CSBC Supported Publications

Publications

  • 2023 | Single-Cell Kinetic Modeling of β-Lapachone Metabolism in Head and Neck Squamous Cell Carcinoma. Raddatz, AD, Furdui, CM, Bey, EA, Kemp, ML Antioxidants (Basel) 12 (3): . doi: 10.3390/antiox12030741. PubMed PMID:36978989 PubMed Central PMC10045120
  • 2023 | SEACells infers transcriptional and epigenomic cellular states from single-cell genomics data. Persad, S, Choo, ZN, Dien, C, Sohail, N, Masilionis, I, Chaligné, R, Nawy, T, Brown, CC, Sharma, R, Pe'er, I, Setty, M, Pe'er, D Nat Biotechnol : . doi: 10.1038/s41587-023-01716-9. PubMed PMID:36973557
  • 2023 | A survey of open questions in adaptive therapy: Bridging mathematics and clinical translation. West, J, Adler, F, Gallaher, J, Strobl, M, Brady-Nicholls, R, Brown, J, Roberson-Tessi, M, Kim, E, Noble, R, Viossat, Y, Basanta, D, Anderson, ARA Elife 12 : . doi: 10.7554/eLife.84263. PubMed PMID:36952376 PubMed Central PMC10036119
  • 2023 | Automated assembly of molecular mechanisms at scale from text mining and curated databases. Bachman, JA, Gyori, BM, Sorger, PK Mol Syst Biol : e11325. doi: 10.15252/msb.202211325. PubMed PMID:36938926
  • 2023 | Involvement of Epithelial-Mesenchymal Transition Genes in Small Cell Lung Cancer Phenotypic Plasticity. Groves, SM, Panchy, N, Tyson, DR, Harris, LA, Quaranta, V, Hong, T Cancers (Basel) 15 (5): . doi: 10.3390/cancers15051477. PubMed PMID:36900269 PubMed Central PMC10001072
  • 2023 | Structural biology at the scale of proteomes. Bouatta, N, AlQuraishi, M Nat Struct Mol Biol 30 (2): 129-130. doi: 10.1038/s41594-023-00924-w. PubMed PMID:36797377
  • 2023 | Elephant TP53-RETROGENE 9 induces transcription-independent apoptosis at the mitochondria. Preston, AJ, Rogers, A, Sharp, M, Mitchell, G, Toruno, C, Barney, BB, Donovan, LN, Bly, J, Kennington, R, Payne, E, Iovino, A, Furukawa, G, Robinson, R, Shamloo, B, Buccilli, M, Anders, R, Eckstein, S, Fedak, EA, Wright, T, Maley, CC, Kiso, WK, Schmitt, D, Malkin, D, Schiffman, JD, Abegglen, LM Cell Death Discov 9 (1): 66. doi: 10.1038/s41420-023-01348-7. PubMed PMID:36797268 PubMed Central PMC9935553
  • 2023 | PrePCI: A structure- and chemical similarity-informed database of predicted protein compound interactions. Trudeau, SJ, Hwang, H, Mathur, D, Begum, K, Petrey, D, Murray, D, Honig, B Protein Sci 32 (4): e4594. doi: 10.1002/pro.4594. PubMed PMID:36776141 PubMed Central PMC10019447
  • 2023 | Alignment, segmentation and neighborhood analysis in cyclic immunohistochemistry data using CASSATT. Brockman, AA, Khurana, R, Bartkowiak, T, Thomas, PL, Sivagnanam, S, Betts, CB, Coussens, LM, Lovly, CM, Irish, JM, Ihrie, RA Cytometry B Clin Cytom : . doi: 10.1002/cyto.b.22114. PubMed PMID:36748312
  • 2023 | A biochemical necroptosis model explains cell-type-specific responses to cell death cues. Ildefonso, GV, Oliver Metzig, M, Hoffmann, A, Harris, LA, Lopez, CF Biophys J 122 (5): 817-834. doi: 10.1016/j.bpj.2023.01.035. PubMed PMID:36710493 PubMed Central PMC10027451
