Searching journal content for articles similar to Jain et al. 12 (2): 325.

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  1. Method: SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification
    • Manuel Tardaguila,
    • Lorena de la Fuente,
    • Cristina Marti,
    • Cécile Pereira,
    • Francisco Jose Pardo-Palacios,
    • Hector del Risco,
    • Marc Ferrell,
    • Maravillas Mellado,
    • Marissa Macchietto,
    • Kenneth Verheggen,
    • Mariola Edelmann,
    • Iakes Ezkurdia,
    • Jesus Vazquez,
    • Michael Tress,
    • Ali Mortazavi,
    • Lennart Martens,
    • Susana Rodriguez-Navarro,
    • Victoria Moreno-Manzano,
    • and Ana Conesa
    Genome Res. March 2018 28: 396-411; Published in Advance February 9, 2018, doi:10.1101/gr.222976.117
    ...combinations of existing splice sites, resulting more frequently in novel ORFs than novel UTRs, and are enriched in both general metabolic and neural-specific functions. We show that these new transcripts have a major impact in the correct quantification of transcript levels by state-of-the-art short...
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  2. Methods: RNAi Microarray Analysis in Cultured Mammalian Cells
    • Spyro Mousses,
    • Natasha J. Caplen,
    • Robert Cornelison,
    • Don Weaver,
    • Mark Basik,
    • Sampsa Hautaniemi,
    • Abdel G. Elkahloun,
    • Roberto A. Lotufo,
    • Ashish Choudary,
    • Edward R. Dougherty,
    • Ed Suh,
    • and Olli Kallioniemi
    Genome Res. October 2003 13: 2341-2347; doi:10.1101/gr.1478703
    ...users are able to load, retrieve, and update experiment information in the database via a Web interface. View larger version: In this window In a new window Figure 3 Single-cell level quantification of RNAi on a microarray platform. The imaging and quantification of fluorescence in HeLa/d2eGFP cells...
  3. Methods: Microarray-based multicycle-enrichment of genomic subsets for targeted next-generation sequencing
    • Daniel Summerer,
    • Haiguo Wu,
    • Bettina Haase,
    • Yang Cheng,
    • Nadine Schracke,
    • Cord F. Stähler,
    • Mark S. Chee,
    • Peer F. Stähler,
    • and Markus Beier
    Genome Res. September 2009 19: 1616-1621; Published in Advance July 28, 2009, doi:10.1101/gr.091942.109
    ...Microarray-based multicycle-enrichment of genomic subsets for targeted next-generation sequencing Daniel Summerer 1 , 4 , Haiguo Wu 2 , Bettina Haase 1 , Yang Cheng 1 , Nadine Schracke 1 , Cord F. Stähler 1 , Mark S. Chee 3...
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  4. Methods: Automatic analysis of dividing cells in live cell movies to detect mitotic delays and correlate phenotypes in time
    • Nathalie Harder,
    • Felipe Mora-Bermúdez,
    • William J. Godinez,
    • Annelie Wünsche,
    • Roland Eils,
    • Jan Ellenberg,
    • and Karl Rohr
    Genome Res. November 2009 19: 2113-2124; Published in Advance October 1, 2009, doi:10.1101/gr.092494.109
    ...this limitation and present a fully automatic approach to determine morphological and temporal phenotypes by accurately computing and analyzing the lengths of normal and, if present, abnormal mitotic phases and their temporal correlation. Our approach is based on three-dimensional (3D) multicell confocal...
  5. Methods: Quantification of Multiple Gene Expression in Individual Cells
    • António Peixoto,
    • Marta Monteiro,
    • Benedita Rocha,
    • and Henrique Veiga-Fernandes
    Genome Res. October 2004 14: 1938-1947; doi:10.1101/gr.2890204
    ...Quantification of Multiple Gene Expression in Individual Cells António Peixoto , Marta Monteiro , Benedita Rocha 1 , and Henrique Veiga-Fernandes INSERM U591, Institut Necker, Paris, 75015 France Abstract Quantitative gene...
