TY - JOUR AU - Goodwin, S. AU - McPherson, J. D. AU - McCombie, W. R. PY - 2016 DA - 2016// TI - Coming of age: ten years of next-generation sequencing technologies JO - Nat Rev Genet VL - 17 UR - https://doi.org/10.1038/nrg.2016.49 DO - 10.1038/nrg.2016.49 ID - Goodwin2016 ER - TY - JOUR AU - van Dam, S. AU - Vosa, U. AU - van der Graaf, A. AU - Franke, L. AU - de Magalhaes, J. P. PY - 2018 DA - 2018// TI - Gene co-expression analysis for functional classification and gene–disease predictions JO - Brief Bioinform VL - 19 ID - van Dam2018 ER - TY - JOUR AU - Shapiro, E. AU - Biezuner, T. AU - Linnarsson, S. PY - 2013 DA - 2013// TI - Single-cell sequencing-based technologies will revolutionize whole-organism science JO - Nat Rev Genet VL - 14 UR - https://doi.org/10.1038/nrg3542 DO - 10.1038/nrg3542 ID - Shapiro2013 ER - TY - JOUR AU - Navin, N. AU - Kendall, J. AU - Troge, J. AU - Andrews, P. AU - Rodgers, L. AU - McIndoo, J. AU - Cook, K. AU - Stepansky, A. AU - Levy, D. AU - Esposito, D. PY - 2011 DA - 2011// TI - Tumour evolution inferred by single-cell sequencing JO - Nature VL - 472 UR - https://doi.org/10.1038/nature09807 DO - 10.1038/nature09807 ID - Navin2011 ER - TY - JOUR AU - Fischer, D. S. AU - Fiedler, A. K. AU - Kernfeld, E. M. AU - Genga, R. M. AU - Bastidas-Ponce, A. AU - Bakhti, M. AU - Lickert, H. AU - Hasenauer, J. AU - Maehr, R. AU - Theis, F. J. PY - 2019 DA - 2019// TI - Inferring population dynamics from single-cell rna-sequencing time series data JO - Nat Biotechnol VL - 37 UR - https://doi.org/10.1038/s41587-019-0088-0 DO - 10.1038/s41587-019-0088-0 ID - Fischer2019 ER - TY - JOUR AU - Li, W. AU - Kang, S. AU - Liu, C. -. C. AU - Zhang, S. AU - Shi, Y. AU - Liu, Y. AU - Zhou, X. J. PY - 2013 DA - 2013// TI - High-resolution functional annotation of human transcriptome: predicting isoform functions by a novel multiple instance-based label propagation method JO - Nucleic Acids Res VL - 42 UR - https://doi.org/10.1093/nar/gkt1362 DO - 10.1093/nar/gkt1362 ID - Li2013 ER - TY - JOUR AU - Wang, Z. AU - Fang, H. AU - Tang, N. L. -. S. AU - Deng, M. PY - 2017 DA - 2017// TI - Vcnet: vector-based gene co-expression network construction and its application to RNA-seq data JO - Bioinformatics VL - 33 UR - https://doi.org/10.1093/bioinformatics/btx131 DO - 10.1093/bioinformatics/btx131 ID - Wang2017 ER - TY - JOUR AU - Bian, S. AU - Hou, Y. AU - Zhou, X. AU - Li, X. AU - Yong, J. AU - Wang, Y. AU - Wang, W. AU - Yan, J. AU - Hu, B. AU - Guo, H. PY - 2018 DA - 2018// TI - Single-cell multiomics sequencing and analyses of human colorectal cancer JO - Science VL - 362 UR - https://doi.org/10.1126/science.aao3791 DO - 10.1126/science.aao3791 ID - Bian2018 ER - TY - JOUR AU - Pearson, K. PY - 1895 DA - 1895// TI - Vii. note on regression and inheritance in the case of two parents JO - Proc R Soc Lond VL - 58 UR - https://doi.org/10.1098/rspl.1895.0041 