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Research: Global identification of mammalian host and nested gene pairs reveal tissue-specific transcriptional interplay
- Bertille Montibus,
- James A. Cain,
- Rocio T. Martinez-Nunez,
- and Rebecca J. Oakey
Genome Res. December 2024 34: 2163-2175; Published in Advance November 22, 2024, doi:10.1101/gr.279430.124
...a filter of a minimum of 1% of the cells of the data set which had to have robust expression for both the host and the nested gene, selecting 34 pairs. Finally, expression above the threshold for both the host and the nested gene allows the identification of cells which coexpress the pair. Expression above...
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Method: Accurate fusion transcript identification from long- and short-read isoform sequencing at bulk or single-cell resolution
- Qian Qin,
- Victoria Popic,
- Kirsty Wienand,
- Houlin Yu,
- Emily White,
- Akanksha Khorgade,
- Asa Shin,
- Christophe Georgescu,
- Catarina D. Campbell,
- Arthur Dondi,
- Niko Beerenwinkel,
- Francisca Vazquez,
- Aziz M. Al'Khafaji,
- and Brian J. Haas
Genome Res. April 2025 35: 967-986; Published in Advance March 14, 2025, doi:10.1101/gr.279200.124
...-read fusion identificationIn exploring the fusion isoforms identified by CTAT-LR-Fusion using combined long and short reads we found 213 fusion genes with 288 fusion splicing isoforms having both short- and long-read alignments together supporting each of the fusion transcript breakpoints. Fusion expression...
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Method: Subgenomic RNA identification in SARS-CoV-2 genomic sequencing data
- Matthew D. Parker,
- Benjamin B. Lindsey,
- Shay Leary,
- Silvana Gaudieri,
- Abha Chopra,
- Matthew Wyles,
- Adrienn Angyal,
- Luke R. Green,
- Paul Parsons,
- Rachel M. Tucker,
- Rebecca Brown,
- Danielle Groves,
- Katie Johnson,
- Laura Carrilero,
- Joe Heffer,
- David G. Partridge,
- Cariad Evans,
- Mohammad Raza,
- Alexander J. Keeley,
- Nikki Smith,
- Ana Da Silva Filipe,
- James G. Shepherd,
- Chris Davis,
- Sahan Bennett,
- Vattipally B. Sreenu,
- Alain Kohl,
- Elihu Aranday-Cortes,
- Lily Tong,
- Jenna Nichols,
- Emma C. Thomson,
- The COVID-19 Genomics UK (COG-UK) Consortium,
- Dennis Wang,
- Simon Mallal,
- and Thushan I. de Silva
Genome Res. April 2021 31: 645-658; Published in Advance March 15, 2021, doi:10.1101/gr.268110.120
...it to sequencing data from an in vitro infection time course using VeroE6 cells that were either WT, overexpressing ACE2, or overexpressing ACE2 and TMPRSS2 (Hoffmann et al. 2020). ACE2 and TMPRSS2 coexpressing cells have the most obviously altered sgRNA kinetics, with the peak level of sgRNA occurring at 48 h...
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Method: Scalable cell-specific coexpression networks for granular regulatory pattern discovery with NeighbourNet
- Yidi Deng,
- Jiadong Mao,
- Jarny Choi,
- and Kim-Anh Le Cao
Genome Res. March 5, 2026 gr.281171.125; Published in Advance March 5, 2026, doi:10.1101/gr.281171.125
...’s effectiveness through three case studies on transcription factor activity prediction, 29 early haematopoiesis, and tumour microenvironments. Provided as an R package, NNet offers 30 a novel framework for exploring cellular variation in coexpression and integrates seamlessly 31 with existing single-cell analysis...
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Method: Identification of phenotype-specific networks from paired gene expression–cell shape imaging data
- Charlie George Barker,
- Eirini Petsalaki,
- Girolamo Giudice,
- Julia Sero,
- Emmanuel Nsa Ekpenyong,
- Chris Bakal,
- and Evangelia Petsalaki
Genome Res. April 2022 32: 750-765; Published in Advance February 23, 2022, doi:10.1101/gr.276059.121
...for further experimental studies to understand and therapeutically target the links between cell shape, cell signaling, and gene regulation in the context of breast cancer.MethodsWGCNA analysisUsing weighted correlation network analysis, we performed coexpression module identification using the R package...