  • 2023 | Neutrophil-activating therapy for the treatment of cancer. Linde, IL, Prestwood, TR, Qiu, J, Pilarowski, G, Linde, MH, Zhang, X, Shen, L, Reticker-Flynn, NE, Chiu, DK, Sheu, LY, Van Deursen, S, Tolentino, LL, Song, WC, Engleman, EG Cancer Cell 41 (2): 356-372.e10. doi: 10.1016/j.ccell.2023.01.002. PubMed PMID:36706760 PubMed Central PMC9968410
  • 2023 | Massively parallel knock-in engineering of human T cells. Dai, X, Park, JJ, Du, Y, Na, Z, Lam, SZ, Chow, RD, Renauer, PA, Gu, J, Xin, S, Chu, Z, Liao, C, Clark, P, Zhao, H, Slavoff, S, Chen, S Nat Biotechnol : . doi: 10.1038/s41587-022-01639-x. PubMed PMID:36702900
  • 2023 | Mechanistic model of MAPK signaling reveals how allostery and rewiring contribute to drug resistance. Fröhlich, F, Gerosa, L, Muhlich, J, Sorger, PK Mol Syst Biol 19 (2): e10988. doi: 10.15252/msb.202210988. PubMed PMID:36700386 PubMed Central PMC9912026
  • 2023 | Oncogenic PKA signaling increases c-MYC protein expression through multiple targetable mechanisms. Chan, GKL, Maisel, S, Hwang, YC, Pascual, BC, Wolber, RRB, Vu, P, Patra, KC, Bouhaddou, M, Kenerson, HL, Lim, HC, Long, D, Yeung, RS, Sethupathy, P, Swaney, DL, Krogan, NJ, Turnham, RE, Riehle, KJ, Scott, JD, Bardeesy, N, Gordan, JD Elife 12 : . doi: 10.7554/eLife.69521. PubMed PMID:36692000 PubMed Central PMC9925115
  • 2023 | Outcomes and clinicopathologic characteristics associated with disseminated tumor cells in bone marrow after neoadjuvant chemotherapy in high-risk early stage breast cancer: the I-SPY SURMOUNT study. Magbanua, MJM, van 't Veer, L, Clark, AS, Chien, AJ, Boughey, JC, Han, HS, Wallace, A, Beckwith, H, Liu, MC, Yau, C, Wileyto, EP, Ordonez, A, Solanki, TI, Hsiao, F, Lee, JC, Basu, A, Brown Swigart, L, Perlmutter, J, Delson, AL, Bayne, L, Deluca, S, Yee, SS, Carpenter, EL, Esserman, LJ, Park, JW, Chodosh, LA, DeMichele, A Breast Cancer Res Treat 198 (2): 383-390. doi: 10.1007/s10549-022-06803-0. PubMed PMID:36689092
  • 2023 | Panobinostat Induced Spatial In Situ Biomarkers Predictive of Anti-PD-1 Efficacy in Mouse Mammary Carcinoma. Tatarova, Z, Blumberg, DC, Bensen, A, Mills, GB, Jonas, O Cells 12 (2): . doi: 10.3390/cells12020308. PubMed PMID:36672243 PubMed Central PMC9856407
  • 2023 | Multiplexed 3D atlas of state transitions and immune interaction in colorectal cancer. Lin, JR, Wang, S, Coy, S, Chen, YA, Yapp, C, Tyler, M, Nariya, MK, Heiser, CN, Lau, KS, Santagata, S, Sorger, PK Cell 186 (2): 363-381.e19. doi: 10.1016/j.cell.2022.12.028. PubMed PMID:36669472 PubMed Central PMC10019067
  • 2023 | A multiplexed in vivo approach to identify driver genes in small cell lung cancer. Lee, MC, Cai, H, Murray, CW, Li, C, Shue, YT, Andrejka, L, He, AL, Holzem, AME, Drainas, AP, Ko, JH, Coles, GL, Kong, C, Zhu, S, Zhu, C, Wang, J, van de Rijn, M, Petrov, DA, Winslow, MM, Sage, J Cell Rep 42 (1): 111990. doi: 10.1016/j.celrep.2023.111990. PubMed PMID:36640300 PubMed Central PMC9972901
  • 2023 | Live Cell Lineage Tracing of Dormant Cancer Cells. Kim, H, Wirasaputra, A, Mohammadi, F, Kundu, AN, Esteves, JAE, Heiser, LM, Meyer, AS, Peyton, SR Adv Healthc Mater : e2202275. doi: 10.1002/adhm.202202275. PubMed PMID:36625629
