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Method: Early feature extraction drives model performance in high-resolution chromatin accessibility prediction
- Aayush Grover,
- Till Muser,
- Liine Kasak,
- Lin Zhang,
- Ekaterina Krymova,
- and Valentina Boeva
Genome Res. March 2026 36: 619-629; Published in Advance January 12, 2026, doi:10.1101/gr.281042.125
...architectures—CNNs, recurrent neural networks (specifically, long short-term memory, LSTM), and dCNNs, for high-resolution chromatin accessibility prediction. Building on this, we incorporate ConvNeXt V2 (Woo et al. 2023) blocks, originally developed for vision tasks, as feature extractors across all...
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Method: EnDeep4mC predicts DNA N⁴-methylcytosine sites using a dual-adaptive feature encoding framework in deep ensembles
- Shuyu Zhang,
- Quan Zou,
- Mengting Niu,
- Zhibin Lv,
- Antony Stalin,
- and Ximei Luo
Genome Res. March 2026 36: 589-599; Published in Advance February 17, 2026, doi:10.1101/gr.280977.125
...sequential information retention, and the second (64 units) performs feature abstraction. The recurrent dropout (rate = 0.1) and batch normalization were introduced to enhance the generalization.The Transformer model features a multilayer encoder with multihead attention (two heads) and a feed...
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Research: Large palindromes on the primate X Chromosome are preserved by natural selection
- Emily K. Jackson,
- Daniel W. Bellott,
- Ting-Jan Cho,
- Helen Skaletsky,
- Jennifer F. Hughes,
- Tatyana Pyntikova,
- and David C. Page
Genome Res. August 2021 31: 1337-1352; Published in Advance July 21, 2021, doi:10.1101/gr.275188.120
...-to-arm identity and was orthologous to human palindrome P10 (Supplemental Fig. S5). In total, we discovered 21 palindromes in chimpanzee and 18 palindromes in rhesus macaque, demonstrating that X-linked palindromes are not unique to humans but represent a common feature of primate X Chromosomes, at least to Old...
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Research: Transcriptional modulation unique to vulnerable motor neurons predicts ALS across species and SOD1 mutations
- Irene Mei,
- Susanne Nichterwitz,
- Melanie Leboeuf,
- Jik Nijssen,
- Isadora Lenoel,
- Dirk Repsilber,
- Christian S. Lobsiger,
- and Eva Hedlund
Genome Res. September 2025 35: 1975-1991; Published in Advance July 17, 2025, doi:10.1101/gr.279501.124
...subjected the neurons to Smart-seq2 poly(A)-based RNA sequencing (Fig. 1A; Supplemental Fig. S1). Reads uniquely mapped to the mouse (69.7 ± 0.50% mean ± SEM) were used for further analyses (Supplemental Fig. S2A). Samples clustered by cell type with a Pearson's correlation of at least 0...
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Method: A high-throughput screening method for selecting feature SNPs to evaluate breed diversity and infer ancestry
- Meilin Zhang,
- Heng Du,
- Yu Zhang,
- Yue Zhuo,
- Zhen Liu,
- Yahui Xue,
- Lei Zhou,
- Sixuan Zhou,
- Wanying Li,
- and Jian-Feng Liu
Genome Res. August 2025 35: 1875-1886; Published in Advance July 15, 2025, doi:10.1101/gr.280176.124
...studies and ancestry inference becomes critically important. Here, we develop a method, HITSNP, that combines feature selection and machine learning algorithms to select high-representative SNPs that can effectively estimate breed diversity and infer ancestry. HITSNP outperforms existing feature selection...
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Research: Long-read genome assembly of the insect model organism Tribolium castaneum reveals spread of satellite DNA in gene-rich regions by recurrent burst events
- Marin Volarić,
- Evelin Despot-Slade,
- Damira Veseljak,
- Brankica Mravinac,
- and Nevenka Meštrović
Genome Res. November 2024 34: 1878-1894; Published in Advance October 22, 2024, doi:10.1101/gr.279225.124
...that the presence of relatively numerous and abundant satDNAs in euchromatin is not a unique feature of the T. castaneum but that the absence of satDNAs in these regions in some other assemblies is a consequence of significant gaps caused by assembling difficulties. We therefore believe that the strategy...
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Method: Latent feature extraction with a prior-based self-attention framework for spatial transcriptomics
- Zhen Li,
- Xiaoyang Chen,
- Xuegong Zhang,
- Rui Jiang,
- and Shengquan Chen
Genome Res. October 2023 33: 1757-1773; Published in Advance October 30, 2023, doi:10.1101/gr.277891.123
...data, self-attention mechanism (Liu et al. 2021) to capture spatial patterns, and a ripple walk sampler (Bai et al. 2021) to enable scalable subgraph-based training and prediction. Featured as the first ST method which integrates reference data from various sources, PAST aims to extract latent...
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Research: Assessment of palindromes as platforms for DNA amplification in breast cancer
- Jamie Guenthoer,
- Scott J. Diede,
- Hisashi Tanaka,
- Xiaoyu Chai,
- Li Hsu,
- Stephen J. Tapscott,
- and Peggy L. Porter
Genome Res. February 2012 22: 232-245; Published in Advance July 13, 2011, doi:10.1101/gr.117226.110
...associate palindromes with copy-number gains. We next profiled palindromes and copy-number gains in a set of breast cancer cell lines and primary tumors, focusing on chromosomes 8, 11, and 12, which contain genes that are recurrently amplified in breast tumors and strongly implicated in breast tumorigenesis...
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Research: L1 retrotransposition is a common feature of mammalian hepatocarcinogenesis
- Stephanie N. Schauer,
- Patricia E. Carreira,
- Ruchi Shukla,
- Daniel J. Gerhardt,
- Patricia Gerdes,
- Francisco J. Sanchez-Luque,
- Paola Nicoli,
- Michaela Kindlova,
- Serena Ghisletti,
- Alexandre Dos Santos,
- Delphine Rapoud,
- Didier Samuel,
- Jamila Faivre,
- Adam D. Ewing,
- Sandra R. Richardson,
- and Geoffrey J. Faulkner
Genome Res. May 2018 28: 639-653; Published in Advance April 11, 2018, doi:10.1101/gr.226993.117
.... This study reveals L1 mobilization as a common feature of hepatocarcinogenesis in mammals, demonstrating that the phenomenon is not restricted to human viral HCC etiologies and is encountered in murine liver tumors.Transposable element (TE) sequences make up at least half of the human and mouse s (Lander et...
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Research: Unique genetic basis of the distinct antibiotic potency of high acetic acid production in the probiotic yeast Saccharomyces cerevisiae var. boulardii
- Benjamin Offei,
- Paul Vandecruys,
- Stijn De Graeve,
- María R. Foulquié-Moreno,
- and Johan M. Thevelein
Genome Res. September 2019 29: 1478-1494; Published in Advance August 29, 2019, doi:10.1101/gr.243147.118
...unusually high levels of acetic acid, which is strongly inhibitory to bacterial growth in agar-well diffusion assays and could be vital for its unique application as a probiotic among yeasts. Using pooled-segregant whole- sequence analysis with S. boulardii and S. cerevisiae parent strains, we succeeded...
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