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Erratum: The Systems Biology Graphical Notation

Nicolas Le Novère
Michael Hucka
Hiroaki Kitano
Amendments and Corrections01 Sept 2009
Nature Biotechnology

Volume: 27, P: 864
Allele-specific analysis of DNA replication origins in mammalian cells

DNA sequences contribute to the location and timing of replication origin firings. Here by allele-specific analysis, the authors show that replication asynchrony is associated with small cumulative variations in the initiation efficiency of origins, rather than with the activation of dormant origins.

Boris Bartholdy
Rituparna Mukhopadhyay
Eric E. Bouhassira
ResearchOpen Access19 May 2015
Nature Communications

Volume: 6, P: 1-12
A dual role of Cohesin in DNA DSB repair

Cohesin plays a crucial role in both chromosome organization and DNA repair. Here the authors find that cohesin mediated genome architecture prevents interactions between damaged chromatin. In contrast cohesin phosphorylation appears to primarily impact DNA repair speed.

Michael Fedkenheuer
Yafang Shang
Rafael Casellas
ResearchOpen Access20 Jan 2025
Nature Communications

Volume: 16, P: 1-11
Selective interactions at pre-replication complexes categorize baseline and dormant origins

Dormant replication origins begin DNA synthesis under replication stress and are inactive in unperturbed cells. Here, the authors show that phospho-RecQL4 helicase blocks dormant origins’ activation by the Treslin/MTBP complex, facilitating its redistribution to activate dormant origins upon stress.

Bhushan L. Thakur
Christophe E. Redon
Mirit I. Aladjem
ResearchOpen Access03 May 2025
Nature Communications

Volume: 16, P: 1-15
Mechanism for local attenuation of DNA replication at double-strand breaks

DNA double-strand breaks induce local genome maintenance and inhibition of replication initiation at nearby topologically associating domains without affecting global DNA synthesis.

Robin Sebastian
Eric G. Sun
Mirit I. Aladjem
Research19 Feb 2025
Nature

Volume: 639, P: 1084-1092
D-2-hydroxyglutarate impairs DNA repair through epigenetic reprogramming

The oncometabolite D-2-HG has been implicated in compromising DNA repair pathway. Here the authors show D-2-HG leads to genome-wide DNA hypermethylation and loss of CTCF coverage, which impairs the assembly of the homologous recombination DNA repair machinery and associated topology adjustment.

Fengchao Lang
Karambir Kaur
Chunzhang Yang
ResearchOpen Access07 Feb 2025
Nature Communications

Volume: 16, P: 1-13
Replication in context: dynamic regulation of DNA replication patterns in metazoans

Spatial and temporal patterns of metazoan DNA replication are emerging as being dynamically regulated by tissue-specific and developmental cues, and by epigenetic modifications. These features might allow coordination with transcription and chromatin assembly, and enable changes in gene expression patterns.

Mirit I. Aladjem
Reviews10 Jul 2007
Nature Reviews Genetics

Volume: 8, P: 588-600
Preventing gene silencing with human replicators

Haiqing Fu
Lixin Wang
Mirit I Aladjem
Research09 Apr 2006
Nature Biotechnology

Volume: 24, P: 572-576
Regulation of cell cycle drivers by Cullin-RING ubiquitin ligases

Sang-Min Jang
Christophe E. Redon
Mirit I. Aladjem
ReviewsOpen Access02 Oct 2020
Experimental & Molecular Medicine

Volume: 52, P: 1637-1651
Correction: Corrigendum: The BioPAX community standard for pathway data sharing

Emek Demir
Michael P Cary
Gary D Bader
Amendments and Corrections07 Dec 2010
Nature Biotechnology

Volume: 28, P: 1308
Correction: Corrigendum: The BioPAX community standard for pathway data sharing

Emek Demir
Michael P Cary
Gary D Bader
Amendments and Corrections10 Apr 2012
Nature Biotechnology

Volume: 30, P: 365
The epigenetic regulator LSH maintains fork protection and genomic stability via MacroH2A deposition and RAD51 filament formation

LSH/HELLS is a chromatin remodeler promoting incorporation of histone variant macroH2A. Here the authors reveal a role for LSH in genome stability, in protecting nascent DNA at stalled forks mediated by macroH2A deposition and RAD51 filament formation.

Xiaoping Xu
Kai Ni
Kathrin Muegge
ResearchOpen Access10 Jun 2021
Nature Communications

Volume: 12, P: 1-16
The RepID–CRL4 ubiquitin ligase complex regulates metaphase to anaphase transition via BUB3 degradation

The spindle assembly checkpoint (SAC) safeguards chromosome segregation by regulating the anaphase promoting complex/cyclosome (APC/C), allowing chromosomes to correctly attach to mitotic spindles. Here the authors reveal a role for Cullin–RING ubiquitin ligase complex 4 (CRL4) in regulating metaphase to anaphase transition via BUB3 degradation.

