CSBC Supported Publications

Publications

  • 2019 | Computational algorithms for in silico profiling of activating mutations in cancer. Jordan, EJ, Patil, K, Suresh, K, Park, JH, Mosse, YP, Lemmon, MA, Radhakrishnan, R Cell. Mol. Life Sci. : . doi: 10.1007/s00018-019-03097-2. PubMed PMID:30982079
  • 2019 | Shallow Sparsely-Connected Autoencoders for Gene Set Projection. Gold, MP, LeNail, A, Fraenkel, E Pac Symp Biocomput 24 : 374-385. . PubMed PMID:30963076 PubMed Central PMC6417803
  • 2019 | In vivo profiling of metastatic double knockouts through CRISPR-Cpf1 screens. Chow, RD, Wang, G, Ye, L, Codina, A, Kim, HR, Shen, L, Dong, MB, Errami, Y, Chen, S Nat. Methods : . doi: 10.1038/s41592-019-0371-5. PubMed PMID:30962622
  • 2019 | Tissue-specific oncogenic activity of K-RasA146T. Poulin, EJ, Bera, AK, Lu, J, Lin, YJ, Strasser, SD, Paulo, JA, Huang, TQ, Morales, C, Yan, W, Cook, J, Nowak, JA, Brubaker, DK, Joughin, BA, Johnson, CW, DeStefanis, RA, Ghazi, PC, Gondi, S, Wales, TE, Iacob, RE, Bogdanova, L, Gierut, JJ, Li, Y, Engen, JR, Perez-Mancera, PA, Braun, BS, Gygi, SP, Lauffenburger, DA, Westover, KD, Haigis, KM Cancer Discov : . doi: 10.1158/2159-8290.CD-18-1220. PubMed PMID:30952657
  • 2019 | SOX11 hypermethylation as a tumor biomarker in endometrial cancer. Shan, T, Uyar, DS, Wang, LS, Mutch, DG, Huang, TH, Rader, JS, Sheng, X, Huang, YW Biochimie 162 : 8-14. doi: 10.1016/j.biochi.2019.03.019. PubMed PMID:30935961
  • 2019 | Moving Toward a Consensus DSC-MRI Protocol: Validation of a Low-Flip Angle Single-Dose Option as a Reference Standard for Brain Tumors. Schmainda, KM, Prah, MA, Hu, LS, Quarles, CC, Semmineh, N, Rand, SD, Connelly, JM, Anderies, B, Zhou, Y, Liu, Y, Logan, B, Stokes, A, Baird, G, Boxerman, JL AJNR Am J Neuroradiol 40 (4): 626-633. doi: 10.3174/ajnr.A6015. PubMed PMID:30923088 PubMed Central PMC6461489
  • 2019 | Stress-Induced Evolutionary Innovation: A Mechanism for the Origin of Cell Types. Wagner, GP, Erkenbrack, EM, Love, AC Bioessays 41 (4): e1800188. doi: 10.1002/bies.201800188. PubMed PMID:30919472
  • 2019 | Acquisition of a hybrid E/M state is essential for tumorigenicity of basal breast cancer cells. Kröger, C, Afeyan, A, Mraz, J, Eaton, EN, Reinhardt, F, Khodor, YL, Thiru, P, Bierie, B, Ye, X, Burge, CB, Weinberg, RA Proc. Natl. Acad. Sci. U.S.A. 116 (15): 7353-7362. doi: 10.1073/pnas.1812876116. PubMed PMID:30910979 PubMed Central PMC6462070
  • 2019 | In situ 10-cell RNA sequencing in tissue and tumor biopsy samples. Singh, S, Wang, L, Schaff, DL, Sutcliffe, MD, Koeppel, AF, Kim, J, Onengut-Gumuscu, S, Park, KS, Zong, H, Janes, KA Sci Rep 9 (1): 4836. doi: 10.1038/s41598-019-41235-9. PubMed PMID:30894605 PubMed Central PMC6426952
  • 2019 | The gut microbiome and response to immune checkpoint inhibitors: preclinical and clinical strategies. Gong, J, Chehrazi-Raffle, A, Placencio-Hickok, V, Guan, M, Hendifar, A, Salgia, R Clin Transl Med 8 (1): 9. doi: 10.1186/s40169-019-0225-x. PubMed PMID:30887236 PubMed Central PMC6423251
  • 2019 | Higher order genomic organization and epigenetic control maintain cellular identity and prevent breast cancer. Fritz, AJ, Gillis, NE, Gerrard, DL, Rodriguez, PD, Hong, D, Rose, JT, Ghule, PN, Bolf, EL, Gordon, JA, Tye, CE, Boyd, JR, Tracy, KM, Nickerson, JA, van Wijnen, AJ, Imbalzano, AN, Heath, JL, Frietze, SE, Zaidi, SK, Carr, FE, Lian, JB, Stein, JL, Stein, GS Genes Chromosomes Cancer : . doi: 10.1002/gcc.22731. PubMed PMID:30873710
  • 2019 | Computational KIR copy number discovery reveals interaction between inhibitory receptor burden and survival. Pyke, RM, Genolet, R, Harari, A, Coukos, G, Gfeller, D, Carter, H Pac Symp Biocomput 24 : 148-159. . PubMed PMID:30864318 PubMed Central PMC6417817
  • 2019 | A multi-targeted probe-based strategy to identify signaling vulnerabilities in cancers. Rao, S, Du, G, Hafner, M, Subramanian, K, Sorger, PK, Gray, NS J. Biol. Chem. : . doi: 10.1074/jbc.RA118.006805. PubMed PMID:30858179
  • 2019 | Modeling differentiation-state transitions linked to therapeutic escape in triple-negative breast cancer. Chapman, MP, Risom, T, Aswani, AJ, Langer, EM, Sears, RC, Tomlin, CJ PLoS Comput. Biol. 15 (3): e1006840. doi: 10.1371/journal.pcbi.1006840. PubMed PMID:30856168 PubMed Central PMC6428348
  • 2019 | Multiparameter MRI Predictors of Long-Term Survival in Glioblastoma Multiforme. Stringfield, O, Arrington, JA, Johnston, SK, Rognin, NG, Peeri, NC, Balagurunathan, Y, Jackson, PR, Clark-Swanson, KR, Swanson, KR, Egan, KM, Gatenby, RA, Raghunand, N Tomography 5 (1): 135-144. doi: 10.18383/j.tom.2018.00052. PubMed PMID:30854451 PubMed Central PMC6403044
  • 2019 | Exceptional response and multisystem autoimmune-like toxicities associated with the same T cell clone in a patient with uveal melanoma treated with immune checkpoint inhibitors. Rapisuwon, S, Izar, B, Batenchuk, C, Avila, A, Mei, S, Sorger, P, Parks, JM, Cooper, SJ, Wagner, D, Zeck, JC, Charabaty, AJ, Atkins, MB J Immunother Cancer 7 (1): 61. doi: 10.1186/s40425-019-0533-0. PubMed PMID:30832716 PubMed Central PMC6399858
  • 2019 | Accurate Patient-Specific Machine Learning Models of Glioblastoma Invasion Using Transfer Learning. Hu, LS, Yoon, H, Eschbacher, JM, Baxter, LC, Dueck, AC, Nespodzany, A, Smith, KA, Nakaji, P, Xu, Y, Wang, L, Karis, JP, Hawkins-Daarud, AJ, Singleton, KW, Jackson, PR, Anderies, BJ, Bendok, BR, Zimmerman, RS, Quarles, C, Porter-Umphrey, AB, Mrugala, MM, Sharma, A, Hoxworth, JM, Sattur, MG, Sanai, N, Koulemberis, PE, Krishna, C, Mitchell, JR, Wu, T, Tran, NL, Swanson, KR, Li, J AJNR Am J Neuroradiol 40 (3): 418-425. doi: 10.3174/ajnr.A5981. PubMed PMID:30819771 PubMed Central PMC6474354
  • 2019 | Structure of the IFNγ receptor complex guides design of biased agonists. Mendoza, JL, Escalante, NK, Jude, KM, Sotolongo Bellon, J, Su, L, Horton, TM, Tsutsumi, N, Berardinelli, SJ, Haltiwanger, RS, Piehler, J, Engleman, EG, Garcia, KC Nature 567 (7746): 56-60. doi: 10.1038/s41586-019-0988-7. PubMed PMID:30814731
  • 2018 | Mismatch repair deficiency in high-grade meningioma: a rare but recurrent event associated with dramatic immune activation and clinical response to PD-1 blockade. Dunn, IF, Du, Z, Touat, M, Sisti, MB, Wen, PY, Umeton, R, Dubuc, AM, Ducar, M, Canoll, PD, Severson, E, Elvin, JA, Ramkissoon, SH, Lin, JR, Cabrera, L, Acevedo, B, Sorger, PK, Ligon, KL, Santagata, S, Reardon, DA JCO Precis Oncol 2018 : . doi: 10.1200/PO.18.00190. PubMed PMID:30801050 PubMed Central PMC6383717
  • 2019 | Lesion Dynamics Under Varying Paracrine PDGF Signaling in Brain Tissue. Massey, SC, Hawkins-Daarud, A, Gallaher, J, Anderson, ARA, Canoll, P, Swanson, KR Bull. Math. Biol. : . doi: 10.1007/s11538-019-00587-z. PubMed PMID:30796683
  • 2019 | The Role of the Microbiome in Cancer Initiation and Progression: How Microbes and Cancer Cells Utilize Excess Energy and Promote One Another's Growth. Whisner, CM, Athena Aktipis, C Curr Nutr Rep 8 (1): 42-51. doi: 10.1007/s13668-019-0257-2. PubMed PMID:30758778 PubMed Central PMC6426824
  • 2019 | Ventricular-Subventricular Zone Contact by Glioblastoma is Not Associated with Molecular Signatures in Bulk Tumor Data. Mistry, AM, Wooten, DJ, Davis, LT, Mobley, BC, Quaranta, V, Ihrie, RA Sci Rep 9 (1): 1842. doi: 10.1038/s41598-018-37734-w. PubMed PMID:30755636 PubMed Central PMC6372607
  • 2019 | Acidification of Tumor at Stromal Boundaries Drives Transcriptome Alterations Associated with Aggressive Phenotypes. Rohani, N, Hao, L, Alexis, MS, Joughin, BA, Krismer, K, Moufarrej, MN, Soltis, AR, Lauffenburger, DA, Yaffe, MB, Burge, CB, Bhatia, SN, Gertler, FB Cancer Res. 79 (8): 1952-1966. doi: 10.1158/0008-5472.CAN-18-1604. PubMed PMID:30755444 PubMed Central PMC6467770
  • 2019 | Immune and genomic correlates of response to anti-PD-1 immunotherapy in glioblastoma. Zhao, J, Chen, AX, Gartrell, RD, Silverman, AM, Aparicio, L, Chu, T, Bordbar, D, Shan, D, Samanamud, J, Mahajan, A, Filip, I, Orenbuch, R, Goetz, M, Yamaguchi, JT, Cloney, M, Horbinski, C, Lukas, RV, Raizer, J, Rae, AI, Yuan, J, Canoll, P, Bruce, JN, Saenger, YM, Sims, P, Iwamoto, FM, Sonabend, AM, Rabadan, R Nat. Med. 25 (3): 462-469. doi: 10.1038/s41591-019-0349-y. PubMed PMID:30742119
  • 2019 | Noninvasive monitoring of single-cell mechanics by acoustic scattering. Kang, JH, Miettinen, TP, Chen, L, Olcum, S, Katsikis, G, Doyle, PS, Manalis, SR Nat. Methods 16 (3): 263-269. doi: 10.1038/s41592-019-0326-x. PubMed PMID:30742041 PubMed Central PMC6420125