DO - 10.1098/rspl.1895.0041 ID - Pearson1895 ER - TY - JOUR AU - Reshef, D. N. AU - Reshef, Y. A. AU - Finucane, H. K. AU - Grossman, S. R. AU - McVean, G. AU - Turnbaugh, P. J. AU - Lander, E. S. AU - Mitzenmacher, M. AU - Sabeti, P. C. PY - 2011 DA - 2011// TI - Detecting novel associations in large data sets JO - Science VL - 334 UR - https://doi.org/10.1126/science.1205438 DO - 10.1126/science.1205438 ID - Reshef2011 ER - TY - JOUR AU - Lan, C. AU - Peng, H. AU - Hutvagner, G. AU - Li, J. PY - 2019 DA - 2019// TI - Construction of competing endogenous rna networks from paired rna-seq data sets by pointwise mutual information JO - BMC Genomics VL - 20 ID - Lan2019 ER - TY - JOUR AU - Robert, P. AU - Escoufier, Y. PY - 1976 DA - 1976// TI - A unifying tool for linear multivariate statistical methods: the rv-coefficient JO - J R Stat Soc: Ser C: Appl Stat VL - 25 ID - Robert1976 ER - TY - JOUR AU - Ramsay, J. AU - ten Berge, J. AU - Styan, G. PY - 1984 DA - 1984// TI - Matrix correlation JO - Psychometrika VL - 49 UR - https://doi.org/10.1007/BF02306029 DO - 10.1007/BF02306029 ID - Ramsay1984 ER - TY - JOUR AU - Smilde, A. K. AU - Kiers, H. A. AU - Bijlsma, S. AU - Rubingh, C. AU - Van Erk, M. PY - 2008 DA - 2008// TI - Matrix correlations for high-dimensional data: the modified rv-coefficient JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btn634 DO - 10.1093/bioinformatics/btn634 ID - Smilde2008 ER - TY - JOUR AU - Aben, N. AU - Westerhuis, J. A. AU - Song, Y. AU - Kiers, H. A. AU - Michaut, M. AU - Smilde, A. K. AU - Wessels, L. F. PY - 2018 DA - 2018// TI - Itop: inferring the topology of omics data JO - Bioinformatics VL - 34 UR - https://doi.org/10.1093/bioinformatics/bty636 DO - 10.1093/bioinformatics/bty636 ID - Aben2018 ER - TY - JOUR AU - Borzou, A. AU - Yousefi, R. AU - Sadygov, R. G. PY - 2019 DA - 2019// TI - Another look at matrix correlations JO - Bioinformatics VL - 35 UR - https://doi.org/10.1093/bioinformatics/btz281 DO - 10.1093/bioinformatics/btz281 ID - Borzou2019 ER - TY - STD TI - Wang D, Zou X, Au KF. A network-based computational framework to predict and differentiate functions for gene isoforms using exon-level expression data. Methods. 2020. https://doi.org/10.1016/j.ymeth.2020.06.005. ID - ref17 ER - TY - STD TI - de Torrenté L, Zimmerman S, Suzuki M, Christopeit M, Greally JM, Mar JC. The shape of gene expression distributions matter: how incorporating distribution shape improves the interpretation of cancer transcriptomic data. bioRxiv. 