Computational methods for characterizing and learning from heterogeneous cell signaling data
Tài liệu tham khảo
Min, 2020, Temporal integration of mitogen history in mother cells controls proliferation of daughter cells, Science, 368, 1261, 10.1126/science.aay8241
Miura, 2018, Cell-to-Cell heterogeneity in p38-mediated cross-inhibition of JNK causes stochastic cell death, Cell Rep, 24, 2658, 10.1016/j.celrep.2018.08.020
Spencer, 2009, Non-genetic origins of cell-to-cell variability in TRAIL-induced apoptosis, Nature, 459, 428, 10.1038/nature08012
Jolly, 2015, Implications of the hybrid epithelial/mesenchymal phenotype in metastasis, Front Oncol, 5, 10.3389/fonc.2015.00155
Jolly, 2017, EMT and MET: necessary or permissive for metastasis?, Mol Oncol, 11, 755, 10.1002/1878-0261.12083
Okabe, 2008, Characteristics of dasatinib- and imatinib-resistant chronic myelogenous leukemia cells, Clin Canc Res, 14, 6181, 10.1158/1078-0432.CCR-08-0461
Sharma, 2010, A chromatin-mediated reversible drug-tolerant state in cancer cell subpopulations, Cell, 141, 69, 10.1016/j.cell.2010.02.027
Bedard, 2013, Tumour heterogeneity in the clinic, Nature, 501, 355, 10.1038/nature12627
Elowitz, 2002, Stochastic gene expression in a single cell, Science, 297, 1183, 10.1126/science.1070919
Swain, 2002, Intrinsic and extrinsic contributions to stochasticity in gene expression, Proc Natl Acad Sci Unit States Am, 99, 12795, 10.1073/pnas.162041399
Sumit, 2019, A two-pulse cellular stimulation test elucidates variability and mechanisms in signaling pathways, Biophys J, 116, 962, 10.1016/j.bpj.2019.01.022
Lin, 2019, Mapping the stochastic sequence of individual ligand-receptor binding events to cellular activation: T cells act on the rare events, Sci Signal, 12, 10.1126/scisignal.aat8715
Soltani, 2016, Intercellular variability in protein levels from stochastic expression and noisy cell cycle processes, PLoS Comput Biol, 12, 10.1371/journal.pcbi.1004972
Bialek, 2005, Physical limits to biochemical signaling, Proc Natl Acad Sci Unit States Am, 102, 10040, 10.1073/pnas.0504321102
Lestas, 2010, Fundamental limits on the suppression of molecular fluctuations, Nature, 467, 174, 10.1038/nature09333
Spinosa, 2019, Short-term cellular memory tunes the signaling responses of the chemokine receptor CXCR4, Sci Signal, 12, 10.1126/scisignal.aaw4204
Yuan, 2011, Cell-to-Cell variability in PI3K protein level regulates PI3K-akt pathway activity in cell populations, Curr Biol, 21, 173, 10.1016/j.cub.2010.12.047
Lee, 2012, Sequential application of anticancer drugs enhances cell death by rewiring apoptotic signaling networks, Cell, 149, 780, 10.1016/j.cell.2012.03.031
Morton, 2014, A nanoparticle-based combination chemotherapy delivery system for enhanced tumor killing by dynamic rewiring of signaling pathways, Sci Signal, 7, 10.1126/scisignal.2005261
Robinson, 2012, Computational analysis of high-throughput flow cytometry data, Expet Opin Drug Discov, 7, 679, 10.1517/17460441.2012.693475
Chen, 2019, Single-cell RNA-seq technologies and related computational data analysis, Front Genet, 10, 317, 10.3389/fgene.2019.00317
Gordonov, 2016, Time series modeling of live-cell shape dynamics for image-based phenotypic profiling, Integr Biol, 8, 73, 10.1039/C5IB00283D
Zhou, 2012, Visualizing dynamic activities of signaling enzymes using genetically encodable fret-based biosensors, 317, 10.1016/B978-0-12-391857-4.00016-1
Regot, 2014, High-sensitivity measurements of multiple kinase activities in live single cells, Cell, 157, 1724, 10.1016/j.cell.2014.04.039
Pargett, 2018, Live-cell imaging and analysis with multiple genetically encoded reporters, Curr Protoc Cell Biol, 78, 10.1002/cpcb.38
Abramoff, 2004, Image processing with ImageJ, Biophot Int, 11, 36
McQuin, 2018, CellProfiler 3.0: next-generation image processing for biology, PLoS Biol, 16, 10.1371/journal.pbio.2005970
Tian, 2020, EllipTrack: a global-local cell-tracking pipeline for 2D fluorescence time-lapse microscopy, Cell Rep, 32, 107984, 10.1016/j.celrep.2020.107984
Tinevez, 2017, TrackMate: an open and extensible platform for single-particle tracking, Methods, 115, 80, 10.1016/j.ymeth.2016.09.016
Gerosa, 2020, Receptor-driven ERK pulses reconfigure MAPK signaling and enable persistence of drug-adapted BRAF-mutant melanoma cells, Cell Syst, 11, 478, 10.1016/j.cels.2020.10.002
