CSBC Supported Publications

Publications

  • 2022 | 2-Hydroxyglutarate destabilizes chromatin regulatory landscape and lineage fidelity to promote cellular heterogeneity. Kusi, M, Zand, M, Lin, LL, Chen, M, Lopez, A, Lin, CL, Wang, CM, Lucio, ND, Kirma, NB, Ruan, J, Huang, TH, Mitsuya, K Cell Rep 38 (2): 110220. doi: 10.1016/j.celrep.2021.110220. PubMed PMID:35021081
  • 2022 | Spatial transcriptomics using combinatorial fluorescence spectral and lifetime encoding, imaging and analysis. Vu, T, Vallmitjana, A, Gu, J, La, K, Xu, Q, Flores, J, Zimak, J, Shiu, J, Hosohama, L, Wu, J, Douglas, C, Waterman, ML, Ganesan, A, Hedde, PN, Gratton, E, Zhao, W Nat Commun 13 (1): 169. doi: 10.1038/s41467-021-27798-0. PubMed PMID:35013281
  • 2022 | Independent Drug Action in Combination Therapy: Implications for Precision Oncology. Plana, D, Palmer, AC, Sorger, PK Cancer Discov : . doi: 10.1158/2159-8290.CD-21-0212. PubMed PMID:34983746
  • 2022 | Fluctuating methylation clocks for cell lineage tracing at high temporal resolution in human tissues. Gabbutt, C, Schenck, RO, Weisenberger, DJ, Kimberley, C, Berner, A, Househam, J, Lakatos, E, Robertson-Tessi, M, Martin, I, Patel, R, Clark, SK, Latchford, A, Barnes, CP, Leedham, SJ, Anderson, ARA, Graham, TA, Shibata, D Nat Biotechnol : . doi: 10.1038/s41587-021-01109-w. PubMed PMID:34980912
  • 2022 | Author Correction: Towards community-driven metadata standards for light microscopy: tiered specifications extending the OME model. Hammer, M, Huisman, M, Rigano, A, Boehm, U, Chambers, JJ, Gaudreault, N, North, AJ, Pimentel, JA, Sudar, D, Bajcsy, P, Brown, CM, Corbett, AD, Faklaris, O, Lacoste, J, Laude, A, Nelson, G, Nitschke, R, Farzam, F, Smith, CS, Grunwald, D, Strambio-De-Castillia, C Nat Methods : . doi: 10.1038/s41592-021-01386-y. PubMed PMID:34980906
  • 2021 | Combination treatment optimization using a pan-cancer pathway model. Schmucker, R, Farina, G, Faeder, J, Fröhlich, F, Saglam, AS, Sandholm, T PLoS Comput Biol 17 (12): e1009689. doi: 10.1371/journal.pcbi.1009689. PubMed PMID:34962919 PubMed Central PMC8747684
  • 2022 | [18F]Fluoro-DCP, a first generation PET radiotracer for monitoring protein sulfenylation in vivo. Solingapuram Sai, KK, Chen, X, Li, Z, Zhu, C, Shukla, K, Forshaw, TE, Wu, H, Vance, SA, Pathirannahel, BL, Madonna, M, Dewhirst, MW, Tsang, AW, Poole, LB, Ramanujam, N, King, SB, Furdui, CM Redox Biol 49 : 102218. doi: 10.1016/j.redox.2021.102218. PubMed PMID:34952463 PubMed Central PMC8715125
  • 2021 | Spatial structure governs the mode of tumour evolution. Noble, R, Burri, D, Le Sueur, C, Lemant, J, Viossat, Y, Kather, JN, Beerenwinkel, N Nat Ecol Evol : . doi: 10.1038/s41559-021-01615-9. PubMed PMID:34949822
  • 2021 | Influence of Estrogen Treatment on ESR1+ and ESR1- Cells in ER+ Breast Cancer: Insights from Single-Cell Analysis of Patient-Derived Xenograft Models. Mori, H, Saeki, K, Chang, G, Wang, J, Wu, X, Hsu, PY, Kanaya, N, Wang, X, Somlo, G, Nakamura, M, Bild, A, Chen, S Cancers (Basel) 13 (24): . doi: 10.3390/cancers13246375. PubMed PMID:34944995 PubMed Central PMC8699443
