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

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Cited by:

  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. 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.
  11. 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.
  12. 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.
  13. 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.
  14. 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.
  15. 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.
  16. 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.
  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. 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.
  19. 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.
  20. 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.
  21. 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.
  22. 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.
  23. 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.
  24. 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.
  25. repec:jss:jstsof:37:i01 is not listed on IDEAS
  26. Hirose, Kei & Fujisawa, Hironori & Sese, Jun, 2017. "Robust sparse Gaussian graphical modeling," Journal of Multivariate Analysis, Elsevier, vol. 161(C), pages 172-190.
  27. 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.
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