CSBC Supported Publications

Publications

  • 2022 | UnMICST: Deep learning with real augmentation for robust segmentation of highly multiplexed images of human tissues. Yapp, C, Novikov, E, Jang, WD, Vallius, T, Chen, YA, Cicconet, M, Maliga, Z, Jacobson, CA, Wei, D, Santagata, S, Pfister, H, Sorger, PK Commun Biol 5 (1): 1263. doi: 10.1038/s42003-022-04076-3. PubMed PMID:36400937 PubMed Central PMC9674686
  • 2022 | A lineage tree-based hidden Markov model quantifies cellular heterogeneity and plasticity. Mohammadi, F, Visagan, S, Gross, SM, Karginov, L, Lagarde, JC, Heiser, LM, Meyer, AS Commun Biol 5 (1): 1258. doi: 10.1038/s42003-022-04208-9. PubMed PMID:36396800 PubMed Central PMC9671968
  • 2022 | The need for evolutionary theory in cancer research. Boddy, AM Eur J Epidemiol : . doi: 10.1007/s10654-022-00936-8. PubMed PMID:36385398
  • 2022 | Multiplexed and reproducible high content screening of live and fixed cells using Dye Drop. Mills, CE, Subramanian, K, Hafner, M, Niepel, M, Gerosa, L, Chung, M, Victor, C, Gaudio, B, Yapp, C, Nirmal, AJ, Clark, N, Sorger, PK Nat Commun 13 (1): 6918. doi: 10.1038/s41467-022-34536-7. PubMed PMID:36376301 PubMed Central PMC9663587
  • 2022 | A Robust Personalized Classification Method for Breast Cancer Metastasis Prediction. Adnan, N, Najnin, T, Ruan, J Cancers (Basel) 14 (21): . doi: 10.3390/cancers14215327. PubMed PMID:36358745 PubMed Central PMC9658757
  • 2022 | Spatial genomics maps the structure, nature and evolution of cancer clones. Lomakin, A, Svedlund, J, Strell, C, Gataric, M, Shmatko, A, Rukhovich, G, Park, JS, Ju, YS, Dentro, S, Kleshchevnikov, V, Vaskivskyi, V, Li, T, Bayraktar, OA, Pinder, S, Richardson, AL, Santagata, S, Campbell, PJ, Russnes, H, Gerstung, M, Nilsson, M, Yates, LR Nature 611 (7936): 594-602. doi: 10.1038/s41586-022-05425-2. PubMed PMID:36352222 PubMed Central PMC9668746
  • 2022 | Systems approaches to uncovering the contribution of environment-mediated drug resistance. Creixell, M, Kim, H, Mohammadi, F, Peyton, SR, Meyer, AS Curr Opin Solid State Mater Sci 26 (5): . doi: 10.1016/j.cossms.2022.101005. PubMed PMID:36321161 PubMed Central PMC9620953
  • 2022 | Protocol to dissociate, process, and analyze the human lung tissue using single-cell RNA-seq. Quintanal-Villalonga, Á, Chan, JM, Masilionis, I, Gao, VR, Xie, Y, Allaj, V, Chow, A, Poirier, JT, Pe'er, D, Rudin, CM, Mazutis, L STAR Protoc 3 (4): 101776. doi: 10.1016/j.xpro.2022.101776. PubMed PMID:36313536 PubMed Central PMC9597186
  • 2022 | Patient-Specific Mathematical Model of the Clear Cell Renal Cell Carcinoma Microenvironment. Sofia, D, Mohammad Mirzaei, N, Shahriyari, L J Pers Med 12 (10): . doi: 10.3390/jpm12101681. PubMed PMID:36294824 PubMed Central PMC9605269
  • 2022 | Resistance to ATR Inhibitors Is Mediated by Loss of the Nonsense-Mediated Decay Factor UPF2. O'Leary, PC, Chen, H, Doruk, YU, Williamson, T, Polacco, B, McNeal, AS, Shenoy, T, Kale, N, Carnevale, J, Stevenson, E, Quigley, DA, Chou, J, Feng, FY, Swaney, DL, Krogan, NJ, Kim, M, Diolaiti, ME, Ashworth, A Cancer Res 82 (21): 3950-3961. doi: 10.1158/0008-5472.CAN-21-4335. PubMed PMID:36273492 PubMed Central PMC9633439