  • 2021 | Disruption of Circadian Rhythms by Ambient Light during Neurodevelopment Leads to Autistic-like Molecular and Behavioral Alterations in Adult Mice. Fang, K, Liu, D, Pathak, SS, Yang, B, Li, J, Karthikeyan, R, Chao, OY, Yang, YM, Jin, VX, Cao, R Cells 10 (12): . doi: 10.3390/cells10123314. PubMed PMID:34943821 PubMed Central PMC8699695
  • 2022 | Hierarchical regulation of the resting and activated T cell epigenome by major transcription factor families. Zhong, Y, Walker, SK, Pritykin, Y, Leslie, CS, Rudensky, AY, van der Veeken, J Nat Immunol 23 (1): 122-134. doi: 10.1038/s41590-021-01086-x. PubMed PMID:34937932 PubMed Central PMC8712421
  • 2021 | Stress generation, relaxation and size control in confined tumor growth. Yan, H, Ramirez-Guerrero, D, Lowengrub, J, Wu, M PLoS Comput Biol 17 (12): e1009701. doi: 10.1371/journal.pcbi.1009701. PubMed PMID:34932555 PubMed Central PMC8726498
  • 2021 | Differential pre-malignant programs and microenvironment chart distinct paths to malignancy in human colorectal polyps. Chen, B, Scurrah, CR, McKinley, ET, Simmons, AJ, Ramirez-Solano, MA, Zhu, X, Markham, NO, Heiser, CN, Vega, PN, Rolong, A, Kim, H, Sheng, Q, Drewes, JL, Zhou, Y, Southard-Smith, AN, Xu, Y, Ro, J, Jones, AL, Revetta, F, Berry, LD, Niitsu, H, Islam, M, Pelka, K, Hofree, M, Chen, JH, Sarkizova, S, Ng, K, Giannakis, M, Boland, GM, Aguirre, AJ, Anderson, AC, Rozenblatt-Rosen, O, Regev, A, Hacohen, N, Kawasaki, K, Sato, T, Goettel, JA, Grady, WM, Zheng, W, Washington, MK, Cai, Q, Sears, CL, Goldenring, JR, Franklin, JL, Su, T, Huh, WJ, Vandekar, S, Roland, JT, Liu, Q, Coffey, RJ, Shrubsole, MJ, Lau, KS Cell 184 (26): 6262-6280.e26. doi: 10.1016/j.cell.2021.11.031. PubMed PMID:34910928
  • 2021 | A pan-cancer immunogenomic atlas for immune checkpoint blockade immunotherapy. Yang, J, Zhao, S, Wang, J, Sheng, Q, Liu, Q, Shyr, Y Cancer Res : . doi: 10.1158/0008-5472.CAN-21-2335. PubMed PMID:34903605
  • 2021 | Microenvironment drives cell state, plasticity, and drug response in pancreatic cancer. Raghavan, S, Winter, PS, Navia, AW, Williams, HL, DenAdel, A, Lowder, KE, Galvez-Reyes, J, Kalekar, RL, Mulugeta, N, Kapner, KS, Raghavan, MS, Borah, AA, Liu, N, Väyrynen, SA, Costa, AD, Ng, RWS, Wang, J, Hill, EK, Ragon, DY, Brais, LK, Jaeger, AM, Spurr, LF, Li, YY, Cherniack, AD, Booker, MA, Cohen, EF, Tolstorukov, MY, Wakiro, I, Rotem, A, Johnson, BE, McFarland, JM, Sicinska, ET, Jacks, TE, Sullivan, RJ, Shapiro, GI, Clancy, TE, Perez, K, Rubinson, DA, Ng, K, Cleary, JM, Crawford, L, Manalis, SR, Nowak, JA, Wolpin, BM, Hahn, WC, Aguirre, AJ, Shalek, AK Cell 184 (25): 6119-6137.e26. doi: 10.1016/j.cell.2021.11.017. PubMed PMID:34890551
  • 2021 | Multicellular modules as clinical diagnostic and therapeutic targets. Baertsch, MA, Nolan, GP, Hickey, JW Trends Cancer : . doi: 10.1016/j.trecan.2021.11.004. PubMed PMID:34872889
