Emergence and evolutionary analysis of the human DDR network: implications in comparative genomics and downstream analyses.

PubWeight™: 0.78‹?›

🔗 View Article (PMC 3969565)

Published in Mol Biol Evol on January 16, 2014

Authors

Aida Arcas1, Oscar Fernández-Capetillo, Ildefonso Cases, Ana M Rojas

Author Affiliations

1: Computational Cell Biology Group, Institute for Predictive and Personalized Medicine of Cancer, Badalona, Spain.

Articles cited by this

Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A (1998) 192.97

MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics (2003) 130.85

An integrated encyclopedia of DNA elements in the human genome. Nature (2012) 64.73

MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res (2005) 31.64

DNA double-stranded breaks induce histone H2AX phosphorylation on serine 139. J Biol Chem (1998) 28.13

Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc Natl Acad Sci U S A (1999) 22.80

The DNA-damage response in human biology and disease. Nature (2009) 17.86

Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J Mol Biol (2001) 16.47

The DNA damage response: making it safe to play with knives. Mol Cell (2010) 16.13

Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics (2006) 14.96

ATR: an essential regulator of genome integrity. Nat Rev Mol Cell Biol (2008) 11.86

Ensembl 2013. Nucleic Acids Res (2012) 11.70

53BP1 inhibits homologous recombination in Brca1-deficient cells by blocking resection of DNA breaks. Cell (2010) 8.70

Evidence for a clade of nematodes, arthropods and other moulting animals. Nature (1997) 7.28

RAP80 targets BRCA1 to specific ubiquitin structures at DNA damage sites. Science (2007) 6.70

Horizontal gene transfer in eukaryotic evolution. Nat Rev Genet (2008) 6.21

Dynamics of DNA damage response proteins at DNA breaks: a focus on protein modifications. Genes Dev (2011) 5.60

The Trichoplax genome and the nature of placozoans. Nature (2008) 5.56

Endonucleolytic function of MutLalpha in human mismatch repair. Cell (2006) 5.07

Human SLX4 is a Holliday junction resolvase subunit that binds multiple DNA repair/recombination endonucleases. Cell (2009) 5.05

Repair and genetic consequences of endogenous DNA base damage in mammalian cells. Annu Rev Genet (2004) 5.04

Mammalian SUMO E3-ligases PIAS1 and PIAS4 promote responses to DNA double-strand breaks. Nature (2009) 4.30

A role for the Tip60 histone acetyltransferase in the acetylation and activation of ATM. Proc Natl Acad Sci U S A (2005) 4.24

More than just a focus: The chromatin response to DNA damage and its role in genome integrity maintenance. Nat Cell Biol (2011) 4.23

Mechanisms and functions of DNA mismatch repair. Cell Res (2008) 4.16

Strength in numbers: preventing rereplication via multiple mechanisms in eukaryotic cells. Genes Dev (2007) 4.11

Alignment uncertainty and genomic analysis. Science (2008) 4.09

Transcription-coupled nucleotide excision repair in mammalian cells: molecular mechanisms and biological effects. Cell Res (2008) 3.83

A phylogenomic study of DNA repair genes, proteins, and processes. Mutat Res (1999) 3.67

The SUMO modification pathway is involved in the BRCA1 response to genotoxic stress. Nature (2009) 3.62

Functional organization of the S. cerevisiae phosphorylation network. Cell (2009) 3.15

Kinases that control the cell cycle in response to DNA damage: Chk1, Chk2, and MK2. Curr Opin Cell Biol (2009) 3.15

The SMC5/6 complex maintains telomere length in ALT cancer cells through SUMOylation of telomere-binding proteins. Nat Struct Mol Biol (2007) 3.15

Mre11-Rad50-Nbs1 is a keystone complex connecting DNA repair machinery, double-strand break signaling, and the chromatin template. Biochem Cell Biol (2007) 3.13

A cell-based screen identifies ATR inhibitors with synthetic lethal properties for cancer-associated mutations. Nat Struct Mol Biol (2011) 3.10

The cellular response to DNA double-strand breaks: defining the sensors and mediators. Trends Cell Biol (2003) 2.95

A double Holliday junction dissolvasome comprising BLM, topoisomerase IIIalpha, and BLAP75. J Biol Chem (2006) 2.69

Repair of DNA double strand breaks by non-homologous end joining. Biochimie (2003) 2.65

The annealing helicase SMARCAL1 maintains genome integrity at stalled replication forks. Genes Dev (2009) 2.50

The universal distribution of evolutionary rates of genes and distinct characteristics of eukaryotic genes of different apparent ages. Proc Natl Acad Sci U S A (2009) 2.50

MERIT40 facilitates BRCA1 localization and DNA damage repair. Genes Dev (2009) 2.49

BLAP18/RMI2, a novel OB-fold-containing protein, is an essential component of the Bloom helicase-double Holliday junction dissolvasome. Genes Dev (2008) 2.29

