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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
.... Here, we present an encoder-only transformer model for assembly polishing called DeepPolisher, which predicts corrections to the underlying sequence using Pacific Biosciences (PacBio) HiFi read alignments to a diploid assembly. Our pipeline introduces a method, PHAsing Reads in Areas Of Homozygosity...
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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
...that are further compounded by the higher cost of spatial data compared to traditional single-cell data. To overcome this challenge, we introduce spRefine, a deep learning framework that leverages genomic language models to jointly denoise and impute spatial transcriptomic data. Our results demonstrate that sp...
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Method: Accurate detection of tandem repeats from error-prone sequences with EquiRep
- Zhezheng Song,
- Tasfia Zahin,
- Xiang Li,
- and Mingfu Shao
Genome Res. December 2025 35: 2714-2721; Published in Advance August 21, 2025, doi:10.1101/gr.280750.125
..., Nguyen N, Diekhans M, Zerbino D, Haussler D. 2011b. Cactus: algorithms for multiple sequence alignment. Genome Res 21: 1512–1528. doi:10.1101/gr.123356.111 ↵R Core Team. 2021. R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna. https...
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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
.... The ensemble and multi-ref strategies leveraged the advantages of both reference data sets, thereby correcting the misannotated cell types. Moreover, CAMUS perfectly aligned the ranking of these four scenarios (i.e., reference 1 only, reference 2 only, ensemble, and multi-ref) with their actual annotation...
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Method: Genetics-driven risk predictions leveraging the Mendelian randomization framework
- Daniel Sens,
- Liubov Shilova,
- Ludwig Gräf,
- Maria Grebenshchikova,
- Bjoern M. Eskofier,
- and Francesco Paolo Casale
Genome Res. September 2024 34: 1276-1285; Published in Advance September 27, 2024, doi:10.1101/gr.279252.124
...of Management, Technical University of Munich, 80333 Munich, Germany Corresponding author: francescopaolo.casale@helmholtz-munich.deAbstractAccurate predictive models of future disease onset are crucial for effective preventive healthcare, yet longitudinal data sets linking early risk factors to subsequent...
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Method: Protein domain embeddings for fast and accurate similarity search
- Benjamin Giovanni Iovino,
- Haixu Tang,
- and Yuzhen Ye
Genome Res. September 2024 34: 1434-1444; Published in Advance September 5, 2024, doi:10.1101/gr.279127.124
...Benjamin Giovanni Iovino, Haixu Tang and Yuzhen Ye Luddy School of Informatics, Computing and Engineering, Indiana University, Bloomington, Indiana 47408, USA Corresponding author: yye@iu.eduAbstractRecently developed protein language models have enabled a variety of applications with the protein...
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Method: Nanopore-based consensus sequencing enables accurate multimodal tumor cell-free DNA profiling
- Li-Ting Chen,
- Myrthe Jager,
- Dàmi Rebergen,
- Geertruid J. Brink,
- Tom van den Ende,
- Willem Vanderlinden,
- Pauline Kolbeck,
- Marc Pagès-Gallego,
- Ymke van der Pol,
- Nicolle Besselink,
- Norbert Moldovan,
- Nizar Hami,
- Wigard P. Kloosterman,
- Hanneke van Laarhoven,
- Florent Mouliere,
- Ronald Zweemer,
- Jan Lipfert,
- Sarah Derks,
- Alessio Marcozzi,
- and Jeroen de Ridder
Genome Res. April 2025 35: 886-899; Published in Advance January 13, 2025, doi:10.1101/gr.279144.124
...are essential for detecting TFs below 3%. NanoRCS provides an opportunity for cost-effective and rapid sample processing, which aligns well with clinical needs, particularly in settings where quick and accurate cancer monitoring is essential for personalized treatment strategies.A recent advancement in cancer...
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Method: Accurate allocation of multimapped reads enables regulatory element analysis at repeats
- Alexis Morrissey,
- Jeffrey Shi,
- Daniela Q. James,
- and Shaun Mahony
Genome Res. June 2024 34: 937-951; Published in Advance July 10, 2024, doi:10.1101/gr.278638.123
...genomics analysis pipelines discard “multimapped” reads that align equally well to multiple genomic locations. Because multimapped reads arise predominantly from repeats, current analysis pipelines fail to detect a substantial portion of regulatory events that occur in repetitive regions. To address...
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Method: A deconvolution framework that uses single-cell sequencing plus a small benchmark data set for accurate analysis of cell type ratios in complex tissue samples
- Shuai Guo,
- Xiaoqian Liu,
- Xuesen Cheng,
- Yujie Jiang,
- Shuangxi Ji,
- Qingnan Liang,
- Andrew Koval,
- Yumei Li,
- Leah A. Owen,
- Ivana K. Kim,
- Ana Aparicio,
- Sanghoon Lee,
- Anil K. Sood,
- Scott Kopetz,
- John Paul Shen,
- John N. Weinstein,
- Margaret M. DeAngelis,
- Rui Chen,
- and Wenyi Wang
Genome Res. January 2025 35: 147-161; Published in Advance November 25, 2024, doi:10.1101/gr.278822.123
...be leveraged to accurately deconvolve large bulk cohorts acquired through either surgical or biopsy samples. DeMixSC's enhanced deconvolution accuracy can improve the reliability of downstream cell type–specific DE analysis with any methods that rely on estimated cell type proportions (Luca et al. 2021; Wang...
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Method: Fast and accurate out-of-core PCA framework for large scale biobank data
- Zilong Li,
- Jonas Meisner,
- and Anders Albrechtsen
Genome Res. September 2023 33: 1599-1608; Published in Advance August 24, 2023, doi:10.1101/gr.277525.122
...a window-based optimization scheme that enables accelerated convergence while improving the accuracy. Additionally, PCAone incorporates out-of-core and multithreaded implementations for the existing Implicitly Restarted Arnoldi Method (IRAM) and RSVD. Through comprehensive evaluations using multiple large...

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