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Method: Combining DNA and protein alignments to improve genome annotation with LiftOn
- Kuan-Hao Chao,
- Jakob M. Heinz,
- Celine Hoh,
- Alan Mao,
- Alaina Shumate,
- Mihaela Pertea,
- and Steven L. Salzberg
Genome Res. February 2025 35: 311-325; Published in Advance December 27, 2024, doi:10.1101/gr.279620.124
...and protein sequence alignment to generate protein-coding gene annotations that maximize similarity to the reference proteins; (2) it checks alternative ORFs for truncated proteins to identify the ORF that yields the longest match to the reference protein; (3) similarly to Liftoff, it finds extra copies...
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Mini-Review: Evolution of genome-wide methylation profiling technologies
- Carolina Montano and
- Winston Timp
Genome Res. April 2025 35: 572-582; doi:10.1101/gr.278407.123
..., Gendron TF, Prudencio M, McLaughlin IJ, Bowman B, Seetin M, DeJesus-Hernandez M, et al. 2018. Long-read sequencing across the C9orf72 ‘GGGGCC’ repeat expansion: implications for clinical use and genetic discovery efforts in human disease. Mol Neurodegener 13: 46. doi:10.1186/s13024-018-0274-4 ↵Eggermann T...
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Resource: CGC1, a new reference genome for Caenorhabditis elegans
- Kazuki Ichikawa,
- Massa J. Shoura,
- Karen L. Artiles,
- Dae-Eun Jeong,
- Chie Owa,
- Haruka Kobayashi,
- Yoshihiko Suzuki,
- Manami Kanamori,
- Yu Toyoshima,
- Yuichi Iino,
- Ann E. Rougvie,
- Lamia Wahba,
- Andrew Z. Fire,
- Erich M. Schwarz,
- and Shinichi Morishita
Genome Res. August 2025 35: 1902-1918; Published in Advance July 15, 2025, doi:10.1101/gr.280274.124
.... An independent assembly of the 5S rDNA locus with Nanopore reads from the N2 strain by Ding et al. (2022) estimated 167 consecutive 5S rDNA units. These results demonstrate the importance of Nanopore ultralong reads for properly assembling large tandemly repeated genomic sequences.The complete sequences of the p...
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Research: Genome-wide nucleosome and transcription factor responses to genetic perturbations reveal chromatin-mediated mechanisms of transcriptional regulation
- Kevin Moyung,
- Yulong Li,
- Heather K. MacAlpine,
- Alexander J. Hartemink,
- and David M. MacAlpine
Genome Res. January 2026 36: 115-128; Published in Advance December 9, 2025, doi:10.1101/gr.279637.124
...are excluded). Each row represents a mutant, and the x-axis represents genomic locations (base pairs) grouped by chromosome. (D) Deletion of CBF1 results in a loss of TF occupancy and inward shifting of nucleosomes at the MET10 locus (in contrast, this effect is not seen when BAS1 or MBP1, e.g., are deleted...
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Resource: Building better genome annotations across the tree of life
- Adam H. Freedman and
- Timothy B. Sackton
Genome Res. May 2025 35: 1261-1276; Published in Advance April 15, 2025, doi:10.1101/gr.280377.124
...assessments of protein-coding and transcriptome annotations separately. To add CDS annotations to StringTie and Scallop annotations, we used TransDecoder (https://github.com/TransDecoder/TransDecoder) to predict open reading frames (ORFs) and explicitly label features as CDS or UTR. Although there are other...
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Method: Accurate and fast graph-based pangenome annotation and clustering with ggCaller
- Samuel T. Horsfield,
- Gerry Tonkin-Hill,
- Nicholas J. Croucher,
- and John A. Lees
Genome Res. September 2023 33: 1622-1637; Published in Advance August 24, 2023, doi:10.1101/gr.277733.123
...1. ggCaller workflow. ggCaller can be split into two sections: ORF identification (steps 1–4) and ORF clustering + filtering (steps 5–8). (1) DBG is generated from assemblies by Bifrost. (2) All stop codons are identified, and stop frequency is calculated (total number of stop codons in DBG / total...
