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Review: Understanding isoform expression by pairing long-read sequencing with single-cell and spatial transcriptomics
- Natan Belchikov,
- Justine Hsu,
- Xiang Jennie Li,
- Julien Jarroux,
- Wen Hu,
- Anoushka Joglekar,
- and Hagen U. Tilgner
Genome Res. November 2024 34: 1735-1746; doi:10.1101/gr.279640.124
...of single-cell technology with the long-range information offered by long-read sequencing has resulted in new insights into the transcriptomes of disease-relevant systems with heterogeneous cell populations. In cancer, transcriptomic variation among cells can be layered on top of genomic variation. Short...
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Method: A Bayesian framework for inferring dynamic intercellular interactions from time-series single-cell data
- Cameron Park,
- Shouvik Mani,
- Nicolas Beltran-Velez,
- Katie Maurer,
- Teddy Huang,
- Shuqiang Li,
- Satyen Gohil,
- Kenneth J. Livak,
- David A. Knowles,
- Catherine J. Wu,
- and Elham Azizi
Genome Res. September 2024 34: 1384-1396; Published in Advance September 5, 2024, doi:10.1101/gr.279126.124
...on databases compiled from limited contexts. We introduce DIISCO, a Bayesian framework designed to characterize the temporal dynamics of cellular interactions using single-cell RNA-sequencing data from multiple time points. Our method utilizes structured Gaussian process regression to unveil time...
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Research: Genetic control of the dynamic transcriptional response to immune stimuli and glucocorticoids at single-cell resolution
- Justyna A. Resztak,
- Julong Wei,
- Samuele Zilioli,
- Edward Sendler,
- Adnan Alazizi,
- Henriette E. Mair-Meijers,
- Peijun Wu,
- Xiaoquan Wen,
- Richard B. Slatcher,
- Xiang Zhou,
- Francesca Luca,
- and Roger Pique-Regi
Genome Res. June 2023 33: 839-856; Published in Advance July 13, 2023, doi:10.1101/gr.276765.122
...to this work. Corresponding authors: fluca@wayne.edu, rpique@wayne.eduAbstractSynthetic glucocorticoids, such as dexamethasone, have been used as a treatment for many immune conditions, such as asthma and, more recently, severe COVID-19. Single-cell data can capture more fine-grained details on transcriptional...
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Method: Ultra-long sequencing for contiguous haplotype resolution of the human immunoglobulin heavy-chain locus
- Mari B. Gornitzka,
- Egil Røsjø,
- Uddalok Jana,
- Easton E. Ford,
- Alan Tourancheau,
- William D. Lees,
- Zachary Vanwinkle,
- Melissa L. Smith,
- Corey T. Watson,
- and Andreas Lossius
Genome Res. October 2025 35: 2240-2251; Published in Advance August 21, 2025, doi:10.1101/gr.280400.125
...±1 bp of homopolymers ≥5 bp (green), and indels within homopolymers or short tandem repeats of dinucleotide of seven or more repeats (orange).Benchmarking with HG002To further evaluate the performance of our long-read ONT method, we sequenced and assembled the IGH locus for the Genome in a Bottle...
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Method: Systematic identification of interchromosomal interaction networks supports the existence of specialized RNA factories
- Borislav Hrisimirov Hristov,
- William Stafford Noble,
- and Alessandro Bertero
Genome Res. October 2024 34: 1610-1623; Published in Advance September 25, 2024, doi:10.1101/gr.278327.123
...Borislav Hrisimirov Hristov1, William Stafford Noble1,2 and Alessandro Bertero3 1Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA; 2Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, Washington 98195, USA; 3Molecular...
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Resource: Indels, structural variation, and recombination drive genomic diversity in Plasmodium falciparum
- Alistair Miles,
- Zamin Iqbal,
- Paul Vauterin,
- Richard Pearson,
- Susana Campino,
- Michel Theron,
- Kelda Gould,
- Daniel Mead,
- Eleanor Drury,
- John O'Brien,
- Valentin Ruano Rubio,
- Bronwyn MacInnis,
- Jonathan Mwangi,
- Upeka Samarakoon,
- Lisa Ranford-Cartwright,
- Michael Ferdig,
- Karen Hayton,
- Xin-zhuan Su,
- Thomas Wellems,
- Julian Rayner,
- Gil McVean,
- and Dominic Kwiatkowski
Genome Res. September 2016 26: 1288-1299; Published in Advance August 16, 2016, doi:10.1101/gr.203711.115
...Indels, structural variation, and recombination drive genomic diversity in Plasmodium falciparum Alistair Miles 1 , 2 , Zamin Iqbal 3 , Paul Vauterin 1 , Richard Pearson 1 , 2 , Susana Campino 2 , Michel Theron 2 , Kelda...
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Method: Sasquatch: predicting the impact of regulatory SNPs on transcription factor binding from cell- and tissue-specific DNase footprints
- Ron Schwessinger,
- Maria C. Suciu,
- Simon J. McGowan,
- Jelena Telenius,
- Stephen Taylor,
- Doug R. Higgs,
- and Jim R. Hughes
Genome Res. October 2017 27: 1730-1742; Published in Advance September 13, 2017, doi:10.1101/gr.220202.117
...number (2000–3000) and cannot cover the complete regulatory landscape of even a single cell type. Similarly, due to the current incomplete understanding of the sequences used by transcription factors across human development, any dependence on PWM collections will necessarily be skewed and contain many...
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RESEARCH: Gene Discovery by EST Sequencing in Toxoplasma gondiiReveals Sequences Restricted to the Apicomplexa
- James W. Ajioka,
- John C. Boothroyd,
- Brian P. Brunk,
- Adrian Hehl,
- Ledeana Hillier,
- Ian D. Manger,
- Marco Marra,
- G. Christian Overton,
- David S. Roos,
- Kiew-Lian Wan,
- Robert Waterston,
- and L. David Sibley
Genome Res. January 1, 1998 8: 18-28; doi:10.1101/gr.8.1.18
...only distantly to model single-celled organisms ( Gajadhar et al. 1991 ). The phylum Apicomplexa contains numerous parasites of medical and veterinary significance, including Plasmodium (the causative agent of malaria), Eimeria (the causative agent of coccidiosis in domestic animals...

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