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Searching journal content for articles similar to Cai et al. 34 (4): 642.

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  1. LETTER: An Arabidopsis gene network based on the graphical Gaussian model
    • Shisong Ma,
    • Qingqiu Gong,
    • and Hans J. Bohnert
    Genome Res. November 2007 17: 1614-1625; Published in Advance October 5, 2007, doi:10.1101/gr.6911207
    ...as subnetworks and added novel components to known edges. Finally, the network reconciled individual subnetworks in a topology joined at the whole-genome level and provided a general framework that can instruct future studies on plant metabolism and stress responses. The network model is included. Footnotes...
  2. Perspective: Advances in spatial transcriptomic data analysis
    • Ruben Dries,
    • Jiaji Chen,
    • Natalie del Rossi,
    • Mohammed Muzamil Khan,
    • Adriana Sistig,
    • and Guo-Cheng Yuan
    Genome Res. October 2021 31: 1706-1718; doi:10.1101/gr.275224.121
    ..., Stegle O. 2018. Multi-omics factor analysis: a framework for unsupervised integration of multi-omics data sets. Mol Syst Biol 14: e8124. doi:10.15252/msb.20178124 ↵Armingol E, Officer A, Harismendy O, Lewis NE. 2021. Deciphering cell–cell interactions and communication from gene expression. Nat Rev Genet...
    OPEN ACCESS ARTICLE
  3. Method: Efficient computation of Faith's phylogenetic diversity with applications in characterizing microbiomes
    • George Armstrong,
    • Kalen Cantrell,
    • Shi Huang,
    • Daniel McDonald,
    • Niina Haiminen,
    • Anna Paola Carrieri,
    • Qiyun Zhu,
    • Antonio Gonzalez,
    • Imran McGrath,
    • Kristen L. Beck,
    • Daniel Hakim,
    • Aki S. Havulinna,
    • Guillaume Méric,
    • Teemu Niiranen,
    • Leo Lahti,
    • Veikko Salomaa,
    • Mohit Jain,
    • Michael Inouye,
    • Austin D. Swafford,
    • Ho-Cheol Kim,
    • Laxmi Parida,
    • Yoshiki Vázquez-Baeza,
    • and Rob Knight
    Genome Res. November 2021 31: 2131-2137; Published in Advance September 3, 2021, doi:10.1101/gr.275777.121
    ..., Estaki M, Haiminen N, et al. 2021. EMPress enables tree-guided, interactive, and exploratory analyses of multi-omic data sets. mSystems 6: e01216-20. doi:10.1128/mSystems.01216-20 ↵Cordova J, Navarro G. 2016. Simple and efficient fully-functional succinct trees. Theor 656: 135–145. doi:10.1016/j.tcs.2016...
  4. Method: A Bayesian inference transcription factor activity model for the analysis of single-cell transcriptomes
    • Shang Gao,
    • Yang Dai,
    • and Jalees Rehman
    Genome Res. July 2021 31: 1296-1311; Published in Advance June 30, 2021, doi:10.1101/gr.265595.120
    ...to study cellular heterogeneity. One of the challenges in scRNA-seq data analysis is integrating different types of biological data to consistently recognize discrete biological functions and regulatory mechanisms of cells, such as transcription factor activities and gene regulatory networks in distinct...
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