CSBC Supported Publications

Publications

  • 2021 | SAILER: scalable and accurate invariant representation learning for single-cell ATAC-seq processing and integration. Cao, Y, Fu, L, Wu, J, Peng, Q, Nie, Q, Zhang, J, Xie, X Bioinformatics 37 (Suppl_1): i317-i326. doi: 10.1093/bioinformatics/btab303. PubMed PMID:34252968 PubMed Central PMC8275346
  • 2021 | Few-shot learning creates predictive models of drug response that translate from high-throughput screens to individual patients. Ma, J, Fong, SH, Luo, Y, Bakkenist, CJ, Shen, JP, Mourragui, S, Wessels, LFA, Hafner, M, Sharan, R, Peng, J, Ideker, T Nat Cancer 2 (2): 233-244. doi: 10.1038/s43018-020-00169-2. PubMed PMID:34223192 PubMed Central PMC8248912
  • 2021 | Ex Vivo Analysis of Primary Tumor Specimens for Evaluation of Cancer Therapeutics. Tognon, CE, Sears, RC, Mills, GB, Gray, JW, Tyner, JW Annu Rev Cancer Biol 5 : 39-57. doi: 10.1146/annurev-cancerbio-043020-125955. PubMed PMID:34222745 PubMed Central PMC8248658
  • 2021 | CODEX multiplexed tissue imaging with DNA-conjugated antibodies. Black, S, Phillips, D, Hickey, JW, Kennedy-Darling, J, Venkataraaman, VG, Samusik, N, Goltsev, Y, Schürch, CM, Nolan, GP Nat Protoc : . doi: 10.1038/s41596-021-00556-8. PubMed PMID:34215862
  • 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 : . doi: 10.1038/s41588-021-00891-2. PubMed PMID:34211178
  • 2021 | Relevance of circulating hybrid cells as a non-invasive biomarker for myriad solid tumors. Dietz, MS, Sutton, TL, Walker, BS, Gast, CE, Zarour, L, Sengupta, SK, Swain, JR, Eng, J, Parappilly, M, Limbach, K, Sattler, A, Burlingame, E, Chin, Y, Gower, A, Mira, JLM, Sapre, A, Chiu, YJ, Clayburgh, DR, Pommier, SJ, Cetnar, JP, Fischer, JM, Jaboin, JJ, Pommier, RF, Sheppard, BC, Tsikitis, VL, Skalet, AH, Mayo, SC, Lopez, CD, Gray, JW, Mills, GB, Mitri, Z, Chang, YH, Chin, K, Wong, MH Sci Rep 11 (1): 13630. doi: 10.1038/s41598-021-93053-7. PubMed PMID:34211050 PubMed Central PMC8249418
  • 2021 | Specificity of Human Sulfiredoxin for Reductant and Peroxiredoxin Oligomeric State. Forshaw, TE, Reisz, JA, Nelson, KJ, Gumpena, R, Lawson, JR, Jönsson, TJ, Wu, H, Clodfelter, JE, Johnson, LC, Furdui, CM, Lowther, WT Antioxidants (Basel) 10 (6): . doi: 10.3390/antiox10060946. PubMed PMID:34208049 PubMed Central PMC8230665
  • 2021 | Evaluation of Somatic Mutations in Solid Metastatic Pan-Cancer Patients. Roosan, MR, Mambetsariev, I, Pharaon, R, Fricke, J, Baroz, AR, Chao, J, Chen, C, Nasser, MW, Chirravuri-Venkata, R, Jain, M, Smith, L, Yost, SE, Reckamp, KL, Pillai, R, Arvanitis, L, Afkhami, M, Wang, EW, Chung, V, Cristea, M, Fakih, M, Koczywas, M, Massarelli, E, Mortimer, J, Yuan, Y, Batra, SK, Pal, S, Salgia, R Cancers (Basel) 13 (11): . doi: 10.3390/cancers13112776. PubMed PMID:34204917 PubMed Central PMC8199748
  • 2021 | A yeast-optimized single-cell transcriptomics platform elucidates how mycophenolic acid and guanine alter global mRNA levels. Urbonaite, G, Lee, JTH, Liu, P, Parada, GE, Hemberg, M, Acar, M Commun Biol 4 (1): 822. doi: 10.1038/s42003-021-02320-w. PubMed PMID:34193958 PubMed Central PMC8245502
