Searching journal content for articles similar to Pharkya et al. 14 (11): 2367.

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Method: A scalable computational framework for predicting gene expression from candidate cis-regulatory elements
- Qinhu Zhang,
- Siguo Wang,
- Zhipeng Li,
- Wenzheng Bao,
- Wenjian Liu,
- and De-Shuang Huang
Genome Res. February 2026 36: 361-374; Published in Advance January 16, 2026, doi:10.1101/gr.281219.125
...@eitech.edu.cnAbstractDeciphering the relationships between cis-regulatory elements (CREs) and target gene expression has been a long-standing unsolved problem in molecular biology, and the dynamics of CREs in different cell types make this problem more challenging. To address this challenge, we propose a scalable computational framework...
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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
..., requires efficient computational detection methods due to experimental limitations. Although machine learning predictors have been proposed, their performance could be enhanced through systematic optimization of feature encoding schemes. Here, we propose EnDeep4mC, a dual-adaptive framework integrating...
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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
..., Germany Corresponding author: christian.roedelsperger@tuebingen.mpg.deAbstractAll animals live in tight association with complex microbial communities, yet studying the effects of individual bacteria remains challenging. Bacterial feeding nematodes are powerful systems to study host-microbe interactions...
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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
...understanding of aging and cancer processes. Details of model development are discussed in the Methods section.View larger version: In this window In a new window Figure 1. The landscape of spRefine and related applications. (A) The computation framework of spRefine as a tool for imputation and denoising. sp...
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Resource: A systems view on DNA damage response kinetics in Tetrahymena
- Emily Nischwitz,
- Vivien A.C. Schoonenberg,
- Rachel Mullner,
- Albert Fradera-Sola,
- Susanne Zimbelmann,
- Joshua J. Smith,
- and Falk Butter
Genome Res. January 28, 2026 ; Published in Advance January 28, 2026, doi:10.1101/gr.281000.125
...Hospital and Harvard Medical School, Boston, MA 02114, USA; 8Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany Corresponding author: falk.butter@fli.de Article published online before print. Article, supplemental material, and publication date...
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Method: Geometric deep learning framework for de novo genome assembly
- Lovro Vrček,
- Xavier Bresson,
- Thomas Laurent,
- Martin Schmitz,
- Kenji Kawaguchi,
- and Mile Šikić
Genome Res. April 2025 35: 839-849; Published in Advance October 29, 2024, doi:10.1101/gr.279307.124
...Geometric deep learning framework for de novo assembly Lovro Vrček1,2, Xavier Bresson3, Thomas Laurent4, Martin Schmitz1,3, Kenji Kawaguchi3 and Mile Šikić1,2 1Genome Institute of Singapore, A*STAR, Singapore 138672; 2Faculty of Electrical Engineering and Computing, University of Zagreb, 10000...
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Method: A novel multislice framework for precision 3D spatial domain reconstruction and disease pathology analysis
- Daijun Zhang,
- Ren Qi,
- Xun Lan,
- and Bin Liu
Genome Res. August 2025 35: 1794-1808; Published in Advance July 14, 2025, doi:10.1101/gr.280281.124
...of tissues, providing novel insights into cellular architecture within intricate biological systems (Berglund et al. 2020; Piwecka et al. 2023). In this study, STMSC, a novel multislice joint analysis framework with a precorrection mechanism, was introduced to overcome the limitations of traditional methods...
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Method: Exon Nomenclature And Classification of Transcripts (ENACT) provides a systematic framework to annotate exon attributes
- Paras Verma,
- Deeksha Thakur,
- Deepanshi Awasthi,
- and Shashi Bhushan Pandit
Genome Res. June 2025 35: 1440-1455; Published in Advance May 7, 2025, doi:10.1101/gr.279878.124
....To achieve the integration of this distinct information, we developed the exon nomenclature and classification of transcripts (ENACT) framework. ENACT's systematic translation-focused, exon-centric design streamlines the computational tracking of exonic loci while facilitating the manual and automatic...
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Method: ESICCC as a systematic computational framework for evaluation, selection, and integration of cell-cell communication inference methods
- Jiaxin Luo,
- Minghua Deng,
- Xuegong Zhang,
- and Xiaoqiang Sun
Genome Res. October 2023 33: 1788-1805; Published in Advance October 12, 2023, doi:10.1101/gr.278001.123
..., stability, and usability have not been comprehensively evaluated and compared, which significantly impedes the development, assessment, and application of CCC inference methods. To address this challenging gap, in this paper, we have proposed a systematic computational framework, ESICCC, for evaluating...
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Method: Accurate estimation of intraspecific microbial gene content variation in metagenomic data with MIDAS v3 and StrainPGC
- Byron J. Smith,
- Chunyu Zhao,
- Veronika Dubinkina,
- Xiaofan Jin,
- Liron Zahavi,
- Saar Shoer,
- Jacqueline Moltzau-Anderson,
- Eran Segal,
- and Katherine S. Pollard
Genome Res. May 2025 35: 1247-1260; Published in Advance April 10, 2025, doi:10.1101/gr.279543.124
...-pure gene content (StrainPGC), a computational method designed to accurately estimate the gene content of individual microbial strains. StrainPGC leverages modern strain tracking tools to separate samples into strain-pure subsets in order to combine data from pan profiling across multiple metas. We also...
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