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Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles

Citations

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Cited by:

  1. Ning Wang & Diane Lefaudeux & Anup Mazumder & Jingyi Jessica Li & Alexander Hoffmann, 2021. "Identifying the combinatorial control of signal-dependent transcription factors," PLOS Computational Biology, Public Library of Science, vol. 17(6), pages 1-29, June.
  2. Xiaomeng Zhang & Bin Shao & Yangle Wu & Ouyang Qi, 2013. "A Reverse Engineering Approach to Optimize Experiments for the Construction of Biological Regulatory Networks," PLOS ONE, Public Library of Science, vol. 8(9), pages 1-9, September.
  3. Shiori Sagawa & Morgan N Price & Adam M Deutschbauer & Adam P Arkin, 2017. "Validating regulatory predictions from diverse bacteria with mutant fitness data," PLOS ONE, Public Library of Science, vol. 12(5), pages 1-14, May.
  4. Guibo Ye & Mengfan Tang & Jian-Feng Cai & Qing Nie & Xiaohui Xie, 2013. "Low-Rank Regularization for Learning Gene Expression Programs," PLOS ONE, Public Library of Science, vol. 8(12), pages 1-9, December.
  5. Joeri Ruyssinck & Vân Anh Huynh-Thu & Pierre Geurts & Tom Dhaene & Piet Demeester & Yvan Saeys, 2014. "NIMEFI: Gene Regulatory Network Inference using Multiple Ensemble Feature Importance Algorithms," PLOS ONE, Public Library of Science, vol. 9(3), pages 1-13, March.
  6. Takanori Hasegawa & Rui Yamaguchi & Masao Nagasaki & Satoru Miyano & Seiya Imoto, 2014. "Inference of Gene Regulatory Networks Incorporating Multi-Source Biological Knowledge via a State Space Model with L1 Regularization," PLOS ONE, Public Library of Science, vol. 9(8), pages 1-19, August.
  7. Mingyi Wang & Jerome Verdier & Vagner A Benedito & Yuhong Tang & Jeremy D Murray & Yinbing Ge & Jörg D Becker & Helena Carvalho & Christian Rogers & Michael Udvardi & Ji He, 2013. "LegumeGRN: A Gene Regulatory Network Prediction Server for Functional and Comparative Studies," PLOS ONE, Public Library of Science, vol. 8(7), pages 1-7, July.
  8. Yichao Han & Wanji Li & Alden Filko & Jingyao Li & Fuzhong Zhang, 2023. "Genome-wide promoter responses to CRISPR perturbations of regulators reveal regulatory networks in Escherichia coli," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
  9. Miles A Miller & Xiao-Jiang Feng & Genyuan Li & Herschel A Rabitz, 2012. "Identifying Biological Network Structure, Predicting Network Behavior, and Classifying Network State With High Dimensional Model Representation (HDMR)," PLOS ONE, Public Library of Science, vol. 7(6), pages 1-19, June.
  10. Ruonan Wu & Michelle R. Davison & William C. Nelson & Montana L. Smith & Mary S. Lipton & Janet K. Jansson & Ryan S. McClure & Jason E. McDermott & Kirsten S. Hofmockel, 2023. "Hi-C metagenome sequencing reveals soil phage–host interactions," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
  11. Ambroise Jérôme & Robert Annie & Macq Benoit & Gala Jean-Luc, 2012. "Transcriptional Network Inference from Functional Similarity and Expression Data: A Global Supervised Approach," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 11(1), pages 1-24, January.
  12. Holger Weishaupt & Patrik Johansson & Christopher Engström & Sven Nelander & Sergei Silvestrov & Fredrik J Swartling, 2017. "Loss of Conservation of Graph Centralities in Reverse-engineered Transcriptional Regulatory Networks," Methodology and Computing in Applied Probability, Springer, vol. 19(4), pages 1089-1105, December.
  13. repec:plo:pcbi00:1004295 is not listed on IDEAS
  14. repec:jss:jstsof:37:i01 is not listed on IDEAS
