CSBC Supported Publications

Publications

  • 2021 | Elevated fibroblast growth factor-inducible 14 expression transforms proneural-like gliomas into more aggressive and lethal brain cancer. Connolly, NP, Galisteo, R, Xu, S, Bar, EE, Peng, S, Tran, NL, Ames, HM, Kim, AJ, Woodworth, GF, Winkles, JA Glia : . doi: 10.1002/glia.24018. PubMed PMID:33991013
  • 2021 | Therapeutically reprogrammed nutrient signalling enhances nanoparticulate albumin bound drug uptake and efficacy in KRAS-mutant cancer. Li, R, Ng, TSC, Wang, SJ, Prytyskach, M, Rodell, CB, Mikula, H, Kohler, RH, Garlin, MA, Lauffenburger, DA, Parangi, S, Dinulescu, DM, Bardeesy, N, Weissleder, R, Miller, MA Nat Nanotechnol : . doi: 10.1038/s41565-021-00897-1. PubMed PMID:33958764
  • 2021 | Systematic interrogation of mutation groupings reveals divergent downstream expression programs within key cancer genes. Grzadkowski, MR, Holly, HD, Somers, J, Demir, E BMC Bioinformatics 22 (1): 233. doi: 10.1186/s12859-021-04147-y. PubMed PMID:33957863 PubMed Central PMC8101181
  • 2021 | Evolution of delayed resistance to immunotherapy in a melanoma responder. Liu, D, Lin, JR, Robitschek, EJ, Kasumova, GG, Heyde, A, Shi, A, Kraya, A, Zhang, G, Moll, T, Frederick, DT, Chen, YA, Wang, S, Schapiro, D, Ho, LL, Bi, K, Sahu, A, Mei, S, Miao, B, Sharova, T, Alvarez-Breckenridge, C, Stocking, JH, Kim, T, Fadden, R, Lawrence, D, Hoang, MP, Cahill, DP, Malehmir, M, Nowak, MA, Brastianos, PK, Lian, CG, Ruppin, E, Izar, B, Herlyn, M, Van Allen, EM, Nathanson, K, Flaherty, KT, Sullivan, RJ, Kellis, M, Sorger, PK, Boland, GM Nat Med : . doi: 10.1038/s41591-021-01331-8. PubMed PMID:33941922
  • 2021 | ZTCG: Viruses expand the genetic alphabet. Grome, MW, Isaacs, FJ Science 372 (6541): 460-461. doi: 10.1126/science.abh3571. PubMed PMID:33926938
  • 2021 | A Crisis-Responsive Framework for Medical Device Development Applied to the COVID-19 Pandemic. Antonini, MJ, Plana, D, Srinivasan, S, Atta, L, Achanta, A, Yang, H, Cramer, AK, Freake, J, Sinha, MS, Yu, SH, LeBoeuf, NR, Linville-Engler, B, Sorger, PK Front Digit Health 3 : . doi: 10.3389/fdgth.2021.617106. PubMed PMID:33899045 PubMed Central PMC8064560
  • 2021 | Disruption of the HER3-PI3K-mTOR oncogenic signaling axis and PD-1 blockade as a multimodal precision immunotherapy in head and neck cancer. Wang, Z, Goto, Y, Allevato, MM, Wu, VH, Saddawi-Konefka, R, Gilardi, M, Alvarado, D, Yung, BS, O'Farrell, A, Molinolo, AA, Duvvuri, U, Grandis, JR, Califano, JA, Cohen, EEW, Gutkind, JS Nat Commun 12 (1): 2383. doi: 10.1038/s41467-021-22619-w. PubMed PMID:33888713 PubMed Central PMC8062674
  • 2021 | Dual blockade of EGFR and CDK4/6 delays head and neck squamous cell carcinoma progression by inducing metabolic rewiring. Chaudhary, S, Pothuraju, R, Rachagani, S, Siddiqui, JA, Atri, P, Mallya, K, Nasser, MW, Sayed, Z, Lyden, ER, Smith, L, Gupta, SD, Ralhan, R, Lakshmanan, I, Jones, DT, Ganti, AK, Macha, MA, Batra, SK Cancer Lett 510 : 79-92. doi: 10.1016/j.canlet.2021.04.004. PubMed PMID:33878394
  • 2021 | Utility of Circulating Tumor DNA in Identifying Somatic Mutations and Tracking Tumor Evolution in Patients with Non-small Cell Lung Cancer. Roosan, MR, Mambetsariev, I, Pharaon, R, Fricke, J, Husain, H, Reckamp, KL, Koczywas, M, Massarelli, E, Bild, AH, Salgia, R Chest : . doi: 10.1016/j.chest.2021.04.016. PubMed PMID:33878340
  • 2021 | A theoretical analysis of tumour containment. Viossat, Y, Noble, R Nat Ecol Evol : . doi: 10.1038/s41559-021-01428-w. PubMed PMID:33846605
  • 2021 | Automated quality control and cell identification of droplet-based single-cell data using dropkick. Heiser, CN, Wang, VM, Chen, B, Hughey, JJ, Lau, KS Genome Res : . doi: 10.1101/gr.271908.120. PubMed PMID:33837131
  • 2020 | Spatial mapping of single cells in the Drosophila embryo from transcriptomic data based on topological consistency. Zand, M, Ruan, J F1000Res 9 : 1014. doi: 10.12688/f1000research.24163.2. PubMed PMID:33824719 PubMed Central PMC7993407
  • 2021 | Normal tissue architecture determines the evolutionary course of cancer. West, J, Schenck, RO, Gatenbee, C, Robertson-Tessi, M, Anderson, ARA Nat Commun 12 (1): 2060. doi: 10.1038/s41467-021-22123-1. PubMed PMID:33824323 PubMed Central PMC8024392
  • 2021 | De novo Powered Air-Purifying Respirator Design and Fabrication for Pandemic Response. Kothakonda, A, Atta, L, Plana, D, Ward, F, Davis, C, Cramer, A, Moran, R, Freake, J, Tian, E, Mazor, O, Gorelik, P, Van, C, Hansen, C, Yang, H, Sinha, MS, Li, J, Yu, SH, LeBoeuf, NR, Sorger, PK medRxiv : . doi: 10.1101/2021.03.25.21252076. PubMed PMID:33821290 PubMed Central PMC8020994
  • 2021 | A survey of multiscale modeling: Foundations, historical milestones, current status, and future prospects. Radhakrishnan, R AIChE J 67 (3): e17026. doi: 10.1002/aic.17026. PubMed PMID:33790479 PubMed Central PMC7988612
  • 2021 | Creating collaboration by breaking down scientific barriers. Fabius, JM, Krogan, NJ Cell 184 (9): 2271-2275. doi: 10.1016/j.cell.2021.02.022. PubMed PMID:33765441
  • 2021 | Time-resolved phosphoproteomics reveals scaffolding and catalysis-responsive patterns of SHP2-dependent signaling. Vemulapalli, V, Chylek, LA, Erickson, A, Pfeiffer, A, Gabriel, KH, LaRochelle, J, Subramanian, K, Cao, R, Stegmaier, K, Mohseni, M, LaMarche, MJ, Acker, MG, Sorger, PK, Gygi, SP, Blacklow, SC Elife 10 : . doi: 10.7554/eLife.64251. PubMed PMID:33755016 PubMed Central PMC8024022
  • 2021 | RNA-based therapies: A cog in the wheel of lung cancer defense. Khan, P, Siddiqui, JA, Lakshmanan, I, Ganti, AK, Salgia, R, Jain, M, Batra, SK, Nasser, MW Mol Cancer 20 (1): 54. doi: 10.1186/s12943-021-01338-2. PubMed PMID:33740988 PubMed Central PMC7977189
  • 2021 | Targeting immunosuppressive macrophages overcomes PARP inhibitor resistance in BRCA1-associated triple-negative breast cancer. Mehta, AK, Cheney, EM, Hartl, CA, Pantelidou, C, Oliwa, M, Castrillon, JA, Lin, JR, Hurst, KE, de Oliveira Taveira, M, Johnson, NT, Oldham, WM, Kalocsay, M, Berberich, MJ, Boswell, SA, Kothari, A, Johnson, S, Dillon, DA, Lipschitz, M, Rodig, S, Santagata, S, Garber, JE, Tung, N, Yélamos, J, Thaxton, JE, Mittendorf, EA, Sorger, PK, Shapiro, GI, Guerriero, JL Nat Cancer 2 (1): 66-82. doi: 10.1038/s43018-020-00148-7. PubMed PMID:33738458 PubMed Central PMC7963404
  • 2021 | stochprofML: stochastic profiling using maximum likelihood estimation in R. Amrhein, L, Fuchs, C BMC Bioinformatics 22 (1): 123. doi: 10.1186/s12859-021-03970-7. PubMed PMID:33722188 PubMed Central PMC7958472
  • 2020 | Flipped Science Fair: Engaging Middle-School Students in STEM while Training Researchers in Science Communication. Benedetti, L, Crouse, RB J STEM Outreach 3 (1): . doi: 10.15695/jstem/v3i1.10. PubMed PMID:33718806 PubMed Central PMC7951179
  • 2021 | Novel evolutionary dynamics of small populations in breast cancer adjuvant and neoadjuvant therapy. Artzy-Randrup, Y, Epstein, T, Brown, JS, Costa, RLB, Czerniecki, BJ, Gatenby, RA NPJ Breast Cancer 7 (1): 26. doi: 10.1038/s41523-021-00230-y. PubMed PMID:33707440 PubMed Central PMC7952601
  • 2021 | ATM and ATR Activation Through Crosstalk Between DNA Damage Response Pathways. Fedak, EA, Adler, FR, Abegglen, LM, Schiffman, JD Bull Math Biol 83 (4): 38. doi: 10.1007/s11538-021-00868-6. PubMed PMID:33704589 PubMed Central PMC8051223
  • 2021 | Knowledge-based classification of fine-grained immune cell types in single-cell RNA-Seq data. Liu, X, Gosline, SJC, Pflieger, LT, Wallet, P, Iyer, A, Guinney, J, Bild, AH, Chang, JT Brief Bioinform : . doi: 10.1093/bib/bbab039. PubMed PMID:33681983
