Searching journal content for articles similar to Gissi and Pesole 13 (9): 2203.

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  1. Method: Mapping and quantifying nascent transcript start sites using TT-TSS-seq
    • Eleanor Elgood Hunt,
    • Claudia Vivori,
    • Richard Mitter,
    • Vedis Agnadottir,
    • and Folkert J. van Werven
    Genome Res. March 2026 36: 600-610; Published in Advance February 17, 2026, doi:10.1101/gr.280726.125
    ...was applied. (E) Genomic locations of detected tags. Tag counts were normalized using the DESeq2 median-of-ratios approach using a threshold of n = 3 counts.Multiple steps of the TSS-seq protocol were optimized, including fragmentation, reverse transcription, RNA clean-up, PCR, and DNA size selection...
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  2. Perspective: Notable challenges posed by long-read sequencing for the study of transcriptional diversity and genome annotation
    • Carolina Monzó,
    • Adam Frankish,
    • and Ana Conesa
    Genome Res. April 2025 35: 583-592; Published in Advance March 3, 2025, doi:10.1101/gr.279865.124
    ...sequence tags (ESTs) and cDNAs, with fewer than 0.5 M cDNAs and ∼8.5 M ESTs ever captured. In an era of relative data sparsity, annotating every transcript detected was a plausible goal notwithstanding the immaturity of much of the software and computational tooling supporting the annotation effort...
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  3. Method: Evaluation of strategies for evidence-driven genome annotation using long-read RNA-seq
    • Alejandro Paniagua,
    • Cristina Agustín-García,
    • Francisco J. Pardo-Palacios,
    • Thomas Brown,
    • Maite De Maria,
    • Nancy D. Denslow,
    • Camila J. Mazzoni,
    • and Ana Conesa
    Genome Res. April 2025 35: 1053-1064; Published in Advance December 23, 2024, doi:10.1101/gr.279864.124
    ...Biosciences (PacBio) Sequel II CCS, and data processing methods influence evidence-driven annotation using long reads. Incorporating PacBio transcripts into our annotation pipeline significantly outperformed traditional methods, such as ab initio predictions and short-read-based annotations. We applied...
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  4. Method: Robust and efficient annotation of cell states through gene signature scoring
    • Laure Ciernik,
    • Agnieszka Kraft,
    • Florian Barkmann,
    • Josephine Yates,
    • and Valentina Boeva
    Genome Res. March 2026 36: 630-644; Published in Advance February 18, 2026, doi:10.1101/gr.280926.125
    ....DiscussionIn this study, we systematically evaluated scRNA-seq gene signature scoring methods for unsupervised cell annotation, an approach widely used in single-cell studies to characterize cellular populations. In the context of cancer research, in which transcriptional programs and diverse cellular states are strongly...
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  5. Resource: Generation and analysis of a mouse multitissue genome annotation atlas
    • Matthew Adams and
    • Christopher Vollmers
    Genome Res. November 2024 34: 2108-2117; Published in Advance October 23, 2024, doi:10.1101/gr.279217.124
    ...will be a valuable resource for genomics research by, for example, complementing existing annotations with tissue-specific information for transcriptome-dependent RNA-seq analysis by tools like Salmon (Patro et al. 2017) and kallisto (Bray et al. 2016). Further, by identifying more accurate transcript ends, TAMI...
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  6. Research: Stable genome structures in living fossil fishes
    • Cheng Wang,
    • Chase D. Brownstein,
    • Wenjun Chen,
    • Zufa Ding,
    • Dan Yu,
    • Yu Deng,
    • Chenguang Feng,
    • Thomas J. Near,
    • Shunping He,
    • and Liandong Yang
    Genome Res. February 2026 36: 318-329; Published in Advance January 13, 2026, doi:10.1101/gr.280800.125
    ...assessed s by mapping Illumina short reads to the assembled s with BWA (Li and Durbin 2009) using default parameters. We also mapped all transcripts assembled from RNA-seq reads to the using BLAST (v35.1) (Kent 2002).Repeat and protein-coding gene annotationFor repeat sequence annotation, we used...
  7. Method: Combining DNA and protein alignments to improve genome annotation with LiftOn
    • Kuan-Hao Chao,
    • Jakob M. Heinz,
    • Celine Hoh,
    • Alan Mao,
    • Alaina Shumate,
    • Mihaela Pertea,
    • and Steven L. Salzberg
    Genome Res. February 2025 35: 311-325; Published in Advance December 27, 2024, doi:10.1101/gr.279620.124
    ...alignments, and other evidence to create annotation at the scale, although these systems primarily annotate protein-coding genes. RNA sequencing (RNA-seq) can more accurately identify exon–intron structure because it directly captures gene transcripts after splicing has removed introns, although RNA-seq may...
  8. 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
    ...Highly accurate reference and method selection for universal cross–data set cell type annotation with CAMUS Qunlun Shen1,2, Shuqin Zhang1,3 and Shihua Zhang2,4,5 1School of Mathematical Sciences, Fudan University, Shanghai 200433, China; 2State Key Laboratory of Mathematical Sciences, Academy...
  9. Resource: Integrative chromatin state annotation of 234 human ENCODE4 cell types using Segway
    • Marjan Farahbod,
    • Aboud Diab,
    • Paul Sud,
    • Meenakshi S. Kagda,
    • Ian Whaling,
    • Mehdi Foroozandeh,
    • Ishan Goel,
    • Habib Daneshpajouh,
    • Benjamin Hitz,
    • J. Michael Cherry,
    • and Maxwell W. Libbrecht
    Genome Res. October 6, 2025 gr.280633.125; Published in Advance October 6, 2025, doi:10.1101/gr.280633.125
    ...4 Segway and higher prediction values for Epimap annotations. 9 We hypothesized that our higher accuracy at detecting transcription-associated activity derives from the use of genomic signals rather than binarized peak calls, leading to increased sensitivity for enhancer activity. To evaluate...
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  10. Method: Robust chromatin state annotation
    • Mehdi Foroozandeh Shahraki,
    • Marjan Farahbod,
    • and Maxwell W. Libbrecht
    Genome Res. March 2024 34: 469-483; Published in Advance March 21, 2024, doi:10.1101/gr.278343.123
    ...recapitulate known biology, and the annotations accurately represent many genomic phenomena, including transcription (Zhang and Hardison 2017; Libbrecht et al. 2019, 2021). However, results are often dissimilar between SAGA methods and hyperparameter settings of a given method (Hoffman et al. 2013; Zhang...
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