  • 2019 | Excessive Cell Growth Causes Cytoplasm Dilution And Contributes to Senescence. Neurohr, GE, Terry, RL, Lengefeld, J, Bonney, M, Brittingham, GP, Moretto, F, Miettinen, TP, Vaites, LP, Soares, LM, Paulo, JA, Harper, JW, Buratowski, S, Manalis, S, van Werven, FJ, Holt, LJ, Amon, A Cell 176 (5): 1083-1097.e18. doi: 10.1016/j.cell.2019.01.018. PubMed PMID:30739799 PubMed Central PMC6386581
  • 2019 | Metabolic plasticity meets gene regulation. Paudel, BB, Quaranta, V Proc. Natl. Acad. Sci. U.S.A. 116 (9): 3370-3372. doi: 10.1073/pnas.1900169116. PubMed PMID:30737291 PubMed Central PMC6397587
  • 2019 | Robust Cell Detection and Segmentation for Image Cytometry Reveal Th17 Cell Heterogeneity. Tsujikawa, T, Thibault, G, Azimi, V, Sivagnanam, S, Banik, G, Means, C, Kawashima, R, Clayburgh, DR, Gray, JW, Coussens, LM, Chang, YH Cytometry A 95 (4): 389-398. doi: 10.1002/cyto.a.23726. PubMed PMID:30714674 PubMed Central PMC6461524
  • 2018 | Evolutionary Stem Cell Poker and Cancer Risks: The Paradox of The Large And Small Intestines. Shibata, D Curr Pathobiol Rep 6 (3): 193-198. doi: 10.1007/s40139-018-0176-8. PubMed PMID:30713810 PubMed Central PMC6350825
  • 2019 | Optofluidic real-time cell sorter for longitudinal CTC studies in mouse models of cancer. Hamza, B, Ng, SR, Prakadan, SM, Delgado, FF, Chin, CR, King, EM, Yang, LF, Davidson, SM, DeGouveia, KL, Cermak, N, Navia, AW, Winter, PS, Drake, RS, Tammela, T, Li, CM, Papagiannakopoulos, T, Gupta, AJ, Shaw Bagnall, J, Knudsen, SM, Vander Heiden, MG, Wasserman, SC, Jacks, T, Shalek, AK, Manalis, SR Proc. Natl. Acad. Sci. U.S.A. 116 (6): 2232-2236. doi: 10.1073/pnas.1814102116. PubMed PMID:30674677 PubMed Central PMC6369805
  • 2019 | Experimental microdissection enables functional harmonisation of pancreatic cancer subtypes. Maurer, C, Holmstrom, SR, He, J, Laise, P, Su, T, Ahmed, A, Hibshoosh, H, Chabot, JA, Oberstein, PE, Sepulveda, AR, Genkinger, JM, Zhang, J, Iuga, AC, Bansal, M, Califano, A, Olive, KP Gut : . doi: 10.1136/gutjnl-2018-317706. PubMed PMID:30658994
  • 2018 | Distinct Phenotypic Clusters of Glioblastoma Growth and Response Kinetics Predict Survival. Rayfield, CA, Grady, F, De Leon, G, Rockne, R, Carrasco, E, Jackson, P, Vora, M, Johnston, SK, Hawkins-Daarud, A, Clark-Swanson, KR, Whitmire, S, Gamez, ME, Porter, A, Hu, L, Gonzalez-Cuyar, L, Bendok, B, Vora, S, Swanson, KR JCO Clin Cancer Inform 2 : 1-14. doi: 10.1200/CCI.17.00080. PubMed PMID:30652553 PubMed Central PMC6358416
  • 2019 | Modeling Tumor Phenotypes In Vitro with Three-Dimensional Bioprinting. Langer, EM, Allen-Petersen, BL, King, SM, Kendsersky, ND, Turnidge, MA, Kuziel, GM, Riggers, R, Samatham, R, Amery, TS, Jacques, SL, Sheppard, BC, Korkola, JE, Muschler, JL, Thibault, G, Chang, YH, Gray, JW, Presnell, SC, Nguyen, DG, Sears, RC Cell Rep 26 (3): 608-623.e6. doi: 10.1016/j.celrep.2018.12.090. PubMed PMID:30650355 PubMed Central PMC6366459
  • 2019 | Microtubule regulators act in the nervous system to modulate fat metabolism and longevity through DAF-16 in C. elegans. Xu, A, Zhang, Z, Ko, SH, Fisher, AL, Liu, Z, Chen, L Aging Cell 18 (2): e12884. doi: 10.1111/acel.12884. PubMed PMID:30638295 PubMed Central PMC6413656
  • 2019 | Single-cell microRNA-mRNA co-sequencing reveals non-genetic heterogeneity and mechanisms of microRNA regulation. Wang, N, Zheng, J, Chen, Z, Liu, Y, Dura, B, Kwak, M, Xavier-Ferrucio, J, Lu, YC, Zhang, M, Roden, C, Cheng, J, Krause, DS, Ding, Y, Fan, R, Lu, J Nat Commun 10 (1): 95. doi: 10.1038/s41467-018-07981-6. PubMed PMID:30626865 PubMed Central PMC6327095
  • 2019 | Prognostic Gene Discovery in Glioblastoma Patients using Deep Learning. Wong, KK, Rostomily, R, Wong, STC Cancers (Basel) 11 (1): . doi: 10.3390/cancers11010053. PubMed PMID:30626092 PubMed Central PMC6356839
  • 2019 | Elucidating synergistic dependencies in lung adenocarcinoma by proteome-wide signaling-network analysis. Bansal, M, He, J, Peyton, M, Kustagi, M, Iyer, A, Comb, M, White, M, Minna, JD, Califano, A PLoS ONE 14 (1): e0208646. doi: 10.1371/journal.pone.0208646. PubMed PMID:30615629 PubMed Central PMC6322741
  • 2019 | Peroxiredoxins in Cancer and Response to Radiation Therapies. Forshaw, TE, Holmila, R, Nelson, KJ, Lewis, JE, Kemp, ML, Tsang, AW, Poole, LB, Lowther, WT, Furdui, CM Antioxidants (Basel) 8 (1): . doi: 10.3390/antiox8010011. PubMed PMID:30609657 PubMed Central PMC6356878
  • 2019 | GRB7 dependent proliferation of basal-like, HER-2 positive human breast cancer cell lines is mediated in part by HER-1 signaling. Luoh, SW, Wagoner, W, Wang, X, Hu, Z, Lai, X, Chin, K, Sears, R, Ramsey, E Mol. Carcinog. : . doi: 10.1002/mc.22963. PubMed PMID:30604896
  • 2018 | Life History Trade-Offs in Tumors. Boddy, AM, Huang, W, Aktipis, A Curr Pathobiol Rep 6 (4): 201-207. doi: 10.1007/s40139-018-0188-4. PubMed PMID:30595969 PubMed Central PMC6290708
  • 2019 | Arrestin-3 scaffolding of the JNK3 cascade suggests a mechanism for signal amplification. Perry, NA, Kaoud, TS, Ortega, OO, Kaya, AI, Marcus, DJ, Pleinis, JM, Berndt, S, Chen, Q, Zhan, X, Dalby, KN, Lopez, CF, Iverson, TM, Gurevich, VV Proc. Natl. Acad. Sci. U.S.A. 116 (3): 810-815. doi: 10.1073/pnas.1819230116. PubMed PMID:30591558 PubMed Central PMC6338856
  • 2019 | Targeting NAD+ Metabolism to Enhance Radiation Therapy Responses. Lewis, JE, Singh, N, Holmila, RJ, Sumer, BD, Williams, NS, Furdui, CM, Kemp, ML, Boothman, DA Semin Radiat Oncol 29 (1): 6-15. doi: 10.1016/j.semradonc.2018.10.009. PubMed PMID:30573185 PubMed Central PMC6310039
  • 2019 | Phf6 Loss Enhances HSC Self-Renewal Driving Tumor Initiation and Leukemia Stem Cell Activity in T-ALL. Wendorff, AA, Quinn, SA, Rashkovan, M, Madubata, CJ, Ambesi-Impiombato, A, Litzow, MR, Tallman, MS, Paietta, E, Paganin, M, Basso, G, Gastier-Foster, JM, Loh, ML, Rabadan, R, Van Vlierberghe, P, Ferrando, AA Cancer Discov 9 (3): 436-451. doi: 10.1158/2159-8290.CD-18-1005. PubMed PMID:30567843 PubMed Central PMC6425751
  • 2019 | Three-dimensional analysis reveals altered chromatin interaction by enhancer inhibitors harbors TCF7L2-regulated cancer gene signature. Gerrard, DL, Wang, Y, Gaddis, M, Zhou, Y, Wang, J, Witt, H, Lin, S, Farnham, PJ, Jin, VX, Frietze, SE J. Cell. Biochem. 120 (3): 3056-3070. doi: 10.1002/jcb.27449. PubMed PMID:30548288
  • 2019 | Tumor growth and calcification in evolving microenvironmental geometries. Chen, Y, Lowengrub, JS J. Theor. Biol. 463 : 138-154. doi: 10.1016/j.jtbi.2018.12.006. PubMed PMID:30528340
  • 2018 | NSD2 is a conserved driver of metastatic prostate cancer progression. Aytes, A, Giacobbe, A, Mitrofanova, A, Ruggero, K, Cyrta, J, Arriaga, J, Palomero, L, Farran-Matas, S, Rubin, MA, Shen, MM, Califano, A, Abate-Shen, C Nat Commun 9 (1): 5201. doi: 10.1038/s41467-018-07511-4. PubMed PMID:30518758 PubMed Central PMC6281610
  • 2018 | Spontaneous migration of cellular aggregates from giant keratocytes to running spheroids. Beaune, G, Blanch-Mercader, C, Douezan, S, Dumond, J, Gonzalez-Rodriguez, D, Cuvelier, D, Ondarçuhu, T, Sens, P, Dufour, S, Murrell, MP, Brochard-Wyart, F Proc. Natl. Acad. Sci. U.S.A. 115 (51): 12926-12931. doi: 10.1073/pnas.1811348115. PubMed PMID:30504144 PubMed Central PMC6304987
  • 2019 | Biomarker-driven strategy for MCL1 inhibition in T-cell lymphomas. Koch, R, Christie, AL, Crombie, JL, Palmer, AC, Plana, D, Shigemori, K, Morrow, SN, Van Scoyk, A, Wu, W, Brem, EA, Secrist, JP, Drew, L, Schuller, AG, Cidado, J, Letai, A, Weinstock, DM Blood 133 (6): 566-575. doi: 10.1182/blood-2018-07-865527. PubMed PMID:30498064 PubMed Central PMC6367646
  • 2018 | Tumour heterogeneity and metastasis at single-cell resolution. Lawson, DA, Kessenbrock, K, Davis, RT, Pervolarakis, N, Werb, Z Nat. Cell Biol. 20 (12): 1349-1360. doi: 10.1038/s41556-018-0236-7. PubMed PMID:30482943
  • 2018 | Linking single-cell measurements of mass, growth rate, and gene expression. Kimmerling, RJ, Prakadan, SM, Gupta, AJ, Calistri, NL, Stevens, MM, Olcum, S, Cermak, N, Drake, RS, Pelton, K, De Smet, F, Ligon, KL, Shalek, AK, Manalis, SR Genome Biol. 19 (1): 207. doi: 10.1186/s13059-018-1576-0. PubMed PMID:30482222 PubMed Central PMC6260722