  • 2022 | Publisher Correction: Single-sequence protein structure prediction using a language model and deep learning. Chowdhury, R, Bouatta, N, Biswas, S, Floristean, C, Kharkar, A, Roy, K, Rochereau, C, Ahdritz, G, Zhang, J, Church, GM, Sorger, PK, AlQuraishi, M Nat Biotechnol 40 (11): 1692. doi: 10.1038/s41587-022-01556-z. PubMed PMID:36253538
  • 2022 | Spatial epitope barcoding reveals clonal tumor patch behaviors. Rovira-Clavé, X, Drainas, AP, Jiang, S, Bai, Y, Baron, M, Zhu, B, Dallas, AE, Lee, MC, Chu, TP, Holzem, A, Ayyagari, R, Bhattacharya, D, McCaffrey, EF, Greenwald, NF, Markovic, M, Coles, GL, Angelo, M, Bassik, MC, Sage, J, Nolan, GP Cancer Cell 40 (11): 1423-1439.e11. doi: 10.1016/j.ccell.2022.09.014. PubMed PMID:36240778 PubMed Central PMC9673683
  • 2022 | Single-sequence protein structure prediction using a language model and deep learning. Chowdhury, R, Bouatta, N, Biswas, S, Floristean, C, Kharkar, A, Roy, K, Rochereau, C, Ahdritz, G, Zhang, J, Church, GM, Sorger, PK, AlQuraishi, M Nat Biotechnol 40 (11): 1617-1623. doi: 10.1038/s41587-022-01432-w. PubMed PMID:36192636
  • 2022 | Association of adenosine signaling gene signature with estrogen receptor-positive breast and prostate cancer bone metastasis. Shropshire, DB, Acosta, FM, Fang, K, Benavides, J, Sun, LZ, Jin, VX, Jiang, JX Front Med (Lausanne) 9 : 965429. doi: 10.3389/fmed.2022.965429. PubMed PMID:36186774 PubMed Central PMC9520286
  • 2022 | Exploiting endogenous and therapy-induced apoptotic vulnerabilities in immunoglobulin light chain amyloidosis with BH3 mimetics. Fraser, CS, Spetz, JKE, Qin, X, Presser, A, Choiniere, J, Li, C, Yu, S, Blevins, F, Hata, AN, Miller, JW, Bradshaw, GA, Kalocsay, M, Sanchorawala, V, Sarosiek, S, Sarosiek, KA Nat Commun 13 (1): 5789. doi: 10.1038/s41467-022-33461-z. PubMed PMID:36184661 PubMed Central PMC9527241
  • 2022 | Computational multiplex panel reduction to maximize information retention in breast cancer tissue microarrays. Ternes, L, Lin, JR, Chen, YA, Gray, JW, Chang, YH PLoS Comput Biol 18 (9): e1010505. doi: 10.1371/journal.pcbi.1010505. PubMed PMID:36178966 PubMed Central PMC9555662
  • 2022 | Oncometabolite d-2HG alters T cell metabolism to impair CD8+ T cell function. Notarangelo, G, Spinelli, JB, Perez, EM, Baker, GJ, Kurmi, K, Elia, I, Stopka, SA, Baquer, G, Lin, JR, Golby, AJ, Joshi, S, Baron, HF, Drijvers, JM, Georgiev, P, Ringel, AE, Zaganjor, E, McBrayer, SK, Sorger, PK, Sharpe, AH, Wucherpfennig, KW, Santagata, S, Agar, NYR, Suvà, ML, Haigis, MC Science 377 (6614): 1519-1529. doi: 10.1126/science.abj5104. PubMed PMID:36173860 PubMed Central PMC9629749
  • 2022 | Visinity: Visual Spatial Neighborhood Analysis for Multiplexed Tissue Imaging Data. Warchol, S, Krueger, R, Nirmal, AJ, Gaglia, G, Jessup, J, Ritch, CC, Hoffer, J, Muhlich, J, Burger, ML, Jacks, T, Santagata, S, Sorger, PK, Pfister, H IEEE Trans Vis Comput Graph PP : . doi: 10.1109/TVCG.2022.3209378. PubMed PMID:36170403
  • 2022 | Integrated analysis of multimodal single-cell data with structural similarity. Cao, Y, Fu, L, Wu, J, Peng, Q, Nie, Q, Zhang, J, Xie, X Nucleic Acids Res : . doi: 10.1093/nar/gkac781. PubMed PMID:36130281
