CSBC Supported Publications

Publications

  • 2022 | A conserved YAP/Notch/REST network controls the neuroendocrine cell fate in the lungs. Shue, YT, Drainas, AP, Li, NY, Pearsall, SM, Morgan, D, Sinnott-Armstrong, N, Hipkins, SQ, Coles, GL, Lim, JS, Oro, AE, Simpson, KL, Dive, C, Sage, J Nat Commun 13 (1): 2690. doi: 10.1038/s41467-022-30416-2. PubMed PMID:35577801
  • 2022 | In Reply: TP53 Alteration Status and Tumor Mutational Burden Score: Prevalence and Prognosis in Head and Neck Squamous Cell Carcinoma. Burcher, KM, Wilson, HL, Gavrila, E, Abreu, A, D'Agostino, RB, Zhang, W, Porosnicu, M Oncologist : . doi: 10.1093/oncolo/oyac088. PubMed PMID:35552454
  • 2022 | A framework for multiplex imaging optimization and reproducible analysis. Eng, J, Bucher, E, Hu, Z, Zheng, T, Gibbs, SL, Chin, K, Gray, JW Commun Biol 5 (1): 438. doi: 10.1038/s42003-022-03368-y. PubMed PMID:35545666 PubMed Central PMC9095647
  • 2022 | Single-cell monitoring of dry mass and dry mass density reveals exocytosis of cellular dry contents in mitosis. Miettinen, TP, Ly, KS, Lam, A, Manalis, SR Elife 11 : . doi: 10.7554/eLife.76664. PubMed PMID:35535854 PubMed Central PMC9090323
  • 2022 | Meningioma DNA methylation groups identify biological drivers and therapeutic vulnerabilities. Choudhury, A, Magill, ST, Eaton, CD, Prager, BC, Chen, WC, Cady, MA, Seo, K, Lucas, CG, Casey-Clyde, TJ, Vasudevan, HN, Liu, SJ, Villanueva-Meyer, JE, Lam, TC, Pu, JK, Li, LF, Leung, GK, Swaney, DL, Zhang, MY, Chan, JW, Qiu, Z, Martin, MV, Susko, MS, Braunstein, SE, Bush, NAO, Schulte, JD, Butowski, N, Sneed, PK, Berger, MS, Krogan, NJ, Perry, A, Phillips, JJ, Solomon, DA, Costello, JF, McDermott, MW, Rich, JN, Raleigh, DR Nat Genet 54 (5): 649-659. doi: 10.1038/s41588-022-01061-8. PubMed PMID:35534562
  • 2022 | Overcoming differential tumor penetration of BRAF inhibitors using computationally guided combination therapy. Ng, TSC, Hu, H, Kronister, S, Lee, C, Li, R, Gerosa, L, Stopka, SA, Burgenske, DM, Khurana, I, Regan, MS, Vallabhaneni, S, Putta, N, Scott, E, Matvey, D, Giobbie-Hurder, A, Kohler, RH, Sarkaria, JN, Parangi, S, Sorger, PK, Agar, NYR, Jacene, HA, Sullivan, RJ, Buchbinder, E, Mikula, H, Weissleder, R, Miller, MA Sci Adv 8 (17): eabl6339. doi: 10.1126/sciadv.abl6339. PubMed PMID:35486732 PubMed Central PMC9054019
  • 2022 | Somatic whole genome dynamics of precancer in Barrett's esophagus reveals features associated with disease progression. Paulson, TG, Galipeau, PC, Oman, KM, Sanchez, CA, Kuhner, MK, Smith, LP, Hadi, K, Shah, M, Arora, K, Shelton, J, Johnson, M, Corvelo, A, Maley, CC, Yao, X, Sanghvi, R, Venturini, E, Emde, AK, Hubert, B, Imielinski, M, Robine, N, Reid, BJ, Li, X Nat Commun 13 (1): 2300. doi: 10.1038/s41467-022-29767-7. PubMed PMID:35484108 PubMed Central PMC9050715
  • 2022 | Cell type and gene expression deconvolution with BayesPrism enables Bayesian integrative analysis across bulk and single-cell RNA sequencing in oncology. Chu, T, Wang, Z, Pe'er, D, Danko, CG Nat Cancer 3 (4): 505-517. doi: 10.1038/s43018-022-00356-3. PubMed PMID:35469013 PubMed Central PMC9046084
