Risultati della ricerca - Leonardo Collado‐Torres

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  1. 1
    recount workflow: Accessing over 70,000 human RNA-seq samples with Bioconductor

    recount workflow: Accessing over 70,000 human RNA-seq samples with Bioconductor di Leonardo Collado‐Torres, Abhinav Nellore, Andrew E. Jaffe

    Pubblicazione 2017
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  2. 2
    Improving the value of public RNA-seq expression data by phenotype prediction

    Improving the value of public RNA-seq expression data by phenotype prediction di Shannon Ellis, Leonardo Collado‐Torres, Andrew E. Jaffe, Jeffrey T. Leek

    Pubblicazione 2018
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  3. 3
    Interspecies interactions that result in<i>Bacillus subtilis</i>forming biofilms are mediated mainly by members of its own genus

    Interspecies interactions that result in<i>Bacillus subtilis</i>forming biofilms are mediated mainly by members of its own genus di Elizabeth A. Shank, Vanja Klepac‐Ceraj, Leonardo Collado‐Torres, Gordon E. Powers, Richard Losick, Roberto Kolter

    Pubblicazione 2011
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  4. 4
    SynGAP isoforms differentially regulate synaptic plasticity and dendritic development

    SynGAP isoforms differentially regulate synaptic plasticity and dendritic development di Yoichi Araki, Ingie Hong, Timothy R. Gamache, Shaowen Ju, Leonardo Collado‐Torres, Joo Heon Shin, Richard L. Huganir

    Pubblicazione 2020
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  5. 5
    Challenges and opportunities to computationally deconvolve heterogeneous tissue with varying cell sizes using single-cell RNA-sequencing datasets

    Challenges and opportunities to computationally deconvolve heterogeneous tissue with varying cell sizes using single-cell RNA-sequencing datasets di Sean K. Maden, Sang Ho Kwon, Louise A. Huuki-Myers, Leonardo Collado‐Torres, Stephanie C. Hicks, Kristen R. Maynard

    Pubblicazione 2023
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  6. 6
    Rail-RNA: scalable analysis of RNA-seq splicing and coverage

    Rail-RNA: scalable analysis of RNA-seq splicing and coverage di Abhinav Nellore, Leonardo Collado‐Torres, Andrew E. Jaffe, José Alquicira‐Hernandez, Christopher Wilks, Jacob Pritt, James T. Morton, Jeffrey T. Leek, Ben Langmead

    Pubblicazione 2016
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  7. 7
    Reproducible RNA-seq analysis using recount2

    Reproducible RNA-seq analysis using recount2 di Leonardo Collado‐Torres, Abhinav Nellore, Kai Kammers, Shannon Ellis, Margaret A. Taub, Kasper D. Hansen, Andrew E. Jaffe, Ben Langmead, Jeffrey T. Leek

    Pubblicazione 2017
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  8. 8
    Flexible expressed region analysis for RNA-seq with<tt>derfinder</tt>

    Flexible expressed region analysis for RNA-seq with<tt>derfinder</tt> di Leonardo Collado‐Torres, Abhinav Nellore, Alyssa C. Frazee, Christopher Wilks, Michael I. Love, Ben Langmead, Rafael A. Irizarry, Jeffrey T. Leek, Andrew E. Jaffe

    Pubblicazione 2016
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  9. 9
    SpatialExperiment: infrastructure for spatially-resolved transcriptomics data in R using Bioconductor

    SpatialExperiment: infrastructure for spatially-resolved transcriptomics data in R using Bioconductor di Dario Righelli, Lukas M. Weber, Helena L. Crowell, Brenda Pardo, Leonardo Collado‐Torres, Shila Ghazanfar, Aaron T. L. Lun, Stephanie C. Hicks, Davide Risso

    Pubblicazione 2022
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  10. 10
    spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data

    spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data di Brenda Pardo, Abby Spangler, Lukas M. Weber, Stephanie C. Page, Stephanie C. Hicks, Andrew E. Jaffe, Keri Martinowich, Kristen R. Maynard, Leonardo Collado‐Torres

    Pubblicazione 2022
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  11. 11
    Human splicing diversity and the extent of unannotated splice junctions across human RNA-seq samples on the Sequence Read Archive

    Human splicing diversity and the extent of unannotated splice junctions across human RNA-seq samples on the Sequence Read Archive di Abhinav Nellore, Andrew E. Jaffe, Jean‐Philippe Fortin, José Alquicira‐Hernandez, Leonardo Collado‐Torres, Siruo Wang, Robert A. Phillips, Nishika Karbhari, Kasper D. Hansen, Ben Langmead, Jeffrey T. Leek

    Pubblicazione 2016
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  12. 12
    Comprehensive assessment of multiple biases in small RNA sequencing reveals significant differences in the performance of widely used methods

