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Method: Full-resolution HLA and KIR gene annotations for human genome assemblies
- Ying Zhou,
- Li Song,
- and Heng Li
Genome Res. November 2024 34: 1931-1941; Published in Advance June 5, 2024, doi:10.1101/gr.278985.124
...We applied Immuannot to 212 full- haploid assemblies, including HPRC (n = 94) (Liao et al. 2023), CPC (n = 114) (Gao et al. 2023), CHM13.0 (Nurk et al. 2022), GRCh38.p14 (Schneider et al. 2017), and CN-T2T (n = 2) (He et al. 2023); 50 KIR reference contigs; and six HLA reference assemblies (Houwaart et al...
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Research: Leveraging the T2T assembly to resolve rare and pathogenic inversions in reference genome gaps
- Kristine Bilgrav Saether,
- Jesper Eisfeldt,
- Jesse D. Bengtsson,
- Ming Yin Lun,
- Christopher M. Grochowski,
- Medhat Mahmoud,
- Hsiao-Tuan Chao,
- Jill A. Rosenfeld,
- Pengfei Liu,
- Marlene Ek,
- Jakob Schuy,
- Adam Ameur,
- Hongzheng Dai,
- Undiagnosed Diseases Network,
- James Paul Hwang,
- Fritz J. Sedlazeck,
- Weimin Bi,
- Ronit Marom,
- Josephine Wincent,
- Ann Nordgren,
- Claudia M.B. Carvalho,
- and Anna Lindstrand
Genome Res. November 2024 34: 1785-1797; Published in Advance November 1, 2024, doi:10.1101/gr.279346.124
..., GRCh38, T2T-CHM13) and a reference agnostic analysis was needed. One of these cases, an INV9 mappable only in de novo assembled lrGS data using T2T-CHM13 disrupts EHMT1 consistent with a Mendelian diagnosis (Kleefstra syndrome 1; MIM#610253). Next, by pairwise comparison between T2T-CHM13, GRCh37...
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Method: Genetic complexity of killer-cell immunoglobulin-like receptor genes in human pangenome assemblies
- Tsung-Kai Hung,
- Wan-Chi Liu,
- Sheng-Kai Lai,
- Hui-Wen Chuang,
- Yi-Che Lee,
- Hong-Ye Lin,
- Chia-Lang Hsu,
- Chien-Yu Chen,
- Ya-Chien Yang,
- Jacob Shujui Hsu,
- and Pei-Lung Chen
Genome Res. August 2024 34: 1211-1223; Published in Advance September 9, 2024, doi:10.1101/gr.278358.123
.... S1A).KIR alleles of human reference sWe compared the SKIRT KIR allele annotations for GRCh37 (hg19) (Church et al. 2011), GRCh38 (hg38) (Schneider et al. 2017), and T2T CHM13v2.0 (hs1) (Nurk et al. 2022) with the latest GENCODE annotations available on the UCSC Genome Browser (Kent et al. 2002...
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Method: De novo reconstruction of satellite repeat units from sequence data
- Yujie Zhang,
- Justin Chu,
- Haoyu Cheng,
- and Heng Li
Genome Res. November 2023 33: 1994-2001; Published in Advance November 2, 2023, doi:10.1101/gr.278005.123
...and de novo haploid assemblies demonstrates the enduring quality of the reference assembly. Genome Res 27: 849–864. doi:10.1101/gr.213611.116 ↵Sevim V, Bashir A, Chin C-S, Miga KH. 2016. Alpha-CENTAURI: assessing novel centromeric repeat sequence variation with long read sequencing. Bioinformatics 32...
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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
.... 2020; Glinos et al. 2022; Veiga et al. 2022; Zhang et al. 2022), and represents a data source of great value for the de novo annotation of the Earth BioGenome Project (Lawniczak et al. 2022). Despite its strengths, LRS presents several shortcomings. The quality of long-read RNA sequencing (lr...
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Method: The Nubeam reference-free approach to analyze metagenomic sequencing reads
- Hang Dai and
- Yongtao Guan
Genome Res. September 2020 30: 1364-1375; Published in Advance September 3, 2020, doi:10.1101/gr.261750.120
...(SEM 13%), but mapping rates vary for samples from different body habitats (Supplemental Fig. S1). The inadequacy of the reference s and mapping bias both contribute to the high percentage of unmapped reads (Nayfach and Pollard 2016). We would like to mention here that the most recent de novo assembly...
