Imaging 69 : 49-56. doi: 10.1016/j.mri.2020.03.002. PubMed PMID:32179095 PubMed Central PMC7237274
  • 2020 | Somatic selection distinguishes oncogenes and tumor suppressor genes. Chandrashekar, P, Ahmadinejad, N, Wang, J, Sekulic, A, Egan, JB, Asmann, YW, Kumar, S, Maley, C, Liu, L Bioinformatics 36 (6): 1712-1717. doi: 10.1093/bioinformatics/btz851. PubMed PMID:32176769
  • 2020 | RESTORE: Robust intEnSiTy nORmalization mEthod for multiplexed imaging. Chang, YH, Chin, K, Thibault, G, Eng, J, Burlingame, E, Gray, JW Commun Biol 3 (1): 111. doi: 10.1038/s42003-020-0828-1. PubMed PMID:32152447 PubMed Central PMC7062831
  • 2020 | Minimal barriers to invasion during human colorectal tumor growth. Ryser, MD, Mallo, D, Hall, A, Hardman, T, King, LM, Tatishchev, S, Sorribes, IC, Maley, CC, Marks, JR, Hwang, ES, Shibata, D Nat Commun 11 (1): 1280. doi: 10.1038/s41467-020-14908-7. PubMed PMID:32152322 PubMed Central PMC7062901
  • 2020 | Transcriptional diversity and bioenergetic shift in human breast cancer metastasis revealed by single-cell RNA sequencing. Davis, RT, Blake, K, Ma, D, Gabra, MBI, Hernandez, GA, Phung, AT, Yang, Y, Maurer, D, Lefebvre, AEYT, Alshetaiwi, H, Xiao, Z, Liu, J, Locasale, JW, Digman, MA, Mjolsness, E, Kong, M, Werb, Z, Lawson, DA Nat. Cell Biol. 22 (3): 310-320. doi: 10.1038/s41556-020-0477-0. PubMed PMID:32144411
  • 2020 | Response and mechanisms of resistance to larotrectinib and selitrectinib in metastatic undifferentiated sarcoma harboring oncogenic fusion of NTRK1. Hemming, ML, Nathenson, MJ, Lin, JR, Mei, S, Du, Z, Malik, K, Marino-Enriquez, A, Jagannathan, JP, Sorger, PK, Bertagnolli, M, Sicinska, E, Demetri, GD, Santagata, S JCO Precis Oncol 4 : 79-90. doi: 10.1200/po.19.00287. PubMed PMID:32133433 PubMed Central PMC7055910
  • 2020 | Imaging of intratumoral heterogeneity in high-grade glioma. Hu, LS, Hawkins-Daarud, A, Wang, L, Li, J, Swanson, KR Cancer Lett. 477 : 97-106. doi: 10.1016/j.canlet.2020.02.025. PubMed PMID:32112907 PubMed Central PMC7108976
  • 2020 | The Cancer Microbiome: Distinguishing Direct and Indirect Effects Requires a Systemic View. Xavier, JB, Young, VB, Skufca, J, Ginty, F, Testerman, T, Pearson, AT, Macklin, P, Mitchell, A, Shmulevich, I, Xie, L, Caporaso, JG, Crandall, KA, Simone, NL, Godoy-Vitorino, F, Griffin, TJ, Whiteson, KL, Gustafson, HH, Slade, DJ, Schmidt, TM, Walther-Antonio, MRS, Korem, T, Webb-Robertson, BM, Styczynski, MP, Johnson, WE, Jobin, C, Ridlon, JM, Koh, AY, Yu, M, Kelly, L, Wargo, JA Trends Cancer 6 (3): 192-204. doi: 10.1016/j.trecan.2020.01.004. PubMed PMID:32101723 PubMed Central PMC7098063
  • 2020 | Measuring single cell divisions in human tissues from multi-region sequencing data. Werner, B, Case, J, Williams, MJ, Chkhaidze, K, Temko, D, Fernández-Mateos, J, Cresswell, GD, Nichol, D, Cross, W, Spiteri, I, Huang, W, Tomlinson, IPM, Barnes, CP, Graham, TA, Sottoriva, A Nat Commun 11 (1): 1035. doi: 10.1038/s41467-020-14844-6. PubMed PMID:32098957 PubMed Central PMC7042311
  • 2020 | Shaping Chromatin States in Prostate Cancer by Pioneer Transcription Factors. Hankey, W, Chen, Z, Wang, Q Cancer Res. 80 (12): 2427-2436. doi: 10.1158/0008-5472.CAN-19-3447. PubMed PMID:32094298 PubMed Central PMC7299826