  • 2018 | Epigenetic Heterogeneity in Human Colorectal Tumors Reveals Preferential Conservation And Evidence of Immune Surveillance. Ryser, MD, Yu, M, Grady, W, Siegmund, K, Shibata, D Sci Rep 8 (1): 17292. doi: 10.1038/s41598-018-35621-y. PubMed PMID:30470817 PubMed Central PMC6251922
  • 2018 | Entropy production rate is maximized in non-contractile actomyosin. Seara, DS, Yadav, V, Linsmeier, I, Tabatabai, AP, Oakes, PW, Tabei, SMA, Banerjee, S, Murrell, MP Nat Commun 9 (1): 4948. doi: 10.1038/s41467-018-07413-5. PubMed PMID:30470750 PubMed Central PMC6251913
  • 2019 | Single-Cell Mass Cytometry of Archived Human Epithelial Tissue for Decoding Cancer Signaling Pathways. Scurrah, CR, Simmons, AJ, Lau, KS Methods Mol. Biol. 1884 : 215-229. doi: 10.1007/978-1-4939-8885-3_15. PubMed PMID:30465206 PubMed Central PMC6282860
  • 2018 | Microfluidic active loading of single cells enables analysis of complex clinical specimens. Calistri, NL, Kimmerling, RJ, Malinowski, SW, Touat, M, Stevens, MM, Olcum, S, Ligon, KL, Manalis, SR Nat Commun 9 (1): 4784. doi: 10.1038/s41467-018-07283-x. PubMed PMID:30429479 PubMed Central PMC6235965
  • 2018 | Analysis of Single-Cell RNA-Seq Identifies Cell-Cell Communication Associated with Tumor Characteristics. Kumar, MP, Du, J, Lagoudas, G, Jiao, Y, Sawyer, A, Drummond, DC, Lauffenburger, DA, Raue, A Cell Rep 25 (6): 1458-1468.e4. doi: 10.1016/j.celrep.2018.10.047. PubMed PMID:30404002
  • 2019 | Adipokines Deregulate Cellular Communication via Epigenetic Repression of Gap Junction Loci in Obese Endometrial Cancer. Polusani, SR, Huang, YW, Huang, G, Chen, CW, Wang, CM, Lin, LL, Osmulski, P, Lucio, ND, Liu, L, Hsu, YT, Zhou, Y, Lin, CL, Aguilera-Barrantes, I, Valente, PT, Kost, ER, Chen, CL, Shim, EY, Lee, SE, Ruan, J, Gaczynska, ME, Yan, P, Goodfellow, PJ, Mutch, DG, Jin, VX, Nicholson, BJ, Huang, TH, Kirma, NB Cancer Res. 79 (1): 196-208. doi: 10.1158/0008-5472.CAN-18-1615. PubMed PMID:30389702
  • 2019 | Activation of PP2A and Inhibition of mTOR Synergistically Reduce MYC Signaling and Decrease Tumor Growth in Pancreatic Ductal Adenocarcinoma. Allen-Petersen, BL, Risom, T, Feng, Z, Wang, Z, Jenny, ZP, Thoma, MC, Pelz, KR, Morton, JP, Sansom, OJ, Lopez, CD, Sheppard, B, Christensen, DJ, Ohlmeyer, M, Narla, G, Sears, RC Cancer Res. 79 (1): 209-219. doi: 10.1158/0008-5472.CAN-18-0717. PubMed PMID:30389701 PubMed Central PMC6318036
  • 2018 | SJARACNe: a scalable software tool for gene network reverse engineering from big data. Khatamian, A, Paull, EO, Califano, A, Yu, J Bioinformatics : . doi: 10.1093/bioinformatics/bty907. PubMed PMID:30388204
  • 2018 | Post-translational modification localizes MYC to the nuclear pore basket to regulate a subset of target genes involved in cellular responses to environmental signals. Su, Y, Pelz, C, Huang, T, Torkenczy, K, Wang, X, Cherry, A, Daniel, CJ, Liang, J, Nan, X, Dai, MS, Adey, A, Impey, S, Sears, RC Genes Dev. 32 (21-22): 1398-1419. doi: 10.1101/gad.314377.118. PubMed PMID:30366908 PubMed Central PMC6217735
  • 2018 | A METHOD FOR QUANTIFICATION OF CALPONIN EXPRESSION IN MYOEPITHELIAL CELLS IN IMMUNOHISTOCHEMICAL IMAGES OF DUCTAL CARCINOMA IN SITU. Gray, E, Mitchell, E, Jindal, S, Schedin, P, Chang, YH Proc IEEE Int Symp Biomed Imaging 2018 : 796-799. doi: 10.1109/ISBI.2018.8363692. PubMed PMID:30364524 PubMed Central PMC6196724
  • 2018 | Quantitative assessment of cell population diversity in single-cell landscapes. Liu, Q, Herring, CA, Sheng, Q, Ping, J, Simmons, AJ, Chen, B, Banerjee, A, Li, W, Gu, G, Coffey, RJ, Shyr, Y, Lau, KS PLoS Biol. 16 (10): e2006687. doi: 10.1371/journal.pbio.2006687. PubMed PMID:30346945 PubMed Central PMC6211764
  • 2018 | Insights into Bidirectional Gene Expression Control Using the Canonical GAL1/GAL10 Promoter. Elison, GL, Xue, Y, Song, R, Acar, M Cell Rep 25 (3): 737-748.e4. doi: 10.1016/j.celrep.2018.09.050. PubMed PMID:30332652 PubMed Central PMC6263159
  • 2019 | Identification of the Fraction of Indolent Tumors and Associated Overdiagnosis in Breast Cancer Screening Trials. Ryser, MD, Gulati, R, Eisenberg, MC, Shen, Y, Hwang, ES, Etzioni, RB Am. J. Epidemiol. 188 (1): 197-205. doi: 10.1093/aje/kwy214. PubMed PMID:30325415 PubMed Central PMC6321806
  • 2018 | Optimization of Acquisition and Analysis Methods for Clinical Dynamic Susceptibility Contrast MRI Using a Population-Based Digital Reference Object. Semmineh, NB, Bell, LC, Stokes, AM, Hu, LS, Boxerman, JL, Quarles, CC AJNR Am J Neuroradiol 39 (11): 1981-1988. doi: 10.3174/ajnr.A5827. PubMed PMID:30309842 PubMed Central PMC6239921
  • 2019 | Decidualization of Human Endometrial Stromal Fibroblasts is a Multiphasic Process Involving Distinct Transcriptional Programs. Rytkönen, KT, Erkenbrack, EM, Poutanen, M, Elo, LL, Pavlicev, M, Wagner, GP Reprod Sci 26 (3): 323-336. doi: 10.1177/1933719118802056. PubMed PMID:30309298
  • 2018 | Cross-talk among writers, readers, and erasers of m6A regulates cancer growth and progression. Panneerdoss, S, Eedunuri, VK, Yadav, P, Timilsina, S, Rajamanickam, S, Viswanadhapalli, S, Abdelfattah, N, Onyeagucha, BC, Cui, X, Lai, Z, Mohammad, TA, Gupta, YK, Huang, TH, Huang, Y, Chen, Y, Rao, MK Sci Adv 4 (10): eaar8263. doi: 10.1126/sciadv.aar8263. PubMed PMID:30306128 PubMed Central PMC6170038
  • 2018 | Typing tumors using pathways selected by somatic evolution. Wang, S, Ma, J, Zhang, W, Shen, JP, Huang, J, Peng, J, Ideker, T Nat Commun 9 (1): 4159. doi: 10.1038/s41467-018-06464-y. PubMed PMID:30297789 PubMed Central PMC6175900
  • 2018 | SHIFT: speedy histopathological-to-immunofluorescent translation of whole slide images using conditional generative adversarial networks. Burlingame, EA, Margolin, AA, Gray, JW, Chang, YH Proc SPIE Int Soc Opt Eng 10581 : . doi: 10.1117/12.2293249. PubMed PMID:30283195 PubMed Central PMC6166432
  • 2018 | Dynamics and Determinants of HPV Infection: The Michigan HPV and Oropharyngeal Cancer (M-HOC) Study. Eisenberg, MC, Campredon, LP, Brouwer, AF, Walline, HM, Marinelli, BM, Lau, YK, Thomas, TB, Delinger, RL, Sullivan, TS, Yost, ML, Goudsmit, CM, Carey, TE, Meza, R BMJ Open 8 (10): e021618. doi: 10.1136/bmjopen-2018-021618. PubMed PMID:30282679 PubMed Central PMC6169774
  • 2019 | Remodeling of the Collagen Matrix in Aging Skin Promotes Melanoma Metastasis and Affects Immune Cell Motility. Kaur, A, Ecker, BL, Douglass, SM, Kugel, CH 3rd, Webster, MR, Almeida, FV, Somasundaram, R, Hayden, J, Ban, E, Ahmadzadeh, H, Franco-Barraza, J, Shah, N, Mellis, IA, Keeney, F, Kossenkov, A, Tang, HY, Yin, X, Liu, Q, Xu, X, Fane, M, Brafford, P, Herlyn, M, Speicher, DW, Wargo, JA, Tetzlaff, MT, Haydu, LE, Raj, A, Shenoy, V, Cukierman, E, Weeraratna, AT Cancer Discov 9 (1): 64-81. doi: 10.1158/2159-8290.CD-18-0193. PubMed PMID:30279173 PubMed Central PMC6328333
  • 2018 | Cooperation of dual modes of cell motility promotes epithelial stress relaxation to accelerate wound healing. Staddon, MF, Bi, D, Tabatabai, AP, Ajeti, V, Murrell, MP, Banerjee, S PLoS Comput. Biol. 14 (10): e1006502. doi: 10.1371/journal.pcbi.1006502. PubMed PMID:30273354 PubMed Central PMC6181425
  • 2018 | Cooperation of loss of NKX3.1 and inflammation in prostate cancer initiation. Le Magnen, C, Virk, RK, Dutta, A, Kim, JY, Panja, S, Lopez-Bujanda, ZA, Califano, A, Drake, CG, Mitrofanova, A, Abate-Shen, C Dis Model Mech 11 (11): . doi: 10.1242/dmm.035139. PubMed PMID:30266798 PubMed Central PMC6262819
  • 2018 | Multi-component gene network design as a survival strategy in diverse environments. Luo, X, Song, R, Acar, M BMC Syst Biol 12 (1): 85. doi: 10.1186/s12918-018-0609-3. PubMed PMID:30257679 PubMed Central PMC6158886
  • 2018 | Synthesizing Signaling Pathways from Temporal Phosphoproteomic Data. Köksal, AS, Beck, K, Cronin, DR, McKenna, A, Camp, ND, Srivastava, S, MacGilvray, ME, Bodík, R, Wolf-Yadlin, A, Fraenkel, E, Fisher, J, Gitter, A Cell Rep 24 (13): 3607-3618. doi: 10.1016/j.celrep.2018.08.085. PubMed PMID:30257219 PubMed Central PMC6295338
  • 2018 | Bidirectional Adaptive Signaling between cancer and stromal cells: mechanisms and therapeutics. Boutchueng-Djidjou, M, Rix, U, Haura, EB Expert Rev Proteomics 15 (9): 697-699. doi: 10.1080/14789450.2018.1521276. PubMed PMID:30251554 PubMed Central PMC6435031
  • 2019 | Somatic cell evolution: how to improve with age. Shibata, D J. Pathol. 247 (1): 3-5. doi: 10.1002/path.5173. PubMed PMID:30246391 PubMed Central PMC6428591
