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Research: Strong bias in long-read sequencing prevents assembly of Drosophila melanogaster Y-linked genes
- A. Bernardo Carvalho,
- Bernard Y. Kim,
- and Fabiana Uno
Genome Res. January 2026 36: 71-82; Published in Advance October 1, 2025, doi:10.1101/gr.280604.125
..., the clearest one against GA-rich repeats in the human . However, our study reveals a systematic failure of both technologies to sequence and assemble specific exons of Drosophila melanogaster genes, indicating an overlooked limitation. Namely, multiple Y-linked exons are nearly or completely absent from raw...
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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
..., hinging on the precise binding of transcription factors (TFs) and cofactors to gene regulatory elements such as promoters and enhancers. Although it is relatively routine to profile -wide DNA binding landscapes of proteins, identifying the specific proteins that bind to, and regulate the transcription of...
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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
...a large gene family. By combining the advantages of DNA and protein sequence alignment, LiftOn generates better protein-coding gene annotation than either alignment method can achieve on its own.ResultsIn our experiments below, we demonstrate how LiftOn can yield substantial improvements in mapping...
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RECOMB 2022 Special/Methods: Learning probabilistic protein–DNA recognition codes from DNA-binding specificities using structural mappings
- Joshua L. Wetzel,
- Kaiqian Zhang,
- and Mona Singh
Genome Res. September 2022 32: 1776-1786; Published in Advance September 19, 2022, doi:10.1101/gr.276606.122
...are expressed in each spatiotemporal context, mutations—within either TFs themselves or the particular genomic regions that they are intended to interact with—can alter gene expression programs and lead to disease phenotypes (for review, see Lee and Young 2013). Because of the central importance of TF–DNA...
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Research: The grasshopper genome reveals long-term gene content conservation of the X Chromosome and temporal variation in X Chromosome evolution
- Xinghua Li,
- Judith E. Mank,
- and Liping Ban
Genome Res. July 2024 34: 997-1007; Published in Advance August 5, 2024, doi:10.1101/gr.278794.123
...library and satellite DNA library and the Dfam_Consensus (Storer et al. 2021) and the Repbase libraries (Bao et al. 2015), we estimated the repeat content of the assembled using RepeatMasker (Smit et al. 2013–2015). Ab initio gene prediction was performed using AUGUSTUS (Stanke et al. 2008). Genome...
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Research: Dynamic DNA N⁶-adenine methylation (6mA) governs the encystment process, showcased in the unicellular eukaryote Pseudocohnilembus persalinus
- Yongqiang Liu,
- Junhua Niu,
- Fei Ye,
- Therese Solberg,
- Borong Lu,
- Chundi Wang,
- Mariusz Nowacki,
- and Shan Gao
Genome Res. February 2024 34: 256-271; Published in Advance March 12, 2024, doi:10.1101/gr.278796.123
...the importance of unravelling the complex network of factors involved in DNA methylation maintenance and regulation of the encystment process.Based on our findings, we propose an encystment–excystment cycle model involving 6mA-regulated gene expression (Fig. 7): Once trophonts are induced by an exogenous trigger...
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Method: Nematode gene annotation by machine-learning-assisted proteotranscriptomics enables proteome-wide evolutionary analysis
- Alejandro Ceron-Noriega,
- Miguel V. Almeida,
- Michal Levin,
- and Falk Butter
Genome Res. January 2023 33: 112-128; Published in Advance January 18, 2023, doi:10.1101/gr.277070.122
...this process to the ecology or biology of C. japonica. Nevertheless, common knockout phenotypes of these genes are related to slow growth and larva viability. In general, we found ribosomal proteins under positive selection in the nematodes C. briggsae, C. drosophilae, C. inopinata, O. tipulae, P. pacificus, R...
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Methods: Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training
- Vardges Ter-Hovhannisyan,
- Alexandre Lomsadze,
- Yury O. Chernoff,
- and Mark Borodovsky
Genome Res. December 2008 18: 1979-1990; Published in Advance August 29, 2008, doi:10.1101/gr.081612.108
...is ready for the next iteration. Preparation of test sets Expressed sequence tags (ESTs) data were available for each of the 16 fungal species (Supplemental Table S2). For assessment of the algorithm performance, we used EST validated genes identified by a local pipeline mapping EST to genomic DNA (A...
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Resource: mGene: Accurate SVM-based gene finding with an application to nematode genomes
- Gabriele Schweikert,
- Alexander Zien,
- Georg Zeller,
- Jonas Behr,
- Christoph Dieterich,
- Cheng Soon Ong,
- Petra Philips,
- Fabio De Bona,
- Lisa Hartmann,
- Anja Bohlen,
- Nina Krüger,
- Sören Sonnenburg,
- and Gunnar Rätsch
Genome Res. November 2009 19: 2133-2143; Published in Advance June 29, 2009, doi:10.1101/gr.090597.108
...are called upon to fill the gap. Recently, computational gene finding has experienced a major breakthrough by adopting discriminative machine learning techniques (Brent 2008). In contrast to generative gene-finding methods, which jointly model the DNA sequence itself together with its segmentation into gene...
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Methods: Ab initio identification of functionally interacting pairs of cis-regulatory elements
- Brad A. Friedman,
- Michael B. Stadler,
- Noam Shomron,
- Ye Ding,
- and Christopher B. Burge
Genome Res. October 2008 18: 1643-1651; Published in Advance September 17, 2008, doi:10.1101/gr.080085.108
...Graph, a software toolbox that generates for each gene a graph-based representation of its transcript variants (R. Sandberg and M.B. Stadler, unpubl.). SpliceGraph databases for human and mouse genes were constructed using spliced alignments of cDNAs and ESTs to the human and mouse s from the University...

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