  • 2022 | A community-based approach to image analysis of cells, tissues and tumors. CSBC/PS-ON Image Analysis Working Group, Vizcarra, JC, Burlingame, EA, Hug, CB, Goltsev, Y, White, BS, Tyson, DR, Sokolov, A Comput Med Imaging Graph 95 : 102013. doi: 10.1016/j.compmedimag.2021.102013. PubMed PMID:34864359 PubMed Central PMC8761177
  • 2021 | Towards community-driven metadata standards for light microscopy: tiered specifications extending the OME model. Hammer, M, Huisman, M, Rigano, A, Boehm, U, Chambers, JJ, Gaudreault, N, North, AJ, Pimentel, JA, Sudar, D, Bajcsy, P, Brown, CM, Corbett, AD, Faklaris, O, Lacoste, J, Laude, A, Nelson, G, Nitschke, R, Farzam, F, Smith, CS, Grunwald, D, Strambio-De-Castillia, C Nat Methods 18 (12): 1427-1440. doi: 10.1038/s41592-021-01327-9. PubMed PMID:34862501
  • 2021 | Shape matters: morphological metrics of glioblastoma imaging abnormalities as biomarkers of prognosis. Curtin, L, Whitmire, P, White, H, Bond, KM, Mrugala, MM, Hu, LS, Swanson, KR Sci Rep 11 (1): 23202. doi: 10.1038/s41598-021-02495-6. PubMed PMID:34853344 PubMed Central PMC8636508
  • 2021 | Single-Cell RNA-Seq Analysis Reveals the Acquisition of Cancer Stem Cell Traits and Increase of Cell-Cell Signaling during EMT Progression. Bocci, F, Zhou, P, Nie, Q Cancers (Basel) 13 (22): . doi: 10.3390/cancers13225726. PubMed PMID:34830900 PubMed Central PMC8616061
  • 2021 | Relationship between Tumor Mutational Burden, PD-L1, Patient Characteristics, and Response to Immune Checkpoint Inhibitors in Head and Neck Squamous Cell Carcinoma. Burcher, KM, Lantz, JW, Gavrila, E, Abreu, A, Burcher, JT, Faucheux, AT, Xie, A, Jackson, C, Song, AH, Hughes, RT, Lycan, T Jr, Bunch, PM, Furdui, CM, Topaloglu, U, D'Agostino, RB Jr, Zhang, W, Porosnicu, M Cancers (Basel) 13 (22): . doi: 10.3390/cancers13225733. PubMed PMID:34830888 PubMed Central PMC8616373
  • 2021 | Phenotypic Consequences of SLC25A40-ABCB1 Fusions beyond Drug Resistance in High-Grade Serous Ovarian Cancer. Pishas, KI, Cowley, KJ, Pandey, A, Hoang, T, Beach, JA, Luu, J, Vary, R, Smith, LK, Shembrey, CE, Rashoo, N, White, MO, Simpson, KJ, Bild, A, Griffiths, JI, Cheasley, D, Campbell, I, Bowtell, DDL, Christie, EL Cancers (Basel) 13 (22): . doi: 10.3390/cancers13225644. PubMed PMID:34830797 PubMed Central PMC8616176
  • 2021 | MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging. Schapiro, D, Sokolov, A, Yapp, C, Chen, YA, Muhlich, JL, Hess, J, Creason, AL, Nirmal, AJ, Baker, GJ, Nariya, MK, Lin, JR, Maliga, Z, Jacobson, CA, Hodgman, MW, Ruokonen, J, Farhi, SL, Abbondanza, D, McKinley, ET, Persson, D, Betts, C, Sivagnanam, S, Regev, A, Goecks, J, Coffey, RJ, Coussens, LM, Santagata, S, Sorger, PK Nat Methods : . doi: 10.1038/s41592-021-01308-y. PubMed PMID:34824477
  • 2021 | A multi-scale map of cell structure fusing protein images and interactions. Qin, Y, Huttlin, EL, Winsnes, CF, Gosztyla, ML, Wacheul, L, Kelly, MR, Blue, SM, Zheng, F, Chen, M, Schaffer, LV, Licon, K, Bäckström, A, Vaites, LP, Lee, JJ, Ouyang, W, Liu, SN, Zhang, T, Silva, E, Park, J, Pitea, A, Kreisberg, JF, Gygi, SP, Ma, J, Harper, JW, Yeo, GW, Lafontaine, DLJ, Lundberg, E, Ideker, T Nature 600 (7889): 536-542. doi: 10.1038/s41586-021-04115-9. PubMed PMID:34819669