  15. Kannan Venkateshan & Tegner Jesper, 2016. "Adaptive input data transformation for improved network reconstruction with information theoretic algorithms," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 15(6), pages 507-520, December.
  16. Hirose, Kei & Fujisawa, Hironori & Sese, Jun, 2017. "Robust sparse Gaussian graphical modeling," Journal of Multivariate Analysis, Elsevier, vol. 161(C), pages 172-190.
  17. Fei Liu & Shao-Wu Zhang & Wei-Feng Guo & Ze-Gang Wei & Luonan Chen, 2016. "Inference of Gene Regulatory Network Based on Local Bayesian Networks," PLOS Computational Biology, Public Library of Science, vol. 12(8), pages 1-17, August.
  18. repec:plo:pone00:0013080 is not listed on IDEAS
  19. Maghsoodi, Masoume, 2016. "A New Method to Build Gene Regulation Network Based on Fuzzy Hierarchical Clustering Methods," MPRA Paper 79743, University Library of Munich, Germany.
  20. Daniel E Carlin & Evan O Paull & Kiley Graim & Christopher K Wong & Adrian Bivol & Peter Ryabinin & Kyle Ellrott & Artem Sokolov & Joshua M Stuart, 2017. "Prophetic Granger Causality to infer gene regulatory networks," PLOS ONE, Public Library of Science, vol. 12(12), pages 1-21, December.
  21. Hossein Zare & Mostafa Kaveh & Arkady Khodursky, 2011. "Inferring a Transcriptional Regulatory Network from Gene Expression Data Using Nonlinear Manifold Embedding," PLOS ONE, Public Library of Science, vol. 6(8), pages 1-7, August.
  22. repec:plo:pcbi00:1005379 is not listed on IDEAS
  23. Tom Wilderjans & Dirk Depril & Iven Van Mechelen, 2013. "Additive Biclustering: A Comparison of One New and Two Existing ALS Algorithms," Journal of Classification, Springer;The Classification Society, vol. 30(1), pages 56-74, April.
  24. Ming Hu & Zhaohui S Qin, 2009. "Query Large Scale Microarray Compendium Datasets Using a Model-Based Bayesian Approach with Variable Selection," PLOS ONE, Public Library of Science, vol. 4(2), pages 1-11, February.
  25. Benafsh Husain & F Alex Feltus, 2019. "EdgeScaping: Mapping the spatial distribution of pairwise gene expression intensities," PLOS ONE, Public Library of Science, vol. 14(8), pages 1-15, August.
  26. Shuhei Kimura & Masanao Sato & Mariko Okada-Hatakeyama, 2013. "Inference of Vohradský's Models of Genetic Networks by Solving Two-Dimensional Function Optimization Problems," PLOS ONE, Public Library of Science, vol. 8(12), pages 1-11, December.
  27. Lulu Shang & Jennifer A Smith & Xiang Zhou, 2020. "Leveraging gene co-expression patterns to infer trait-relevant tissues in genome-wide association studies," PLOS Genetics, Public Library of Science, vol. 16(4), pages 1-30, April.
  28. repec:plo:pcbi00:1000340 is not listed on IDEAS
  29. Diambra, L., 2011. "Coarse-grain reconstruction of genetic networks from expression levels," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 390(11), pages 2198-2207.
  30. Zhen Yang & Yen‐Yi Ho, 2022. "Modeling dynamic correlation in zero‐inflated bivariate count data with applications to single‐cell RNA sequencing data," Biometrics, The International Biometric Society, vol. 78(2), pages 766-776, June.
  31. Marco Grimaldi & Roberto Visintainer & Giuseppe Jurman, 2011. "RegnANN: Reverse Engineering Gene Networks Using Artificial Neural Networks," PLOS ONE, Public Library of Science, vol. 6(12), pages 1-19, December.
  32. Scott Christley & Qing Nie & Xiaohui Xie, 2009. "Incorporating Existing Network Information into Gene Network Inference," PLOS ONE, Public Library of Science, vol. 4(8), pages 1-13, August.
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