  • 2022 | Post-infusion CAR TReg cells identify patients resistant to CD19-CAR therapy. Good, Z, Spiegel, JY, Sahaf, B, Malipatlolla, MB, Ehlinger, ZJ, Kurra, S, Desai, MH, Reynolds, WD, Wong Lin, A, Vandris, P, Wu, F, Prabhu, S, Hamilton, MP, Tamaresis, JS, Hanson, PJ, Patel, S, Feldman, SA, Frank, MJ, Baird, JH, Muffly, L, Claire, GK, Craig, J, Kong, KA, Wagh, D, Coller, J, Bendall, SC, Tibshirani, RJ, Plevritis, SK, Miklos, DB, Mackall, CL Nat Med 28 (9): 1860-1871. doi: 10.1038/s41591-022-01960-7. PubMed PMID:36097223
  • 2022 | In Vitro Reconstitution of the Actin Cytoskeleton Inside Giant Unilamellar Vesicles. Chen, S, Sun, ZG, Murrell, MP J Vis Exp (186): . doi: 10.3791/64026. PubMed PMID:36094272
  • 2022 | Design principles to assemble drug combinations for effective tuberculosis therapy using interpretable pairwise drug response measurements. Larkins-Ford, J, Degefu, YN, Van, N, Sokolov, A, Aldridge, BB Cell Rep Med 3 (9): 100737. doi: 10.1016/j.xcrm.2022.100737. PubMed PMID:36084643 PubMed Central PMC9512659
  • 2022 | Proteotype coevolution and quantitative diversity across 11 mammalian species. Ba, Q, Hei, Y, Dighe, A, Li, W, Maziarz, J, Pak, I, Wang, S, Wagner, GP, Liu, Y Sci Adv 8 (36): eabn0756. doi: 10.1126/sciadv.abn0756. PubMed PMID:36083897 PubMed Central PMC9462687
  • 2022 | A Review of the Role of Oral Microbiome in the Development, Detection, and Management of Head and Neck Squamous Cell Cancers. Burcher, KM, Burcher, JT, Inscore, L, Bloomer, CH, Furdui, CM, Porosnicu, M Cancers (Basel) 14 (17): . doi: 10.3390/cancers14174116. PubMed PMID:36077651 PubMed Central PMC9454796
  • 2022 | PyBioPAX: biological pathway exchange in Python. Gyori, BM, Hoyt, CT J Open Source Softw 7 (71): . doi: 10.21105/joss.04136. PubMed PMID:36071952 PubMed Central PMC9447860
  • 2022 | Novel antigen-presenting cell imparts Treg-dependent tolerance to gut microbiota. Akagbosu, B, Tayyebi, Z, Shibu, G, Paucar Iza, YA, Deep, D, Parisotto, YF, Fisher, L, Pasolli, HA, Thevin, V, Elmentaite, R, Knott, M, Hemmers, S, Jahn, L, Friedrich, C, Verter, J, Wang, ZM, van den Brink, M, Gasteiger, G, Grünewald, TGP, Marie, JC, Leslie, C, Rudensky, AY, Brown, CC Nature 610 (7933): 752-760. doi: 10.1038/s41586-022-05309-5. PubMed PMID:36070798 PubMed Central PMC9605865
  • 2022 | Changes in chromatin accessibility are not concordant with transcriptional changes for single-factor perturbations. Kiani, K, Sanford, EM, Goyal, Y, Raj, A Mol Syst Biol 18 (9): e10979. doi: 10.15252/msb.202210979. PubMed PMID:36069349 PubMed Central PMC9450098
  • 2022 | Systematic replication enables normalization of high-throughput imaging assays. Hunt, GJ, Dane, MA, Korkola, JE, Heiser, LM, Gagnon-Bartsch, JA Bioinformatics 38 (21): 4934-4940. doi: 10.1093/bioinformatics/btac606. PubMed PMID:36063034 PubMed Central PMC9620822
  • 2022 | Quantification of spatial subclonal interactions enhancing the invasive phenotype of pediatric glioma. Tari, H, Kessler, K, Trahearn, N, Werner, B, Vinci, M, Jones, C, Sottoriva, A Cell Rep 40 (9): 111283. doi: 10.1016/j.celrep.2022.111283. PubMed PMID:36044867 PubMed Central PMC9449134
