HMS LINCS publications

Last updated January 27, 2017

Fallahi-Sichani, M., Becker, V., Izar, B., Baker, G.J., Lin, J.R., Boswell, S.A., Shah, P., Rotem, A., Garraway, L.A., and Sorger, P.K. (2017) Adaptive resistance of melanoma cells to RAF inhibition via reversible induction of a slowly dividing de‐differentiated state. Mol Syst Biol. 13(1):905. doi:10.15252/msb.20166796 PMID:28069687 PMCID:PMC5248573 Explore
Jones, D.S., Jenney, A.P., Swantek, J.L., Burke, J.M., Lauffenburger, D.A., and Sorger, P.K. (2017) Profiling drugs for rheumatoid arthritis that inhibit synovial fibroblast activation. Nat Chem Biol. 13(1):38-45. doi:10.1038/nchembio.2211 PMID:27820799 Explore
Erickson, B.K., Rose, C.M., Braun, C.R., Erickson, A.R., Knott, J., McAlister, G.C., Wühr, M.,
Paulo, J.A., Everley, R.A., and Gygi, S.P. (2016) A Strategy to Combine Sample Multiplexing with
Targeted Proteomics Assays for High-Throughput Protein Signature Characterization. Mol Cell. 65(2):361-370. doi:10.1016/j.molcel.2016.12.005 PMID:28065596 PMCID:PMC5250569
Everley, R.A., Huttlin, E.L., Erickson, A.R., Beausoleil, S.A., and Gygi, S.P. (2016) Neutral loss is a very common occurrence in phosphotyrosine-containing peptides labeled with isobaric tags. J Proteome Res. 16(2):1069-1076. doi:10.1021/acs.jproteome.6b00487 PMID:27978624
Lin, J.R., Fallahi-Sichani, M., Chen, J.Y., and Sorger, P.K. (2016) Cyclic Immunofluorescence (CycIF), a highly multiplexed method for single-cell imaging. Curr Protoc Chem Biol. 8(4):251-264. doi:10.1002/cpch.14 PMID:27925668 PMCID:PMC5233430 Explore
Shi, T., Niepel, M., McDermott, J.E., Gao, Y., Nicora, C.D., Chrisler, W.B., Markillie, L.M., Petyuk, V.A., Smith, R.D., Rodland, K.D., Sorger, P.K., Qian, W.J., and Wiley, H.S. (2016) Conservation of protein abundance patterns reveals the regulatory architecture of the EGFR-MAPK pathway. Sci Signal. 9(436):rs6. doi:10.1126/scisignal.aaf0891 PMID:27405981 PMCID:PMC5036860
Hafner, M., Niepel, M., Chung, M., and Sorger, P.K. (2016) Growth rate inhibition metrics correct for confounders in measuring sensitivity to cancer drugs. Nat Methods. 13(6):521-527. doi:10.1038/nmeth.3853 PMID:27135972 PMCID:PMC4887336 Explore
Sokolov, A., Carlin, D.E., Paull, E.O., Baertsch, R., and Stuart, J.M. (2016) Pathway-Based Genomics Prediction using Generalized Elastic Net. PLoS Comput Biol. 12(3): e10004790. doi:10.1371/journal.pcbi.1004790 PMID:26960204 PMCID:PMC4784899
Sokolov, A., Paull, E.O., and Stuart, J.M. (2016) One-class detection of cell states in tumor subtypes. Pac Symp Biocomput. 21:405-16 PMID:26776204 PMCID:PMC4856035
Lin, J.-R., Fallahi-Sichani, M., and Sorger, P.K. (2015) Highly multiplexed imaging of single cells using a high-throughput cyclic immunofluorescence method. Nat Commun. 6, Article number: 8390 doi:10.1038/ncomms9390 PMID:26399630 PMCID:PMC4587398 Explore
Roux, J., Hafner, M., Bandara, S., Sims, J.J., Hudson, H., Chai, D.H., and Sorger, P.K. (2015) Fractional killing arises from cell-to-cell variability in overcoming a caspase activity threshold. Mol Syst Biol. 11:803. doi:10.15252/msb.20145584 PMID:25953765 PMCID:PMC4461398 Explore