  • 2020 | Defining the emergence of myeloid-derived suppressor cells in breast cancer using single-cell transcriptomics. Alshetaiwi, H, Pervolarakis, N, McIntyre, LL, Ma, D, Nguyen, Q, Rath, JA, Nee, K, Hernandez, G, Evans, K, Torosian, L, Silva, A, Walsh, C, Kessenbrock, K Sci Immunol 5 (44): . doi: 10.1126/sciimmunol.aay6017. PubMed PMID:32086381 PubMed Central PMC7219211
  • 2020 | Kernel Differential Subgraph Analysis to Reveal the Key Period Affecting Glioblastoma. Xie, J, Sun, J, Feng, J, Yang, F, Wang, J, Wen, T, Nie, Q Biomolecules 10 (2): . doi: 10.3390/biom10020318. PubMed PMID:32079293 PubMed Central PMC7072688
  • 2020 | A census of pathway maps in cancer systems biology. Kuenzi, BM, Ideker, T Nat. Rev. Cancer 20 (4): 233-246. doi: 10.1038/s41568-020-0240-7. PubMed PMID:32066900 PubMed Central PMC7224610
  • 2020 | Exploration of Cell Development Pathways through High-Dimensional Single Cell Analysis in Trajectory Space. Dermadi, D, Bscheider, M, Bjegovic, K, Lazarus, NH, Szade, A, Hadeiba, H, Butcher, EC iScience 23 (2): 100842. doi: 10.1016/j.isci.2020.100842. PubMed PMID:32058956 PubMed Central PMC6997593
  • 2020 | Robustness and applicability of transcription factor and pathway analysis tools on single-cell RNA-seq data. Holland, CH, Tanevski, J, Perales-Patón, J, Gleixner, J, Kumar, MP, Mereu, E, Joughin, BA, Stegle, O, Lauffenburger, DA, Heyn, H, Szalai, B, Saez-Rodriguez, J Genome Biol. 21 (1): 36. doi: 10.1186/s13059-020-1949-z. PubMed PMID:32051003 PubMed Central PMC7017576
  • 2020 | Precision medicine and actionable alterations in lung cancer: A single institution experience. Mambetsariev, I, Wang, Y, Chen, C, Nadaf, S, Pharaon, R, Fricke, J, Amanam, I, Amini, A, Bild, A, Chu, P, Erhunmwunsee, L, Kim, J, Munu, J, Pillai, R, Raz, D, Sampath, S, Vora, L, Qiu, F, Smith, L, Batra, SK, Massarelli, E, Koczywas, M, Reckamp, K, Salgia, R PLoS ONE 15 (2): e0228188. doi: 10.1371/journal.pone.0228188. PubMed PMID:32045431 PubMed Central PMC7012442
  • 2020 | Regenerative lineages and immune-mediated pruning in lung cancer metastasis. Laughney, AM, Hu, J, Campbell, NR, Bakhoum, SF, Setty, M, Lavallée, VP, Xie, Y, Masilionis, I, Carr, AJ, Kottapalli, S, Allaj, V, Mattar, M, Rekhtman, N, Xavier, JB, Mazutis, L, Poirier, JT, Rudin, CM, Pe'er, D, Massagué, J Nat. Med. 26 (2): 259-269. doi: 10.1038/s41591-019-0750-6. PubMed PMID:32042191 PubMed Central PMC7021003
  • 2020 | CLEAR: coverage-based limiting-cell experiment analysis for RNA-seq. Walker, LA, Sovic, MG, Chiang, CL, Hu, E, Denninger, JK, Chen, X, Kirby, ED, Byrd, JC, Muthusamy, N, Bundschuh, R, Yan, P J Transl Med 18 (1): 63. doi: 10.1186/s12967-020-02247-6. PubMed PMID:32039730 PubMed Central PMC7008572
  • 2020 | Paradoxical Role for Wild-Type p53 in Driving Therapy Resistance in Melanoma. Webster, MR, Fane, ME, Alicea, GM, Basu, S, Kossenkov, AV, Marino, GE, Douglass, SM, Kaur, A, Ecker, BL, Gnanapradeepan, K, Ndoye, A, Kugel, C, Valiga, A, Palmer, J, Liu, Q, Xu, X, Morris, J, Yin, X, Wu, H, Xu, W, Zheng, C, Karakousis, GC, Amaravadi, RK, Mitchell, TC, Almeida, FV, Xiao, M, Rebecca, VW, Wang, YJ, Schuchter, LM, Herlyn, M, Murphy, ME, Weeraratna, AT Mol. Cell 77 (3): 681. doi: 10.1016/j.molcel.2020.01.005. PubMed PMID:32032511 PubMed Central PMC7441646
