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Next-Generation DNA Sequencing/Review: Microbial community profiling for human microbiome projects: Tools, techniques, and challenges
- Micah Hamady and
- Rob Knight
Genome Res. July 2009 19: 1141-1152; Published in Advance April 21, 2009, doi:10.1101/gr.085464.108
...microbes as unimportant: Many pathogens are rare and can be detected at low levels using PCRbased assays in clinically relevant settings. Thus, the appropriate trade-off between depth of coverage and number of samples is likely to vary depending on the goal of the study. It is likely that the frequent...
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Method: High-resolution spatial transcriptomics in fixed tissue using a cost-effective PCL-seq workflow
- Xue Dong,
- Mengzhu Hu,
- Xiaonan Cui,
- Wenjian Zhou,
- Jingtao Cai,
- Guangyao Mao,
- and Weiyang Shi
Genome Res. September 2025 35: 2052-2063; Published in Advance August 5, 2025, doi:10.1101/gr.279906.124
...regions (Fig. 4E). To further analyze these DEGs, we consulted the Gene Ontology (GO) database (https://geneontology.org/) for gene sets associated with limb and spine development. Key GO terms, including those related to limb development (GO:0060173) and spine development (GO:0060996), were retrieved...
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Research: Modeling alternative translation initiation sites in plants reveals evolutionarily conserved cis-regulatory codes in eukaryotes
- Ting-Ying Wu,
- Ya-Ru Li,
- Kai-Jyun Chang,
- Jhen-Cheng Fang,
- Daisuke Urano,
- and Ming-Jung Liu
Genome Res. February 2024 34: 272-285; Published in Advance March 13, 2024, doi:10.1101/gr.278100.123
...and machine learning, we developed models for predicting alternative TISs in the tomato (Solanum lycopersicum). Distinct feature sets were predictive of AUG and nonAUG TISs in 5′ untranslated regions and coding sequences, including a novel CU-rich sequence that promoted plant TIS activity, a translational...
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Resource: The SynMall resource for characterizing the functional impact of synonymous variation
- Chen Ye,
- Xiaoyan Li,
- Na Cheng,
- Yansen Su,
- and Junfeng Xia
Genome Res. February 2026 36: 421-431; Published in Advance December 17, 2025, doi:10.1101/gr.281257.125
...assessment. At the protein level, SynMall adopts an advanced model capable of extracting rich structural information from standalone protein sequences.To demonstrate the utility of the feature module, we analyze a curated data set (Supplemental Methods) using extracted DNA, RNA, and protein features. We...
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Resource: Quadrupia provides a comprehensive catalog of G-quadruplexes across genomes from the tree of life
- Nikol Chantzi,
- Akshatha Nayak,
- Fotis A. Baltoumas,
- Eleni Aplakidou,
- Shiau Wei Liew,
- Jesslyn Elvaretta Galuh,
- Michail Patsakis,
- Austin Montgomery,
- Camille Moeckel,
- Ioannis Mouratidis,
- Saiful Arefeen Sazed,
- Wilfried Guiblet,
- Panagiotis Karmiris-Obratański,
- Guliang Wang,
- Apostolos Zaravinos,
- Karen M. Vasquez,
- Chun Kit Kwok,
- Georgios A. Pavlopoulos,
- and Ilias Georgakopoulos-Soares
Genome Res. November 2025 35: 2578-2600; Published in Advance August 26, 2025, doi:10.1101/gr.279790.124
..., there are different databases available incorporating the identification of potential G4 DNA-forming sequences in different organisms; however, all available data sets cover a small number of species or taxa. Zhong et al. (2023) constructed G4Bank, a G4 database containing 6 million G4s across 13 species (Zhong et al...
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Resource: High-quality assembly of the Chinese white truffle genome and recalibrated divergence time estimate provide insight into the evolutionary dynamics of Tuberaceae
- Jacopo Martelossi,
- Jacopo Vujovic,
- Yue Huang,
- Alessia Tatti,
- Kaiwei Xu,
- Federico Puliga,
- Yuanxue Chen,
- Omar Rota Stabelli,
- Fabrizio Ghiselli,
- Xiaoping Zhang,
- and Alessandra Zambonelli
Genome Res. November 2025 35: 2601-2616; Published in Advance August 21, 2025, doi:10.1101/gr.280368.124
...; Miyauchi et al. 2020) have demonstrated that high TE content and a reduced set of plant cell wall–degrading enzymes are recurring genomic features among ECM fungi. As all known Tuberaceae species exhibit an ECM lifestyle (Bonito and Smith 2016), this family represents a valuable model for investigating...
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Mini-Review: A Hitchhiker's Guide to long-read genomic analysis
- Medhat Mahmoud,
- Daniel P. Agustinho,
- and Fritz J. Sedlazeck
Genome Res. April 2025 35: 545-558; doi:10.1101/gr.279975.124
...-based approach (Guo et al. 2018). In addition, specific methods such as StrSpy leverage TRs’ high variability between individuals for forensic applications by targeting only a small set of TRs (Hall et al. 2022). A significant challenge in TR detection lies in the inconsistent definition of repeat units across...
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Method: Inferring and comparing metabolism across heterogeneous sets of annotated genomes using AuCoMe
- Arnaud Belcour,
- Jeanne Got,
- Méziane Aite,
- Ludovic Delage,
- Jonas Collén,
- Clémence Frioux,
- Catherine Leblanc,
- Simon M. Dittami,
- Samuel Blanquart,
- Gabriel V. Markov,
- and Anne Siegel
Genome Res. June 2023 33: 972-987; Published in Advance July 19, 2023, doi:10.1101/gr.277056.122
...and is able to aggregate heterogeneous information in both prokaryote and eukaryote data sets. AuCoMe combines metabolic network reconstruction, propagation, and verification of annotations. The method automatizes the strategy of transferring information from the annotations of the s and complements...
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Method: Analyzing rare mutations in metagenomes assembled using long and accurate reads
- Marcus W. Fedarko,
- Mikhail Kolmogorov,
- and Pavel A. Pevzner
Genome Res. November/December 2022 32: 2119-2133; Published in Advance November 23, 2022, doi:10.1101/gr.276917.122
...of “complete metagenomics” by enabling complete or nearly complete assemblies of hundreds of MAGs from a single HiFi data set (Kolmogorov et al. 2020; Bickhart et al. 2022; Kim et al. 2022). This shift allows fundamentally new possibilities in the analysis of metas.Identifying rare mutations in metagenomic...
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Research: Population genomics reveals mechanisms and dynamics of de novo expressed open reading frame emergence in Drosophila melanogaster
- Anna Grandchamp,
- Lucas Kühl,
- Marie Lebherz,
- Kathrin Brüggemann,
- John Parsch,
- and Erich Bornberg-Bauer
Genome Res. June 2023 33: 872-890; Published in Advance July 13, 2023, doi:10.1101/gr.277482.122
...ORFs and the ORFs that they detected, we found that 64 ORFs were common to the two data sets (Supplemental Table S27), all of them being shared by several lines. As we show in this manuscript, most neORFs are line specific. This result suggests that most line-specific neORFs are not yet widely translated. Another...

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