Searching journal content for articles similar to McCue et al. 12 (10): 1523.

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  1. Method: k-mer cross-species profiling reveals taxon-specific TE expansions accompanied by KZFP co-option and functional impacts in ruminants
    • Pengju Zhao,
    • Jiayi He,
    • Chen Peng,
    • Yuelang Zhang,
    • Chong Wang,
    • Dongyou Yu,
    • Lingzhao Fang,
    • and Zhengguang Wang
    Genome Res. March 23, 2026 gr.281289.125; Published in Advance March 23, 2026, doi:10.1101/gr.281289.125
    ...k-mer cross-species profiling reveals taxon-specific TE expansions accompanied 1 by KZFP co-option and functional impacts in ruminants 2 3 Pengju Zhao1,2*, Jiayi He1,2, Chen Peng1,2, Yuelang Zhang1,2, Chong Wang1,2, 4 Dongyou Yu1,2, Lingzhao Fang3*, Zhengguang Wang1,2* 5 6 1Hainan Institute...
    ACCEPTED MANUSCRIPT
  2. Method: Domain-adaptive neural networks improve cross-species prediction of transcription factor binding
    • Kelly Cochran,
    • Divyanshi Srivastava,
    • Avanti Shrikumar,
    • Akshay Balsubramani,
    • Ross C. Hardison,
    • Anshul Kundaje,
    • and Shaun Mahony
    Genome Res. March 2022 32: 512-523; Published in Advance January 18, 2022, doi:10.1101/gr.275394.121
    ...species should generalize to closely matched cell types in a related species. To assess the viability of cross-species TF binding prediction, we train neural networks to discriminate ChIP-seq peak locations from genomic background and evaluate their performance within and across species. Cross-species...
  3. Method: Cross-species cell-type assignment from single-cell RNA-seq data by a heterogeneous graph neural network
    • Xingyan Liu,
    • Qunlun Shen,
    • and Shihua Zhang
    Genome Res. January 2023 33: 96-111; Published in Advance December 16, 2022, doi:10.1101/gr.276868.122
    ...equally to this work. Corresponding author: zsh@amss.ac.cnAbstractCross-species comparative analyses of single-cell RNA sequencing (scRNA-seq) data allow us to explore, at single-cell resolution, the origins of the cellular diversity and evolutionary mechanisms that shape cellular form and function. Cell...
  4. Method: Cross-species analysis of enhancer logic using deep learning
    • Liesbeth Minnoye,
    • Ibrahim Ihsan Taskiran,
    • David Mauduit,
    • Maurizio Fazio,
    • Linde Van Aerschot,
    • Gert Hulselmans,
    • Valerie Christiaens,
    • Samira Makhzami,
    • Monika Seltenhammer,
    • Panagiotis Karras,
    • Aline Primot,
    • Edouard Cadieu,
    • Ellen van Rooijen,
    • Jean-Christophe Marine,
    • Giorgia Egidy,
    • Ghanem-Elias Ghanem,
    • Leonard Zon,
    • Jasper Wouters,
    • and Stein Aerts
    Genome Res. December 2020 30: 1815-1834; Published in Advance July 30, 2020, doi:10.1101/gr.260844.120
    ...identity. A better understanding of how enhancers work will improve the interpretation of noncoding variation and empower the generation of cell type–specific drivers for gene therapy. Here, we explore the combination of deep learning and cross-species chromatin accessibility profiling to build explainable...
    OPEN ACCESS ARTICLE
  5. Method: Characterizing the targets of transcription regulators by aggregating ChIP-seq and perturbation expression data sets
    • Alexander Morin,
    • Eric Ching-Pan Chu,
    • Aman Sharma,
    • Alex Adrian-Hamazaki,
    • and Paul Pavlidis
    Genome Res. May 2023 33: 763-778; Published in Advance June 12, 2023, doi:10.1101/gr.277273.122
    ...underlying gene expression programs is of considerable interest to contemporary experimental and computational biology. A fundamental objective is to map the relationships between transcription regulators (TRs) and the sets of gene targets they functionally influence. TRs, which include DNA sequence...
  6. Resource: Improved exome prioritization of disease genes through cross-species phenotype comparison
    • Peter N. Robinson,
    • Sebastian Köhler,
    • Anika Oellrich,
    • Sanger Mouse Genetics Project,
    • Kai Wang,
    • Christopher J. Mungall,
    • Suzanna E. Lewis,
    • Nicole Washington,
    • Sebastian Bauer,
    • Dominik Seelow,
    • Peter Krawitz,
    • Christian Gilissen,
    • Melissa Haendel,
    • and Damian Smedley
    Genome Res. February 2014 24: 340-348; Published in Advance October 25, 2013, doi:10.1101/gr.160325.113
    ...Improved exome prioritization of disease genes through cross-species phenotype comparison Peter N. Robinson 1 , 2 , 3 , 10 , Sebastian Köhler 1 , 2 , Anika Oellrich 4 , Sanger Mouse Genetics Project 4 , Kai Wang 5 , Christopher J...
    OPEN ACCESS ARTICLE
  7. Research: Transposon insertional mutagenesis in Saccharomyces uvarum reveals trans-acting effects influencing species-dependent essential genes
    • Monica R. Sanchez,
    • Celia Payen,
    • Frances Cheong,
    • Blake T. Hovde,
    • Sarah Bissonnette,
    • Adam P. Arkin,
    • Jeffrey M. Skerker,
    • Rachel B. Brem,
    • Amy A. Caudy,
    • and Maitreya J. Dunham
    Genome Res. March 2019 29: 396-406; Published in Advance January 11, 2019, doi:10.1101/gr.232330.117
    ...were capable of cross-species complementation, demonstrating that trans-acting factors that are background-dependent contribute to differential gene essentiality. This study shows that direct experimental testing of gene disruption phenotypes across species can inform comparative genomic analyses...
  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
    .... To this end, we present a cross–data set cell type annotation methodology with a universal reference data and method selection strategy (CAMUS) to achieve highly accurate and efficient annotations. We demonstrate the advantages of CAMUS by conducting comprehensive analyses on 672 pairs of cross-species sc...
  9. Methods: Identification and analysis of ancestral hominoid transcriptome inferred from cross-species transcript and processed pseudogene comparisons
    • Yao-Ting Huang,
    • Feng-Chi Chen,
    • Chiuan-Jung Chen,
    • Hsin-Liang Chen,
    • and Trees-Juen Chuang
    Genome Res. July 2008 18: 1163-1170; Published in Advance March 27, 2008, doi:10.1101/gr.075556.107
    ...Identification and analysis of ancestral hominoid transcriptome inferred from cross-species transcript and processed pseudogene comparisons Yao-Ting Huang 1 , 2 , Feng-Chi Chen 3 , 4 , 5 , Chiuan-Jung Chen 1 , Hsin-Liang Chen 1 , and Trees...
    OPEN ACCESS ARTICLE
  10. Method: Modeling leaderless transcription and atypical genes results in more accurate gene prediction in prokaryotes
    • Alexandre Lomsadze,
    • Karl Gemayel,
    • Shiyuyun Tang,
    • and Mark Borodovsky
    Genome Res. July 2018 28: 1079-1089; Published in Advance May 17, 2018, doi:10.1101/gr.230615.117
    ...that are difficult to filter out as false positives.An extension of GeneMarkS (known as GeneMarkS+) integrates external evidence, such as similarity to cross-species protein at a protein level or predicted RNA genes and CRISPR sequences, into ab initio gene prediction. In the NCBI annotation pipeline, Gene...
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