  • 2021 | Computational studies of anaplastic lymphoma kinase mutations reveal common mechanisms of oncogenic activation. Patil, K, Jordan, EJ, Park, JH, Suresh, K, Smith, CM, Lemmon, AA, Mossé, YP, Lemmon, MA, Radhakrishnan, R Proc Natl Acad Sci U S A 118 (10): . doi: 10.1073/pnas.2019132118. PubMed PMID:33674381 PubMed Central PMC7958353
  • 2021 | A CRISPR RNA-binding protein screen reveals regulators of RUNX1 isoform generation. Davis, AG, Einstein, JM, Zheng, D, Jayne, ND, Fu, XD, Tian, B, Yeo, GW, Zhang, DE Blood Adv 5 (5): 1310-1323. doi: 10.1182/bloodadvances.2020002090. PubMed PMID:33656539 PubMed Central PMC7948294
  • 2021 | Multimodal pooled Perturb-CITE-seq screens in patient models define mechanisms of cancer immune evasion. Frangieh, CJ, Melms, JC, Thakore, PI, Geiger-Schuller, KR, Ho, P, Luoma, AM, Cleary, B, Jerby-Arnon, L, Malu, S, Cuoco, MS, Zhao, M, Ager, CR, Rogava, M, Hovey, L, Rotem, A, Bernatchez, C, Wucherpfennig, KW, Johnson, BE, Rozenblatt-Rosen, O, Schadendorf, D, Regev, A, Izar, B Nat Genet 53 (3): 332-341. doi: 10.1038/s41588-021-00779-1. PubMed PMID:33649592
  • 2021 | Unmasking the immune microecology of ductal carcinoma in situ with deep learning. Narayanan, PL, Raza, SEA, Hall, AH, Marks, JR, King, L, West, RB, Hernandez, L, Guppy, N, Dowsett, M, Gusterson, B, Maley, C, Hwang, ES, Yuan, Y NPJ Breast Cancer 7 (1): 19. doi: 10.1038/s41523-020-00205-5. PubMed PMID:33649333 PubMed Central PMC7921670
  • 2021 | Variability within rare cell states enables multiple paths toward drug resistance. Emert, BL, Cote, CJ, Torre, EA, Dardani, IP, Jiang, CL, Jain, N, Shaffer, SM, Raj, A Nat Biotechnol : . doi: 10.1038/s41587-021-00837-3. PubMed PMID:33619394
  • 2021 | Stability Analysis of a Signaling Circuit with Dual Species of GTPase Switches. Stolerman, LM, Ghosh, P, Rangamani, P Bull Math Biol 83 (4): 34. doi: 10.1007/s11538-021-00864-w. PubMed PMID:33609194
  • 2021 | Regulation of PTEN translation by PI3K signaling maintains pathway homeostasis. Mukherjee, R, Vanaja, KG, Boyer, JA, Gadal, S, Solomon, H, Chandarlapaty, S, Levchenko, A, Rosen, N Mol Cell 81 (4): 708-723.e5. doi: 10.1016/j.molcel.2021.01.033. PubMed PMID:33606974
  • 2021 | An in vitro vascularized micro-tumor model of human colorectal cancer recapitulates in vivo responses to standard-of-care therapy. Hachey, SJ, Movsesyan, S, Nguyen, QH, Burton-Sojo, G, Tankazyan, A, Wu, J, Hoang, T, Zhao, D, Wang, S, Hatch, MM, Celaya, E, Gomez, S, Chen, GT, Davis, RT, Nee, K, Pervolarakis, N, Lawson, DA, Kessenbrock, K, Lee, AP, Lowengrub, J, Waterman, ML, Hughes, CCW Lab Chip 21 (7): 1333-1351. doi: 10.1039/d0lc01216e. PubMed PMID:33605955
  • 2021 | Design and Characterization of an Intracellular Covalent Ligand for CC Chemokine Receptor 2. Ortiz Zacarías, NV, Chahal, KK, Šimková, T, van der Horst, C, Zheng, Y, Inoue, A, Theunissen, E, Mallee, L, van der Es, D, Louvel, J, IJzerman, AP, Handel, TM, Kufareva, I, Heitman, LH J Med Chem 64 (5): 2608-2621. doi: 10.1021/acs.jmedchem.0c01137. PubMed PMID:33600174 PubMed Central PMC7958898
  • 2021 | Uncertainty quantification in the radiogenomics modeling of EGFR amplification in glioblastoma. Hu, LS, Wang, L, Hawkins-Daarud, A, Eschbacher, JM, Singleton, KW, Jackson, PR, Clark-Swanson, K, Sereduk, CP, Peng, S, Wang, P, Wang, J, Baxter, LC, Smith, KA, Mazza, GL, Stokes, AM, Bendok, BR, Zimmerman, RS, Krishna, C, Porter, AB, Mrugala, MM, Hoxworth, JM, Wu, T, Tran, NL, Swanson, KR, Li, J Sci Rep 11 (1): 3932. doi: 10.1038/s41598-021-83141-z. PubMed PMID:33594116 PubMed Central PMC7886858
  • 2021 | Machine learning identifies candidates for drug repurposing in Alzheimer's disease. Rodriguez, S, Hug, C, Todorov, P, Moret, N, Boswell, SA, Evans, K, Zhou, G, Johnson, NT, Hyman, BT, Sorger, PK, Albers, MW, Sokolov, A Nat Commun 12 (1): 1033. doi: 10.1038/s41467-021-21330-0. PubMed PMID:33589615 PubMed Central PMC7884393
  • 2021 | Leveraging Single-Cell Approaches in Cancer Precision Medicine. Nath, A, Bild, AH Trends Cancer 7 (4): 359-372. doi: 10.1016/j.trecan.2021.01.007. PubMed PMID:33563578 PubMed Central PMC7969443
  • 2021 | Evolved Resistance to Placental Invasion Secondarily Confers Increased Survival in Melanoma Patients. Suhail, Y, Afzal, J, Kshitiz, J Clin Med 10 (4): . doi: 10.3390/jcm10040595. PubMed PMID:33562461 PubMed Central PMC7915120
  • 2021 | Consensus Recommendations for MRI and PET Imaging of Primary Central Nervous System Lymphoma: Guideline Statement from the International Primary CNS Lymphoma Collaborative Group (IPCG). Barajas, RF Jr, Politi, LS, Anzalone, N, Schöder, H, Fox, CP, Boxerman, JL, Kaufmann, TJ, Quarles, CC, Ellingson, BM, Auer, D, Andronesi, OC, Ferreri, AJM, Mrugala, MM, Grommes, C, Neuwelt, EA, Ambady, P, Rubenstein, JL, Illerhaus, G, Nagane, M, Batchelor, TT, Hu, LS Neuro Oncol : . doi: 10.1093/neuonc/noab020. PubMed PMID:33560416
  • 2021 | shinyDepMap, a tool to identify targetable cancer genes and their functional connections from Cancer Dependency Map data. Shimada, K, Bachman, JA, Muhlich, JL, Mitchison, TJ Elife 10 : . doi: 10.7554/eLife.57116. PubMed PMID:33554860 PubMed Central PMC7924953
  • 2021 | Highly multiplexed tissue imaging using repeated oligonucleotide exchange reaction. Kennedy-Darling, J, Bhate, SS, Hickey, JW, Black, S, Barlow, GL, Vazquez, G, Venkataraaman, VG, Samusik, N, Goltsev, Y, Schürch, CM, Nolan, GP Eur J Immunol 51 (5): 1262-1277. doi: 10.1002/eji.202048891. PubMed PMID:33548142
  • 2021 | A gene-environment-induced epigenetic program initiates tumorigenesis. Alonso-Curbelo, D, Ho, YJ, Burdziak, C, Maag, JLV, Morris, JP 4th, Chandwani, R, Chen, HA, Tsanov, KM, Barriga, FM, Luan, W, Tasdemir, N, Livshits, G, Azizi, E, Chun, J, Wilkinson, JE, Mazutis, L, Leach, SD, Koche, R, Pe'er, D, Lowe, SW Nature 590 (7847): 642-648. doi: 10.1038/s41586-020-03147-x. PubMed PMID:33536616
  • 2021 | A Leucine-Rich Repeat Protein Provides a SHOC2 the RAS Circuit: a Structure-Function Perspective. Kwon, JJ, Hahn, WC Mol Cell Biol 41 (4): . doi: 10.1128/MCB.00627-20. PubMed PMID:33526449 PubMed Central PMC8088128
  • 2021 | The improbable targeted therapy: KRAS as an emerging target in non-small cell lung cancer (NSCLC). Salgia, R, Pharaon, R, Mambetsariev, I, Nam, A, Sattler, M Cell Rep Med 2 (1): 100186. doi: 10.1016/j.xcrm.2020.100186. PubMed PMID:33521700 PubMed Central PMC7817862
  • 2021 | Optimal experimental design for mathematical models of haematopoiesis. Lomeli, LM, Iniguez, A, Tata, P, Jena, N, Liu, ZY, Van Etten, R, Lander, AD, Shahbaba, B, Lowengrub, JS, Minin, VN J R Soc Interface 18 (174): 20200729. doi: 10.1098/rsif.2020.0729. PubMed PMID:33499768 PubMed Central PMC7879761
  • 2021 | PEtab-Interoperable specification of parameter estimation problems in systems biology. Schmiester, L, Schälte, Y, Bergmann, FT, Camba, T, Dudkin, E, Egert, J, Fröhlich, F, Fuhrmann, L, Hauber, AL, Kemmer, S, Lakrisenko, P, Loos, C, Merkt, S, Müller, W, Pathirana, D, Raimúndez, E, Refisch, L, Rosenblatt, M, Stapor, PL, Städter, P, Wang, D, Wieland, FG, Banga, JR, Timmer, J, Villaverde, AF, Sahle, S, Kreutz, C, Hasenauer, J, Weindl, D PLoS Comput Biol 17 (1): e1008646. doi: 10.1371/journal.pcbi.1008646. PubMed PMID:33497393 PubMed Central PMC7864467