  • 2021 | Robust IgM responses following intravenous vaccination with Bacille Calmette-Guérin associate with prevention of Mycobacterium tuberculosis infection in macaques. Irvine, EB, O'Neil, A, Darrah, PA, Shin, S, Choudhary, A, Li, W, Honnen, W, Mehra, S, Kaushal, D, Gideon, HP, Flynn, JL, Roederer, M, Seder, RA, Pinter, A, Fortune, S, Alter, G Nat Immunol 22 (12): 1515-1523. doi: 10.1038/s41590-021-01066-1. PubMed PMID:34811542 PubMed Central PMC8642241
  • 2021 | Disruption of β-Catenin-Dependent Wnt Signaling in Colon Cancer Cells Remodels the Microenvironment to Promote Tumor Invasion. Chen, GT, Tifrea, DF, Murad, R, Habowski, AN, Lyou, Y, Duong, MR, Hosohama, L, Mortazavi, A, Edwards, RA, Waterman, ML Mol Cancer Res : . doi: 10.1158/1541-7786.MCR-21-0349. PubMed PMID:34799404
  • 2021 | UFold: fast and accurate RNA secondary structure prediction with deep learning. Fu, L, Cao, Y, Wu, J, Peng, Q, Nie, Q, Xie, X Nucleic Acids Res : . doi: 10.1093/nar/gkab1074. PubMed PMID:34792173
  • 2021 | Upregulation of DNA repair genes and cell extrusion underpin the remarkable radiation resistance of Trichoplax adhaerens. Fortunato, A, Fleming, A, Aktipis, A, Maley, CC PLoS Biol 19 (11): e3001471. doi: 10.1371/journal.pbio.3001471. PubMed PMID:34788294 PubMed Central PMC8635375
  • 2021 | Therapeutic implications of activating noncanonical PIK3CA mutations in head and neck squamous cell carcinoma. Jin, N, Keam, B, Cho, J, Lee, MJ, Kim, HR, Torosyan, H, Jura, N, Ng, PK, Mills, GB, Li, H, Zeng, Y, Barbash, Z, Tarcic, G, Kang, H, Bauman, JE, Kim, MO, VanLandingham, NK, Swaney, DL, Krogan, NJ, Johnson, DE, Grandis, JR J Clin Invest 131 (22): . doi: 10.1172/JCI150335. PubMed PMID:34779417 PubMed Central PMC8592538
  • 2021 | Model-based assessment of mammalian cell metabolic functionalities using omics data. Richelle, A, Kellman, BP, Wenzel, AT, Chiang, AWT, Reagan, T, Gutierrez, JM, Joshi, C, Li, S, Liu, JK, Masson, H, Lee, J, Li, Z, Heirendt, L, Trefois, C, Juarez, EF, Bath, T, Borland, D, Mesirov, JP, Robasky, K, Lewis, NE Cell Rep Methods 1 (3): . doi: 10.1016/j.crmeth.2021.100040. PubMed PMID:34761247 PubMed Central PMC8577426
  • 2021 | Structures of the HER2-HER3-NRG1β complex reveal a dynamic dimer interface. Diwanji, D, Trenker, R, Thaker, TM, Wang, F, Agard, DA, Verba, KA, Jura, N Nature 600 (7888): 339-343. doi: 10.1038/s41586-021-04084-z. PubMed PMID:34759323
  • 2021 | Mapping the evolution of T cell states during response and resistance to adoptive cellular therapy. Bachireddy, P, Azizi, E, Burdziak, C, Nguyen, VN, Ennis, CS, Maurer, K, Park, CY, Choo, ZN, Li, S, Gohil, SH, Ruthen, NG, Ge, Z, Keskin, DB, Cieri, N, Livak, KJ, Kim, HT, Neuberg, DS, Soiffer, RJ, Ritz, J, Alyea, EP, Pe'er, D, Wu, CJ Cell Rep 37 (6): 109992. doi: 10.1016/j.celrep.2021.109992. PubMed PMID:34758319
  • 2021 | Directional Gaussian Mixture Models of the Gut Microbiome Elucidate Microbial Spatial Structure. Pasarkar, AP, Joseph, TA, Pe'er, I mSystems 6 (6): e0081721. doi: 10.1128/mSystems.00817-21. PubMed PMID:34751587 PubMed Central PMC8577282
