Jill P. Mesirov
University of California, San Diego
Publications 224
#1Konstantin Okonechnikov (DKFZ: German Cancer Research Center)H-Index: 3
#2Jens-Martin Hübner (DKFZ: German Cancer Research Center)H-Index: 1
Last.Jesse R. Dixon (Salk Institute for Biological Studies)H-Index: 15
view all 13 authors...
Signaling pathways are orchestrated by post-translational modifications (PTMs) such as phosphorylation. However, pathway analysis of PTM datasets generated by mass spectrometry (MS)-based proteomics is typically performed at a gene-centric level due to the lack of appropriately curated PTM signature databases and bioinformatic tools that leverage PTM site-specific information. Here we present the first version of PTMsigDB, a database of modification site-specific signatures of perturbations, kin...
#1Clarence K. Mah (UCSD: University of California, San Diego)H-Index: 2
#2Jill P. Mesirov (UCSD: University of California, San Diego)H-Index: 71
Last.Lukas Chavez (UCSD: University of California, San Diego)H-Index: 25
view all 3 authors...
Illumina Infinium DNA methylation arrays are a cost-effective technology to measure DNA methylation at CpG sites genome-wide and across cohorts of normal and cancer samples. While copy number alterations are commonly inferred from array-CGH, SNP arrays, or whole-genome DNA sequencing, Illumina Infinium DNA methylation arrays have been shown to detect copy number alterations at comparable sensitivity. Here we present an accessible, interactive GenePattern notebook for the analysis of copy number ...
#1Steven E. Brenner (University of California, Berkeley)H-Index: 55
#2Martha L. Bulyk (Brigham and Women's Hospital)H-Index: 48
Last.Predrag Radivojac (IU: Indiana University)H-Index: 41
view all 6 authors...
#1Daniel E. Carlin (UCSD: University of California, San Diego)H-Index: 11
#2Forrest Kim (UCSD: University of California, San Diego)
Last.Jill P. Mesirov (UCSD: University of California, San Diego)H-Index: 71
view all 4 authors...
We present a unified GenomeSpace recipe that combines the results of a high throughput CRISPR genetic screen and a biological network to return a subnetwork that suggests a mechanistic explanation of the screen’s results. The explanatory subnetwork is found by network propagation, a popular systems biology approach. We demonstrate our pipeline on an alpha toxin screen, revealing a subnetwork that is both highly interconnected and highly enriched for hits in the screen.
#1Tenley C. ArcherH-Index: 11
#2Tobias Ehrenberger (MIT: Massachusetts Institute of Technology)H-Index: 8
Last.Divya Ramamoorthy (MIT: Massachusetts Institute of Technology)H-Index: 2
view all 31 authors...
Summary There is a pressing need to identify therapeutic targets in tumors with low mutation rates such as the malignant pediatric brain tumor medulloblastoma. To address this challenge, we quantitatively profiled global proteomes and phospho-proteomes of 45 medulloblastoma samples. Integrated analyses revealed that tumors with similar RNA expression vary extensively at the post-transcriptional and post-translational levels. We identified distinct pathways associated with two subsets of SHH tumo...
#1Clarence K. Mah (UCSD: University of California, San Diego)H-Index: 2
#2Thorin Tabor (UCSD: University of California, San Diego)H-Index: 2
Last.Michael M. Reich (UCSD: University of California, San Diego)H-Index: 2
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Single-cell RNA sequencing (scRNA-seq) has emerged as a popular method to profile gene expression at the resolution of individual cells. While there have been methods and software specifically developed to analyze scRNA-seq data, they are most accessible to users who program. We have created a scRNA-seq clustering analysis GenePattern Notebook that provides an interactive, easy-to-use interface for data analysis and exploration of scRNA-Seq data, without the need to write or view any code. The n...