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Method: Targeted single-cell RNA sequencing of transcription factors enhances the identification of cell types and trajectories
- Alexandra Pokhilko,
- Adam E. Handel,
- Fabiola Curion,
- Viola Volpato,
- Emma S. Whiteley,
- Sunniva Bøstrand,
- Sarah E. Newey,
- Colin J. Akerman,
- Caleb Webber,
- Michael B. Clark,
- Rory Bowden,
- and M. Zameel Cader
Genome Res. June 2021 31: 1069-1081; Published in Advance May 19, 2021, doi:10.1101/gr.273961.120
...-capture-imputed networks. (E) Enrichment of the cluster subnetworks in TF PPIs (TF networks), for pre-capture (PRE) and imputed (POST) networks. The circle sizes show the number of genes in each TF PPI term.TF capture facilitates the identification of TFs associated with developmental trajectoriesTo explore...
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Research: Identification of a primitive intestinal transcription factor network shared between esophageal adenocarcinoma and its precancerous precursor state
- Connor Rogerson,
- Edward Britton,
- Sarah Withey,
- Neil Hanley,
- Yeng S. Ang,
- and Andrew D. Sharrocks
Genome Res. May 2019 29: 723-736; Published in Advance April 8, 2019, doi:10.1101/gr.243345.118
...other germ layers, for example, brain (ectoderm) or heart ventricle, adrenal, or kidney (mesoderm) (Supplemental Fig. S3). However, strong coexpression was not observed in any single tissue type. To explore this further, we integrated the human embryonic data with RNA-seq from differentiating human...
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Research: The identification and functional annotation of RNA structures conserved in vertebrates
- Stefan E. Seemann,
- Aashiq H. Mirza,
- Claus Hansen,
- Claus H. Bang-Berthelsen,
- Christian Garde,
- Mikkel Christensen-Dalsgaard,
- Elfar Torarinsson,
- Zizhen Yao,
- Christopher T. Workman,
- Flemming Pociot,
- Henrik Nielsen,
- Niels Tommerup,
- Walter L. Ruzzo,
- and Jan Gorodkin
Genome Res. August 2017 27: 1371-1383; Published in Advance May 9, 2017, doi:10.1101/gr.208652.116
...and sequencebased alignments (Managadze et al. 2011) have indicated that RNA secondary structures are depleted in lncRNAs (Ulitsky and Bartel 2013). The low sequence conservation of most lncRNAs, while complicating identification of CRSs, does not preclude their existence, such as in telomerase RNA (structurally...
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Method: SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification
- Manuel Tardaguila,
- Lorena de la Fuente,
- Cristina Marti,
- Cécile Pereira,
- Francisco Jose Pardo-Palacios,
- Hector del Risco,
- Marc Ferrell,
- Maravillas Mellado,
- Marissa Macchietto,
- Kenneth Verheggen,
- Mariola Edelmann,
- Iakes Ezkurdia,
- Jesus Vazquez,
- Michael Tress,
- Ali Mortazavi,
- Lennart Martens,
- Susana Rodriguez-Navarro,
- Victoria Moreno-Manzano,
- and Ana Conesa
Genome Res. March 2018 28: 396-411; Published in Advance February 9, 2018, doi:10.1101/gr.222976.117
...for the identification of AS events such as exon skipping or intron retention and have established the involvement of AS in many biological processes. However, both technologies have serious limitations for the reconstruction of the actual expressed transcripts, as short reads break the continuity of the transcript...
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Resource: Interspecies systems biology links bacterial metabolic pathways to nematode gene expression, chemotaxis behavior, and survival
- Marina Athanasouli,
- Tobias Loschko,
- and Christian Rödelsperger
Genome Res. October 2025 35: 2363-2374; Published in Advance August 5, 2025, doi:10.1101/gr.280848.125
...coexpression modules with differential responses to environmental microbiota. Third, we link the microbial and host transcriptome data by predicting a global map of more than 2800 metabolic interactions. These interactions represent statistical associations between variation in bacterial metabolic potential...

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