CSBC Supported Publications

Publications

  • 2021 | Simplifying the development of portable, scalable, and reproducible workflows. Piccolo, SR, Ence, ZE, Anderson, EC, Chang, JT, Bild, AH Elife 10 : . doi: 10.7554/eLife.71069. PubMed PMID:34643507
  • 2021 | Differentiable biology: using deep learning for biophysics-based and data-driven modeling of molecular mechanisms. AlQuraishi, M, Sorger, PK Nat Methods 18 (10): 1169-1180. doi: 10.1038/s41592-021-01283-4. PubMed PMID:34608321
  • 2021 | Determinants of SARS-CoV-2 entry and replication in airway mucosal tissue and susceptibility in smokers. Nakayama, T, Lee, IT, Jiang, S, Matter, MS, Yan, CH, Overdevest, JB, Wu, CT, Goltsev, Y, Shih, LC, Liao, CK, Zhu, B, Bai, Y, Lidsky, P, Xiao, Y, Zarabanda, D, Yang, A, Easwaran, M, Schürch, CM, Chu, P, Chen, H, Stalder, AK, McIlwain, DR, Borchard, NA, Gall, PA, Dholakia, SS, Le, W, Xu, L, Tai, CJ, Yeh, TH, Erickson-Direnzo, E, Duran, JM, Mertz, KD, Hwang, PH, Haslbauer, JD, Jackson, PK, Menter, T, Andino, R, Canoll, PD, DeConde, AS, Patel, ZM, Tzankov, A, Nolan, GP, Nayak, JV Cell Rep Med : 100421. doi: 10.1016/j.xcrm.2021.100421. PubMed PMID:34604819 PubMed Central PMC8479532
  • 2021 | Atlas of clinically distinct cell states and ecosystems across human solid tumors. Luca, BA, Steen, CB, Matusiak, M, Azizi, A, Varma, S, Zhu, C, Przybyl, J, Espín-Pérez, A, Diehn, M, Alizadeh, AA, van de Rijn, M, Gentles, AJ, Newman, AM Cell : . doi: 10.1016/j.cell.2021.09.014. PubMed PMID:34597583
  • 2021 | A protein network map of head and neck cancer reveals PIK3CA mutant drug sensitivity. Swaney, DL, Ramms, DJ, Wang, Z, Park, J, Goto, Y, Soucheray, M, Bhola, N, Kim, K, Zheng, F, Zeng, Y, McGregor, M, Herrington, KA, O'Keefe, R, Jin, N, VanLandingham, NK, Foussard, H, Von Dollen, J, Bouhaddou, M, Jimenez-Morales, D, Obernier, K, Kreisberg, JF, Kim, M, Johnson, DE, Jura, N, Grandis, JR, Gutkind, JS, Ideker, T, Krogan, NJ Science 374 (6563): eabf2911. doi: 10.1126/science.abf2911. PubMed PMID:34591642
  • 2021 | Interpretation of cancer mutations using a multiscale map of protein systems. Zheng, F, Kelly, MR, Ramms, DJ, Heintschel, ML, Tao, K, Tutuncuoglu, B, Lee, JJ, Ono, K, Foussard, H, Chen, M, Herrington, KA, Silva, E, Liu, SN, Chen, J, Churas, C, Wilson, N, Kratz, A, Pillich, RT, Patel, DN, Park, J, Kuenzi, B, Yu, MK, Licon, K, Pratt, D, Kreisberg, JF, Kim, M, Swaney, DL, Nan, X, Fraley, SI, Gutkind, JS, Krogan, NJ, Ideker, T Science 374 (6563): eabf3067. doi: 10.1126/science.abf3067. PubMed PMID:34591613
  • 2021 | A protein interaction landscape of breast cancer. Kim, M, Park, J, Bouhaddou, M, Kim, K, Rojc, A, Modak, M, Soucheray, M, McGregor, MJ, O'Leary, P, Wolf, D, Stevenson, E, Foo, TK, Mitchell, D, Herrington, KA, Muñoz, DP, Tutuncuoglu, B, Chen, KH, Zheng, F, Kreisberg, JF, Diolaiti, ME, Gordan, JD, Coppé, JP, Swaney, DL, Xia, B, van 't Veer, L, Ashworth, A, Ideker, T, Krogan, NJ Science 374 (6563): eabf3066. doi: 10.1126/science.abf3066. PubMed PMID:34591612