  • 2018 | A Loss of Epigenetic Control Can Promote Cell Death through Reversing the Balance of Pathways in a Signaling Network. Vanaja, KG, Timp, W, Feinberg, AP, Levchenko, A Mol. Cell 72 (1): 60-70.e3. doi: 10.1016/j.molcel.2018.08.025. PubMed PMID:30244832 PubMed Central PMC6219618
  • 2018 | Differentiation-state plasticity is a targetable resistance mechanism in basal-like breast cancer. Risom, T, Langer, EM, Chapman, MP, Rantala, J, Fields, AJ, Boniface, C, Alvarez, MJ, Kendsersky, ND, Pelz, CR, Johnson-Camacho, K, Dobrolecki, LE, Chin, K, Aswani, AJ, Wang, NJ, Califano, A, Lewis, MT, Tomlin, CJ, Spellman, PT, Adey, A, Gray, JW, Sears, RC Nat Commun 9 (1): 3815. doi: 10.1038/s41467-018-05729-w. PubMed PMID:30232459 PubMed Central PMC6145927
  • 2018 | A Human Adult Stem Cell Signature Marks Aggressive Variants across Epithelial Cancers. Smith, BA, Balanis, NG, Nanjundiah, A, Sheu, KM, Tsai, BL, Zhang, Q, Park, JW, Thompson, M, Huang, J, Witte, ON, Graeber, TG Cell Rep 24 (12): 3353-3366.e5. doi: 10.1016/j.celrep.2018.08.062. PubMed PMID:30232014 PubMed Central PMC6382070
  • 2018 | The effect of cellular context on miR-155-mediated gene regulation in four major immune cell types. Hsin, JP, Lu, Y, Loeb, GB, Leslie, CS, Rudensky, AY Nat. Immunol. 19 (10): 1137-1145. doi: 10.1038/s41590-018-0208-x. PubMed PMID:30224821 PubMed Central PMC6158091
  • 2018 | Computational measurement of tumor immune microenvironment in gastric adenocarcinomas. Chang, YH, Heo, YJ, Cho, J, Song, SY, Lee, J, Kim, KM Sci Rep 8 (1): 13887. doi: 10.1038/s41598-018-32299-0. PubMed PMID:30224753 PubMed Central PMC6141531
  • 2018 | PDZ-RhoGEF Is a Signaling Effector for TROY-Induced Glioblastoma Cell Invasion and Survival. Ding, Z, Dhruv, H, Kwiatkowska-Piwowarczyk, A, Ruggieri, R, Kloss, J, Symons, M, Pirrotte, P, Eschbacher, JM, Tran, NL, Loftus, JC Neoplasia 20 (10): 1045-1058. doi: 10.1016/j.neo.2018.08.008. PubMed PMID:30219706 PubMed Central PMC6140379
  • 2018 | Multiple Routes to Oncogenesis Are Promoted by the Human Papillomavirus-Host Protein Network. Eckhardt, M, Zhang, W, Gross, AM, Von Dollen, J, Johnson, JR, Franks-Skiba, KE, Swaney, DL, Johnson, TL, Jang, GM, Shah, PS, Brand, TM, Archambault, J, Kreisberg, JF, Grandis, JR, Ideker, T, Krogan, NJ Cancer Discov 8 (11): 1474-1489. doi: 10.1158/2159-8290.CD-17-1018. PubMed PMID:30209081 PubMed Central PMC6375299
  • 2018 | Proteomics, Post-translational Modifications, and Integrative Analyses Reveal Molecular Heterogeneity within Medulloblastoma Subgroups. Archer, TC, Ehrenberger, T, Mundt, F, Gold, MP, Krug, K, Mah, CK, Mahoney, EL, Daniel, CJ, LeNail, A, Ramamoorthy, D, Mertins, P, Mani, DR, Zhang, H, Gillette, MA, Clauser, K, Noble, M, Tang, LC, Pierre-François, J, Silterra, J, Jensen, J, Tamayo, P, Korshunov, A, Pfister, SM, Kool, M, Northcott, PA, Sears, RC, Lipton, JO, Carr, SA, Mesirov, JP, Pomeroy, SL, Fraenkel, E Cancer Cell 34 (3): 396-410.e8. doi: 10.1016/j.ccell.2018.08.004. PubMed PMID:30205044 PubMed Central PMC6372116
  • 2018 | Extravasation of Brownian Spheroidal Nanoparticles through Vascular Pores. Shah, PN, Lin, TY, Aanei, IL, Klass, SH, Smith, BR, Shaqfeh, ESG Biophys. J. 115 (6): 1103-1115. doi: 10.1016/j.bpj.2018.07.038. PubMed PMID:30201266 PubMed Central PMC6139985
  • 2018 | A threonine zipper that mediates protein-protein interactions: Structure and prediction. Oi, C, Treado, JD, Levine, ZA, Lim, CS, Knecht, KM, Xiong, Y, O'Hern, CS, Regan, L Protein Sci. 27 (11): 1969-1977. doi: 10.1002/pro.3505. PubMed PMID:30198622 PubMed Central PMC6201716
  • 2018 | Allergic inflammatory memory in human respiratory epithelial progenitor cells. Ordovas-Montanes, J, Dwyer, DF, Nyquist, SK, Buchheit, KM, Vukovic, M, Deb, C, Wadsworth, MH 2nd, Hughes, TK, Kazer, SW, Yoshimoto, E, Cahill, KN, Bhattacharyya, N, Katz, HR, Berger, B, Laidlaw, TM, Boyce, JA, Barrett, NA, Shalek, AK Nature 560 (7720): 649-654. doi: 10.1038/s41586-018-0449-8. PubMed PMID:30135581 PubMed Central PMC6133715
  • 2018 | Homeobox oncogene activation by pan-cancer DNA hypermethylation. Su, J, Huang, YH, Cui, X, Wang, X, Zhang, X, Lei, Y, Xu, J, Lin, X, Chen, K, Lv, J, Goodell, MA, Li, W Genome Biol. 19 (1): 108. doi: 10.1186/s13059-018-1492-3. PubMed PMID:30097071 PubMed Central PMC6085761
  • 2018 | A Visually Apparent and Quantifiable CT Imaging Feature Identifies Biophysical Subtypes of Pancreatic Ductal Adenocarcinoma. Koay, EJ, Lee, Y, Cristini, V, Lowengrub, JS, Kang, Y, Lucas, FAS, Hobbs, BP, Ye, R, Elganainy, D, Almahariq, M, Amer, AM, Chatterjee, D, Yan, H, Park, PC, Rios Perez, MV, Li, D, Garg, N, Reiss, KA, Yu, S, Chauhan, A, Zaid, M, Nikzad, N, Wolff, RA, Javle, M, Varadhachary, GR, Shroff, RT, Das, P, Lee, JE, Ferrari, M, Maitra, A, Taniguchi, CM, Kim, MP, Crane, CH, Katz, MH, Wang, H, Bhosale, P, Tamm, EP, Fleming, JB Clin. Cancer Res. 24 (23): 5883-5894. doi: 10.1158/1078-0432.CCR-17-3668. PubMed PMID:30082477 PubMed Central PMC6279613
  • 2018 | Deep Profiling of Mouse Splenic Architecture with CODEX Multiplexed Imaging. Goltsev, Y, Samusik, N, Kennedy-Darling, J, Bhate, S, Hale, M, Vazquez, G, Black, S, Nolan, GP Cell 174 (4): 968-981.e15. doi: 10.1016/j.cell.2018.07.010. PubMed PMID:30078711 PubMed Central PMC6086938
  • 2018 | Quantitative Yeast Genetic Interaction Profiling of Bacterial Effector Proteins Uncovers a Role for the Human Retromer in Salmonella Infection. Patrick, KL, Wojcechowskyj, JA, Bell, SL, Riba, MN, Jing, T, Talmage, S, Xu, P, Cabello, AL, Xu, J, Shales, M, Jimenez-Morales, D, Ficht, TA, de Figueiredo, P, Samuel, JE, Li, P, Krogan, NJ, Watson, RO Cell Syst 7 (3): 323-338.e6. doi: 10.1016/j.cels.2018.06.010. PubMed PMID:30077634 PubMed Central PMC6160342
  • 2018 | Sno-derived RNAs are prevalent molecular markers of cancer immunity. Chow, RD, Chen, S Oncogene 37 (50): 6442-6462. doi: 10.1038/s41388-018-0420-z. PubMed PMID:30072739 PubMed Central PMC6294694
  • 2018 | Programmable DNA repair with CRISPRa/i enhanced homology-directed repair efficiency with a single Cas9. Ye, L, Wang, C, Hong, L, Sun, N, Chen, D, Chen, S, Han, F Cell Discov 4 : 46. doi: 10.1038/s41421-018-0049-7. PubMed PMID:30062046 PubMed Central PMC6056518
  • 2018 | Transmission of rhinovirus in the Utah BIG-LoVE families: Consequences of age and household structure. Adler, FR, Stockmann, C, Ampofo, K, Pavia, AT, Byington, CL PLoS ONE 13 (7): e0199388. doi: 10.1371/journal.pone.0199388. PubMed PMID:30044794 PubMed Central PMC6059387
  • 2018 | Single-cell transcriptome analysis of lineage diversity in high-grade glioma. Yuan, J, Levitin, HM, Frattini, V, Bush, EC, Boyett, DM, Samanamud, J, Ceccarelli, M, Dovas, A, Zanazzi, G, Canoll, P, Bruce, JN, Lasorella, A, Iavarone, A, Sims, PA Genome Med 10 (1): 57. doi: 10.1186/s13073-018-0567-9. PubMed PMID:30041684 PubMed Central PMC6058390
  • 2019 | CIRCOAST: a statistical hypothesis test for cellular colocalization with network structures. Corliss, BA, Ray, HC, Patrie, JT, Mansour, J, Kesting, S, Park, JH, Rohde, G, Yates, PA, Janes, KA, Peirce, SM Bioinformatics 35 (3): 506-514. doi: 10.1093/bioinformatics/bty638. PubMed PMID:30032263 PubMed Central PMC6361237
  • 2018 | Live-Cell Imaging of Chromatin Condensation Dynamics by CRISPR. Xue, Y, Acar, M iScience 4 : 216-235. doi: 10.1016/j.isci.2018.06.001. PubMed PMID:30027155 PubMed Central PMC6048970
  • 2018 | A simple and robust procedure for preparing graphene-oxide cryo-EM grids. Palovcak, E, Wang, F, Zheng, SQ, Yu, Z, Li, S, Betegon, M, Bulkley, D, Agard, DA, Cheng, Y J. Struct. Biol. 204 (1): 80-84. doi: 10.1016/j.jsb.2018.07.007. PubMed PMID:30017701 PubMed Central PMC6119484
  • 2018 | Immune reprogramming via PD-1 inhibition enhances early-stage lung cancer survival. Markowitz, GJ, Havel, LS, Crowley, MJ, Ban, Y, Lee, SB, Thalappillil, JS, Narula, N, Bhinder, B, Elemento, O, Wong, ST, Gao, D, Altorki, NK, Mittal, V JCI Insight 3 (13): . doi: 10.1172/jci.insight.96836. PubMed PMID:29997286 PubMed Central PMC6101707
  • 2018 | The Cytoscape Automation app article collection. Demchak, B, Otasek, D, Pico, AR, Bader, GD, Ono, K, Settle, B, Sage, E, Morris, JH, Longabaugh, W, Lopes, C, Kucera, M, Treister, A, Schwikowski, B, Molenaar, P, Ideker, T F1000Res 7 : 800. doi: 10.12688/f1000research.15355.1. PubMed PMID:29983926 PubMed Central PMC6013757