  • 2021 | Narrative online guides for the interpretation of digital-pathology images and tissue-atlas data. Rashid, R, Chen, YA, Hoffer, J, Muhlich, JL, Lin, JR, Krueger, R, Pfister, H, Mitchell, R, Santagata, S, Sorger, PK Nat Biomed Eng : . doi: 10.1038/s41551-021-00789-8. PubMed PMID:34750536
  • 2021 | Myeloid antigen-presenting cell niches sustain antitumor T cells and license PD-1 blockade via CD28 costimulation. Duraiswamy, J, Turrini, R, Minasyan, A, Barras, D, Crespo, I, Grimm, AJ, Casado, J, Genolet, R, Benedetti, F, Wicky, A, Ioannidou, K, Castro, W, Neal, C, Moriot, A, Renaud-Tissot, S, Anstett, V, Fahr, N, Tanyi, JL, Eiva, MA, Jacobson, CA, Montone, KT, Westergaard, MCW, Svane, IM, Kandalaft, LE, Delorenzi, M, Sorger, PK, Färkkilä, A, Michielin, O, Zoete, V, Carmona, SJ, Foukas, PG, Powell, DJ Jr, Rusakiewicz, S, Doucey, MA, Dangaj Laniti, D, Coukos, G Cancer Cell 39 (12): 1623-1642.e20. doi: 10.1016/j.ccell.2021.10.008. PubMed PMID:34739845
  • 2021 | Transcription recycling assays identify PAF1 as a driver for RNA Pol II recycling. Chen, Z, Hankey, W, Zhao, Y, Groth, J, Huang, F, Wang, H, Campos, AR, Huang, J, Roeder, RG, Wang, Q Nat Commun 12 (1): 6318. doi: 10.1038/s41467-021-26604-1. PubMed PMID:34732721 PubMed Central PMC8566496
  • 2021 | Rare t(X;14)(q28;q32) translocation reveals link between MTCP1 and chronic lymphocytic leukemia. Walker, JS, Hing, ZA, Sher, S, Cronin, J, Williams, K, Harrington, B, Skinner, JN, Cempre, CB, Gregory, CT, Pan, A, Yano, M, Beaver, LP, Walker, BR, Labanowska, JM, Heerema, NA, Mrózek, K, Woyach, JA, Ruppert, AS, Lehman, A, Ozer, HG, Coppola, V, Yan, P, Byrd, JC, Blachly, JS, Lapalombella, R Nat Commun 12 (1): 6338. doi: 10.1038/s41467-021-26400-x. PubMed PMID:34732719 PubMed Central PMC8566464
  • 2021 | Global characterization of macrophage polarization mechanisms and identification of M2-type polarization inhibitors. He, L, Jhong, JH, Chen, Q, Huang, KY, Strittmatter, K, Kreuzer, J, DeRan, M, Wu, X, Lee, TY, Slavov, N, Haas, W, Marneros, AG Cell Rep 37 (5): 109955. doi: 10.1016/j.celrep.2021.109955. PubMed PMID:34731634
  • 2021 | Serial single-cell genomics reveals convergent subclonal evolution of resistance as early-stage breast cancer patients progress on endocrine plus CDK4/6 therapy. Griffiths, JI, Chen, J, Cosgrove, PA, O'Dea, A, Sharma, P, Ma, C, Trivedi, M, Kalinsky, K, Wisinski, KB, O'Regan, R, Makhoul, I, Spring, LM, Bardia, A, Adler, FR, Cohen, AL, Chang, JT, Khan, QJ, Bild, AH Nat Cancer 2 (6): 658-671. doi: 10.1038/s43018-021-00215-7. PubMed PMID:34712959 PubMed Central PMC8547038
  • 2021 | Single-Cell Transcriptomics Reveals a Conserved Metaplasia Program in Pancreatic Injury. Ma, Z, Lytle, NK, Chen, B, Jyotsana, N, Novak, SW, Cho, CJ, Caplan, L, Ben-Levy, O, Neininger, AC, Burnette, DT, Trinh, VQ, Tan, MCB, Patterson, EA, Arrojo E Drigo, R, Giraddi, RR, Ramos, C, Means, AL, Matsumoto, I, Manor, U, Mills, JC, Goldenring, JR, Lau, KS, Wahl, GM, DelGiorno, KE Gastroenterology : . doi: 10.1053/j.gastro.2021.10.027. PubMed PMID:34695382