  • 2020 | New Approaches to SCLC Therapy: From the Laboratory to the Clinic. Poirier, JT, George, J, Owonikoko, TK, Berns, A, Brambilla, E, Byers, LA, Carbone, D, Chen, HJ, Christensen, CL, Dive, C, Farago, AF, Govindan, R, Hann, C, Hellmann, MD, Horn, L, Johnson, JE, Ju, YS, Kang, S, Krasnow, M, Lee, J, Lee, SH, Lehman, J, Lok, B, Lovly, C, MacPherson, D, McFadden, D, Minna, J, Oser, M, Park, K, Park, KS, Pommier, Y, Quaranta, V, Ready, N, Sage, J, Scagliotti, G, Sos, ML, Sutherland, KD, Travis, WD, Vakoc, CR, Wait, SJ, Wistuba, I, Wong, KK, Zhang, H, Daigneault, J, Wiens, J, Rudin, CM, Oliver, TG J Thorac Oncol 15 (4): 520-540. doi: 10.1016/j.jtho.2020.01.016. PubMed PMID:32018053 PubMed Central PMC7263769
  • 2020 | Distribution and storage of inflammatory memory in barrier tissues. Ordovas-Montanes, J, Beyaz, S, Rakoff-Nahoum, S, Shalek, AK Nat. Rev. Immunol. 20 (5): 308-320. doi: 10.1038/s41577-019-0263-z. PubMed PMID:32015472
  • 2020 | HSF1 phase transition mediates stress adaptation and cell fate decisions. Gaglia, G, Rashid, R, Yapp, C, Joshi, GN, Li, CG, Lindquist, SL, Sarosiek, KA, Whitesell, L, Sorger, PK, Santagata, S Nat. Cell Biol. 22 (2): 151-158. doi: 10.1038/s41556-019-0458-3. PubMed PMID:32015439 PubMed Central PMC7135912
  • 2020 | Immunological Fingerprints of Controllers Developing Neutralizing HIV-1 Antibodies. Martin-Gayo, E, Gao, C, Chen, HR, Ouyang, Z, Kim, D, Kolb, KE, Shalek, AK, Walker, BD, Lichterfeld, M, Yu, XG Cell Rep 30 (4): 984-996.e4. doi: 10.1016/j.celrep.2019.12.087. PubMed PMID:31995767 PubMed Central PMC6990401
  • 2020 | Fragile epitopes-Antibody's guess is as good as yours. Janes, KA Sci Signal 13 (616): . doi: 10.1126/scisignal.aaz8130. PubMed PMID:31992582 PubMed Central PMC7231929
  • 2020 | Single-Cell Proteomic Profiling Identifies Combined AXL and JAK1 Inhibition as a Novel Therapeutic Strategy for Lung Cancer. Taverna, JA, Hung, CN, DeArmond, DT, Chen, M, Lin, CL, Osmulski, PA, Gaczynska, ME, Wang, CM, Lucio, ND, Chou, CW, Chen, CL, Nazarullah, A, Lampkin, SR, Qiu, L, Bearss, DJ, Warner, S, Whatcott, CJ, Mouritsen, L, Wade, M, Weitman, S, Mesa, RA, Kirma, NB, Chao, WT, Huang, TH Cancer Res. 80 (7): 1551-1563. doi: 10.1158/0008-5472.CAN-19-3183. PubMed PMID:31992541 PubMed Central PMC7127959
  • 2020 | Astrocytic trans-Differentiation Completes a Multicellular Paracrine Feedback Loop Required for Medulloblastoma Tumor Growth. Yao, M, Ventura, PB, Jiang, Y, Rodriguez, FJ, Wang, L, Perry, JSA, Yang, Y, Wahl, K, Crittenden, RB, Bennett, ML, Qi, L, Gong, CC, Li, XN, Barres, BA, Bender, TP, Ravichandran, KS, Janes, KA, Eberhart, CG, Zong, H Cell 180 (3): 502-520.e19. doi: 10.1016/j.cell.2019.12.024. PubMed PMID:31983537 PubMed Central PMC7259679
  • 2020 | Prediction of Benefit from Checkpoint Inhibitors in Mismatch Repair Deficient Metastatic Colorectal Cancer: Role of Tumor Infiltrating Lymphocytes. Loupakis, F, Depetris, I, Biason, P, Intini, R, Prete, AA, Leone, F, Lombardi, P, Filippi, R, Spallanzani, A, Cascinu, S, Bonetti, LR, Maddalena, G, Valeri, N, Sottoriva, A, Zapata, L, Salmaso, R, Munari, G, Rugge, M, Dei Tos, AP, Golovato, J, Sanborn, JZ, Nguyen, A, Schirripa, M, Zagonel, V, Lonardi, S, Fassan, M Oncologist 25 (6): 481-487. doi: 10.1634/theoncologist.2019-0611. PubMed PMID:31967692 PubMed Central PMC7288636
  • 2020 | Receptor-based mechanism of relative sensing and cell memory in mammalian signaling networks. Lyashenko, E, Niepel, M, Dixit, PD, Lim, SK, Sorger, PK, Vitkup, D Elife 9 : . doi: 10.7554/eLife.50342. PubMed PMID:31961323 PubMed Central PMC7046471
  • 2020 | Mix and Match: Phenotypic Coexistence as a Key Facilitator of Cancer Invasion. Strobl, MAR, Krause, AL, Damaghi, M, Gillies, R, Anderson, ARA, Maini, PK Bull. Math. Biol. 82 (1): 15. doi: 10.1007/s11538-019-00675-0. PubMed PMID:31953602 PubMed Central PMC6968991