  • 2021 | Measuring kinetics and metastatic propensity of CTCs by blood exchange between mice. Hamza, B, Miller, AB, Meier, L, Stockslager, M, Ng, SR, King, EM, Lin, L, DeGouveia, KL, Mulugeta, N, Calistri, NL, Strouf, H, Bray, C, Rodriguez, F, Freed-Pastor, WA, Chin, CR, Jaramillo, GC, Burger, ML, Weinberg, RA, Shalek, AK, Jacks, T, Manalis, SR Nat Commun 12 (1): 5680. doi: 10.1038/s41467-021-25917-5. PubMed PMID:34584084
  • 2021 | ENDLESS FORMS MOST BEAUTIFUL: A GARDEN SHOWS THAT CANCER IS A PART OF LIFE. Winfrey, P, Robertson, C, Maley, C, Aktipis, A Leonardo (Oxf) 54 (4): 398-401. doi: 10.1162/leon_a_01915. PubMed PMID:34565895 PubMed Central PMC8460130
  • 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, Li, Y, Sinha, MS, Li, J, Yu, SH, LeBoeuf, NR, Sorger, PK Front Bioeng Biotechnol 9 : 690905. doi: 10.3389/fbioe.2021.690905. PubMed PMID:34552915 PubMed Central PMC8450396
  • 2021 | Hi-C profiling of cancer spheroids identifies 3D-growth-specific chromatin interactions in breast cancer endocrine resistance. Li, J, Fang, K, Choppavarapu, L, Yang, K, Yang, Y, Wang, J, Cao, R, Jatoi, I, Jin, VX Clin Epigenetics 13 (1): 175. doi: 10.1186/s13148-021-01167-6. PubMed PMID:34535185 PubMed Central PMC8447690
  • 2021 | Predator-Prey in Tumor-Immune Interactions: A Wrong Model or Just an Incomplete One?. Kareva, I, Luddy, KA, O'Farrelly, C, Gatenby, RA, Brown, JS Front Immunol 12 : 668221. doi: 10.3389/fimmu.2021.668221. PubMed PMID:34531851 PubMed Central PMC8438324
  • 2021 | Do mechanisms matter? Comparing cancer treatment strategies across mathematical models and outcome objectives. Buhler, CK, Terry, RS, Link, KG, Adler, FR Math Biosci Eng 18 (5): 6305-6327. doi: 10.3934/mbe.2021315. PubMed PMID:34517535
  • 2021 | Programmatic modeling for biological systems. Lubbock, ALR, Lopez, CF Curr Opin Syst Biol 27 : . doi: 10.1016/j.coisb.2021.05.004. PubMed PMID:34485764 PubMed Central PMC8411905
  • 2021 | Phosphoproteomics: a valuable tool for uncovering molecular signaling in cancer cells. Gerritsen, JS, White, FM Expert Rev Proteomics 18 (8): 661-674. doi: 10.1080/14789450.2021.1976152. PubMed PMID:34468274
  • 2021 | NucHMM: a method for quantitative modeling of nucleosome organization identifying functional nucleosome states distinctly associated with splicing potentiality. Fang, K, Li, T, Huang, Y, Jin, VX Genome Biol 22 (1): 250. doi: 10.1186/s13059-021-02465-1. PubMed PMID:34446075 PubMed Central PMC8390234
  • 2021 | Predicting functional consequences of mutations using molecular interaction network features. Ozturk, K, Carter, H Hum Genet : . doi: 10.1007/s00439-021-02329-5. PubMed PMID:34432150
  • 2021 | Modeling the effects of EMT-immune dynamics on carcinoma disease progression. Bergman, DR, Karikomi, MK, Yu, M, Nie, Q, MacLean, AL Commun Biol 4 (1): 983. doi: 10.1038/s42003-021-02499-y. PubMed PMID:34408236 PubMed Central PMC8373868
  • 2021 | Age-dependent regulation of SARS-CoV-2 cell entry genes and cell death programs correlates with COVID-19 severity. Inde, Z, Croker, BA, Yapp, C, Joshi, GN, Spetz, J, Fraser, C, Qin, X, Xu, L, Deskin, B, Ghelfi, E, Webb, G, Carlin, AF, Zhu, YP, Leibel, SL, Garretson, AF, Clark, AE, Duran, JM, Pretorius, V, Crotty-Alexander, LE, Li, C, Lee, JC, Sodhi, C, Hackam, DJ, Sun, X, Hata, AN, Kobzik, L, Miller, J, Park, JA, Brownfield, D, Jia, H, Sarosiek, KA Sci Adv 7 (34): . doi: 10.1126/sciadv.abf8609. PubMed PMID:34407940 PubMed Central PMC8373124