  • 2018 | DNA concentration from self samples for HPV testing. Meza, R, Lau, YK, Thomas, TB, Carey, TE, Walline, HM, Eisenberg, MC Int. J. Cancer 143 (11): 3036-3037. doi: 10.1002/ijc.31666. PubMed PMID:29978468 PubMed Central PMC6235705
  • 2018 | Single-Cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment. Azizi, E, Carr, AJ, Plitas, G, Cornish, AE, Konopacki, C, Prabhakaran, S, Nainys, J, Wu, K, Kiseliovas, V, Setty, M, Choi, K, Fromme, RM, Dao, P, McKenney, PT, Wasti, RC, Kadaveru, K, Mazutis, L, Rudensky, AY, Pe'er, D Cell 174 (5): 1293-1308.e36. doi: 10.1016/j.cell.2018.05.060. PubMed PMID:29961579 PubMed Central PMC6348010
  • 2018 | Recovering Gene Interactions from Single-Cell Data Using Data Diffusion. van Dijk, D, Sharma, R, Nainys, J, Yim, K, Kathail, P, Carr, AJ, Burdziak, C, Moon, KR, Chaffer, CL, Pattabiraman, D, Bierie, B, Mazutis, L, Wolf, G, Krishnaswamy, S, Pe'er, D Cell 174 (3): 716-729.e27. doi: 10.1016/j.cell.2018.05.061. PubMed PMID:29961576
  • 2018 | Classifying tumors by supervised network propagation. Zhang, W, Ma, J, Ideker, T Bioinformatics 34 (13): i484-i493. doi: 10.1093/bioinformatics/bty247. PubMed PMID:29949979 PubMed Central PMC6022559
  • 2018 | Synthetic Lethal Networks for Precision Oncology: Promises and Pitfalls. Shen, JP, Ideker, T J. Mol. Biol. 430 (18 Pt A): 2900-2912. doi: 10.1016/j.jmb.2018.06.026. PubMed PMID:29932943 PubMed Central PMC6097899
  • 2018 | Kinase Substrate Profiling Using a Proteome-wide Serine-Oriented Human Peptide Library. Barber, KW, Miller, CJ, Jun, JW, Lou, HJ, Turk, BE, Rinehart, J Biochemistry 57 (31): 4717-4725. doi: 10.1021/acs.biochem.8b00410. PubMed PMID:29920078
  • 2018 | A precision oncology approach to the pharmacological targeting of mechanistic dependencies in neuroendocrine tumors. Alvarez, MJ, Subramaniam, PS, Tang, LH, Grunn, A, Aburi, M, Rieckhof, G, Komissarova, EV, Hagan, EA, Bodei, L, Clemons, PA, Dela Cruz, FS, Dhall, D, Diolaiti, D, Fraker, DA, Ghavami, A, Kaemmerer, D, Karan, C, Kidd, M, Kim, KM, Kim, HC, Kunju, LP, Langel, Ü, Li, Z, Lee, J, Li, H, LiVolsi, V, Pfragner, R, Rainey, AR, Realubit, RB, Remotti, H, Regberg, J, Roses, R, Rustgi, A, Sepulveda, AR, Serra, S, Shi, C, Yuan, X, Barberis, M, Bergamaschi, R, Chinnaiyan, AM, Detre, T, Ezzat, S, Frilling, A, Hommann, M, Jaeger, D, Kim, MK, Knudsen, BS, Kung, AL, Leahy, E, Metz, DC, Milsom, JW, Park, YS, Reidy-Lagunes, D, Schreiber, S, Washington, K, Wiedenmann, B, Modlin, I, Califano, A Nat. Genet. 50 (7): 979-989. doi: 10.1038/s41588-018-0138-4. PubMed PMID:29915428 PubMed Central PMC6421579
  • 2018 | The Emerging Potential for Network Analysis to Inform Precision Cancer Medicine. Ozturk, K, Dow, M, Carlin, DE, Bejar, R, Carter, H J. Mol. Biol. 430 (18 Pt A): 2875-2899. doi: 10.1016/j.jmb.2018.06.016. PubMed PMID:29908887 PubMed Central PMC6097914
  • 2018 | Case Studies of Gastric, Lung, and Oral Cancer Connect Etiologic Agent Prevalence to Cancer Incidence. Brouwer, AF, Eisenberg, MC, Meza, R Cancer Res. 78 (12): 3386-3396. doi: 10.1158/0008-5472.CAN-17-3467. PubMed PMID:29907681 PubMed Central PMC6007874
  • 2018 | Visible Machine Learning for Biomedicine. Yu, MK, Ma, J, Fisher, J, Kreisberg, JF, Raphael, BJ, Ideker, T Cell 173 (7): 1562-1565. doi: 10.1016/j.cell.2018.05.056. PubMed PMID:29906441
  • 2018 | Managing Patients With Relapsed Small-Cell Lung Cancer. Gong, J, Salgia, R J Oncol Pract 14 (6): 359-366. doi: 10.1200/JOP.18.00204. PubMed PMID:29894664 PubMed Central PMC6002253
  • 2018 | The Spatiotemporal Evolution of Lymph Node Spread in Early Breast Cancer. Barry, P, Vatsiou, A, Spiteri, I, Nichol, D, Cresswell, GD, Acar, A, Trahearn, N, Hrebien, S, Garcia-Murillas, I, Chkhaidze, K, Ermini, L, Huntingford, IS, Cottom, H, Zabaglo, L, Koelble, K, Khalique, S, Rusby, JE, Muscara, F, Dowsett, M, Maley, CC, Natrajan, R, Yuan, Y, Schiavon, G, Turner, N, Sottoriva, A Clin. Cancer Res. 24 (19): 4763-4770. doi: 10.1158/1078-0432.CCR-17-3374. PubMed PMID:29891724 PubMed Central PMC6296441
  • 2018 | Encoding human serine phosphopeptides in bacteria for proteome-wide identification of phosphorylation-dependent interactions. Barber, KW, Muir, P, Szeligowski, RV, Rogulina, S, Gerstein, M, Sampson, JR, Isaacs, FJ, Rinehart, J Nat. Biotechnol. 36 (7): 638-644. doi: 10.1038/nbt.4150. PubMed PMID:29889213
  • 2018 | Scarless genome editing: progress towards understanding genotype-phenotype relationships. Elison, GL, Acar, M Curr. Genet. 64 (6): 1229-1238. doi: 10.1007/s00294-018-0850-8. PubMed PMID:29872908 PubMed Central PMC6281794
  • 2018 | Harnessing single-cell genomics to improve the physiological fidelity of organoid-derived cell types. Mead, BE, Ordovas-Montanes, J, Braun, AP, Levy, LE, Bhargava, P, Szucs, MJ, Ammendolia, DA, MacMullan, MA, Yin, X, Hughes, TK, Wadsworth, MH 2nd, Ahmad, R, Rakoff-Nahoum, S, Carr, SA, Langer, R, Collins, JJ, Shalek, AK, Karp, JM BMC Biol. 16 (1): 62. doi: 10.1186/s12915-018-0527-2. PubMed PMID:29871632 PubMed Central PMC5989470
  • 2018 | Mechanisms for the epigenetic inheritance of stress response in single cells. Xue, Y, Acar, M Curr. Genet. 64 (6): 1221-1228. doi: 10.1007/s00294-018-0849-1. PubMed PMID:29846762 PubMed Central PMC6215725
  • 2018 | Diverse AR-V7 cistromes in castration-resistant prostate cancer are governed by HoxB13. Chen, Z, Wu, D, Thomas-Ahner, JM, Lu, C, Zhao, P, Zhang, Q, Geraghty, C, Yan, PS, Hankey, W, Sunkel, B, Cheng, X, Antonarakis, ES, Wang, QE, Liu, Z, Huang, TH, Jin, VX, Clinton, SK, Luo, J, Huang, J, Wang, Q Proc. Natl. Acad. Sci. U.S.A. 115 (26): 6810-6815. doi: 10.1073/pnas.1718811115. PubMed PMID:29844167 PubMed Central PMC6042123
  • 2018 | The complex ecosystem in non small cell lung cancer invasion. Haney, S, Konen, J, Marcus, AI, Bazhenov, M PLoS Comput. Biol. 14 (5): e1006131. doi: 10.1371/journal.pcbi.1006131. PubMed PMID:29795571 PubMed Central PMC5991406
  • 2018 | Profiling human breast epithelial cells using single cell RNA sequencing identifies cell diversity. Nguyen, QH, Pervolarakis, N, Blake, K, Ma, D, Davis, RT, James, N, Phung, AT, Willey, E, Kumar, R, Jabart, E, Driver, I, Rock, J, Goga, A, Khan, SA, Lawson, DA, Werb, Z, Kessenbrock, K Nat Commun 9 (1): 2028. doi: 10.1038/s41467-018-04334-1. PubMed PMID:29795293 PubMed Central PMC5966421
  • 2018 | Microbial Interactions in the Cystic Fibrosis Airway. Granchelli, AM, Adler, FR, Keogh, RH, Kartsonaki, C, Cox, DR, Liou, TG J. Clin. Microbiol. 56 (8): . doi: 10.1128/JCM.00354-18. PubMed PMID:29769279 PubMed Central PMC6062800
  • 2018 | Programmable sequential mutagenesis by inducible Cpf1 crRNA array inversion. Chow, RD, Kim, HR, Chen, S Nat Commun 9 (1): 1903. doi: 10.1038/s41467-018-04158-z. PubMed PMID:29765043 PubMed Central PMC5954137
  • 2018 | Spatial mutation patterns as markers of early colorectal tumor cell mobility. Ryser, MD, Min, BH, Siegmund, KD, Shibata, D Proc. Natl. Acad. Sci. U.S.A. 115 (22): 5774-5779. doi: 10.1073/pnas.1716552115. PubMed PMID:29760052 PubMed Central PMC5984490
  • 2018 | GFPT2-Expressing Cancer-Associated Fibroblasts Mediate Metabolic Reprogramming in Human Lung Adenocarcinoma. Zhang, W, Bouchard, G, Yu, A, Shafiq, M, Jamali, M, Shrager, JB, Ayers, K, Bakr, S, Gentles, AJ, Diehn, M, Quon, A, West, RB, Nair, V, van de Rijn, M, Napel, S, Plevritis, SK Cancer Res. 78 (13): 3445-3457. doi: 10.1158/0008-5472.CAN-17-2928. PubMed PMID:29760045 PubMed Central PMC6030462
  • 2018 | Spectrum and prevalence of genetic predisposition in medulloblastoma: a retrospective genetic study and prospective validation in a clinical trial cohort. Waszak, SM, Northcott, PA, Buchhalter, I, Robinson, GW, Sutter, C, Groebner, S, Grund, KB, Brugières, L, Jones, DTW, Pajtler, KW, Morrissy, AS, Kool, M, Sturm, D, Chavez, L, Ernst, A, Brabetz, S, Hain, M, Zichner, T, Segura-Wang, M, Weischenfeldt, J, Rausch, T, Mardin, BR, Zhou, X, Baciu, C, Lawerenz, C, Chan, JA, Varlet, P, Guerrini-Rousseau, L, Fults, DW, Grajkowska, W, Hauser, P, Jabado, N, Ra, YS, Zitterbart, K, Shringarpure, SS, De La Vega, FM, Bustamante, CD, Ng, HK, Perry, A, MacDonald, TJ, Hernáiz Driever, P, Bendel, AE, Bowers, DC, McCowage, G, Chintagumpala, MM, Cohn, R, Hassall, T, Fleischhack, G, Eggen, T, Wesenberg, F, Feychting, M, Lannering, B, Schüz, J, Johansen, C, Andersen, TV, Röösli, M, Kuehni, CE, Grotzer, M, Kjaerheim, K, Monoranu, CM, Archer, TC, Duke, E, Pomeroy, SL, Shelagh, R, Frank, S, Sumerauer, D, Scheurlen, W, Ryzhova, MV, Milde, T, Kratz, CP, Samuel, D, Zhang, J, Solomon, DA, Marra, M, Eils, R, Bartram, CR, von Hoff, K, Rutkowski, S, Ramaswamy, V, Gilbertson, RJ, Korshunov, A, Taylor, MD, Lichter, P, Malkin, D, Gajjar, A, Korbel, JO, Pfister, SM Lancet Oncol. 19 (6): 785-798. doi: 10.1016/S1470-2045(18)30242-0. PubMed PMID:29753700 PubMed Central PMC5984248