  • 2020 | Towards Multidrug Adaptive Therapy. West, J, You, L, Zhang, J, Gatenby, RA, Brown, JS, Newton, PK, Anderson, ARA Cancer Res. 80 (7): 1578-1589. doi: 10.1158/0008-5472.CAN-19-2669. PubMed PMID:31948939 PubMed Central PMC7307613
  • 2020 | Mass cytometry defines distinct immune profile in germinal center B-cell lymphomas. Roussel, M, Lhomme, F, Roe, CE, Bartkowiak, T, Gravelle, P, Laurent, C, Fest, T, Irish, JM Cancer Immunol. Immunother. 69 (3): 407-420. doi: 10.1007/s00262-019-02464-z. PubMed PMID:31919622
  • 2020 | Biophysical prediction of protein-peptide interactions and signaling networks using machine learning. Cunningham, JM, Koytiger, G, Sorger, PK, AlQuraishi, M Nat. Methods 17 (2): 175-183. doi: 10.1038/s41592-019-0687-1. PubMed PMID:31907444 PubMed Central PMC7004877
  • 2019 | Wound Healing Coordinates Actin Architectures to Regulate Mechanical Work. Ajeti, V, Tabatabai, AP, Fleszar, AJ, Staddon, MF, Seara, DS, Suarez, C, Yousafzai, MS, Bi, D, Kovar, DR, Banerjee, S, Murrell, MP Nat Phys 15 : 696-705. doi: 10.1038/s41567-019-0485-9. PubMed PMID:31897085 PubMed Central PMC6939997
  • 2019 | Energy oversupply to tissues: a single mechanism possibly underlying multiple cancer risk factors. Wu, DJ, Aktipis, A, Pepper, JW Evol Med Public Health 2019 (1): 9-16. doi: 10.1093/emph/eoz004. PubMed PMID:31893122 PubMed Central PMC6379718
  • 2020 | Interactive Multiresolution Visualization of Cellular Network Processes. Ortega, OO, Lopez, CF iScience 23 (1): 100748. doi: 10.1016/j.isci.2019.100748. PubMed PMID:31884165 PubMed Central PMC6941861
  • 2020 | Inhibition of Haspin Kinase Promotes Cell-Intrinsic and Extrinsic Antitumor Activity. Melms, JC, Vallabhaneni, S, Mills, CE, Yapp, C, Chen, JY, Morelli, E, Waszyk, P, Kumar, S, Deming, D, Moret, N, Rodriguez, S, Subramanian, K, Rogava, M, Cartwright, ANR, Luoma, A, Mei, S, Brinker, TJ, Miller, DM, Spektor, A, Schadendorf, D, Riggi, N, Wucherpfennig, KW, Sorger, PK, Izar, B Cancer Res. 80 (4): 798-810. doi: 10.1158/0008-5472.CAN-19-2330. PubMed PMID:31882401 PubMed Central PMC7029677
  • 2020 | Topological Tumor Graphs: A Graph-Based Spatial Model to Infer Stromal Recruitment for Immunosuppression in Melanoma Histology. Failmezger, H, Muralidhar, S, Rullan, A, de Andrea, CE, Sahai, E, Yuan, Y Cancer Res. 80 (5): 1199-1209. doi: 10.1158/0008-5472.CAN-19-2268. PubMed PMID:31874858
  • 2019 | Robust latent-variable interpretation of in vivo regression models by nested resampling. Caulk, AW, Janes, KA Sci Rep 9 (1): 19671. doi: 10.1038/s41598-019-55796-2. PubMed PMID:31873087 PubMed Central PMC6928252
  • 2020 | Amino and PEG-amino graphene oxide grids enrich and protect samples for high-resolution single particle cryo-electron microscopy. Wang, F, Yu, Z, Betegon, M, Campbell, MG, Aksel, T, Zhao, J, Li, S, Douglas, SM, Cheng, Y, Agard, DA J. Struct. Biol. 209 (2): 107437. doi: 10.1016/j.jsb.2019.107437. PubMed PMID:31866389 PubMed Central PMC7272056
  • 2020 | Maximum Entropy Framework for Predictive Inference of Cell Population Heterogeneity and Responses in Signaling Networks. Dixit, PD, Lyashenko, E, Niepel, M, Vitkup, D Cell Syst 10 (2): 204-212.e8. doi: 10.1016/j.cels.2019.11.010. PubMed PMID:31864963 PubMed Central PMC7047530
