Searching journal content for articles similar to Kaplan and Linial 16 (11): 1431.

Displaying results 1-10 of 4523
For checked items
  1. Method: Balancing gene ontology annotation specificity in protein function prediction based on the protein sequence large graph
    • Jiangyi Shao,
    • Shutao Chen,
    • Ziwen Wang,
    • Zixu Chen,
    • and Bin Liu
    Genome Res. April 15, 2026 gr.280816.125; Published in Advance April 15, 2026, doi:10.1101/gr.280816.125
    ...these challenges explicit. 162 We define Gene Ontology (GO) annotation as a hierarchical multi-label 163 classification problem (Kabir and Shehu 2022). Let 𝐱 = [𝐴1, 𝐴2, … , 𝐴𝐿] denote a 164 protein sequence of length 𝐿, where each 𝐴𝑖 represents one of the 21 standard amino 165 acids(Yang et al. 2020). Let...
    ACCEPTED MANUSCRIPT
  2. Method: Fast and space-efficient taxonomic classification of long reads with hierarchical interleaved XOR filters
    • Jens-Uwe Ulrich and
    • Bernhard Y. Renard
    Genome Res. June 2024 34: 914-924; Published in Advance June 17, 2024, doi:10.1101/gr.278623.123
    ...taxonomic classification methods have large computational requirements. This issue motivated us to develop a new data structure for fast and memory-efficient querying of long reads. Here, we present Taxor as a new tool for long-read metagenomic classification using a hierarchical interleaved XOR filter data...
  3. Research: Comprehensive functional annotation of ESR1-driven enhancers in breast cancer reveals hierarchical activity independent of genomic and epigenomic contexts
    • Yanis Zekri,
    • Sebastian Gregoricchio,
    • Elif Yapıcı,
    • Chia-Chi Flora Huang,
    • Tunç Morova,
    • Umut Berkay Altıntaş,
    • Gozde Korkmaz,
    • Nathan A. Lack,
    • and Wilbert Zwart
    Genome Res. July 2025 35: 1530-1543; Published in Advance June 10, 2025, doi:10.1101/gr.280320.124
    ...and inactive ERBS did (Fig. 1G).To assess the correlation between STARR-seq-based ERBS annotation and enhancer activity within the native chromatin context, we analyzed GRO-seq signal (GEO; GSE27463) (Hah et al. 2011) at ERBS following E2 stimulation, as enhancer transcription is a well-established readout...
  4. 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
    ...al. 2023), and RefSeq (Pruitt et al. 2007). Additionally, we show that LiftOn is effective for mapping annotation between members of nonhuman species, including Mus musculus (mouse), Apis mellifera (honey bee), Arabidopsis thaliana (thale cress), and Oryza sativa (rice). To demonstrate Lift...
  5. 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
    ..., particularly for unsupervised cellular state annotation based on maximum signature score values. However, this application requires robust and comparable score distributions across diverse signatures and experimental conditions. Our systematic evaluation of established scoring methodologies—Seurat, SCANPY...
    OPEN ACCESS ARTICLE
  6. 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
    ...@iisermohali.ac.inAbstractIsoform diversity is known to enhance a gene's functional repertoire by producing protein variants with distinct functional implications. Despite numerous studies on transcriptome diversifying processes (alternative splicing/transcription), understanding their extent and correlated impact on proteome diversity...
  7. 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
    ...samples in which supportive reads were observed. (C) Structural category classification and intersection of 50 loci from the WTC11 samples that were not identified by any transcript identification tool but were manually annotated by GENCODE. These loci were selected for having mapped reads across all six...
    OPEN ACCESS ARTICLE
  8. 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
    ...'s organisms, herald a new era of possibilities and requirements for annotation. Traditionally, annotation has relied on ab initio algorithms alone or combined with short-read sequencing and proteomics data to improve gene predictions. However, with the increased availability and throughput of lr...
    OPEN ACCESS ARTICLE
  9. Research: Hierarchical architecture of neo-sex chromosomes and accelerated adaptive evolution in tortricid moths
    • Fangyuan Yang,
    • Li-Jun Cao,
    • Petr Nguyen,
    • Zhong-Zheng Ma,
    • Jin-Cui Chen,
    • Wei Song,
    • and Shu-Jun Wei
    Genome Res. January 2025 35: 66-77; Published in Advance January 6, 2025, doi:10.1101/gr.279569.124
    ...∼124 million years ago, accompanied by an SA fusion between the Merian elements M(20 + 17) and MZ. In contrast to partial autosomal fusions, the fused neo-Z Chromosome developed a hierarchical architecture, in which the three elements exhibit heterogeneous sequence features and evolutionary patterns...
  10. Method: Nematode gene annotation by machine-learning-assisted proteotranscriptomics enables proteome-wide evolutionary analysis
    • Alejandro Ceron-Noriega,
    • Miguel V. Almeida,
    • Michal Levin,
    • and Falk Butter
    Genome Res. January 2023 33: 112-128; Published in Advance January 18, 2023, doi:10.1101/gr.277070.122
    ...of nematodes is believed to date back to ∼650–750 million years, generating a large and phylogenetically diverse group to be explored. However, for most species high-quality gene annotations are incomprehensive or missing. Combining short-read RNA sequencing with mass spectrometry–based proteomics and machine...
For checked items

Search Results

Next 10 » New Search

Modify Results

Citation format:
Results / page:
Results order:

This search

  • Alert me when new articles matching this search are published
  • Download all citations on this page to my citation manager

Preprint Server



Current Issue

  1. April 2026, 36 (4)
  1. Current Issue
  1. Alert me to new issues of Genome Research