  • 2021 | A community challenge to evaluate RNA-seq, fusion detection, and isoform quantification methods for cancer discovery. Creason, A, Haan, D, Dang, K, Chiotti, KE, Inkman, M, Lamb, A, Yu, T, Hu, Y, Norman, TC, Buchanan, A, van Baren, J, Spangler, R, Rollins, MR, Spellman, PT, Rozanov, D, Zhang, J, Maher, CA, Caloian, C, Watson, JD, Uhrig, S, Haas, BJ, Jain, M, Akeson, M, Ahsen, ME, SMC-RNA Challenge Participants, Stolovitzky, G, Guinney, J, Boutros, PC, Stuart, JM, Ellrott, K Cell Syst : . doi: 10.1016/j.cels.2021.05.021. PubMed PMID:34146471
  • 2021 | A new method to accurately identify single nucleotide variants using small FFPE breast samples. Fortunato, A, Mallo, D, Rupp, SM, King, LM, Hardman, T, Lo, JY, Hall, A, Marks, JR, Hwang, ES, Maley, CC Brief Bioinform : . doi: 10.1093/bib/bbab221. PubMed PMID:34117742
  • 2021 | 3D Printed frames to enable reuse and improve the fit of N95 and KN95 respirators. McAvoy, M, Bui, AN, Hansen, C, Plana, D, Said, JT, Yu, Z, Yang, H, Freake, J, Van, C, Krikorian, D, Cramer, A, Smith, L, Jiang, L, Lee, KJ, Li, SJ, Beller, B, Huggins, K, Short, MP, Yu, SH, Mostaghimi, A, Sorger, PK, LeBoeuf, NR BMC Biomed Eng 3 (1): 10. doi: 10.1186/s42490-021-00055-7. PubMed PMID:34099062 PubMed Central PMC8182357
  • 2021 | SARS-CoV-2 infects human pancreatic β cells and elicits β cell impairment. Wu, CT, Lidsky, PV, Xiao, Y, Lee, IT, Cheng, R, Nakayama, T, Jiang, S, Demeter, J, Bevacqua, RJ, Chang, CA, Whitener, RL, Stalder, AK, Zhu, B, Chen, H, Goltsev, Y, Tzankov, A, Nayak, JV, Nolan, GP, Matter, MS, Andino, R, Jackson, PK Cell Metab : . doi: 10.1016/j.cmet.2021.05.013. PubMed PMID:34081912 PubMed Central PMC8130512
  • 2021 | Unsupervised logic-based mechanism inference for network-driven biological processes. Prugger, M, Einkemmer, L, Beik, SP, Wasdin, PT, Harris, LA, Lopez, CF PLoS Comput Biol 17 (6): e1009035. doi: 10.1371/journal.pcbi.1009035. PubMed PMID:34077417 PubMed Central PMC8202945
  • 2021 | Molecular and Clinical Features of Hospital Admissions in Patients with Thoracic Malignancies on Immune Checkpoint Inhibitors. Zhao, D, Li, H, Mambetsariev, I, Chen, C, Pharaon, R, Fricke, J, Baroz, AR, Kulkarni, P, Xing, Y, Massarelli, E, Koczywas, M, Reckamp, KL, Margolin, K, Salgia, R Cancers (Basel) 13 (11): . doi: 10.3390/cancers13112653. PubMed PMID:34071259 PubMed Central PMC8198372
  • 2021 | Contacts with macrophages promote an aggressive nanomechanical phenotype of circulating tumor cells in prostate cancer. Osmulski, PA, Cunsolo, A, Chen, M, Qian, Y, Lin, CL, Hung, CN, Mahalingam, D, Kirma, NB, Chen, CL, Taverna, JA, Liss, MA, Thompson, IM, Huang, TH, Gaczynska, ME Cancer Res : . doi: 10.1158/0008-5472.CAN-20-3595. PubMed PMID:34045187
  • 2021 | Thunor: visualization and analysis of high-throughput dose-response datasets. Lubbock, ALR, Harris, LA, Quaranta, V, Tyson, DR, Lopez, CF Nucleic Acids Res 49 (W1): W633-W640. doi: 10.1093/nar/gkab424. PubMed PMID:34038546 PubMed Central PMC8265171