  • 2021 | Opposing immune and genetic mechanisms shape oncogenic programs in synovial sarcoma. Jerby-Arnon, L, Neftel, C, Shore, ME, Weisman, HR, Mathewson, ND, McBride, MJ, Haas, B, Izar, B, Volorio, A, Boulay, G, Cironi, L, Richman, AR, Broye, LC, Gurski, JM, Luo, CC, Mylvaganam, R, Nguyen, L, Mei, S, Melms, JC, Georgescu, C, Cohen, O, Buendia-Buendia, JE, Segerstolpe, A, Sud, M, Cuoco, MS, Labes, D, Gritsch, S, Zollinger, DR, Ortogero, N, Beechem, JM, Petur Nielsen, G, Chebib, I, Nguyen-Ngoc, T, Montemurro, M, Cote, GM, Choy, E, Letovanec, I, Cherix, S, Wagle, N, Sorger, PK, Haynes, AB, Mullen, JT, Stamenkovic, I, Rivera, MN, Kadoch, C, Wucherpfennig, KW, Rozenblatt-Rosen, O, Suvà, ML, Riggi, N, Regev, A Nat Med 27 (2): 289-300. doi: 10.1038/s41591-020-01212-6. PubMed PMID:33495604
  • 2021 | GECO: gene expression clustering optimization app for non-linear data visualization of patterns. Habowski, AN, Habowski, TJ, Waterman, ML BMC Bioinformatics 22 (1): 29. doi: 10.1186/s12859-020-03951-2. PubMed PMID:33494695 PubMed Central PMC7831185
  • 2021 | Conversion of Existing UVB Phototherapy Units to UVC Germicidal Chambers for N95 Decontamination: Lessons Learned. Kassamali, B, Yu, Z, Davis, C, Carmack, M, Bui, AN, Said, JT, Plana, D, Yang, H, Sorger, P, LeBoeuf, NR, LaChance, AH Photobiomodul Photomed Laser Surg 39 (2): 83-85. doi: 10.1089/photob.2020.4968. PubMed PMID:33481669 PubMed Central PMC8106246
  • 2021 | Analysis of SteraMist ionized hydrogen peroxide technology in the sterilization of N95 respirators and other PPE. Cramer, AK, Plana, D, Yang, H, Carmack, MM, Tian, E, Sinha, MS, Krikorian, D, Turner, D, Mo, J, Li, J, Gupta, R, Manning, H, Bourgeois, FT, Yu, SH, Sorger, PK, LeBoeuf, NR Sci Rep 11 (1): 2051. doi: 10.1038/s41598-021-81365-7. PubMed PMID:33479334 PubMed Central PMC7819989
  • 2021 | Topsentinol L Trisulfate, a Marine Natural Product That Targets Basal-like and Claudin-Low Breast Cancers. El-Chaar, NN, Smith, TE, Shrestha, G, Piccolo, SR, Harper, MK, Van Wagoner, RM, Lu, Z, Venancio, AR, Ireland, CM, Bild, AH, Moos, PJ Mar Drugs 19 (1): . doi: 10.3390/md19010041. PubMed PMID:33477536 PubMed Central PMC7831112
  • 2021 | Personalized Genome-Scale Metabolic Models Identify Targets of Redox Metabolism in Radiation-Resistant Tumors. Lewis, JE, Forshaw, TE, Boothman, DA, Furdui, CM, Kemp, ML Cell Syst 12 (1): 68-81.e11. doi: 10.1016/j.cels.2020.12.001. PubMed PMID:33476554 PubMed Central PMC7905848
  • 2021 | The harsh microenvironment in early breast cancer selects for a Warburg phenotype. Damaghi, M, West, J, Robertson-Tessi, M, Xu, L, Ferrall-Fairbanks, MC, Stewart, PA, Persi, E, Fridley, BL, Altrock, PM, Gatenby, RA, Sims, PA, Anderson, ARA, Gillies, RJ Proc Natl Acad Sci U S A 118 (3): . doi: 10.1073/pnas.2011342118. PubMed PMID:33452133 PubMed Central PMC7826394
  • 2021 | HAND1 and BARX1 Act as Transcriptional and Anatomic Determinants of Malignancy in Gastrointestinal Stromal Tumor. Hemming, ML, Coy, S, Lin, JR, Andersen, JL, Przybyl, J, Mazzola, E, Abdelhamid Ahmed, AH, van de Rijn, M, Sorger, PK, Armstrong, SA, Demetri, GD, Santagata, S Clin Cancer Res 27 (6): 1706-1719. doi: 10.1158/1078-0432.CCR-20-3538. PubMed PMID:33451979 PubMed Central PMC7956056
  • 2021 | Small-cell lung cancer. Rudin, CM, Brambilla, E, Faivre-Finn, C, Sage, J Nat Rev Dis Primers 7 (1): 3. doi: 10.1038/s41572-020-00235-0. PubMed PMID:33446664
  • 2021 | Genomic Alterations during the In Situ to Invasive Ductal Breast Carcinoma Transition Shaped by the Immune System. Trinh, A, Gil Del Alcazar, CR, Shukla, SA, Chin, K, Chang, YH, Thibault, G, Eng, J, Jovanović, B, Aldaz, CM, Park, SY, Jeong, J, Wu, C, Gray, J, Polyak, K Mol Cancer Res 19 (4): 623-635. doi: 10.1158/1541-7786.MCR-20-0949. PubMed PMID:33443130 PubMed Central PMC8026652
  • 2020 | Co-stimulatory and co-inhibitory immune markers in solid tumors with MET alterations. Reckamp, KL, McQuerry, JA, Mambetsariev, I, Pharaon, R, Yost, SE, Fricke, J, Mirzapoiazova, T, Pillai, RK, Khan, Z, Fakih, M, Yuan, Y, Koczywas, M, Massarelli, E, Kulkarni, P, Pal, SK, Sattler, M, Bild, A, Salgia, R Future Sci OA 7 (2): FSO662. doi: 10.2144/fsoa-2020-0159. PubMed PMID:33437521 PubMed Central PMC7787173
  • 2021 | A modular master regulator landscape controls cancer transcriptional identity. Paull, EO, Aytes, A, Jones, SJ, Subramaniam, PS, Giorgi, FM, Douglass, EF, Tagore, S, Chu, B, Vasciaveo, A, Zheng, S, Verhaak, R, Abate-Shen, C, Alvarez, MJ, Califano, A Cell 184 (2): 334-351.e20. doi: 10.1016/j.cell.2020.11.045. PubMed PMID:33434495 PubMed Central PMC8103356
  • 2021 | Mass spectrometry-based protein-protein interaction networks for the study of human diseases. Richards, AL, Eckhardt, M, Krogan, NJ Mol Syst Biol 17 (1): e8792. doi: 10.15252/msb.20188792. PubMed PMID:33434350 PubMed Central PMC7803364
  • 2021 | Mammalian cell proliferation requires noncatalytic functions of O-GlcNAc transferase. Levine, ZG, Potter, SC, Joiner, CM, Fei, GQ, Nabet, B, Sonnett, M, Zachara, NE, Gray, NS, Paulo, JA, Walker, S Proc Natl Acad Sci U S A 118 (4): . doi: 10.1073/pnas.2016778118. PubMed PMID:33419956 PubMed Central PMC7848692
  • 2021 | HiDeF: identifying persistent structures in multiscale 'omics data. Zheng, F, Zhang, S, Churas, C, Pratt, D, Bahar, I, Ideker, T Genome Biol 22 (1): 21. doi: 10.1186/s13059-020-02228-4. PubMed PMID:33413539 PubMed Central PMC7789082
  • 2021 | Genetic screening for single-cell variability modulators driving therapy resistance. Torre, EA, Arai, E, Bayatpour, S, Jiang, CL, Beck, LE, Emert, BL, Shaffer, SM, Mellis, IA, Fane, ME, Alicea, GM, Budinich, KA, Weeraratna, AT, Shi, J, Raj, A Nat Genet 53 (1): 76-85. doi: 10.1038/s41588-020-00749-z. PubMed PMID:33398196 PubMed Central PMC7796998
  • 2021 | The aging transcriptome and cellular landscape of the human lung in relation to SARS-CoV-2. Chow, RD, Majety, M, Chen, S Nat Commun 12 (1): 4. doi: 10.1038/s41467-020-20323-9. PubMed PMID:33397975 PubMed Central PMC7782551
  • 2021 | Metastasis and Immune Evasion from Extracellular cGAMP Hydrolysis. Li, J, Duran, MA, Dhanota, N, Chatila, WK, Bettigole, SE, Kwon, J, Sriram, RK, Humphries, MP, Salto-Tellez, M, James, JA, Hanna, MG, Melms, JC, Vallabhaneni, S, Litchfield, K, Usaite, I, Biswas, D, Bareja, R, Li, HW, Martin, ML, Dorsaint, P, Cavallo, JA, Li, P, Pauli, C, Gottesdiener, L, DiPardo, BJ, Hollmann, TJ, Merghoub, T, Wen, HY, Reis-Filho, JS, Riaz, N, Su, SM, Kalbasi, A, Vasan, N, Powell, SN, Wolchok, JD, Elemento, O, Swanton, C, Shoushtari, AN, Parkes, EE, Izar, B, Bakhoum, SF Cancer Discov 11 (5): 1212-1227. doi: 10.1158/2159-8290.CD-20-0387. PubMed PMID:33372007 PubMed Central PMC8102348
  • 2020 | Predicting transcription factor binding in single cells through deep learning. Fu, L, Zhang, L, Dollinger, E, Peng, Q, Nie, Q, Xie, X Sci Adv 6 (51): . doi: 10.1126/sciadv.aba9031. PubMed PMID:33355120
  • 2020 | Two Stream Active Query Suggestion for Active Learning in Connectomics. Lin, Z, Wei, D, Jang, WD, Zhou, S, Chen, X, Wang, X, Schalek, R, Berger, D, Matejek, B, Kamentsky, L, Peleg, A, Haehn, D, Jones, T, Parag, T, Lichtman, J, Pfister, H Comput Vis ECCV 12363 : 103-120. doi: 10.1007/978-3-030-58523-5_7. PubMed PMID:33345257 PubMed Central PMC7746018
  • 2020 | Prolonged survival and response to tepotinib in a non-small-cell lung cancer patient with brain metastases harboring MET exon 14 mutation: a research report. Roth, KG, Mambetsariev, I, Salgia, R Cold Spring Harb Mol Case Stud 6 (6): . doi: 10.1101/mcs.a005785. PubMed PMID:33335011 PubMed Central PMC7784494
  • 2020 | SECAT: Quantifying Protein Complex Dynamics across Cell States by Network-Centric Analysis of SEC-SWATH-MS Profiles. Rosenberger, G, Heusel, M, Bludau, I, Collins, BC, Martelli, C, Williams, EG, Xue, P, Liu, Y, Aebersold, R, Califano, A Cell Syst 11 (6): 589-607.e8. doi: 10.1016/j.cels.2020.11.006. PubMed PMID:33333029 PubMed Central PMC8034988
