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Journal Articles

Sanchez-Alvarez, M. & Bakal, C. (2018). PERK links the clock and protein stress in cancer. Nat cell biol, Vol.20 (1), pp. 4-5.

Sanchez-Alvarez, M., Del Pozo, M.A. & Bakal, C. (2018). Publisher Correction: AKT-mTOR signaling modulates the dynamics of IRE1 RNAse activity by regulating ER-mitochondria contacts. Sci rep, Vol.8 (1), p. 6476.  show abstract

Spill, F., Bakal, C. & Mak, M. (2018). Mechanical and Systems Biology of Cancer. Comput struct biotechnol j, Vol.16, pp. 237-245.  show abstract

Asghar, U.S., Barr, A.R., Cutts, R., Beaney, M., Babina, I., Sampath, D., Giltnane, J., Lacap, J.A., Crocker, L., Young, A., et al. (2017). Single-Cell Dynamics Determines Response to CDK4/6 Inhibition in Triple-Negative Breast Cancer. Clin cancer res, Vol.23 (18), pp. 5561-5572.  show abstract

Cooper, S., Barr, A.R., Glen, R. & Bakal, C. (2017). NucliTrack: an integrated nuclei tracking application. Bioinformatics, Vol.33 (20), pp. 3320-3322.  show abstract

Barr, A.R., Cooper, S., Heldt, F.S., Butera, F., Stoy, H., Mansfeld, J., Novák, B. & Bakal, C. (2017). DNA damage during S-phase mediates the proliferation-quiescence decision in the subsequent G1 via p21 expression. Nat commun, Vol.8, p. 14728.  show abstract

Sero, J.E. & Bakal, C. (2017). Multiparametric Analysis of Cell Shape Demonstrates that β-PIX Directly Couples YAP Activation to Extracellular Matrix Adhesion. Cell syst, Vol.4 (1), pp. 84-96.e6.  show abstract

Sanchez-Alvarez, M., Del Pozo, M.A. & Bakal, C. (2017). AKT-mTOR signaling modulates the dynamics of IRE1 RNAse activity by regulating ER-mitochondria contacts. Sci rep, Vol.7 (1), p. 16497.  show abstract

Natrajan, R., Sailem, H., Mardakheh, F.K., Arias Garcia, M., Tape, C.J., Dowsett, M., Bakal, C. & Yuan, Y. (2016). Microenvironmental Heterogeneity Parallels Breast Cancer Progression: A Histology-Genomic Integration Analysis. Plos med, Vol.13 (2), p. e1001961.  show abstract

Mardakheh, F.K., Sailem, H.Z., Kümper, S., Tape, C.J., McCully, R.R., Paul, A., Anjomani-Virmouni, S., Jørgensen, C., Poulogiannis, G., Marshall, C.J., et al. (2016). Proteomics profiling of interactome dynamics by colocalisation analysis (COLA). Mol biosyst, Vol.13 (1), pp. 92-105.  show abstract

Sailem, H.Z., Cooper, S. & Bakal, C. (2016). Visualizing quantitative microscopy data: History and challenges. Crit rev biochem mol biol, Vol.51 (2), pp. 96-101.  show abstract

Sero, J.E., Sailem, H.Z., Ardy, R.C., Almuttaqi, H., Zhang, T. & Bakal, C. (2015). Cell shape and the microenvironment regulate nuclear translocation of NF-κB in breast epithelial and tumor cells. Mol syst biol, Vol.11 (1), p. 790.  show abstract

Barr, A.R. & Bakal, C. (2015). A sensitised RNAi screen reveals a ch-TOG genetic interaction network required for spindle assembly. Sci rep, Vol.5, p. 10564.  show abstract

Sero, J.E., Sailem, H.Z., Ardy, R.C., Almuttaqi, H., Zhang, T. & Bakal, C. (2015). Cell shape and the microenvironment regulate nuclear translocation of NF-κB in breast epithelial and tumor cells. Mol syst biol, Vol.11 (3), p. 790.  show abstract

Cooper, S., Sadok, A., Bousgouni, V. & Bakal, C. (2015). Apolar and polar transitions drive the conversion between amoeboid and mesenchymal shapes in melanoma cells. Mol biol cell, Vol.26 (22), pp. 4163-4170.  show abstract

Sailem, H.Z., Sero, J.E. & Bakal, C. (2015). Visualizing cellular imaging data using PhenoPlot. Nat commun, Vol.6, p. 5825.  show abstract

Sanchez-Alvarez, M., Zhang, Q., Finger, F., Wakelam, M.J. & Bakal, C. (2015). Cell cycle progression is an essential regulatory component of phospholipid metabolism and membrane homeostasis. Open biol, Vol.5 (9), p. 150093.  show abstract

Yin, Z., Sailem, H., Sero, J., Ardy, R., Wong, S.T. & Bakal, C. (2014). How cells explore shape space: a quantitative statistical perspective of cellular morphogenesis. Bioessays, Vol.36 (12), pp. 1195-1203.  show abstract

