STEM: a tool for the analysis of short time series gene expression data von Ernst, Jason, Bar-Joseph, Ziv

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Algorithms in nature: the convergence of systems biology and computational thinking von Navlakha, Saket, Bar‐Joseph, Ziv

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Deep learning for inferring gene relationships from single-cell expression data von Yuan, Ye, Bar-Joseph, Ziv

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GCNG: graph convolutional networks for inferring gene interaction from spatial transcriptomics data von Yuan, Ye, Bar-Joseph, Ziv

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Construction of integrated microRNA and mRNA immune cell signatures to predict survival of patients with breast and ovarian cancer von Ray, Mondira, Ruffalo, Matthew M., Bar‐Joseph, Ziv

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Evaluation of different biological data and computational classification methods for use in protein interaction prediction von Qi, Yanjun, Bar-Joseph, Ziv, Klein-Seetharaman, Judith

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Transcriptional regulatory model of fibrosis progression in the human lung von McDonough, John E, Ahangari, Farida, Li, Qin, Jain, Siddhartha, Verleden, Stijn E, Herazo-Maya, Jose, Vukmirovic, Milica, DeIuliis, Giuseppe, Tzouvelekis, Argyrios, Tanabe, Naoya, Chu, Fanny, Yan, Xiting, Verschakelen, Johny, Homer, Robert J, Manatakis, Dimitris V, Zhang, Junke, Ding, Jun, Maes, Karen, De Sadeleer, Laurens, Vos, Robin, Neyrinck, Arne, Benos, Panayiotis V, Bar-Joseph, Ziv, Tantin, Dean, Hogg, James C, Vanaudenaerde, Bart M, Wuyts, Wim A, Kaminski, Naftali

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CINS: Cell Interaction Network inference from Single cell expression data von Yuan, Ye, Cosme, Jr, Carlos, Adams, Taylor Sterling, Schupp, Jonas, Sakamoto, Koji, Xylourgidis, Nikos, Ruffalo, Matthew, Li, Jiachen, Kaminski, Naftali, Bar-Joseph, Ziv

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Single-cell lineage tracing by integrating CRISPR-Cas9 mutations with transcriptomic data von Zafar, Hamim, Lin, Chieh, Bar-Joseph, Ziv

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Tradeoffs between Dense and Replicate Sampling Strategies for High-Throughput Time Series Experiments von Sefer, Emre, Kleyman, Michael, Bar-Joseph, Ziv

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Analyzing time series gene expression data von Bar-Joseph, Ziv

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SCODE: an efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation von Matsumoto, Hirotaka, Kiryu, Hisanori, Furusawa, Chikara, Ko, Minoru S H, Ko, Shigeru B H, Gouda, Norio, Hayashi, Tetsutaro, Nikaido, Itoshi

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scSTEM: clustering pseudotime ordered single-cell data von Song, Qi, Wang, Jingtao, Bar-Joseph, Ziv

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Iterative point set registration for aligning scRNA-seq data von Alavi, Amir, Bar-Joseph, Ziv

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A transcription factor hierarchy defines an environmental stress response network von Song, Liang, Huang, Shao-shan Carol, Wise, Aaron, Castanon, Rosa, Nery, Joseph R., Chen, Huaming, Watanabe, Marina, Thomas, Jerushah, Bar-Joseph, Ziv, Ecker, Joseph R.

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Backup in gene regulatory networks explains differences between binding and knockout results von Gitter, Anthony, Siegfried, Zehava, Klutstein, Michael, Fornes, Oriol, Oliva, Baldo, Simon, Itamar, Bar‐Joseph, Ziv

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Protein interaction disruption in cancer von Ruffalo, Matthew, Bar-Joseph, Ziv

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A web server for comparative analysis of single-cell RNA-seq data von Alavi, Amir, Ruffalo, Matthew, Parvangada, Aiyappa, Huang, Zhilin, Bar-Joseph, Ziv

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Inferring TF activation order in time series scRNA-Seq studies von Lin, Chieh, Ding, Jun, Bar-Joseph, Ziv

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Membrane marker selection for segmenting single cell spatial proteomics data von Dayao, Monica T., Brusko, Maigan, Wasserfall, Clive, Bar-Joseph, Ziv

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