  • 2021 | The vascular niche in next generation microphysiological systems. Ewald, ML, Chen, YH, Lee, AP, Hughes, CCW Lab Chip 21 (17): 3244-3262. doi: 10.1039/d1lc00530h. PubMed PMID:34396383
  • 2021 | Detailed Balance Broken by Catch Bond Kinetics Enables Mechanical-Adaptation in Active Materials. Tabatabai, AP, Seara, DS, Tibbs, J, Yadav, V, Linsmeier, I, Murrell, MP Adv Funct Mater 31 (10): . doi: 10.1002/adfm.202006745. PubMed PMID:34393691 PubMed Central PMC8357268
  • 2021 | KITlow Cells Mediate Imatinib Resistance in Gastrointestinal Stromal Tumor. Banerjee, S, Yoon, H, Ting, S, Tang, CM, Yebra, M, Wenzel, AT, Yeerna, H, Mesirov, JP, Wechsler-Reya, RJ, Tamayo, P, Sicklick, JK Mol Cancer Ther 20 (10): 2035-2048. doi: 10.1158/1535-7163.MCT-20-0973. PubMed PMID:34376580 PubMed Central PMC8492542
  • 2021 | Recombination and lineage-specific mutations linked to the emergence of SARS-CoV-2. Patiño-Galindo, JÁ, Filip, I, Chowdhury, R, Maranas, CD, Sorger, PK, AlQuraishi, M, Rabadan, R Genome Med 13 (1): 124. doi: 10.1186/s13073-021-00943-6. PubMed PMID:34362430 PubMed Central PMC8343217
  • 2021 | Unsupervised machine learning reveals key immune cell subsets in COVID-19, rhinovirus infection, and cancer therapy. Barone, SM, Paul, AG, Muehling, LM, Lannigan, JA, Kwok, WW, Turner, RB, Woodfolk, JA, Irish, JM Elife 10 : . doi: 10.7554/eLife.64653. PubMed PMID:34350827 PubMed Central PMC8370768
  • 2021 | A domain damage index to prioritizing the pathogenicity of missense variants. Chen, HC, Wang, J, Liu, Q, Shyr, Y Hum Mutat 42 (11): 1503-1517. doi: 10.1002/humu.24269. PubMed PMID:34350656
  • 2021 | PD-L1 is upregulated via BRD2 in head and neck squamous cell carcinoma models of acquired cetuximab resistance. Bhola, NE, Njatcha, C, Hu, L, Lee, ED, Shiah, JV, Kim, MO, Johnson, DE, Grandis, JR Head Neck 43 (11): 3364-3373. doi: 10.1002/hed.26827. PubMed PMID:34346116
  • 2021 | Sensitivity to targeted therapy differs between HER2-amplified breast cancer cells harboring kinase and helical domain mutations in PIK3CA. Garay, JP, Smith, R, Devlin, K, Hollern, DP, Liby, T, Liu, M, Boddapati, S, Watson, SS, Esch, A, Zheng, T, Thompson, W, Babcock, D, Kwon, S, Chin, K, Heiser, L, Gray, JW, Korkola, JE Breast Cancer Res 23 (1): 81. doi: 10.1186/s13058-021-01457-0. PubMed PMID:34344439 PubMed Central PMC8336338
  • 2021 | Protein structure prediction by AlphaFold2: are attention and symmetries all you need?. Bouatta, N, Sorger, P, AlQuraishi, M Acta Crystallogr D Struct Biol 77 (Pt 8): 982-991. doi: 10.1107/S2059798321007531. PubMed PMID:34342271 PubMed Central PMC8329862
  • 2021 | MuSyC is a consensus framework that unifies multi-drug synergy metrics for combinatorial drug discovery. Wooten, DJ, Meyer, CT, Lubbock, ALR, Quaranta, V, Lopez, CF Nat Commun 12 (1): 4607. doi: 10.1038/s41467-021-24789-z. PubMed PMID:34326325 PubMed Central PMC8322415