  • 2021 | Evolution of core archetypal phenotypes in progressive high grade serous ovarian cancer. Nath, A, Cosgrove, PA, Mirsafian, H, Christie, EL, Pflieger, L, Copeland, B, Majumdar, S, Cristea, MC, Han, ES, Lee, SJ, Wang, EW, Fereday, S, Traficante, N, Salgia, R, Werner, T, Cohen, AL, Moos, P, Chang, JT, Bowtell, DDL, Bild, AH Nat Commun 12 (1): 3039. doi: 10.1038/s41467-021-23171-3. PubMed PMID:34031395 PubMed Central PMC8144406
  • 2021 | Detection of Post-translational Modifications on MYC. Daniel, CJ, Sun, XX, Chen, Y, Zhang, X, Dai, MS, Sears, RC Methods Mol Biol 2318 : 69-85. doi: 10.1007/978-1-0716-1476-1_5. PubMed PMID:34019287
  • 2021 | Single-cell characterization of macrophages in glioblastoma reveals MARCO as a mesenchymal pro-tumor marker. Chen, AX, Gartrell, RD, Zhao, J, Upadhyayula, PS, Zhao, W, Yuan, J, Minns, HE, Dovas, A, Bruce, JN, Lasorella, A, Iavarone, A, Canoll, P, Sims, PA, Rabadan, R Genome Med 13 (1): 88. doi: 10.1186/s13073-021-00906-x. PubMed PMID:34011400 PubMed Central PMC8136167
  • 2021 | Membrane signalosome: where biophysics meets systems biology. Kandy, SK, Janmey, PA, Radhakrishnan, R Curr Opin Syst Biol 25 : 34-41. doi: 10.1016/j.coisb.2021.02.001. PubMed PMID:33997528 PubMed Central PMC8117111
  • 2021 | Elevated fibroblast growth factor-inducible 14 expression transforms proneural-like gliomas into more aggressive and lethal brain cancer. Connolly, NP, Galisteo, R, Xu, S, Bar, EE, Peng, S, Tran, NL, Ames, HM, Kim, AJ, Woodworth, GF, Winkles, JA Glia 69 (9): 2199-2214. doi: 10.1002/glia.24018. PubMed PMID:33991013
  • 2021 | Integration of machine learning and genome-scale metabolic modeling identifies multi-omics biomarkers for radiation resistance. Lewis, JE, Kemp, ML Nat Commun 12 (1): 2700. doi: 10.1038/s41467-021-22989-1. PubMed PMID:33976213 PubMed Central PMC8113601
  • 2021 | DebarcodeR increases fluorescent cell barcoding capacity and accuracy. Reisman, BJ, Barone, SM, Bachmann, BO, Irish, JM Cytometry A : . doi: 10.1002/cyto.a.24363. PubMed PMID:33960644
  • 2021 | Therapeutically reprogrammed nutrient signalling enhances nanoparticulate albumin bound drug uptake and efficacy in KRAS-mutant cancer. Li, R, Ng, TSC, Wang, SJ, Prytyskach, M, Rodell, CB, Mikula, H, Kohler, RH, Garlin, MA, Lauffenburger, DA, Parangi, S, Dinulescu, DM, Bardeesy, N, Weissleder, R, Miller, MA Nat Nanotechnol 16 (7): 830-839. doi: 10.1038/s41565-021-00897-1. PubMed PMID:33958764
  • 2021 | Systematic interrogation of mutation groupings reveals divergent downstream expression programs within key cancer genes. Grzadkowski, MR, Holly, HD, Somers, J, Demir, E BMC Bioinformatics 22 (1): 233. doi: 10.1186/s12859-021-04147-y. PubMed PMID:33957863 PubMed Central PMC8101181
