Research graph
References from Computational biology approaches for mapping transcriptional regulatory networks. Local targets link to admitted publications; unresolved targets remain external evidence.
Qualitative analysis of gene networks
1998 · External reference
10.1073/pnas.0408031102
10.1073/pnas.0408031102 · External reference
10.1196/annals.1407.021
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10.1002/(sici)1521-1878(199805)20:5<433::aid-bies10>3.0.co;2-2
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10.1038/ng881
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10.1126/science.298.5594.824
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10.1126/science.1089769 · External reference
10.1016/j.cell.2005.08.020
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10.1038/nature13972
10.1038/nature13972 · External reference
Unresolved reference
2020 · External reference
10.1016/s0022-2836(02)00994-4
10.1016/s0022-2836(02)00994-4 · External reference
10.1038/nrg2102
10.1038/nrg2102 · External reference
Dynamical roles of biological regulatory circuits
10.1093/bib/bbm028 · 2007 · External reference
10.1101/gr.197590.115
10.1101/gr.197590.115 · External reference
10.1016/j.jmb.2005.12.003
10.1016/j.jmb.2005.12.003 · External reference
10.1126/science.1069883
10.1126/science.1069883 · External reference
Core transcriptional regulatory circuitry in human hepatocytes
2006 · External reference
10.1016/j.ccr.2012.06.007
10.1016/j.ccr.2012.06.007 · External reference
10.1016/j.neuron.2017.04.022
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10.1242/dev.157420 · External reference
10.1038/ng941
10.1038/ng941 · External reference
10.1073/pnas.231608898
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10.1016/s0303-2647(98)00087-2
10.1016/s0303-2647(98)00087-2 · External reference
10.1038/nbt890
10.1038/nbt890 · External reference
10.1038/nbt.2463
10.1038/nbt.2463 · External reference
10.1093/nar/gkv1156
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10.1186/1752-0509-6-104
10.1186/1752-0509-6-104 · External reference
10.7717/peerj.1525
10.7717/peerj.1525 · External reference
Going the distance for protein function prediction: a new distance metric for protein interaction networks) going the distance for protein function prediction: a new distance metric for protein interaction networks
10.1371/journal.pone.0076339 · 2013 · External reference
Reconstructing dynamic regulatory maps
10.1038/msb4100115 · 2007 · External reference
10.1093/bioinformatics/btn273
10.1093/bioinformatics/btn273 · External reference
10.1093/nar/26.1.55
10.1093/nar/26.1.55 · External reference
DISTILLER: A data integration framework to reveal condition dependency of complex regulons in Escherichia coli
10.1186/gb-2009-10-3-r27 · 2009 · External reference
A semi-supervised method for predicting transcription factor-gene interactions in Escherichia coli
10.1371/journal.pcbi.1000044 · 2008 · External reference
10.1016/j.cell.2015.05.056
10.1016/j.cell.2015.05.056 · External reference
10.1038/ng1165
10.1038/ng1165 · External reference
10.1371/journal.pone.0012776
10.1371/journal.pone.0012776 · External reference
10.1093/bioinformatics/bty916
10.1093/bioinformatics/bty916 · External reference
10.1093/bioinformatics/btz950
10.1093/bioinformatics/btz950 · External reference
Trustful Inference of Gene REgulation using Stability Selection
10.1186/1752-0509-6-145 · 2012 · External reference
10.1016/j.cell.2011.01.004
10.1016/j.cell.2011.01.004 · External reference
10.1038/s41592-019-0509-5
10.1038/s41592-019-0509-5 · External reference
10.1038/nature13668
10.1038/nature13668 · External reference
10.1038/nmeth.3799
10.1038/nmeth.3799 · External reference
10.1038/nature11247
10.1038/nature11247 · External reference
10.1038/s41586-020-03145-z
10.1038/s41586-020-03145-z · External reference
10.1101/gr.203679.115
10.1101/gr.203679.115 · External reference
10.1016/j.sbi.2004.05.004
10.1016/j.sbi.2004.05.004 · External reference
10.1038/nature08533
10.1038/nature08533 · External reference
10.1038/nature11245
10.1038/nature11245 · External reference
10.1038/nature12337
10.1038/nature12337 · External reference
10.1038/ng873
10.1038/ng873 · External reference
10.1016/j.csbj.2019.07.001
10.1016/j.csbj.2019.07.001 · External reference
10.1038/nprot.2006.106
10.1038/nprot.2006.106 · External reference
10.1371/journal.pbio.0050008
10.1371/journal.pbio.0050008 · External reference
Inferring gene regulatory networks by ANOVA
10.1093/bioinformatics/bts143 · 2012 · External reference
CoExpNetViz: Comparative co-expression networks construction and visualization tool
10.3389/fpls.2015.01194 · 2016 · External reference
10.1093/bioinformatics/btw216
10.1093/bioinformatics/btw216 · External reference
10.1038/nmeth.2016
10.1038/nmeth.2016 · External reference
10.1038/nmeth.4463
10.1038/nmeth.4463 · External reference
Advances to Bayesian network inference for generating causal networks from observational biological data
10.1093/bioinformatics/bth448 · 2004 · External reference
10.1093/bioinformatics/btn658
10.1093/bioinformatics/btn658 · External reference
10.1038/nsmb.1995
10.1038/nsmb.1995 · External reference