Fallahi-Sichani, M., Moerke, N.J., Niepel, M., Zhang, T., Gray, N.S., and Sorger, P.K. (2015) Systematic analysis of BRAFV600E melanomas reveals a role for JNK/c-Jun pathway in adaptive resistance to drug-induced apoptosis. Mol Syst Biol. 11(3):797. doi:10.15252/msb.20145877 PMID:25814555 PMCID:PMC4380931 Explore
Gujral, T.S., Chan, M., Peshkin, L., Sorger, P.K., Kirschner, M.W., and MacBeath, G. (2014) A noncanonical frizzled2 pathway regulates epithelial-mesenchymal transition and metastasis. Cell. 159(4), 844-56. doi:10.1016/j.cell.2014.10.032 PMID:25417160 PMCID:PMC4243058
Niepel, M., Hafner, M., Pace, E.A., Chung, M., Chai, D.H., Zhou, L., Muhlich, J.L., Schoeberl, B., and Sorger, P.K. (2014) Analysis of growth factor signaling in genetically diverse breast cancer lines. BMC Biol. 12, 20. doi:10.1186/1741-7007-12-20 PMID:24655548 PMCID:PMC4234128 Explore
Vempati, U.D., Chung, C., Mader, C., Koleti, A., Datar, N., Vidović, D., Wrobel, D., Erickson, S., Muhlich, J.L., Berriz, G., Benes, C.H., Subramanian, A., Pillai, A., Shamu, C.E., and Schürer, S.C. (2014) Metadata Standard and Data Exchange Specifications to Describe, Model, and Integrate Complex and Diverse High-Throughput Screening Data from the Library of Integrated Network-based Cellular Signatures (LINCS). J Biomol Screen. 19, 803-816. doi:10.1177/1087057114522514 PMID:24518066
Duan, Q., Flynn, C., Niepel, M., Hafner, M., Muhlich, J.L., Fernandez, N.F., Rouillard, A.D., Tan, C.M., Chen, E.Y., Golub, T.R., Sorger, P.K., Subramanian, A., and Ma’ayan, A. (2014) LINCS Canvas Browser: interactive web app to query, browse and interrogate LINCS L1000 gene expression signatures. Nucleic Acids Res 42, W449-60. doi:10.1093/nar/gku476 PMID:24906883 PMCID:PMC4086130
Tang, Y. (2014) A one-step imaging assay to monitor cell cycle state and apoptosis in mammalian cells. Curr Protoc Chem Biol. 6(1):1-5. doi:10.1002/9780470559277.ch130140. PMID:24652619 PMCID:PMC4016950 Explore
Paull, E.O., Carlin, D.E., Niepel, M., Sorger, P.K., Haussler, D., and Stuart, J.M. (2013) Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Events (TieDIE). Bioinformatics. 29, 2757–2764. doi:10.1093/bioinformatics/btt471 PMID:23986566 PMCID:PMC3799471 Explore
Niepel, M., Hafner, M., Pace, E.A., Chung, M., Chai, D.H., Zhou, L., Schoeberl, B., and Sorger, P.K. (2013) Profiles of Basal and Stimulated Receptor Signaling Networks Predict Drug Response in Breast Cancer Lines. Sci Signal. 6, ra84. doi:10.1126/scisignal.2004379 PMID:24065145 PMCID:PMC3845839 Explore
Fallahi-Sichani, M., Honarnejad, S., Heiser, L.M., Gray, J.W. & Sorger, P.K. (2013) Metrics other than potency reveal systematic variation in responses to cancer drugs. Nat Chem Biol. 9, 708–714. doi:10.1038/nchembio.1337 PMID:24013279 PMCID:PMC3947796 Explore
