2016 LSP Publications

 

Cyclic Immunofluorescence (CycIF), A Highly Multiplexed Method for Single-cell Imaging. Lin, J.-R., Fallahi-Sichani, M., Chen, J.-Y., and Sorger, P.K. (2016). Curr. Protoc. Chem. Biol. 8, 251–264 http://dx.doi.org/10.1002/cpch.14

Application of small RNA sequencing to identify microRNAs in acute kidney injury and fibrosis. Pellegrini, K.L., Gerlach, C.V., Craciun, F.L., Ramachandran, K., Bijol, V., Kissick, H.T., and Vaidya, V.S. (2016). Toxicol. Appl. Pharmacol. 312, 42–52 http://dx.doi.org/10.1016/j.taap.2015.12.002

Environmental exposure to arsenic and chromium in children is associated with kidney injury molecule-1. Cárdenas-González, M., Osorio-Yáñez, C., Gaspar-Ramírez, O., Pavković, M., Ochoa-Martínez, A., López-Ventura, D., Medeiros, M., Barbier, O.C., Pérez-Maldonado, I.N., Sabbisetti, V.S., et al. (2016a). Environ. Res. 150, 653–662  View PDF

A High-Throughput Screening Assay to Identify Kidney Toxic Compounds. Ramm, S., Adler, M., and Vaidya, V.S. (2016a). Curr. Protoc. Toxicol. 69, 9.10.1–9.10.26 http://dx.doi.org/10.1002/cptx.12

Conservation of protein abundance patterns reveals the regulatory architecture of the EGFR-MAPK pathway. 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., et al. (2016). Sci. Signal. 9, rs6 http://dx.doi.org/10.1126/scisignal.aaf0891

Innate immune memory and homeostasis may be conferred through crosstalk between the TLR3 and TLR7 pathways. Liu, B., Liu, Q., Yang, L., Palaniappan, S.K., Bahar, I., Thiagarajan, P.S., and Ding, J.L. (2016). Sci. Signal. 9, ra70  View PDF

RNA-binding Protein Musashi Homologue 1 Regulates Kidney Fibrosis by Translational Inhibition of p21 and Numb mRNA. Jadhav, S., Ajay, A.K., Trivedi, P., Seematti, J., Pellegrini, K., Craciun, F., and Vaidya, V.S. (2016). J. Biol. Chem. 291, 14085–14094 http://dx.doi.org/10.1074/jbc.M115.713289

Detection of Drug-Induced Acute Kidney Injury in Humans Using Urinary KIM-1, miR-21, -200c, and -423. Pavkovic, M., Robinson-Cohen, C., Chua, A.S., Nicoara, O., Cárdenas-González, M., Bijol, V., Ramachandran, K., Hampson, L., Pirmohamed, M., Antoine, D.J., et al. (2016). Toxicol. Sci. 152, 205–213  View PDF

MicroRNAs and drug-induced kidney injury. Pavkovic, M., and Vaidya, V.S. (2016). Pharmacol. Ther. 163, 48–57  View PDF

Functional and cellular consequences of covalent target protein modification by furan in rat liver. Ramm, S., Limbeck, E., and Mally, A. (2016b). Toxicology 361-362, 49–61 http://dx.doi.org/10.1016/j.tox.2016.06.018

Growth rate inhibition metrics correct for confounders in measuring sensitivity to cancer drugs. Hafner, M., Niepel, M., Chung, M., and Sorger, P.K. (2016). Nat. Methods 13, 521–527 http://dx.doi.org/10.1038/nmeth.3853

Reproducibility will only come with data liberation. AlQuraishi, M., and Sorger, P.K. (2016). Sci. Transl. Med. 8, 339ed7 http://dx.doi.org/10.1126/scitranslmed.aaf0968

Structural Basis for Substrate Selectivity of the E3 Ligase COP1. Uljon, S., Xu, X., Durzynska, I., Stein, S., Adelmant, G., Marto, J.A., Pear, W.S., and Blacklow, S.C. (2016). Structure 24, 687–696  View PDF

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq. Tirosh, I., Izar, B., Prakadan, S.M., Wadsworth, M.H., 2nd, Treacy, D., Trombetta, J.J., Rotem, A., Rodman, C., Lian, C., Murphy, G., et al. (2016). Science 352, 189–196  View PDF

A Quantitative Approach to Screen for Nephrotoxic Compounds In Vitro. Adler, M., Ramm, S., Hafner, M., Muhlich, J.L., Gottwald, E.M., Weber, E., Jaklic, A., Ajay, A.K., Svoboda, D., Auerbach, S., et al. (2016). J. Am. Soc. Nephrol. 27, 1015–1028  http://dx.doi.org/10.1681/ASN.2015010060

Overcoming Therapeutic Resistance in HER2-Positive Breast Cancers with CDK4/6 Inhibitors. Goel, S., Wang, Q., Watt, A.C., Tolaney, S.M., Dillon, D.A., Li, W., Ramm, S., Palmer, A.C., Yuzugullu, H., Varadan, V., et al. (2016). Cancer Cell 29, 255–269  View PDF

Pathway-Based Genomics Prediction using Generalized Elastic Net. Sokolov, A., Carlin, D.E., Paull, E.O., Baertsch, R., and Stuart, J.M. (2016a). PLoS Comput. Biol. 12, e1004790  View PDF

Sub-chronic exposure to fluoride impacts the response to a subsequent nephrotoxic treatment with gentamicin. Cárdenas-González, M., Jacobo Estrada, T., Rodríguez-Muñoz, R., Barrera-Chimal, J., Bobadilla, N.A., Barbier, O.C., and Del Razo, L.M. (2016b). J. Appl. Toxicol. 36, 309–319 http://dx.doi.org/10.1002/jat.3186

Chemical probes: The many genes of drug mechanism. Palmer, A.C. (2016). Nat. Chem. Biol. 12, 57–58 http://dx.doi.org/10.1038/nchembio.2010

Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments. Chait, R., Palmer, A.C., Yelin, I., and Kishony, R. (2016). Nat. Commun. 7, 10333  View PDF

One-class detection of cell states in tumor subtypes. Sokolov, A., Paull, E.O., and Stuart, J.M. (2016b). Pac. Symp. Biocomput. 21, 405–416  View PDF