Activity‐regulated gene expression across cell types of the mouse hippocampus
Nelson, Erik D., Maynard, Kristen R., Nicholas, Kyndall R., Tran, Matthew N., Divecha, Heena R., Collado‐Torres, Leonardo, Hicks, Stephanie C., Martinowich, Keri
Published in Hippocampus (01.09.2023)
Published in Hippocampus (01.09.2023)
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Integrated Transcriptomic and Proteomic Analysis of Primary Human Umbilical Vein Endothelial Cells
Madugundu, Anil K., Na, Chan Hyun, Nirujogi, Raja Sekhar, Renuse, Santosh, Kim, Kwang Pyo, Burns, Kathleen H., Wilks, Christopher, Langmead, Ben, Ellis, Shannon E., Collado‐Torres, Leonardo, Halushka, Marc K., Kim, Min‐Sik, Pandey, Akhilesh
Published in Proteomics (Weinheim) (01.08.2019)
Published in Proteomics (Weinheim) (01.08.2019)
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recount3: summaries and queries for large-scale RNA-seq expression and splicing
Wilks, Christopher, Zheng, Shijie C, Chen, Feng Yong, Charles, Rone, Solomon, Brad, Ling, Jonathan P, Imada, Eddie Luidy, Zhang, David, Joseph, Lance, Leek, Jeffrey T, Jaffe, Andrew E, Nellore, Abhinav, Collado-Torres, Leonardo, Hansen, Kasper D, Langmead, Ben
Published in Genome Biology (29.11.2021)
Published in Genome Biology (29.11.2021)
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Journal Article
Developmental and genetic regulation of the human cortex transcriptome illuminate schizophrenia pathogenesis
Jaffe, Andrew E., Straub, Richard E., Shin, Joo Heon, Tao, Ran, Gao, Yuan, Collado-Torres, Leonardo, Kam-Thong, Tony, Xi, Hualin S., Quan, Jie, Chen, Qiang, Colantuoni, Carlo, Ulrich, William S., Maher, Brady J., Deep-Soboslay, Amy, Cross, Alan J., Brandon, Nicholas J., Leek, Jeffrey T., Hyde, Thomas M., Kleinman, Joel E., Weinberger, Daniel R.
Published in Nature neuroscience (01.08.2018)
Published in Nature neuroscience (01.08.2018)
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spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data
Pardo, Brenda, Spangler, Abby, Weber, Lukas M, Page, Stephanie C, Hicks, Stephanie C, Jaffe, Andrew E, Martinowich, Keri, Maynard, Kristen R, Collado-Torres, Leonardo
Published in BMC genomics (10.06.2022)
Published in BMC genomics (10.06.2022)
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BiocMAP: a Bioconductor-friendly, GPU-accelerated pipeline for bisulfite-sequencing data
Eagles, Nicholas J, Wilton, Richard, Jaffe, Andrew E, Collado-Torres, Leonardo
Published in BMC bioinformatics (13.09.2023)
Published in BMC bioinformatics (13.09.2023)
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Journal Article
Regional Heterogeneity in Gene Expression, Regulation, and Coherence in the Frontal Cortex and Hippocampus across Development and Schizophrenia
Collado-Torres, Leonardo, Burke, Emily E., Peterson, Amy, Shin, JooHeon, Straub, Richard E., Rajpurohit, Anandita, Semick, Stephen A., Ulrich, William S., Price, Amanda J., Valencia, Cristian, Tao, Ran, Deep-Soboslay, Amy, Hyde, Thomas M., Kleinman, Joel E., Weinberger, Daniel R., Jaffe, Andrew E.
Published in Neuron (Cambridge, Mass.) (17.07.2019)
Published in Neuron (Cambridge, Mass.) (17.07.2019)
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Comprehensive assessment of multiple biases in small RNA sequencing reveals significant differences in the performance of widely used methods
Wright, Carrie, Rajpurohit, Anandita, Burke, Emily E, Williams, Courtney, Collado-Torres, Leonardo, Kimos, Martha, Brandon, Nicholas J, Cross, Alan J, Jaffe, Andrew E, Weinberger, Daniel R, Shin, Joo Heon
Published in BMC genomics (21.06.2019)
Published in BMC genomics (21.06.2019)
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Challenges and opportunities to computationally deconvolve heterogeneous tissue with varying cell sizes using single-cell RNA-sequencing datasets
Maden, Sean K, Kwon, Sang Ho, Huuki-Myers, Louise A, Collado-Torres, Leonardo, Hicks, Stephanie C, Maynard, Kristen R
Published in Genome Biology (14.12.2023)
Published in Genome Biology (14.12.2023)
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Journal Article
Integrated DNA methylation and gene expression profiling across multiple brain regions implicate novel genes in Alzheimer’s disease
Semick, Stephen A., Bharadwaj, Rahul A., Collado-Torres, Leonardo, Tao, Ran, Shin, Joo Heon, Deep-Soboslay, Amy, Weiss, James R., Weinberger, Daniel R., Hyde, Thomas M., Kleinman, Joel E., Jaffe, Andrew E., Mattay, Venkata S.