  • 2021 | Assessing the filtration efficiency and regulatory status of N95s and nontraditional filtering face-piece respirators available during the COVID-19 pandemic. Plana, D, Tian, E, Cramer, AK, Yang, H, Carmack, MM, Sinha, MS, Bourgeois, FT, Yu, SH, Masse, P, Boyer, J, Kim, M, Mo, J, LeBoeuf, NR, Li, J, Sorger, PK BMC Infect Dis 21 (1): 712. doi: 10.1186/s12879-021-06008-8. PubMed PMID:34325673 PubMed Central PMC8319695
  • 2021 | Toward uncharted territory of cellular heterogeneity: advances and applications of single-cell RNA-seq. Lieberman, B, Kusi, M, Hung, CN, Chou, CW, He, N, Ho, YY, Taverna, JA, Huang, THM, Chen, CL J Transl Genet Genom 5 : 1-21. doi: 10.20517/jtgg.2020.51. PubMed PMID:34322662 PubMed Central PMC8315474
  • 2020 | ACDC: Automated Cell Detection and Counting for Time-Lapse Fluorescence Microscopy. Rundo, L, Tangherloni, A, Tyson, DR, Betta, R, Militello, C, Spolaor, S, Nobile, MS, Besozzi, D, Lubbock, ALR, Quaranta, V, Mauri, G, Lopez, CF, Cazzaniga, P Appl Sci (Basel) 10 (18): . doi: 10.3390/app10186187. PubMed PMID:34306736 PubMed Central PMC8297459
  • 2021 | Tepoxalin increases chemotherapy efficacy in drug-resistant breast cancer cells overexpressing the multidrug transporter gene ABCB1. McQuerry, JA, Chen, J, Chang, JT, Bild, AH Transl Oncol 14 (10): 101181. doi: 10.1016/j.tranon.2021.101181. PubMed PMID:34298440 PubMed Central PMC8322466
  • 2021 | Phosphorylated WNK kinase networks in recoded bacteria recapitulate physiological function. Schiapparelli, P, Pirman, NL, Mohler, K, Miranda-Herrera, PA, Zarco, N, Kilic, O, Miller, C, Shah, SR, Rogulina, S, Hungerford, W, Abriola, L, Hoyer, D, Turk, BE, Guerrero-Cázares, H, Isaacs, FJ, Quiñones-Hinojosa, A, Levchenko, A, Rinehart, J Cell Rep 36 (3): 109416. doi: 10.1016/j.celrep.2021.109416. PubMed PMID:34289367 PubMed Central PMC8379681
  • 2021 | Computing the Riemannian curvature of image patch and single-cell RNA sequencing data manifolds using extrinsic differential geometry. Sritharan, D, Wang, S, Hormoz, S Proc Natl Acad Sci U S A 118 (29): . doi: 10.1073/pnas.2100473118. PubMed PMID:34272279 PubMed Central PMC8307776
  • 2021 | SAILER: scalable and accurate invariant representation learning for single-cell ATAC-seq processing and integration. Cao, Y, Fu, L, Wu, J, Peng, Q, Nie, Q, Zhang, J, Xie, X Bioinformatics 37 (Suppl_1): i317-i326. doi: 10.1093/bioinformatics/btab303. PubMed PMID:34252968 PubMed Central PMC8275346
  • 2021 | Landscape of innate lymphoid cells in human head and neck cancer reveals divergent NK cell states in the tumor microenvironment. Moreno-Nieves, UY, Tay, JK, Saumyaa, S, Horowitz, NB, Shin, JH, Mohammad, IA, Luca, B, Mundy, DC, Gulati, GS, Bedi, N, Chang, S, Chen, C, Kaplan, MJ, Rosenthal, EL, Holsinger, FC, Divi, V, Baik, FM, Sirjani, DB, Gentles, AJ, Newman, AM, Freud, AG, Sunwoo, JB Proc Natl Acad Sci U S A 118 (28): . doi: 10.1073/pnas.2101169118. PubMed PMID:34244432 PubMed Central PMC8285950