  • 2019 | An ultrasensitive fiveplex activity assay for cellular kinases. Smolko, CM, Janes, KA Sci Rep 9 (1): 19409. doi: 10.1038/s41598-019-55998-8. PubMed PMID:31857650 PubMed Central PMC6923413
  • 2019 | Highly multiplexed immunofluorescence images and single-cell data of immune markers in tonsil and lung cancer. Rashid, R, Gaglia, G, Chen, YA, Lin, JR, Du, Z, Maliga, Z, Schapiro, D, Yapp, C, Muhlich, J, Sokolov, A, Sorger, P, Santagata, S Sci Data 6 (1): 323. doi: 10.1038/s41597-019-0332-y. PubMed PMID:31848351 PubMed Central PMC6917801
  • 2019 | Single-cell connectomic analysis of adult mammalian lungs. Raredon, MSB, Adams, TS, Suhail, Y, Schupp, JC, Poli, S, Neumark, N, Leiby, KL, Greaney, AM, Yuan, Y, Horien, C, Linderman, G, Engler, AJ, Boffa, DJ, Kluger, Y, Rosas, IO, Levchenko, A, Kaminski, N, Niklason, LE Sci Adv 5 (12): eaaw3851. doi: 10.1126/sciadv.aaw3851. PubMed PMID:31840053 PubMed Central PMC6892628
  • 2019 | Individual Cells Can Resolve Variations in Stimulus Intensity along the IGF-PI3K-AKT Signaling Axis. Gross, SM, Dane, MA, Bucher, E, Heiser, LM Cell Syst 9 (6): 580-588.e4. doi: 10.1016/j.cels.2019.11.005. PubMed PMID:31838146 PubMed Central PMC7081831
  • 2020 | Paradoxical Role for Wild-Type p53 in Driving Therapy Resistance in Melanoma. Webster, MR, Fane, ME, Alicea, GM, Basu, S, Kossenkov, AV, Marino, GE, Douglass, SM, Kaur, A, Ecker, BL, Gnanapradeepan, K, Ndoye, A, Kugel, C, Valiga, A, Palmer, J, Liu, Q, Xu, X, Morris, J, Yin, X, Wu, H, Xu, W, Zheng, C, Karakousis, GC, Amaravadi, RK, Mitchell, TC, Almeida, FV, Xiao, M, Rebecca, VW, Wang, YJ, Schuchter, LM, Herlyn, M, Murphy, ME, Weeraratna, AT Mol. Cell 77 (3): 633-644.e5. doi: 10.1016/j.molcel.2019.11.009. PubMed PMID:31836388 PubMed Central PMC7419227
  • 2019 | Axon-like protrusions promote small cell lung cancer migration and metastasis. Yang, D, Qu, F, Cai, H, Chuang, CH, Lim, JS, Jahchan, N, Grüner, BM, S Kuo, C, Kong, C, Oudin, MJ, Winslow, MM, Sage, J Elife 8 : . doi: 10.7554/eLife.50616. PubMed PMID:31833833 PubMed Central PMC6940020
  • 2019 | Disruption of Broad Epigenetic Domains in PDAC Cells by HAT Inhibitors. Gerrard, DL, Boyd, JR, Stein, GS, Jin, VX, Frietze, S Epigenomes 3 (2): . doi: 10.3390/epigenomes3020011. PubMed PMID:31815011 PubMed Central PMC6897394
  • 2020 | Torin2 Exploits Replication and Checkpoint Vulnerabilities to Cause Death of PI3K-Activated Triple-Negative Breast Cancer Cells. Chopra, SS, Jenney, A, Palmer, A, Niepel, M, Chung, M, Mills, C, Sivakumaren, SC, Liu, Q, Chen, JY, Yapp, C, Asara, JM, Gray, NS, Sorger, PK Cell Syst 10 (1): 66-81.e11. doi: 10.1016/j.cels.2019.11.001. PubMed PMID:31812693 PubMed Central PMC7000271
  • 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 | Inferring reaction network structure from single-cell, multiplex data, using toric systems theory. Wang, S, Lin, JR, Sontag, ED, Sorger, PK PLoS Comput. Biol. 15 (12): e1007311. doi: 10.1371/journal.pcbi.1007311. PubMed PMID:31809500 PubMed Central PMC6919632
  • 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 PubMed Central PMC6966510
  • 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
  • 2020 | Cooperative inflammation: The recruitment of inflammatory signaling in marsupial and eutherian pregnancy. Stadtmauer, DJ, Wagner, GP J. Reprod. Immunol. 137 : 102626. doi: 10.1016/j.jri.2019.102626. PubMed PMID:31783286 PubMed Central PMC7028515
