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Genome Biology|March 8, 2022
TraSig: inferring cell-cell interactions from pseudotime ordering of scRNA-Seq dataDongshunyi Li, Jeremy J Velazquez, Jun Ding, et al.Genome Research|January 11, 2018
Reconstructing differentiation networks and their regulation from time series single-cell expression dataJun Ding, Bruce J Aronow, Naftali Kaminski, et al.Genome Biology|December 11, 2020
GCNG: graph convolutional networks for inferring gene interaction from spatial transcriptomics dataYe Yuan, Ziv Bar-JosephBriefings in Bioinformatics|April 20, 2021
Deep learning of gene relationships from single cell time-course expression dataYe Yuan, Ziv Bar-JosephMolecular Systems Biology|November 10, 2011
Algorithms in nature: the convergence of systems biology and computational thinkingSaket Navlakha, Ziv Bar-JosephMethods in Molecular Biology (Clifton, N.J.)|August 4, 2015
The SDREM Method for Reconstructing Signaling and Regulatory Response Networks: Applications for Studying Disease ProgressionAnthony Gitter, Ziv Bar-JosephIEEE/ACM Transactions on Computational Biology and Bioinformatics|May 3, 2008
Extracting dynamics from static cancer expression dataAnupam Gupta, Ziv Bar-JosephBioinformatics (Oxford, England)|July 2, 2013
Identifying proteins controlling key disease signaling pathwaysAnthony Gitter, Ziv Bar-JosephJournal of Computational Biology : a Journal of Computational Molecular Cell Biology|April 7, 2015
cDREM: inferring dynamic combinatorial gene regulationAaron Wise, Ziv Bar-JosephPageof 385