  • 2021 | Few-shot learning creates predictive models of drug response that translate from high-throughput screens to individual patients. Ma, J, Fong, SH, Luo, Y, Bakkenist, CJ, Shen, JP, Mourragui, S, Wessels, LFA, Hafner, M, Sharan, R, Peng, J, Ideker, T Nat Cancer 2 (2): 233-244. doi: 10.1038/s43018-020-00169-2. PubMed PMID:34223192 PubMed Central PMC8248912
  • 2021 | Ex Vivo Analysis of Primary Tumor Specimens for Evaluation of Cancer Therapeutics. Tognon, CE, Sears, RC, Mills, GB, Gray, JW, Tyner, JW Annu Rev Cancer Biol 5 : 39-57. doi: 10.1146/annurev-cancerbio-043020-125955. PubMed PMID:34222745 PubMed Central PMC8248658
  • 2021 | Inhibition of YTHDF2 triggers proteotoxic cell death in MYC-driven breast cancer. Einstein, JM, Perelis, M, Chaim, IA, Meena, JK, Nussbacher, JK, Tankka, AT, Yee, BA, Li, H, Madrigal, AA, Neill, NJ, Shankar, A, Tyagi, S, Westbrook, TF, Yeo, GW Mol Cell 81 (15): 3048-3064.e9. doi: 10.1016/j.molcel.2021.06.014. PubMed PMID:34216543 PubMed Central PMC8359670
  • 2021 | Reconstructing single-cell karyotype alterations in colorectal cancer identifies punctuated and gradual diversification patterns. Bollen, Y, Stelloo, E, van Leenen, P, van den Bos, M, Ponsioen, B, Lu, B, van Roosmalen, MJ, Bolhaqueiro, ACF, Kimberley, C, Mossner, M, Cross, WCH, Besselink, NJM, van der Roest, B, Boymans, S, Oost, KC, de Vries, SG, Rehmann, H, Cuppen, E, Lens, SMA, Kops, GJPL, Kloosterman, WP, Terstappen, LWMM, Barnes, CP, Sottoriva, A, Graham, TA, Snippert, HJG Nat Genet 53 (8): 1187-1195. doi: 10.1038/s41588-021-00891-2. PubMed PMID:34211178 PubMed Central PMC8346364
  • 2021 | Relevance of circulating hybrid cells as a non-invasive biomarker for myriad solid tumors. Dietz, MS, Sutton, TL, Walker, BS, Gast, CE, Zarour, L, Sengupta, SK, Swain, JR, Eng, J, Parappilly, M, Limbach, K, Sattler, A, Burlingame, E, Chin, Y, Gower, A, Mira, JLM, Sapre, A, Chiu, YJ, Clayburgh, DR, Pommier, SJ, Cetnar, JP, Fischer, JM, Jaboin, JJ, Pommier, RF, Sheppard, BC, Tsikitis, VL, Skalet, AH, Mayo, SC, Lopez, CD, Gray, JW, Mills, GB, Mitri, Z, Chang, YH, Chin, K, Wong, MH Sci Rep 11 (1): 13630. doi: 10.1038/s41598-021-93053-7. PubMed PMID:34211050 PubMed Central PMC8249418
  • 2021 | Specificity of Human Sulfiredoxin for Reductant and Peroxiredoxin Oligomeric State. Forshaw, TE, Reisz, JA, Nelson, KJ, Gumpena, R, Lawson, JR, Jönsson, TJ, Wu, H, Clodfelter, JE, Johnson, LC, Furdui, CM, Lowther, WT Antioxidants (Basel) 10 (6): . doi: 10.3390/antiox10060946. PubMed PMID:34208049 PubMed Central PMC8230665
  • 2021 | Evaluation of Somatic Mutations in Solid Metastatic Pan-Cancer Patients. Roosan, MR, Mambetsariev, I, Pharaon, R, Fricke, J, Baroz, AR, Chao, J, Chen, C, Nasser, MW, Chirravuri-Venkata, R, Jain, M, Smith, L, Yost, SE, Reckamp, KL, Pillai, R, Arvanitis, L, Afkhami, M, Wang, EW, Chung, V, Cristea, M, Fakih, M, Koczywas, M, Massarelli, E, Mortimer, J, Yuan, Y, Batra, SK, Pal, S, Salgia, R Cancers (Basel) 13 (11): . doi: 10.3390/cancers13112776. PubMed PMID:34204917 PubMed Central PMC8199748
  • 2021 | A yeast-optimized single-cell transcriptomics platform elucidates how mycophenolic acid and guanine alter global mRNA levels. Urbonaite, G, Lee, JTH, Liu, P, Parada, GE, Hemberg, M, Acar, M Commun Biol 4 (1): 822. doi: 10.1038/s42003-021-02320-w. PubMed PMID:34193958 PubMed Central PMC8245502