  • 2020 | How Has the COVID-19 Pandemic Changed How You Will Approach Research and Lab Work in the Future?. Haynes, K, Yau, C, Bild, A, Laughney, A, Morsut, L, Yang, X, Zaugg, J, Hsu, P, Pancaldi, V, Iyer-Biswas, S Cell Syst 11 (6): 550-554. doi: 10.1016/j.cels.2020.11.011. PubMed PMID:33333028 PubMed Central PMC7833873
  • 2020 | Addressing BBB Heterogeneity: A New Paradigm for Drug Delivery to Brain Tumors. Griffith, JI, Rathi, S, Zhang, W, Zhang, W, Drewes, LR, Sarkaria, JN, Elmquist, WF Pharmaceutics 12 (12): . doi: 10.3390/pharmaceutics12121205. PubMed PMID:33322488 PubMed Central PMC7763839
  • 2021 | Transcriptional response modules characterize IL-1β and IL-6 activity in COVID-19. Bell, LCK, Meydan, C, Kim, J, Foox, J, Butler, D, Mason, CE, Shapira, SD, Noursadeghi, M, Pollara, G iScience 24 (1): 101896. doi: 10.1016/j.isci.2020.101896. PubMed PMID:33319166 PubMed Central PMC7721347
  • 2021 | A Call to Action: Dismantling Racial Injustices in Preclinical Research and Clinical Care of Black Patients Living with Small Cell Lung Cancer. Thomas, PL, Madubata, CJ, Aldrich, MC, Lee, MM, Owonikoko, TK, Minna, JD, Rudin, CM, Sage, J, Lovly, CM Cancer Discov 11 (2): 240-244. doi: 10.1158/2159-8290.CD-20-1592. PubMed PMID:33318034 PubMed Central PMC7858238
  • 2020 | Automated Measurements of Key Morphological Features of Human Embryos for IVF. Leahy, BD, Jang, WD, Yang, HY, Struyven, R, Wei, D, Sun, Z, Lee, KR, Royston, C, Cam, L, Kalma, Y, Azem, F, Ben-Yosef, D, Pfister, H, Needleman, D Med Image Comput Comput Assist Interv 12265 : 25-35. doi: 10.1007/978-3-030-59722-1_3. PubMed PMID:33313603 PubMed Central PMC7732604
  • 2020 | Obesity Shapes Metabolism in the Tumor Microenvironment to Suppress Anti-Tumor Immunity. Ringel, AE, Drijvers, JM, Baker, GJ, Catozzi, A, García-Cañaveras, JC, Gassaway, BM, Miller, BC, Juneja, VR, Nguyen, TH, Joshi, S, Yao, CH, Yoon, H, Sage, PT, LaFleur, MW, Trombley, JD, Jacobson, CA, Maliga, Z, Gygi, SP, Sorger, PK, Rabinowitz, JD, Sharpe, AH, Haigis, MC Cell 183 (7): 1848-1866.e26. doi: 10.1016/j.cell.2020.11.009. PubMed PMID:33301708 PubMed Central PMC8064125
  • 2020 | Methodological Advancements for Investigating Intra-tumoral Heterogeneity in Breast Cancer at the Bench and Bedside. Baek, M, Chang, JT, Echeverria, GV J Mammary Gland Biol Neoplasia 25 (4): 289-304. doi: 10.1007/s10911-020-09470-3. PubMed PMID:33300087 PubMed Central PMC7960623
  • 2020 | Transcriptional response modules characterise IL-1β and IL-6 activity in COVID-19. Bell, LC, Meydan, C, Kim, J, Foox, J, Butler, D, Mason, CE, Shapira, SD, Noursadeghi, M, Pollara, G bioRxiv : . doi: 10.1101/2020.07.22.202275. PubMed PMID:33299992 PubMed Central PMC7724660
  • 2021 | Melanoma Cell Intrinsic GABAA Receptor Enhancement Potentiates Radiation and Immune Checkpoint Inhibitor Response by Promoting Direct and T Cell-Mediated Antitumor Activity. Pomeranz Krummel, DA, Nasti, TH, Kaluzova, M, Kallay, L, Bhattacharya, D, Melms, JC, Izar, B, Xu, M, Burnham, A, Ahmed, T, Li, G, Lawson, D, Kowalski, J, Cao, Y, Switchenko, JM, Ionascu, D, Cook, JM, Medvedovic, M, Jenkins, A, Khan, MK, Sengupta, S Int J Radiat Oncol Biol Phys 109 (4): 1040-1053. doi: 10.1016/j.ijrobp.2020.10.025. PubMed PMID:33289666
  • 2020 | Gene regulation gravitates toward either addition or multiplication when combining the effects of two signals. Sanford, EM, Emert, BL, Coté, A, Raj, A Elife 9 : . doi: 10.7554/eLife.59388. PubMed PMID:33284110 PubMed Central PMC7771960
  • 2021 | Can some microbes promote host stress and benefit evolutionarily from this strategy?. Aktipis, A, Guevara Beltran, D Bioessays 43 (1): e2000188. doi: 10.1002/bies.202000188. PubMed PMID:33283894
  • 2020 | MitoEM Dataset: Large-scale 3D Mitochondria Instance Segmentation from EM Images. Wei, D, Lin, Z, Franco-Barranco, D, Wendt, N, Liu, X, Yin, W, Huang, X, Gupta, A, Jang, WD, Wang, X, Arganda-Carreras, I, Lichtman, JW, Pfister, H Med Image Comput Comput Assist Interv 12265 : 66-76. doi: 10.1007/978-3-030-59722-1_7. PubMed PMID:33283212 PubMed Central PMC7713709
  • 2020 | Channel Embedding for Informative Protein Identification from Highly Multiplexed Images. Magid, SA, Jang, WD, Schapiro, D, Wei, D, Tompkin, J, Sorger, PK, Pfister, H Med Image Comput Comput Assist Interv 12265 : 3-13. doi: 10.1007/978-3-030-59722-1_1. PubMed PMID:33283211 PubMed Central PMC7713713
  • 2020 | Assessment of Prognostic Value of Cystic Features in Glioblastoma Relative to Sex and Treatment With Standard-of-Care. Curtin, L, Whitmire, P, Rickertsen, CR, Mazza, GL, Canoll, P, Johnston, SK, Mrugala, MM, Swanson, KR, Hu, LS Front Oncol 10 : 580750. doi: 10.3389/fonc.2020.580750. PubMed PMID:33282737 PubMed Central PMC7705378
  • 2021 | Pharmacologic Screening Identifies Metabolic Vulnerabilities of CD8+ T Cells. Drijvers, JM, Gillis, JE, Muijlwijk, T, Nguyen, TH, Gaudiano, EF, Harris, IS, LaFleur, MW, Ringel, AE, Yao, CH, Kurmi, K, Juneja, VR, Trombley, JD, Haigis, MC, Sharpe, AH Cancer Immunol Res 9 (2): 184-199. doi: 10.1158/2326-6066.CIR-20-0384. PubMed PMID:33277233 PubMed Central PMC7864883
  • 2020 | VISTA: VIsual Semantic Tissue Analysis for pancreatic disease quantification in murine cohorts. Ternes, L, Huang, G, Lanciault, C, Thibault, G, Riggers, R, Gray, JW, Muschler, J, Chang, YH Sci Rep 10 (1): 20904. doi: 10.1038/s41598-020-78061-3. PubMed PMID:33262400 PubMed Central PMC7708430
  • 2021 | Clinical Efficacy and Molecular Response Correlates of the WEE1 Inhibitor Adavosertib Combined with Cisplatin in Patients with Metastatic Triple-Negative Breast Cancer. Keenan, TE, Li, T, Vallius, T, Guerriero, JL, Tayob, N, Kochupurakkal, B, Davis, J, Pastorello, R, Tahara, RK, Anderson, L, Conway, J, He, MX, Shannon, E, Godin, RE, Sorger, PK, D'Andrea, A, Overmoyer, B, Winer, EP, Mittendorf, EA, Van Allen, EM, Shapiro, GI, Tolaney, SM Clin Cancer Res 27 (4): 983-991. doi: 10.1158/1078-0432.CCR-20-3089. PubMed PMID:33257427 PubMed Central PMC7887044
  • 2020 | Head and neck squamous cell carcinoma. Johnson, DE, Burtness, B, Leemans, CR, Lui, VWY, Bauman, JE, Grandis, JR Nat Rev Dis Primers 6 (1): 92. doi: 10.1038/s41572-020-00224-3. PubMed PMID:33243986 PubMed Central PMC7944998
  • 2020 | The gut microbiota is associated with immune cell dynamics in humans. Schluter, J, Peled, JU, Taylor, BP, Markey, KA, Smith, M, Taur, Y, Niehus, R, Staffas, A, Dai, A, Fontana, E, Amoretti, LA, Wright, RJ, Morjaria, S, Fenelus, M, Pessin, MS, Chao, NJ, Lew, M, Bohannon, L, Bush, A, Sung, AD, Hohl, TM, Perales, MA, van den Brink, MRM, Xavier, JB Nature 588 (7837): 303-307. doi: 10.1038/s41586-020-2971-8. PubMed PMID:33239790 PubMed Central PMC7725892
  • 2021 | Concurrent Dexamethasone Limits the Clinical Benefit of Immune Checkpoint Blockade in Glioblastoma. Iorgulescu, JB, Gokhale, PC, Speranza, MC, Eschle, BK, Poitras, MJ, Wilkens, MK, Soroko, KM, Chhoeu, C, Knott, A, Gao, Y, Lim-Fat, MJ, Baker, GJ, Bonal, DM, Nguyen, QD, Grant, GRL, Ligon, KL, Sorger, PK, Chiocca, EA, Anderson, AC, Kirschmeier, PT, Sharpe, AH, Freeman, GJ, Reardon, DA Clin Cancer Res 27 (1): 276-287. doi: 10.1158/1078-0432.CCR-20-2291. PubMed PMID:33239433 PubMed Central PMC8034990
  • 2021 | A `one-two punch' therapy strategy to target chemoresistance in estrogen receptor positive breast cancer. Chi, F, Liu, J, Brady, SW, Cosgrove, PA, Nath, A, McQuerry, JA, Majumdar, S, Moos, PJ, Chang, JT, Kahn, M, Bild, AH Transl Oncol 14 (1): 100946. doi: 10.1016/j.tranon.2020.100946. PubMed PMID:33221681 PubMed Central PMC7689336