  • 2022 | Microbench: automated metadata management for systems biology benchmarking and reproducibility in Python. Lubbock, ALR, Lopez, CF Bioinformatics 38 (20): 4823-4825. doi: 10.1093/bioinformatics/btac580. PubMed PMID:36000837 PubMed Central PMC9563693
  • 2022 | Homeostasis limits keratinocyte evolution. Schenck, RO, Kim, E, Bravo, RR, West, J, Leedham, S, Shibata, D, Anderson, ARA Proc Natl Acad Sci U S A 119 (35): e2006487119. doi: 10.1073/pnas.2006487119. PubMed PMID:35998218 PubMed Central PMC9436311
  • 2021 | Primary central nervous system lymphoma: advances in MRI and PET imaging. Ambady, P, Hu, LS, Politi, LS, Anzalone, N, Barajas, RF Jr Ann Lymphoma 5 : . doi: 10.21037/aol-20-53. PubMed PMID:35994050 PubMed Central PMC9387672
  • 2022 | Archetype tasks link intratumoral heterogeneity to plasticity and cancer hallmarks in small cell lung cancer. Groves, SM, Ildefonso, GV, McAtee, CO, Ozawa, PMM, Ireland, AS, Stauffer, PE, Wasdin, PT, Huang, X, Qiao, Y, Lim, JS, Bader, J, Liu, Q, Simmons, AJ, Lau, KS, Iams, WT, Hardin, DP, Saff, EB, Holmes, WR, Tyson, DR, Lovly, CM, Rathmell, JC, Marth, G, Sage, J, Oliver, TG, Weaver, AM, Quaranta, V Cell Syst 13 (9): 690-710.e17. doi: 10.1016/j.cels.2022.07.006. PubMed PMID:35981544 PubMed Central PMC9615940
  • 2022 | Lineage plasticity in prostate cancer depends on JAK/STAT inflammatory signaling. Chan, JM, Zaidi, S, Love, JR, Zhao, JL, Setty, M, Wadosky, KM, Gopalan, A, Choo, ZN, Persad, S, Choi, J, LaClair, J, Lawrence, KE, Chaudhary, O, Xu, T, Masilionis, I, Linkov, I, Wang, S, Lee, C, Barlas, A, Morris, MJ, Mazutis, L, Chaligne, R, Chen, Y, Goodrich, DW, Karthaus, WR, Pe'er, D, Sawyers, CL Science 377 (6611): 1180-1191. doi: 10.1126/science.abn0478. PubMed PMID:35981096 PubMed Central PMC9653178
  • 2022 | Alveolar macrophages in early stage COPD show functional deviations with properties of impaired immune activation. Baßler, K, Fujii, W, Kapellos, TS, Dudkin, E, Reusch, N, Horne, A, Reiz, B, Luecken, MD, Osei-Sarpong, C, Warnat-Herresthal, S, Bonaguro, L, Schulte-Schrepping, J, Wagner, A, Günther, P, Pizarro, C, Schreiber, T, Knoll, R, Holsten, L, Kröger, C, De Domenico, E, Becker, M, Händler, K, Wohnhaas, CT, Baumgartner, F, Köhler, M, Theis, H, Kraut, M, Wadsworth, MH 2nd, Hughes, TK, Ferreira, HJ, Hinkley, E, Kaltheuner, IH, Geyer, M, Thiele, C, Shalek, AK, Feißt, A, Thomas, D, Dickten, H, Beyer, M, Baum, P, Yosef, N, Aschenbrenner, AC, Ulas, T, Hasenauer, J, Theis, FJ, Skowasch, D, Schultze, JL Front Immunol 13 : 917232. doi: 10.3389/fimmu.2022.917232. PubMed PMID:35979364 PubMed Central PMC9377018
  • 2022 | Metabolic analyses reveal dysregulated NAD+ metabolism and altered mitochondrial state in ulcerative colitis. Kang, YH, Tucker, SA, Quevedo, SF, Inal, A, Korzenik, JR, Haigis, MC PLoS One 17 (8): e0273080. doi: 10.1371/journal.pone.0273080. PubMed PMID:35976971 PubMed Central PMC9385040