  • 2023 | Multimodal single-cell and whole-genome sequencing of small, frozen clinical specimens. Wang, Y, Fan, JL, Melms, JC, Amin, AD, Georgis, Y, Barrera, I, Ho, P, Tagore, S, Abril-Rodríguez, G, He, S, Jin, Y, Biermann, J, Hofree, M, Caprio, L, Berhe, S, Khan, SA, Henick, BS, Ribas, A, Macosko, EZ, Chen, F, Taylor, AM, Schwartz, GK, Carvajal, RD, Azizi, E, Izar, B Nat Genet 55 (1): 19-25. doi: 10.1038/s41588-022-01268-9. PubMed PMID:36624340
  • 2022 | Evolutionary Analysis of TCGA Data Using Over- and Under- Mutated Genes Identify Key Molecular Pathways and Cellular Functions in Lung Cancer Subtypes. Freischel, AR, Teer, JK, Luddy, K, Cunningham, J, Artzy-Randrup, Y, Epstein, T, Tsai, KY, Berglund, A, Cleveland, JL, Gillies, RJ, Brown, JS, Gatenby, RA Cancers (Basel) 15 (1): . doi: 10.3390/cancers15010018. PubMed PMID:36612014 PubMed Central PMC9817988
  • 2023 | Bifurcation analysis of a free boundary model of vascular tumor growth with a necrotic core and chemotaxis. Lu, MJ, Hao, W, Hu, B, Li, S J Math Biol 86 (1): 19. doi: 10.1007/s00285-022-01862-9. PubMed PMID:36609586
  • 2023 | Metabolic regulation of species-specific developmental rates. Diaz-Cuadros, M, Miettinen, TP, Skinner, OS, Sheedy, D, Díaz-García, CM, Gapon, S, Hubaud, A, Yellen, G, Manalis, SR, Oldham, WM, Pourquié, O Nature 613 (7944): 550-557. doi: 10.1038/s41586-022-05574-4. PubMed PMID:36599986 PubMed Central PMC9944513
  • 2023 | MicroRNA-1 attenuates the growth and metastasis of small cell lung cancer through CXCR4/FOXM1/RRM2 axis. Khan, P, Siddiqui, JA, Kshirsagar, PG, Venkata, RC, Maurya, SK, Mirzapoiazova, T, Perumal, N, Chaudhary, S, Kanchan, RK, Fatima, M, Khan, MA, Rehman, AU, Lakshmanan, I, Mahapatra, S, Talmon, GA, Kulkarni, P, Ganti, AK, Jain, M, Salgia, R, Batra, SK, Nasser, MW Mol Cancer 22 (1): 1. doi: 10.1186/s12943-022-01695-6. PubMed PMID:36597126 PubMed Central PMC9811802
  • 2023 | Efficient computation of adjoint sensitivities at steady-state in ODE models of biochemical reaction networks. Lakrisenko, P, Stapor, P, Grein, S, Paszkowski, Ł, Pathirana, D, Fröhlich, F, Lines, GT, Weindl, D, Hasenauer, J PLoS Comput Biol 19 (1): e1010783. doi: 10.1371/journal.pcbi.1010783. PubMed PMID:36595539 PubMed Central PMC9838866
  • 2022 | Accurate genome-wide genotyping from archival tissue to explore the contribution of common genetic variants to pre-cancer outcomes. Nachmanson, D, Pagadala, M, Steward, J, Cheung, C, Bruce, LK, Lee, NQ, O'Keefe, TJ, Lin, GY, Hasteh, F, Morris, GP, Carter, H, Harismendy, O J Transl Med 20 (1): 623. doi: 10.1186/s12967-022-03810-z. PubMed PMID:36575447 PubMed Central PMC9793518
  • 2023 | Learning cell identity in immunology, neuroscience, and cancer. Medina, S, Ihrie, RA, Irish, JM Semin Immunopathol 45 (1): 3-16. doi: 10.1007/s00281-022-00976-y. PubMed PMID:36534139 PubMed Central PMC9762661
  • 2022 | Causal inference in medical records and complementary systems pharmacology for metformin drug repurposing towards dementia. Charpignon, ML, Vakulenko-Lagun, B, Zheng, B, Magdamo, C, Su, B, Evans, K, Rodriguez, S, Sokolov, A, Boswell, S, Sheu, YH, Somai, M, Middleton, L, Hyman, BT, Betensky, RA, Finkelstein, SN, Welsch, RE, Tzoulaki, I, Blacker, D, Das, S, Albers, MW Nat Commun 13 (1): 7652. doi: 10.1038/s41467-022-35157-w. PubMed PMID:36496454 PubMed Central PMC9741618