  • 2021 | Evolution of delayed resistance to immunotherapy in a melanoma responder. Liu, D, Lin, JR, Robitschek, EJ, Kasumova, GG, Heyde, A, Shi, A, Kraya, A, Zhang, G, Moll, T, Frederick, DT, Chen, YA, Wang, S, Schapiro, D, Ho, LL, Bi, K, Sahu, A, Mei, S, Miao, B, Sharova, T, Alvarez-Breckenridge, C, Stocking, JH, Kim, T, Fadden, R, Lawrence, D, Hoang, MP, Cahill, DP, Malehmir, M, Nowak, MA, Brastianos, PK, Lian, CG, Ruppin, E, Izar, B, Herlyn, M, Van Allen, EM, Nathanson, K, Flaherty, KT, Sullivan, RJ, Kellis, M, Sorger, PK, Boland, GM Nat Med 27 (6): 985-992. doi: 10.1038/s41591-021-01331-8. PubMed PMID:33941922
  • 2021 | Impact of HER2 heterogeneity on treatment response of early-stage HER2-positive breast cancer: phase II neoadjuvant clinical trial of T-DM1 combined with pertuzumab. Metzger Filho, O, Viale, G, Stein, S, Trippa, L, Yardley, DA, Mayer, IA, Abramson, VG, Arteaga, CL, Spring, LM, Waks, AG, Wrabel, E, DeMeo, MK, Bardia, A, Dell'Orto, P, Russo, L, King, TA, Polyak, K, Michor, F, Winer, EP, Krop, IE Cancer Discov : . doi: 10.1158/2159-8290.CD-20-1557. PubMed PMID:33941592
  • 2021 | ZTCG: Viruses expand the genetic alphabet. Grome, MW, Isaacs, FJ Science 372 (6541): 460-461. doi: 10.1126/science.abh3571. PubMed PMID:33926938
  • 2021 | COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets. Delorey, TM, Ziegler, CGK, Heimberg, G, Normand, R, Yang, Y, Segerstolpe, Å, Abbondanza, D, Fleming, SJ, Subramanian, A, Montoro, DT, Jagadeesh, KA, Dey, KK, Sen, P, Slyper, M, Pita-Juárez, YH, Phillips, D, Biermann, J, Bloom-Ackermann, Z, Barkas, N, Ganna, A, Gomez, J, Melms, JC, Katsyv, I, Normandin, E, Naderi, P, Popov, YV, Raju, SS, Niezen, S, Tsai, LT, Siddle, KJ, Sud, M, Tran, VM, Vellarikkal, SK, Wang, Y, Amir-Zilberstein, L, Atri, DS, Beechem, J, Brook, OR, Chen, J, Divakar, P, Dorceus, P, Engreitz, JM, Essene, A, Fitzgerald, DM, Fropf, R, Gazal, S, Gould, J, Grzyb, J, Harvey, T, Hecht, J, Hether, T, Jané-Valbuena, J, Leney-Greene, M, Ma, H, McCabe, C, McLoughlin, DE, Miller, EM, Muus, C, Niemi, M, Padera, R, Pan, L, Pant, D, Pe'er, C, Pfiffner-Borges, J, Pinto, CJ, Plaisted, J, Reeves, J, Ross, M, Rudy, M, Rueckert, EH, Siciliano, M, Sturm, A, Todres, E, Waghray, A, Warren, S, Zhang, S, Zollinger, DR, Cosimi, L, Gupta, RM, Hacohen, N, Hibshoosh, H, Hide, W, Price, AL, Rajagopal, J, Tata, PR, Riedel, S, Szabo, G, Tickle, TL, Ellinor, PT, Hung, D, Sabeti, PC, Novak, R, Rogers, R, Ingber, DE, Jiang, ZG, Juric, D, Babadi, M, Farhi, SL, Izar, B et al. Nature 595 (7865): 107-113. doi: 10.1038/s41586-021-03570-8. PubMed PMID:33915569
  • 2021 | A molecular single-cell lung atlas of lethal COVID-19. Melms, JC, Biermann, J, Huang, H, Wang, Y, Nair, A, Tagore, S, Katsyv, I, Rendeiro, AF, Amin, AD, Schapiro, D, Frangieh, CJ, Luoma, AM, Filliol, A, Fang, Y, Ravichandran, H, Clausi, MG, Alba, GA, Rogava, M, Chen, SW, Ho, P, Montoro, DT, Kornberg, AE, Han, AS, Bakhoum, MF, Anandasabapathy, N, Suárez-Fariñas, M, Bakhoum, SF, Bram, Y, Borczuk, A, Guo, XV, Lefkowitch, JH, Marboe, C, Lagana, SM, Del Portillo, A, Zorn, E, Markowitz, GS, Schwabe, RF, Schwartz, RE, Elemento, O, Saqi, A, Hibshoosh, H, Que, J, Izar, B Nature 595 (7865): 114-119. doi: 10.1038/s41586-021-03569-1. PubMed PMID:33915568