  • 2018 | Inflammatory signatures distinguish metabolic health in African American women with obesity. Denis, GV, Sebastiani, P, Bertrand, KA, Strissel, KJ, Tran, AH, Slama, J, Medina, ND, Andrieu, G, Palmer, JR PLoS ONE 13 (5): e0196755. doi: 10.1371/journal.pone.0196755. PubMed PMID:29738558 PubMed Central PMC5940209
  • 2018 | Pan-cancer transcriptional signatures predictive of oncogenic mutations reveal that Fbw7 regulates cancer cell oxidative metabolism. Davis, RJ, Gönen, M, Margineantu, DH, Handeli, S, Swanger, J, Hoellerbauer, P, Paddison, PJ, Gu, H, Raftery, D, Grim, JE, Hockenbery, DM, Margolin, AA, Clurman, BE Proc. Natl. Acad. Sci. U.S.A. 115 (21): 5462-5467. doi: 10.1073/pnas.1718338115. PubMed PMID:29735700
  • 2018 | Cancer CRISPR Screens In Vivo. Chow, RD, Chen, S Trends Cancer 4 (5): 349-358. doi: 10.1016/j.trecan.2018.03.002. PubMed PMID:29709259 PubMed Central PMC5935117
  • 2018 | The number of titrated microRNA species dictates ceRNA regulation. Chiu, HS, Martínez, MR, Komissarova, EV, Llobet-Navas, D, Bansal, M, Paull, EO, Silva, J, Yang, X, Sumazin, P, Califano, A Nucleic Acids Res. 46 (9): 4354-4369. doi: 10.1093/nar/gky286. PubMed PMID:29684207 PubMed Central PMC5961349
  • 2018 | Heritable stress response dynamics revealed by single-cell genealogy. Chatterjee, M, Acar, M Sci Adv 4 (4): e1701775. doi: 10.1126/sciadv.1701775. PubMed PMID:29675464 PubMed Central PMC5906080
  • 2018 | Integrative analysis reveals functional and regulatory roles of H3K79me2 in mediating alternative splicing. Li, T, Liu, Q, Garza, N, Kornblau, S, Jin, VX Genome Med 10 (1): 30. doi: 10.1186/s13073-018-0538-1. PubMed PMID:29665865 PubMed Central PMC5902843
  • 2018 | Quantitative assessment of protein activity in orphan tissues and single cells using the metaVIPER algorithm. Ding, H, Douglass, EF Jr, Sonabend, AM, Mela, A, Bose, S, Gonzalez, C, Canoll, PD, Sims, PA, Alvarez, MJ, Califano, A Nat Commun 9 (1): 1471. doi: 10.1038/s41467-018-03843-3. PubMed PMID:29662057 PubMed Central PMC5902599
  • 2018 | DRUG-NEM: Optimizing drug combinations using single-cell perturbation response to account for intratumoral heterogeneity. Anchang, B, Davis, KL, Fienberg, HG, Williamson, BD, Bendall, SC, Karacosta, LG, Tibshirani, R, Nolan, GP, Plevritis, SK Proc. Natl. Acad. Sci. U.S.A. 115 (18): E4294-E4303. doi: 10.1073/pnas.1711365115. PubMed PMID:29654148 PubMed Central PMC5939057
  • 2018 | Value-based genomics. Gong, J, Pan, K, Fakih, M, Pal, S, Salgia, R Oncotarget 9 (21): 15792-15815. doi: 10.18632/oncotarget.24353. PubMed PMID:29644010 PubMed Central PMC5884665
  • 2018 | Disruption of NSD1 in Head and Neck Cancer Promotes Favorable Chemotherapeutic Responses Linked to Hypomethylation. Bui, N, Huang, JK, Bojorquez-Gomez, A, Licon, K, Sanchez, KS, Tang, SN, Beckett, AN, Wang, T, Zhang, W, Shen, JP, Kreisberg, JF, Ideker, T Mol. Cancer Ther. 17 (7): 1585-1594. doi: 10.1158/1535-7163.MCT-17-0937. PubMed PMID:29636367 PubMed Central PMC6030464
  • 2018 | The Immune Landscape of Cancer. Thorsson, V, Gibbs, DL, Brown, SD, Wolf, D, Bortone, DS, Ou Yang, TH, Porta-Pardo, E, Gao, GF, Plaisier, CL, Eddy, JA, Ziv, E, Culhane, AC, Paull, EO, Sivakumar, IKA, Gentles, AJ, Malhotra, R, Farshidfar, F, Colaprico, A, Parker, JS, Mose, LE, Vo, NS, Liu, J, Liu, Y, Rader, J, Dhankani, V, Reynolds, SM, Bowlby, R, Califano, A, Cherniack, AD, Anastassiou, D, Bedognetti, D, Rao, A, Chen, K, Krasnitz, A, Hu, H, Malta, TM, Noushmehr, H, Pedamallu, CS, Bullman, S, Ojesina, AI, Lamb, A, Zhou, W, Shen, H, Choueiri, TK, Weinstein, JN, Guinney, J, Saltz, J, Holt, RA, Rabkin, CE, Cancer Genome Atlas Research Network, Lazar, AJ, Serody, JS, Demicco, EG, Disis, ML, Vincent, BG, Shmulevich, L Immunity 48 (4): 812-830.e14. doi: 10.1016/j.immuni.2018.03.023. PubMed PMID:29628290 PubMed Central PMC5982584
  • 2018 | A CLK3-HMGA2 Alternative Splicing Axis Impacts Human Hematopoietic Stem Cell Molecular Identity throughout Development. Cesana, M, Guo, MH, Cacchiarelli, D, Wahlster, L, Barragan, J, Doulatov, S, Vo, LT, Salvatori, B, Trapnell, C, Clement, K, Cahan, P, Tsanov, KM, Sousa, PM, Tazon-Vega, B, Bolondi, A, Giorgi, FM, Califano, A, Rinn, JL, Meissner, A, Hirschhorn, JN, Daley, GQ Cell Stem Cell 22 (4): 575-588.e7. doi: 10.1016/j.stem.2018.03.012. PubMed PMID:29625070 PubMed Central PMC5957284
  • 2018 | A global transcriptional network connecting noncoding mutations to changes in tumor gene expression. Zhang, W, Bojorquez-Gomez, A, Velez, DO, Xu, G, Sanchez, KS, Shen, JP, Chen, K, Licon, K, Melton, C, Olson, KM, Yu, MK, Huang, JK, Carter, H, Farley, EK, Snyder, M, Fraley, SI, Kreisberg, JF, Ideker, T Nat. Genet. 50 (4): 613-620. doi: 10.1038/s41588-018-0091-2. PubMed PMID:29610481 PubMed Central PMC5893414
  • 2018 | pyNBS: a Python implementation for network-based stratification of tumor mutations. Huang, JK, Jia, T, Carlin, DE, Ideker, T Bioinformatics 34 (16): 2859-2861. doi: 10.1093/bioinformatics/bty186. PubMed PMID:29608663 PubMed Central PMC6084608
  • 2018 | Systematic Evaluation of Molecular Networks for Discovery of Disease Genes. Huang, JK, Carlin, DE, Yu, MK, Zhang, W, Kreisberg, JF, Tamayo, P, Ideker, T Cell Syst 6 (4): 484-495.e5. doi: 10.1016/j.cels.2018.03.001. PubMed PMID:29605183 PubMed Central PMC5920724
  • 2018 | Automated brightfield morphometry of 3D organoid populations by OrganoSeg. Borten, MA, Bajikar, SS, Sasaki, N, Clevers, H, Janes, KA Sci Rep 8 (1): 5319. doi: 10.1038/s41598-017-18815-8. PubMed PMID:29593296 PubMed Central PMC5871765
  • 2018 | A Nonquiescent "Idling" Population State in Drug-Treated, BRAF-Mutated Melanoma. Paudel, BB, Harris, LA, Hardeman, KN, Abugable, AA, Hayford, CE, Tyson, DR, Quaranta, V Biophys. J. 114 (6): 1499-1511. doi: 10.1016/j.bpj.2018.01.016. PubMed PMID:29590606 PubMed Central PMC5883941
  • 2018 | Topotaxis: A New Mechanism of Directed Cell Migration in Topographic ECM Gradients. Park, J, Kim, DH, Levchenko, A Biophys. J. 114 (6): 1257-1263. doi: 10.1016/j.bpj.2017.11.3813. PubMed PMID:29590582 PubMed Central PMC5883610
  • 2018 | iterClust: a statistical framework for iterative clustering analysis. Ding, H, Wang, W, Califano, A Bioinformatics 34 (16): 2865-2866. doi: 10.1093/bioinformatics/bty176. PubMed PMID:29579153 PubMed Central PMC6084607
  • 2018 | Microenvironment-Mediated Mechanisms of Resistance to HER2 Inhibitors Differ between HER2+ Breast Cancer Subtypes. Watson, SS, Dane, M, Chin, K, Tatarova, Z, Liu, M, Liby, T, Thompson, W, Smith, R, Nederlof, M, Bucher, E, Kilburn, D, Whitman, M, Sudar, D, Mills, GB, Heiser, LM, Jonas, O, Gray, JW, Korkola, JE Cell Syst 6 (3): 329-342.e6. doi: 10.1016/j.cels.2018.02.001. PubMed PMID:29550255 PubMed Central PMC5927625
  • 2018 | Single-cell RNA sequencing reveals gene expression signatures of breast cancer-associated endothelial cells. Sun, Z, Wang, CY, Lawson, DA, Kwek, S, Velozo, HG, Owyong, M, Lai, MD, Fong, L, Wilson, M, Su, H, Werb, Z, Cooke, DL Oncotarget 9 (13): 10945-10961. doi: 10.18632/oncotarget.23760. PubMed PMID:29541388 PubMed Central PMC5834272
  • 2018 | Cross-Cohort Analysis Identifies a TEAD4-MYCN Positive Feedback Loop as the Core Regulatory Element of High-Risk Neuroblastoma. Rajbhandari, P, Lopez, G, Capdevila, C, Salvatori, B, Yu, J, Rodriguez-Barrueco, R, Martinez, D, Yarmarkovich, M, Weichert-Leahey, N, Abraham, BJ, Alvarez, MJ, Iyer, A, Harenza, JL, Oldridge, D, De Preter, K, Koster, J, Asgharzadeh, S, Seeger, RC, Wei, JS, Khan, J, Vandesompele, J, Mestdagh, P, Versteeg, R, Look, AT, Young, RA, Iavarone, A, Lasorella, A, Silva, JM, Maris, JM, Califano, A Cancer Discov 8 (5): 582-599. doi: 10.1158/2159-8290.CD-16-0861. PubMed PMID:29510988 PubMed Central PMC5967627
  • 2018 | Using deep learning to model the hierarchical structure and function of a cell. Ma, J, Yu, MK, Fong, S, Ono, K, Sage, E, Demchak, B, Sharan, R, Ideker, T Nat. Methods 15 (4): 290-298. doi: 10.1038/nmeth.4627. PubMed PMID:29505029 PubMed Central PMC5882547
