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Resource: Identification of protein features encoded by alternative exons using Exon Ontology
- Léon-Charles Tranchevent,
- Fabien Aubé,
- Louis Dulaurier,
- Clara Benoit-Pilven,
- Amandine Rey,
- Arnaud Poret,
- Emilie Chautard,
- Hussein Mortada,
- François-Olivier Desmet,
- Fatima Zahra Chakrama,
- Maira Alejandra Moreno-Garcia,
- Evelyne Goillot,
- Stéphane Janczarski,
- Franck Mortreux,
- Cyril F. Bourgeois,
- and Didier Auboeuf
Genome Res. June 2017 27: 1087-1097; Published in Advance April 18, 2017, doi:10.1101/gr.212696.116
...,C). These include protein domains with catalytic, binding, receptor, and transporter activities and protein regions containing subcellular localization signals, structural features, and experimentally validated post-translational modifications (PTMs). Each class of protein features was next divided into categories...
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Methods: Automatic analysis of dividing cells in live cell movies to detect mitotic delays and correlate phenotypes in time
- Nathalie Harder,
- Felipe Mora-Bermúdez,
- William J. Godinez,
- Annelie Wünsche,
- Roland Eils,
- Jan Ellenberg,
- and Karl Rohr
Genome Res. November 2009 19: 2113-2124; Published in Advance October 1, 2009, doi:10.1101/gr.092494.109
...migration dynamics (e.g., Chen et al. 2009). Automated classification methods have also been used on static images to distinguish different phenotype classes, providing information on the structure and location of subcellular phenotypes at a single cell level (e.g., Conrad et al. 2004; Huang and Murphy 2004...
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Methods: Identification of novel mammalian growth regulatory factors by genome-scale quantitative image analysis
- Josephine N. Harada,
- Kristen E. Bower,
- Anthony P. Orth,
- Scott Callaway,
- Christian G. Nelson,
- Casey Laris,
- John B. Hogenesch,
- Peter K. Vogt,
- and Sumit K. Chanda
Genome Res. August 2005 15: 1136-1144; Published in Advance July 15, 2005, doi:10.1101/gr.3889305
...in sensitivity, as well as rare-event detection. Furthermore, this technology can uniquely enable the quantitative analysis of certain discrete molecular phenotypes at the level of an individual cell, such as changes in subcellular localization, morphological alterations, cellular migration, or cytoskeletal...
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Method: Integration of hyperspectral imaging and transcriptomics from individual cells with SpectralSeq
- Yike Xie,
- Abbas Habibalahi,
- Ayad G. Anwer,
- Kanu Wahi,
- Jacqueline Bailey,
- Francis Lin,
- Catherine Gatt,
- Emma M.V. Johansson,
- Tatyana Chtanova,
- Jeff Holst,
- Ewa Goldys,
- and Fabio Zanini
Genome Res. August 2025 35: 1809-1820; Published in Advance July 8, 2025, doi:10.1101/gr.280014.124
...cytometabolic heterogeneity (Gosnell et al. 2016b; Campbell et al. 2019; Bertoldo et al. 2020). This technique can assign each cell multiple features related to morphology, spectral profile, and combinations of the two (e.g., spectral features with a specific subcellular localization). Hyperspectral data...
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Research: Single-cell spatial transcriptomics reveals a dystrophic trajectory following a developmental bifurcation of myoblast cell fates in facioscapulohumeral muscular dystrophy
- Lujia Chen,
- Xiangduo Kong,
- Kevin G. Johnston,
- Ali Mortazavi,
- Todd C. Holmes,
- Zhiqun Tan,
- Kyoko Yokomori,
- and Xiangmin Xu
Genome Res. May 2024 34: 665-679; Published in Advance May 22, 2024, doi:10.1101/gr.278717.123
...profiling of RNA transcripts at a subcellular resolution. We simultaneously examined spatial distributions of 140 genes, including 24 direct DUX4 targets, in in vitro differentiated myotubes and unfused mononuclear cells (MNCs) of control, isogenic D4Z4 contraction mutant and FSHD patient samples, as well...