  • 2022 | DLL3 regulates Notch signaling in small cell lung cancer. Kim, JW, Ko, JH, Sage, J iScience 25 (12): 105603. doi: 10.1016/j.isci.2022.105603. PubMed PMID:36483011 PubMed Central PMC9722452
  • 2023 | Elevated Methionine Flux Drives Pyroptosis Evasion in Persister Cancer Cells. El-Kenawi, A, Berglund, A, Estrella, V, Zhang, Y, Liu, M, Putney, RM, Yoder, SJ, Johnson, J, Brown, J, Gatenby, R Cancer Res 83 (5): 720-734. doi: 10.1158/0008-5472.CAN-22-1002. PubMed PMID:36480167 PubMed Central PMC9978888
  • 2022 | Texture-based Error Analysis for Image Super-Resolution. Magid, SA, Lin, Z, Wei, D, Zhang, Y, Gu, J, Pfister, H Proc IEEE Comput Soc Conf Comput Vis Pattern Recognit 2022 : 2108-2117. doi: 10.1109/cvpr52688.2022.00216. PubMed PMID:36465475 PubMed Central PMC9719360
  • 2022 | Lactate-dependent chaperone-mediated autophagy induces oscillatory HIF-1α activity promoting proliferation of hypoxic cells. Kshitiz,, Afzal, J, Suhail, Y, Chang, H, Hubbi, ME, Hamidzadeh, A, Goyal, R, Liu, Y, Sun, P, Nicoli, S, Dang, CV, Levchenko, A Cell Syst 13 (12): 1048-1064.e7. doi: 10.1016/j.cels.2022.11.003. PubMed PMID:36462504 PubMed Central PMC10012408
  • 2022 | Double knockout CRISPR screen for cancer resistance to T cell cytotoxicity. Park, JJ, Codina, A, Ye, L, Lam, S, Guo, J, Clark, P, Zhou, X, Peng, L, Chen, S J Hematol Oncol 15 (1): 172. doi: 10.1186/s13045-022-01389-y. PubMed PMID:36456981 PubMed Central PMC9716677
  • 2022 | The genomic and immune landscape of long-term survivors of high-grade serous ovarian cancer. Garsed, DW, Pandey, A, Fereday, S, Kennedy, CJ, Takahashi, K, Alsop, K, Hamilton, PT, Hendley, J, Chiew, YE, Traficante, N, Provan, P, Ariyaratne, D, Au-Yeung, G, Bateman, NW, Bowes, L, Brand, A, Christie, EL, Cunningham, JM, Friedlander, M, Grout, B, Harnett, P, Hung, J, McCauley, B, McNally, O, Piskorz, AM, Saner, FAM, Vierkant, RA, Wang, C, Winham, SJ, Pharoah, PDP, Brenton, JD, Conrads, TP, Maxwell, GL, Ramus, SJ, Pearce, CL, Pike, MC, Nelson, BH, Goode, EL, DeFazio, A, Bowtell, DDL Nat Genet 54 (12): 1853-1864. doi: 10.1038/s41588-022-01230-9. PubMed PMID:36456881
  • 2022 | Spatial intra-tumor heterogeneity is associated with survival of lung adenocarcinoma patients. Wu, HJ, Temko, D, Maliga, Z, Moreira, AL, Sei, E, Minussi, DC, Dean, J, Lee, C, Xu, Q, Hochart, G, Jacobson, CA, Yapp, C, Schapiro, D, Sorger, PK, Seeley, EH, Navin, N, Downey, RJ, Michor, F Cell Genom 2 (8): . doi: 10.1016/j.xgen.2022.100165. PubMed PMID:36419822 PubMed Central PMC9681138
  • 2022 | The Adaptive Potential of Nonheritable Somatic Mutations. Majic, P, Erten, EY, Payne, JL Am Nat 200 (6): 755-772. doi: 10.1086/721766. PubMed PMID:36409982
  • 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
  • 2023 | OncoLoop: A Network-Based Precision Cancer Medicine Framework. Vasciaveo, A, Arriaga, JM, de Almeida, FN, Zou, M, Douglass, EF, Picech, F, Shibata, M, Rodriguez-Calero, A, de Brot, S, Mitrofanova, A, Chua, CW, Karan, C, Realubit, R, Pampou, S, Kim, JY, Afari, SN, Mukhammadov, T, Zanella, L, Corey, E, Alvarez, MJ, Rubin, MA, Shen, MM, Califano, A, Abate-Shen, C Cancer Discov 13 (2): 386-409. doi: 10.1158/2159-8290.CD-22-0342. PubMed PMID:36374194 PubMed Central PMC9905319