  • 2021 | Targeting Pyruvate Kinase M2 Phosphorylation Reverses Aggressive Cancer Phenotypes. Apostolidi, M, Vathiotis, IA, Muthusamy, V, Gaule, P, Gassaway, BM, Rimm, DL, Rinehart, J Cancer Res 81 (16): 4346-4359. doi: 10.1158/0008-5472.CAN-20-4190. PubMed PMID:34185676 PubMed Central PMC8373815
  • 2021 | A community challenge to evaluate RNA-seq, fusion detection, and isoform quantification methods for cancer discovery. Creason, A, Haan, D, Dang, K, Chiotti, KE, Inkman, M, Lamb, A, Yu, T, Hu, Y, Norman, TC, Buchanan, A, van Baren, MJ, Spangler, R, Rollins, MR, Spellman, PT, Rozanov, D, Zhang, J, Maher, CA, Caloian, C, Watson, JD, Uhrig, S, Haas, BJ, Jain, M, Akeson, M, Ahsen, ME, SMC-RNA Challenge Participants, Stolovitzky, G, Guinney, J, Boutros, PC, Stuart, JM, Ellrott, K Cell Syst 12 (8): 827-838.e5. doi: 10.1016/j.cels.2021.05.021. PubMed PMID:34146471 PubMed Central PMC8376800
  • 2021 | HER2 Isoforms Uniquely Program Intratumor Heterogeneity and Predetermine Breast Cancer Trajectories During the Occult Tumorigenic Phase. Ginzel, JD, Acharya, CR, Lubkov, V, Mori, H, Boone, PG, Rochelle, LK, Roberts, WL, Everitt, JI, Hartman, ZC, Crosby, EJ, Barak, LS, Caron, MG, Chen, JQ, Hubbard, NE, Cardiff, RD, Borowsky, AD, Lyerly, HK, Snyder, JC Mol Cancer Res 19 (10): 1699-1711. doi: 10.1158/1541-7786.MCR-21-0215. PubMed PMID:34131071 PubMed Central PMC8507429
  • 2021 | Immu-Mela: An open resource for exploring immunotherapy-related multidimensional genomic profiles in melanoma. Yang, J, Zhao, S, Wang, J, Sheng, Q, Liu, Q, Shyr, Y J Genet Genomics 48 (5): 361-368. doi: 10.1016/j.jgg.2021.03.016. PubMed PMID:34127402 PubMed Central PMC8349898
  • 2021 | A new method to accurately identify single nucleotide variants using small FFPE breast samples. Fortunato, A, Mallo, D, Rupp, SM, King, LM, Hardman, T, Lo, JY, Hall, A, Marks, JR, Hwang, ES, Maley, CC Brief Bioinform : . doi: 10.1093/bib/bbab221. PubMed PMID:34117742
  • 2021 | Molecular omics resources should require sex annotation: a call for action. Bond, KM, McCarthy, MM, Rubin, JB, Swanson, KR Nat Methods 18 (6): 585-588. doi: 10.1038/s41592-021-01168-6. PubMed PMID:34099934
  • 2021 | 3D Printed frames to enable reuse and improve the fit of N95 and KN95 respirators. McAvoy, M, Bui, AN, Hansen, C, Plana, D, Said, JT, Yu, Z, Yang, H, Freake, J, Van, C, Krikorian, D, Cramer, A, Smith, L, Jiang, L, Lee, KJ, Li, SJ, Beller, B, Huggins, K, Short, MP, Yu, SH, Mostaghimi, A, Sorger, PK, LeBoeuf, NR BMC Biomed Eng 3 (1): 10. doi: 10.1186/s42490-021-00055-7. PubMed PMID:34099062 PubMed Central PMC8182357
  • 2021 | SARS-CoV-2 infects human pancreatic β cells and elicits β cell impairment. Wu, CT, Lidsky, PV, Xiao, Y, Lee, IT, Cheng, R, Nakayama, T, Jiang, S, Demeter, J, Bevacqua, RJ, Chang, CA, Whitener, RL, Stalder, AK, Zhu, B, Chen, H, Goltsev, Y, Tzankov, A, Nayak, JV, Nolan, GP, Matter, MS, Andino, R, Jackson, PK Cell Metab 33 (8): 1565-1576.e5. doi: 10.1016/j.cmet.2021.05.013. PubMed PMID:34081912 PubMed Central PMC8130512