  • 2019 | Multifaceted function of YAP/TEAD on chromatin:prospects of 'A non-canonical role of YAP/TEAD is required for activation of estrogen-regulated enhancers in breast cancer'. Chen, L, Liu, Z J Mol Cell Biol 11 (12): 1101-1103. doi: 10.1093/jmcb/mjz106. PubMed PMID:31774121 PubMed Central PMC6934152
  • 2019 | Evolution of placental invasion and cancer metastasis are causally linked. Kshitiz,, Afzal, J, Maziarz, JD, Hamidzadeh, A, Liang, C, Erkenbrack, EM, Kim, HN, 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 PubMed Central PMC7340496
  • 2020 | 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. 130 (1): 231-246. doi: 10.1172/JCI126390. PubMed PMID:31763993 PubMed Central PMC6934197
  • 2019 | Dynamic motions of molecular motors in the actin cytoskeleton. Jung, W, Tabatabai, AP, Thomas, JJ, Tabei, SMA, Murrell, MP, Kim, T Cytoskeleton (Hoboken) 76 (11-12): 517-531. doi: 10.1002/cm.21582. PubMed PMID:31758841 PubMed Central PMC7439601
  • 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 | A curative combination cancer therapy achieves high fractional cell killing through low cross-resistance and drug additivity. Palmer, AC, Chidley, C, Sorger, PK Elife 8 : . doi: 10.7554/eLife.50036. PubMed PMID:31742555 PubMed Central PMC6897534
  • 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 | CXCR3: Here to stay to enhance cancer immunotherapy?. Rogava, M, Izar, B EBioMedicine 49 : 11-12. doi: 10.1016/j.ebiom.2019.09.044. PubMed PMID:31690542 PubMed Central PMC6945198
  • 2019 | Pericytes enable effective angiogenesis in the presence of proinflammatory signals. Kang, TY, Bocci, F, Jolly, MK, Levine, H, Onuchic, JN, Levchenko, A Proc. Natl. Acad. Sci. U.S.A. 116 (47): 23551-23561. doi: 10.1073/pnas.1913373116. PubMed PMID:31685607 PubMed Central PMC6876202
  • 2019 | Superpixel-Based Conditional Random Fields (SuperCRF): Incorporating Global and Local Context for Enhanced Deep Learning in Melanoma Histopathology. Zormpas-Petridis, K, Failmezger, H, Raza, SEA, Roxanis, I, Jamin, Y, Yuan, Y Front Oncol 9 : 1045. doi: 10.3389/fonc.2019.01045. PubMed PMID:31681583 PubMed Central PMC6798642
  • 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 PubMed Central PMC7060040
  • 2019 | Systems-level network modeling of Small Cell Lung Cancer subtypes identifies master regulators and destabilizers. Wooten, DJ, Groves, SM, Tyson, DR, Liu, Q, Lim, JS, Albert, R, Lopez, CF, Sage, J, Quaranta, V PLoS Comput. Biol. 15 (10): e1007343. doi: 10.1371/journal.pcbi.1007343. PubMed PMID:31671086 PubMed Central PMC6860456
  • 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 | Transcriptional Basis of Mouse and Human Dendritic Cell Heterogeneity. Brown, CC, Gudjonson, H, Pritykin, Y, Deep, D, Lavallée, VP, Mendoza, A, Fromme, R, Mazutis, L, Ariyan, C, Leslie, C, Pe'er, D, Rudensky, AY Cell 179 (4): 846-863.e24. doi: 10.1016/j.cell.2019.09.035. PubMed PMID:31668803 PubMed Central PMC6838684
  • 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 | Cochlear Place of Stimulation Is One Determinant of Cochlear Implant Sound Quality. Dorman, MF, Cook Natale, S, Baxter, L, Zeitler, DM, Carlson, ML, Noble, JH Audiol. Neurootol. 24 (5): 264-269. doi: 10.1159/000503217. PubMed PMID:31661682
  • 2020 | 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 33 (2): 439-446. doi: 10.1007/s10278-019-00282-4. PubMed PMID:31654174 PubMed Central PMC7165226