  • 2020 | Comparing the Efficacy of Cancer Therapies between Subgroups in Basket Trials. Palmer, AC, Plana, D, Sorger, PK Cell Syst 11 (5): 449-460.e2. doi: 10.1016/j.cels.2020.09.003. PubMed PMID:33220857 PubMed Central PMC8022348
  • 2020 | Epigenetic landscape of small cell lung cancer: small image of a giant recalcitrant disease. Khan, P, Siddiqui, JA, Maurya, SK, Lakshmanan, I, Jain, M, Ganti, AK, Salgia, R, Batra, SK, Nasser, MW Semin Cancer Biol : . doi: 10.1016/j.semcancer.2020.11.006. PubMed PMID:33220460
  • 2020 | Does placental invasiveness lead to higher rates of malignant transformation in mammals?: Response to: 'Available data suggests positive relationship between placental invasion an malignancy'. Boddy, AM, Abegglen, LM, Aktipis, A, Schiffman, JD, Maley, CC, Witte, C Evol Med Public Health 2020 (1): 215-216. doi: 10.1093/emph/eoaa025. PubMed PMID:33214902 PubMed Central PMC7658549
  • 2020 | Transmissible cancers and the evolution of sex under the Red Queen hypothesis. Aubier, TG, Galipaud, M, Erten, EY, Kokko, H PLoS Biol 18 (11): e3000916. doi: 10.1371/journal.pbio.3000916. PubMed PMID:33211684 PubMed Central PMC7676742
  • 2020 | Lifetime cancer prevalence and life history traits in mammals. Boddy, AM, Abegglen, LM, Pessier, AP, Aktipis, A, Schiffman, JD, Maley, CC, Witte, C Evol Med Public Health 2020 (1): 187-195. doi: 10.1093/emph/eoaa015. PubMed PMID:33209304 PubMed Central PMC7652303
  • 2020 | Inflammasomes within Hyperactive Murine Dendritic Cells Stimulate Long-Lived T Cell-Mediated Anti-tumor Immunity. Zhivaki, D, Borriello, F, Chow, OA, Doran, B, Fleming, I, Theisen, DJ, Pallis, P, Shalek, AK, Sokol, CL, Zanoni, I, Kagan, JC Cell Rep 33 (7): 108381. doi: 10.1016/j.celrep.2020.108381. PubMed PMID:33207188 PubMed Central PMC7727444
  • 2020 | A Random Matrix Theory Approach to Denoise Single-Cell Data. Aparicio, L, Bordyuh, M, Blumberg, AJ, Rabadan, R Patterns (N Y) 1 (3): 100035. doi: 10.1016/j.patter.2020.100035. PubMed PMID:33205104 PubMed Central PMC7660363
  • 2020 | The MOBSTER R package for tumour subclonal deconvolution from bulk DNA whole-genome sequencing data. Caravagna, G, Sanguinetti, G, Graham, TA, Sottoriva, A BMC Bioinformatics 21 (1): 531. doi: 10.1186/s12859-020-03863-1. PubMed PMID:33203356 PubMed Central PMC7672894
  • 2021 | Immune Checkpoint Inhibitors for the Treatment of Cancer: Clinical Impact and Mechanisms of Response and Resistance. Bagchi, S, Yuan, R, Engleman, EG Annu Rev Pathol 16 : 223-249. doi: 10.1146/annurev-pathol-042020-042741. PubMed PMID:33197221
  • 2020 | High-Spatial-Resolution Multi-Omics Sequencing via Deterministic Barcoding in Tissue. Liu, Y, Yang, M, Deng, Y, Su, G, Enninful, A, Guo, CC, Tebaldi, T, Zhang, D, Kim, D, Bai, Z, Norris, E, Pan, A, Li, J, Xiao, Y, Halene, S, Fan, R Cell 183 (6): 1665-1681.e18. doi: 10.1016/j.cell.2020.10.026. PubMed PMID:33188776 PubMed Central PMC7736559
  • 2020 | Nonstructural Protein 1 of SARS-CoV-2 Is a Potent Pathogenicity Factor Redirecting Host Protein Synthesis Machinery toward Viral RNA. Yuan, S, Peng, L, Park, JJ, Hu, Y, Devarkar, SC, Dong, MB, Shen, Q, Wu, S, Chen, S, Lomakin, IB, Xiong, Y Mol Cell 80 (6): 1055-1066.e6. doi: 10.1016/j.molcel.2020.10.034. PubMed PMID:33188728 PubMed Central PMC7833686
  • 2021 | Clinical Trial Metrics: The Complexity of Conducting Clinical Trials in North American Cancer Centers. Lee, C, Werner, TL, Deal, AM, Krise-Confair, CJ, Bentz, TA, Cummings, TM, Grant, SC, Lee, AB, Moehle, J, Moffett, K, Peck, H, Williamson, S, Zafirovski, A, Shaw, K, Hofacker, JK JCO Oncol Pract 17 (1): e77-e93. doi: 10.1200/OP.20.00501. PubMed PMID:33186085
  • 2021 | Evolution of Embryo Implantation Was Enabled by the Origin of Decidual Stromal Cells in Eutherian Mammals. Chavan, AR, Griffith, OW, Stadtmauer, DJ, Maziarz, J, Pavlicev, M, Fishman, R, Koren, L, Romero, R, Wagner, GP Mol Biol Evol 38 (3): 1060-1074. doi: 10.1093/molbev/msaa274. PubMed PMID:33185661 PubMed Central PMC7947829
  • 2020 | Hyperprogression on immunotherapy with complete response to chemotherapy in a NSCLC patient with high PD-L1 and STK11: A case report. Fricke, J, Mambetsariev, I, Pharaon, R, Subbiah, S, Rajurkar, S, Salgia, R Medicine (Baltimore) 99 (46): e22323. doi: 10.1097/MD.0000000000022323. PubMed PMID:33181636 PubMed Central PMC7668523
  • 2020 | The Transcription Factor Foxp3 Shapes Regulatory T Cell Identity by Tuning the Activity of trans-Acting Intermediaries. van der Veeken, J, Glasner, A, Zhong, Y, Hu, W, Wang, ZM, Bou-Puerto, R, Charbonnier, LM, Chatila, TA, Leslie, CS, Rudensky, AY Immunity 53 (5): 971-984.e5. doi: 10.1016/j.immuni.2020.10.010. PubMed PMID:33176163
  • 2021 | Turnover Modulates the Need for a Cost of Resistance in Adaptive Therapy. Strobl, MAR, West, J, Viossat, Y, Damaghi, M, Robertson-Tessi, M, Brown, JS, Gatenby, RA, Maini, PK, Anderson, ARA Cancer Res 81 (4): 1135-1147. doi: 10.1158/0008-5472.CAN-20-0806. PubMed PMID:33172930
  • 2020 | The effects of age and systemic metabolism on anti-tumor T cell responses. Drijvers, JM, Sharpe, AH, Haigis, MC Elife 9 : . doi: 10.7554/eLife.62420. PubMed PMID:33170123 PubMed Central PMC7655106
  • 2021 | Chromatin regulatory genes differentially interact in networks to facilitate distinct GAL1 activity and noise profiles. Moreno, DF, Acar, M Curr Genet 67 (2): 267-281. doi: 10.1007/s00294-020-01124-5. PubMed PMID:33159551 PubMed Central PMC8035145
  • 2020 | Defining the Teratoma as a Model for Multi-lineage Human Development. McDonald, D, Wu, Y, Dailamy, A, Tat, J, Parekh, U, Zhao, D, Hu, M, Tipps, A, Zhang, K, Mali, P Cell 183 (5): 1402-1419.e18. doi: 10.1016/j.cell.2020.10.018. PubMed PMID:33152263 PubMed Central PMC7704916
  • 2020 | IFITM3 functions as a PIP3 scaffold to amplify PI3K signalling in B cells. Lee, J, Robinson, ME, Ma, N, Artadji, D, Ahmed, MA, Xiao, G, Sadras, T, Deb, G, Winchester, J, Cosgun, KN, Geng, H, Chan, LN, Kume, K, Miettinen, TP, Zhang, Y, Nix, MA, Klemm, L, Chen, CW, Chen, J, Khairnar, V, Wiita, AP, Thomas-Tikhonenko, A, Farzan, M, Jung, JU, Weinstock, DM, Manalis, SR, Diamond, MS, Vaidehi, N, Müschen, M Nature 588 (7838): 491-497. doi: 10.1038/s41586-020-2884-6. PubMed PMID:33149299 PubMed Central PMC8087162
  • 2020 | Systematic elucidation of neuron-astrocyte interaction in models of amyotrophic lateral sclerosis using multi-modal integrated bioinformatics workflow. Mishra, V, Re, DB, Le Verche, V, Alvarez, MJ, Vasciaveo, A, Jacquier, A, Doulias, PT, Greco, TM, Nizzardo, M, Papadimitriou, D, Nagata, T, Rinchetti, P, Perez-Torres, EJ, Politi, KA, Ikiz, B, Clare, K, Than, ME, Corti, S, Ischiropoulos, H, Lotti, F, Califano, A, Przedborski, S Nat Commun 11 (1): 5579. doi: 10.1038/s41467-020-19177-y. PubMed PMID:33149111 PubMed Central PMC7642391
  • 2020 | Rapid progression of disease from immunotherapy following targeted therapy: insights into treatment management and sequence. Pharaon, R, Mambetsariev, I, Fricke, J, Salgia, R J Thorac Dis 12 (9): 5096-5103. doi: 10.21037/jtd.2019.08.14. PubMed PMID:33145086 PubMed Central PMC7578509
  • 2020 | Role of immunotherapy and co-mutations on KRAS-mutant non-small cell lung cancer survival. Amanam, I, Mambetsariev, I, Gupta, R, Achuthan, S, Wang, Y, Pharaon, R, Massarelli, E, Koczywas, M, Reckamp, K, Salgia, R J Thorac Dis 12 (9): 5086-5095. doi: 10.21037/jtd.2020.04.18. PubMed PMID:33145085 PubMed Central PMC7578487