  • 2021 | A Crisis-Responsive Framework for Medical Device Development Applied to the COVID-19 Pandemic. Antonini, MJ, Plana, D, Srinivasan, S, Atta, L, Achanta, A, Yang, H, Cramer, AK, Freake, J, Sinha, MS, Yu, SH, LeBoeuf, NR, Linville-Engler, B, Sorger, PK Front Digit Health 3 : . doi: 10.3389/fdgth.2021.617106. PubMed PMID:33899045 PubMed Central PMC8064560
  • 2021 | A unified atlas of CD8 T cell dysfunctional states in cancer and infection. Pritykin, Y, van der Veeken, J, Pine, AR, Zhong, Y, Sahin, M, Mazutis, L, Pe'er, D, Rudensky, AY, Leslie, CS Mol Cell 81 (11): 2477-2493.e10. doi: 10.1016/j.molcel.2021.03.045. PubMed PMID:33891860
  • 2021 | Disruption of the HER3-PI3K-mTOR oncogenic signaling axis and PD-1 blockade as a multimodal precision immunotherapy in head and neck cancer. Wang, Z, Goto, Y, Allevato, MM, Wu, VH, Saddawi-Konefka, R, Gilardi, M, Alvarado, D, Yung, BS, O'Farrell, A, Molinolo, AA, Duvvuri, U, Grandis, JR, Califano, JA, Cohen, EEW, Gutkind, JS Nat Commun 12 (1): 2383. doi: 10.1038/s41467-021-22619-w. PubMed PMID:33888713 PubMed Central PMC8062674
  • 2021 | Dual blockade of EGFR and CDK4/6 delays head and neck squamous cell carcinoma progression by inducing metabolic rewiring. Chaudhary, S, Pothuraju, R, Rachagani, S, Siddiqui, JA, Atri, P, Mallya, K, Nasser, MW, Sayed, Z, Lyden, ER, Smith, L, Gupta, SD, Ralhan, R, Lakshmanan, I, Jones, DT, Ganti, AK, Macha, MA, Batra, SK Cancer Lett 510 : 79-92. doi: 10.1016/j.canlet.2021.04.004. PubMed PMID:33878394 PubMed Central PMC8153085
  • 2021 | Usefulness of Circulating Tumor DNA in Identifying Somatic Mutations and Tracking Tumor Evolution in Patients with Non-Small Cell Lung Cancer. Roosan, MR, Mambetsariev, I, Pharaon, R, Fricke, J, Husain, H, Reckamp, KL, Koczywas, M, Massarelli, E, Bild, AH, Salgia, R Chest : . doi: 10.1016/j.chest.2021.04.016. PubMed PMID:33878340
  • 2021 | Single-cell sequencing links multiregional immune landscapes and tissue-resident T cells in ccRCC to tumor topology and therapy efficacy. Krishna, C, DiNatale, RG, Kuo, F, Srivastava, RM, Vuong, L, Chowell, D, Gupta, S, Vanderbilt, C, Purohit, TA, Liu, M, Kansler, E, Nixon, BG, Chen, YB, Makarov, V, Blum, KA, Attalla, K, Weng, S, Salmans, ML, Golkaram, M, Liu, L, Zhang, S, Vijayaraghavan, R, Pawlowski, T, Reuter, V, Carlo, MI, Voss, MH, Coleman, J, Russo, P, Motzer, RJ, Li, MO, Leslie, CS, Chan, TA, Hakimi, AA Cancer Cell 39 (5): 662-677.e6. doi: 10.1016/j.ccell.2021.03.007. PubMed PMID:33861994 PubMed Central PMC8268947
  • 2021 | The AMBRA1 E3 ligase adaptor regulates the stability of cyclin D. Chaikovsky, AC, Li, C, Jeng, EE, Loebell, S, Lee, MC, Murray, CW, Cheng, R, Demeter, J, Swaney, DL, Chen, SH, Newton, BW, Johnson, JR, Drainas, AP, Shue, YT, Seoane, JA, Srinivasan, P, He, A, Yoshida, A, Hipkins, SQ, McCrea, E, Poltorack, CD, Krogan, NJ, Diehl, JA, Kong, C, Jackson, PK, Curtis, C, Petrov, DA, Bassik, MC, Winslow, MM, Sage, J Nature 592 (7856): 794-798. doi: 10.1038/s41586-021-03474-7. PubMed PMID:33854239 PubMed Central PMC8246597