  • 2019 | Analysis of tumour ecological balance reveals resource-dependent adaptive strategies of ovarian cancer. Nawaz, S, Trahearn, NA, Heindl, A, Banerjee, S, Maley, CC, Sottoriva, A, Yuan, Y EBioMedicine 48 : 224-235. doi: 10.1016/j.ebiom.2019.10.001. PubMed PMID:31648981 PubMed Central PMC6838425
  • 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 | Induction of metabolic quiescence defines the transitional to follicular B cell switch. Farmer, JR, Allard-Chamard, H, Sun, N, Ahmad, M, Bertocchi, A, Mahajan, VS, Aicher, T, Arnold, J, Benson, MD, Morningstar, J, Barmettler, S, Yuen, G, Murphy, SJH, Walter, JE, Ghebremichael, M, Shalek, AK, Batista, F, Gerszten, R, Pillai, S Sci Signal 12 (604): . doi: 10.1126/scisignal.aaw5573. PubMed PMID:31641080 PubMed Central PMC7301641
  • 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 | Unified rational protein engineering with sequence-based deep representation learning. Alley, EC, Khimulya, G, Biswas, S, AlQuraishi, M, Church, GM Nat. Methods 16 (12): 1315-1322. doi: 10.1038/s41592-019-0598-1. PubMed PMID:31636460 PubMed Central PMC7067682
  • 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 PubMed Central PMC7208439
  • 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 | Ultrahigh-Density Screens for Genome-Wide Yeast EMAPs in a Single Plate. Licon, K, Shen, JP, Munson, BP, Michaca, M, Fassino, C, Fassino, L, Kreisberg, JF, Ideker, T Methods Mol. Biol. 2049 : 73-85. doi: 10.1007/978-1-4939-9736-7_4. PubMed PMID:31602605 PubMed Central PMC7423300
  • 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
  • 2020 | 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 33 (2): 279-292. 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 | Qualifying antibodies for image-based immune profiling and multiplexed tissue imaging. Du, Z, Lin, JR, Rashid, R, Maliga, Z, Wang, S, Aster, JC, Izar, B, Sorger, PK, Santagata, S Nat Protoc 14 (10): 2900-2930. doi: 10.1038/s41596-019-0206-y. PubMed PMID:31534232 PubMed Central PMC6959005
  • 2019 | T Cell Activation Depends on Extracellular Alanine. Ron-Harel, N, Ghergurovich, JM, Notarangelo, G, LaFleur, MW, Tsubosaka, Y, Sharpe, AH, Rabinowitz, JD, Haigis, MC Cell Rep 28 (12): 3011-3021.e4. doi: 10.1016/j.celrep.2019.08.034. PubMed PMID:31533027 PubMed Central PMC6934407
  • 2019 | PTPN2 regulates the generation of exhausted CD8+ T cell subpopulations and restrains tumor immunity. LaFleur, MW, Nguyen, TH, Coxe, MA, Miller, BC, Yates, KB, Gillis, JE, Sen, DR, Gaudiano, EF, Al Abosy, R, Freeman, GJ, Haining, WN, Sharpe, AH Nat. Immunol. 20 (10): 1335-1347. doi: 10.1038/s41590-019-0480-4. PubMed PMID:31527834 PubMed Central PMC6754306
  • 2019 | HiLDA: a statistical approach to investigate differences in mutational signatures. Yang, Z, Pandey, P, Shibata, D, Conti, DV, Marjoram, P, Siegmund, KD PeerJ 7 : e7557. doi: 10.7717/peerj.7557. PubMed PMID:31523512 PubMed Central PMC6717498
  • 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
  • 2020 | Facetto: Combining Unsupervised and Supervised Learning for Hierarchical Phenotype Analysis in Multi-Channel Image Data. Krueger, R, Beyer, J, Jang, WD, Kim, NW, Sokolov, A, Sorger, PK, Pfister, H IEEE Trans Vis Comput Graph 26 (1): 227-237. doi: 10.1109/TVCG.2019.2934547. PubMed PMID:31514138 PubMed Central PMC7045445
