CSBC Supported Publications

Publications

  • 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 : . doi: 10.1126/science.abc4776. PubMed PMID:32434946 PubMed Central PMC7243369
  • 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. : . doi: 10.1038/s41556-020-0514-z. PubMed PMID:32424275
  • 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
  • 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 : . doi: 10.1038/s41592-020-0818-8. PubMed PMID:32341544
  • 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
  • 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 : . doi: 10.1002/cncr.32903. PubMed PMID:32315457
  • 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
  • 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 | 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 | 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 | 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. : . doi: 10.1016/j.addr.2020.03.003. PubMed PMID:32217069
  • 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 | 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 | 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. : . doi: 10.1158/0008-5472.CAN-19-3447. PubMed PMID:32094298
  • 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 | 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
  • 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 | 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 | 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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 | 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 | 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
  • 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 | 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, Vander Heiden, MG, 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 | 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
  • 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 | 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
  • 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
  • 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 | Signal integration and information transfer in an allosterically regulated network. Shockley, EM, Rouzer, CA, Marnett, LJ, Deeds, EJ, Lopez, CF NPJ Syst Biol Appl 5 : 23. doi: 10.1038/s41540-019-0100-9. PubMed PMID:31341635 PubMed Central PMC6639376
  • 2020 | The Mitochondrion as an Emerging Therapeutic Target in Cancer. Roth, KG, Mambetsariev, I, Kulkarni, P, Salgia, R Trends Mol Med 26 (1): 119-134. doi: 10.1016/j.molmed.2019.06.009. PubMed PMID:31327706 PubMed Central PMC6938552
  • 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 | Targeted treatment of papillary craniopharyngiomas harboring BRAF V600E mutations. Juratli, TA, Jones, PS, Wang, N, Subramanian, M, Aylwin, SJB, Odia, Y, Rostami, E, Gudjonsson, O, Shaw, BL, Cahill, DP, Galanis, E, Barker, FG 2nd, Santagata, S, Brastianos, PK Cancer 125 (17): 2910-2914. doi: 10.1002/cncr.32197. PubMed PMID:31314136 PubMed Central PMC7032527
