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Large-Scale Uniform Analysis of Cancer Whole Genomes in Multiple Computing Environments

https://doi.org/10.1101/161638
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Inferred edges come from two machine sources: sweeps of open repository metadata (mostly SSRN and Zenodo), and a bulk OpenAlex citation snapshot. Every row below is labelled with the one it came from. Neither is a complete citation index — absence here is not evidence of absence.

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/0471250953.bi1507s52openalex-snapshot
cgpPindel: Identifying Somatically Acquired Insertion and Deletion Events from Paired End Sequencing
inferredcites →https://doi.org/10.1002/cpbi.17openalex-snapshot
ascatNgs: Identifying Somatically Acquired Copy‐Number Alterations from Whole‐Genome Sequencing Data
inferredcites →https://doi.org/10.1002/cpbi.20openalex-snapshot
cgpCaVEManWrapper: Simple Execution of CaVEMan in Order to Detect Somatic Single Nucleotide Variants in NGS Data
inferredcites →https://doi.org/10.1038/nbt.2514openalex-snapshot
Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples
inferredcites →https://doi.org/10.1038/ncomms10001openalex-snapshot
A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing
inferredcites →https://doi.org/10.1038/ng.2761openalex-snapshot
Enabling transparent and collaborative computational analysis of 12 tumor types within The Cancer Genome Atlas
inferredcites →https://doi.org/10.1038/ng.2764openalex-snapshot
The Cancer Genome Atlas Pan-Cancer analysis project
inferredcites →https://doi.org/10.1038/ng.3036openalex-snapshot
Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications
inferredcites →https://doi.org/10.1093/bioinformatics/bts378openalex-snapshot
DELLY: structural variant discovery by integrated paired-end and split-read analysis
inferredcites →https://doi.org/10.1093/bioinformatics/btw111openalex-snapshot
VariantBam: filtering and profiling of next-generational sequencing data using region-specific rules
inferredcites →https://doi.org/10.1093/database/bau093openalex-snapshot
The Cancer Genomics Hub (CGHub): overcoming cancer through the power of torrential data
inferredcites →https://doi.org/10.1093/nar/gks1443openalex-snapshot
Discovery and characterization of artifactual mutations in deep coverage targeted capture sequencing data due to oxidative DNA damage during sample preparation
inferredcites →https://doi.org/10.1186/1471-2105-11-s12-s2openalex-snapshot
SeqWare Query Engine: storing and searching sequence data in the cloud
inferredcites →https://doi.org/10.1186/gm262openalex-snapshot
Towards a data sharing Code of Conduct for international genomic research
inferredcites →https://doi.org/10.1186/s13059-016-1029-6openalex-snapshot
MuSE: accounting for tumor heterogeneity using a sample-specific error model improves sensitivity and specificity in mutation calling from sequencing data
inferredcites →https://doi.org/10.12688/f1000research.10137.1openalex-snapshot
The Dockstore: enabling modular, community-focused sharing of Docker-based genomics tools and workflows
inferredcites →https://doi.org/10.6084/m9.figshare.963153.v1openalex-snapshot
Aligning sequence reads, clone sequences and assembly con*gs with BWA-MEM