Tan, C. M., Chen, E. Y., Dannenfelser, R., Clark, N. R., and Ma’ayan, A. (2013) Network2Canvas: network visualization on a canvas with enrichment analysis. Bioinformatics. 29, 1872–1878. doi:10.1093/bioinformatics/btt319 PMID:23749960 PMCID:PMC3712222
Duan, Q., Kou, Y., Clark, N.R., Gordonov, S., and Ma’ayan, A. (2013) Metasignatures identify two major subtypes of breast cancer. CPT Pharmacometrics Syst Pharmacol. 2, e35. doi:10.1038/psp.2013.11 PMID:23836026 PMCID:PMC3615534
Tang, Y., Xie, T., Florian, S., Moerke, N., Shamu, C., Benes, C., and Mitchison, T.J. (2013) Differential Determinants of Cancer Cell Insensitivity to Antimitotic Drugs Discriminated by a One-Step Cell Imaging Assay. J Biomol Screen. 18, 1062-71. doi:10.1177/1087057113493804 PMID:23788527 PMCID:PMC3783590 Explore
Wong, C.K., Vaske, C.J., Ng, S., Sanborn, J.Z., Benz, S.C., Haussler, D., and Stuart, J.M. (2013) The UCSC Interaction Browser: multidimensional data views in pathway context. Nucleic Acids Res. 41, W218–W224. doi:10.1093/nar/gkt473 PMID:23748957 PMCID:PMC3692096
McAllister, F.E., Niepel, M., Haas, W., Huttlin, E., Sorger, P.K., and Gygi, S.P. (2013) Mass Spectrometry Based Method to Increase Throughput for Kinome Analyses Using ATP Probes. Anal Chem. 85, 4666–4674. doi:10.1021/ac303478g PMID:23607489 PMCID:PMC3771683 Explore
Chen, E.Y., Tan, C.M., Kou, Y., Duan, Q., Wang, Z., Meirelles, G.V., Clark, N.R., and Ma’ayan, A. (2013) Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. BMC Bioinformatics. 14, 128. doi:10.1186/1471-2105-14-128 PMID:23586463 PMCID:PMC3637064
Liu, Q., Xu, C., Kirubakaran, S., Zhang, X., Hur, W., Liu, Y., Kwiatkowski, N.P., Wang, J., Westover, K.D., Gao, P., Ercan, D., Niepel, M., Thoreen, C.C., Kang, S.A., Patricelli, M.P., Wang, Y., Tupper, T., Altabef, A., Kawamura, H., Held, K.D., Chou, D.M., Elledge, S.J., Janne, P.A., Wong, K.K., Sabatini, D.M., and Gray N.S. (2013) Characterization of Torin2, an ATP-competitive inhibitor of mTOR, ATM and ATR. Cancer Res. 73:2574-86. doi:10.1158/0008-5472.CAN-12-1702 PMID:23436801 PMCID:PMC3760004
Corcoran, R.B., Cheng, K.A., Hata, A.N., Faber, A.C., Ebi, H., Coffee, E.M., Greninger, P., Brown, R.D., Godfrey, J.T., Cohoon, T.J., Song, Y., Lifshits, E., Hung, K.E., Shioda, T., Dias-Santagata, D., Singh, A., Settleman, J., Benes, C.H., Mino-Kenudson, M., Wong, K.K., and Engelman, J.A. (2013) Synthetic Lethal Interaction of Combined BCL-XL and MEK Inhibition Promotes Tumor Regressions in KRAS Mutant Cancer Models. Cancer Cell. 23, 121–128. doi:10.1016/j.ccr.2012.11.007 PMID:23245996 PMCID:PMC3667614
Jenkins, S.L. and Ma’ayan, A. (2013) Systems pharmacology meets predictive, preventive, personalized and participatory medicine. Pharmacogenomics. 14, 119–122. doi:10.2217/pgs.12.186 PMID:23327571 PMCID:PMC3605723
Clark, N.R., Dannenfelser, R., Tan, C.M., Komosinski, M.E., and Ma’ayan, A. (2012) Sets2Networks: network inference from repeated observations of sets. BMC Syst Biol. 6, 89. doi:10.1186/1752-0509-6-89 PMID:22824380 PMCID:PMC3443648