  • 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 | Engineered 3D Model of Cancer Stem Cell Enrichment and Chemoresistance. Ward Rashidi, MR, Mehta, P, Bregenzer, M, Raghavan, S, Fleck, EM, Horst, EN, Harissa, Z, Ravikumar, V, Brady, S, Bild, A, Rao, A, Buckanovich, RJ, Mehta, G Neoplasia 21 (8): 822-836. doi: 10.1016/j.neo.2019.06.005. PubMed PMID:31299607 PubMed Central PMC6624324
  • 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 | Dynamic secretome of bone marrow-derived stromal cells reveals a cardioprotective biochemical cocktail. Kshitiz,, Ellison, DD, Suhail, Y, Afzal, J, Woo, L, Kilic, O, Spees, J, Levchenko, A Proc. Natl. Acad. Sci. U.S.A. 116 (28): 14374-14383. doi: 10.1073/pnas.1902598116. PubMed PMID:31239339 PubMed Central PMC6628676
  • 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 | ProteinNet: a standardized data set for machine learning of protein structure. AlQuraishi, M BMC Bioinformatics 20 (1): 311. doi: 10.1186/s12859-019-2932-0. PubMed PMID:31185886 PubMed Central PMC6560865
  • 2019 | 3D Analysis of Multi-cellular Responses to Chemoattractant Gradients. Kang, TY, Ellison, D, Lee, SH, Ewald, AJ, Levchenko, A J Vis Exp (147): . doi: 10.3791/59226. PubMed PMID:31180367
  • 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 | Multiomics Profiling Establishes the Polypharmacology of FDA-Approved CDK4/6 Inhibitors and the Potential for Differential Clinical Activity. Hafner, M, Mills, CE, Subramanian, K, Chen, C, Chung, M, Boswell, SA, Everley, RA, Liu, C, Walmsley, CS, Juric, D, Sorger, PK Cell Chem Biol 26 (8): 1067-1080.e8. doi: 10.1016/j.chembiol.2019.05.005. PubMed PMID:31178407 PubMed Central PMC6936329
  • 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
  • 2020 | An update on the CNS manifestations of neurofibromatosis type 2. Coy, S, Rashid, R, Stemmer-Rachamimov, A, Santagata, S Acta Neuropathol. 139 (4): 643-665. doi: 10.1007/s00401-019-02029-5. PubMed PMID:31161239 PubMed Central PMC7038792
  • 2019 | Mapping phospho-catalytic dependencies of therapy-resistant tumours reveals actionable vulnerabilities. Coppé, JP, Mori, M, Pan, B, Yau, C, Wolf, DM, Ruiz-Saenz, A, Brunen, D, Prahallad, A, Cornelissen-Steijger, P, Kemper, K, Posch, C, Wang, C, Dreyer, CA, Krijgsman, O, Lee, PRE, Chen, Z, Peeper, DS, Moasser, MM, Bernards, R, van 't Veer, LJ Nat. Cell Biol. 21 (6): 778-790. doi: 10.1038/s41556-019-0328-z. PubMed PMID:31160710 PubMed Central PMC7170003