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1002/cpbi.39openalex-snapshot
Using the Seven Bridges Cancer Genomics Cloud to Access and Analyze Petabytes of Cancer Data
inferred← citeshttps://doi.org/10.1002/cpmb.49openalex-snapshot
Making Use of Cancer Genomic Databases
inferred← citeshttps://doi.org/10.1016/j.ebiom.2020.102659openalex-snapshot
Classification of primary liver cancer with immunosuppression mechanisms and correlation with genomic alterations
inferred← citeshttps://doi.org/10.1016/j.tig.2018.12.006openalex-snapshot
Data Lakes, Clouds, and Commons: A Review of Platforms for Analyzing and Sharing Genomic Data
inferred← citeshttps://doi.org/10.1038/nrg.2017.113openalex-snapshot
Cloud computing for genomic data analysis and collaboration
inferred← citeshttps://doi.org/10.1038/s41467-019-13885-wopenalex-snapshot
High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations
inferred← citeshttps://doi.org/10.1038/s41467-020-19633-9openalex-snapshot
XPC deficiency increases risk of hematologic malignancies through mutator phenotype and characteristic mutational signature
inferred← citeshttps://doi.org/10.1038/s41598-019-55636-3openalex-snapshot
Deep whole-genome sequencing of 3 cancer cell lines on 2 sequencing platforms
inferred← citeshttps://doi.org/10.1097/ppo.0000000000000318openalex-snapshot
Progress Toward Cancer Data Ecosystems
inferred← citeshttps://doi.org/10.1101/163907openalex-snapshot
A user’s guide to the online resources for data exploration, visualization, and discovery for the Pan-Cancer Analysis of Whole Genomes project (PCAWG)
inferred← citeshttps://doi.org/10.1101/185736openalex-snapshot
Enabling rapid cloud-based analysis of thousands of human genomes via Butler
inferred← citeshttps://doi.org/10.1101/2022.05.10.491431openalex-snapshot
RNA-sequencing as an expression-informed alternative for somatic variant detection and cancer driver identification
inferred← citeshttps://doi.org/10.1101/225441openalex-snapshot
Assessing the Gene Regulatory Landscape in 1,188 Human Tumors
inferred← citeshttps://doi.org/10.1101/280446openalex-snapshot
Passenger mutations in 2500 cancer genomes: Overall molecular functional impact and consequences
inferred← citeshttps://doi.org/10.1101/322859openalex-snapshot
The Repertoire of Mutational Signatures in Human Cancer
inferred← citeshttps://doi.org/10.1101/761510openalex-snapshot
Improving personalized prediction of cancer prognoses with clonal evolution models
inferred← citeshttps://doi.org/10.1101/gr.231696.117openalex-snapshot
Aberrant PRDM9 expression impacts the pan-cancer genomic landscape
inferred← citeshttps://doi.org/10.1109/escience.2018.00064openalex-snapshot
A portable and scalable workflow for detecting structural variants in whole-genome sequencing data
inferred← citeshttps://doi.org/10.1186/s13059-019-1818-9openalex-snapshot
Global impact of somatic structural variation on the DNA methylome of human cancers
inferred← citeshttps://doi.org/10.1186/s13073-019-0695-xopenalex-snapshot
FIREVAT: finding reliable variants without artifacts in human cancer samples using etiologically relevant mutational signatures
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1008777openalex-snapshot
Assessing the contribution of tumor mutational phenotypes to cancer progression risk
inferred← citeshttps://doi.org/10.3410/f.734944792.793567131openalex-snapshot
Faculty Opinions recommendation of Data lakes, clouds, and commons: A review of platforms for analyzing and sharing genomic data.
inferred← citeshttps://doi.org/10.48550/arxiv.1809.01699openalex-snapshot
Data Lakes, Clouds and Commons: A Review of Platforms for Analyzing and Sharing Genomic Data
inferred← citeshttps://doi.org/10.7287/peerj.8214v0.1/reviews/1openalex-snapshot
Peer Review #1 of "sv-callers: a highly portable parallel workflow for structural variant detection in whole-genome sequence data (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.8214v0.1/reviews/2openalex-snapshot
Peer Review #2 of "sv-callers: a highly portable parallel workflow for structural variant detection in whole-genome sequence data (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.8214v0.2/reviews/1openalex-snapshot
Peer Review #1 of "sv-callers: a highly portable parallel workflow for structural variant detection in whole-genome sequence data (v0.2)"
inferred← citeshttps://doi.org/10.7287/peerj.8214v0.2/reviews/3openalex-snapshot
Peer Review #3 of "sv-callers: a highly portable parallel workflow for structural variant detection in whole-genome sequence data (v0.2)"
inferred← citeshttps://doi.org/10.7717/peerj.8214openalex-snapshot
sv-callers: a highly portable parallel workflow for structural variant detection in whole-genome sequence data
Editorial review for independent work. ICSAC — the Institute for Complexity Science and Advanced Computing — runs a structured editorial panel for researchers publishing outside journals, and publishes on CiteStamp rails. Submission is free and goes through ORCID: icsacinstitute.org/submit.