Last updated November 11, 2017

Phase II Publications





Hafner, M., Mills, C.E., Subramanian, K., Chen, C., Chung, M., Boswell, S.A., Everley, R.A., Walmsley, C.S., Juric, D., and Sorger, P.K. (2017) Therapeutically advantageous secondary targets of abemaciclib identified by multi-omics profiling of CDK4/6 inhibitors. bioRxiv
Niepel, M., Heiser, L.M., Hafner, M., Williams, E.H., Chung, M., Barrette, A.M., Stern, A.D., Hu, B., LINCS Consortium, Gray, J.W., Birtwistle, M.R., Heiser, L.M., and Sorger, P.K. (2017). A multi-center study on factors influencing the reproducibility of drug-response studies in cancer cell lines. bioRxiv
Clark, N.A., Hafner, M., Kouril, M., Williams, E.H., Muhlich, J.L., Pilarczyk, M., Niepel, M., Sorger, P.K., and Medvedovic, M. (2017) GRcalculator: an online tool for calculating and mining drug-response data. BMC Cancer 17(1):698. doi:10.1186/s12885-017-3689-3 PMID:29065900 PMCID:PMC5655815
Hafner, M., Heiser, L.M., Williams, E.H., Niepel, M., Wang, N.J., Korkola, J.E., Gray, J.W., and Sorger, P.K. (2017) Quantification of sensitivity and resistance of breast cancer cell lines to anti-cancer drugs using GR metrics. Sci Data 4:170166. doi:10.1038/sdata.2017.166 PMID:29112189 PMCID:PMC5674849
Niepel, M., Hafner, M., Duan, Q., Wang, Z., Paull, E.O., Chung, M., Lu, X., Stuart, J.M., Golub, T.R., Subramanian, A., Ma’ayan, A., and Sorger, P.K. (2017) Common and cell-type specific responses to anti-cancer drugs revealed by high throughput transcript profiling. Nat Commun 8(1):1186. doi:10.1038/s41467-017-01383-w PMID:29084964 PMCID:PMC5662764
Werbin, J.L., Avendano, M.S., Becker, V., Jungmann, R., Yin, P., Danuser, G., and Sorger, P.K. (2017) Multiplexed Exchange-PAINT imaging reveals ligand-dependent EGFR and Met interactions in the plasma membrane. Sci Rep 7(1):12150. doi:10.1038/s41598-017-12257-y PMID:28939861 PMCID:PMC5610318
Niepel, M., Hafner, M., Chung, M., and Sorger, P.K. (2017) Measuring cancer drug sensitivity and resistance in cultured cells. Curr Protoc Chem Biol 19;9(2):55-74. doi:10.1002/cpch.21. PMID:28628199 PMCID:PMC5538315
Hafner, M., Niepel, M., Subramanian, K., and Sorger, P.K. (2017) Designing drug response experiments and quantifying their results. Curr Protoc Chem Biol 9(2):96-116. doi:10.1002/cpch.19 PMID:28628201
Hafner, M., Niepel, M., and Sorger, P.K. (2017) Alternative drug sensitivity metrics improve preclinical cancer pharmacogenomics. Nat Biotechnol. 35(6):500-502. doi:10.1038/nbt.3882 PMID:28591115 PMCID:PMC5668135
Graim, K., Liu, T.T., Achrol, A.S., Paull, E.O., Newton, Y., Chang, S.D., Harsh IV, G.R., Cordero, S.P., Rubin, D.L., and Stuart, J.M. (2017) Revealing cancer subtypes with higher-order correlations applied to imaging and omics data. BMC Med Genomics. 10(1):20. doi:10.1186/s12920-017-0256-3 PMID:28359308 PMCID:PMC5374737
Tan, L., Gurbani, D., Weisberg, E.L., Jones, D.S., Rao, S., Singer, W.D., Bernard, F.M., Mowafy, S., Jenney, A., Du, G., Nonami, A., Griffin, J.D., Lauffenburger, D.A., Westover, K.D., Sorger, P.K., and Gray, N.S. (2017) Studies of TAK1-centered polypharmacology with novel covalent TAK1 inhibitors. Bioorg Med Chem. 25(4):1320-1328. doi:10.1016/j.bmc.2016.11.034 PMID:28038940
Tan, L., Gurbani, D., Weisberg, E.L., Hunter, J.C., Li, L., Jones, D.S., Ficarro, S.B., Mowafy, S., Tam, C.P., Rao, S., Du, G., Griffin, J.D., Sorger, P.K., Marto, J.A., Westover, K.D., and Gray, N.S. (2017) Structure-guided development of covalent TAK1 inhibitors. Bioorg Med Chem. 25(3):838-846. doi:10.1016/j.bmc.2016.11.035 PMID:28011204 PMCID:PMC5484537
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
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 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. (2017) 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
Chong, C.R., Bahcall, M., Capelletti, M., Kosaka, T., Ercan, D., Sim, T., Sholl, L.M., Nishino, M., Johnson, B.E., Gray, N.S., and Jänne, P.A. (2017) Identification of Existing Drugs That Effectively Target NTRK1 and ROS1 Rearrangements in Lung Cancer. Clin Cancer Res. 23(1):204-213. doi:10.1158/1078-0432.CCR-15-1601 PMID:27370605 PMCID:PMC5203969
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 PMCID:PMC5372219 Explore
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. 6:8390. 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

Featured Pilot Phase Publications

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
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
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
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
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
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
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
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
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

See the complete list of HMS LINCS Pilot Phase publications and other related publications here.