  • 2019 | Neuronal differentiation and cell-cycle programs mediate response to BET-bromodomain inhibition in MYC-driven medulloblastoma. Bandopadhayay, P, Piccioni, F, O'Rourke, R, Ho, P, Gonzalez, EM, Buchan, G, Qian, K, Gionet, G, Girard, E, Coxon, M, Rees, MG, Brenan, L, Dubois, F, Shapira, O, Greenwald, NF, Pages, M, Balboni Iniguez, A, Paolella, BR, Meng, A, Sinai, C, Roti, G, Dharia, NV, Creech, A, Tanenbaum, B, Khadka, P, Tracy, A, Tiv, HL, Hong, AL, Coy, S, Rashid, R, Lin, JR, Cowley, GS, Lam, FC, Goodale, A, Lee, Y, Schoolcraft, K, Vazquez, F, Hahn, WC, Tsherniak, A, Bradner, JE, Yaffe, MB, Milde, T, Pfister, SM, Qi, J, Schenone, M, Carr, SA, Ligon, KL, Kieran, MW, Santagata, S, Olson, JM, Gokhale, PC, Jaffe, JD, Root, DE, Stegmaier, K, Johannessen, CM, Beroukhim, R Nat Commun 10 (1): 2400. doi: 10.1038/s41467-019-10307-9. PubMed PMID:31160565 PubMed Central PMC6546744
  • 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
  • 2019 | Augmentation of HIV-specific T cell function by immediate treatment of hyperacute HIV-1 infection. Ndhlovu, ZM, Kazer, SW, Nkosi, T, Ogunshola, F, Muema, DM, Anmole, G, Swann, SA, Moodley, A, Dong, K, Reddy, T, Brockman, MA, Shalek, AK, Ndung'u, T, Walker, BD Sci Transl Med 11 (493): . doi: 10.1126/scitranslmed.aau0528. PubMed PMID:31118290 PubMed Central PMC6901350
  • 2019 | NeoPredPipe: high-throughput neoantigen prediction and recognition potential pipeline. Schenck, RO, Lakatos, E, Gatenbee, C, Graham, TA, Anderson, ARA BMC Bioinformatics 20 (1): 264. doi: 10.1186/s12859-019-2876-4. PubMed PMID:31117948 PubMed Central PMC6532147
  • 2019 | AlphaFold at CASP13. AlQuraishi, M Bioinformatics 35 (22): 4862-4865. doi: 10.1093/bioinformatics/btz422. PubMed PMID:31116374 PubMed Central PMC6907002
  • 2019 | Characterizing ABC-Transporter Substrate-Likeness Using a Clean-Slate Genetic Background. Sokolov, A, Ashenden, S, Sahin, N, Lewis, R, Erdem, N, Ozaltan, E, Bender, A, Roth, FP, Cokol, M Front Pharmacol 10 : 448. doi: 10.3389/fphar.2019.00448. PubMed PMID:31105571 PubMed Central PMC6494965
  • 2019 | Time-dependent antagonist-agonist switching in receptor tyrosine kinase-mediated signaling. Ghosh, A, Radhakrishnan, R BMC Bioinformatics 20 (1): 242. doi: 10.1186/s12859-019-2816-3. PubMed PMID:31092187 PubMed Central PMC6521356
  • 2019 | Single-Cell Analysis of the Liver Epithelium Reveals Dynamic Heterogeneity and an Essential Role for YAP in Homeostasis and Regeneration. Pepe-Mooney, BJ, Dill, MT, Alemany, A, Ordovas-Montanes, J, Matsushita, Y, Rao, A, Sen, A, Miyazaki, M, Anakk, S, Dawson, PA, Ono, N, Shalek, AK, van Oudenaarden, A, Camargo, FD Cell Stem Cell 25 (1): 23-38.e8. doi: 10.1016/j.stem.2019.04.004. PubMed PMID:31080134 PubMed Central PMC6814390
  • 2019 | Adaptation of Human iPSC-Derived Cardiomyocytes to Tyrosine Kinase Inhibitors Reduces Acute Cardiotoxicity via Metabolic Reprogramming. Wang, H, Sheehan, RP, Palmer, AC, Everley, RA, Boswell, SA, Ron-Harel, N, Ringel, AE, Holton, KM, Jacobson, CA, Erickson, AR, Maliszewski, L, Haigis, MC, Sorger, PK Cell Syst 8 (5): 412-426.e7. doi: 10.1016/j.cels.2019.03.009. PubMed PMID:31078528 PubMed Central PMC6657491
  • 2019 | Picturing Polarized Myeloid Phagocytes and Regulatory Cells by Mass Cytometry. Roussel, M, Bartkowiak, T, Irish, JM Methods Mol. Biol. 1989 : 217-226. doi: 10.1007/978-1-4939-9454-0_14. PubMed PMID:31077108 PubMed Central PMC6886519