2019;572693. https://doi.org/10.1101/572693. ID - ref18 ER - TY - JOUR AU - Yalamanchili, H. K. AU - Li, Z. AU - Wang, P. AU - Wong, M. P. AU - Yao, J. AU - Wang, J. PY - 2014 DA - 2014// TI - Splicenet: recovering splicing isoform-specific differential gene networks from rna-seq data of normal and diseased samples JO - Nucleic Acids Res VL - 42 UR - https://doi.org/10.1093/nar/gku577 DO - 10.1093/nar/gku577 ID - Yalamanchili2014 ER - TY - JOUR AU - Network, C. G. A. R. PY - 2011 DA - 2011// TI - Integrated genomic analyses of ovarian carcinoma JO - Nature VL - 474 UR - https://doi.org/10.1038/nature10166 DO - 10.1038/nature10166 ID - Network2011 ER - TY - JOUR AU - Ramirez, R. N. AU - El-Ali, N. C. AU - Mager, M. A. AU - Wyman, D. AU - Conesa, A. AU - Mortazavi, A. PY - 2017 DA - 2017// TI - Dynamic gene regulatory networks of human myeloid differentiation JO - Cell Syst VL - 4 UR - https://doi.org/10.1016/j.cels.2017.03.005 DO - 10.1016/j.cels.2017.03.005 ID - Ramirez2017 ER - TY - JOUR AU - Okuda, T. AU - Nishimura, M. AU - Nakao, M. AU - Fujitaa, Y. PY - 2001 DA - 2001// TI - Runx1/aml1: A central player in hematopoiesis JO - Int J Hematol VL - 74 UR - https://doi.org/10.1007/BF02982057 DO - 10.1007/BF02982057 ID - Okuda2001 ER - TY - JOUR AU - Oeckinghaus, A. AU - Ghosh, S. PY - 2009 DA - 2009// TI - The nf- κb family of transcription factors and its regulation JO - Cold Spring Harb Perspect Biol VL - 1 UR - https://doi.org/10.1101/cshperspect.a000034 DO - 10.1101/cshperspect.a000034 ID - Oeckinghaus2009 ER - TY - JOUR AU - Klampfer, L. PY - 2006 DA - 2006// TI - Signal transducers and activators of transcription (stats): Novel targets of chemopreventive and chemotherapeutic drugs JO - Curr Cancer Drug Targets VL - 6 UR - https://doi.org/10.2174/156800906776056491 DO - 10.2174/156800906776056491 ID - Klampfer2006 ER - TY - JOUR AU - Wu, C. AU - Zhang, Q. AU - Jiang, Y. AU - Ma, S. PY - 2018 DA - 2018// TI - Robust network-based analysis of the associations between (epi) genetic measurements JO - J Multivar Anal VL - 168 UR - https://doi.org/10.1016/j.jmva.2018.06.009 DO - 10.1016/j.jmva.2018.06.009 ID - Wu2018 ER - TY - JOUR AU - Wu, C. AU - Shi, X. AU - Cui, Y. AU - Ma, S. PY - 2015 DA - 2015// TI - A penalized robust semiparametric approach for gene–environment interactions JO - Stat Med VL - 34 UR - https://doi.org/10.1002/sim.6609 DO - 10.1002/sim.6609 ID - Wu2015 ER - TY - STD TI - Wu C, Zhong P-S, Cui Y. Additive varying-coefficient model for nonlinear gene-environment interactions. Stat Appl Genet Mol Biol. 2018;17(2). https://doi.org/10.1515/sagmb-2017-0008. ID - ref27 ER - TY - JOUR AU - Wu, C. AU - Jiang, Y. AU - Ren, J. AU - Cui, Y. AU - Ma, S. PY - 2018 DA - 2018// TI - Dissecting gene-environment interactions: A penalized robust approach accounting for hierarchical structures JO - Stat Med VL - 37 UR - https://doi.org/10.1002/sim.7518 DO - 10.1002/sim.7518 ID - Wu2018 ER - TY - JOUR AU - Ren, J. AU - Zhou, F. AU - Li, X. AU - Chen, Q. AU - Zhang, H. AU - Ma, S. AU - Jiang, Y. AU - Wu, C. PY - 2020 DA - 2020// TI - Semiparametric bayesian variable selection for gene-environment interactions JO - Stat Med VL - 39 UR - https://doi.org/10.1002/sim.8434 DO - 10.1002/sim.8434 ID - Ren2020 ER -