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Research: Age-dependent mutational loads in human tRNA genes are tumor-specific and result in chimeric tRNA sequences that could disrupt the genetic code
- Marina Murillo,
- Marina Salvadores,
- Aina Vaquer Picó,
- Lina Tsapanou,
- Adrian Gabriel Torres,
- Fran Supek,
- and Lluis Ribas de Pouplana
Genome Res. April 15, 2026 gr.281022.125; Published in Advance April 15, 2026, doi:10.1101/gr.281022.125
...2023). However, some ARS do 14 not interact with the anticodon sequence of their cognate tRNAs, and mutations at these anticodons 15 can lead to chimeric tRNAs that cause amino acid substitutions throughout the proteome (Geslain et 16 al. 2010; Parisien et al. 2013; Reverendo et al. 2014; Santos et al...
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Method: Accurate detection of tandem repeats from error-prone sequences with EquiRep
- Zhezheng Song,
- Tasfia Zahin,
- Xiang Li,
- and Mingfu Shao
Genome Res. December 2025 35: 2714-2721; Published in Advance August 21, 2025, doi:10.1101/gr.280750.125
..., USA ↵3 These authors contributed equally to this work. Corresponding author: mxs2589@psu.eduAbstractA tandem repeat is a sequence of nucleotides that appear as multiple contiguous, near-identical copies arranged consecutively. Tandem repeats are widespread across natural s, play critical roles...
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Method: k-mer manifold approximation and projection for visualizing DNA sequences
- Chengbo Fu,
- Einari A. Niskanen,
- Gong-Hong Wei,
- Zhirong Yang,
- Marta Sanvicente-García,
- Marc Güell,
- and Lu Cheng
Genome Res. May 2025 35: 1234-1246; Published in Advance April 10, 2025, doi:10.1101/gr.279458.124
..., Universitat Pompeu Fabra, 08003 Barcelona, Spain; 8Institució Catalana de Recerca i Estudis Avançats, ICREA, 08003 Barcelona, Spain Corresponding author: lu.cheng.ac@gmail.comAbstractIdentifying and illustrating patterns in DNA sequences are crucial tasks in various biological data analyses. In this task...
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Method: Identification of the shortest species-specific oligonucleotide sequences
- Ioannis Mouratidis,
- Maxwell A. Konnaris,
- Nikol Chantzi,
- Candace S.Y. Chan,
- Michail Patsakis,
- Kimonas Provatas,
- Austin Montgomery,
- Fotis A. Baltoumas,
- Congzhou M. Sha,
- Manvita Mareboina,
- Georgios A. Pavlopoulos,
- Dionysios V. Chartoumpekis,
- and Ilias Georgakopoulos-Soares
Genome Res. February 2025 35: 279-295; Published in Advance January 2, 2025, doi:10.1101/gr.280070.124
...contributed equally to this work. Corresponding authors: ipm5219@psu.edu, izg5139@psu.eduAbstractDespite the exponential increase in sequencing information driven by massively parallel DNA sequencing technologies, universal and succinct genomic fingerprints for each organism are still missing. Identifying...
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Method: A simple method for finding related sequences by adding probabilities of alternative alignments
- Martin C. Frith
Genome Res. August 2024 34: 1165-1173; Published in Advance August 16, 2024, doi:10.1101/gr.279464.124
...: mcfrith@edu.k.u-tokyo.ac.jpAbstractThe main way of analyzing genetic sequences is by finding sequence regions that are related to each other. There are many methods to do that, usually based on this idea: Find an alignment of two sequence regions, which would be unlikely to exist between unrelated...
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Review: Advancing genomic technologies and clinical awareness accelerates discovery of disease-associated tandem repeat sequences
- Terence Gall-Duncan,
- Nozomu Sato,
- Ryan K.C. Yuen,
- and Christopher E. Pearson
Genome Res. January 2022 32: 1-27; Published in Advance December 29, 2021, doi:10.1101/gr.269530.120
...-causing repeat expansion loci accelerated through technological advances in DNA sequencing and computational analyses. Between 2019 and 2021, 17 new disease-causing TR expansions were reported, totaling 63 TR loci (>69 diseases), with a likelihood of more discoveries, and in more organisms. Recent and historical...
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Method: Reference-informed prediction of alternative splicing and splicing-altering mutations from sequences
- Chencheng Xu,
- Suying Bao,
- Ye Wang,
- Wenxing Li,
- Hao Chen,
- Yufeng Shen,
- Tao Jiang,
- and Chaolin Zhang
Genome Res. July 2024 34: 1052-1065; Published in Advance July 26, 2024, doi:10.1101/gr.279044.124
...in higher eukaryotes, and mutations causing dysregulated splicing underlie a range of genetic diseases. Computational prediction of alternative splicing from genomic sequences not only provides insight into gene-regulatory mechanisms but also helps identify disease-causing mutations and drug targets...
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Method: Aligning distant sequences to graphs using long seed sketches
- Amir Joudaki,
- Alexandru Meterez,
- Harun Mustafa,
- Ragnar Groot Koerkamp,
- André Kahles,
- and Gunnar Rätsch
Genome Res. July 2023 33: 1208-1217; Published in Advance April 18, 2023, doi:10.1101/gr.277659.123
...Institute of Bioinformatics, Lausanne 1015, Switzerland; 4ETH AI Center, 8092 Zurich, Switzerland ↵5 These authors contributed equally to this work. Corresponding authors: andre.kahles@inf.ethz.ch, raetsch@inf.ethz.chAbstractSequence-to-graph alignment is crucial for applications such as variant genotyping...
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Resource: Long-read assembly and comparative evidence-based reanalysis of Cryptosporidium genome sequences reveal expanded transporter repertoire and duplication of entire chromosome ends including subtelomeric regions
- Rodrigo P. Baptista,
- Yiran Li,
- Adam Sateriale,
- Mandy J. Sanders,
- Karen L. Brooks,
- Alan Tracey,
- Brendan R.E. Ansell,
- Aaron R. Jex,
- Garrett W. Cooper,
- Ethan D. Smith,
- Rui Xiao,
- Jennifer E. Dumaine,
- Peter Georgeson,
- Bernard J. Pope,
- Matthew Berriman,
- Boris Striepen,
- James A. Cotton,
- and Jessica C. Kissinger
Genome Res. January 2022 32: 203-213; Published in Advance November 11, 2021, doi:10.1101/gr.275325.121
...3. CpIA assembly and annotation reveal new transporters. The numbers of transporters correspond to the counts of genes encoding each type of transporter protein: (ABC) ATP-binding cassette transporter; (MFS) major facilitator superfamily; (DMT) divalent metal transporter; (AAAP) amino acid...
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Method: Unraveling the palindromic and nonpalindromic motifs of retroviral integration site sequences by statistical mixture models
- Dalibor Miklík,
- Jiří Grim,
- Daniel Elleder,
- and Jiří Hejnar
Genome Res. August 2023 33: 1395-1408; Published in Advance July 18, 2023, doi:10.1101/gr.277694.123
...Academy of Sciences, Prague 8, 182 08, Czech Republic Corresponding author: jiri.hejnar@img.cas.czAbstractA weak palindromic nucleotide motif is the hallmark of retroviral integration site alignments. Given that the majority of target sequences are not palindromic, the current model explains the symmetry...
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