  • 2019 | Going to extremes: determinants of extraordinary response and survival in patients with cancer. Saner, FAM, Herschtal, A, Nelson, BH, deFazio, A, Goode, EL, Ramus, SJ, Pandey, A, Beach, JA, Fereday, S, Berchuck, A, Lheureux, S, Pearce, CL, Pharoah, PD, Pike, MC, Garsed, DW, Bowtell, DDL Nat. Rev. Cancer 19 (6): 339-348. doi: 10.1038/s41568-019-0145-5. PubMed PMID:31076661 PubMed Central PMC7255796
  • 2019 | Return to the Sea, Get Huge, Beat Cancer: An Analysis of Cetacean Genomes Including an Assembly for the Humpback Whale (Megaptera novaeangliae). Tollis, M, Robbins, J, Webb, AE, Kuderna, LFK, Caulin, AF, Garcia, JD, Bèrubè, M, Pourmand, N, Marques-Bonet, T, O'Connell, MJ, Palsbøll, PJ, Maley, CC Mol. Biol. Evol. 36 (8): 1746-1763. doi: 10.1093/molbev/msz099. PubMed PMID:31070747 PubMed Central PMC6657726
  • 2019 | Multiplexed, Sequential Secretion Analysis of the Same Single Cells Reveals Distinct Effector Response Dynamics Dependent on the Initial Basal State. Chen, Z, Lu, Y, Zhang, K, Xiao, Y, Lu, J, Fan, R Adv Sci (Weinh) 6 (9): 1801361. doi: 10.1002/advs.201801361. PubMed PMID:31065513 PubMed Central PMC6498135
  • 2019 | Mammalian cell growth dynamics in mitosis. Miettinen, TP, Kang, JH, Yang, LF, Manalis, SR Elife 8 : . doi: 10.7554/eLife.44700. PubMed PMID:31063131 PubMed Central PMC6534395
  • 2019 | Measuring Clonal Evolution in Cancer with Genomics. Williams, MJ, Sottoriva, A, Graham, TA Annu Rev Genomics Hum Genet 20 : 309-329. doi: 10.1146/annurev-genom-083117-021712. PubMed PMID:31059289
  • 2019 | The Small GTPase ARF6 Activates PI3K in Melanoma to Induce a Prometastatic State. Yoo, JH, Brady, SW, Acosta-Alvarez, L, Rogers, A, Peng, J, Sorensen, LK, Wolff, RK, Mleynek, T, Shin, D, Rich, CP, Kircher, DA, Bild, A, Odelberg, SJ, Li, DY, Holmen, SL, Grossmann, AH Cancer Res. 79 (11): 2892-2908. doi: 10.1158/0008-5472.CAN-18-3026. PubMed PMID:31048499 PubMed Central PMC7197377
  • 2019 | Mechanisms of Lymphoma Clearance Induced by High-Dose Alkylating Agents. Lossos, C, Liu, Y, Kolb, KE, Christie, AL, Van Scoyk, A, Prakadan, SM, Shigemori, K, Stevenson, KE, Morrow, S, Plana, OD, Fraser, C, Jones, KL, Liu, H, Pallasch, CP, Modiste, R, Nguyen, QD, Craig, JW, Morgan, EA, Vega, F, Aster, JC, Sarosiek, KA, Shalek, AK, Hemann, MT, Weinstock, DM Cancer Discov 9 (7): 944-961. doi: 10.1158/2159-8290.CD-18-1393. PubMed PMID:31040105 PubMed Central PMC6606344
  • 2019 | Seq-Well: A Sample-Efficient, Portable Picowell Platform for Massively Parallel Single-Cell RNA Sequencing. Aicher, TP, Carroll, S, Raddi, G, Gierahn, T, Wadsworth, MH 2nd, Hughes, TK, Love, C, Shalek, AK Methods Mol. Biol. 1979 : 111-132. doi: 10.1007/978-1-4939-9240-9_8. PubMed PMID:31028635
  • 2019 | Natural Genetic Variation Reveals Key Features of Epigenetic and Transcriptional Memory in Virus-Specific CD8 T Cells. van der Veeken, J, Zhong, Y, Sharma, R, Mazutis, L, Dao, P, Pe'er, D, Leslie, CS, Rudensky, AY Immunity 50 (5): 1202-1217.e7. doi: 10.1016/j.immuni.2019.03.031. PubMed PMID:31027997 PubMed Central PMC7023907