  • 2021 | A theoretical analysis of tumour containment. Viossat, Y, Noble, R Nat Ecol Evol 5 (6): 826-835. doi: 10.1038/s41559-021-01428-w. PubMed PMID:33846605
  • 2021 | Beyond Programmed Death-Ligand 1: B7-H6 Emerges as a Potential Immunotherapy Target in SCLC. Thomas, PL, Groves, SM, Zhang, YK, Li, J, Gonzalez-Ericsson, P, Sivagnanam, S, Betts, CB, Chen, HC, Liu, Q, Lowe, C, Chen, H, Boyd, KL, Kopparapu, PR, Yan, Y, Coussens, LM, Quaranta, V, Tyson, DR, Iams, W, Lovly, CM J Thorac Oncol 16 (7): 1211-1223. doi: 10.1016/j.jtho.2021.03.011. PubMed PMID:33839362 PubMed Central PMC8222171
  • 2021 | Automated quality control and cell identification of droplet-based single-cell data using dropkick. Heiser, CN, Wang, VM, Chen, B, Hughey, JJ, Lau, KS Genome Res : . doi: 10.1101/gr.271908.120. PubMed PMID:33837131
  • 2020 | Spatial mapping of single cells in the Drosophila embryo from transcriptomic data based on topological consistency. Zand, M, Ruan, J F1000Res 9 : 1014. doi: 10.12688/f1000research.24163.2. PubMed PMID:33824719 PubMed Central PMC7993407
  • 2021 | Normal tissue architecture determines the evolutionary course of cancer. West, J, Schenck, RO, Gatenbee, C, Robertson-Tessi, M, Anderson, ARA Nat Commun 12 (1): 2060. doi: 10.1038/s41467-021-22123-1. PubMed PMID:33824323 PubMed Central PMC8024392
  • 2021 | De novo Powered Air-Purifying Respirator Design and Fabrication for Pandemic Response. Kothakonda, A, Atta, L, Plana, D, Ward, F, Davis, C, Cramer, A, Moran, R, Freake, J, Tian, E, Mazor, O, Gorelik, P, Van, C, Hansen, C, Yang, H, Sinha, MS, Li, J, Yu, SH, LeBoeuf, NR, Sorger, PK medRxiv : . doi: 10.1101/2021.03.25.21252076. PubMed PMID:33821290 PubMed Central PMC8020994
  • 2021 | A survey of multiscale modeling: Foundations, historical milestones, current status, and future prospects. Radhakrishnan, R AIChE J 67 (3): e17026. doi: 10.1002/aic.17026. PubMed PMID:33790479 PubMed Central PMC7988612
  • 2021 | Creating collaboration by breaking down scientific barriers. Fabius, JM, Krogan, NJ Cell 184 (9): 2271-2275. doi: 10.1016/j.cell.2021.02.022. PubMed PMID:33765441
  • 2021 | Time-resolved phosphoproteomics reveals scaffolding and catalysis-responsive patterns of SHP2-dependent signaling. Vemulapalli, V, Chylek, LA, Erickson, A, Pfeiffer, A, Gabriel, KH, LaRochelle, J, Subramanian, K, Cao, R, Stegmaier, K, Mohseni, M, LaMarche, MJ, Acker, MG, Sorger, PK, Gygi, SP, Blacklow, SC Elife 10 : . doi: 10.7554/eLife.64251. PubMed PMID:33755016 PubMed Central PMC8024022
  • | Integrating 3D structural information into systems biology. Murray, D, Petrey, D, Honig, B J Biol Chem 296 : 100562. doi: 10.1016/j.jbc.2021.100562. PubMed PMID:33744294 PubMed Central PMC8095114
  • 2021 | RNA-based therapies: A cog in the wheel of lung cancer defense. Khan, P, Siddiqui, JA, Lakshmanan, I, Ganti, AK, Salgia, R, Jain, M, Batra, SK, Nasser, MW Mol Cancer 20 (1): 54. doi: 10.1186/s12943-021-01338-2. PubMed PMID:33740988 PubMed Central PMC7977189