  • 2022 | Single cell spatial analysis reveals the topology of immunomodulatory purinergic signaling in glioblastoma. Coy, S, Wang, S, Stopka, SA, Lin, JR, Yapp, C, Ritch, CC, Salhi, L, Baker, GJ, Rashid, R, Baquer, G, Regan, M, Khadka, P, Cole, KA, Hwang, J, Wen, PY, Bandopadhayay, P, Santi, M, De Raedt, T, Ligon, KL, Agar, NYR, Sorger, PK, Touat, M, Santagata, S Nat Commun 13 (1): 4814. doi: 10.1038/s41467-022-32430-w. PubMed PMID:35973991 PubMed Central PMC9381513
  • 2022 | Of Elephants and Other Mammals: A Comparative Review of Reproductive Tumors and Potential Impact on Conservation. Abegglen, LM, Harrison, TM, Moresco, A, Fowles, JS, Troan, BV, Kiso, WK, Schmitt, D, Boddy, AM, Schiffman, JD Animals (Basel) 12 (15): . doi: 10.3390/ani12152005. PubMed PMID:35953994 PubMed Central PMC9367617
  • 2022 | Mapping nucleosome and chromatin architectures: A survey of computational methods. Fang, K, Wang, J, Liu, L, Jin, VX Comput Struct Biotechnol J 20 : 3955-3962. doi: 10.1016/j.csbj.2022.07.037. PubMed PMID:35950186 PubMed Central PMC9340519
  • 2022 | Pathogenic variants damage cell composition and single cell transcription in cardiomyopathies. Reichart, D, Lindberg, EL, Maatz, H, Miranda, AMA, Viveiros, A, Shvetsov, N, Gärtner, A, Nadelmann, ER, Lee, M, Kanemaru, K, Ruiz-Orera, J, Strohmenger, V, DeLaughter, DM, Patone, G, Zhang, H, Woehler, A, Lippert, C, Kim, Y, Adami, E, Gorham, JM, Barnett, SN, Brown, K, Buchan, RJ, Chowdhury, RA, Constantinou, C, Cranley, J, Felkin, LE, Fox, H, Ghauri, A, Gummert, J, Kanda, M, Li, R, Mach, L, McDonough, B, Samari, S, Shahriaran, F, Yapp, C, Stanasiuk, C, Theotokis, PI, Theis, FJ, van den Bogaerdt, A, Wakimoto, H, Ware, JS, Worth, CL, Barton, PJR, Lee, YA, Teichmann, SA, Milting, H, Noseda, M, Oudit, GY, Heinig, M, Seidman, JG, Hubner, N, Seidman, CE Science 377 (6606): eabo1984. doi: 10.1126/science.abo1984. PubMed PMID:35926050 PubMed Central PMC9528698
  • 2022 | Early on-treatment transcriptional profiling as a tool for improving pathological response prediction in HER2-positive inflammatory breast cancer. Pernas, S, Guerriero, JL, Naumenko, S, Goel, S, Regan, MM, Hu, J, Harrison, BT, Lynce, F, Lin, NU, Partridge, A, Morikawa, A, Hutchinson, J, Mittendorf, EA, Sokolov, A, Overmoyer, B Ther Adv Med Oncol 14 : 17588359221113269. doi: 10.1177/17588359221113269. PubMed PMID:35923923 PubMed Central PMC9340890
  • 2022 | Multipair Förster Resonance Energy Transfer via Spectrally Resolved Single-Molecule Detection. Phelps, C, Huang, T, Wang, J, Nan, X J Phys Chem B 126 (31): 5765-5771. doi: 10.1021/acs.jpcb.2c03249. PubMed PMID:35897122 PubMed Central PMC9377335
  • 2022 | Nanoscopic Spatial Association between Ras and Phosphatidylserine on the Cell Membrane Studied with Multicolor Super Resolution Microscopy. Koester, AM, Tao, K, Szczepaniak, M, Rames, MJ, Nan, X Biomolecules 12 (8): . doi: 10.3390/biom12081033. PubMed PMID:35892343 PubMed Central PMC9332490
  • 2022 | ECM dimensionality tunes actin tension to modulate endoplasmic reticulum function and spheroid phenotypes of mammary epithelial cells. Kai, F, Ou, G, Tourdot, RW, Stashko, C, Gaietta, G, Swift, MF, Volkmann, N, Long, AF, Han, Y, Huang, HH, Northey, JJ, Leidal, AM, Viasnoff, V, Bryant, DM, Guo, W, Wiita, AP, Guo, M, Dumont, S, Hanein, D, Radhakrishnan, R, Weaver, VM EMBO J 41 (17): e109205. doi: 10.15252/embj.2021109205. PubMed PMID:35880301 PubMed Central PMC9434103