  • 2020 | Identifying the spatial and temporal dynamics of molecularly-distinct glioblastoma sub-populations. Morris, B, Curtin, L, Hawkins-Daarud, A, Hubbard, ME, Rahman, R, Smith, SJ, Auer, D, Tran, NL, Hu, LS, Eschbacher, JM, Smith, KA, Stokes, A, Swanson, KR, Owen, MR Math Biosci Eng 17 (5): 4905-4941. doi: 10.3934/mbe.2020267. PubMed PMID:33120534
  • 2020 | ACE2 localizes to the respiratory cilia and is not increased by ACE inhibitors or ARBs. Lee, IT, Nakayama, T, Wu, CT, Goltsev, Y, Jiang, S, Gall, PA, Liao, CK, Shih, LC, Schürch, CM, McIlwain, DR, Chu, P, Borchard, NA, Zarabanda, D, Dholakia, SS, Yang, A, Kim, D, Chen, H, Kanie, T, Lin, CD, Tsai, MH, Phillips, KM, Kim, R, Overdevest, JB, Tyler, MA, Yan, CH, Lin, CF, Lin, YT, Bau, DT, Tsay, GJ, Patel, ZM, Tsou, YA, Tzankov, A, Matter, MS, Tai, CJ, Yeh, TH, Hwang, PH, Nolan, GP, Nayak, JV, Jackson, PK Nat Commun 11 (1): 5453. doi: 10.1038/s41467-020-19145-6. PubMed PMID:33116139 PubMed Central PMC7595232
  • 2020 | Epigenetic Mechanisms Contribute to Evolutionary Adaptation of Gene Network Activity under Environmental Selection. Luo, X, Song, R, Moreno, DF, Ryu, HY, Hochstrasser, M, Acar, M Cell Rep 33 (4): 108306. doi: 10.1016/j.celrep.2020.108306. PubMed PMID:33113358 PubMed Central PMC7656290
  • 2020 | Receptor-Driven ERK Pulses Reconfigure MAPK Signaling and Enable Persistence of Drug-Adapted BRAF-Mutant Melanoma Cells. Gerosa, L, Chidley, C, Fröhlich, F, Sanchez, G, Lim, SK, Muhlich, J, Chen, JY, Vallabhaneni, S, Baker, GJ, Schapiro, D, Atanasova, MI, Chylek, LA, Shi, T, Yi, L, Nicora, CD, Claas, A, Ng, TSC, Kohler, RH, Lauffenburger, DA, Weissleder, R, Miller, MA, Qian, WJ, Wiley, HS, Sorger, PK Cell Syst 11 (5): 478-494.e9. doi: 10.1016/j.cels.2020.10.002. PubMed PMID:33113355 PubMed Central PMC8009031
  • 2020 | WNT Signaling Driven by R-spondin 1 and LGR6 in High-grade Serous Ovarian Cancer. Lee, S, Jun, J, Kim, WJ, Tamayo, P, Howell, SB Anticancer Res 40 (11): 6017-6028. doi: 10.21873/anticanres.14623. PubMed PMID:33109540
  • 2020 | sFRP2 Supersedes VEGF as an Age-related Driver of Angiogenesis in Melanoma, Affecting Response to Anti-VEGF Therapy in Older Patients. Fane, ME, Ecker, BL, Kaur, A, Marino, GE, Alicea, GM, Douglass, SM, Chhabra, Y, Webster, MR, Marshall, A, Colling, R, Espinosa, O, Coupe, N, Maroo, N, Campo, L, Middleton, MR, Corrie, P, Xu, X, Karakousis, GC, Weeraratna, AT Clin Cancer Res 26 (21): 5709-5719. doi: 10.1158/1078-0432.CCR-20-0446. PubMed PMID:33097493 PubMed Central PMC7642114
  • 2020 | Predicting Drug Response and Synergy Using a Deep Learning Model of Human Cancer Cells. Kuenzi, BM, Park, J, Fong, SH, Sanchez, KS, Lee, J, Kreisberg, JF, Ma, J, Ideker, T Cancer Cell 38 (5): 672-684.e6. doi: 10.1016/j.ccell.2020.09.014. PubMed PMID:33096023 PubMed Central PMC7737474
  • 2020 | Multiscale community detection in Cytoscape. Singhal, A, Cao, S, Churas, C, Pratt, D, Fortunato, S, Zheng, F, Ideker, T PLoS Comput Biol 16 (10): e1008239. doi: 10.1371/journal.pcbi.1008239. PubMed PMID:33095781 PubMed Central PMC7584444
  • 2020 | Pharmacologic profiling of patient-derived xenograft models of primary treatment-naïve triple-negative breast cancer. Powell, RT, Redwood, A, Liu, X, Guo, L, Cai, S, Zhou, X, Tu, Y, Zhang, X, Qi, Y, Jiang, Y, Echeverria, G, Feng, N, Ma, X, Giuliani, V, Marszalek, JR, Heffernan, TP, Vellano, CP, White, JB, Stephan, C, Davies, PJ, Moulder, S, Symmans, WF, Chang, JT, Piwnica-Worms, H Sci Rep 10 (1): 17899. doi: 10.1038/s41598-020-74882-4. PubMed PMID:33087803 PubMed Central PMC7578025
  • 2020 | Mechanism of action biomarkers predicting response to AKT inhibition in the I-SPY 2 breast cancer trial. Wolf, DM, Yau, C, Wulfkuhle, J, Brown-Swigart, L, Gallagher, RI, Magbanua, MJM, O'Grady, N, Hirst, G, I-SPY 2 TRIAL Investigators, Asare, S, Tripathy, D, Berry, D, Esserman, L, Chien, AJ, Petricoin, EF 3rd, van 't Veer, L NPJ Breast Cancer 6 : 48. doi: 10.1038/s41523-020-00189-2. PubMed PMID:33083527 PubMed Central PMC7532145
  • 2020 | Divergent Resistance Mechanisms to Immunotherapy Explain Responses in Different Skin Cancers. Dollinger, E, Bergman, D, Zhou, P, Atwood, SX, Nie, Q Cancers (Basel) 12 (10): . doi: 10.3390/cancers12102946. PubMed PMID:33065980 PubMed Central PMC7599806
  • 2020 | Vascular Disease and Thrombosis in SARS-CoV-2-Infected Rhesus Macaques. Aid, M, Busman-Sahay, K, Vidal, SJ, Maliga, Z, Bondoc, S, Starke, C, Terry, M, Jacobson, CA, Wrijil, L, Ducat, S, Brook, OR, Miller, AD, Porto, M, Pellegrini, KL, Pino, M, Hoang, TN, Chandrashekar, A, Patel, S, Stephenson, K, Bosinger, SE, Andersen, H, Lewis, MG, Hecht, JL, Sorger, PK, Martinot, AJ, Estes, JD, Barouch, DH Cell 183 (5): 1354-1366.e13. doi: 10.1016/j.cell.2020.10.005. PubMed PMID:33065030 PubMed Central PMC7546181
  • 2020 | SHIFT: speedy histological-to-immunofluorescent translation of a tumor signature enabled by deep learning. Burlingame, EA, McDonnell, M, Schau, GF, Thibault, G, Lanciault, C, Morgan, T, Johnson, BE, Corless, C, Gray, JW, Chang, YH Sci Rep 10 (1): 17507. doi: 10.1038/s41598-020-74500-3. PubMed PMID:33060677 PubMed Central PMC7566625
  • 2020 | An Integrative Gene Expression and Mathematical Flux Balance Analysis Identifies Targetable Redox Vulnerabilities in Melanoma Cells. Paudel, BB, Lewis, JE, Hardeman, KN, Hayford, CE, Robbins, CJ, Stauffer, PE, Codreanu, SG, Sherrod, SD, McLean, JA, Kemp, ML, Quaranta, V Cancer Res 80 (20): 4565-4577. doi: 10.1158/0008-5472.CAN-19-3588. PubMed PMID:33060170
  • 2021 | A Sweep of Earth's Virome Reveals Host-Guided Viral Protein Structural Mimicry and Points to Determinants of Human Disease. Lasso, G, Honig, B, Shapira, SD Cell Syst 12 (1): 82-91.e3. doi: 10.1016/j.cels.2020.09.006. PubMed PMID:33053371 PubMed Central PMC7552982
  • 2020 | Dynamics of nevus development implicate cell cooperation in the growth arrest of transformed melanocytes. Ruiz-Vega, R, Chen, CF, Razzak, E, Vasudeva, P, Krasieva, TB, Shiu, J, Caldwell, MG, Yan, H, Lowengrub, J, Ganesan, AK, Lander, AD Elife 9 : . doi: 10.7554/eLife.61026. PubMed PMID:33047672 PubMed Central PMC7553774
  • 2020 | Functional Precision Medicine Identifies New Therapeutic Candidates for Medulloblastoma. Rusert, JM, Juarez, EF, Brabetz, S, Jensen, J, Garancher, A, Chau, LQ, Tacheva-Grigorova, SK, Wahab, S, Udaka, YT, Finlay, D, Seker-Cin, H, Reardon, B, Gröbner, S, Serrano, J, Ecker, J, Qi, L, Kogiso, M, Du, Y, Baxter, PA, Henderson, JJ, Berens, ME, Vuori, K, Milde, T, Cho, YJ, Li, XN, Olson, JM, Reyes, I, Snuderl, M, Wong, TC, Dimmock, DP, Nahas, SA, Malicki, D, Crawford, JR, Levy, ML, Van Allen, EM, Pfister, SM, Tamayo, P, Kool, M, Mesirov, JP, Wechsler-Reya, RJ Cancer Res 80 (23): 5393-5407. doi: 10.1158/0008-5472.CAN-20-1655. PubMed PMID:33046443 PubMed Central PMC7718387
  • 2020 | Landscape of coordinated immune responses to H1N1 challenge in humans. Rahil, Z, Leylek, R, Schürch, CM, Chen, H, Bjornson-Hooper, Z, Christensen, SR, Gherardini, PF, Bhate, SS, Spitzer, MH, Fragiadakis, GK, Mukherjee, N, Kim, N, Jiang, S, Yo, J, Gaudilliere, B, Affrime, M, Bock, B, Hensley, SE, Idoyaga, J, Aghaeepour, N, Kim, K, Nolan, GP, McIlwain, DR J Clin Invest 130 (11): 5800-5816. doi: 10.1172/JCI137265. PubMed PMID:33044226 PubMed Central PMC7598057
  • 2020 | Monitoring and modeling of lymphocytic leukemia cell bioenergetics reveals decreased ATP synthesis during cell division. Kang, JH, Katsikis, G, Li, Z, Sapp, KM, Stockslager, MA, Lim, D, Vander Heiden, MG, Yaffe, MB, Manalis, SR, Miettinen, TP Nat Commun 11 (1): 4983. doi: 10.1038/s41467-020-18769-y. PubMed PMID:33020492 PubMed Central PMC7536222
  • 2020 | Robust edge-based biomarker discovery improves prediction of breast cancer metastasis. Adnan, N, Lei, C, Ruan, J BMC Bioinformatics 21 (Suppl 14): 359. doi: 10.1186/s12859-020-03692-2. PubMed PMID:32998692 PubMed Central PMC7526355