Sailem, H., Bousgouni, V., Cooper, S. & Bakal, C. (2014). Cross-talk between Rho and Rac GTPases drives deterministic exploration of cellular shape space and morphological heterogeneity. Open biol, Vol.4, p. 130132.  show abstract

Sanchez-Alvarez, M., Finger, F., Arias-Garcia, M.D., Bousgouni, V., Pascual-Vargas, P. & Bakal, C. (2014). Signaling networks converge on TORC1-SREBP activity to promote endoplasmic reticulum homeostasis. Plos one, Vol.9 (7), p. e101164.  show abstract

Yin, Z., Sadok, A., Sailem, H., McCarthy, A., Xia, X., Li, F., Garcia, M.A., Evans, L., Barr, A.R., Perrimon, N., et al. (2013). A screen for morphological complexity identifies regulators of switch-like transitions between discrete cell shapes. Nature cell biology, Vol.15 (7), pp. 860-+.

Evans, L., Sailem, H., Vargas, P.P. & Bakal, C. (2013). Inferring signalling networks from images. J microsc, Vol.252 (1), pp. 1-7.  show abstract

Bakal, C. (2013). Chris Bakal: Look and learn. Journal of cell biology, Vol.203 (3), pp. 378-379.

Bakal, C. (2013). Chris Bakal: Look and learn Interviewed by Caitlin Sedwick. J cell biol, Vol.203 (3), pp. 378-379.

Meiri, D., Marshall, C.B., Greeve, M.A., Kim, B., Balan, M., Suarez, F., Bakal, C., Wu, C., Larose, J., Fine, N., et al. (2012). Mechanistic insight into the microtubule and actin cytoskeleton coupling through dynein-dependent RhoGEF inhibition. Mol cell, Vol.45 (5), pp. 642-655.  show abstract

Garcia, M.A., Alvarez, M.S., Sailem, H., Bousgouni, V., Sero, J. & Bakal, C. (2012). Differential RNAi screening provides insights into the rewiring of signalling networks during oxidative stress. Mol biosyst, Vol.8 (10), pp. 2605-2613.  show abstract

Barr, A.R. & Bakal, C. (2012). A direct look at RNAi screens. Mol syst biol, Vol.8, p. 580.

Meiri, D., Marshall, C.B., Greeve, M.A., Kim, B., Balan, M., Suarez, F., Bakal, C., Wu, C., LaRose, J., Fine, N., et al. (2012). Mechanistic Insight into the Microtubule and Actin Cytoskeleton Coupling through Dynein-Dependent RhoGEF Inhibition (vol 45, pg 642, 2012). Molecular cell, Vol.45 (6), pp. 844-844.

Bakal, C. (2012). Dynamic systems. Genome biol, Vol.13 (1), p. 312.  show abstract

Evans, L. & Bakal, C. (2012). High-Content Combinatorial RNAi Screens Reveal the Regulation of Cytokinesis by Rho-family GTPase Signalling Networks in Drosophila. Molecular biology of the cell, Vol.23.

Bakal, C. (2011). Drosophila RNAi screening in a postgenomic world. Brief funct genomics, Vol.10 (4), pp. 197-205.  show abstract

Sero, J.E., Thodeti, C.K., Mammoto, A., Bakal, C., Thomas, S. & Ingber, D.E. (2011). Paxillin mediates sensing of physical cues and regulates directional cell motility by controlling lamellipodia positioning. Plos one, Vol.6 (12), p. e28303.  show abstract

Nir, O., Bakal, C., Perrimon, N. & Berger, B. (2010). Inference of RhoGAP/GTPase regulation using single-cell morphological data from a combinatorial RNAi screen. Genome res, Vol.20 (3), pp. 372-380.  show abstract

Bakal, C. & Perrimon, N. (2010). Realizing the promise of RNAi high throughput screening. Dev cell, Vol.18 (4), pp. 506-507.  show abstract

Mohr, S., Bakal, C. & Perrimon, N. (2010). Genomic screening with RNAi: results and challenges. Annu rev biochem, Vol.79, pp. 37-64.  show abstract

Kaplow, I.M., Singh, R., Friedman, A., Bakal, C., Perrimon, N. & Berger, B. (2009). RNAiCut: automated detection of significant genes from functional genomic screens. Nat methods, Vol.6 (7), pp. 476-477.

Griffin, R., Sustar, A., Bonvin, M., Binari, R., del Valle Rodriguez, A., Hohl, A.M., Bateman, J.R., Villalta, C., Heffern, E., Grunwald, D., et al. (2009). The twin spot generator for differential Drosophila lineage analysis. Nat methods, Vol.6 (8), pp. 600-602.  show abstract

Yin, Z., Zhou, X., Bakal, C., Li, F., Sun, Y., Perrimon, N. & Wong, S.T. (2008). Using iterative cluster merging with improved gap statistics to perform online phenotype discovery in the context of high-throughput RNAi screens. Bmc bioinformatics, Vol.9, p. 264.  show abstract

Bakal, C., Linding, R., Llense, F., Heffern, E., Martin-Blanco, E., Pawson, T. & Perrimon, N. (2008). Phosphorylation networks regulating JNK activity in diverse genetic backgrounds. Science, Vol.322 (5900), pp. 453-456.  show abstract