  6. Research: Mapping multitissue regulatory variants reveals a liver-centric coexpression network associated with duck egg-laying performance
    • Yang Xi,
    • Jingjing Qi,
    • Zhao Yang,
    • Yutian Zeng,
    • Huicong Zhang,
    • Qiuyu Tao,
    • Mengru Xu,
    • Anqi Huang,
    • Shenqiang Hu,
    • Chunchun Han,
    • Lili Bai,
    • Jiwei Hu,
    • Jiwen Wang,
    • Liang Li,
    • Lingzhao Fang,
    • and Hehe Liu
    Genome Res. October 2025 35: 2211-2225; Published in Advance September 10, 2025, doi:10.1101/gr.280345.124
    ...of each week. The horizontal and vertical axes represent the weeks and average egg production, respectively. (C) The sample clustering by PCA based on the quantification results of different molecular phenotypes. The diagrams from top to bottom represent clustering results based on gene expression...
  7. Mini-Review: The additional diagnostic yield of long-read sequencing in undiagnosed rare diseases
    • Giulia F. Del Gobbo and
    • Kym M. Boycott
    Genome Res. April 2025 35: 559-571; Published in Advance February 3, 2025, doi:10.1101/gr.279970.124
    ...assessing SR-GS for the diagnosis of NDDs, LRS was necessary to fully resolve complex SVs in four patients, supporting its specific added yield over SRS (Sanchis-Juan et al. 2023). Additional examples of LRS revealing greater complexity of SVs and/or fine-mapping breakpoints to clarify and confirm...
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  8. Method: A deconvolution framework that uses single-cell sequencing plus a small benchmark data set for accurate analysis of cell type ratios in complex tissue samples
    • Shuai Guo,
    • Xiaoqian Liu,
    • Xuesen Cheng,
    • Yujie Jiang,
    • Shuangxi Ji,
    • Qingnan Liang,
    • Andrew Koval,
    • Yumei Li,
    • Leah A. Owen,
    • Ivana K. Kim,
    • Ana Aparicio,
    • Sanghoon Lee,
    • Anil K. Sood,
    • Scott Kopetz,
    • John Paul Shen,
    • John N. Weinstein,
    • Margaret M. DeAngelis,
    • Rui Chen,
    • and Wenyi Wang
    Genome Res. January 2025 35: 147-161; Published in Advance November 25, 2024, doi:10.1101/gr.278822.123
    ...and Nekrutenko 2021). We, therefore, expect that the reference matrices derived from sc/snRNA-seq data will not fully represent cell type–specific expression profiles in bulk samples (Cobos et al. 2023; Hippen et al. 2023). Given such discrepancies, the performance of existing deconvolution methods...
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  9. Method: Proxy panels enable privacy-aware outsourcing of genotype imputation
    • Degui Zhi,
    • Xiaoqian Jiang,
    • and Arif Harmanci
    Genome Res. February 2025 35: 326-339; Published in Advance January 10, 2025, doi:10.1101/gr.278934.124
    ...infrastructure to process proxy panel data. It is, however, necessary to establish the infrastructure at each data owner/controller to perform automatic proxy panel generation; that is, every time imputation is initiated, a reference panel must be processed to generate the proxy panels. The successful adoption...
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  10. Method: Assessing transcriptomic reidentification risks using discriminative sequence models
    • Shuvom Sadhuka,
    • Daniel Fridman,
    • Bonnie Berger,
    • and Hyunghoon Cho
    Genome Res. July 2023 33: 1101-1112; Published in Advance August 4, 2023, doi:10.1101/gr.277699.123
    ...expression level measurements obtained via microarray or RNA sequencing experiments; that is, e(j) ∈ ℝG, where G is the number of genes (e.g., around 20,000).For each individual gene expression profile , the attacker scores all candidate genotype profiles according to some match score function M(x(i), e...
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