Searching journal content for articles similar to Misra et al. 12 (7): 1112.

Displaying results 1-10 of 90
For checked items
  1. Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
    • Andrew D. Bates,
    • Dawid Grzela,
    • Maciej Studzian,
    • Louise Brennan,
    • Moli Williams,
    • Conor Fawcett,
    • Beth Hammond,
    • Manreen Grewal,
    • Marcin Ratajewski,
    • Lukasz Pulaski,
    • and Urszula L. McClurg
    Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
    ...relevance, integrating the origin of DNA and protein elements (cis and trans) to evaluate false-positive and false-negative risks across experimental systems. Moreover, we explore how perturbation strategies—gain and loss of function—can complement steady-state profiling to establish causality in gene...
    OPEN ACCESS ARTICLE
  2. Method: A best-match approach for gene set analyses in embedding spaces
    • Lechuan Li,
    • Ruth Dannenfelser,
    • Charlie Cruz,
    • and Vicky Yao
    Genome Res. September 2024 34: 1421-1433; Published in Advance September 4, 2024, doi:10.1101/gr.279141.124
    ...data into more accessible lower-dimensional spaces. Applications of embedding methods to biological data have demonstrated that gene embeddings can effectively capture physical, structural, and functional relationships between genes. However, this utility has been primarily realized by using gene...
    OPEN ACCESS ARTICLE
  3. Research: Suv39h-catalyzed H3K9me3 is critical for euchromatic genome organization and the maintenance of gene transcription
    • Christine R. Keenan,
    • Hannah D. Coughlan,
    • Nadia Iannarella,
    • Andres Tapia del Fierro,
    • Andrew Keniry,
    • Timothy M. Johanson,
    • Wing Fuk Chan,
    • Alexandra L. Garnham,
    • Lachlan W. Whitehead,
    • Marnie E. Blewitt,
    • Gordon K. Smyth,
    • and Rhys S. Allan
    Genome Res. April 2024 34: 556-571; Published in Advance May 6, 2024, doi:10.1101/gr.279119.124
    ...examined the large-scale genomic compartments of the interaction space comprising the euchromatic, gene-dense, so-called A compartment and the gene-poor, heterochromatic B compartment. We found a relatively large amount of compartment switching between the Suv39DKO and control DP thymocytes (∼1...
    OPEN ACCESS ARTICLE
  4. Method: Data integration and inference of gene regulation using single-cell temporal multimodal data with scTIE
    • Yingxin Lin,
    • Tung-Yu Wu,
    • Xi Chen,
    • Sheng Wan,
    • Brian Chao,
    • Jingxue Xin,
    • Jean Y.H. Yang,
    • Wing H. Wong,
    • and Y.X. Rachel Wang
    Genome Res. January 2024 34: 119-133; Published in Advance December 15, 2023, doi:10.1101/gr.277960.123
    ...genes (HVGs) as input through a pair of coupled batchnorm layers to account for large variations in gene expression levels, making it more robust and generalizable. Third, scTIE provides the means to extract interpretable features from the common embedding space by linking the developmental trajectories...
    OPEN ACCESS ARTICLE
  5. Method: Identification of phenotype-specific networks from paired gene expression–cell shape imaging data
    • Charlie George Barker,
    • Eirini Petsalaki,
    • Girolamo Giudice,
    • Julia Sero,
    • Emmanuel Nsa Ekpenyong,
    • Chris Bakal,
    • and Evangelia Petsalaki
    Genome Res. April 2022 32: 750-765; Published in Advance February 23, 2022, doi:10.1101/gr.276059.121
    ...-related morphology enables a cell to become more susceptible to EMT, thus reinforcing their metastatic fate. This analysis was extended by Sailem and Bakal (2017), who combined cell-shape features collected from image analysis with microarray expression data for breast cancer cell lines to create a shape–gene...
    OPEN ACCESS ARTICLE
  6. Method: netNMF-sc: leveraging gene–gene interactions for imputation and dimensionality reduction in single-cell expression analysis
    • Rebecca Elyanow,
    • Bianca Dumitrascu,
    • Barbara E. Engelhardt,
    • and Benjamin J. Raphael
    Genome Res. February 2020 30: 195-204; Published in Advance January 28, 2020, doi:10.1101/gr.251603.119
    ...-out values in the transcript count matrix X. H is useful for clustering and visualizing cells in lower-dimensional space, whereas WH is useful for downstream analysis such as quantifying gene–gene correlations.We also derive a formulation of netNMF-sc with the Euclidean distance cost function (Supplemental...
  7. Research: Three-dimensional modeling of the P. falciparum genome during the erythrocytic cycle reveals a strong connection between genome architecture and gene expression
    • Ferhat Ay,
    • Evelien M. Bunnik,
    • Nelle Varoquaux,
    • Sebastiaan M. Bol,
    • Jacques Prudhomme,
    • Jean-Philippe Vert,
    • William Stafford Noble,
    • and Karine G. Le Roch
    Genome Res. June 2014 24: 974-988; Published in Advance March 26, 2014, doi:10.1101/gr.169417.113
    ...Three-dimensional modeling of the P. falciparum genome during the erythrocytic cycle reveals a strong connection between genome architecture and gene expression Ferhat Ay 1 , 7 , Evelien M. Bunnik 2 , 7 , Nelle Varoquaux 3 , 4 , 5 , 7...
  8. METHODS: Spectral Biclustering of Microarray Data: Coclustering Genes and Conditions
    • Yuval Kluger,
    • Ronen Basri,
    • Joseph T. Chang,
    • and Mark Gerstein
    Genome Res. April 1, 2003 13: 703-716; doi:10.1101/gr.648603
    ...the assumed structure of these data (e.g., whether they can be organized in a checkerboard pattern), and to design a clustering algorithm that is suitable for this structure. In particular, in analyzing microarray cancer data sets we may wish to identify both clusters of genes that participate in common...
  9. Research: Diverse gene reprogramming events occur in the same spatial clusters of distal regulatory elements
    • Ofir Hakim,
    • Myong-Hee Sung,
    • Ty C. Voss,
    • Erik Splinter,
    • Sam John,
    • Peter J. Sabo,
    • Robert E. Thurman,
    • John A. Stamatoyannopoulos,
    • Wouter de Laat,
    • and Gordon L. Hager
    Genome Res. May 2011 21: 697-706; Published in Advance April 6, 2011, doi:10.1101/gr.111153.110
    ...features of the linear genome are organized in the three-dimensional nuclear space in the context of rapid gene regulation. We found that the transcriptional response to GR occurs without dramatic nuclear reorganization. Moreover, contrary to the view of transcription-driven organization, even genes...
  10. Methods: Subsystem Identification Through Dimensionality Reduction of Large-Scale Gene Expression Data
    • Philip M. Kim and
    • Bruce Tidor
    Genome Res. July 2003 13: 1706-1718; doi:10.1101/gr.903503
    ...expression for each gene comprising the feature represented. Selection of NMF Dimensionality An essential feature of the NMF approach is that it reduces the data set from its full dimensionality (original data space) to a lower dimensional NMF space. Initial calculations were performed to select...
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. March 2026, 36 (3)
  1. Current Issue
  1. Alert me to new issues of Genome Research