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   https://doi.org/10.1038/s43586-021-00046-x  

   Garenne, David; Haines, Matthew C.; Romantseva, Eugenia F.; Freemont, Paul; Strychalski, Elizabeth A.; Noireaux, Vincent (December 2021, Nature Reviews Methods Primers)

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2. Hyperbolic geometry of gene expression

   https://doi.org/10.1016/j.isci.2021.102225  

   Zhou, Yuansheng; Sharpee, Tatyana O. (March 2021, iScience)

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3. Compensatory Evolution of Gene Expression

   https://doi.org/10.1016/j.tig.2019.09.008  

   Signor, Sarah A.; Nuzhdin, Sergey V. (December 2019, Trends in Genetics)
4. Differential Expression Gene Explorer (DrEdGE): a tool for generating interactive online visualizations of gene expression datasets

   https://doi.org/10.1093/bioinformatics/btz972  

   Tintori, Sophia C.; Golden, Patrick; Goldstein, Bob; Wren, ed., Jonathan (January 2020, Bioinformatics)

   Abstract SummaryDifferential Expression Gene Explorer (DrEdGE) is a web-based tool that guides genomicists through easily creating interactive online data visualizations, which colleagues can query according to their own conditions to discover genes, samples or patterns of interest. We demonstrate DrEdGE’s features with three example websites generated from publicly available datasets—human neuronal tissue, mouse embryonic tissue and Caenorhabditis elegans whole embryos. DrEdGE increases the utility of large genomics datasets by removing technical obstacles to independent exploration. Availability and implementationFreely available at http://dredge.bio.unc.edu. Supplementary informationSupplementary data are available at Bioinformatics online. 

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5. Single‐parent expression drives dynamic gene expression complementation in maize hybrids

   https://doi.org/10.1111/tpj.15042  

   Li, Zhi; Zhou, Peng; Della Coletta, Rafael; Zhang, Tifu; Brohammer, Alex B.; H. O’Connor, Christine; Vaillancourt, Brieanne; Lipzen, Anna; Daum, Chris; Barry, Kerrie; et al (November 2020, The Plant Journal)

   SUMMARY Single‐parent expression (SPE) is defined as gene expression in only one of the two parents. SPE can arise from differential expression between parental alleles, termed non‐presence/absence (non‐PAV) SPE, or from the physical absence of a gene in one parent, termed PAV SPE. We used transcriptome data of diverseZea mays(maize) inbreds and hybrids, including 401 samples from five different tissues, to test for differences between these types of SPE genes. Although commonly observed, SPE is highly genotype and tissue specific. A positive correlation was observed between the genetic distance of the two inbred parents and the number of SPE genes identified. Regulatory analysis showed that PAV SPE and non‐PAV SPE genes are mainly regulated byciseffects, with a small fraction undertransregulation. Polymorphic transposable element insertions in promoter sequences contributed to the high level ofcisregulation for PAV SPE and non‐PAV SPE genes. PAV SPE genes were more frequently expressed in hybrids than non‐PAV SPE genes. The expression of parentally silent alleles in hybrids of non‐PAV SPE genes was relatively rare but occurred in most hybrids. Non‐PAV SPE genes with expression of the silent allele in hybrids are more likely to exhibit above high parent expression level than hybrids that do not express the silent allele, leading to non‐additive expression. This study provides a comprehensive understanding of the nature of non‐PAV SPE and PAV SPE genes and their roles in gene expression complementation in maize hybrids. 

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