  • 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 | Phenotypic plasticity and genetic control in colorectal cancer evolution. Househam, J, Heide, T, Cresswell, GD, Spiteri, I, Kimberley, C, Zapata, L, Lynn, C, James, C, Mossner, M, Fernandez-Mateos, J, Vinceti, A, Baker, AM, Gabbutt, C, Berner, A, Schmidt, M, Chen, B, Lakatos, E, Gunasri, V, Nichol, D, Costa, H, Mitchinson, M, Ramazzotti, D, Werner, B, Iorio, F, Jansen, M, Caravagna, G, Barnes, CP, Shibata, D, Bridgewater, J, Rodriguez-Justo, M, Magnani, L, Sottoriva, A, Graham, TA Nature 611 (7937): 744-753. doi: 10.1038/s41586-022-05311-x. PubMed PMID:36289336 PubMed Central PMC9684078
  • 2022 | The co-evolution of the genome and epigenome in colorectal cancer. Heide, T, Househam, J, Cresswell, GD, Spiteri, I, Lynn, C, Mossner, M, Kimberley, C, Fernandez-Mateos, J, Chen, B, Zapata, L, James, C, Barozzi, I, Chkhaidze, K, Nichol, D, Gunasri, V, Berner, A, Schmidt, M, Lakatos, E, Baker, AM, Costa, H, Mitchinson, M, Piazza, R, Jansen, M, Caravagna, G, Ramazzotti, D, Shibata, D, Bridgewater, J, Rodriguez-Justo, M, Magnani, L, Graham, TA, Sottoriva, A Nature 611 (7937): 733-743. doi: 10.1038/s41586-022-05202-1. PubMed PMID:36289335 PubMed Central PMC9684080
  • 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 | 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 | Scalable and model-free detection of spatial patterns and colocalization. Liu, Q, Hsu, CY, Shyr, Y Genome Res 32 (9): 1736-1745. doi: 10.1101/gr.276851.122. PubMed PMID:36223499 PubMed Central PMC9528978
  • 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 PubMed Central PMC10043053
  • 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 50 (21): e121. doi: 10.1093/nar/gkac781. PubMed PMID:36130281 PubMed Central PMC9757079
  • 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 | 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
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  • 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
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  • 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
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  • 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 19 (2): 635-648. doi: 10.1007/s13311-022-01207-w. PubMed PMID:35226341 PubMed Central PMC9226224
  • 2022 | Treatment of immune checkpoint inhibitor-mediated psoriasis: A systematic review. Said, JT, Elman, SA, Perez-Chada, LM, Mita, C, Merola, JF, LeBoeuf, NR J Am Acad Dermatol 87 (2): 399-400. doi: 10.1016/j.jaad.2022.02.030. PubMed PMID:35218852 PubMed Central PMC9973559
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  • 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 PubMed Central PMC9288111
  • 2022 | Leveraging modeling and simulation to optimize the therapeutic window for epigenetic modifier drugs. Walz, AC, Van De Vyver, AJ, Yu, L, Birtwistle, MR, Krogan, NJ, Bouhaddou, M Pharmacol Ther 235 : 108162. doi: 10.1016/j.pharmthera.2022.108162. PubMed PMID:35189161 PubMed Central PMC9292061
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