BioJazz: in silico evolution of cellular networks with unbounded complexity using rule-based modeling.

Abstract:

:Systems biologists aim to decipher the structure and dynamics of signaling and regulatory networks underpinning cellular responses; synthetic biologists can use this insight to alter existing networks or engineer de novo ones. Both tasks will benefit from an understanding of which structural and dynamic features of networks can emerge from evolutionary processes, through which intermediary steps these arise, and whether they embody general design principles. As natural evolution at the level of network dynamics is difficult to study, in silico evolution of network models can provide important insights. However, current tools used for in silico evolution of network dynamics are limited to ad hoc computer simulations and models. Here we introduce BioJazz, an extendable, user-friendly tool for simulating the evolution of dynamic biochemical networks. Unlike previous tools for in silico evolution, BioJazz allows for the evolution of cellular networks with unbounded complexity by combining rule-based modeling with an encoding of networks that is akin to a genome. We show that BioJazz can be used to implement biologically realistic selective pressures and allows exploration of the space of network architectures and dynamics that implement prescribed physiological functions. BioJazz is provided as an open-source tool to facilitate its further development and use. Source code and user manuals are available at: http://oss-lab.github.io/biojazz and http://osslab.lifesci.warwick.ac.uk/BioJazz.aspx.

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

Feng S,Ollivier JF,Swain PS,Soyer OS

doi

10.1093/nar/gkv595

subject

Has Abstract

pub_date

2015-10-30 00:00:00

pages

e123

issue

19

eissn

0305-1048

issn

1362-4962

pii

gkv595

journal_volume

43

pub_type

杂志文章
  • Distinct promoter elements mediate the co-operative effect of Brn-3a and p53 on the p21 promoter and their antagonism on the Bax promoter.

    abstract::Although the promoters of both the Bax and p21 genes are activated by p53, they differ in the effect on this activation of the POU family transcription factor Brn-3a. Thus, Brn-3a inhibits activation of the Bax promoter by p53 but enhances the ability of p53 to activate the p21 promoter. We demonstrate that repression...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkf610

    authors: Perez-Sanchez C,Budhram-Mahadeo VS,Latchman DS

    更新日期:2002-11-15 00:00:00

  • Expression and replication of the hepatitis B virus genome under foreign promoter control.

    abstract::A novel expression system was established that allows expression and propagation of the human hepatitis B virus (HBV) genome in cultured animal cells. An overlength HBV genome encoding the viral pregenomic RNA was put under transcriptional control of the human metallothionein IIA promoter thereby replacing the endogen...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/15.24.10117

    authors: Junker M,Galle P,Schaller H

    更新日期:1987-12-23 00:00:00

  • The conserved ribonuclease aCPSF1 triggers genome-wide transcription termination of Archaea via a 3'-end cleavage mode.

    abstract::Transcription termination defines accurate transcript 3'-ends and ensures programmed transcriptomes, making it critical to life. However, transcription termination mechanisms remain largely unknown in Archaea. Here, we reported the physiological significance of the newly identified general transcription termination fa...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkaa702

    authors: Yue L,Li J,Zhang B,Qi L,Li Z,Zhao F,Li L,Zheng X,Dong X

    更新日期:2020-09-25 00:00:00

  • Studies on transfer ribonucleic acids and related compounds. 8(1). Further studies on aromatic phosphoramidates as a protecting group for phosphomonoesters.

    abstract::Stability of aromatic phosphoramidates was studied using 2',3'-O-dibenzoyluridine 5'-phosphoramidates and N,2',3'-O-tribenzoylcytidine 5'-phosphate. The effect of dicyclohexylcarbodiimide in this mixture was investigated. Decomposition of the anilidate was slower in the presence of DCC. Substituted anilidates of uridi...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/1.2.223

    authors: Otsuka E,Honda A,Shigyo H,Morioka S,Sugiyama T

    更新日期:1974-02-01 00:00:00

  • The cellular abundance of the essential transcription termination factor TTF-I regulates ribosome biogenesis and is determined by MDM2 ubiquitinylation.

    abstract::The ARF tumour suppressor stabilizes p53 by negatively regulating the E3 ubiquitin ligase MDM2 to promote cell cycle arrest and cell death. However, ARF is also able to arrest cell proliferation by inhibiting ribosome biogenesis. In greater part this is achieved by targeting the transcription termination factor I (TTF...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gks198

    authors: Lessard F,Stefanovsky V,Tremblay MG,Moss T

    更新日期:2012-07-01 00:00:00

  • Methyl transferases induced during chemical adaptation of M. luteus.