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Resource: The western redcedar genome reveals low genetic diversity in a self-compatible conifer
- Tal J. Shalev,
- Omnia Gamal El-Dien,
- Macaire M.S. Yuen,
- Shu Shengqiang,
- Shaun D. Jackman,
- René L. Warren,
- Lauren Coombe,
- Lise van der Merwe,
- Ada Stewart,
- Lori B. Boston,
- Christopher Plott,
- Jerry Jenkins,
- Guifen He,
- Juying Yan,
- Mi Yan,
- Jie Guo,
- Jesse W. Breinholt,
- Leandro G. Neves,
- Jane Grimwood,
- Loren H. Rieseberg,
- Jeremy Schmutz,
- Inanc Birol,
- Matias Kirst,
- Alvin D. Yanchuk,
- Carol Ritland,
- John H. Russell,
- and Joerg Bohlmann
Genome Res. October 2022 32: 1952-1964; Published in Advance September 15, 2022, doi:10.1101/gr.276358.121
..._EST v2.6, and EXONERATE and PASA (Haas et al. 2003) assembly ORFs. The best-scored predictions for each locus were selected and improved by PASA, adding UTRs, splicing correction, and alternative transcripts. All software was run using default parameters. Detailed RNA extraction, sequencing...
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Resource: Comprehensive, integrated, and phased whole-genome analysis of the primary ENCODE cell line K562
- Bo Zhou,
- Steve S. Ho,
- Stephanie U. Greer,
- Xiaowei Zhu,
- John M. Bell,
- Joseph G. Arthur,
- Noah Spies,
- Xianglong Zhang,
- Seunggyu Byeon,
- Reenal Pattni,
- Noa Ben-Efraim,
- Michael S. Haney,
- Rajini R. Haraksingh,
- Giltae Song,
- Hanlee P. Ji,
- Dimitri Perrin,
- Wing H. Wong,
- Alexej Abyzov,
- and Alexander E. Urban
Genome Res. March 2019 29: 472-484; Published in Advance February 8, 2019, doi:10.1101/gr.234948.118
...(blue), and a 163-kb tandem duplication (green). This rearrangement resides on the nonduplicated haplotype of this triploid region. ORC6 is located entirely within the 63-kb inversion on 16q11.2 and is “deleted” by the left breakpoint of the 125-kb inversion, which also inverts MYLK3. C16orf8...
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Resource: Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci
- Jonathan M. Mudge,
- Irwin Jungreis,
- Toby Hunt,
- Jose Manuel Gonzalez,
- James C. Wright,
- Mike Kay,
- Claire Davidson,
- Stephen Fitzgerald,
- Ruth Seal,
- Susan Tweedie,
- Liang He,
- Robert M. Waterhouse,
- Yue Li,
- Elspeth Bruford,
- Jyoti S. Choudhary,
- Adam Frankish,
- and Manolis Kellis
Genome Res. December 2019 29: 2073-2087; Published in Advance September 19, 2019, doi:10.1101/gr.246462.118
...-generation transcriptomic data sets, and mass spectrometry evidence of translation for several new genes. Our discoveries required simultaneous comparative annotation of other vertebrate s, which we show is essential to remove spurious ORFs and to distinguish coding from pseudogene regions. Our new coding regions help...
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Methods: Gene and alternative splicing annotation with AIR
- Liliana Florea,
- Valentina Di Francesco,
- Jason Miller,
- Russell Turner,
- Alison Yao,
- Michael Harris,
- Brian Walenz,
- Clark Mobarry,
- Gennady V. Merkulov,
- Rosane Charlab,
- Ian Dew,
- Zuoming Deng,
- Sorin Istrail,
- Peter Li,
- and Granger Sutton
Genome Res. January 2005 15: 54-66; doi:10.1101/gr.2889405
...the number of exactly identified splice junctions. Lastly, to measure the effects of splice junction and alignment inaccuracies on the open reading frame (ORF) and on the resulting protein product, we compared the two sets of ORFs and their protein translations. As shown in Table 4 , AIR produced...

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