Co-expression networks reveal the tissue-specific regulation of transcription and splicing. Co-expression networks reveal tissue-specific
2016 · External reference
10.1126/science.1081900
10.1126/science.1081900 · External reference
The inferelator: An algorithn for learning parsimonious regulatory networks from systems-biology data sets de novo
10.1186/gb-2006-7-5-r36 · 2006 · External reference
10.1126/science.181.4097.310
10.1126/science.181.4097.310 · External reference
Logical modelling of regulatory networks with GINsim 2.3
10.1016/j.biosystems.2009.04.008 · 2009 · External reference
The CoLoMoTo interactive notebook: Accessible and reproducible computational analyses for qualitative biological networks
10.3389/fphys.2018.00680 · 2018 · External reference
Genetic network analyzer: A tool for the qualitative modeling and simulation of bacterial regulatory networks
10.1007/978-1-61779-361-5_22 · 2012 · External reference
10.1038/nbt.2635
10.1038/nbt.2635 · External reference
10.1126/science.290.5500.2306
10.1126/science.290.5500.2306 · External reference
10.1101/gad.1509607
10.1101/gad.1509607 · External reference
10.1101/gr.7090407
10.1101/gr.7090407 · External reference
10.1101/gr.127191.111
10.1101/gr.127191.111 · External reference
Improved reconstruction of in silico gene regulatory networks by integrating knockout and perturbation data
10.1371/journal.pone.0008121 · 2010 · External reference
10.1016/j.cell.2014.02.054
10.1016/j.cell.2014.02.054 · External reference
10.1101/gr.1239303
10.1101/gr.1239303 · External reference
10.1126/science.1246949
10.1126/science.1246949 · External reference
10.1126/science.aat8464
10.1126/science.aat8464 · External reference
10.1101/gr.092759.109
10.1101/gr.092759.109 · External reference
A geometric approach to characterize the functional identity of single cells
10.1038/s41467-018-03933-2 · 2018 · External reference
10.1016/j.cels.2019.10.007
10.1016/j.cels.2019.10.007 · External reference
10.1016/j.cels.2017.08.014
10.1016/j.cels.2017.08.014 · External reference
10.1038/nbt.3154
10.1038/nbt.3154 · External reference
10.1093/bioinformatics/btx194
10.1093/bioinformatics/btx194 · External reference
10.1371/journal.pcbi.1007644
10.1371/journal.pcbi.1007644 · External reference
Benchmarking joint multi-omics dimensionality reduction approaches for the study of cancer
10.1038/s41467-020-20430-7 · 2021 · External reference
Evaluating methods of inferring gene regulatory networks highlights their lack of performance for single cell gene expression data
10.1186/s12859-018-2217-z · 2018 · External reference
10.1038/s41592-019-0690-6
10.1038/s41592-019-0690-6 · External reference
10.1038/msb.2010.31
10.1038/msb.2010.31 · External reference
10.1126/science.1247363
10.1126/science.1247363 · External reference
Sharing and specificity of co-expression networks across 35 human tissues
10.1371/journal.pcbi.1004220 · 2015 · External reference
The role of transcription in shaping the spatial organization of the genome
2019 · External reference
10.1038/nature11082
10.1038/nature11082 · External reference
10.1038/nature11049
10.1038/nature11049 · External reference
Contro155osomes
2014 · External reference
10.1016/j.celrep.2012.09.022
10.1016/j.celrep.2012.09.022 · External reference
10.1038/nature11212
10.1038/nature11212 · External reference
10.1038/s41586-020-2493-4
10.1038/s41586-020-2493-4 · External reference
10.1016/j.cell.2013.09.053
10.1016/j.cell.2013.09.053 · External reference
10.1073/pnas.1016071107
10.1073/pnas.1016071107 · External reference
10.1016/j.cell.2012.08.026
10.1016/j.cell.2012.08.026 · External reference
10.1016/j.celrep.2018.01.075
10.1016/j.celrep.2018.01.075 · External reference
Bromodomain and extraterminal proteins foster the core transcriptional regulatory programs and confer vulnerability in liposarcoma
2019 · External reference
10.1016/j.ccell.2019.06.002
10.1016/j.ccell.2019.06.002 · External reference
10.1016/j.cell.2016.12.013
10.1016/j.cell.2016.12.013 · External reference
10.1016/j.ccell.2020.12.003
10.1016/j.ccell.2020.12.003 · External reference
10.1016/j.exphem.2017.06.001
10.1016/j.exphem.2017.06.001 · External reference
10.1093/nar/gky317
10.1093/nar/gky317 · External reference
10.1101/gr.260877.120
10.1101/gr.260877.120 · External reference
10.1016/j.cels.2017.06.015
10.1016/j.cels.2017.06.015 · External reference
10.1101/394205
10.1101/394205 · External reference
10.1186/gb-2011-12-8-r83
10.1186/gb-2011-12-8-r83 · External reference
10.1016/j.cell.2017.10.049
10.1016/j.cell.2017.10.049 · External reference
Lisa: inferring transcriptional regulators through integrative modeling of public chromatin accessibility and ChIP-seq data
2020 · External reference
10.1016/j.ymeth.2019.07.014
10.1016/j.ymeth.2019.07.014 · External reference
10.1038/nature11981
10.1038/nature11981 · External reference
10.1038/s41590-017-0012-z
10.1038/s41590-017-0012-z · External reference
Distinctive roles of age, sex, and genetics in shaping transcriptional variation of human immune responses to microbial challenges
10.1073/pnas.1714765115 · 2018 · External reference
10.1016/j.cels.2018.01.009
10.1016/j.cels.2018.01.009 · External reference
10.2217/pgs-2018-0008
10.2217/pgs-2018-0008 · External reference