  • 2021 | Targeting immunosuppressive macrophages overcomes PARP inhibitor resistance in BRCA1-associated triple-negative breast cancer. Mehta, AK, Cheney, EM, Hartl, CA, Pantelidou, C, Oliwa, M, Castrillon, JA, Lin, JR, Hurst, KE, de Oliveira Taveira, M, Johnson, NT, Oldham, WM, Kalocsay, M, Berberich, MJ, Boswell, SA, Kothari, A, Johnson, S, Dillon, DA, Lipschitz, M, Rodig, S, Santagata, S, Garber, JE, Tung, N, Yélamos, J, Thaxton, JE, Mittendorf, EA, Sorger, PK, Shapiro, GI, Guerriero, JL Nat Cancer 2 (1): 66-82. doi: 10.1038/s43018-020-00148-7. PubMed PMID:33738458 PubMed Central PMC7963404
  • 2021 | Leukocyte Heterogeneity in Pancreatic Ductal Adenocarcinoma: Phenotypic and Spatial Features Associated with Clinical Outcome. Liudahl, SM, Betts, CB, Sivagnanam, S, Morales-Oyarvide, V, da Silva, A, Yuan, C, Hwang, S, Grossblatt-Wait, A, Leis, KR, Larson, W, Lavoie, MB, Robinson, P, Dias Costa, A, Väyrynen, SA, Clancy, TE, Rubinson, DA, Link, J, Keith, D, Horton, W, Tempero, MA, Vonderheide, RH, Jaffee, EM, Sheppard, B, Goecks, J, Sears, RC, Park, BS, Mori, M, Nowak, JA, Wolpin, BM, Coussens, LM Cancer Discov : . doi: 10.1158/2159-8290.CD-20-0841. PubMed PMID:33727309
  • 2021 | stochprofML: stochastic profiling using maximum likelihood estimation in R. Amrhein, L, Fuchs, C BMC Bioinformatics 22 (1): 123. doi: 10.1186/s12859-021-03970-7. PubMed PMID:33722188 PubMed Central PMC7958472
  • 2020 | Flipped Science Fair: Engaging Middle-School Students in STEM while Training Researchers in Science Communication. Benedetti, L, Crouse, RB J STEM Outreach 3 (1): . doi: 10.15695/jstem/v3i1.10. PubMed PMID:33718806 PubMed Central PMC7951179
  • 2021 | Pontin Functions as A Transcriptional Co-activator for Retinoic Acid-induced HOX Gene Expression. Tang, D, Zhang, Z, Zboril, E, Wetzel, MD, Xu, X, Zhang, W, Chen, L, Liu, Z J Mol Biol 433 (14): 166928. doi: 10.1016/j.jmb.2021.166928. PubMed PMID:33713676 PubMed Central PMC8184613
  • 2021 | Novel evolutionary dynamics of small populations in breast cancer adjuvant and neoadjuvant therapy. Artzy-Randrup, Y, Epstein, T, Brown, JS, Costa, RLB, Czerniecki, BJ, Gatenby, RA NPJ Breast Cancer 7 (1): 26. doi: 10.1038/s41523-021-00230-y. PubMed PMID:33707440 PubMed Central PMC7952601
  • 2021 | ATM and ATR Activation Through Crosstalk Between DNA Damage Response Pathways. Fedak, EA, Adler, FR, Abegglen, LM, Schiffman, JD Bull Math Biol 83 (4): 38. doi: 10.1007/s11538-021-00868-6. PubMed PMID:33704589 PubMed Central PMC8051223
  • 2021 | Knowledge-based classification of fine-grained immune cell types in single-cell RNA-Seq data. Liu, X, Gosline, SJC, Pflieger, LT, Wallet, P, Iyer, A, Guinney, J, Bild, AH, Chang, JT Brief Bioinform : . doi: 10.1093/bib/bbab039. PubMed PMID:33681983
  • 2021 | Computational studies of anaplastic lymphoma kinase mutations reveal common mechanisms of oncogenic activation. Patil, K, Jordan, EJ, Park, JH, Suresh, K, Smith, CM, Lemmon, AA, Mossé, YP, Lemmon, MA, Radhakrishnan, R Proc Natl Acad Sci U S A 118 (10): . doi: 10.1073/pnas.2019132118. PubMed PMID:33674381 PubMed Central PMC7958353
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