  • 2018 | In vivo systems biology approaches to chronic immune/inflammatory pathophysiology. Starchenko, A, Lauffenburger, DA Curr. Opin. Biotechnol. 52 : 9-16. doi: 10.1016/j.copbio.2018.02.006. PubMed PMID:29494996
  • 2018 | BET proteins in abnormal metabolism, inflammation, and the breast cancer microenvironment. Andrieu, GP, Shafran, JS, Deeney, JT, Bharadwaj, KR, Rangarajan, A, Denis, GV J. Leukoc. Biol. 104 (2): 265-274. doi: 10.1002/JLB.5RI0917-380RR. PubMed PMID:29493812 PubMed Central PMC6134394
  • 2018 | Brain cancer genomics and epigenomics. Archer, TC, Sengupta, S, Pomeroy, SL Handb Clin Neurol 148 : 785-797. doi: 10.1016/B978-0-444-64076-5.00050-8. PubMed PMID:29478614
  • 2018 | Differential expression of the TWEAK receptor Fn14 in IDH1 wild-type and mutant gliomas. Hersh, DS, Peng, S, Dancy, JG, Galisteo, R, Eschbacher, JM, Castellani, RJ, Heath, JE, Legesse, T, Kim, AJ, Woodworth, GF, Tran, NL, Winkles, JA J. Neurooncol. 138 (2): 241-250. doi: 10.1007/s11060-018-2799-3. PubMed PMID:29453678 PubMed Central PMC6047063
  • 2018 | Combinatorial CRISPR-Cas9 Metabolic Screens Reveal Critical Redox Control Points Dependent on the KEAP1-NRF2 Regulatory Axis. Zhao, D, Badur, MG, Luebeck, J, Magaña, JH, Birmingham, A, Sasik, R, Ahn, CS, Ideker, T, Metallo, CM, Mali, P Mol. Cell 69 (4): 699-708.e7. doi: 10.1016/j.molcel.2018.01.017. PubMed PMID:29452643 PubMed Central PMC5819357
  • 2018 | The ABCs of PTMs. Barber, KW, Rinehart, J Nat. Chem. Biol. 14 (3): 188-192. doi: 10.1038/nchembio.2572. PubMed PMID:29443972 PubMed Central PMC5979263
  • 2018 | Comprehensive characterisation of compartment-specific long non-coding RNAs associated with pancreatic ductal adenocarcinoma. Arnes, L, Liu, Z, Wang, J, Maurer, C, Sagalovskiy, I, Sanchez-Martin, M, Bommakanti, N, Garofalo, DC, Balderes, DA, Sussel, L, Olive, KP, Rabadan, R Gut : . doi: 10.1136/gutjnl-2017-314353. PubMed PMID:29440233 PubMed Central PMC6086768
  • 2018 | Cross-talk Signaling between HER3 and HPV16 E6 and E7 Mediates Resistance to PI3K Inhibitors in Head and Neck Cancer. Brand, TM, Hartmann, S, Bhola, NE, Li, H, Zeng, Y, O'Keefe, RA, Ranall, MV, Bandyopadhyay, S, Soucheray, M, Krogan, NJ, Kemp, C, Duvvuri, U, LaVallee, T, Johnson, DE, Ozbun, MA, Bauman, JE, Grandis, JR Cancer Res. 78 (9): 2383-2395. doi: 10.1158/0008-5472.CAN-17-1672. PubMed PMID:29440171
  • 2018 | BET Proteins Exhibit Transcriptional and Functional Opposition in the Epithelial-to-Mesenchymal Transition. Andrieu, GP, Denis, GV Mol. Cancer Res. 16 (4): 580-586. doi: 10.1158/1541-7786.MCR-17-0568. PubMed PMID:29437854 PubMed Central PMC5882530
  • 2018 | A drift-diffusion checkpoint model predicts a highly variable and growth-factor-sensitive portion of the cell cycle G1 phase. Jones, ZW, Leander, R, Quaranta, V, Harris, LA, Tyson, DR PLoS ONE 13 (2): e0192087. doi: 10.1371/journal.pone.0192087. PubMed PMID:29432467 PubMed Central PMC5809023
  • 2018 | Comparing side chain packing in soluble proteins, protein-protein interfaces, and transmembrane proteins. Gaines, JC, Acebes, S, Virrueta, A, Butler, M, Regan, L, O'Hern, CS Proteins 86 (5): 581-591. doi: 10.1002/prot.25479. PubMed PMID:29427530 PubMed Central PMC5912992
  • 2018 | Targeting minimal residual disease: a path to cure?. Luskin, MR, Murakami, MA, Manalis, SR, Weinstock, DM Nat. Rev. Cancer 18 (4): 255-263. doi: 10.1038/nrc.2017.125. PubMed PMID:29376520 PubMed Central PMC6398166
  • 2018 | N-Carboxyanhydride Polymerization of Glycopolypeptides That Activate Antigen-Presenting Cells through Dectin-1 and Dectin-2. Zhou, MN, Delaveris, CS, Kramer, JR, Kenkel, JA, Engleman, EG, Bertozzi, CR Angew. Chem. Int. Ed. Engl. 57 (12): 3137-3142. doi: 10.1002/anie.201713075. PubMed PMID:29370452 PubMed Central PMC5842139
  • 2018 | Discovering Altered Regulation and Signaling Through Network-based Integration of Transcriptomic, Epigenomic, and Proteomic Tumor Data. Kedaigle, AJ, Fraenkel, E Methods Mol. Biol. 1711 : 13-26. doi: 10.1007/978-1-4939-7493-1_2. PubMed PMID:29344883 PubMed Central PMC6309679
  • 2018 | Clonal evolution mechanisms in NT5C2 mutant-relapsed acute lymphoblastic leukaemia. Tzoneva, G, Dieck, CL, Oshima, K, Ambesi-Impiombato, A, Sánchez-Martín, M, Madubata, CJ, Khiabanian, H, Yu, J, Waanders, E, Iacobucci, I, Sulis, ML, Kato, M, Koh, K, Paganin, M, Basso, G, Gastier-Foster, JM, Loh, ML, Kirschner-Schwabe, R, Mullighan, CG, Rabadan, R, Ferrando, AA Nature 553 (7689): 511-514. doi: 10.1038/nature25186. PubMed PMID:29342136 PubMed Central PMC5931372
  • 2018 | HIF signaling in osteoblast-lineage cells promotes systemic breast cancer growth and metastasis in mice. Devignes, CS, Aslan, Y, Brenot, A, Devillers, A, Schepers, K, Fabre, S, Chou, J, Casbon, AJ, Werb, Z, Provot, S Proc. Natl. Acad. Sci. U.S.A. 115 (5): E992-E1001. doi: 10.1073/pnas.1718009115. PubMed PMID:29339479 PubMed Central PMC5798374
  • 2018 | Cancer-associated fibroblasts regulate endothelial adhesion protein LPP to promote ovarian cancer chemoresistance. Leung, CS, Yeung, TL, Yip, KP, Wong, KK, Ho, SY, Mangala, LS, Sood, AK, Lopez-Berestein, G, Sheng, J, Wong, ST, Birrer, MJ, Mok, SC J. Clin. Invest. 128 (2): 589-606. doi: 10.1172/JCI95200. PubMed PMID:29251630 PubMed Central PMC5785271
  • 2018 | Single-Cell RNA-seq Reveals a Subpopulation of Prostate Cancer Cells with Enhanced Cell-Cycle-Related Transcription and Attenuated Androgen Response. Horning, AM, Wang, Y, Lin, CK, Louie, AD, Jadhav, RR, Hung, CN, Wang, CM, Lin, CL, Kirma, NB, Liss, MA, Kumar, AP, Sun, L, Liu, Z, Chao, WT, Wang, Q, Jin, VX, Chen, CL, Huang, TH Cancer Res. 78 (4): 853-864. doi: 10.1158/0008-5472.CAN-17-1924. PubMed PMID:29233929 PubMed Central PMC5983359
  • 2017 | A new method for post-translationally labeling proteins in live cells for fluorescence imaging and tracking. Hinrichsen, M, Lenz, M, Edwards, JM, Miller, OK, Mochrie, SGJ, Swain, PS, Schwarz-Linek, U, Regan, L Protein Eng. Des. Sel. 30 (12): 771-780. doi: 10.1093/protein/gzx059. PubMed PMID:29228311
  • 2018 | Tamoxifen Resistance in Breast Cancer Is Regulated by the EZH2-ERα-GREB1 Transcriptional Axis. Wu, Y, Zhang, Z, Cenciarini, ME, Proietti, CJ, Amasino, M, Hong, T, Yang, M, Liao, Y, Chiang, HC, Kaklamani, VG, Jeselsohn, R, Vadlamudi, RK, Huang, TH, Li, R, De Angelis, C, Fu, X, Elizalde, PV, Schiff, R, Brown, M, Xu, K Cancer Res. 78 (3): 671-684. doi: 10.1158/0008-5472.CAN-17-1327. PubMed PMID:29212856 PubMed Central PMC5967248
  • 2018 | Vimentin Is Required for Lung Adenocarcinoma Metastasis via Heterotypic Tumor Cell-Cancer-Associated Fibroblast Interactions during Collective Invasion. Richardson, AM, Havel, LS, Koyen, AE, Konen, JM, Shupe, J, Wiles, WG 4th, Martin, WD, Grossniklaus, HE, Sica, G, Gilbert-Ross, M, Marcus, AI Clin. Cancer Res. 24 (2): 420-432. doi: 10.1158/1078-0432.CCR-17-1776. PubMed PMID:29208669 PubMed Central PMC5771825
  • 2017 | Quantitative, in situ analysis of mRNAs and proteins with subcellular resolution. Kwon, S, Chin, K, Nederlof, M, Gray, JW Sci Rep 7 (1): 16459. doi: 10.1038/s41598-017-16492-1. PubMed PMID:29184166 PubMed Central PMC5705767
  • 2017 | Tumor-Suppressor Inactivation of GDF11 Occurs by Precursor Sequestration in Triple-Negative Breast Cancer. Bajikar, SS, Wang, CC, Borten, MA, Pereira, EJ, Atkins, KA, Janes, KA Dev. Cell 43 (4): 418-435.e13. doi: 10.1016/j.devcel.2017.10.027. PubMed PMID:29161592 PubMed Central PMC5726799
  • 2018 | Unsupervised Trajectory Analysis of Single-Cell RNA-Seq and Imaging Data Reveals Alternative Tuft Cell Origins in the Gut. Herring, CA, Banerjee, A, McKinley, ET, Simmons, AJ, Ping, J, Roland, JT, Franklin, JL, Liu, Q, Gerdes, MJ, Coffey, RJ, Lau, KS Cell Syst 6 (1): 37-51.e9. doi: 10.1016/j.cels.2017.10.012. PubMed PMID:29153838 PubMed Central PMC5799016
  • 2017 | Precise Editing at DNA Replication Forks Enables Multiplex Genome Engineering in Eukaryotes. Barbieri, EM, Muir, P, Akhuetie-Oni, BO, Yellman, CM, Isaacs, FJ Cell 171 (6): 1453-1467.e13. doi: 10.1016/j.cell.2017.10.034. PubMed PMID:29153834 PubMed Central PMC5995112
  • 2017 | Determining therapeutic susceptibility in multiple myeloma by single-cell mass accumulation. Cetin, AE, Stevens, MM, Calistri, NL, Fulciniti, M, Olcum, S, Kimmerling, RJ, Munshi, NC, Manalis, SR Nat Commun 8 (1): 1613. doi: 10.1038/s41467-017-01593-2. PubMed PMID:29151572 PubMed Central PMC5694762