Bakal, C., Aach, J., Church, G. & Perrimon, N. (2007). Quantitative morphological signatures define local signaling networks regulating cell morphology. Science, Vol.316 (5832), pp. 1753-1756.  show abstract

Tsuchihara, K., Lapin, V., Bakal, C., Okada, H., Brown, L., Hirota-Tsuchihara, M., Zaugg, K., Ho, A., Itie-Youten, A., Harris-Brandts, M., et al. (2005). Ckap2 regulates aneuploidy, cell cycling, and cell death in a p53-dependent manner. Cancer res, Vol.65 (15), pp. 6685-6691.  show abstract

Bakal, C.J., Finan, D., LaRose, J., Wells, C.D., Gish, G., Kulkarni, S., DeSepulveda, P., Wilde, A. & Rottapel, R. (2005). The Rho GTP exchange factor Lfc promotes spindle assembly in early mitosis. Proc natl acad sci u s a, Vol.102 (27), pp. 9529-9534.  show abstract

Hara, H., Bakal, C., Wada, T., Bouchard, D., Rottapel, R., Saito, T. & Penninger, J.M. (2004). The molecular adapter Carma1 controls entry of IkappaB kinase into the central immune synapse. J exp med, Vol.200 (9), pp. 1167-1177.  show abstract

Okada, H., Bakal, C., Shahinian, A., Elia, A., Wakeham, A., Suh, W.-., Duncan, G.S., Ciofani, M., Rottapel, R., Zúñiga-Pflücker, J.C., et al. (2004). Survivin loss in thymocytes triggers p53-mediated growth arrest and p53-independent cell death. J exp med, Vol.199 (3), pp. 399-410.  show abstract

Hara, H., Wada, T., Bakal, C., Kozieradzki, I., Suzuki, S., Suzuki, N., Nghiem, M., Griffiths, E.K., Krawczyk, C., Bauer, B., et al. (2003). The MAGUK family protein CARD11 is essential for lymphocyte activation. Immunity, Vol.18 (6), pp. 763-775.  show abstract

Bakal, C.J. & Davies, J.E. (2000). No longer an exclusive club: eukaryotic signalling domains in bacteria. Trends cell biol, Vol.10 (1), pp. 32-38.  show abstract

Heldt, F.S., Barr, A.R., Cooper, S., Bakal, C. & Novák, B. A comprehensive model for the proliferation-quiescence decision in response to endogenous DNA damage in human cells. Proc natl acad sci u s a, Vol.115 (10), pp. 2532-2537.  show abstract

Pascual-Vargas, P., Cooper, S., Sero, J., Bousgouni, V., Arias-Garcia, M. & Bakal, C. RNAi screens for Rho GTPase regulators of cell shape and YAP/TAZ localisation in triple negative breast cancer. Sci data, Vol.4, p. 170018.  show abstract

Cooper, S. & Bakal, C. Accelerating Live Single-Cell Signalling Studies. Trends biotechnol, Vol.35 (5), pp. 422-433.  show abstract

Sailem, H.Z. & Bakal, C. Identification of clinically predictive metagenes that encode components of a network coupling cell shape to transcription by image-omics. Genome res, Vol.27 (2), pp. 196-207.  show abstract

Barr, A.R., Heldt, F.S., Zhang, T., Bakal, C. & Novák, B. A Dynamical Framework for the All-or-None G1/S Transition. Cell syst, Vol.2 (1), pp. 27-37.  show abstract


Conferences

Sailem, H., Arias-Garcia, M., Bakal, C., Zisserman, A., Rittscher, J. & IEEE, (2017). Discovery of Rare Phenotypes in Cellular Images Using Weakly Supervised Deep Learning, 2017 IEEE INTERNATIONAL CONFERENCE ON COMPUTER VISION WORKSHOPS (ICCVW 2017), , pp.49-55.

Sero, J.E. & Bakal, C. (2016). Multiparametric analysis of cell morphology shows that beta-PIX, Cdc42, Rac1, and PAK2 drive YAP activation in breast epithelial cells., MOLECULAR BIOLOGY OF THE CELL, Vol.27.

Lin, C., Hong, P., Bakal, C. & Perrimon, N. (2010). Novel Morphological Phenotypes Discovery in High-Content Screens Using Underused Features., BICoB, , pp.184-189.

Baym, M., Bakal, C., Perrimon, N. & Berger, B. (2008). High-resolution Modeling of cellular signaling networks, Presented at 12th Annual International Conference on Research Computational Molecular Biology, Singapore, SINGAPORE. RESEARCH IN COMPUTATIONAL MOLECULAR BIOLOGY, PROCEEDINGS, Vol.4955, pp.257-271.

Yin, Z., Zhou, X.B., Bakal, C., Li, F.H., Sun, Y.X., Perrimon, N. & Wong, S.T. (2007). Online phenotype discovery in high-content RNAi screens using gap statistics, Presented at International Symposium on Computational Models for Life Science, Queensland, AUSTRALIA. COMPUTATIONAL MODELS FOR LIFE SCIENCES (CMLS 07), Vol.952, pp.86-95.

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