Published in Acta neuropathologica (01.04.2019)
Published in Acta neuropathologica (01.04.2019)
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Journal Article
Genetics and Brain Transcriptomics of Completed Suicide
Punzi, Giovanna, Ursini, Gianluca, Chen, Qiang, Radulescu, Eugenia, Tao, Ran, Huuki, Louise A, Di Carlo, Pasquale, Collado-Torres, Leonardo, Shin, Joo Heon, Catanesi, Roberto, Jaffe, Andrew E, Hyde, Thomas M, Kleinman, Joel E, Mackay, Trudy F C, Weinberger, Daniel R
Published in The American journal of psychiatry (01.03.2022)
Published in The American journal of psychiatry (01.03.2022)
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Journal Article
Divergent neuronal DNA methylation patterns across human cortical development reveal critical periods and a unique role of CpH methylation
Price, Amanda J, Collado-Torres, Leonardo, Ivanov, Nikolay A, Xia, Wei, Burke, Emily E, Shin, Joo Heon, Tao, Ran, Ma, Liang, Jia, Yankai, Hyde, Thomas M, Kleinman, Joel E, Weinberger, Daniel R, Jaffe, Andrew E
Published in Genome Biology (26.09.2019)
Published in Genome Biology (26.09.2019)
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Journal Article
SynGAP isoforms differentially regulate synaptic plasticity and dendritic development
Araki, Yoichi, Hong, Ingie, Gamache, Timothy R, Ju, Shaowen, Collado-Torres, Leonardo, Shin, Joo Heon, Huganir, Richard L
Published in eLife (24.06.2020)
Published in eLife (24.06.2020)
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Journal Article
Data-driven identification of total RNA expression genes for estimation of RNA abundance in heterogeneous cell types highlighted in brain tissue
Huuki-Myers, Louise A, Montgomery, Kelsey D, Kwon, Sang Ho, Page, Stephanie C, Hicks, Stephanie C, Maynard, Kristen R, Collado-Torres, Leonardo
Published in Genome Biology (16.10.2023)
Published in Genome Biology (16.10.2023)
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Journal Article
Genome-wide sequencing-based identification of methylation quantitative trait loci and their role in schizophrenia risk
Perzel Mandell, Kira A., Eagles, Nicholas J., Wilton, Richard, Price, Amanda J., Semick, Stephen A., Collado-Torres, Leonardo, Ulrich, William S., Tao, Ran, Han, Shizhong, Szalay, Alexander S., Hyde, Thomas M., Kleinman, Joel E., Weinberger, Daniel R., Jaffe, Andrew E.
Published in Nature communications (02.09.2021)
Published in Nature communications (02.09.2021)
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Human splicing diversity and the extent of unannotated splice junctions across human RNA-seq samples on the Sequence Read Archive
Nellore, Abhinav, Jaffe, Andrew E, Fortin, Jean-Philippe, Alquicira-Hernández, José, Collado-Torres, Leonardo, Wang, Siruo, Phillips, III, Robert A, Karbhari, Nishika, Hansen, Kasper D, Langmead, Ben, Leek, Jeffrey T
Published in Genome Biology (30.12.2016)
Published in Genome Biology (30.12.2016)
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Interspecies interactions that result in Bacillus subtilis forming biofilms are mediated mainly by members of its own genus
Shank, Elizabeth A, Klepac-Ceraj, Vanja, Collado-Torres, Leonardo, Powers, Gordon E, Losick, Richard, Kolter, Roberto
Published in Proceedings of the National Academy of Sciences - PNAS (29.11.2011)
Published in Proceedings of the National Academy of Sciences - PNAS (29.11.2011)
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SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor-powered RNA-seq analyses
Eagles, Nicholas J, Burke, Emily E, Leonard, Jacob, Barry, Brianna K, Stolz, Joshua M, Huuki, Louise, Phan, BaDoi N, Serrato, Violeta Larios, Gutiérrez-Millán, Everardo, Aguilar-Ordoñez, Israel, Jaffe, Andrew E, Collado-Torres, Leonardo
Published in BMC bioinformatics (01.05.2021)
Published in BMC bioinformatics (01.05.2021)
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Journal Article
Sex affects transcriptional associations with schizophrenia across the dorsolateral prefrontal cortex, hippocampus, and caudate nucleus
Benjamin, Kynon J. M., Arora, Ria, Feltrin, Arthur S., Pertea, Geo, Giles, Hunter H., Stolz, Joshua M., D’Ignazio, Laura, Collado-Torres, Leonardo, Shin, Joo Heon, Ulrich, William S., Hyde, Thomas M., Kleinman, Joel E., Weinberger, Daniel R., Paquola, Apuã C. M., Erwin, Jennifer A.
Published in Nature communications (10.05.2024)
Published in Nature communications (10.05.2024)
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Journal Article
Recounting the FANTOM CAGE-Associated Transcriptome
Imada, Eddie Luidy, Sanchez, Diego Fernando, Collado-Torres, Leonardo, Wilks, Christopher, Matam, Tejasvi, Dinalankara, Wikum, Stupnikov, Aleksey, Lobo-Pereira, Francisco, Yip, Chi-Wai, Yasuzawa, Kayoko, Kondo, Naoto, Itoh, Masayoshi, Suzuki, Harukazu, Kasukawa, Takeya, Hon, Chung-Chau, de Hoon, Michiel J L, Shin, Jay W, Carninci, Piero, Jaffe, Andrew E, Leek, Jeffrey T, Favorov, Alexander, Franco, Gloria R, Langmead, Ben, Marchionni, Luigi
Published in Genome research (01.07.2020)
Published in Genome research (01.07.2020)
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