  • | How Should Cancer Models Be Constructed?. Beckman, RA, Kareva, I, Adler, FR Cancer Control 27 (1): 1073274820962008. doi: 10.1177/1073274820962008. PubMed PMID:32991214 PubMed Central PMC7791451
  • 2020 | Considerations for the Selection and Use of Disinfectants Against SARS-CoV-2 in a Health Care Setting. Tyan, K, Levin, A, Avalos-Pacheco, A, Plana, D, Rand, EA, Yang, H, Maliszewski, LE, Chylek, LA, Atta, L, Tye, MA, Carmack, MM, Oglesby, NS, Burgin, S, Yu, SH, LeBoeuf, NR, Kemp, JM Open Forum Infect Dis 7 (9): ofaa396. doi: 10.1093/ofid/ofaa396. PubMed PMID:32989420 PubMed Central PMC7499694
  • 2021 | A web tool for the design of prime-editing guide RNAs. Chow, RD, Chen, JS, Shen, J, Chen, S Nat Biomed Eng 5 (2): 190-194. doi: 10.1038/s41551-020-00622-8. PubMed PMID:32989284 PubMed Central PMC7882013
  • 2020 | Gene selection for optimal prediction of cell position in tissues from single-cell transcriptomics data. Tanevski, J, Nguyen, T, Truong, B, Karaiskos, N, Ahsen, ME, Zhang, X, Shu, C, Xu, K, Liang, X, Hu, Y, Pham, HV, Xiaomei, L, Le, TD, Tarca, AL, Bhatti, G, Romero, R, Karathanasis, N, Loher, P, Chen, Y, Ouyang, Z, Mao, D, Zhang, Y, Zand, M, Ruan, J, Hafemeister, C, Qiu, P, Tran, D, Nguyen, T, Gabor, A, Yu, T, Guinney, J, Glaab, E, Krause, R, Banda, P, DREAM SCTC Consortium, Stolovitzky, G, Rajewsky, N, Saez-Rodriguez, J, Meyer, P Life Sci Alliance 3 (11): . doi: 10.26508/lsa.202000867. PubMed PMID:32972997 PubMed Central PMC7536825
  • 2020 | Menin and Menin-Associated Proteins Coregulate Cancer Energy Metabolism. Chou, CW, Tan, X, Hung, CN, Lieberman, B, Chen, M, Kusi, M, Mitsuya, K, Lin, CL, Morita, M, Liu, Z, Chen, CL, Huang, TH Cancers (Basel) 12 (9): . doi: 10.3390/cancers12092715. PubMed PMID:32971831 PubMed Central PMC7564175
  • 2020 | The 3D genomic landscape of differential response to EGFR/HER2 inhibition in endocrine-resistant breast cancer cells. Yang, Y, Choppavarapu, L, Fang, K, Naeini, AS, Nosirov, B, Li, J, Yang, K, He, Z, Zhou, Y, Schiff, R, Li, R, Hu, Y, Wang, J, Jin, VX Biochim Biophys Acta Gene Regul Mech 1863 (11): 194631. doi: 10.1016/j.bbagrm.2020.194631. PubMed PMID:32956836 PubMed Central PMC7686120
  • 2020 | Leveraging correlations between variants in polygenic risk scores to detect heterogeneity in GWAS cohorts. Yuan, J, Xing, H, Lamy, AL, Schizophrenia Working Group of the Psychiatric Genomics Consortium, Lencz, T, Pe'er, I PLoS Genet 16 (9): e1009015. doi: 10.1371/journal.pgen.1009015. PubMed PMID:32956347 PubMed Central PMC7529195
  • 2020 | Application of simultaneous selective pressures slows adaptation. Merlo, LMF, Sprouffske, K, Howard, TC, Gardiner, KL, Caulin, AF, Blum, SM, Evans, P, Bedalov, A, Sniegowski, PD, Maley, CC Evol Appl 13 (7): 1615-1625. doi: 10.1111/eva.13062. PubMed PMID:32952608 PubMed Central PMC7484835
  • 2020 | A Non-genetic Mechanism Involving the Integrin β4/Paxillin Axis Contributes to Chemoresistance in Lung Cancer. Mohanty, A, Nam, A, Pozhitkov, A, Yang, L, Srivastava, S, Nathan, A, Wu, X, Mambetsariev, I, Nelson, M, Subbalakshmi, AR, Guo, L, Nasser, MW, Batra, SK, Orban, J, Jolly, MK, Massarelli, E, Kulkarni, P, Salgia, R iScience 23 (9): 101496. doi: 10.1016/j.isci.2020.101496. PubMed PMID:32947124 PubMed Central PMC7502350
  • 2020 | The transcriptomic response of cells to a drug combination is more than the sum of the responses to the monotherapies. Diaz, JE, Ahsen, ME, Schaffter, T, Chen, X, Realubit, RB, Karan, C, Califano, A, Losic, B, Stolovitzky, G Elife 9 : . doi: 10.7554/eLife.52707. PubMed PMID:32945258 PubMed Central PMC7546737
  • 2020 | A Phosphoramidate Strategy Enables Membrane Permeability of a Non-nucleotide Inhibitor of the Prolyl Isomerase Pin1. Schwarz, DMC, Williams, SK, Dillenburg, M, Wagner, CR, Gestwicki, JE ACS Med Chem Lett 11 (9): 1704-1710. doi: 10.1021/acsmedchemlett.0c00170. PubMed PMID:32944137 PubMed Central PMC7488286
  • 2020 | Integrating Mathematical Modeling with High-Throughput Imaging Explains How Polyploid Populations Behave in Nutrient-Sparse Environments. Kimmel, GJ, Dane, M, Heiser, LM, Altrock, PM, Andor, N Cancer Res 80 (22): 5109-5120. doi: 10.1158/0008-5472.CAN-20-1231. PubMed PMID:32938640 PubMed Central PMC7671819
  • 2021 | Diversity in cancer invasion phenotypes indicates specific stroma regulated programs. Novin, A, Suhail, Y, Ajeti, V, Goyal, R, Wali, K, Seck, A, Jackson, A, Kshitiz, Hum Cell 34 (1): 111-121. doi: 10.1007/s13577-020-00427-6. PubMed PMID:32935295
  • 2020 | Age-dependent regulation of SARS-CoV-2 cell entry genes and cell death programs correlates with COVID-19 disease severity. Inde, Z, Yapp, C, Joshi, GN, Spetz, J, Fraser, C, Deskin, B, Ghelfi, E, Sodhi, C, Hackam, D, Kobzik, L, Croker, B, Brownfield, D, Jia, H, Sarosiek, KA bioRxiv : . doi: 10.1101/2020.09.13.276923. PubMed PMID:32935109 PubMed Central PMC7491524
  • 2020 | Searching for Goldilocks: How Evolution and Ecology Can Help Uncover More Effective Patient-Specific Chemotherapies. Park, DS, Luddy, KA, Robertson-Tessi, M, O'Farrelly, C, Gatenby, RA, Anderson, ARA Cancer Res 80 (23): 5147-5154. doi: 10.1158/0008-5472.CAN-19-3981. PubMed PMID:32934022
  • 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 52 (10): 1057-1066. doi: 10.1038/s41588-020-0687-1. PubMed PMID:32929288 PubMed Central PMC7610467
  • 2021 | 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 39 (2): 215-224. doi: 10.1038/s41587-020-0652-7. PubMed PMID:32929263 PubMed Central PMC7878435
  • 2020 | Exercise and immunometabolic regulation in cancer. Koelwyn, GJ, Zhuang, X, Tammela, T, Schietinger, A, Jones, LW Nat Metab 2 (9): 849-857. doi: 10.1038/s42255-020-00277-4. PubMed PMID:32929232
  • 2020 | General and robust covalently linked graphene oxide affinity grids for high-resolution cryo-EM. Wang, F, Liu, Y, Yu, Z, Li, S, Feng, S, Cheng, Y, Agard, DA Proc Natl Acad Sci U S A 117 (39): 24269-24273. doi: 10.1073/pnas.2009707117. PubMed PMID:32913054 PubMed Central PMC7533693
  • 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
  • 2020 | SYLARAS: A Platform for the Statistical Analysis and Visual Display of Systemic Immunoprofiling Data and Its Application to Glioblastoma. Baker, GJ, Muhlich, JL, Palaniappan, SK, Moore, JK, Davis, SH, Santagata, S, Sorger, PK Cell Syst 11 (3): 272-285.e9. doi: 10.1016/j.cels.2020.08.001. PubMed PMID:32898474 PubMed Central PMC7565356
  • 2020 | CRISPR-GEMM Pooled Mutagenic Screening Identifies KMT2D as a Major Modulator of Immune Checkpoint Blockade. Wang, G, Chow, RD, Zhu, L, Bai, Z, Ye, L, Zhang, F, Renauer, PA, Dong, MB, Dai, X, Zhang, X, Du, Y, Cheng, Y, Niu, L, Chu, Z, Kim, K, Liao, C, Clark, P, Errami, Y, Chen, S Cancer Discov 10 (12): 1912-1933. doi: 10.1158/2159-8290.CD-19-1448. PubMed PMID:32887696 PubMed Central PMC7710536
  • 2020 | Publisher Correction: 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): 495. doi: 10.1038/s42003-020-01237-0. PubMed PMID:32884070 PubMed Central PMC7471919
  • 2020 | Subclonal reconstruction of tumors by using machine learning and population genetics. Caravagna, G, Heide, T, Williams, MJ, Zapata, L, Nichol, D, Chkhaidze, K, Cross, W, Cresswell, GD, Werner, B, Acar, A, Chesler, L, Barnes, CP, Sanguinetti, G, Graham, TA, Sottoriva, A Nat Genet 52 (9): 898-907. doi: 10.1038/s41588-020-0675-5. PubMed PMID:32879509 PubMed Central PMC7610388
