On the public citation graph

Pan-cancer analysis of whole genomes reveals driver rearrangements promoted by LINE-1 retrotransposition in human tumours

https://doi.org/10.1101/179705
0 signed · 99 inferred · view as graph

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.

Is this your work? Sign in with ORCID and put your name on the claims that are yours.
Claim with ORCID
Reference health. See whether every reference in this work resolves to a known work and none has been retracted — and get a dated CiteStamped badge you can embed.
See reference health

What this work says

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

inferredcites →https://doi.org/10.1002/humu.20307openalex-snapshot
dbRIP: A highly integrated database of retrotransposon insertion polymorphisms in humans
inferredcites →https://doi.org/10.1016/j.cell.2007.05.009openalex-snapshot
High-Resolution Profiling of Histone Methylations in the Human Genome
inferredcites →https://doi.org/10.1016/j.cell.2010.05.021openalex-snapshot
LINE-1 Retrotransposition Activity in Human Genomes
inferredcites →https://doi.org/10.1016/j.cell.2012.04.023openalex-snapshot
The Life History of 21 Breast Cancers
inferredcites →https://doi.org/10.1016/j.cell.2015.12.050openalex-snapshot
Mutational Strand Asymmetries in Cancer Genomes Reveal Mechanisms of DNA Damage and Repair
inferredcites →https://doi.org/10.1016/j.cell.2017.07.003openalex-snapshot
Clustered Mutation Signatures Reveal that Error-Prone DNA Repair Targets Mutations to Active Genes
inferredcites →https://doi.org/10.1016/j.jgg.2011.09.002openalex-snapshot
Dysregulation of CDK8 and Cyclin C in tumorigenesis
inferredcites →https://doi.org/10.1016/s0022-2836(05)80360-2openalex-snapshot
Basic Local Alignment Search Tool
inferredcites →https://doi.org/10.1016/s0092-8674(02)00828-0openalex-snapshot
Genomic Deletions Created upon LINE-1 Retrotransposition
inferredcites →https://doi.org/10.1016/s0092-8674(02)00839-5openalex-snapshot
Human L1 Retrotransposition Is Associated with Genetic Instability In Vivo
inferredcites →https://doi.org/10.1016/s0168-9525(00)02024-2openalex-snapshot
EMBOSS: The European Molecular Biology Open Software Suite
inferredcites →https://doi.org/10.1016/s1535-6108(02)00094-6openalex-snapshot
Telomere dysfunction provokes regional amplification and deletion in cancer genomes
inferredcites →https://doi.org/10.1038/35020592openalex-snapshot
Telomere dysfunction promotes non-reciprocal translocations and epithelial cancers in mice
inferredcites →https://doi.org/10.1038/35057062openalex-snapshot
Initial sequencing and analysis of the human genome
inferredcites →https://doi.org/10.1038/nature08822openalex-snapshot
The landscape of somatic copy-number alteration across human cancers
inferredcites →https://doi.org/10.1038/nature09460openalex-snapshot
The patterns and dynamics of genomic instability in metastatic pancreatic cancer
inferredcites →https://doi.org/10.1038/nature11003openalex-snapshot
The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity
inferredcites →https://doi.org/10.1038/nature11247openalex-snapshot
An integrated encyclopedia of DNA elements in the human genome
inferredcites →https://doi.org/10.1038/nature11404openalex-snapshot
Comprehensive genomic characterization of squamous cell lung cancers
inferredcites →https://doi.org/10.1038/nature12213openalex-snapshot
Mutational heterogeneity in cancer and the search for new cancer-associated genes
inferredcites →https://doi.org/10.1038/nature13115openalex-snapshot
Constitutional and somatic rearrangement of chromosome 21 in acute lymphoblastic leukaemia
inferredcites →https://doi.org/10.1038/nature13385openalex-snapshot
Comprehensive molecular profiling of lung adenocarcinoma
inferredcites →https://doi.org/10.1038/nature14129openalex-snapshot
Comprehensive genomic characterization of head and neck squamous cell carcinomas
inferredcites →https://doi.org/10.1038/nature15394openalex-snapshot
An integrated map of structural variation in 2,504 human genomes