    abstract::Three peaks of methyltransferase activity specific for MNNG alkylated DNA have been identified from extracts of chemically adapted M. luteus. They are designated as TI to TIII in order to their elution from a Sephadex G-75 column. The first one of these peaks has been purified to homogeneity. TI, is an inducible, unus...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/15.22.9471

    authors: Riazuddin S,Athar A,Sohail A

    更新日期:1987-11-25 00:00:00

  • Accurate and rapid modeling of iron-bleomycin-induced DNA damage using tethered duplex oligonucleotides and electrospray ionization ion trap mass spectrometric analysis.

    abstract::Bleomycin B(2)(BLM) in the presence of iron [Fe(II)] and O(2)catalyzes single-stranded (ss) and double-stranded (ds) cleavage of DNA. Electrospray ionization ion trap mass spectrometry was used to monitor these cleavage processes. Two duplex oligonucleotides containing an ethylene oxide tether between both strands wer...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/28.9.1978

    authors: Harsch A,Marzilli LA,Bunt RC,Stubbe J,Vouros P

    更新日期:2000-05-01 00:00:00

  • Mutational analysis of the reverse transcriptase and ribonuclease H domains of the human foamy virus.

    abstract::Human foamy or spuma virus (HFV) codes for a distinct set of pol gen products. To determine the minimal requirements for the HFV enzymatic activities, defined residues of the reverse transcriptase (RT) and ribo-nuclease H (RNase H) domain of the HFV pol gene were mutated by site-specific PCR mutagenesis. The mutant ge...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/23.14.2621

    authors: Kögel D,Aboud M,Flügel RM

    更新日期:1995-07-25 00:00:00

  • DNA intercalation without flipping in the specific ThaI-DNA complex.

    abstract::The PD-(D/E)XK type II restriction endonuclease ThaI cuts the target sequence CG/CG with blunt ends. Here, we report the 1.3 Å resolution structure of the enzyme in complex with substrate DNA and a sodium or calcium ion taking the place of a catalytic magnesium ion. The structure identifies Glu54, Asp82 and Lys93 as t...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkq834

    authors: Firczuk M,Wojciechowski M,Czapinska H,Bochtler M

    更新日期:2011-01-01 00:00:00

  • 3' processing of pre-mRNA plays a major role in proliferation-dependent regulation of histone gene expression.

    abstract::A short histone-like fusion RNA, generated when the RNA 3' processing signal from a mouse histone H4 gene is inserted into a heterologous transcription unit, becomes correctly down-regulated in G1-arrested cells of a temperature-sensitive mouse mastocytoma cell cycle mutant (21-Tb; Stauber et al., EMBO J. 5, 3297-3303...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/16.20.9399

    authors: Stauber C,Schümperli D

    更新日期:1988-10-25 00:00:00

  • SpliceInfo: an information repository for mRNA alternative splicing in human genome.

    abstract::We have developed an information repository named SpliceInfo to collect the occurrences of the four major alternative-splicing (AS) modes in human genome; these include exon skipping, 5'-alternative splicing, 3'-alternative splicing and intron retention. The dataset is derived by comparing the nucleotide and protein s...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gki129

    authors: Huang HD,Horng JT,Lin FM,Chang YC,Huang CC

    更新日期:2005-01-01 00:00:00

  • Force-activated DNA substrates for probing individual proteins interacting with single-stranded DNA.

    abstract::Single-molecule force spectroscopy provides insight into how proteins bind to and move along DNA. Such studies often embed a single-stranded (ss) DNA region within a longer double-stranded (ds) DNA molecule. Yet, producing these substrates remains laborious and inefficient, particularly when using the traditional thre...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkx761

    authors: Okoniewski SR,Uyetake L,Perkins TT

    更新日期:2017-10-13 00:00:00

  • mRNA transfection of a novel TAL effector nuclease (TALEN) facilitates efficient knockout of HIV co-receptor CCR5.

    abstract::Homozygosity for a natural deletion variant of the HIV-coreceptor molecule CCR5, CCR5Δ32, confers resistance toward HIV infection. Allogeneic stem cell transplantation from a CCR5Δ32-homozygous donor has resulted in the first cure from HIV ('Berlin patient'). Based thereon, genetic disruption of CCR5 using designer nu...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkv469

    authors: Mock U,Machowicz R,Hauber I,Horn S,Abramowski P,Berdien B,Hauber J,Fehse B

    更新日期:2015-06-23 00:00:00

  • Analysis of the attachment of replicating DNA to a nuclear matrix in mammalian interphase nuclei.

