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Complex correlations: replication timing and mutational landscapes during cancer and genome evolution
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review article
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title
Complex correlations: replication timing and mutational landscapes during cancer and genome evolution
(English)
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PubMed
author name string
Jiao Sima
series ordinal
1
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David M. Gilbert
series ordinal
2
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Crossref
language of work or name
English
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publication date
April 2014
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published in
Current Opinion in Genetics & Development
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volume
25
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PubMed
page(s)
93-100
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PubMed
cites work
Mutational heterogeneity in cancer and the search for new cancer-associated genes
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Tissue-specific spatial organization of genomes
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Comprehensive mapping of long-range interactions reveals folding principles of the human genome
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7 April 2017
Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions
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The landscape of somatic copy-number alteration across human cancers
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Transcription-coupled DNA repair: two decades of progress and surprises
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Late-replicating CNVs as a source of new genes
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Genomic basis of aromatase excess syndrome: recombination- and replication-mediated rearrangements leading to CYP19A1 overexpression
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KDM4A lysine demethylase induces site-specific copy gain and rereplication of regions amplified in tumors
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Bubble-seq analysis of the human genome reveals distinct chromatin-mediated mechanisms for regulating early- and late-firing origins
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28 September 2017
Translesion DNA polymerases
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PubMed Central
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28 September 2017
Relative proximity of chromosome territories influences chromosome exchange partners in radiation-induced chromosome rearrangements in primary human bronchial epithelial cells.
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28 September 2017
Next-generation sequencing of paired tyrosine kinase inhibitor-sensitive and -resistant EGFR mutant lung cancer cell lines identifies spectrum of DNA changes associated with drug resistance
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28 September 2017
Transcription-replication encounters, consequences and genomic instability
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DNA replication timing and higher-order nuclear organization determine single-nucleotide substitution patterns in cancer genomes
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28 September 2017
DNA replication timing, genome stability and cancer: late and/or delayed DNA replication timing is associated with increased genomic instability.
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28 September 2017
Single-stranded annealing induced by re-initiation of replication origins provides a novel and efficient mechanism for generating copy number expansion via non-allelic homologous recombination
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28 September 2017
Genomic hallmarks of genes involved in chromosomal translocations in hematological cancer
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28 September 2017
Differential relationship of DNA replication timing to different forms of human mutation and variation
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28 September 2017
Alterations in replication timing of cancer-related genes in malignant human breast cancer cells
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28 September 2017
Three-dimensional genome architecture influences partner selection for chromosomal translocations in human disease
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28 September 2017
Close proximity to Igh is a contributing factor to AID-mediated translocations.
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PubMed Central
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28 September 2017
Mouse model of endemic Burkitt translocations reveals the long-range boundaries of Ig-mediated oncogene deregulation
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28 September 2017
Abnormal developmental control of replication-timing domains in pediatric acute lymphoblastic leukemia
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28 September 2017
Model for MLL translocations in therapy-related leukemia involving topoisomerase IIβ-mediated DNA strand breaks and gene proximity
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28 September 2017
Distinct contributions of replication and transcription to mutation rate variation of human genomes
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28 September 2017
Y-family DNA polymerases and their role in tolerance of cellular DNA damage.
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28 September 2017
Spatial organization of the mouse genome and its role in recurrent chromosomal translocations
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28 September 2017
Evidence for sequential and increasing activation of replication origins along replication timing gradients in the human genome
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4140690
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28 September 2017
DNA replication timing and long-range DNA interactions predict mutational landscapes of cancer genomes
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4140690
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28 September 2017
High order chromatin architecture shapes the landscape of chromosomal alterations in cancer
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PubMed Central
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28 September 2017
Drosophila duplication hotspots are associated with late-replicating regions of the genome
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4140690
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28 September 2017
Genome-wide translocation sequencing reveals mechanisms of chromosome breaks and rearrangements in B cells
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4140690
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28 September 2017
Translocation-capture sequencing reveals the extent and nature of chromosomal rearrangements in B lymphocytes
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4140690
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28 September 2017
Mutation rates across budding yeast chromosome VI are correlated with replication timing
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4140690
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28 September 2017
Chromatin signatures of the Drosophila replication program
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4140690
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28 September 2017
Comparative analysis of DNA replication timing reveals conserved large-scale chromosomal architecture.