inferredcites →https://doi.org/10.1038/ncomms4644openalex-snapshot
Processed pseudogenes acquired somatically during cancer development
inferredcites →https://doi.org/10.1038/ng.3984openalex-snapshot
Computational correction of copy number effect improves specificity of CRISPR–Cas9 essentiality screens in cancer cells
inferredcites →https://doi.org/10.1038/ng0597-37openalex-snapshot
Many human L1 elements are capable of retrotransposition
inferredcites →https://doi.org/10.1038/ng0694-143openalex-snapshot
A new retrotransposable human L1 element from the LRE2 locus on chromosome 1q produces a chimaeric insertion
inferredcites →https://doi.org/10.1038/nn.4388openalex-snapshot
L1-associated genomic regions are deleted in somatic cells of the healthy human brain
inferredcites →https://doi.org/10.1038/nprot.2012.016openalex-snapshot
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
inferredcites →https://doi.org/10.1038/nrc.2017.35openalex-snapshot
Transposable elements in cancer
inferredcites →https://doi.org/10.1038/nrc1299openalex-snapshot
A census of human cancer genes
inferredcites →https://doi.org/10.1038/nrm.2016.171openalex-snapshot
Telomeres in cancer: tumour suppression and genome instability
inferredcites →https://doi.org/10.1038/nrm.2017.48openalex-snapshot
Non-homologous DNA end joining and alternative pathways to double-strand break repair
inferredcites →https://doi.org/10.1038/s41586-020-1969-6openalex-snapshot
Pan-cancer analysis of whole genomes
inferredcites →https://doi.org/10.1056/nejmra1510092openalex-snapshot
Mobile DNA in Health and Disease
inferredcites →https://doi.org/10.1073/pnas.0831042100openalex-snapshot
Hot L1s account for the bulk of retrotransposition in the human population
inferredcites →https://doi.org/10.1093/bib/bbs017openalex-snapshot
Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration
inferredcites →https://doi.org/10.1093/bioinformatics/btp324openalex-snapshot
Fast and accurate short read alignment with Burrows–Wheeler transform
inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot
The Sequence Alignment/Map format and SAMtools
inferredcites →https://doi.org/10.1093/bioinformatics/btp698openalex-snapshot
Fast and accurate long-read alignment with Burrows–Wheeler transform
inferredcites →https://doi.org/10.1093/bioinformatics/btr509openalex-snapshot
A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data
inferredcites →https://doi.org/10.1093/bioinformatics/btr708openalex-snapshot
ART: a next-generation sequencing read simulator
inferredcites →https://doi.org/10.1093/bioinformatics/bts480openalex-snapshot
Snakemake—a scalable bioinformatics workflow engine
inferredcites →https://doi.org/10.1093/bioinformatics/bts635openalex-snapshot
STAR: ultrafast universal RNA-seq aligner
inferredcites →https://doi.org/10.1093/bioinformatics/btu638openalex-snapshot
HTSeq—a Python framework to work with high-throughput sequencing data
inferredcites →https://doi.org/10.1093/bioinformatics/bty191openalex-snapshot
Minimap2: pairwise alignment for nucleotide sequences
inferredcites →https://doi.org/10.1093/hmg/8.8.1557openalex-snapshot
Full-Length Human L1 Insertions Retain the Capacity for High Frequency Retrotransposition in Cultured Cells
inferredcites →https://doi.org/10.1093/nar/gkh340openalex-snapshot
MUSCLE: multiple sequence alignment with high accuracy and high throughput
inferredcites →https://doi.org/10.1093/nar/gki718openalex-snapshot
Genomic rearrangements by LINE-1 insertion-mediated deletion in the human and chimpanzee lineages
inferredcites →https://doi.org/10.1093/nar/gkj522openalex-snapshot
Gamma radiation increases endonuclease-dependent L1 retrotransposition in a cultured cell assay
inferredcites →https://doi.org/10.1093/nar/gkm317openalex-snapshot
Endonuclease-independent insertion provides an alternative pathway for L1 retrotransposition in the human genome
inferredcites →https://doi.org/10.1093/nar/gkq603openalex-snapshot
ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data
inferredcites →https://doi.org/10.1093/nar/gks596openalex-snapshot
Primer3—new capabilities and interfaces
inferredcites →https://doi.org/10.1093/nar/gkv1189openalex-snapshot
Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a026372openalex-snapshot
L1 (LINE-1) Retrotransposon Evolution and Amplification in Recent Human History
inferredcites →https://doi.org/10.1101/162784openalex-snapshot
Pan-cancer analysis of whole genomes
inferredcites →https://doi.org/10.1101/183889openalex-snapshot
Genomic basis for RNA alterations revealed by whole-genome analyses of 27 cancer types
inferredcites →https://doi.org/10.1101/187609openalex-snapshot
Selective and mechanistic sources of recurrent rearrangements across the cancer genome
inferredcites →https://doi.org/10.1101/190330openalex-snapshot
The whole-genome panorama of cancer drivers
inferredcites →https://doi.org/10.1101/gad.266098.115openalex-snapshot
p53 genes function to restrain mobile elements
inferredcites →https://doi.org/10.1101/gr.074492.107openalex-snapshot
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
inferredcites →https://doi.org/10.1101/gr.106419.110openalex-snapshot
High-throughput sequencing reveals extensive variation in human-specific L1 content in individual human genomes
inferredcites →https://doi.org/10.1101/gr.135350.111openalex-snapshot
GENCODE: The reference human genome annotation for The ENCODE Project
inferredcites →https://doi.org/10.1101/gr.145235.112openalex-snapshot
Extensive somatic L1 retrotransposition in colorectal tumors
inferredcites →https://doi.org/10.1101/gr.163659.113openalex-snapshot
Somatic retrotransposition in human cancer revealed by whole-genome and exome sequencing
inferredcites →https://doi.org/10.1101/gr.229202openalex-snapshot
BLAT —The BLAST -Like Alignment Tool
inferredcites →https://doi.org/10.1101/gr.231837.117openalex-snapshot
Immune signatures correlate with L1 retrotransposition in gastrointestinal cancers
inferredcites →https://doi.org/10.1126/science.1089670openalex-snapshot
Mobile Elements: Drivers of Genome Evolution
inferredcites →https://doi.org/10.1126/science.1222077openalex-snapshot
Landscape of Somatic Retrotransposition in Human Cancers
inferredcites →https://doi.org/10.1126/science.1251343openalex-snapshot
Extensive transduction of nonrepetitive DNA mediated by L1 retrotransposition in cancer genomes
inferredcites →https://doi.org/10.1126/science.283.5407.1530openalex-snapshot
Exon Shuffling by L1 Retrotransposition
inferredcites →https://doi.org/10.1128/mcb.25.17.7780-7795.2005openalex-snapshot
Multiple Fates of L1 Retrotransposition Intermediates in Cultured Human Cells
inferredcites →https://doi.org/10.1158/1538-7445.am2018-3000openalex-snapshot
Abstract 3000: Pervasive intra-tumour heterogeneity and subclonal selection across cancer types
inferredcites →https://doi.org/10.1186/1476-4598-3-12openalex-snapshot
L1 and HERV-W retrotransposons are hypomethylated in human ovarian carcinomas.
inferredcites →https://doi.org/10.1186/1751-0473-9-13openalex-snapshot
biobambam: tools for read pair collation based algorithms on BAM files
inferredcites →https://doi.org/10.1186/1759-8753-5-20openalex-snapshot
Processed pseudogene insertions in somatic cells
inferredcites →https://doi.org/10.1186/gb-2013-14-3-r22openalex-snapshot
Retrotransposition of gene transcripts leads to structural variation in mammalian genomes
inferredcites →https://doi.org/10.1186/gb-2013-14-4-r36openalex-snapshot
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
inferredcites →https://doi.org/10.1371/journal.pgen.1002236openalex-snapshot
A Comprehensive Map of Mobile Element Insertion Polymorphisms in Humans
inferredcites →https://doi.org/10.18632/oncotarget.18412openalex-snapshot
CDKN2A methylation in esophageal cancer: a meta-analysis
inferredcites →https://doi.org/10.7554/elife.30058openalex-snapshot
LINE-1 protein localization and functional dynamics during the cell cycle