    abstract::The attachment of replicating DNA to a rapidly sedimenting nuclear structure was investigated by digestion with various nucleases. When DNA was gradually removed by DNase I, pulse label incorporated during either 1 min or during 1 hour in the presence of arabinosylcytosine, remained preferentially attached to the nucl...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/6.1.219

    authors: Dijkwel PA,Mullenders LH,Wanka F

    更新日期:1979-01-01 00:00:00

  • Distinct transcriptional regulatory modules underlie STAT3's cell type-independent and cell type-specific functions.

    abstract::Transcription factors (TFs) regulate gene expression by binding to short DNA sequence motifs, yet their binding specificities alone cannot explain how certain TFs drive a diversity of biological processes. In order to investigate the factors that control the functions of the pleiotropic TF STAT3, we studied its genome...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gks1300

    authors: Hutchins AP,Diez D,Takahashi Y,Ahmad S,Jauch R,Tremblay ML,Miranda-Saavedra D

    更新日期:2013-02-01 00:00:00

  • EASI--enrichment of alternatively spliced isoforms.

    abstract::Alternative splicing produces more than one protein from the majority of genes and the rarer forms can have dominant functions. Instability of alternative transcripts can also hinder the study of regulation of gene expression by alternative splicing. To investigate the true extent of alternative splicing we have devel...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkl592

    authors: Venables JP,Burn J

    更新日期:2006-01-01 00:00:00

  • 5' flanking sequence and genomic structure of Egr-1, a murine mitogen inducible zinc finger encoding gene.

    abstract::Egr-1 is a murine zinc finger encoding cDNA whose expression is modulated by a variety of ligand-receptor interactions and is often coregulated with c-fos (1). This study reports the isolation of a mouse Egr-1 genomic clone, its intron-exon structure, and 935 bp of 5' flanking sequence. The gene spans about 3.8 kb and...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/16.18.8835

    authors: Tsai-Morris CH,Cao XM,Sukhatme VP

    更新日期:1988-09-26 00:00:00

  • Phosphorylated (pT371)TRF1 is recruited to sites of DNA damage to facilitate homologous recombination and checkpoint activation.

    abstract::TRF1, a duplex telomeric DNA-binding protein, plays an important role in telomere metabolism. We have previously reported that a fraction of endogenous TRF1 can stably exist free of telomere chromatin when it is phosphorylated at T371 by Cdk1; however, the role of this telomere-free (pT371)TRF1 has yet to be fully cha...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkt775

    authors: McKerlie M,Walker JR,Mitchell TR,Wilson FR,Zhu XD

    更新日期:2013-12-01 00:00:00

  • GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions.

    abstract::Improving the accuracy of prediction of gene starts is one of a few remaining open problems in computer prediction of prokaryotic genes. Its difficulty is caused by the absence of relatively strong sequence patterns identifying true translation initiation sites. In the current paper we show that the accuracy of gene s...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/29.12.2607

    authors: Besemer J,Lomsadze A,Borodovsky M

    更新日期:2001-06-15 00:00:00

  • The DNA dioxygenase ALKBH2 protects Arabidopsis thaliana against methylation damage.

    abstract::The Escherichia coli AlkB protein (EcAlkB) is a DNA repair enzyme which reverses methylation damage such as 1-methyladenine (1-meA) and 3-methylcytosine (3-meC). The mammalian AlkB homologues ALKBH2 and ALKBH3 display EcAlkB-like repair activity in vitro, but their substrate specificities are different, and ALKBH2 is ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gks327

    authors: Meza TJ,Moen MN,Vågbø CB,Krokan HE,Klungland A,Grini PE,Falnes PØ

    更新日期:2012-08-01 00:00:00

  • Functional analysis of the tobacco mosaic virus tRNA-like structure in cytoplasmic gene regulation.

    abstract::The 3'-untranslated region (UTR) of tobacco mosaic virus (TMV), which terminates in a tRNA-like structure, functionally substitutes for a poly(A) tail in both plant and animal cells. The addition of the TMV 3'-UTR to chimeric mRNA constructs increases their expression up to 100-fold, increasing both translational effi...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/19.18.5031

    authors: Gallie DR,Feder JN,Schimke RT,Walbot V

    更新日期:1991-09-25 00:00:00

  • PeroxisomeDB: a database for the peroxisomal proteome, functional genomics and disease.

    abstract::Peroxisomes are essential organelles of eukaryotic origin, ubiquitously distributed in cells and organisms, playing key roles in lipid and antioxidant metabolism. Loss or malfunction of peroxisomes causes more than 20 fatal inherited conditions. We have created a peroxisomal database (http://www.peroxisomeDB.org) that...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkl935

    authors: Schlüter A,Fourcade S,Domènech-Estévez E,Gabaldón T,Huerta-Cepas J,Berthommier G,Ripp R,Wanders RJ,Poch O,Pujol A