  • 2022 | High inter-follicular spatial co-localization of CD8+FOXP3+ with CD4+CD8+ cells predicts favorable outcome in follicular lymphoma. Hagos, YB, Akarca, AU, Ramsay, A, Rossi, RL, Pomplun, S, Ngai, V, Moioli, A, Gianatti, A, Mcnamara, C, Rambaldi, A, Quezada, SA, Linch, D, Gritti, G, Yuan, Y, Marafioti, T Hematol Oncol : . doi: 10.1002/hon.3003. PubMed PMID:35451108
  • 2022 | Real-time luminescence enables continuous drug-response analysis in adherent and suspension cell lines. Wandishin, CM, Robbins, CJ, Tyson, DR, Harris, LA, Quaranta, V Cancer Biol Ther 23 (1): 358-368. doi: 10.1080/15384047.2022.2065182. PubMed PMID:35443861 PubMed Central PMC9037430
  • 2022 | A whole genome CRISPR screen identifies AHR loss as a mechanism of PARP7 inhibitor resistance. Chen, H, Diolaiti, ME, O'Leary, PC, Rojc, A, Krogan, NJ, Kim, M, Ashworth, A Mol Cancer Ther : . doi: 10.1158/1535-7163.MCT-21-0841. PubMed PMID:35439318
  • 2022 | Aspirin's effect on kinetic parameters of cells contributes to its role in reducing incidence of advanced colorectal adenomas, shown by a multiscale computational study. Wang, Y, Boland, CR, Goel, A, Wodarz, D, Komarova, NL Elife 11 : . doi: 10.7554/eLife.71953. PubMed PMID:35416770 PubMed Central PMC9007589
  • 2022 | Lineage tracing in human tissues. Gabbutt, C, Wright, NA, Baker, AM, Shibata, D, Graham, TA J Pathol : . doi: 10.1002/path.5911. PubMed PMID:35415852
  • 2022 | Phosphorylated MED1 links transcription recycling and cancer growth. Chen, Z, Ye, Z, Soccio, RE, Nakadai, T, Hankey, W, Zhao, Y, Huang, F, Yuan, F, Wang, H, Cui, Z, Sunkel, B, Wu, D, Dzeng, RK, Thomas-Ahner, JM, Huang, THM, Clinton, SK, Huang, J, Lazar, MA, Jin, VX, Roeder, RG, Wang, Q Nucleic Acids Res 50 (8): 4450-4463. doi: 10.1093/nar/gkac246. PubMed PMID:35394046 PubMed Central PMC9071494
  • 2022 | Structure-based design of CDC42 effector interaction inhibitors for the treatment of cancer. Jahid, S, Ortega, JA, Vuong, LM, Acquistapace, IM, Hachey, SJ, Flesher, JL, La Serra, MA, Brindani, N, La Sala, G, Manigrasso, J, Arencibia, JM, Bertozzi, SM, Summa, M, Bertorelli, R, Armirotti, A, Jin, R, Liu, Z, Chen, CF, Edwards, R, Hughes, CCW, De Vivo, M, Ganesan, AK Cell Rep 39 (1): 110641. doi: 10.1016/j.celrep.2022.110641. PubMed PMID:35385746
  • 2022 | Cell type determination for cardiac differentiation occurs soon after seeding of human-induced pluripotent stem cells. Jiang, CL, Goyal, Y, Jain, N, Wang, Q, Truitt, RE, Coté, AJ, Emert, B, Mellis, IA, Kiani, K, Yang, W, Jain, R, Raj, A Genome Biol 23 (1): 90. doi: 10.1186/s13059-022-02654-6. PubMed PMID:35382863 PubMed Central PMC8985385
  • 2022 | T-cell dysfunction upon expression of MYC with altered phosphorylation at Threonine 58 and Serine 62. Daniel, CJ, Pelz, C, Wang, X, Munks, MW, Ko, A, Murugan, D, Byers, SA, Juarez, E, Taylor, KL, Fan, G, Coussens, LM, Link, JM, Sears, RC Mol Cancer Res : . doi: 10.1158/1541-7786.MCR-21-0560. PubMed PMID:35380701
  • 2022 | Immunosuppressive niche engineering at the onset of human colorectal cancer. Gatenbee, CD, Baker, AM, Schenck, RO, Strobl, M, West, J, Neves, MP, Hasan, SY, Lakatos, E, Martinez, P, Cross, WCH, Jansen, M, Rodriguez-Justo, M, Whelan, CJ, Sottoriva, A, Leedham, S, Robertson-Tessi, M, Graham, TA, Anderson, ARA Nat Commun 13 (1): 1798. doi: 10.1038/s41467-022-29027-8. PubMed PMID:35379804 PubMed Central PMC8979971