  • 2019 | Clonal hematopoiesis of indeterminate potential and its impact on patient trajectories after stem cell transplantation. Park, DS, Akuffo, AA, Muench, DE, Grimes, HL, Epling-Burnette, PK, Maini, PK, Anderson, ARA, Bonsall, MB PLoS Comput. Biol. 15 (4): e1006913. doi: 10.1371/journal.pcbi.1006913. PubMed PMID:31026273 PubMed Central PMC6505959
  • 2019 | Ex vivo Dynamics of Human Glioblastoma Cells in a Microvasculature-on-a-Chip System Correlates with Tumor Heterogeneity and Subtypes. Xiao, Y, Kim, D, Dura, B, Zhang, K, Yan, R, Li, H, Han, E, Ip, J, Zou, P, Liu, J, Chen, AT, Vortmeyer, AO, Zhou, J, Fan, R Adv Sci (Weinh) 6 (8): 1801531. doi: 10.1002/advs.201801531. PubMed PMID:31016107 PubMed Central PMC6468969
  • 2019 | Improved model prediction of glioma growth utilizing tissue-specific boundary effects. Jacobs, J, Rockne, RC, Hawkins-Daarud, AJ, Jackson, PR, Johnston, SK, Kinahan, P, Swanson, KR Math Biosci 312 : 59-66. doi: 10.1016/j.mbs.2019.04.004. PubMed PMID:31009624
  • 2019 | End-to-End Differentiable Learning of Protein Structure. AlQuraishi, M Cell Syst 8 (4): 292-301.e3. doi: 10.1016/j.cels.2019.03.006. PubMed PMID:31005579 PubMed Central PMC6513320
  • 2019 | Resistance to neoadjuvant chemotherapy in triple-negative breast cancer mediated by a reversible drug-tolerant state. Echeverria, GV, Ge, Z, Seth, S, Zhang, X, Jeter-Jones, S, Zhou, X, Cai, S, Tu, Y, McCoy, A, Peoples, M, Sun, Y, Qiu, H, Chang, Q, Bristow, C, Carugo, A, Shao, J, Ma, X, Harris, A, Mundi, P, Lau, R, Ramamoorthy, V, Wu, Y, Alvarez, MJ, Califano, A, Moulder, SL, Symmans, WF, Marszalek, JR, Heffernan, TP, Chang, JT, Piwnica-Worms, H Sci Transl Med 11 (488): . doi: 10.1126/scitranslmed.aav0936. PubMed PMID:30996079 PubMed Central PMC6541393
  • 2019 | BRCA1 mutations attenuate super-enhancer function and chromatin looping in haploinsufficient human breast epithelial cells. Zhang, X, Wang, Y, Chiang, HC, Hsieh, YP, Lu, C, Park, BH, Jatoi, I, Jin, VX, Hu, Y, Li, R Breast Cancer Res. 21 (1): 51. doi: 10.1186/s13058-019-1132-1. PubMed PMID:30995943 PubMed Central PMC6472090
  • 2019 | The 2019 mathematical oncology roadmap. Rockne, RC, Hawkins-Daarud, A, Swanson, KR, Sluka, JP, Glazier, JA, Macklin, P, Hormuth, DA, Jarrett, AM, Lima, EABF, Tinsley Oden, J, Biros, G, Yankeelov, TE, Curtius, K, Al Bakir, I, Wodarz, D, Komarova, N, Aparicio, L, Bordyuh, M, Rabadan, R, Finley, SD, Enderling, H, Caudell, J, Moros, EG, Anderson, ARA, Gatenby, RA, Kaznatcheev, A, Jeavons, P, Krishnan, N, Pelesko, J, Wadhwa, RR, Yoon, N, Nichol, D, Marusyk, A, Hinczewski, M, Scott, JG Phys Biol 16 (4): 041005. doi: 10.1088/1478-3975/ab1a09. PubMed PMID:30991381 PubMed Central PMC6655440