  • 2020 | Inference and multiscale model of epithelial-to-mesenchymal transition via single-cell transcriptomic data. Sha, Y, Wang, S, Zhou, P, Nie, Q Nucleic Acids Res 48 (17): 9505-9520. doi: 10.1093/nar/gkaa725. PubMed PMID:32870263 PubMed Central PMC7515733
  • 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 | Identifying the Potential Mechanism of Action of SNPs Associated With Breast Cancer Susceptibility With GVITamIN. Nguyen, AP, Nicoletti, P, Arnol, D, Califano, A, Rodríguez Martínez, M Front Bioeng Biotechnol 8 : 798. doi: 10.3389/fbioe.2020.00798. PubMed PMID:32850701 PubMed Central PMC7417307
  • 2020 | α-Ketoglutarate attenuates Wnt signaling and drives differentiation in colorectal cancer. Tran, TQ, Hanse, EA, Habowski, AN, Li, H, Gabra, MBI, Yang, Y, Lowman, XH, Ooi, AM, Liao, SY, Edwards, RA, Waterman, ML, Kong, M Nat Cancer 1 (3): 345-358. doi: 10.1038/s43018-020-0035-5. PubMed PMID:32832918 PubMed Central PMC7442208
  • 2020 | Hypoxia: Friend or Foe for drug delivery in Pancreatic Cancer. Shah, VM, Sheppard, BC, Sears, RC, Alani, AW Cancer Lett 492 : 63-70. doi: 10.1016/j.canlet.2020.07.041. PubMed PMID:32822815 PubMed Central PMC7879337
  • 2020 | The evolution of metapopulation dynamics and the number of stem cells in intestinal crypts and other tissue structures in multicellular bodies. Birtwell, D, Luebeck, G, Maley, CC Evol Appl 13 (7): 1771-1783. doi: 10.1111/eva.13069. PubMed PMID:32821281 PubMed Central PMC7428809
  • 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 | Kinetics of receptor tyrosine kinase activation define ERK signaling dynamics. Kiyatkin, A, van Alderwerelt van Rosenburgh, IK, Klein, DE, Lemmon, MA Sci Signal 13 (645): . doi: 10.1126/scisignal.aaz5267. PubMed PMID:32817373 PubMed Central PMC7521189
  • 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 | Modeling and analysis of Hi-C data by HiSIF identifies characteristic promoter-distal loops. Zhou, Y, Cheng, X, Yang, Y, Li, T, Li, J, Huang, TH, Wang, J, Lin, S, Jin, VX Genome Med 12 (1): 69. doi: 10.1186/s13073-020-00769-8. PubMed PMID:32787954 PubMed Central PMC7425017
  • 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 | Unsupervised machine learning reveals key immune cell subsets in COVID-19, rhinovirus infection, and cancer therapy. Barone, SM, Paul, AGA, Muehling, LM, Lannigan, JA, Kwok, WW, Turner, RB, Woodfolk, JA, Irish, JM bioRxiv : . doi: 10.1101/2020.07.31.190454. PubMed PMID:32766581 PubMed Central PMC7402038
  • 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 26 (10): 1609-1615. doi: 10.1038/s41591-020-1021-2. PubMed PMID:32747830 PubMed Central PMC7809634
  • 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, Muszynski, 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 80 (19): 4278-4287. doi: 10.1158/0008-5472.CAN-19-3850. PubMed PMID:32747364 PubMed Central PMC7541581
  • 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 PubMed Central PMC7496637
  • 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 | Multiscale modeling of protein membrane interactions for nanoparticle targeting in drug delivery. Eckmann, DM, Bradley, RP, Kandy, SK, Patil, K, Janmey, PA, Radhakrishnan, R Curr Opin Struct Biol 64 : 104-110. doi: 10.1016/j.sbi.2020.06.023. PubMed PMID:32731155 PubMed Central PMC7666034
  • 2021 | Refined cut-off for TP53 immunohistochemistry improves prediction of TP53 mutation status in ovarian mucinous tumors: implications for outcome analyses. Kang, EY, Cheasley, D, LePage, C, Wakefield, MJ, da Cunha Torres, M, Rowley, S, Salazar, C, Xing, Z, Allan, P, Bowtell, DDL, Mes-Masson, AM, Provencher, DM, Rahimi, K, Kelemen, LE, Fasching, PA, Doherty, JA, Goodman, MT, Goode, EL, Deen, S, Pharoah, PDP, Brenton, JD, Sieh, W, Mateoiu, C, Sundfeldt, K, Cook, LS, Le, ND, Anglesio, MS, Gilks, CB, Huntsman, DG, Kennedy, CJ, Traficante, N, Australian Ovarian Cancer Study, DeFazio, A, Kaufmann, S, Churchman, M, Gourley, C, Stephens, AN, Meagher, NS, Ramus, SJ, Antill, YC, Campbell, I, Scott, CL, Köbel, M, Gorringe, KL, GAMuT Collaborators Mod Pathol 34 (1): 194-206. doi: 10.1038/s41379-020-0618-9. PubMed PMID:32724153
  • 2020 | Tuft Cells Inhibit Pancreatic Tumorigenesis in Mice by Producing Prostaglandin D2. DelGiorno, KE, Chung, CY, Vavinskaya, V, Maurer, HC, Novak, SW, Lytle, NK, Ma, Z, Giraddi, RR, Wang, D, Fang, L, Naeem, RF, Andrade, LR, Ali, WH, Tseng, H, Tsui, C, Gubbala, VB, Ridinger-Saison, M, Ohmoto, M, Erikson, GA, O'Connor, C, Shokhirev, MN, Hah, N, Urade, Y, Matsumoto, I, Kaech, SM, Singh, PK, Manor, U, Olive, KP, Wahl, GM Gastroenterology 159 (5): 1866-1881.e8. doi: 10.1053/j.gastro.2020.07.037. PubMed PMID:32717220 PubMed Central PMC7680354
  • 2020 | Menstruation: science and society. Critchley, HOD, Babayev, E, Bulun, SE, Clark, S, Garcia-Grau, I, Gregersen, PK, Kilcoyne, A, Kim, JJ, Lavender, M, Marsh, EE, Matteson, KA, Maybin, JA, Metz, CN, Moreno, I, Silk, K, Sommer, M, Simon, C, Tariyal, R, Taylor, HS, Wagner, GP, Griffith, LG Am J Obstet Gynecol 223 (5): 624-664. doi: 10.1016/j.ajog.2020.06.004. PubMed PMID:32707266 PubMed Central PMC7661839
  • 2020 | Leukemia-Associated Rho Guanine Nucleotide Exchange Factor and Ras Homolog Family Member C Play a Role in Glioblastoma Cell Invasion and Resistance. Ding, Z, Dong, Z, Yang, Y, Fortin Ensign, SP, Sabit, H, Nakada, M, Ruggieri, R, Kloss, JM, Symons, M, Tran, NL, Loftus, JC Am J Pathol 190 (10): 2165-2176. doi: 10.1016/j.ajpath.2020.07.005. PubMed PMID:32693062 PubMed Central PMC7527857
  • 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 PubMed Central PMC7747770
  • 2020 | TROY signals through JAK1-STAT3 to promote glioblastoma cell migration and resistance. Ding, Z, Kloss, JM, Tuncali, S, Tran, NL, Loftus, JC Neoplasia 22 (9): 352-364. doi: 10.1016/j.neo.2020.06.005. PubMed PMID:32629176 PubMed Central PMC7338993
  • 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 | Select Stabilization of a Tumor-Suppressive PP2A Heterotrimer. Shah, VM, English, IA, Sears, RC Trends Pharmacol Sci 41 (9): 595-597. doi: 10.1016/j.tips.2020.06.008. PubMed PMID:32624198 PubMed Central PMC8106543
  • 2020 | Visualizing Human Colorectal Cancer Intratumor Heterogeneity with Phylogeography. Shibata, D iScience 23 (7): 101304. doi: 10.1016/j.isci.2020.101304. PubMed PMID:32623333 PubMed Central PMC7334596
  • 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 | YAP Enhances Tumor Cell Dissemination by Promoting Intravascular Motility and Reentry into Systemic Circulation. Benjamin, DC, Kang, JH, Hamza, B, King, EM, Lamar, JM, Manalis, SR, Hynes, RO Cancer Res 80 (18): 3867-3879. doi: 10.1158/0008-5472.CAN-20-0212. PubMed PMID:32591412 PubMed Central PMC7501173
  • 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 | Mass measurements during lymphocytic leukemia cell polyploidization decouple cell cycle- and cell size-dependent growth. Mu, L, Kang, JH, Olcum, S, Payer, KR, Calistri, NL, Kimmerling, RJ, Manalis, SR, Miettinen, TP Proc Natl Acad Sci U S A 117 (27): 15659-15665. doi: 10.1073/pnas.1922197117. PubMed PMID:32581119 PubMed Central PMC7355023
  • 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 PubMed Central PMC7723336
  • 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 | Exploiting collateral sensitivity controls growth of mixed culture of sensitive and resistant cells and decreases selection for resistant cells in a cell line model. Grolmusz, VK, Chen, J, Emond, R, Cosgrove, PA, Pflieger, L, Nath, A, Moos, PJ, Bild, AH Cancer Cell Int 20 : 253. doi: 10.1186/s12935-020-01337-1. PubMed PMID:32565737 PubMed Central PMC7301982
  • 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
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