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PubMed Central
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28 September 2017
Evolutionarily conserved replication timing profiles predict long-range chromatin interactions and distinguish closely related cell types
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PubMed Central
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28 September 2017
Mutational bias shaping fly copy number variation: implications for genome evolution
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28 September 2017
Maintaining genome stability at the replication fork
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PubMed Central
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28 September 2017
Impact of replication timing on non-CpG and CpG substitution rates in mammalian genomes
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28 September 2017
Sequencing newly replicated DNA reveals widespread plasticity in human replication timing
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28 September 2017
Nuclear receptor-induced chromosomal proximity and DNA breaks underlie specific translocations in cancer
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28 September 2017
Genome-wide dynamics of replication timing revealed by in vitro models of mouse embryogenesis
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28 September 2017
Induced chromosomal proximity and gene fusions in prostate cancer
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PubMed Central
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28 September 2017
Replication timing and transcriptional control: beyond cause and effect--part II.
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28 September 2017
Chromatin state marks cell-type- and gender-specific replication of the Drosophila genome
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28 September 2017
ReplicationDomain: a visualization tool and comparative database for genome-wide replication timing data
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28 September 2017
Global reorganization of replication domains during embryonic stem cell differentiation
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4140690
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28 September 2017
ATM signaling facilitates repair of DNA double-strand breaks associated with heterochromatin
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4140690
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28 September 2017
Global chromatin compaction limits the strength of the DNA damage response
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4140690
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28 September 2017
Myc dynamically and preferentially relocates to a transcription factory occupied by Igh
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4140690
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28 September 2017
Pan-S replication patterns and chromosomal domains defined by genome-tiling arrays of ENCODE genomic areas
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4140690
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28 September 2017
The critical mutagenic translesion DNA polymerase Rev1 is highly expressed during G(2)/M phase rather than S phase
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4140690
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28 September 2017
Intermingling of chromosome territories in interphase suggests role in translocations and transcription-dependent associations
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4140690
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28 September 2017
Preferential occurrence of chromosome breakpoints within early replicating regions in neuroblastoma
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4140690
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28 September 2017
DNA polymerase clamp shows little turnover at established replication sites but sequential de novo assembly at adjacent origin clusters
1 reference
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4140690
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28 September 2017
Conservation of relative chromosome positioning in normal and cancer cells
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4140690
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28 September 2017
The supply of exogenous deoxyribonucleotides accelerates the speed of the replication fork in early S-phase
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4140690
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28 September 2017
A possible function of constitutive heterochromatin: the bodyguard hypothesis
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4140690
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28 September 2017
The Npl3 hnRNP prevents R-loop-mediated transcription-replication conflicts and genome instability
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PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4140690
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31 May 2018
Spatial dynamics of chromosome translocations in living cells.
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4140690
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31 May 2018
Human mutation rate associated with DNA replication timing
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4140690
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31 May 2018
DNA damage tolerance: when it's OK to make mistakes
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31 May 2018
DNA replication timing and selection shape the landscape of nucleotide variation in cancer genomes.
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PubMed Central
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28 November 2018
The mutational profile of the yeast genome is shaped by replication
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4140690
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28 November 2018
Late-replicating domains have higher divergence and diversity in Drosophila melanogaster
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PubMed Central
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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4140690
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28 November 2018
Chromosome-wide assessment of replication timing for human chromosomes 11q and 21q: disease-related genes in timing-switch regions
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28 November 2018
Replication dynamics of the yeast genome.
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28 November 2018
The nuclear topography of ABL, BCR, PML, and RARalpha genes: evidence for gene proximity in specific phases of the cell cycle and stages of hematopoietic differentiation
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28 November 2018
How chromatin prevents genomic rearrangements: locus colocalization induced by transcription factor binding
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https://pubmed.ncbi.nlm.nih.gov/24598232
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12 December 2020
based on heuristic
inferred from PubMed ID database lookup
Proximity of chromosomal loci that participate in radiation-induced rearrangements in human cells
1 reference
stated in
PubMed
reference URL
https://pubmed.ncbi.nlm.nih.gov/24598232
retrieved
12 December 2020
based on heuristic
inferred from PubMed ID database lookup
Analyzing the association of SCNA boundaries with replication timing
1 reference
stated in
PubMed
reference URL
https://pubmed.ncbi.nlm.nih.gov/24598232
retrieved
12 December 2020
based on heuristic
inferred from PubMed ID database lookup
Spatial proximity of translocation-prone gene loci in human lymphomas
1 reference
stated in
PubMed
reference URL
https://pubmed.ncbi.nlm.nih.gov/24598232
retrieved
12 December 2020
based on heuristic
inferred from PubMed ID database lookup
Timing of Replication Is a Determinant of Neutral Substitution Rates but Does Not Explain Slow Y Chromosome Evolution in Rodents
1 reference
stated in
PubMed
reference URL
https://pubmed.ncbi.nlm.nih.gov/24598232
retrieved
12 December 2020
based on heuristic
inferred from PubMed ID database lookup
Identifiers
DOI
10.1016/J.GDE.2013.11.022
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PMC publication ID
4140690
1 reference
stated in
PubMed
PubMed publication ID
24598232
1 reference
stated in
PubMed
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