  • 2021 | Unsupervised logic-based mechanism inference for network-driven biological processes. Prugger, M, Einkemmer, L, Beik, SP, Wasdin, PT, Harris, LA, Lopez, CF PLoS Comput Biol 17 (6): e1009035. doi: 10.1371/journal.pcbi.1009035. PubMed PMID:34077417 PubMed Central PMC8202945
  • 2021 | Molecular and Clinical Features of Hospital Admissions in Patients with Thoracic Malignancies on Immune Checkpoint Inhibitors. Zhao, D, Li, H, Mambetsariev, I, Chen, C, Pharaon, R, Fricke, J, Baroz, AR, Kulkarni, P, Xing, Y, Massarelli, E, Koczywas, M, Reckamp, KL, Margolin, K, Salgia, R Cancers (Basel) 13 (11): . doi: 10.3390/cancers13112653. PubMed PMID:34071259 PubMed Central PMC8198372
  • 2021 | Peptide-tiling screens of cancer drivers reveal oncogenic protein domains and associated peptide inhibitors. Ford, KM, Panwala, R, Chen, DH, Portell, A, Palmer, N, Mali, P Cell Syst 12 (7): 716-732.e7. doi: 10.1016/j.cels.2021.05.002. PubMed PMID:34051140 PubMed Central PMC8298269
  • 2021 | Contacts with Macrophages Promote an Aggressive Nanomechanical Phenotype of Circulating Tumor Cells in Prostate Cancer. Osmulski, PA, Cunsolo, A, Chen, M, Qian, Y, Lin, CL, Hung, CN, Mahalingam, D, Kirma, NB, Chen, CL, Taverna, JA, Liss, MA, Thompson, IM, Huang, TH, Gaczynska, ME Cancer Res 81 (15): 4110-4123. doi: 10.1158/0008-5472.CAN-20-3595. PubMed PMID:34045187 PubMed Central PMC8367292
  • 2021 | Thunor: visualization and analysis of high-throughput dose-response datasets. Lubbock, ALR, Harris, LA, Quaranta, V, Tyson, DR, Lopez, CF Nucleic Acids Res 49 (W1): W633-W640. doi: 10.1093/nar/gkab424. PubMed PMID:34038546 PubMed Central PMC8265171
  • 2021 | Evolution of core archetypal phenotypes in progressive high grade serous ovarian cancer. Nath, A, Cosgrove, PA, Mirsafian, H, Christie, EL, Pflieger, L, Copeland, B, Majumdar, S, Cristea, MC, Han, ES, Lee, SJ, Wang, EW, Fereday, S, Traficante, N, Salgia, R, Werner, T, Cohen, AL, Moos, P, Chang, JT, Bowtell, DDL, Bild, AH Nat Commun 12 (1): 3039. doi: 10.1038/s41467-021-23171-3. PubMed PMID:34031395 PubMed Central PMC8144406
  • 2021 | Detection of Post-translational Modifications on MYC. Daniel, CJ, Sun, XX, Chen, Y, Zhang, X, Dai, MS, Sears, RC Methods Mol Biol 2318 : 69-85. doi: 10.1007/978-1-0716-1476-1_5. PubMed PMID:34019287
  • 2021 | Single-cell characterization of macrophages in glioblastoma reveals MARCO as a mesenchymal pro-tumor marker. Chen, AX, Gartrell, RD, Zhao, J, Upadhyayula, PS, Zhao, W, Yuan, J, Minns, HE, Dovas, A, Bruce, JN, Lasorella, A, Iavarone, A, Canoll, P, Sims, PA, Rabadan, R Genome Med 13 (1): 88. doi: 10.1186/s13073-021-00906-x. PubMed PMID:34011400 PubMed Central PMC8136167
  • 2021 | Membrane signalosome: where biophysics meets systems biology. Kandy, SK, Janmey, PA, Radhakrishnan, R Curr Opin Syst Biol 25 : 34-41. doi: 10.1016/j.coisb.2021.02.001. PubMed PMID:33997528 PubMed Central PMC8117111
  • 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 69 (9): 2199-2214. doi: 10.1002/glia.24018. PubMed PMID:33991013
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