    Comprehensive assessment of multiple biases in small RNA sequencing reveals significant differences in the performance of widely used methods di Carrie Wright, Anandita Rajpurohit, Emily E. Burke, Courtney Williams, Leonardo Collado‐Torres, Martha Kimos, Nicholas J. Brandon, A.J. Cross, Andrew E. Jaffe, Daniel R. Weinberger, Joo Heon Shin

    Pubblicazione 2019
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  13. 13
    Developmental regulation of human cortex transcription and its clinical relevance at single base resolution

    Developmental regulation of human cortex transcription and its clinical relevance at single base resolution di Andrew E. Jaffe, Jooheon Shin, Leonardo Collado‐Torres, Jeffrey T. Leek, Ran Tao, Chao Li, Yuan Gao, Yankai Jia, Brady J. Maher, Thomas M. Hyde, Joel E. Kleinman, Daniel R. Weinberger

    Pubblicazione 2014
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  14. 14
    Altered expression of histamine signaling genes in autism spectrum disorder

    Altered expression of histamine signaling genes in autism spectrum disorder di Carrie Wright, Joo Heon Shin, Anandita Rajpurohit, Amy Deep‐Soboslay, Leonardo Collado‐Torres, Nicholas J. Brandon, Thomas M. Hyde, Joel E. Kleinman, Andrew E. Jaffe, A.J. Cross, Daniel R. Weinberger

    Pubblicazione 2017
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  15. 15
    Large-scale transcriptomic analyses of major depressive disorder reveal convergent dysregulation of synaptic pathways in excitatory neurons

    Large-scale transcriptomic analyses of major depressive disorder reveal convergent dysregulation of synaptic pathways in excitatory neurons di Fernando S. Goes, Leonardo Collado‐Torres, Peter P. Zandi, Louise A. Huuki-Myers, Ran Tao, Andrew E. Jaffe, Geo Pertea, Joo Heon Shin, Daniel R. Weinberger, Joel E. Kleinman, Thomas M. Hyde

    Pubblicazione 2025
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  16. 16
    Integrated DNA methylation and gene expression profiling across multiple brain regions implicate novel genes in Alzheimer’s disease

    Integrated DNA methylation and gene expression profiling across multiple brain regions implicate novel genes in Alzheimer’s disease di Stephen A. Semick, Rahul Bharadwaj, Leonardo Collado‐Torres, Ran Tao, Joo Heon Shin, Amy Deep‐Soboslay, James R. Weiss, Daniel R. Weinberger, Thomas M. Hyde, Joel E. Kleinman, Andrew E. Jaffe, Venkata S. Mattay

    Pubblicazione 2019
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  17. 17
    Incomplete annotation has a disproportionate impact on our understanding of Mendelian and complex neurogenetic disorders

    Incomplete annotation has a disproportionate impact on our understanding of Mendelian and complex neurogenetic disorders di David Zhang, Sebastian Guelfi, Sonia García-Ruiz, Beatrice Costa, Regina H. Reynolds, Karishma D’Sa, Wenfei Liu, Thomas Courtin, Amy Peterson, Andrew E. Jaffe, John Hardy, Juan A. Botía, Leonardo Collado‐Torres, Mina Ryten

    Pubblicazione 2020
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  18. 18
    Divergent neuronal DNA methylation patterns across human cortical development reveal critical periods and a unique role of CpH methylation

    Divergent neuronal DNA methylation patterns across human cortical development reveal critical periods and a unique role of CpH methylation di Amanda J. Price, Leonardo Collado‐Torres, Nikolay A. Ivanov, Wei Xia, Emily E. Burke, Joo Heon Shin, Ran Tao, Liang Ma, Yankai Jia, Thomas M. Hyde, Joel E. Kleinman, Daniel R. Weinberger, Andrew E. Jaffe

    Pubblicazione 2019
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  19. 19
    recount3: summaries and queries for large-scale RNA-seq expression and splicing

    recount3: summaries and queries for large-scale RNA-seq expression and splicing di Christopher Wilks, Shijie Zheng, Feng Yong Chen, Rone Charles, Brad Solomon, Jonathan P. Ling, Eddie L. Imada, David Zhang, Lance Joseph, Jeffrey T. Leek, Andrew E. Jaffe, Abhinav Nellore, Leonardo Collado‐Torres, Kasper D. Hansen, Ben Langmead

    Pubblicazione 2021
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  20. 20
    Benchmark of cellular deconvolution methods using a multi-assay dataset from postmortem human prefrontal cortex

    Benchmark of cellular deconvolution methods using a multi-assay dataset from postmortem human prefrontal cortex di Louise A. Huuki-Myers, Kelsey D. Montgomery, Sang Ho Kwon, Sophia Cinquemani, Nicholas J. Eagles, Daianna González‐Padilla, Sean K. Maden, Joel E. Kleinman, Thomas M. Hyde, Stephanie C. Hicks, Kristen R. Maynard, Leonardo Collado‐Torres

    Pubblicazione 2025
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