  • 2021 | Cell-Cell Communication Networks in Tissue: Toward Quantitatively Linking Structure with Function. Luthria, G, Lauffenburger, D, Miller, MA Curr Opin Syst Biol 27 : . doi: 10.1016/j.coisb.2021.05.002. PubMed PMID:34693081 PubMed Central PMC8530179
  • 2021 | A Mathematical Model of Breast Tumor Progression Based on Immune Infiltration. Mohammad Mirzaei, N, Su, S, Sofia, D, Hegarty, M, Abdel-Rahman, MH, Asadpoure, A, Cebulla, CM, Chang, YH, Hao, W, Jackson, PR, Lee, AV, Stover, DG, Tatarova, Z, Zervantonakis, IK, Shahriyari, L J Pers Med 11 (10): . doi: 10.3390/jpm11101031. PubMed PMID:34683171 PubMed Central PMC8540934
  • | Developmental Stage Classification of Embryos Using Two-Stream Neural Network with Linear-Chain Conditional Random Field. Lukyanenko, S, Jang, WD, Wei, D, Struyven, R, Kim, Y, Leahy, B, Yang, H, Rush, A, Ben-Yosef, D, Needleman, D, Pfister, H Med Image Comput Comput Assist Interv 12908 : 363-372. doi: 10.1007/978-3-030-87237-3_35. PubMed PMID:34671767 PubMed Central PMC8526069
  • 2021 | Multiomics analysis of serial PARP inhibitor treated metastatic TNBC inform on rational combination therapies. Labrie, M, Li, A, Creason, A, Betts, C, Keck, J, Johnson, B, Sivagnanam, S, Boniface, C, Ma, H, Blucher, A, Chang, YH, Chin, K, Vuky, J, Guimaraes, AR, Downey, M, Lim, JY, Gao, L, Siex, K, Parmar, S, Kolodzie, A, Spellman, PT, Goecks, J, Coussens, LM, Corless, CL, Bergan, R, Gray, JW, Mills, GB, Mitri, ZI NPJ Precis Oncol 5 (1): 92. doi: 10.1038/s41698-021-00232-w. PubMed PMID:34667258 PubMed Central PMC8526613
  • 2021 | Regulatory feedback effects on tissue growth dynamics in a two-stage cell lineage model. Wang, MX, Lander, A, Lai, PY Phys Rev E 104 (3-1): 034405. doi: 10.1103/PhysRevE.104.034405. PubMed PMID:34654185 PubMed Central PMC8585573
  • 2021 | Signatures of plasticity, metastasis, and immunosuppression in an atlas of human small cell lung cancer. Chan, JM, Quintanal-Villalonga, Á, Gao, VR, Xie, Y, Allaj, V, Chaudhary, O, Masilionis, I, Egger, J, Chow, A, Walle, T, Mattar, M, Yarlagadda, DVK, Wang, JL, Uddin, F, Offin, M, Ciampricotti, M, Qeriqi, B, Bahr, A, de Stanchina, E, Bhanot, UK, Lai, WV, Bott, MJ, Jones, DR, Ruiz, A, Baine, MK, Li, Y, Rekhtman, N, Poirier, JT, Nawy, T, Sen, T, Mazutis, L, Hollmann, TJ, Pe'er, D, Rudin, CM Cancer Cell 39 (11): 1479-1496.e18. doi: 10.1016/j.ccell.2021.09.008. PubMed PMID:34653364 PubMed Central PMC8628860
  • 2021 | scMRMA: single cell multiresolution marker-based annotation. Li, J, Sheng, Q, Shyr, Y, Liu, Q Nucleic Acids Res : . doi: 10.1093/nar/gkab931. PubMed PMID:34648021
  • 2021 | Systems-level effects of allosteric perturbations to a model molecular switch. Perica, T, Mathy, CJP, Xu, J, Jang, GΜ, Zhang, Y, Kaake, R, Ollikainen, N, Braberg, H, Swaney, DL, Lambright, DG, Kelly, MJS, Krogan, NJ, Kortemme, T Nature 599 (7883): 152-157. doi: 10.1038/s41586-021-03982-6. PubMed PMID:34646016 PubMed Central PMC8571063
  • 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 PubMed Central PMC8514239
