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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. February 3, 2026 ; Published in Advance February 3, 2026, doi:10.1101/gr.281001.125
...transcriptomics. Efforts have beenmade to address the limitations of these two platforms. For imaging-based technologies, researchers utilize reference scRNA-seq data setswith a larger number ofmeasured genes to impute the unmeasured genes in the spatial transcriptomics, whose related methods were already...
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Resource: MPRAbase a Massively Parallel Reporter Assay database
- Jingjing Zhao,
- Fotis A Baltoumas,
- Maxwell A Konnaris,
- Ioannis Mouratidis,
- Zhe Liu,
- Jasmine Sims,
- Vikram Agarwal,
- Georgios A Pavlopoulos,
- Ilias Georgakopoulos-Soares,
- and Nadav Ahituv
Genome Res. April 22, 2025 gr.280387.124; Published in Advance April 22, 2025, doi:10.1101/gr.280387.124
...MPRAbase (https://mprabase.ucsf.edu), a database that harbors 130 experiments, encompassing 17,718,677 sequences tested across 35 cell types and 4 organisms. In addition to storing published data, MPRAbase provides a platform for users to deposit new MPRA data and rapidly disseminate it to the functional...
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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
...a completely defined reference and corresponding isogenic wild-type strain for C. elegans, allowing unique opportunities for model and systems biology.The nematode Caenorhabditis elegans is a model for biology ranging from mechanistic functions of individual proteins and RNAs to multicellular interactions...
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Method: Highly accurate reference and method selection for universal cross–data set cell type annotation with CAMUS
- Qunlun Shen,
- Shuqin Zhang,
- and Shihua Zhang
Genome Res. November 2025 35: 2527-2538; Published in Advance October 1, 2025, doi:10.1101/gr.280821.125
...of various reference–method pairs as inputs (Methods) (Fig. 1A). It initially preclusters cells from query data into several distinct clusters (Fig. 1A) to approximate the cell type composition of the query data. It compares the concordance score between the preclustering and annotation results with various...
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Resource: Interspecies systems biology links bacterial metabolic pathways to nematode gene expression, chemotaxis behavior, and survival
- Marina Athanasouli,
- Tobias Loschko,
- and Christian Rödelsperger
Genome Res. October 2025 35: 2363-2374; Published in Advance August 5, 2025, doi:10.1101/gr.280848.125
...(PeqLab) and a Qubit 2.0 Fluorometer. The samples were shipped to Novogene for library preparation and messenger RNA (mRNA) sequencing. Libraries were sequenced as 150-bp paired-end reads on an Illumina NovoSeq 6000 platform.RNA-seq and coexpression network analysisFor the coexpression analysis, we...
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Resource: Analyzing the large and complex SFARI autism cohort data using the Genotypes and Phenotypes in Families (GPF) platform
- Liubomir Chorbadjiev,
- Murat Cokol,
- Zohar Weinstein,
- Kevin Shi,
- Christopher Fleisch,
- Nikolay Dimitrov,
- Svetlin Mladenov,
- Ivo Todorov,
- Iordan Ivanov,
- Simon Xu,
- Steven Ford,
- Yoon-ha Lee,
- Boris Yamrom,
- Steven Marks,
- Adriana Munoz,
- Alex Lash,
- Natalia Volfovsky,
- and Ivan Iossifov
Genome Res. October 2025 35: 2352-2362; Published in Advance September 16, 2025, doi:10.1101/gr.280356.124
...made it possible to pursue the search for variants associated with complex diseases. However, managing these large-scale data sets requires specialized computational tools to organize and analyze the extensive data. Genotypes and Phenotypes in Families (GPF) is an open-source platform that manages...
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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
..., Rausch T, Gardner EJ, Rodriguez OL, Guo L, Collins RL, et al. 2019. Multi-platform discovery of haplotype-resolved structural variation in human s. Nat Commun 10: 1784. doi:10.1038/s41467-018-08148-z ↵Cheng H, Jarvis ED, Fedrigo O, Koepfli KP, Urban L, Gemmell NJ, Li H. 2022. Haplotype-resolved assembly...
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Research: Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection
- Jian-Hai Chen,
- Patrick Landback,
- Deanna Arsala,
- Alexander Guzzetta,
- Shengqian Xia,
- Jared Atlas,
- Dylan Sosa,
- Yong E. Zhang,
- Jingqiu Cheng,
- Bairong Shen,
- and Manyuan Long
Genome Res. March 2025 35: 379-392; Published in Advance February 14, 2025, doi:10.1101/gr.279498.124
..., or origination stages) from the GenTree database (Zhang et al. 2010; Shao et al. 2019), which is based on Ensembl v95 of human reference version hg38 (Flicek et al. 2014). We then trans-mapped the v95 gene list of GenTree into Ensembl gene annotation (v110). The gene age inference in the GenTree database relied...
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Research: Independent expansion, selection, and hypervariability of the TBC1D3 gene family in humans
- Xavi Guitart,
- David Porubsky,
- DongAhn Yoo,
- Max L. Dougherty,
- Philip C. Dishuck,
- Katherine M. Munson,
- Alexandra P. Lewis,
- Kendra Hoekzema,
- Jordan Knuth,
- Stephen Chang,
- Tomi Pastinen,
- and Evan E. Eichler
Genome Res. November 2024 34: 1798-1810; Published in Advance August 6, 2024, doi:10.1101/gr.279299.124
...this hypothesis (Sabeti et al. 2006). However, the duplicated and highly identical sequences of TBC1D3 copies make assembly impossible with standard short-read sequencing platforms. Instead, researchers have investigated copy-number variation in SD genes using short-read sequencing data to understand patterns...
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Resource: LEMMI: a continuous benchmarking platform for metagenomics classifiers
- Mathieu Seppey,
- Mosè Manni,
- and Evgeny M. Zdobnov
Genome Res. August 2020 30: 1208-1216; Published in Advance July 2, 2020, doi:10.1101/gr.260398.119
...run. This is the best possible benchmark for developers to support their algorithm improvement claims and for advanced users interested in producing their own reference database after selecting the most efficient method.Evaluation of recent methodsThe release of the LEMMI benchmarking platform...
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