  • 2021 | Dynamic High-Pass Filtering and Multi-Spectral Attention for Image Super-Resolution. Magid, SA, Zhang, Y, Wei, D, Jang, WD, Lin, Z, Fu, Y, Pfister, H Proc IEEE Int Conf Comput Vis 2021 : 4268-4277. doi: 10.1109/iccv48922.2021.00425. PubMed PMID:35368831 PubMed Central PMC8969883
  • 2021 | A Tale of Two Histologies: Dissecting the Biology of Lineage Transformation in Lung Cancer. Meador, CB, Lovly, CM Cancer Discov 11 (12): 2962-2964. doi: 10.1158/2159-8290.CD-21-1222. PubMed PMID:35363868 PubMed Central PMC8988434
  • 2022 | Collateral responses to classical cytotoxic chemotherapies are heterogeneous and sensitivities are sparse. Dalin, S, Grauman-Boss, B, Lauffenburger, DA, Hemann, MT Sci Rep 12 (1): 5453. doi: 10.1038/s41598-022-09319-1. PubMed PMID:35361803 PubMed Central PMC8971507
  • 2022 | Dual data and motif clustering improves the modeling and interpretation of phosphoproteomic data. Creixell, M, Meyer, AS Cell Rep Methods 2 (2): . doi: 10.1016/j.crmeth.2022.100167. PubMed PMID:35360705 PubMed Central PMC8967184
  • 2021 | Forecasting cancer: from precision to predictive medicine. Fertig, EJ, Jaffee, EM, Macklin, P, Stearns, V, Wang, C Med (N Y) 2 (9): 1004-1010. doi: 10.1016/j.medj.2021.08.007. PubMed PMID:35330848 PubMed Central PMC8942083
  • 2022 | A multi-encoder variational autoencoder controls multiple transformational features in single-cell image analysis. Ternes, L, Dane, M, Gross, S, Labrie, M, Mills, G, Gray, J, Heiser, L, Chang, YH Commun Biol 5 (1): 255. doi: 10.1038/s42003-022-03218-x. PubMed PMID:35322205 PubMed Central PMC8943013
  • 2022 | Modelling glioma progression, mass effect and intracranial pressure in patient anatomy. Lipková, J, Menze, B, Wiestler, B, Koumoutsakos, P, Lowengrub, JS J R Soc Interface 19 (188): 20210922. doi: 10.1098/rsif.2021.0922. PubMed PMID:35317645 PubMed Central PMC8941421
  • | An in vitro intestinal model captures immunomodulatory properties of the microbiota in inflammation. Lock, JY, Caboni, M, Strandwitz, P, Morrissette, M, DiBona, K, Joughin, BA, Lewis, K, Carrier, RL Gut Microbes 14 (1): 2039002. doi: 10.1080/19490976.2022.2039002. PubMed PMID:35316142 PubMed Central PMC8942420
  • 2022 | Screening for modulators of the cellular composition of gut epithelia via organoid models of intestinal stem cell differentiation. Mead, BE, Hattori, K, Levy, L, Imada, S, Goto, N, Vukovic, M, Sze, D, Kummerlowe, C, Matute, JD, Duan, J, Langer, R, Blumberg, RS, Ordovas-Montanes, J, Yilmaz, ÖH, Karp, JM, Shalek, AK Nat Biomed Eng 6 (4): 476-494. doi: 10.1038/s41551-022-00863-9. PubMed PMID:35314801 PubMed Central PMC9046079
  • 2022 | Reconstructing codependent cellular cross-talk in lung adenocarcinoma using REMI. Yu, A, Li, Y, Li, I, Ozawa, MG, Yeh, C, Chiou, AE, Trope, WL, Taylor, J, Shrager, J, Plevritis, SK Sci Adv 8 (11): eabi4757. doi: 10.1126/sciadv.abi4757. PubMed PMID:35302849 PubMed Central PMC8932661