  • 2021 | Genomic and transcriptomic correlates of immunotherapy response within the tumor microenvironment of leptomeningeal metastases. Prakadan, SM, Alvarez-Breckenridge, CA, Markson, SC, Kim, AE, Klein, RH, Nayyar, N, Navia, AW, Kuter, BM, Kolb, KE, Bihun, I, Mora, JL, Bertalan, MS, Shaw, B, White, M, Kaplan, A, Stocking, JH, Wadsworth, MH 2nd, Lee, EQ, Chukwueke, U, Wang, N, Subramanian, M, Rotem, D, Cahill, DP, Adalsteinsson, VA, Miller, JW, Sullivan, RJ, Carter, SL, Brastianos, PK, Shalek, AK Nat Commun 12 (1): 5955. doi: 10.1038/s41467-021-25860-5. PubMed PMID:34642316 PubMed Central PMC8511044
  • 2021 | Functional drug susceptibility testing using single-cell mass predicts treatment outcome in patient-derived cancer neurosphere models. Stockslager, MA, Malinowski, S, Touat, M, Yoon, JC, Geduldig, J, Mirza, M, Kim, AS, Wen, PY, Chow, KH, Ligon, KL, Manalis, SR Cell Rep 37 (1): 109788. doi: 10.1016/j.celrep.2021.109788. PubMed PMID:34610309
  • 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
  • 2022 | Scope2Screen: Focus+Context Techniques for Pathology Tumor Assessment in Multivariate Image Data. Jessup, J, Krueger, R, Warchol, S, Hoffer, J, Muhlich, J, Ritch, CC, Gaglia, G, Coy, S, Chen, YA, Lin, JR, Santagata, S, Sorger, PK, Pfister, H IEEE Trans Vis Comput Graph 28 (1): 259-269. doi: 10.1109/TVCG.2021.3114786. PubMed PMID:34606456
  • 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 2 (10): 100421. doi: 10.1016/j.xcrm.2021.100421. PubMed PMID:34604819 PubMed Central PMC8479532
  • 2021 | The landscape of tumor cell states and ecosystems in diffuse large B cell lymphoma. Steen, CB, Luca, BA, Esfahani, MS, Azizi, A, Sworder, BJ, Nabet, BY, Kurtz, DM, Liu, CL, Khameneh, F, Advani, RH, Natkunam, Y, Myklebust, JH, Diehn, M, Gentles, AJ, Newman, AM, Alizadeh, AA Cancer Cell 39 (10): 1422-1437.e10. doi: 10.1016/j.ccell.2021.08.011. PubMed PMID:34597589
  • 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 184 (21): 5482-5496.e28. doi: 10.1016/j.cell.2021.09.014. PubMed PMID:34597583 PubMed Central PMC8526411
  • 2021 | Translational biophotonics with Raman imaging: clinical applications and beyond. Pence, IJ, Evans, CL Analyst 146 (21): 6379-6393. doi: 10.1039/d1an00954k. PubMed PMID:34596653 PubMed Central PMC8543123
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  • 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
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  • 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
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  • 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
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  • 2021 | Sequential CRISPR gene editing in human iPSCs charts the clonal evolution of myeloid leukemia and identifies early disease targets. Wang, T, Pine, AR, Kotini, AG, Yuan, H, Zamparo, L, Starczynowski, DT, Leslie, C, Papapetrou, EP Cell Stem Cell 28 (6): 1074-1089.e7. doi: 10.1016/j.stem.2021.01.011. PubMed PMID:33571445 PubMed Central PMC8178190
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