  • 2022 | Cas13d knockdown of lung protease Ctsl prevents and treats SARS-CoV-2 infection. Cui, Z, Zeng, C, Huang, F, Yuan, F, Yan, J, Zhao, Y, Zhou, Y, Hankey, W, Jin, VX, Huang, J, Staats, HF, Everitt, JI, Sempowski, GD, Wang, H, Dong, Y, Liu, SL, Wang, Q Nat Chem Biol 18 (10): 1056-1064. doi: 10.1038/s41589-022-01094-4. PubMed PMID:35879545
  • 2022 | Drug independence and the curability of cancer by combination chemotherapy. Pomeroy, AE, Schmidt, EV, Sorger, PK, Palmer, AC Trends Cancer 8 (11): 915-929. doi: 10.1016/j.trecan.2022.06.009. PubMed PMID:35842290 PubMed Central PMC9588605
  • 2022 | ERK2 MAP kinase regulates SUFU binding by multisite phosphorylation of GLI1. Bardwell, AJ, Wu, B, Sarin, KY, Waterman, ML, Atwood, SX, Bardwell, L Life Sci Alliance 5 (11): . doi: 10.26508/lsa.202101353. PubMed PMID:35831023 PubMed Central PMC9279676
  • 2022 | Fides: Reliable trust-region optimization for parameter estimation of ordinary differential equation models. Fröhlich, F, Sorger, PK PLoS Comput Biol 18 (7): e1010322. doi: 10.1371/journal.pcbi.1010322. PubMed PMID:35830470 PubMed Central PMC9312381
  • 2022 | Tumor cells dictate anti-tumor immune responses by altering pyruvate utilization and succinate signaling in CD8+ T cells. Elia, I, Rowe, JH, Johnson, S, Joshi, S, Notarangelo, G, Kurmi, K, Weiss, S, Freeman, GJ, Sharpe, AH, Haigis, MC Cell Metab 34 (8): 1137-1150.e6. doi: 10.1016/j.cmet.2022.06.008. PubMed PMID:35820416 PubMed Central PMC9357162
  • 2022 | Dissecting the treatment-naive ecosystem of human melanoma brain metastasis. Biermann, J, Melms, JC, Amin, AD, Wang, Y, Caprio, LA, Karz, A, Tagore, S, Barrera, I, Ibarra-Arellano, MA, Andreatta, M, Fullerton, BT, Gretarsson, KH, Sahu, V, Mangipudy, VS, Nguyen, TTT, Nair, A, Rogava, M, Ho, P, Koch, PD, Banu, M, Humala, N, Mahajan, A, Walsh, ZH, Shah, SB, Vaccaro, DH, Caldwell, B, Mu, M, Wünnemann, F, Chazotte, M, Berhe, S, Luoma, AM, Driver, J, Ingham, M, Khan, SA, Rapisuwon, S, Slingluff, CL Jr, Eigentler, T, Röcken, M, Carvajal, R, Atkins, MB, Davies, MA, Agustinus, A, Bakhoum, SF, Azizi, E, Siegelin, M, Lu, C, Carmona, SJ, Hibshoosh, H, Ribas, A, Canoll, P, Bruce, JN, Bi, WL, Agrawal, P, Schapiro, D, Hernando, E, Macosko, EZ, Chen, F, Schwartz, GK, Izar, B Cell 185 (14): 2591-2608.e30. doi: 10.1016/j.cell.2022.06.007. PubMed PMID:35803246 PubMed Central PMC9677434
  • 2022 | A multiplex implantable microdevice assay identifies synergistic combinations of cancer immunotherapies and conventional drugs. Tatarova, Z, Blumberg, DC, Korkola, JE, Heiser, LM, Muschler, JL, Schedin, PJ, Ahn, SW, Mills, GB, Coussens, LM, Jonas, O, Gray, JW Nat Biotechnol : . doi: 10.1038/s41587-022-01379-y. PubMed PMID:35788566
  • 2022 | Oncogenic KRAS G12C: Kinetic and redox characterization of covalent inhibition. Huynh, MV, Parsonage, D, Forshaw, TE, Chirasani, VR, Hobbs, GA, Wu, H, Lee, J, Furdui, CM, Poole, LB, Campbell, SL J Biol Chem 298 (8): 102186. doi: 10.1016/j.jbc.2022.102186. PubMed PMID:35753348 PubMed Central PMC9352912