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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
...in a clear visual improvement of the vertical alignment of the spatial expression data (Fig. 2B).Both FISH- and ISS-based techniques provide single-cell or even subcellular resolution; however, this depends on proper identification of cell morphology. Tracing the cell boundaries—and other cellular structures...
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Method: Pooled protein tagging, cellular imaging, and in situ sequencing for monitoring drug action in real time
- Andreas Reicher,
- Anna Koren,
- and Stefan Kubicek
Genome Res. December 2020 30: 1846-1855; Published in Advance November 17, 2020, doi:10.1101/gr.261503.120
...of Sciences, 1090 Vienna, Austria Corresponding author: skubicek@cemm.oeaw.ac.atAbstractThe levels and subcellular localizations of proteins regulate critical aspects of many cellular processes and can become targets of therapeutic intervention. However, high-throughput methods for the discovery of proteins...
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Method: Spatially resolved whole transcriptome profiling in human and mouse tissue using Digital Spatial Profiling
- Stephanie M. Zimmerman,
- Robin Fropf,
- Bridget R. Kulasekara,
- Maddy Griswold,
- Oliver Appelbe,
- Arya Bahrami,
- Rich Boykin,
- Derek L. Buhr,
- Kit Fuhrman,
- Margaret L. Hoang,
- Quoc Huynh,
- Lesley Isgur,
- Andrew Klock,
- Alecksandr Kutchma,
- Alexa E. Lasley,
- Yan Liang,
- Jill McKay-Fleisch,
- Jeffrey S. Nelson,
- Karen Nguyen,
- Erin Piazza,
- Aric Rininger,
- Daniel R. Zollinger,
- Michael Rhodes,
- and Joseph M. Beechem
Genome Res. October 2022 32: 1892-1905; Published in Advance September 13, 2022, doi:10.1101/gr.276206.121
...fluorescence in situ hybridization (seqFISH) (Chen et al. 2015; Lee et al. 2015; Xia et al. 2019), use rounds of sequential hybridization and imaging to resolve transcripts at single-cell or subcellular resolution. Some imaging methods have shown detection of up to 10,000 targets, but most experiments have...
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Research: A genome-wide long noncoding RNA CRISPRi screen identifies PRANCR as a novel regulator of epidermal homeostasis
- Pengfei Cai,
- Auke B.C. Otten,
- Binbin Cheng,
- Mitsuhiro A. Ishii,
- Wen Zhang,
- Beibei Huang,
- Kun Qu,
- and Bryan K. Sun
Genome Res. January 2020 30: 22-34; Published in Advance December 4, 2019, doi:10.1101/gr.251561.119
...) and are essential to epidermal development (Ivanova et al. 2005). To determine whether PRANCR displayed similar localization, subcellular fractionation was performed, which confirmed the enrichment of PRANCR transcripts in the nucleus (Fig. 5B). Next, we specifically examined the expression of E2F target genes...
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Method: Phenotypic profiling of the human genome reveals gene products involved in plasma membrane targeting of SRC kinases
- Julia Ritzerfeld,
- Steffen Remmele,
- Tao Wang,
- Koen Temmerman,
- Britta Brügger,
- Sabine Wegehingel,
- Stella Tournaviti,
- Jeroen R.P.M. Strating,
- Felix T. Wieland,
- Beate Neumann,
- Jan Ellenberg,
- Chris Lawerenz,
- Jürgen Hesser,
- Holger Erfle,
- Rainer Pepperkok,
- and Walter Nickel
Genome Res. November 2011 21: 1955-1968; Published in Advance July 27, 2011, doi:10.1101/gr.116087.110
...GFP fusion proteins containing either wild-type or mutant forms of the SH4 domains of either HASPB or YES1 were induced for reporter protein expression and subjected to live cell confocal microscopy to determine the subcellular localization of the SH4 fusion proteins. (B) Stable HeLa cells expressing...

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