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Method: Read-level genotyping of short tandem repeats using long reads and single-nucleotide variation with STRkit
- David R. Lougheed,
- Tomi Pastinen,
- and Guillaume Bourque
Genome Res. March 2026 36: 578-588; Published in Advance January 15, 2026, doi:10.1101/gr.280766.125
...outperform ONT data, a pattern that has been observed in other long-read variant call benchmarking (Harvey et al. 2023). With ONT data, our performance gains were larger, achieving a ∼2%–3% higher F1 score (for high-coverage simplex and low-coverage duplex, respectively) than LongTR and narrowing...
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Resource: The PanOryza pangene catalog of Asian cultivated rice
- Bruno Contreras-Moreira,
- Eshan Sharma,
- Shradha Saraf,
- Guy Naamati,
- Parul Gupta,
- Justin Elser,
- Dmytro Chebotarov,
- Kapeel Chougule,
- Zhenyuan Lu,
- Sharon Wei,
- Andrew Olson,
- Ian Tsang,
- Disha Lodha,
- Yong Zhou,
- Zhichao Yu,
- Wen Zhao,
- Jianwei Zhang,
- Sandeep Amberkar,
- Kawinnat Sue-Ob,
- Zhi Sun,
- Maria Martin,
- Kenneth L. McNally,
- Doreen Ware,
- Eric W. Deutsch,
- Dario Copetti,
- Rod A. Wing,
- Pankaj Jaiswal,
- Sarah Dyer,
- and Andrew R. Jones
Genome Res. January 2026 36: 226-238; Published in Advance December 12, 2025, doi:10.1101/gr.280790.125
..., with the latter being the more widely used/reference annotations (for historical reasons).To study genetic variation, significant efforts have been made to identify variants on a large scale from high-throughput short DNA read sequencing, for example, via the 3000 Rice Genomes Project (Li et al. 2014; Wang et al...
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Method: De novo detection of somatic variants in high-quality long-read single-cell RNA sequencing data
- Arthur Dondi,
- Nico Borgsmüller,
- Pedro F. Ferreira,
- Brian J. Haas,
- Francis Jacob,
- Viola Heinzelmann-Schwarz,
- Tumor Profiler Consortium,
- and Niko Beerenwinkel
Genome Res. April 2025 35: 900-913; Published in Advance March 19, 2025, doi:10.1101/gr.279281.124
...and transcriptomic variants. However, those protocols can only capture RNA molecules via their 3′ or 5′ ends, and short-read (SR) scRNA-seq coverage is heavily biased toward the 3′/5′ end of genes. Recently, methods to call SNVs (Zhang et al. 2023; Muyas et al. 2024) and CNAs (Serin Harmanci et al. 2020; Gao et al...
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Research: A prospective trial comparing programmable targeted long-read sequencing and short-read genome sequencing for genetic diagnosis of cerebellar ataxia
- Haloom Rafehi,
- Liam G. Fearnley,
- Justin Read,
- Penny Snell,
- Kayli C. Davies,
- Liam Scott,
- Greta Gillies,
- Genevieve C. Thompson,
- Tess A. Field,
- Aleena Eldo,
- Simon Bodek,
- Ernest Butler,
- Luke Chen,
- John Drago,
- Himanshu Goel,
- Anna Hackett,
- G. Michael Halmagyi,
- Andrew Hannaford,
- Katya Kotschet,
- Kishore R. Kumar,
- Smitha Kumble,
- Matthew Lee-Archer,
- Abhishek Malhotra,
- Mark Paine,
- Michael Poon,
- Kate Pope,
- Katrina Reardon,
- Steven Ring,
- Anne Ronan,
- Matthew Silsby,
- Renee Smyth,
- Chloe Stutterd,
- Mathew Wallis,
- John Waterston,
- Thomas Wellings,
- Kirsty West,
- Christine Wools,
- Kathy H.C. Wu,
- David J. Szmulewicz,
- Martin B. Delatycki,
- Melanie Bahlo,
- and Paul J. Lockhart
Genome Res. April 2025 35: 769-785; Published in Advance February 27, 2025, doi:10.1101/gr.279634.124
...in light green are SCA27B VUS. Triangles indicate low coverage (≤7 reads) on LR-AS, squares indicate non-GAA repeat motifs, and circles samples with coverage >7 reads and GAA motifs. The pathogenic (≥250 repeats) and VUS (≥180 repeats) thresholds are shown as dashed red lines. A 1:1 correlation is shown...