Regulatory ubiquitylation in response to DNA double-strand breaks. DNA Repair (Amst) (2009) 2.17

MOF and histone H4 acetylation at lysine 16 are critical for DNA damage response and double-strand break repair. Mol Cell Biol (2010) 2.03

Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood. Bioinformatics (2010) 1.98

Bacterial DNA repair by non-homologous end joining. Nat Rev Microbiol (2007) 1.94

F-box protein FBXO31 mediates cyclin D1 degradation to induce G1 arrest after DNA damage. Nature (2009) 1.93

A mitotic phosphorylation feedback network connects Cdk1, Plk1, 53BP1, and Chk2 to inactivate the G(2)/M DNA damage checkpoint. PLoS Biol (2010) 1.90

Taking the time to make important decisions: the checkpoint effector kinases Chk1 and Chk2 and the DNA damage response. DNA Repair (Amst) (2009) 1.89

The Chk2 protein kinase. DNA Repair (Amst) (2004) 1.85

Evolution: revisiting the root of the eukaryote tree. Curr Biol (2009) 1.68

More forks on the road to replication stress recovery. J Mol Cell Biol (2011) 1.64

TRF2 functions as a protein hub and regulates telomere maintenance by recognizing specific peptide motifs. Nat Struct Mol Biol (2009) 1.51

TRF2 and apollo cooperate with topoisomerase 2alpha to protect human telomeres from replicative damage. Cell (2010) 1.50

Evolutionary and functional conservation of the DNA non-homologous end-joining protein, XLF/Cernunnos. J Biol Chem (2006) 1.50

Nonhomologous end-joining in bacteria: a microbial perspective. Annu Rev Microbiol (2007) 1.49

53BP1 promotes ATM activity through direct interactions with the MRN complex. EMBO J (2009) 1.47

BRCA2 is ubiquitinated in vivo and interacts with USP11, a deubiquitinating enzyme that exhibits prosurvival function in the cellular response to DNA damage. Mol Cell Biol (2004) 1.44

DNA repair in plants. Chem Rev (2006) 1.30

Regulation of global genome nucleotide excision repair by SIRT1 through xeroderma pigmentosum C. Proc Natl Acad Sci U S A (2010) 1.30

Sensitivity to poly(ADP-ribose) polymerase (PARP) inhibition identifies ubiquitin-specific peptidase 11 (USP11) as a regulator of DNA double-strand break repair. J Biol Chem (2010) 1.26

Snm1B/Apollo mediates replication fork collapse and S Phase checkpoint activation in response to DNA interstrand cross-links. Oncogene (2008) 1.20

SIRT1 negatively regulates the activities, functions, and protein levels of hMOF and TIP60. Mol Cell Biol (2012) 1.15

An end-joining repair mechanism in Escherichia coli. Proc Natl Acad Sci U S A (2010) 1.13

Secret life of genes. Nature (2002) 1.12

ProteinHistorian: tools for the comparative analysis of eukaryote protein origin. PLoS Comput Biol (2012) 0.97

Intrauterine programming of ageing. EMBO Rep (2009) 0.91

Functions and regulation of Artemis: a goddess in the maintenance of genome integrity. J Radiat Res (2010) 0.88

The evolutionary landscape of the chromatin modification machinery reveals lineage specific gains, expansions, and losses. Proteins (2010) 0.87

Genetic analysis of CHK1 and CHK2 homologues revealed a unique cross talk between ATM and ATR pathways in Neurospora crassa. DNA Repair (Amst) (2008) 0.80

The Neurospora crassa UVS-3 epistasis group encodes homologues of the ATR/ATRIP checkpoint control system. DNA Repair (Amst) (2007) 0.76

When it comes to homology, bad habits die hard. Trends Biochem Sci (2009) 0.76

Serine/threonine kinases and E2-ubiquitin conjugating enzymes in Planctomycetes: unexpected findings. Antonie Van Leeuwenhoek (2013) 0.76

Articles by these authors

Increased telomere fragility and fusions resulting from TRF1 deficiency lead to degenerative pathologies and increased cancer in mice. Genes Dev (2009) 2.91

BioLayout(Java): versatile network visualisation of structural and functional relationships. Appl Bioinformatics (2005) 2.26

The Nod-like receptor (NLR) family: a tale of similarities and differences. PLoS One (2008) 1.99

COmplete GENome Tracking (COGENT): a flexible data environment for computational genomics. Bioinformatics (2003) 1.77

Myriads of protein families, and still counting. Genome Biol (2003) 1.75

Heavy metal tolerance and metal homeostasis in Pseudomonas putida as revealed by complete genome analysis. Environ Microbiol (2003) 1.61

Randomised trial of external beam radiotherapy alone or combined with high-dose-rate brachytherapy boost for localised prostate cancer. Radiother Oncol (2012) 1.47

Radiotherapy with concurrent carbogen and nicotinamide in bladder carcinoma. J Clin Oncol (2010) 1.40