Liu, Q., Ren, T., Fresques, T., Oppliger, W., Niles, B.J., Hur, W., Sabatini, D.M., Hall, M.N., Powers, T., and Gray, N.S. (2012) Selective ATP-competitive inhibitors of TOR suppress rapamycin-insensitive function of TORC2 in Saccharomyces cerevisiae. ACS Chem Biol. 7, 982–987. doi:10.1021/cb300058v PMID:22496512 PMCID:PMC3376217
Ni, J., Liu, Q., Xie, S., Carlson, C., Von, T., Vogel, K., Riddle, S., Benes, C., Eck, M., Roberts, T., Gray, N., and Zhao, J. (2012) Functional Characterization of an Isoform-Selective Inhibitor of PI3K-p110β as a Potential Anticancer Agent. Cancer Discov. 2, 425–433. doi:10.1158/2159-8290.CD-12-0003 PMID:22588880 PMCID:PMC3384541
Kirouac, D.C., Saez-Rodriguez, J., Swantek, J., Burke, J.M., Lauffenburger, D.A., and Sorger, P.K. (2012) Creating and analyzing pathway and protein interaction compendia for modelling signal transduction networks. BMC Syst Biol. 6, 29. doi:10.1186/1752-0509-6-29 PMID:22548703 PMCID:PMC3436686
Benes, C.H. (2012) Functionalizing Genomic Data for Personalization of Medicine. Clinical Pharmacol Ther. 93, 309–311. doi:10.1038/clpt.2012.219 PMID:23321554 PMCID:PMC3609407
Garnett, M.J., Edelman, E.J., Heidorn, S.J., Greenman, C.D., Dastur, A., Lau, K.W., Greninger, P., Thompson, I.R., Luo, X., Soares, J., Liu, Q., Iorio, F., Surdez, D., Chen, L., Milano, R.J., Bignell, G.R., Tam, A.T., Davies, H., Stevenson, J.A., Barthorpe, S., Lutz, S.R., Kogera, F., Lawrence, K., McLaren-Douglas, A., Mitropoulos, X., Mironenko, T., Thi, H., Richardson, L., Zhou, W., Jewitt, F., Zhang, T., O’Brien, P., Boisvert, J.L., Price, S., Hur, W., Yang, W., Deng, X., Butler, A., Choi, H.G., Chang, J.W., Baselga, J., Stamenkovic, I., Engelman, J.A., Sharma, S.V., Delattre, O., Saez-Rodriguez, J., Gray, N.S., Settleman, J., Futreal, P.A., Haber, D.A., Stratton, M.R., Ramaswamy, S., McDermott, U., and Benes, C.H. (2012) Systematic identification of genomic markers of drug sensitivity in cancer cells. Nature. 483, 570–575. doi:10.1038/nature11005 PMID:22460902 PMCID:PMC3349233
Liu, Q., Kirubakaran, S., Hur, W., Niepel, M., Westover, K., Thoreen, C.C., Wang, J., Ni, J., Patricelli, M.P., Vogel, K., Riddle, S., Waller, D.L., Traynor, R., Sanda, T., Zhao, Z., Kang, S.A., Zhao, J., Look, A.T., Sorger, P.K., Sabatini, D.M., and Gray, N.S. (2012) Kinome-wide Selectivity Profiling of ATP-competitive Mammalian Target of Rapamycin (mTOR) Inhibitors and Characterization of Their Binding Kinetics. J Biol Chem. 287, 9742–9752. doi:10.1074/jbc.M111.304485 PMID:22223645 PMCID:PMC3322972
Sansone, S.A., Rocca-Serra, P., Field, D., Maguire, E., Taylor, C., Hofmann, O., Fang, H., Neumann, S., Tong, W., Amaral-Zettler, L., Begley, K., Booth, T., Bougueleret, L., Burns, G., Chapman, B., Clark, T., Coleman, L.A., Copeland, J., Das, S., de Daruvar, A., de Matos, P., Dix, I., Edmunds, S., Evelo, C.T., Forster, M.J., Gaudet, P., Gilbert, J., Goble, C., Griffin, J.L., Jacob, D., Kleinjans, J. Harland, L., Haug, K., Hermjakob, H., Ho Sui, S.J., Laederach, A., Liang, S., Marshall, S., McGrath, A., Merrill, E., Reilly, D., Roux, M., Shamu, C.E., Shang, C.A., Steinbeck, C., Trefethen, A., Williams-Jones, B., Wolstencroft, K., Xenarios, I., and Hide, W. (2012) Toward interoperable bioscience data. Nat Genet. 44, 121–126. doi:10.1038/ng.1054 PMID:22281772 PMCID:PMC3428019