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Research: Genotype imputation from low-coverage data for medical and population genetic analyses
- Simone Andrea Biagini,
- Sara Becelaere,
- Mio Aerden,
- Tatjana Jatsenko,
- Laurens Hannes,
- Philip Van Damme,
- Jeroen Breckpot,
- Koenraad Devriendt,
- Bernard Thienpont,
- Joris Robert Vermeesch,
- Isabelle Cleynen,
- and Toomas Kivisild
Genome Res. September 2025 35: 1929-1941; Published in Advance July 22, 2025, doi:10.1101/gr.280175.124
...noninvasive prenatal screening (NIPS) with an average autosomal sequence depth of ∼0.15×. In studies involving ultra-low coverage sequences, conventional approaches to secure genotype accuracy may fail, especially when multiple samples are pooled. To enhance the proportion of high-quality genotypes in large...
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Mini-Review: A Hitchhiker's Guide to long-read genomic analysis
- Medhat Mahmoud,
- Daniel P. Agustinho,
- and Fritz J. Sedlazeck
Genome Res. April 2025 35: 545-558; doi:10.1101/gr.279975.124
..., contributing to a more comprehensive understanding of their roles in health and disease.De novo assembly of long-read dataDe novo assembly, the process of reconstructing complete sequences from raw sequencing reads without a reference , has historically been a significant challenge for short-read sequencing...
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Method: Long-read reconstruction of many diverse haplotypes with devider
- Jim Shaw,
- Christina Boucher,
- Yun William Yu,
- Noelle Noyes,
- and Heng Li
Genome Res. December 2025 35: 2637-2649; Published in Advance September 23, 2025, doi:10.1101/gr.280510.125
...of genetic diversity in microbes, viruses, or even genes.With high-throughput sequencing, we can obtain haplotypes by linking reads that share informative alleles, for example, single-nucleotide polymorphisms (SNPs). Unfortunately, standard de novo short-read or long-read assembly approaches can collapse...
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Method: Genotyping of selected germline adaptive immune system loci using short-read sequencing data
- Michael K.B. Ford,
- Ananth Hari,
- Meredith Yeager,
- Lisa Mirabello,
- Stephen Chanock,
- Ibrahim Numanagić,
- COVNET Consortium,
- and S. Cenk Sahinalp
Genome Res. September 2025 35: 2076-2086; Published in Advance August 5, 2025, doi:10.1101/gr.280314.124
...option is probe-based target sequencing, with either long reads and de novo assembly, as utilized in the IGenotyper approach (Rodriguez et al. 2020, 2022; Gibson et al. 2023; Engelbrecht et al. 2024), or short reads (Lin et al. 2022). Studies using these approaches have successfully found that germline...
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Review: De novo gene birth and the conundrum of ORFan genes in bacteria
- Md. Hassan uz-Zaman and
- Howard Ochman
Genome Res. August 2025 35: 1679-1688; Published in Advance July 10, 2025, doi:10.1101/gr.280157.124
...actually emerges. There are three routes by which ORFans can arise in bacterial s: (1) de novo evolution from noncoding sequences (including noncoding alternative reading frames of functional genes), (2) extreme divergence from other functional genes, and (3) horizontal transfer from a source not present...
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Method: Estimating the size of long tandem repeat expansions from short reads with ScatTR
- Rashid Al-Abri and
- Gamze Gürsoy
Genome Res. December 2025 35: 2701-2713; Published in Advance August 21, 2025, doi:10.1101/gr.280563.125
..., many pathogenic TRs expand to hundreds of base pairs, well above the fragment length in typical short-read data (Hannan 2018). Moreover, these methods are constrained by the length of the TR unit (i.e., motif) they can analyze: STRling is restricted to motifs between 2 and 6 bp, whereas Expansion...
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