  • 2017 | Type II Diabetes and Incidence of Estrogen Receptor Negative Breast Cancer in African American Women. Palmer, JR, Castro-Webb, N, Bertrand, K, Bethea, TN, Denis, GV Cancer Res. 77 (22): 6462-6469. doi: 10.1158/0008-5472.CAN-17-1903. PubMed PMID:29141994 PubMed Central PMC5726548
  • 2018 | Innate and acquired immune surveillance in the postdissemination phase of metastasis. Gonzalez, H, Robles, I, Werb, Z FEBS J. 285 (4): 654-664. doi: 10.1111/febs.14325. PubMed PMID:29131550 PubMed Central PMC5826884
  • 2018 | Diverse Class 2 CRISPR-Cas Effector Proteins for Genome Engineering Applications. Pyzocha, NK, Chen, S ACS Chem. Biol. 13 (2): 347-356. doi: 10.1021/acschembio.7b00800. PubMed PMID:29121460
  • 2018 | A Novel Signaling Complex between TROY and EGFR Mediates Glioblastoma Cell Invasion. Ding, Z, Roos, A, Kloss, J, Dhruv, H, Peng, S, Pirrotte, P, Eschbacher, JM, Tran, NL, Loftus, JC Mol. Cancer Res. 16 (2): 322-332. doi: 10.1158/1541-7786.MCR-17-0454. PubMed PMID:29117939 PubMed Central PMC5805628
  • 2017 | Utilizing networks for differential analysis of chromatin interactions. Liu, L, Ruan, J J Bioinform Comput Biol 15 (6): 1740008. doi: 10.1142/S021972001740008X. PubMed PMID:29113562 PubMed Central PMC5808438
  • 2018 | Modulators of Redox Metabolism in Head and Neck Cancer. Chen, X, Mims, J, Huang, X, Singh, N, Motea, E, Planchon, SM, Beg, M, Tsang, AW, Porosnicu, M, Kemp, ML, Boothman, DA, Furdui, CM Antioxid. Redox Signal. 29 (16): 1660-1690. doi: 10.1089/ars.2017.7423. PubMed PMID:29113454 PubMed Central PMC6207163
  • 2017 | MHC-I Genotype Restricts the Oncogenic Mutational Landscape. Marty, R, Kaabinejadian, S, Rossell, D, Slifker, MJ, van de Haar, J, Engin, HB, de Prisco, N, Ideker, T, Hildebrand, WH, Font-Burgada, J, Carter, H Cell 171 (6): 1272-1283.e15. doi: 10.1016/j.cell.2017.09.050. PubMed PMID:29107334 PubMed Central PMC5711564
  • 2017 | Acceptability of Human Papillomavirus Self-Sampling for Cervical Cancer Screening in an Indigenous Community in Guatemala. Gottschlich, A, Rivera-Andrade, A, Grajeda, E, Alvarez, C, Mendoza Montano, C, Meza, R J Glob Oncol 3 (5): 444-454. doi: 10.1200/JGO.2016.005629. PubMed PMID:29094082 PubMed Central PMC5646882
  • 2017 | Combating subclonal evolution of resistant cancer phenotypes. Brady, SW, McQuerry, JA, Qiao, Y, Piccolo, SR, Shrestha, G, Jenkins, DF, Layer, RM, Pedersen, BS, Miller, RH, Esch, A, Selitsky, SR, Parker, JS, Anderson, LA, Dalley, BK, Factor, RE, Reddy, CB, Boltax, JP, Li, DY, Moos, PJ, Gray, JW, Heiser, LM, Buys, SS, Cohen, AL, Johnson, WE, Quinlan, AR, Marth, G, Werner, TL, Bild, AH Nat Commun 8 (1): 1231. doi: 10.1038/s41467-017-01174-3. PubMed PMID:29093439 PubMed Central PMC5666005
  • 2017 | NDEx 2.0: A Clearinghouse for Research on Cancer Pathways. Pratt, D, Chen, J, Pillich, R, Rynkov, V, Gary, A, Demchak, B, Ideker, T Cancer Res. 77 (21): e58-e61. doi: 10.1158/0008-5472.CAN-17-0606. PubMed PMID:29092941 PubMed Central PMC5679399
  • 2017 | Combining deep learning and coherent anti-Stokes Raman scattering imaging for automated differential diagnosis of lung cancer. Weng, S, Xu, X, Li, J, Wong, STC J Biomed Opt 22 (10): 1-10. doi: 10.1117/1.JBO.22.10.106017. PubMed PMID:29086544 PubMed Central PMC5661703
  • 2017 | Genome-wide prediction of minor-groove electrostatic potential enables biophysical modeling of protein-DNA binding. Chiu, TP, Rao, S, Mann, RS, Honig, B, Rohs, R Nucleic Acids Res. 45 (21): 12565-12576. doi: 10.1093/nar/gkx915. PubMed PMID:29040720 PubMed Central PMC5716191
  • 2017 | A nonimmune function of T cells in promoting lung tumor progression. Green, JA, Arpaia, N, Schizas, M, Dobrin, A, Rudensky, AY J. Exp. Med. 214 (12): 3565-3575. doi: 10.1084/jem.20170356. PubMed PMID:29038367 PubMed Central PMC5716034
  • 2017 | Network modeling of kinase inhibitor polypharmacology reveals pathways targeted in chemical screens. Ursu, O, Gosline, SJC, Beeharry, N, Fink, L, Bhattacharjee, V, Huang, SC, Zhou, Y, Yen, T, Fraenkel, E PLoS ONE 12 (10): e0185650. doi: 10.1371/journal.pone.0185650. PubMed PMID:29023490 PubMed Central PMC5638242
  • 2017 | Systematic, network-based characterization of therapeutic target inhibitors. Shen, Y, Alvarez, MJ, Bisikirska, B, Lachmann, A, Realubit, R, Pampou, S, Coku, J, Karan, C, Califano, A PLoS Comput. Biol. 13 (10): e1005599. doi: 10.1371/journal.pcbi.1005599. PubMed PMID:29023443 PubMed Central PMC5638208
  • 2017 | Brachyury-YAP Regulatory Axis Drives Stemness and Growth in Cancer. Shah, SR, David, JM, Tippens, ND, Mohyeldin, A, Martinez-Gutierrez, JC, Ganaha, S, Schiapparelli, P, Hamilton, DH, Palena, C, Levchenko, A, Quiñones-Hinojosa, A Cell Rep 21 (2): 495-507. doi: 10.1016/j.celrep.2017.09.057. PubMed PMID:29020634 PubMed Central PMC5637538
  • 2018 | Functional Genomics Approach Identifies Novel Signaling Regulators of TGFα Ectodomain Shedding. Wilson, JL, Kefaloyianni, E, Stopfer, L, Harrison, C, Sabbisetti, VS, Fraenkel, E, Lauffenburger, DA, Herrlich, A Mol. Cancer Res. 16 (1): 147-161. doi: 10.1158/1541-7786.MCR-17-0140. PubMed PMID:29018056 PubMed Central PMC5859574
  • 2018 | Is the blood-brain barrier really disrupted in all glioblastomas? A critical assessment of existing clinical data. Sarkaria, JN, Hu, LS, Parney, IF, Pafundi, DH, Brinkmann, DH, Laack, NN, Giannini, C, Burns, TC, Kizilbash, SH, Laramy, JK, Swanson, KR, Kaufmann, TJ, Brown, PD, Agar, NYR, Galanis, E, Buckner, JC, Elmquist, WF Neuro-oncology 20 (2): 184-191. doi: 10.1093/neuonc/nox175. PubMed PMID:29016900 PubMed Central PMC5777482
  • 2017 | EGFR Ligands Differentially Stabilize Receptor Dimers to Specify Signaling Kinetics. Freed, DM, Bessman, NJ, Kiyatkin, A, Salazar-Cavazos, E, Byrne, PO, Moore, JO, Valley, CC, Ferguson, KM, Leahy, DJ, Lidke, DS, Lemmon, MA Cell 171 (3): 683-695.e18. doi: 10.1016/j.cell.2017.09.017. PubMed PMID:28988771 PubMed Central PMC5650921
  • 2017 | Logo2PWM: a tool to convert sequence logo to position weight matrix. Gao, Z, Liu, L, Ruan, J BMC Genomics 18 (Suppl 6): 709. doi: 10.1186/s12864-017-4023-9. PubMed PMID:28984206 PubMed Central PMC5629559
  • 2017 | Pathway Enrichment Analysis with Networks. Liu, L, Wei, J, Ruan, J Genes (Basel) 8 (10): . doi: 10.3390/genes8100246. PubMed PMID:28956817 PubMed Central PMC5664096
  • 2017 | Accelerated parallel algorithm for gene network reverse engineering. He, J, Zhou, Z, Reed, M, Califano, A BMC Syst Biol 11 (Suppl 4): 83. doi: 10.1186/s12918-017-0458-5. PubMed PMID:28950860 PubMed Central PMC5615246
  • 2017 | START: a system for flexible analysis of hundreds of genomic signal tracks in few lines of SQL-like queries. Zhu, X, Zhang, Q, Ho, ED, Yu, KH, Liu, C, Huang, TH, Cheng, AS, Kao, B, Lo, E, Yip, KY BMC Genomics 18 (1): 749. doi: 10.1186/s12864-017-4071-1. PubMed PMID:28938868 PubMed Central PMC5610441
  • 2017 | Single-cell analyses to tailor treatments. Shalek, AK, Benson, M Sci Transl Med 9 (408): . doi: 10.1126/scitranslmed.aan4730. PubMed PMID:28931656 PubMed Central PMC5645080
  • 2018 | Refined karyotype-based prognostic stratification of chronic lymphocytic leukemia with a low- and very-low-risk genetic profile. Giudice, ID, Rigolin, GM, Raponi, S, Cafforio, L, Ilari, C, Wang, J, Bordyuh, M, Piciocchi, A, Marinelli, M, Nanni, M, Tavolaro, S, Filetti, M, Bardi, A, Tammiso, E, Volta, E, Negrini, M, Saccenti, E, Mauro, FR, Rossi, D, Gaidano, G, Guarini, A, Rabadan, R, Cuneo, A, Foà, R Leukemia 32 (2): 543-546. doi: 10.1038/leu.2017.292. PubMed PMID:28924243 PubMed Central PMC5898432
  • 2017 | Bivalent Epigenetic Control of Oncofetal Gene Expression in Cancer. Zaidi, SK, Frietze, SE, Gordon, JA, Heath, JL, Messier, T, Hong, D, Boyd, JR, Kang, M, Imbalzano, AN, Lian, JB, Stein, JL, Stein, GS Mol. Cell. Biol. 37 (23): . doi: 10.1128/MCB.00352-17. PubMed PMID:28923849 PubMed Central PMC5686582
  • 2017 | Classifying the evolutionary and ecological features of neoplasms. Maley, CC, Aktipis, A, Graham, TA, Sottoriva, A, Boddy, AM, Janiszewska, M, Silva, AS, Gerlinger, M, Yuan, Y, Pienta, KJ, Anderson, KS, Gatenby, R, Swanton, C, Posada, D, Wu, CI, Schiffman, JD, Hwang, ES, Polyak, K, Anderson, ARA, Brown, JS, Greaves, M, Shibata, D Nat. Rev. Cancer 17 (10): 605-619. doi: 10.1038/nrc.2017.69. PubMed PMID:28912577 PubMed Central PMC5811185
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