  • 2019 | Leveraging Compound Promiscuity to Identify Targetable Cysteines within the Kinome. Rao, S, Gurbani, D, Du, G, Everley, RA, Browne, CM, Chaikuad, A, Tan, L, Schröder, M, Gondi, S, Ficarro, SB, Sim, T, Kim, ND, Berberich, MJ, Knapp, S, Marto, JA, Westover, KD, Sorger, PK, Gray, NS Cell Chem Biol 26 (6): 818-829.e9. doi: 10.1016/j.chembiol.2019.02.021. PubMed PMID:30982749 PubMed Central PMC6634314
  • 2019 | Computational algorithms for in silico profiling of activating mutations in cancer. Jordan, EJ, Patil, K, Suresh, K, Park, JH, Mosse, YP, Lemmon, MA, Radhakrishnan, R Cell. Mol. Life Sci. 76 (14): 2663-2679. doi: 10.1007/s00018-019-03097-2. PubMed PMID:30982079 PubMed Central PMC6589134
  • 2019 | Single-Cell Protein Secretion Detection and Profiling. Chen, Z, Chen, JJ, Fan, R Annu Rev Anal Chem (Palo Alto Calif) 12 (1): 431-449. doi: 10.1146/annurev-anchem-061318-115055. PubMed PMID:30978293
  • 2019 | Complete Regression of Advanced Pancreatic Ductal Adenocarcinomas upon Combined Inhibition of EGFR and C-RAF. Blasco, MT, Navas, C, Martín-Serrano, G, Graña-Castro, O, Lechuga, CG, Martín-Díaz, L, Djurec, M, Li, J, Morales-Cacho, L, Esteban-Burgos, L, Perales-Patón, J, Bousquet-Mur, E, Castellano, E, Jacob, HKC, Cabras, L, Musteanu, M, Drosten, M, Ortega, S, Mulero, F, Sainz, B Jr, Dusetti, N, Iovanna, J, Sánchez-Bueno, F, Hidalgo, M, Khiabanian, H, Rabadán, R, Al-Shahrour, F, Guerra, C, Barbacid, M Cancer Cell 35 (4): 573-587.e6. doi: 10.1016/j.ccell.2019.03.002. PubMed PMID:30975481
  • 2019 | In vivo profiling of metastatic double knockouts through CRISPR-Cpf1 screens. Chow, RD, Wang, G, Ye, L, Codina, A, Kim, HR, Shen, L, Dong, MB, Errami, Y, Chen, S Nat. Methods 16 (5): 405-408. doi: 10.1038/s41592-019-0371-5. PubMed PMID:30962622 PubMed Central PMC6592845
  • 2019 | Leukemia Inhibitory Factor Promotes Castration-resistant Prostate Cancer and Neuroendocrine Differentiation by Activated ZBTB46. Liu, YN, Niu, S, Chen, WY, Zhang, Q, Tao, Y, Chen, WH, Jiang, KC, Chen, X, Shi, H, Liu, A, Li, J, Li, Y, Lee, YC, Zhang, X, Huang, J Clin. Cancer Res. 25 (13): 4128-4140. doi: 10.1158/1078-0432.CCR-18-3239. PubMed PMID:30962287 PubMed Central PMC7168873
  • 2019 | Tissue-Specific Oncogenic Activity of KRASA146T. Poulin, EJ, Bera, AK, Lu, J, Lin, YJ, Strasser, SD, Paulo, JA, Huang, TQ, Morales, C, Yan, W, Cook, J, Nowak, JA, Brubaker, DK, Joughin, BA, Johnson, CW, DeStefanis, RA, Ghazi, PC, Gondi, S, Wales, TE, Iacob, RE, Bogdanova, L, Gierut, JJ, Li, Y, Engen, JR, Perez-Mancera, PA, Braun, BS, Gygi, SP, Lauffenburger, DA, Westover, KD, Haigis, KM Cancer Discov 9 (6): 738-755. doi: 10.1158/2159-8290.CD-18-1220. PubMed PMID:30952657 PubMed Central PMC6548671
  • 2019 | Temporal dynamic reorganization of 3D chromatin architecture in hormone-induced breast cancer and endocrine resistance. Zhou, Y, Gerrard, DL, Wang, J, Li, T, Yang, Y, Fritz, AJ, Rajendran, M, Fu, X, Stein, G, Schiff, R, Lin, S, Frietze, S, Jin, VX Nat Commun 10 (1): 1522. doi: 10.1038/s41467-019-09320-9. PubMed PMID:30944316 PubMed Central PMC6447566