  • 2022 | Gattaca: Base-Pair Resolution Mutation Tracking for Somatic Evolution Studies using Agent-based Models. Schenck, RO, Brosula, G, West, J, Leedham, S, Shibata, D, Anderson, ARA Mol Biol Evol 39 (4): . doi: 10.1093/molbev/msac058. PubMed PMID:35298641 PubMed Central PMC9034688
  • 2022 | Copper induces cell death by targeting lipoylated TCA cycle proteins. Tsvetkov, P, Coy, S, Petrova, B, Dreishpoon, M, Verma, A, Abdusamad, M, Rossen, J, Joesch-Cohen, L, Humeidi, R, Spangler, RD, Eaton, JK, Frenkel, E, Kocak, M, Corsello, SM, Lutsenko, S, Kanarek, N, Santagata, S, Golub, TR Science 375 (6586): 1254-1261. doi: 10.1126/science.abf0529. PubMed PMID:35298263
  • 2022 | Investigating key cell types and molecules dynamics in PyMT mice model of breast cancer through a mathematical model. Mohammad Mirzaei, N, Changizi, N, Asadpoure, A, Su, S, Sofia, D, Tatarova, Z, Zervantonakis, IK, Chang, YH, Shahriyari, L PLoS Comput Biol 18 (3): e1009953. doi: 10.1371/journal.pcbi.1009953. PubMed PMID:35294447 PubMed Central PMC8959189
  • 2022 | Temporal and spatial topography of cell proliferation in cancer. Gaglia, G, Kabraji, S, Rammos, D, Dai, Y, Verma, A, Wang, S, Mills, CE, Chung, M, Bergholz, JS, Coy, S, Lin, JR, Jeselsohn, R, Metzger, O, Winer, EP, Dillon, DA, Zhao, JJ, Sorger, PK, Santagata, S Nat Cell Biol 24 (3): 316-326. doi: 10.1038/s41556-022-00860-9. PubMed PMID:35292783 PubMed Central PMC8959396
  • 2022 | Phase 2 study of pembrolizumab in patients with recurrent and residual high-grade meningiomas. Brastianos, PK, Kim, AE, Giobbie-Hurder, A, Lee, EQ, Wang, N, Eichler, AF, Chukwueke, U, Forst, DA, Arrillaga-Romany, IC, Dietrich, J, Corbin, Z, Moliterno, J, Baehring, J, White, M, Lou, KW, Larson, J, de Sauvage, MA, Evancic, K, Mora, J, Nayyar, N, Loeffler, J, Oh, K, Shih, HA, Curry, WT, Cahill, DP, Barker, FG, Gerstner, ER, Santagata, S Nat Commun 13 (1): 1325. doi: 10.1038/s41467-022-29052-7. PubMed PMID:35289329 PubMed Central PMC8921328
  • 2022 | Time-series transcriptomics and proteomics reveal alternative modes to decode p53 oscillations. Jiménez, A, Lu, D, Kalocsay, M, Berberich, MJ, Balbi, P, Jambhekar, A, Lahav, G Mol Syst Biol 18 (3): e10588. doi: 10.15252/msb.202110588. PubMed PMID:35285572 PubMed Central PMC8919251
  • 2022 | MITI minimum information guidelines for highly multiplexed tissue images. Schapiro, D, Yapp, C, Sokolov, A, Reynolds, SM, Chen, YA, Sudar, D, Xie, Y, Muhlich, J, Arias-Camison, R, Arena, S, Taylor, AJ, Nikolov, M, Tyler, M, Lin, JR, Burlingame, EA, Human Tumor Atlas Network, Chang, YH, Farhi, SL, Thorsson, V, Venkatamohan, N, Drewes, JL, Pe'er, D, Gutman, DA, Herrmann, MD, Gehlenborg, N, Bankhead, P, Roland, JT, Herndon, JM, Snyder, MP, Angelo, M, Nolan, G, Swedlow, JR, Schultz, N, Merrick, DT, Mazzili, SA, Cerami, E, Rodig, SJ, Santagata, S, Sorger, PK Nat Methods 19 (3): 262-267. doi: 10.1038/s41592-022-01415-4. PubMed PMID:35277708 PubMed Central PMC9009186
  • 2022 | Small Cell Lung Cancer Transformation following Treatment in EGFR-Mutated Non-Small Cell Lung Cancer. Mambetsariev, I, Arvanitis, L, Fricke, J, Pharaon, R, Baroz, AR, Afkhami, M, Koczywas, M, Massarelli, E, Salgia, R J Clin Med 11 (5): . doi: 10.3390/jcm11051429. PubMed PMID:35268520 PubMed Central PMC8911080