Cyclin-dependent kinase inhibitor p21 controls adult neural stem cell expansion by regulating Sox2 gene expression. Cell Stem Cell (2012) 1.33

CARGO: a web portal to integrate customized biological information. Nucleic Acids Res (2007) 1.18

A proteomic characterization of factors enriched at nascent DNA molecules. Cell Rep (2013) 1.15

Overall Cdk activity modulates the DNA damage response in mammalian cells. J Cell Biol (2009) 1.14

Gas1 is related to the glial cell-derived neurotrophic factor family receptors alpha and regulates Ret signaling. J Biol Chem (2006) 1.11

The structure of a tandem pair of spectrin repeats of plectin reveals a modular organization of the plakin domain. J Mol Biol (2007) 1.09

Beyond 100 genomes. Genome Biol (2003) 1.06

TreeDet: a web server to explore sequence space. Nucleic Acids Res (2006) 1.05

ACRATA: a novel electron transfer domain associated to apoptosis and cancer. BMC Cancer (2004) 1.00

The phosphotransferase system formed by PtsP, PtsO, and PtsN proteins controls production of polyhydroxyalkanoates in Pseudomonas putida. J Bacteriol (2007) 0.99

SPOC: a widely distributed domain associated with cancer, apoptosis and transcription. BMC Bioinformatics (2004) 0.95

A 26-gene hypoxia signature predicts benefit from hypoxia-modifying therapy in laryngeal cancer but not bladder cancer. Clin Cancer Res (2013) 0.94

SIREs: searching for iron-responsive elements. Nucleic Acids Res (2010) 0.93

Necrosis predicts benefit from hypoxia-modifying therapy in patients with high risk bladder cancer enrolled in a phase III randomised trial. Radiother Oncol (2013) 0.92

CoGenT++: an extensive and extensible data environment for computational genomics. Bioinformatics (2005) 0.89

Databases of protein-protein interactions and their use in drug discovery. Curr Opin Drug Discov Devel (2009) 0.88

Are promyelocytic leukaemia protein nuclear bodies a scaffold for caspase-2 programmed cell death? Trends Biochem Sci (2007) 0.87

An isoform-specific PDZ-binding motif targets type I PIP5 kinase beta to the uropod and controls polarization of neutrophil-like HL60 cells. FASEB J (2010) 0.86

Late-replicating CNVs as a source of new genes. Biol Open (2013) 0.84

Systemic approaches to biodegradation. FEMS Microbiol Rev (2008) 0.82

Management of cancer of the head and neck--a cocktail with your PORT? N Engl J Med (2004) 0.82

gyrA Mutations associated with nalidixic acid-resistant salmonellae from wild birds. Antimicrob Agents Chemother (2002) 0.81

Sumoylation regulates nuclear localization of repressor DREAM. Biochim Biophys Acta (2010) 0.80

Mature results of a randomized trial of accelerated hyperfractionated versus conventional radiotherapy in head-and-neck cancer. Int J Radiat Oncol Biol Phys (2010) 0.80

Upgrading of residues of bracts, stems and hearts of Cynara cardunculus L. var. scolymus to functional fractions enriched in soluble fiber. Food Funct (2014) 0.79

Chemical and functional properties of cell wall polymers from two cherry varieties at two developmental stages. Carbohydr Polym (2012) 0.78

Carbogen and nicotinamide in locally advanced bladder cancer: early results of a phase-III randomized trial. Radiother Oncol (2008) 0.78

Bionemo: molecular information on biodegradation metabolism. Nucleic Acids Res (2008) 0.77

Acute and late morbidity in the treatment of advanced bladder carcinoma with accelerated radiotherapy, carbogen, and nicotinamide. Cancer (2005) 0.77

Serine/threonine kinases and E2-ubiquitin conjugating enzymes in Planctomycetes: unexpected findings. Antonie Van Leeuwenhoek (2013) 0.76

Two novel missense mutations in iron transport protein transferrin causing hypochromic microcytic anaemia and haemosiderosis: molecular characterization and structural implications. Br J Haematol (2013) 0.75

A common structural scaffold in CTD phosphatases that supports distinct catalytic mechanisms. Proteins (2013) 0.75

Development of a high methoxyl pectin edible film for retention of l-(+)-ascorbic acid. J Agric Food Chem (2009) 0.75

Characterization of acid-extracted pectin-enriched products obtained from red beet (Beta vulgaris L. var. conditiva) and butternut (Cucurbita moschata Duch ex Poiret). J Agric Food Chem (2010) 0.75

Functional analysis of the integration host factor site of the σ(54) Pu promoter of Pseudomonas putida by in vivo UV imprinting. Mol Microbiol (2011) 0.75

Late-replicating CNVs as a source of new genes. Biol Open (2014) 0.75

Hydrolytic and oxidative stability of L-(+)-ascorbic acid supported in pectin films: influence of the macromolecular structure and calcium presence. J Agric Food Chem (2012) 0.75