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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 Lê Cao
Genome Res. March 5, 2026 ; Published in Advance March 5, 2026, doi:10.1101/gr.281171.125
...ran on a RStudio server allocated with four cores of Intel Xeon Gold 6254 @ 3.10GHz CPU. We did not perform parallel computing. Other acronyms: DEGs: differentially expressed genes. PKN: prior knowledge network. Cell-specific coexpression networks Genome Research 5 www..org information on TF...
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Research: Functional genomics analysis of developing zebrafish and human endoderm reveals highly conserved cis-regulatory modules acting during vertebrate organogenesis
- Daniela M. Riley,
- Randa Elsayed,
- Mark D. Walsh,
- Simaran Johal,
- Ying Lin,
- Harry Walton,
- Till Bretschneider,
- Sascha Ott,
- and Andrew C. Nelson
Genome Res. March 4, 2026 ; Published in Advance March 4, 2026, doi:10.1101/gr.280838.125
...and zebrafish endoderm, we used the genomic regions enrichment of annotations tool (GREAT) to perform functional and phenotypic annotation analyses on the common 1701 HCNEs (McLean et al. 2010). Annotation of putative target genes used the “basal plus extension” method in which each gene is assigned a basal...
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Perspective: Notable challenges posed by long-read sequencing for the study of transcriptional diversity and genome annotation
- Carolina Monzó,
- Adam Frankish,
- and Ana Conesa
Genome Res. April 2025 35: 583-592; Published in Advance March 3, 2025, doi:10.1101/gr.279865.124
...have the potential of discarding real biological TD from less abundant transcripts or those present in sample-specific conditions. Therefore, developing accurate algorithms to identify TD represents a new and important challenge for the computational biology and RNA communities.Genome annotation...
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Method: Evaluation of strategies for evidence-driven genome annotation using long-read RNA-seq
- Alejandro Paniagua,
- Cristina Agustín-García,
- Francisco J. Pardo-Palacios,
- Thomas Brown,
- Maite De Maria,
- Nancy D. Denslow,
- Camila J. Mazzoni,
- and Ana Conesa
Genome Res. April 2025 35: 1053-1064; Published in Advance December 23, 2024, doi:10.1101/gr.279864.124
..., Spanish National Research Council, Paterna 46980, Spain; 2Department of Computer Science, Universitat de València, Valencia 46100, Spain; 3Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, 10315 Berlin, Germany; 4Berlin Center for Genomics in Biodiversity Research...
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Method: Integration of transcriptomics and long-read genomics prioritizes structural variants in rare disease
- Tanner D. Jensen,
- Bohan Ni,
- Chloe M. Reuter,
- John E. Gorzynski,
- Sarah Fazal,
- Devon Bonner,
- Rachel A. Ungar,
- Pagé C. Goddard,
- Archana Raja,
- Euan A. Ashley,
- Jonathan A. Bernstein,
- Stephan Zuchner,
- Undiagnosed Diseases Network,
- Michael D. Greicius,
- Stephen B. Montgomery,
- Michael C. Schatz,
- Matthew T. Wheeler,
- and Alexis Battle
Genome Res. April 2025 35: 914-928; Published in Advance March 20, 2025, doi:10.1101/gr.279323.124
...-specific genomic annotations, which significantly outperforms baseline models that do not incorporate expression data. Watershed-SV identified a median of eight high-confidence functional SVs per UDN . Notably, this included compound heterozygous deletions in FAM177A1 shared by two siblings, which were likely...
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Method: GeneMark-ETP significantly improves the accuracy of automatic annotation of large eukaryotic genomes
- Tomáš Brůna,
- Alexandre Lomsadze,
- and Mark Borodovsky
Genome Res. May 2024 34: 757-768; Published in Advance June 12, 2024, doi:10.1101/gr.278373.123
...Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA; 3School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA ↵4 These authors contributed equally to this work. ↵5 Present address: U.S. Department of Energy, Joint Genome Institute...
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Mini-Review: Large-scale genomic analysis of the domestic dog informs biological discovery
- Reuben M. Buckley and
- Elaine A. Ostrander
Genome Res. June 2024 34: 811-821; Published in Advance July 2, 2024, doi:10.1101/gr.278569.123
...drive rare variant discovery and assess the geographic distribution of canine diversity, which identifies Asia as a major source of missing variation. Finally, we review recent comparative genomic analyses that will facilitate annotation of the noncoding in dogs.The domestic dog has increasingly been...
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Perspective: Applications of single-cell genomics and computational strategies to study common disease and population-level variation
- Benjamin J. Auerbach,
- Jian Hu,
- Muredach P. Reilly,
- and Mingyao Li
Genome Res. October 2021 31: 1728-1741; doi:10.1101/gr.275430.121
...Benjamin J. Auerbach1, Jian Hu2, Muredach P. Reilly3 and Mingyao Li2 1Graduate Group in Genomics and Computational Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA; 2Department of Biostatistics, Epidemiology and Informatics, University...
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Method: AIDE: annotation-assisted isoform discovery with high precision
- Wei Vivian Li,
- Shan Li,
- Xin Tong,
- Ling Deng,
- Hubing Shi,
- and Jingyi Jessica Li
Genome Res. December 2019 29: 2056-2072; Published in Advance November 6, 2019, doi:10.1101/gr.251108.119
...[Zerbino et al. 2018], GENCODE [Harrow et al. 2012], and the UCSC Genome Browser [Rosenbloom et al. 2015]) to aid isoform discovery. Existing efforts include two approaches. In the first approach, methods extract the coordinates of gene and exon boundaries, that is, known splicing sites, from annotations...
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Method: BRAKER3: Fully automated genome annotation using RNA-seq and protein evidence with GeneMark-ETP, AUGUSTUS, and TSEBRA
- Lars Gabriel,
- Tomáš Brůna,
- Katharina J. Hoff,
- Matthis Ebel,
- Alexandre Lomsadze,
- Mark Borodovsky,
- and Mario Stanke
Genome Res. May 2024 34: 769-777; Published in Advance June 12, 2024, doi:10.1101/gr.278090.123
...BRAKER3: Fully automated annotation using RNA-seq and protein evidence with GeneMark-ETP, AUGUSTUS, and TSEBRA Lars Gabriel1,2, Tomáš Brůna3, Katharina J. Hoff1,2, Matthis Ebel1,2, Alexandre Lomsadze4, Mark Borodovsky4,5,6 and Mario Stanke1,2,6 1Institute of Mathematics and Computer Science...
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