  • 2022 | Computation and visualization of cell-cell signaling topologies in single-cell systems data using Connectome. Raredon, MSB, Yang, J, Garritano, J, Wang, M, Kushnir, D, Schupp, JC, Adams, TS, Greaney, AM, Leiby, KL, Kaminski, N, Kluger, Y, Levchenko, A, Niklason, LE Sci Rep 12 (1): 4187. doi: 10.1038/s41598-022-07959-x. PubMed PMID:35264704 PubMed Central PMC8906120
  • 2022 | PI3K activation allows immune evasion by promoting an inhibitory myeloid tumor microenvironment. Collins, NB, Al Abosy, R, Miller, BC, Bi, K, Zhao, Q, Quigley, M, Ishizuka, JJ, Yates, KB, Pope, HW, Manguso, RT, Shrestha, Y, Wadsworth, M, Hughes, T, Shalek, AK, Boehm, JS, Hahn, WC, Doench, JG, Haining, WN J Immunother Cancer 10 (3): . doi: 10.1136/jitc-2021-003402. PubMed PMID:35264433 PubMed Central PMC8915320
  • 2022 | INHBA is a mediator of aggressive tumor behavior in HER2+ basal breast cancer. Liu, M, Smith, R, Liby, T, Chiotti, K, López, CS, Korkola, JE Breast Cancer Res 24 (1): 18. doi: 10.1186/s13058-022-01512-4. PubMed PMID:35248133 PubMed Central PMC8898494
  • 2022 | Optimal Strategy and Benefit of Pulsed Therapy Depend On Tumor Heterogeneity and Aggressiveness at Time of Treatment Initiation. Mathur, D, Taylor, BP, Chatila, WK, Scher, HI, Schultz, N, Razavi, P, Xavier, JB Mol Cancer Ther 21 (5): 831-843. doi: 10.1158/1535-7163.MCT-21-0574. PubMed PMID:35247928 PubMed Central PMC9081172
  • 2022 | RAGE Inhibitors as Alternatives to Dexamethasone for Managing Cerebral Edema Following Brain Tumor Surgery. Liu, S, Song, Y, Zhang, IY, Zhang, L, Gao, H, Su, Y, Yang, Y, Yin, S, Zheng, Y, Ren, L, Yin, HH, Pillai, R, Nath, A, Medina, EF, Cosgrove, PA, Bild, AH, Badie, B Neurotherapeutics : . doi: 10.1007/s13311-022-01207-w. PubMed PMID:35226341
  • 2022 | Ras Multimers on the Membrane: Many Ways for a Heart-to-Heart Conversation. Ozdemir, ES, Koester, AM, Nan, X Genes (Basel) 13 (2): . doi: 10.3390/genes13020219. PubMed PMID:35205266 PubMed Central PMC8872464
  • 2022 | Complex effects of kinase localization revealed by compartment-specific regulation of protein kinase A activity. LaCroix, R, Lin, B, Kang, TY, Levchenko, A Elife 11 : . doi: 10.7554/eLife.66869. PubMed PMID:35199643 PubMed Central PMC8871369
  • 2022 | Supporting Computational Apprenticeship Through Educational and Software Infrastructure: A Case Study in a Mathematical Oncology Research Lab. Madamanchi, A, Thomas, M, Magana, A, Heiland, R, Macklin, P PRIMUS (Terre Ht) 32 (3 Pt 2): 446-467. doi: 10.1080/10511970.2021.1881849. PubMed PMID:35197716 PubMed Central PMC8863170
  • 2022 | Piquing our interest: Insights into the role of PEAK3 in signaling and disease. Paul, MD, Torosyan, H, Jura, N Sci Signal 15 (722): eabm9396. doi: 10.1126/scisignal.abm9396. PubMed PMID:35192418
  • 2022 | Natural and Designed Proteins Inspired by Extremotolerant Organisms Can Form Condensates and Attenuate Apoptosis in Human Cells. Veling, MT, Nguyen, DT, Thadani, NN, Oster, ME, Rollins, NJ, Brock, KP, Bethel, NP, Lim, S, Baker, D, Way, JC, Marks, DS, Chang, RL, Silver, PA ACS Synth Biol 11 (3): 1292-1302. doi: 10.1021/acssynbio.1c00572. PubMed PMID:35176859