Zhang, T., Inesta-Vaquera, F., Niepel, M., Zhang, J., Ficarro, S.B., Machleidt, T., Xie, T., Marto, J.A., Kim, N., Sim, T., Laughlin, J.D., Park, H., LoGrasso, P.V., Patricelli, M., Nomanbhoy, T.K., Sorger, P.K., Alessi, D.R., and Gray, N.S. (2012) Discovery of potent and selective covalent inhibitors of JNK. Chem Biol. 19, 140–154. doi:10.1016/j.chembiol.2011.11.010 PMID:22284361 PMCID:PMC3270411
Luckert, K., Gujral, T.S., Chan, M., Sevecka, M., Joos, T.O., Sorger, P.K., Macbeath, G., and Pötz, O. (2012) A dual array-based approach to assess the abundance and posttranslational modification state of signaling proteins. Sci Signal. 5, pl1. doi:10.1126/scisignal.2002372 PMID:22234610 PMCID:PMC3465074
Prill, R.J., Saez-Rodriguez, J., Alexopoulos, L.G., Sorger, P.K., and Stolovitzky, G. (2011) Crowdsourcing network inference: the DREAM predictive signaling network challenge. Sci Signal. 4, mr7. doi:10.1126/scisignal.2002212 PMID:21900204 PMCID:PMC3465072
Millard, B.L., Niepel, M., Menden, M.P., Muhlich, J.L., and Sorger, P.K. (2011) Adaptive informatics for multifactorial and high-content biological data. Nat Methods. 8, 487–493. doi:10.1038/nmeth.1600 PMID:21516115 PMCID:PMC3105758

Other relevant publications

Yang, R., Niepel, M., Mitchison, T.K., and Sorger, P.K. (2010) Dissecting variability in responses to cancer chemotherapy through systems pharmacology. Clin Pharmacol Ther. 88, 34–38. doi:10.1038/clpt.2010.96 PMID:20520606 PMCID:PMC2941986
Alexopoulos, L.G., Saez-Rodriguez, J., Cosgrove, B.D., Lauffenburger, D.A., and Sorger, P.K. (2010) Networks Inferred from Biochemical Data Reveal Profound Differences in Toll-like Receptor and Inflammatory Signaling between Normal and Transformed Hepatocytes. Mol Cell Proteomics. 9(9), 1849-65. doi:10.1074/mcp.M110.000406 PMID:20460255 PMCID:PMC2938121
Chen, W.W., Niepel, M., and Sorger, P.K. (2010) Classic and Contemporary Approaches to Modeling Biochemical Reactions. Genes Dev. 24(17), 1861-75. doi:10.1101/gad.1945410 PMID:20810646 PMCID:PMC2932968
Niepel, M., Spencer, S.L., and Sorger, P.K. (2009) Non-Genetic Cell-to-Cell Variability and the Consequences for Pharmacology. Curr Opin Chem Biol. 13, 556-561. doi:10.1016/j.cbpa.2009.09.015 PMID:19833543 PMCID:PMC2975492
Saez-Rodriguez, J., Alexopoulos, L.G., Epperlein, J., Samaga, R., Lauffenburger, D.A., Klamt, S., and Sorger, P.K. (2009) Discrete Logic Modelling as a Means to Link Protein Signalling Networks with Functional Analysis of Mammalian Signal Transduction. Mol Syst Biol. 5, 331. doi:10.1038/msb.2009.87 PMID:19953085 PMCID:PMC2824489
Gaudet, S., Janes, K.A., Albeck, J.G., Pace, E.A., Lauffenburger, D.A., and Sorger, P.K. (2005) A Compendium of Signals and Responses Triggered by Prodeath and Prosurvival Cytokines. Mol Cell Proteomics. 4, 1569-1590. doi:10.1074/mcp.M500158-MCP200 PMID:16030008