  • 2019 | Progesterone Receptor Attenuates STAT1-Mediated IFN Signaling in Breast Cancer. Goodman, ML, Trinca, GM, Walter, KR, Papachristou, EK, D'Santos, CS, Li, T, Liu, Q, Lai, Z, Chalise, P, Madan, R, Fan, F, Markiewicz, MA, Jin, VX, Carroll, JS, Hagan, CR J. Immunol. 202 (10): 3076-3086. doi: 10.4049/jimmunol.1801152. PubMed PMID:30936295 PubMed Central PMC6504603
  • 2019 | SOX11 hypermethylation as a tumor biomarker in endometrial cancer. Shan, T, Uyar, DS, Wang, LS, Mutch, DG, Huang, TH, Rader, JS, Sheng, X, Huang, YW Biochimie 162 : 8-14. doi: 10.1016/j.biochi.2019.03.019. PubMed PMID:30935961 PubMed Central PMC6561798
  • 2019 | Molecular subtypes of small cell lung cancer: a synthesis of human and mouse model data. Rudin, CM, Poirier, JT, Byers, LA, Dive, C, Dowlati, A, George, J, Heymach, JV, Johnson, JE, Lehman, JM, MacPherson, D, Massion, PP, Minna, JD, Oliver, TG, Quaranta, V, Sage, J, Thomas, RK, Vakoc, CR, Gazdar, AF Nat. Rev. Cancer 19 (5): 289-297. doi: 10.1038/s41568-019-0133-9. PubMed PMID:30926931 PubMed Central PMC6538259
  • 2019 | Moving Toward a Consensus DSC-MRI Protocol: Validation of a Low-Flip Angle Single-Dose Option as a Reference Standard for Brain Tumors. Schmainda, KM, Prah, MA, Hu, LS, Quarles, CC, Semmineh, N, Rand, SD, Connelly, JM, Anderies, B, Zhou, Y, Liu, Y, Logan, B, Stokes, A, Baird, G, Boxerman, JL AJNR Am J Neuroradiol 40 (4): 626-633. doi: 10.3174/ajnr.A6015. PubMed PMID:30923088 PubMed Central PMC6461489
  • 2019 | Stress-Induced Evolutionary Innovation: A Mechanism for the Origin of Cell Types. Wagner, GP, Erkenbrack, EM, Love, AC Bioessays 41 (4): e1800188. doi: 10.1002/bies.201800188. PubMed PMID:30919472 PubMed Central PMC7202399
  • 2019 | Tumorigenesis as the Paradigm of Quasi-neutral Molecular Evolution. Chen, B, Shi, Z, Chen, Q, Shen, X, Shibata, D, Wen, H, Wu, CI Mol. Biol. Evol. 36 (7): 1430-1441. doi: 10.1093/molbev/msz075. PubMed PMID:30912799
  • 2019 | In situ 10-cell RNA sequencing in tissue and tumor biopsy samples. Singh, S, Wang, L, Schaff, DL, Sutcliffe, MD, Koeppel, AF, Kim, J, Onengut-Gumuscu, S, Park, KS, Zong, H, Janes, KA Sci Rep 9 (1): 4836. doi: 10.1038/s41598-019-41235-9. PubMed PMID:30894605 PubMed Central PMC6426952
  • 2019 | Multiple ABCB1 transcriptional fusions in drug resistant high-grade serous ovarian and breast cancer. Christie, EL, Pattnaik, S, Beach, J, Copeland, A, Rashoo, N, Fereday, S, Hendley, J, Alsop, K, Brady, SL, Lamb, G, Pandey, A, deFazio, A, Thorne, H, Bild, A, Bowtell, DDL Nat Commun 10 (1): 1295. doi: 10.1038/s41467-019-09312-9. PubMed PMID:30894541 PubMed Central PMC6426934
  • 2019 | Therapeutic Clues from an Integrated Omic Assessment of East Asian Triple Negative Breast Cancers. Heiser, LM, Mills, GB, Gray, JW Cancer Cell 35 (3): 341-343. doi: 10.1016/j.ccell.2019.02.012. PubMed PMID:30889376 PubMed Central PMC6499473
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