  • 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 | Deoxycytidine Release from Pancreatic Stellate Cells Promotes Gemcitabine Resistance. Dalin, S, Sullivan, MR, Lau, AN, Grauman-Boss, B, Mueller, HS, Kreidl, E, Fenoglio, S, Luengo, A, Lees, JA, Vander Heiden, MG, Lauffenburger, DA, Hemann, MT Cancer Res. 79 (22): 5723-5733. doi: 10.1158/0008-5472.CAN-19-0960. PubMed PMID:31484670 PubMed Central PMC7357734
  • 2019 | A Structure-Informed Atlas of Human-Virus Interactions. Lasso, G, Mayer, SV, Winkelmann, ER, Chu, T, Elliot, O, Patino-Galindo, JA, Park, K, Rabadan, R, Honig, B, Shapira, SD Cell 178 (6): 1526-1541.e16. doi: 10.1016/j.cell.2019.08.005. PubMed PMID:31474372 PubMed Central PMC6736651
  • 2020 | Therapeutic potential of ReACp53 targeting mutant p53 protein in CRPC. Zhang, Y, Xu, L, Chang, Y, Li, Y, Butler, W, Jin, E, Wang, A, Tao, Y, Chen, X, Liang, C, Huang, J Prostate Cancer Prostatic Dis. 23 (1): 160-171. doi: 10.1038/s41391-019-0172-z. PubMed PMID:31471556 PubMed Central PMC7031025
  • 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 | Synthetic Essentiality of Metabolic Regulator PDHK1 in PTEN-Deficient Cells and Cancers. Chatterjee, N, Pazarentzos, E, Mayekar, MK, Gui, P, Allegakoen, DV, Hrustanovic, G, Olivas, V, Lin, L, Verschueren, E, Johnson, JR, Hofree, M, Yan, JJ, Newton, BW, Dollen, JV, Earnshaw, CH, Flanagan, J, Chan, E, Asthana, S, Ideker, T, Wu, W, Suzuki, J, Barad, BA, Kirichok, Y, Fraser, JS, Weiss, WA, Krogan, NJ, Tulpule, A, Sabnis, AJ, Bivona, TG Cell Rep 28 (9): 2317-2330.e8. doi: 10.1016/j.celrep.2019.07.063. PubMed PMID:31461649 PubMed Central PMC6728083
  • 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 | Dynamics of drug response informs rational combination regimens. Paudel, BB, Quaranta, V Sci Signal 12 (595): . doi: 10.1126/scisignal.aax9742. PubMed PMID:31431544
  • 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 | Mission Possible: Advances in MYC Therapeutic Targeting in Cancer. Allen-Petersen, BL, Sears, RC BioDrugs 33 (5): 539-553. doi: 10.1007/s40259-019-00370-5. PubMed PMID:31392631 PubMed Central PMC6790341
  • 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 | scRNABatchQC: multi-samples quality control for single cell RNA-seq data. Liu, Q, Sheng, Q, Ping, J, Ramirez, MA, Lau, KS, Coffey, RJ, Shyr, Y Bioinformatics 35 (24): 5306-5308. doi: 10.1093/bioinformatics/btz601. PubMed PMID:31373345 PubMed Central PMC6954654
  • 2019 | Cancer cell evolution through the ages. Maley, CC, Shibata, D Science 365 (6452): 440-441. doi: 10.1126/science.aay2859. PubMed PMID:31371596 PubMed Central PMC7449598
  • 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 | Cardiolipin-Dependent Properties of Model Mitochondrial Membranes from Molecular Simulations. Wilson, BA, Ramanathan, A, Lopez, CF Biophys. J. 117 (3): 429-444. doi: 10.1016/j.bpj.2019.06.023. PubMed PMID:31349988 PubMed Central PMC6697365
  • 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 | ENvironmental Dynamics Underlying Responsive Extreme Survivors (ENDURES) of Glioblastoma: A Multidisciplinary Team-based, Multifactorial Analytical Approach. Johnston, SK, Whitmire, P, Massey, SC, Kumthekar, P, Porter, AB, Raghunand, N, Gonzalez-Cuyar, LF, Mrugala, MM, Hawkins-Daarud, A, Jackson, PR, Hu, LS, Sarkaria, JN, Wang, L, Gatenby, RA, Egan, KM, Canoll, P, Swanson, KR, ENDURES consortium Am. J. Clin. Oncol. 42 (8): 655-661. doi: 10.1097/COC.0000000000000564. PubMed PMID:31343422 PubMed Central PMC7416695
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