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Method: Minimizing reference bias with an imputed personalized reference
- Kavya Vaddadi,
- Mao-Jan Lin,
- Sina Majidian,
- Taher Mun,
- and Ben Langmead
Genome Res. April 2026 36: 740-753; Published in Advance March 5, 2026, doi:10.1101/gr.280989.125
...Kavya Vaddadi, Mao-Jan Lin, Sina Majidian, Taher Mun and Ben Langmead Department of Computer Science, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA Corresponding author: langmea@cs.jhu.eduAbstractPan indexes reduce reference bias in sequencing data analysis...
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Method: Balancing gene ontology annotation specificity in protein function prediction based on the protein sequence large graph
- Jiangyi Shao,
- Shutao Chen,
- Ziwen Wang,
- Zixu Chen,
- and Bin Liu
Genome Res. April 15, 2026 gr.280816.125; Published in Advance April 15, 2026, doi:10.1101/gr.280816.125
...; Alfatah et 63 al. 2024; Nomburg et al. 2024), ensuring that these functionally critical annotations are 64 not overlooked. We refer to this phenomenon as “specificity imbalance,” encompassing 65 both annotation density imbalance and information content asymmetry across GO terms. 66 This gap...
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Method: Complete genetic and epigenetic architecture of D4Z4 macrosatellites in FSHD, BAMS, and reference cohorts with D4Z4End2End
- Lucinda C. Xiao,
- Ayush Semwal,
- Brianna St John,
- Kathleen Zeglinski,
- Shian Su,
- James Lancaster,
- Shifeng Xue,
- Bruno Reversade,
- Matthew E. Ritchie,
- Frédérique Magdinier,
- Marnie E. Blewitt,
- and Quentin Gouil
Genome Res. April 2026 36: 827-848; Published in Advance March 23, 2026, doi:10.1101/gr.280907.125
...by the Human Pan Reference Consortium (HPRC) (Liao et al. 2023), which have previously been studied in the context of FSHD (Salsi et al. 2023). The pipeline was able to successfully identify and annotate raw reads that spanned complete D4Z4 arrays, enabling accurate D4Z4 counting and resolution of 4q and 10q...
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Method: Robust and efficient annotation of cell states through gene signature scoring
- Laure Ciernik,
- Agnieszka Kraft,
- Florian Barkmann,
- Josephine Yates,
- and Valentina Boeva
Genome Res. March 2026 36: 630-644; Published in Advance February 18, 2026, doi:10.1101/gr.280926.125
...the stability of gene signature scores provided by the most popular cell scoring methods: SCANPY, Seurat, UCell, and JASMINE. Using nine human healthy and cancer scRNA-seq data sets, we find that accurate unsupervised cell-state annotation using gene signature scores is not possible based on scores calculated...
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Method: spRefine denoises and imputes spatial transcriptomic data with a reference-free framework powered by genomic language model
- Tianyu Liu,
- Tinglin Huang,
- Wengong Jin,
- Tinyi Chu,
- Rex Ying,
- and Hongyu Zhao
Genome Res. April 2026 36: 754-768; Published in Advance February 3, 2026, doi:10.1101/gr.281001.125
...in benchmarking analysis (Ding et al. 2024). We used the 10x Visium data set from SpatialLIBD (Maynard et al. 2021) for evaluation. This data set contains multiple slides and also offers expert annotation of spot types to validate the preservation of biological signals. Our selected baselines provide recommended...
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Method: Interactive visualization and interpretation of pangenome graphs by linear reference–based coordinate projection and annotation integration
- Zepu Miao and
- Jia-Xing Yue
Genome Res. February 2025 35: 296-310; Published in Advance January 13, 2025, doi:10.1101/gr.279461.124
...Interactive visualization and interpretation of pan graphs by linear reference–based coordinate projection and annotation integration Zepu Miao and Jia-Xing Yue State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong...
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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
...of CHROMOSOME_I and CHROMOSOME_III. For C. elegans to have a completely accurate reference , the N2 reference assembly needed to be replaced, but the VC2010 assembly could not fully replace it.View this table: In this window In a new window Table 1. Chromosome lengths and tandem repeat lengths of different C...
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Method: Robust chromatin state annotation
- Mehdi Foroozandeh Shahraki,
- Marjan Farahbod,
- and Maxwell W. Libbrecht
Genome Res. March 2024 34: 469-483; Published in Advance March 21, 2024, doi:10.1101/gr.278343.123
...recapitulate known biology, and the annotations accurately represent many genomic phenomena, including transcription (Zhang and Hardison 2017; Libbrecht et al. 2019, 2021). However, results are often dissimilar between SAGA methods and hyperparameter settings of a given method (Hoffman et al. 2013; Zhang...
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Resource: Integrative chromatin state annotation of 234 human ENCODE4 cell types using Segway
- Marjan Farahbod,
- Aboud Diab,
- Paul Sud,
- Meenakshi S. Kagda,
- Ian Whaling,
- Mehdi Foroozandeh,
- Ishan Goel,
- Habib Daneshpajouh,
- Benjamin Hitz,
- J. Michael Cherry,
- and Maxwell W. Libbrecht
Genome Res. October 6, 2025 gr.280633.125; Published in Advance October 6, 2025, doi:10.1101/gr.280633.125
...integrative summary of such data sets. Here, we present the ENCODE4 Catalog of Segway Annotations, a set of sample-specific -wide chromatin state annotations of 234 human biosamples inferred from 1,794 genomics experiments. This catalog identifies genomic elements, accurately captures cell type...
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Method: Highly accurate assembly polishing with DeepPolisher
- Mira Mastoras,
- Mobin Asri,
- Lucas Brambrink,
- Prajna Hebbar,
- Alexey Kolesnikov,
- Daniel E. Cook,
- Maria Nattestad,
- Julian Lucas,
- Taylor S. Won,
- Pi-Chuan Chang,
- Andrew Carroll,
- Benedict Paten,
- Kishwar Shafin,
- and and the Human Pangenome Reference Consortium
Genome Res. July 2025 35: 1595-1608; Published in Advance May 19, 2025, doi:10.1101/gr.280149.124
...The first affiliated hospital of Xi'an Jiaotong University, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China; Corresponding authors: awcarroll@google.com, bpaten@ucsc.edu, shafin@google.comAbstractAccurate assemblies are essential for biological research, but even the highest...

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