  • 2022 | Cancer patient survival can be parametrized to improve trial precision and reveal time-dependent therapeutic effects. Plana, D, Fell, G, Alexander, BM, Palmer, AC, Sorger, PK Nat Commun 13 (1): 873. doi: 10.1038/s41467-022-28410-9. PubMed PMID:35169116 PubMed Central PMC8847344
  • 2022 | Publisher Correction: ERK1/2 phosphorylation predicts survival following anti-PD-1 immunotherapy in recurrent glioblastoma. Arrieta, VA, Chen, AX, Kane, JR, Kang, SJ, Kassab, C, Dmello, C, Zhao, J, Burdett, KB, Upadhyayula, PS, Lee-Chang, C, Shilati, J, Jaishankar, D, Chen, L, Gould, A, Zhang, D, Yuan, J, Zhao, W, Ling, X, Burks, JK, Laffleur, B, Amidei, C, Bruce, JN, Lukas, RV, Yamaguchi, JT, Cieremans, D, Rothschild, G, Basu, U, McCord, M, Brat, DJ, Zhang, H, Cooper, LAD, Zhang, B, Sims, P, Cloughesy, TF, Prins, R, Canoll, P, Stupp, R, Heimberger, AB, Horbinski, C, Iwamoto, FM, Rabadan, R, Sonabend, AM Nat Cancer 3 (3): 373. doi: 10.1038/s43018-022-00343-8. PubMed PMID:35149861
  • 2022 | Three-dimensional spatial transcriptomics uncovers cell type localizations in the human rheumatoid arthritis synovium. Vickovic, S, Schapiro, D, Carlberg, K, Lötstedt, B, Larsson, L, Hildebrandt, F, Korotkova, M, Hensvold, AH, Catrina, AI, Sorger, PK, Malmström, V, Regev, A, Ståhl, PL Commun Biol 5 (1): 129. doi: 10.1038/s42003-022-03050-3. PubMed PMID:35149753 PubMed Central PMC8837632
  • 2022 | Single-cell tumor-immune microenvironment of BRCA1/2 mutated high-grade serous ovarian cancer. Launonen, IM, Lyytikäinen, N, Casado, J, Anttila, EA, Szabó, A, Haltia, UM, Jacobson, CA, Lin, JR, Maliga, Z, Howitt, BE, Strickland, KC, Santagata, S, Elias, K, D'Andrea, AD, Konstantinopoulos, PA, Sorger, PK, Färkkilä, A Nat Commun 13 (1): 835. doi: 10.1038/s41467-022-28389-3. PubMed PMID:35149709 PubMed Central PMC8837628
  • 2022 | Single-Cell Transcriptional Profiling Reveals Signatures of Helper, Effector, and Regulatory MAIT Cells during Homeostasis and Activation. Vorkas, CK, Krishna, C, Li, K, Aubé, J, Fitzgerald, DW, Mazutis, L, Leslie, CS, Glickman, MS J Immunol 208 (5): 1042-1056. doi: 10.4049/jimmunol.2100522. PubMed PMID:35149530 PubMed Central PMC9012082
  • 2022 | Spatial-CUT&Tag: Spatially resolved chromatin modification profiling at the cellular level. Deng, Y, Bartosovic, M, Kukanja, P, Zhang, D, Liu, Y, Su, G, Enninful, A, Bai, Z, Castelo-Branco, G, Fan, R Science 375 (6581): 681-686. doi: 10.1126/science.abg7216. PubMed PMID:35143307
  • 2021 | ERK1/2 phosphorylation predicts survival following anti-PD-1 immunotherapy in recurrent glioblastoma. Arrieta, VA, Chen, AX, Kane, JR, Kang, SJ, Kassab, C, Dmello, C, Zhao, J, Burdett, KB, Upadhyayula, PS, Lee-Chang, C, Shilati, J, Jaishankar, D, Chen, L, Gould, A, Zhang, D, Yuan, J, Zhao, W, Ling, X, Burks, JK, Laffleur, B, Amidei, C, Bruce, JN, Lukas, RV, Yamaguchi, JT, Cieremans, D, Rothschild, G, Basu, U, McCord, M, Brat, DJ, Zhang, H, Cooper, LAD, Zhang, B, Sims, P, Cloughesy, TF, Prins, R, Canoll, P, Stupp, R, Heimberger, AB, Horbinski, C, Iwamoto, FM, Rabadan, R, Sonabend, AM Nat Cancer 2 (12): 1372-1386. doi: 10.1038/s43018-021-00260-2. PubMed PMID:35121903 PubMed Central PMC8818262
