James T Robinson
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Explore the profile of James T Robinson including associated specialties, affiliations and a list of published articles.
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23
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22285
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Recent Articles
1.
Panda A, Suvakov M, Thorvaldsdottir H, Mesirov J, Robinson J, Abyzov A
Bioinformatics
. 2024 Jul;
40(8).
PMID: 39018173
Summary: Copy number variation (CNV) and alteration (CNA) analysis is a crucial component in many genomic studies and its applications span from basic research to clinic diagnostics and personalized medicine....
2.
Chapman O, Luebeck J, Sridhar S, Wong I, Dixit D, Wang S, et al.
Nat Genet
. 2023 Nov;
55(12):2189-2199.
PMID: 37945900
Circular extrachromosomal DNA (ecDNA) in patient tumors is an important driver of oncogenic gene expression, evolution of drug resistance and poor patient outcomes. Applying computational methods for the detection and...
3.
Haas B, Dobin A, Ghandi M, Van Arsdale A, Tickle T, Robinson J, et al.
Cell Rep Methods
. 2023 Jun;
3(5):100467.
PMID: 37323575
Here, we present FusionInspector for characterization and interpretation of candidate fusion transcripts from RNA sequencing (RNA-seq) and exploration of their sequence and expression characteristics. We applied FusionInspector to thousands of...
4.
Okonechnikov K, Camgoz A, Chapman O, Wani S, Park D, Hubner J, et al.
Nat Commun
. 2023 Apr;
14(1):2300.
PMID: 37085539
Ependymoma is a tumor of the brain or spinal cord. The two most common and aggressive molecular groups of ependymoma are the supratentorial ZFTA-fusion associated and the posterior fossa ependymoma...
5.
Robinson J, Thorvaldsdottir H, Turner D, Mesirov J
Bioinformatics
. 2022 Dec;
39(1).
PMID: 36562559
Summary: igv.js is an embeddable JavaScript implementation of the Integrative Genomics Viewer (IGV). It can be easily dropped into any web page with a single line of code and has...
6.
Robinson J, Turner D, Durand N, Thorvaldsdottir H, Mesirov J, Aiden E
Cell Syst
. 2018 Feb;
6(2):256-258.e1.
PMID: 29428417
Contact mapping experiments such as Hi-C explore how genomes fold in 3D. Here, we introduce Juicebox.js, a cloud-based web application for exploring the resulting datasets. Like the original Juicebox application,...
7.
Robinson J, Thorvaldsdottir H, Wenger A, Zehir A, Mesirov J
Cancer Res
. 2017 Nov;
77(21):e31-e34.
PMID: 29092934
Manual review of aligned reads for confirmation and interpretation of variant calls is an important step in many variant calling pipelines for next-generation sequencing (NGS) data. Visual inspection can greatly...
8.
Rao S, Huang S, St Hilaire B, Engreitz J, Perez E, Kieffer-Kwon K, et al.
Cell
. 2017 Oct;
171(2):305-320.e24.
PMID: 28985562
The human genome folds to create thousands of intervals, called "contact domains," that exhibit enhanced contact frequency within themselves. "Loop domains" form because of tethering between two loci-almost always bound...
9.
Yuen R, Merico D, Bookman M, Howe J, Thiruvahindrapuram B, Patel R, et al.
Nat Neurosci
. 2017 Mar;
20(4):602-611.
PMID: 28263302
We are performing whole-genome sequencing of families with autism spectrum disorder (ASD) to build a resource (MSSNG) for subcategorizing the phenotypes and underlying genetic factors involved. Here we report sequencing...
10.
Durand N, Robinson J, Shamim M, Machol I, Mesirov J, Lander E, et al.
Cell Syst
. 2016 Jul;
3(1):99-101.
PMID: 27467250
Hi-C experiments study how genomes fold in 3D, generating contact maps containing features as small as 20 bp and as large as 200 Mb. Here we introduce Juicebox, a tool...