    更新日期:2007-01-01 00:00:00

  • Functional and physical interaction between the histone methyl transferase Suv39H1 and histone deacetylases.

    abstract::The histone methyl transferase Suv39H1 is involved in silencing by pericentric heterochromatin. It specifically methylates K9 of histone H3, thereby creating a high affinity binding site for HP1 proteins. We and others have shown recently that it is also involved in transcriptional repression by the retinoblastoma pro...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/30.2.475

    authors: Vaute O,Nicolas E,Vandel L,Trouche D

    更新日期:2002-01-15 00:00:00

  • siRNA-mediated off-target gene silencing triggered by a 7 nt complementation.

    abstract::A growing body of evidence suggests that siRNA could generate off-target effects through different mechanisms. However, the full impact of off-target gene regulation on phenotypic induction and accordingly on data interpretation in the context of large-scale siRNA library screen has not been reported. Here we report o...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gki762

    authors: Lin X,Ruan X,Anderson MG,McDowell JA,Kroeger PE,Fesik SW,Shen Y

    更新日期:2005-08-09 00:00:00

  • The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants.

    abstract::FASTQ has emerged as a common file format for sharing sequencing read data combining both the sequence and an associated per base quality score, despite lacking any formal definition to date, and existing in at least three incompatible variants. This article defines the FASTQ format, covering the original Sanger stand...

    journal_title:Nucleic acids research

    pub_type: 历史文章,杂志文章,评审

    doi:10.1093/nar/gkp1137

    authors: Cock PJ,Fields CJ,Goto N,Heuer ML,Rice PM

    更新日期:2010-04-01 00:00:00

  • The EcoCyc and MetaCyc databases.

    abstract::EcoCyc is an organism-specific Pathway/Genome Database that describes the metabolic and signal-transduction pathways of Escherichia coli, its enzymes, and-a new addition-its transport proteins. MetaCyc is a new metabolic-pathway database that describes pathways and enzymes of many different organisms, with a microbial...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/28.1.56

    authors: Karp PD,Riley M,Saier M,Paulsen IT,Paley SM,Pellegrini-Toole A

    更新日期:2000-01-01 00:00:00

  • Two promoter elements are necessary and sufficient for expression of the sea urchin U1 snRNA gene.

    abstract::The essential elements of the sea urchin L. variegatus U1 snRNA promoter were mapped by microinjection of a U1 maxigene into sea urchin zygotes. Two elements are required for expression: a distal sequence element (DSE) located between -318 and -300 and a proximal sequence element (PSE) centered at -55. Removal or alte...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/20.14.3743

    authors: Wendelburg BJ,Marzluff WF

    更新日期:1992-07-25 00:00:00

  • Structural properties and gene-silencing activity of chemically modified DNA-RNA hybrids with parallel orientation.

    abstract::We report, herein, a new class of RNAi trigger molecules based on the unconventional parallel hybridization of two oligonucleotide chains. We have prepared and studied several parallel stranded (ps) duplexes, in which the parallel orientation is achieved through incorporation of isoguanine and isocytosine to form reve...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gky024

    authors: Habibian M,Yahyaee-Anzahaee M,Lucic M,Moroz E,Martín-Pintado N,Di Giovanni LD,Leroux JC,Hall J,González C,Damha MJ

    更新日期:2018-02-28 00:00:00

  • Programmed genome rearrangements in Oxytricha produce transcriptionally active extrachromosomal circular DNA.

    abstract::Extrachromosomal circular DNA (eccDNA) is both a driver of eukaryotic genome instability and a product of programmed genome rearrangements, but its extent had not been surveyed in Oxytricha, a ciliate with elaborate DNA elimination and translocation during development. Here, we captured rearrangement-specific circular...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkz725

    authors: Yerlici VT,Lu MW,Hoge CR,Miller RV,Neme R,Khurana JS,Bracht JR,Landweber LF

    更新日期:2019-10-10 00:00:00

  • Impacts of uORF codon identity and position on translation regulation.

    abstract::Translation regulation plays an important role in eukaryotic gene expression. Upstream open reading frames (uORFs) are potent regulatory elements located in 5' mRNA transcript leaders. Translation of uORFs usually inhibit the translation of downstream main open reading frames, but some enhance expression. While a mino...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkz681

    authors: Lin Y,May GE,Kready H,Nazzaro L,Mao M,Spealman P,Creeger Y,McManus CJ

    更新日期:2019-09-26 00:00:00