  • 2021 | Immune-stimulating antibody conjugates elicit robust myeloid activation and durable antitumor immunity. Ackerman, SE, Pearson, CI, Gregorio, JD, Gonzalez, JC, Kenkel, JA, Hartmann, FJ, Luo, A, Ho, PY, LeBlanc, H, Blum, LK, Kimmey, SC, Luo, A, Nguyen, ML, Paik, JC, Sheu, LY, Ackerman, B, Lee, A, Li, H, Melrose, J, Laura, RP, Ramani, VC, Henning, KA, Jackson, DY, Safina, BS, Yonehiro, G, Devens, BH, Carmi, Y, Chapin, SJ, Bendall, SC, Kowanetz, M, Dornan, D, Engleman, EG, Alonso, MN Nat Cancer 2 (1): 18-33. doi: 10.1038/s43018-020-00136-x. PubMed PMID:35121890 PubMed Central PMC9012298
  • 2022 | Tracing the cis-regulatory changes underlying the endometrial control of placental invasion. Suhail, Y, Maziarz, JD, Novin, A, Dighe, A, Afzal, J, Wagner, G, Kshitiz, Proc Natl Acad Sci U S A 119 (6): . doi: 10.1073/pnas.2111256119. PubMed PMID:35110402 PubMed Central PMC8832988
  • 2021 | Paracrine Behaviors Arbitrate Parasite-Like Interactions Between Tumor Subclones. Noble, RJ, Walther, V, Roumestand, C, Hochberg, ME, Hibner, U, Lassus, P Front Ecol Evol 9 : . doi: 10.3389/fevo.2021.675638. PubMed PMID:35096847 PubMed Central PMC8794381
  • 2022 | Modeling of Tumor Growth with Input from Patient-Specific Metabolomic Data. Miller, HA, Lowengrub, J, Frieboes, HB Ann Biomed Eng 50 (3): 314-329. doi: 10.1007/s10439-022-02904-5. PubMed PMID:35083584
  • 2022 | Comprehensive evaluation of noise reduction methods for single-cell RNA sequencing data. Chu, SK, Zhao, S, Shyr, Y, Liu, Q Brief Bioinform 23 (2): . doi: 10.1093/bib/bbab565. PubMed PMID:35048125 PubMed Central PMC8921632
  • 2022 | Predictable Clinical Benefits without Evidence of Synergy in Trials of Combination Therapies with Immune-Checkpoint Inhibitors. Palmer, AC, Izar, B, Hwangbo, H, Sorger, PK Clin Cancer Res 28 (2): 368-377. doi: 10.1158/1078-0432.CCR-21-2275. PubMed PMID:35045958 PubMed Central PMC9068233
  • 2022 | Integrated Proteomics-Based Physical and Functional Mapping of AXL Kinase Signaling Pathways and Inhibitors Define Its Role in Cell Migration. Majumder, A, Hosseinian, S, Stroud, M, Adhikari, E, Saller, JJ, Smith, MA, Zhang, G, Agarwal, S, Creixell, M, Meyer, BS, Kinose, F, Bowers, K, Fang, B, Stewart, PA, Welsh, EA, Boyle, TA, Meyer, AS, Koomen, JM, Haura, EB Mol Cancer Res 20 (4): 542-555. doi: 10.1158/1541-7786.MCR-21-0275. PubMed PMID:35022314 PubMed Central PMC8983558
  • 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 PubMed Central PMC8811753
  • 2022 | From systems to structure - using genetic data to model protein structures. Braberg, H, Echeverria, I, Kaake, RM, Sali, A, Krogan, NJ Nat Rev Genet 23 (6): 342-354. doi: 10.1038/s41576-021-00441-w. PubMed PMID:35013567 PubMed Central PMC8744059
  • 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 PubMed Central PMC8748653
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  • 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
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  • 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
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