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Method: Diffusion-based generation of gene regulatory networks from scRNA-seq data with DigNet
- Chuanyuan Wang and
- Zhi-Ping Liu
Genome Res. February 2025 35: 340-354; Published in Advance December 18, 2024, doi:10.1101/gr.279551.124
...space modeling, DigNet is robust to the presence of noise in scRNA-seq data and the sparsity of GRNs. Benchmark evaluation results against more than a dozen state-of-the-art network inference methods demonstrate that DigNet achieves superior performance across various single-cell GRN reconstruction...
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Method: High-fidelity bidirectional translation between single-cell transcriptomes and DNA methylomes with scBOND
- Kehan Lang,
- Chenyang Jia,
- Siyu Li,
- Yi Guo,
- Dingjun Hu,
- and Shengquan Chen
Genome Res. April 2026 36: 769-784; Published in Advance March 26, 2026, doi:10.1101/gr.281350.125
...(Argelaguet et al. 2019). To ensure robust performance evaluation, we conducted fivefold cross-validation on the data set, using 80% of the cells for training the model and holding out the remaining 20% for translating in each fold. We benchmarked scBOND against two existing methods, scCross (Yang et al. 2024...
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Method: Autoencoders for genomic variation analysis
- Margarita Geleta,
- Daniel Mas Montserrat,
- Xavier Giro-i-Nieto,
- and Alexander G. Ioannidis
Genome Res. February 2026 36: 348-360; Published in Advance January 20, 2026, doi:10.1101/gr.280086.124
...), a multilayer perceptron (MLP) that addresses the geographical coordinate regression problem by estimating a nonlinear function mapping genotypes to locations; and Diet Networks (Romero et al. 2016), which represent another deep-learning-based ancestry classifier within this paradigm of methods. Nevertheless...
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Resource: Assemblathon 1: A competitive assessment of de novo short read assembly methods
- Dent Earl,
- Keith Bradnam,
- John St. John,
- Aaron Darling,
- Dawei Lin,
- Joseph Fass,
- Hung On Ken Yu,
- Vince Buffalo,
- Daniel R. Zerbino,
- Mark Diekhans,
- Ngan Nguyen,
- Pramila Nuwantha Ariyaratne,
- Wing-Kin Sung,
- Zemin Ning,
- Matthias Haimel,
- Jared T. Simpson,
- Nuno A. Fonseca,
- İnanç Birol,
- T. Roderick Docking,
- Isaac Y. Ho,
- Daniel S. Rokhsar,
- Rayan Chikhi,
- Dominique Lavenier,
- Guillaume Chapuis,
- Delphine Naquin,
- Nicolas Maillet,
- Michael C. Schatz,
- David R. Kelley,
- Adam M. Phillippy,
- Sergey Koren,
- Shiaw-Pyng Yang,
- Wei Wu,
- Wen-Chi Chou,
- Anuj Srivastava,
- Timothy I. Shaw,
- J. Graham Ruby,
- Peter Skewes-Cox,
- Miguel Betegon,
- Michelle T. Dimon,
- Victor Solovyev,
- Igor Seledtsov,
- Petr Kosarev,
- Denis Vorobyev,
- Ricardo Ramirez-Gonzalez,
- Richard Leggett,
- Dan MacLean,
- Fangfang Xia,
- Ruibang Luo,
- Zhenyu Li,
- Yinlong Xie,
- Binghang Liu,
- Sante Gnerre,
- Iain MacCallum,
- Dariusz Przybylski,
- Filipe J. Ribeiro,
- Shuangye Yin,
- Ted Sharpe,
- Giles Hall,
- Paul J. Kersey,
- Richard Durbin,
- Shaun D. Jackman,
- Jarrod A. Chapman,
- Xiaoqiu Huang,
- Joseph L. DeRisi,
- Mario Caccamo,
- Yingrui Li,
- David B. Jaffe,
- Richard E. Green,
- David Haussler,
- Ian Korf,
- and Benedict Paten
Genome Res. December 2011 21: 2224-2241; Published in Advance September 16, 2011, doi:10.1101/gr.126599.111
...Illumina HiSeq data set of an unknown, simulated diploid . A total of 41 assemblies from 17 different groups were received. Novel haplotype aware assessments of coverage, contiguity, structure, base calling, and copy number were made. We establish that within this benchmark: (1) It is possible to assemble...
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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
...beads. To focus on individual candidate genes predicted to be bound by the protein of interest, precipitated DNA can be analyzed using qPCR with primers designed specifically against the regulatory sequences of the GOIs. Alternatively, in ChIP-seq following precipitation, cross-links are reversed...
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Method: Integration of high-throughput proteomic data and complementary omics layers with PriOmics
- Robin Kosch,
- Katharina Limm,
- Annette M. Staiger,
- Nadine S. Kurz,
- Nicole Seifert,
- Bence Oláh,
- Stefan Solbrig,
- Viola Poeschel,
- Gerhard Held,
- Marita Ziepert,
- Norbert Schmitz,
- Emil Chteinberg,
- Reiner Siebert,
- Rainer Spang,
- Helena U. Zacharias,
- German Ott,
- Peter J. Oefner,
- and Michael Altenbuchinger
Genome Res. January 2026 36: 197-213; Published in Advance November 18, 2025, doi:10.1101/gr.279487.124
...aggregation faces a more complicated problem, as peptides, especially modified versions, may exhibit different behaviors and functional roles than their nonmodified counterparts. Further, the data quality between both fields differs a lot. Bulk RNA-seq typically provides sufficiently high read counts, whereas...
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Perspective: Tagmentation-based single-cell genomics
- Andrew C. Adey
Genome Res. October 2021 31: 1693-1705; doi:10.1101/gr.275223.121
...to always use HPLC-purified oligonucleotides and perform activity-based quantification using standard adapters and benchmarking against commercially-available options. Other modes of failure include protein that has not properly folded or inaccurate quantification of active enzyme, the latter of which can...
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Method: Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation
- Sergey Koren,
- Brian P. Walenz,
- Konstantin Berlin,
- Jason R. Miller,
- Nicholas H. Bergman,
- and Adam M. Phillippy
Genome Res. May 2017 27: 722-736; Published in Advance March 15, 2017, doi:10.1101/gr.215087.116
...(Chum et al. 2008). Applied to the read overlapping problem, the weighting is a multiplicative combination of the number of occurrences of a k-mer inside a read (the document) and the overall rarity of the k-mer among all reads (the corpus). For document similarity, the intuition is that a rare word...
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Resource: BayesCall: A model-based base-calling algorithm for high-throughput short-read sequencing
- Wei-Chun Kao,
- Kristian Stevens,
- and Yun S. Song
Genome Res. October 2009 19: 1884-1895; Published in Advance August 6, 2009, doi:10.1101/gr.095299.109
..., characterization, and analysis. In this paper, we address an important problem pertinent to data acquisition, namely, developing improved base-calling algorithms for highthroughput sequencing. The main challenges are to reduce the error rate, to assign more accurate base-specific quality scores, and to reduce...

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