Sang-Min Jang
Jenny F. Nathans
Mirit I. Aladjem
ResearchOpen Access07 Jan 2020
Nature Communications

Volume: 11, P: 1-12
The DNA repair endonuclease Mus81 facilitates fast DNA replication in the absence of exogenous damage

Several mechanisms are in place to ensure the accurate and timely replication of the genome as cells progress through S-phase. Here, the authors show that Mus81, an endonuclease involved in the response to DNA damage during replicative stress, also regulates the rate of DNA replication during normal growth.

Haiqing Fu
Melvenia M. Martin
Mirit I. Aladjem
Research16 Apr 2015
Nature Communications

Volume: 6, P: 1-14
BRCA2 associates with MCM10 to suppress PRIMPOL-mediated repriming and single-stranded gap formation after DNA damage

Tumor suppressor BRCA2 is known to stabilize and restart stalled DNA replication forks. Here the authors show that BRCA2 is recruited to the replication fork through its interaction with MCM10 and inhibits Primase-Polymerase-mediated repriming, lesion bypass and single strand DNA gap formation after DNA damage.

Zhihua Kang
Pan Fu
Bing Xia
ResearchOpen Access13 Oct 2021
Nature Communications

Volume: 12, P: 1-12
Dynamics of replication origin over-activation

DNA replication processes are often dysregulated in cancer. Here the authors analyse DNA synthesis patterns in cancer cells undergoing partial genome re-replication to reveal that re-replication exhibits aberrant replication fork dynamics and a skewed distribution of replication initiation that over-duplicates early-replicating genomic regions.

Haiqing Fu
Christophe E. Redon
Mirit I. Aladjem
ResearchOpen Access08 Jun 2021
Nature Communications

Volume: 12, P: 1-15
LibSBGN: Electronic Processing of SBGN maps

Emek Demir
Ugur Dogrusoz
Tobias Czauderna
MultimediaOpen Access08 Sept 2011
Nature Precedings

P: 1
LibSBGN: Electronic Processing of SBGN maps

Emek Demir
Ugur Dogrusoz
Tobias Czauderna
MultimediaOpen Access08 Oct 2010
Nature Precedings

P: 1
A replicator-specific binding protein essential for site-specific initiation of DNA replication in mammalian cells

Origins of mammalian DNA replication are poorly characterised because they lack an Identifiable consensus sequence. Here the authors identify RepID, a protein that binds to a subset of G-rich replication origins and facilitates initiation from those origins.

Ya Zhang
Liang Huang
Mirit I. Aladjem
ResearchOpen Access08 Jun 2016
Nature Communications

Volume: 7, P: 1-14
The replication initiation determinant protein (RepID) modulates replication by recruiting CUL4 to chromatin

RepID has previously been shown to promote origin firing. Here the authors reveal that RepID regulates replication origins via the recruitment of the CRL4 complex, and prevents re-initiation and unscheduled DNA replication.

Sang-Min Jang
Ya Zhang
Mirit I. Aladjem
ResearchOpen Access17 Jul 2018
Nature Communications

Volume: 9, P: 1-13
Order from clutter: selective interactions at mammalian replication origins

Genome-wide mapping, mathematical models and functional genetic analyses suggest that distinct molecular interactions at replication initiation sites underlie the regulation of DNA replication in metazoans. In this Review, the authors discuss recent insights into these DNA–protein interactions, and the genetic and epigenetic features of mammalian replication origins.

Mirit I. Aladjem
Christophe E. Redon
Reviews21 Nov 2016
Nature Reviews Genetics

Volume: 18, P: 101-116
RepID as a potential biomarker and therapeutic target for lung neuroendocrine tumor

Jong-Uk Park
Jae-Hyun Jo
Sang-Min Jang
ResearchOpen Access11 Nov 2024
Scientific Reports

Volume: 14, P: 1-10
The BioPAX community standard for pathway data sharing

Incompatible data storage formats have hindered the sharing and analyses of digital representations of biological pathways. BioPAX is a standardized language supported by >40 databases and software tools for exchanging pathway data.

Emek Demir
Michael P Cary
Gary D Bader
Reviews09 Sept 2010
Nature Biotechnology

Volume: 28, P: 935-942
The Systems Biology Graphical Notation

A group of scientists in the systems biology community propose visual conventions for drawing biological diagrams.

Nicolas Le Novère
Michael Hucka
Hiroaki Kitano
Reviews07 Aug 2009
Nature Biotechnology

Volume: 27, P: 735-741

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