Birtwistle, 2012, Emergence of bimodal cell population responses from the interplay between analog single-cell signaling and protein expression noise, BMC Syst Biol, 6, 109, 10.1186/1752-0509-6-109
Goglia, 2020, A live-cell screen for altered erk dynamics reveals principles of proliferative control, Cell Syst, 10, 240, 10.1016/j.cels.2020.02.005
Aghabozorgi, 2015, Time-series clustering – a decade review, Inf Syst, 53, 16, 10.1016/j.is.2015.04.007
Blum, 2019, Temporal perturbation of ERK dynamics reveals network architecture of FGF2/MAPK signaling, Mol Syst Biol, 15, 10.15252/msb.20198947
Dobrzyński, 2020, Mining single-cell time-series datasets with time course inspector, Bioinformatics, 36, 1968, 10.1093/bioinformatics/btz846
Ramsay, 2005
Chen, 2017, Quantifying infinite-dimensional data: functional data analysis in action, Stat Biosci, 9, 582, 10.1007/s12561-015-9137-5
Sampattavanich, 2018, Encoding growth factor identity in the temporal dynamics of FOXO3 under the combinatorial control of ERK and AKT kinases, Cell Syst, 6, 664, 10.1016/j.cels.2018.05.004
Cheong, 2011, Information transduction capacity of noisy biochemical signaling networks, Science, 334, 354, 10.1126/science.1204553
Selimkhanov, 2014, Accurate information transmission through dynamic biochemical signaling networks, Science, 346, 1370, 10.1126/science.1254933
Keshelava, 2018, High capacity in G protein-coupled receptor signaling, Nat Commun, 9, 876, 10.1038/s41467-018-02868-y
Gross, 2019, Individual cells can resolve variations in stimulus intensity along the IGF-PI3K-akt signaling Axis, Cell Syst, 9, 580, 10.1016/j.cels.2019.11.005
Lopez, 2013, Programming biological models in Python using PySB, Mol Syst Biol, 9, 646, 10.1038/msb.2013.1
Garner, 2016, Information transfer in gonadotropin-releasing hormone (GnRH) signaling, J Biol Chem, 291, 2246, 10.1074/jbc.M115.686964
Iwamoto, 2016, Modeling cellular noise underlying heterogeneous cell responses in the epidermal growth factor signaling pathway, PLoS Comput Biol, 12, 10.1371/journal.pcbi.1005222
Wang, 2019, Roles of cellular heterogeneity, intrinsic and extrinsic noise in variability of p53 oscillation, Sci Rep, 9, 5883, 10.1038/s41598-019-41904-9
Tomida, 2015, Oscillation of p38 activity controls efficient pro-inflammatory gene expression, Nat Commun, 6, 10.1038/ncomms9350
Yao, 2016, Distinct cellular states determine calcium signaling response, Mol Syst Biol, 12, 894, 10.15252/msb.20167137
Hase, 2009, Structure of protein interaction networks and their implications on drug design, PLoS Comput Biol, 5, 10.1371/journal.pcbi.1000550
Jeschke, 2013, Determinants of cell-to-cell variability in protein kinase signaling, PLoS Comput Biol, 9, 10.1371/journal.pcbi.1003357
Lin, 2000, Feature extraction based ON morlet wavelet and its application for mechanical fault diagnosis, J Sound Vib, 234, 135, 10.1006/jsvi.2000.2864
Salamon, 2016, Towards the automatic classification of avian flight calls for bioacoustic monitoring, PLoS One, 11, 10.1371/journal.pone.0166866
Längkvist, 2014, A review of unsupervised feature learning and deep learning for time-series modeling, Pattern Recogn Lett, 42, 11, 10.1016/j.patrec.2014.01.008
Albeck, 2013, Frequency-modulated pulses of ERK activity transmit quantitative proliferation signals, Mol Cell, 49, 249, 10.1016/j.molcel.2012.11.002
Benary, 2020, Disentangling pro-mitotic signaling during cell cycle progression using time-resolved single-cell imaging, Cell Rep, 31, 107514, 10.1016/j.celrep.2020.03.078
Hung, 2017, Akt regulation of glycolysis mediates bioenergetic stability in epithelial cells, eLife, 6, 10.7554/eLife.27293
Lane, 2017, Measuring signaling and RNA-seq in the same cell links gene expression to dynamic patterns of NF-κB activation, Cell Syst, 4, 458, 10.1016/j.cels.2017.03.010
Jetka, 2019, Information-theoretic analysis of multivariate single-cell signaling responses, PLoS Comput Biol, 15, 10.1371/journal.pcbi.1007132
Suderman, 2017, Fundamental trade-offs between information flow in single cells and cellular populations, Proc Natl Acad Sci Unit States Am, 114, 5755, 10.1073/pnas.1615660114
Salis, 2006, Multiscale Hy3S: hybrid stochastic simulation for supercomputers, BMC Bioinf, 7, 93, 10.1186/1471-2105-7-93