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Method: Pan-human consensus genome significantly improves the accuracy of RNA-seq analyses
- Benjamin Kaminow,
- Sara Ballouz,
- Jesse Gillis,
- and Alexander Dobin
Genome Res. April 2022 32: 738-749; Published in Advance March 7, 2022, doi:10.1101/gr.275613.121
..., it is still not without flaws, primarily the lack of variation information. Around 93% of the current GRCh38 assembly is composed of DNA from just 11 individuals (International Human Genome Sequencing Consortium 2001; https://www.ncbi.nlm.nih.gov/grc/help/faq/). Because such a large portion of the reference...
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Review: Genome graphs and the evolution of genome inference
- Benedict Paten,
- Adam M. Novak,
- Jordan M. Eizenga,
- and Erik Garrison
Genome Res. May 2017 27: 665-676; Published in Advance March 30, 2017, doi:10.1101/gr.214155.116
...Human Genome Sequencing Consortium 2001). Over a number of years, the assembly has steadily improved (International Human Genome Sequencing Consortium2004; Church et al. 2011) to the point that the current Genome Reference Consortium (GRC) human assembly, GRCh38 (Schneider et al. 2017), is arguably...
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Method: Comparative Annotation Toolkit (CAT)—simultaneous clade and personal genome annotation
- Ian T. Fiddes,
- Joel Armstrong,
- Mark Diekhans,
- Stefanie Nachtweide,
- Zev N. Kronenberg,
- Jason G. Underwood,
- David Gordon,
- Dent Earl,
- Thomas Keane,
- Evan E. Eichler,
- David Haussler,
- Mario Stanke,
- and Benedict Paten
Genome Res. July 2018 28: 1029-1038; Published in Advance June 8, 2018, doi:10.1101/gr.233460.117
...for comparing genomic features. Bioinformatics 26: 841–842. ↵Schneider VA, Graves-Lindsay T, Howe K, Bouk N, Chen HC, Kitts PA, Murphy TD, Pruitt KD, Thibaud-Nissen F, Albracht D, et al. 2017. Evaluation of GRCh38 and de novo haploid assemblies demonstrates the enduring quality of the reference assembly. Genome...
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Method: Resolving the full spectrum of human genome variation using Linked-Reads
- Patrick Marks,
- Sarah Garcia,
- Alvaro Martinez Barrio,
- Kamila Belhocine,
- Jorge Bernate,
- Rajiv Bharadwaj,
- Keith Bjornson,
- Claudia Catalanotti,
- Josh Delaney,
- Adrian Fehr,
- Ian T. Fiddes,
- Brendan Galvin,
- Haynes Heaton,
- Jill Herschleb,
- Christopher Hindson,
- Esty Holt,
- Cassandra B. Jabara,
- Susanna Jett,
- Nikka Keivanfar,
- Sofia Kyriazopoulou-Panagiotopoulou,
- Monkol Lek,
- Bill Lin,
- Adam Lowe,
- Shazia Mahamdallie,
- Shamoni Maheshwari,
- Tony Makarewicz,
- Jamie Marshall,
- Francesca Meschi,
- Christopher J. O'Keefe,
- Heather Ordonez,
- Pranav Patel,
- Andrew Price,
- Ariel Royall,
- Elise Ruark,
- Sheila Seal,
- Michael Schnall-Levin,
- Preyas Shah,
- David Stafford,
- Stephen Williams,
- Indira Wu,
- Andrew Wei Xu,
- Nazneen Rahman,
- Daniel MacArthur,
- and Deanna M. Church
Genome Res. April 2019 29: 635-645; Published in Advance March 20, 2019, doi:10.1101/gr.234443.118
.... 2014). We chose this call set version as it was the last GIAB data set that did not include 10x data as an input for call set curation. This necessitated the use of GRCh37 as a reference assembly rather than the more current GRCh38 reference assembly, limiting analysis to the 82.67% of SNV calls...
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