  • 2022 | A database of pediatric drug effects to evaluate ontogenic mechanisms from child growth and development. Giangreco, NP, Tatonetti, NP Med (N Y) 3 (8): 579-595.e7. doi: 10.1016/j.medj.2022.06.001. PubMed PMID:35752163 PubMed Central PMC9378670
  • 2022 | Accurate Identification of Subclones in Tumor Genomes. Ahmadinejad, N, Troftgruben, S, Wang, J, Chandrashekar, PB, Dinu, V, Maley, C, Liu, L Mol Biol Evol 39 (7): . doi: 10.1093/molbev/msac136. PubMed PMID:35749590 PubMed Central PMC9260306
  • 2022 | Cancer cells depend on environmental lipids for proliferation when electron acceptors are limited. Li, Z, Ji, BW, Dixit, PD, Tchourine, K, Lien, EC, Hosios, AM, Abbott, KL, Rutter, JC, Westermark, AM, Gorodetsky, EF, Sullivan, LB, Vander Heiden, MG, Vitkup, D Nat Metab 4 (6): 711-723. doi: 10.1038/s42255-022-00588-8. PubMed PMID:35739397
  • 2022 | Integrating multi-omics data reveals function and therapeutic potential of deubiquitinating enzymes. Doherty, LM, Mills, CE, Boswell, SA, Liu, X, Hoyt, CT, Gyori, B, Buhrlage, SJ, Sorger, PK Elife 11 : . doi: 10.7554/eLife.72879. PubMed PMID:35737447 PubMed Central PMC9225015
  • 2022 | A scalable, open-source implementation of a large-scale mechanistic model for single cell proliferation and death signaling. Erdem, C, Mutsuddy, A, Bensman, EM, Dodd, WB, Saint-Antoine, MM, Bouhaddou, M, Blake, RC, Gross, SM, Heiser, LM, Feltus, FA, Birtwistle, MR Nat Commun 13 (1): 3555. doi: 10.1038/s41467-022-31138-1. PubMed PMID:35729113 PubMed Central PMC9213456
  • 2022 | Single-cell characterization of step-wise acquisition of carboplatin resistance in ovarian cancer. Wenzel, AT, Champa, D, Venkatesh, H, Sun, S, Tsai, CY, Mesirov, JP, Bui, JD, Howell, SB, Harismendy, O NPJ Syst Biol Appl 8 (1): 20. doi: 10.1038/s41540-022-00230-z. PubMed PMID:35715421 PubMed Central PMC9206019
  • 2022 | Single-cell profiling of the antigen-specific response to BNT162b2 SARS-CoV-2 RNA vaccine. Kramer, KJ, Wilfong, EM, Voss, K, Barone, SM, Shiakolas, AR, Raju, N, Roe, CE, Suryadevara, N, Walker, LM, Wall, SC, Paulo, A, Schaefer, S, Dahunsi, D, Westlake, CS, Crowe, JE Jr, Carnahan, RH, Rathmell, JC, Bonami, RH, Georgiev, IS, Irish, JM Nat Commun 13 (1): 3466. doi: 10.1038/s41467-022-31142-5. PubMed PMID:35710908 PubMed Central PMC9201272
  • 2022 | Systematically quantifying morphological features reveals constraints on organoid phenotypes. Beck, LE, Lee, J, Coté, C, Dunagin, MC, Lukonin, I, Salla, N, Chang, MK, Hughes, AJ, Mornin, JD, Gartner, ZJ, Liberali, P, Raj, A Cell Syst 13 (7): 547-560.e3. doi: 10.1016/j.cels.2022.05.008. PubMed PMID:35705097 PubMed Central PMC9350855
  • 2022 | Diet, Microbes, and Cancer Across the Tree of Life: a Systematic Review. Kapsetaki, SE, Marquez Alcaraz, G, Maley, CC, Whisner, CM, Aktipis, A Curr Nutr Rep 11 (3): 508-525. doi: 10.1007/s13668-022-00420-5. PubMed PMID:35704266 PubMed Central PMC9197725
  • 2022 | Accurate Identification of Transcription Regulatory Sequences and Genes in Coronaviruses. Zhang, C, Sashittal, P, Xiang, M, Zhang, Y, Kazi, A, El-Kebir, M Mol Biol Evol 39 (7): . doi: 10.1093/molbev/msac133. PubMed PMID:35700225 PubMed Central PMC9214144
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