What points at this work

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

inferred← citeshttps://doi.org/10.1007/s10555-021-09969-zopenalex-snapshot
Decoding human cancer with whole genome sequencing: a review of PCAWG Project studies published in February 2020
inferred← citeshttps://doi.org/10.1016/j.cell.2019.02.012openalex-snapshot
Characterizing Mutational Signatures in Human Cancer Cell Lines Reveals Episodic APOBEC Mutagenesis
inferred← citeshttps://doi.org/10.1016/j.humpath.2019.06.001openalex-snapshot
Expression of L1 retrotransposon open reading frame protein 1 in gynecologic cancers
inferred← citeshttps://doi.org/10.1038/s12276-018-0112-3openalex-snapshot
Patterns and mechanisms of structural variations in human cancer
inferred← citeshttps://doi.org/10.1038/s41467-019-11770-0openalex-snapshot
Retrotransposon insertions can initiate colorectal cancer and are associated with poor survival
inferred← citeshttps://doi.org/10.1038/s41467-020-16546-5openalex-snapshot
The genomic and epigenomic evolutionary history of papillary renal cell carcinomas
inferred← citeshttps://doi.org/10.1038/s41586-020-1969-6openalex-snapshot
Pan-cancer analysis of whole genomes
inferred← citeshttps://doi.org/10.1038/s41588-018-0073-4openalex-snapshot
DNA methylation loss in late-replicating domains is linked to mitotic cell division
inferred← citeshttps://doi.org/10.1038/s41588-019-0551-3openalex-snapshot
Genomic evidence supports a clonal diaspora model for metastases of esophageal adenocarcinoma
inferred← citeshttps://doi.org/10.1038/s41594-020-0372-1openalex-snapshot
Cell fitness screens reveal a conflict between LINE-1 retrotransposition and DNA replication
inferred← citeshttps://doi.org/10.1038/s41594-020-0374-zopenalex-snapshot
BRCA1 and S phase DNA repair pathways restrict LINE-1 retrotransposition in human cells
inferred← citeshttps://doi.org/10.1101/536896openalex-snapshot
Spontaneous retrotranspositions in normal tissues are rare and associated with cell-type-specific differentiation
inferred← citeshttps://doi.org/10.1101/706788openalex-snapshot
Evidence that APP gene copy number changes reflect recombinant vector contamination
inferred← citeshttps://doi.org/10.1101/781013openalex-snapshot
GRIDSS, PURPLE, LINX: Unscrambling the tumor genome via integrated analysis of structural variation and copy number
inferred← citeshttps://doi.org/10.21203/rs.3.rs-136297/v1openalex-snapshot
Annotations of Recurrent Structural Variant Events in Pan-cancer Whole Genome Data for Precision Medicine
inferred← citeshttps://doi.org/10.3410/f.737342811.793574228openalex-snapshot
Faculty Opinions recommendation of Cell fitness screens reveal a conflict between LINE-1 retrotransposition and DNA replication.
inferred← citeshttps://doi.org/10.37349/etat.2024.00261openalex-snapshot
Prospects for breast cancer immunotherapy using microRNAs and transposable elements as objects
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.