L. Collado-Torres
L. Collado-Torres
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SpatialExperiment: infrastructure for spatially resolved transcriptomics data in R using Bioconductor
Summary
SpatialExperiment is a new data infrastructure for storing and accessing spatially resolved transcriptomics data, implemented …
Dario Righelli __*__
,
Lukas M. Weber __*__
,
Helena L. Crowell __*__
,
Brenda Pardo
,
Leonardo Collado-Torres
,
Shila Ghazanfar
,
Aaron T. L. Lun,
,
Stephanie C. Hicks †
,
Davide Risso †
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DOI
Amygdala and anterior cingulate transcriptomes from individuals with bipolar disorder reveal downregulated neuroimmune and synaptic pathways
Recent genetic studies have identified variants associated with bipolar disorder (BD), but it remains unclear how brain gene expression …
Peter P. Zandi
,
Andrew E. Jaffe
,
Fernando S. Goes
,
Emily E. Burke
,
Leonardo Collado-Torres
,
Louise Huuki-Myers
,
Arta Seyedian
,
Yian Lin
,
Fayaz Seifuddin
,
Mehdi Pirooznia
,
Christopher A. Ross
,
Joel E. Kleinman
,
Daniel R. Weinberger
,
Thomas M. Hyde †
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Genetics and Brain Transcriptomics of Completed Suicide
Objective: The authors sought to study the transcriptomic and genomic features of completed suicide by parsing the method chosen, to …
Giovanna Punzi
,
Gianluca Ursini
,
Qiang Chen
,
Eugenia Radulescu
,
Ran Tao
,
Louise A. Huuki
,
Pasquale Di Carlo
,
Leonardo Collado-Torres
,
Joo Heon Shin
,
Roberto Catanesi
,
Andrew E. Jaffe
,
Thomas M. Hyde
,
Joel E. Kleinman
,
Trudy F.C. Mackay
,
Daniel R. Weinberger †
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recount3: summaries and queries for large-scale RNA-seq expression and splicing
We present recount3, a resource consisting of over 750,000 publicly available human and mouse RNA sequencing (RNA-seq) samples …
Christopher Wilks
,
Shijie C. Zheng
,
Feng Yong Chen
,
Rone Charles
,
Brad Solomon
,
Jonathan P. Ling
,
Eddie Luidy Imada
,
David Zhang
,
Lance Joseph
,
Jeffrey T. Leek
,
Andrew E. Jaffe
,
Abhinav Nellore
,
Leonardo Collado-Torres
,
Kasper D. Hansen †
,
Ben Langmead †
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Single-nucleus transcriptome analysis reveals cell-type-specific molecular signatures across reward circuitry in the human brain
Single-cell gene expression technologies are powerful tools to study cell types in the human brain, but efforts have largely focused on …
Matthew N. Tran __*__
,
Kristen R. Maynard __*__
,
Abby Spangler
,
Louise A. Huuki
,
Kelsey D. Montgomery
,
Vijay Sadashivaiah
,
Madhavi Tippani
,
Brianna K. Barry
,
Dana B. Hancock
,
Stephanie C. Hicks
,
Joel E. Kleinman
,
Thomas M. Hyde
,
Leonardo Collado-Torres
,
Andrew E. Jaffe †
,
Keri Martinowich †
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Genome-wide sequencing-based identification of methylation quantitative trait loci and their role in schizophrenia risk
DNA methylation (DNAm) is an epigenetic regulator of gene expression and a hallmark of gene-environment interaction. Using whole-genome …
Kira A. Perzel Mandell
,
Nicholas J. Eagles
,
Richard Wilton
,
Amanda J. Price
,
Stephen A. Semick
,
Leonardo Collado-Torres
,
William S. Ulrich
,
Ran Tao
,
Shizhong Han
,
Alexander S. Szalay
,
Thomas M. Hyde
,
Joel E. Kleinman
,
Daniel R. Weinberger †
,
Andrew E. Jaffe †
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SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/Bioconductor-powered RNA-seq analyses
Background
. RNA sequencing (RNA-seq) is a common and widespread biological assay, and an increasing amount of data is generated with …
Nicholas J. Eagles
,
Emily E. Burke
,
Jacob Leonard
,
Brianna K. Barry
,
Joshua M. Stolz
,
Louise Huuki
,
BaDoi N. Phan
,
Violeta Larios Serrato
,
Everardo Gutiérrez-Millán
,
Israel Aguilar-Ordoñez
,
Andrew E. Jaffe
,
Leonardo Collado-Torres
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Developmental Profile of Psychiatric Risk Associated With Voltage-Gated Cation Channel Activity
Background
. Recent breakthroughs in psychiatric genetics have implicated biological pathways onto which genetic risk for psychiatric …
Nicholas E. Clifton
,
Leonardo Collado-Torres
,
Emily E. Burke
,
Antonio F. Pardiñas
,
Janet C. Harwood
,
Arianna Di Florio
,
James T. R. Walters
,
Michael J. Owen
,
Michael C. O’Donovan
,
Daniel R. Weinberger
,
Peter A. Holmans
,
Andrew E. Jaffe †
,
Jeremy Hall †
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Megadepth: efficient coverage quantification for BigWigs and BAMs
Motivation
. A common way to summarize sequencing datasets is to quantify data lying within genes or other genomic intervals. This can …
Christopher Wilks
,
Omar Ahmed
,
Daniel N Baker
,
David Zhang
,
Leonardo Collado-Torres
,
Ben Langmead
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Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex
We used the 10x Genomics Visium platform to define the spatial topography of gene expression in the six-layered human dorsolateral …
Kristen R Maynard __*__
,
[__Leonardo Collado-Torres__](/authors/admin) __*__
,
Lukas M. Weber
,
Cedric Uytingco
,
Brianna K. Barry
,
Stephen R. Williams
,
Joseph L. Catallini II
,
Matthew N. Tran
,
Zachary Besich
,
Madhavi Tippani
,
Jennifer Chew
,
Yifeng Yin
,
Joel E. Kleinman
,
Thomas M. Hyde
,
Nikhil Rao
,
Stephanie C. Hicks
,
Keri Martinowich †
,
Andrew E Jaffe †
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