Reference health
Horizontal gene transfer and the evolution of transcriptional regulation in Escherichia coli
1 of 61 checkable references need attention · checked 2026-07-22
At the dated check, the references listed below either did not resolve in Crossref or DataCite, or carried a retraction notice. Each one is shown with the registry record that put it there.
4 without a DOI — not checked. A reference deposited without a DOI is never matched by title or guessed at; it stays outside the checked set, and this line discloses that.
References needing attention
does not resolve to a known work10.1101/gr.207502. Article published online before print in January 2002
The 60 checked references that resolve
resolves10.1093/nar/gkg210
Evolution of transcription factors and the gene regulatory network in Escherichia coli
resolves10.1016/j.sbi.2006.04.001
Evolution of transcriptional regulatory networks in microbial genomes
resolves10.1006/jtbi.1996.0016
Evolution of Transcriptional Regulation System through Promiscuous Coupling of Regulatory Proteins with Operons; Suggestion from Proteins Sequence Similarities inEscherichia coli
resolves10.1093/nar/29.3.774
Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes
resolves10.1101/gr.323602
Factors Influencing the Identification of Transcription Factor Binding Sites by Cross-Species Comparison
resolves10.1016/j.tig.2005.01.003
Chromosomal organization is shaped by the transcription regulatory network
resolves10.1038/nbt988
Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairs
resolves10.1186/1471-2148-6-63
resolves10.1371/journal.pcbi.0030175
Orthologous Transcription Factors in Bacteria Have Different Functions and Regulate Different Genes
resolves10.1186/1471-2105-7-201
A phylogenomic gene cluster resource: the Phylogenetically Inferred Groups (PhIGs) database
resolves10.1186/gb-2006-7-7-r62
Co-evolution of transcription factors and their targets depends on mode of regulation
resolves10.1093/nar/gki232
A novel method for accurate operon predictions in all sequenced prokaryotes
resolves10.1093/nar/29.1.22
The COG database: new developments in phylogenetic classification of proteins from complete genomes
resolves10.1038/ng1381
Biased biological functions of horizontally transferred genes in prokaryotic genomes
resolves10.1093/molbev/msl206
Gene Cluster Analysis Method Identifies Horizontally Transferred Genes with High Reliability and Indicates that They Provide the Main Mechanism of Operon Gain in 8 Species of γ-Proteobacteria
resolves10.1128/JB.181.18.5624-5635.1999
Inactivation and Regulation of the Aerobic C
<sub>4</sub>
-Dicarboxylate Transport (
<i>dctA</i>
) Gene of
<i>Escherichia coli</i>
resolves10.1371/journal.pbio.0000019
From Gene Trees to Organismal Phylogeny in Prokaryotes:The Case of the γ-Proteobacteria
resolves10.1073/pnas.0609023104
Hierarchy and feedback in the evolution of the
<i>Escherichia coli</i>
transcription network
resolves10.1128/jb.172.10.5877-5883.1990
A Xanthomonas campestris pv. campestris protein similar to catabolite activation factor is involved in regulation of phytopathogenicity
resolves10.1128/jb.174.16.5457-5461.1992
DNA binding specificity and sequence of Xanthomonas campestris catabolite gene activator protein-like protein
resolves10.1046/j.1365-2958.2000.01849.x
Transcription activation at the <i>Escherichia coli melAB</i> promoter: the role of MelR and the cyclic AMP receptor protein
resolves10.1006/jmbi.1998.2160
A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome 1 1Edited by R. Ebright
resolves10.1093/genetics/143.4.1843
Selfish Operons: Horizontal Transfer May Drive the Evolution of Gene Clusters
resolves10.1016/S0959-437X(99)00025-8
Selfish operons: the evolutionary impact of gene clustering in prokaryotes and eukaryotes
resolves10.1093/nar/gki638
Interruptions in gene expression drive highly expressed operons to the leading strand of DNA replication
resolves10.1101/gr.3368805
Operon formation is driven by co-regulation and not by horizontal gene transfer
resolves10.1073/pnas.0700672104
How gene order is influenced by the biophysics of transcription regulation
resolves10.1126/science.1141967
Probing Transcription Factor Dynamics at the Single-Molecule Level in a Living Cell
resolves10.1038/ng1686
Adaptive evolution of bacterial metabolic networks by horizontal gene transfer
resolves10.1101/gr.4746406
The fate of laterally transferred genes: Life in the fast lane to adaptation or death
resolves10.1093/bioinformatics/18.11.1546
QuickTree: building huge Neighbour-Joining trees of
protein sequences
resolves10.1186/1471-2148-3-2
Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes
resolves10.1093/nar/gkh340
MUSCLE: multiple sequence alignment with high accuracy and high throughput
resolves10.1093/oxfordjournals.molbev.a026334
Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis
resolves10.1093/bioinformatics/18.3.502
TREE-PUZZLE: maximum likelihood phylogenetic analysis using
quartets and parallel computing
resolves10.1080/10635150390235520
A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood
resolves10.1099/ijs.0.02026-0
Distributional profiles of homologous open reading frames among bacterial phyla: implications for vertical and lateral transmission
resolves10.1101/gr.2231904
Bacterial Genomes as New Gene Homes: The Genealogy of ORFans in
<i>E. coli</i>
resolves10.1093/bioinformatics/15.7.563
Identifying DNA and protein patterns with statistically significant alignments of multiple sequences.
resolves10.1128/jb.177.19.5506-5516.1995
Identification and characterization of genes (xapA, xapB, and xapR) involved in xanthosine catabolism in Escherichia coli
The 4 references without a DOI — listed, not checked
no DOI — not checkedHow to Use the MicrobesOnline Tree-Browser. [http://www.microbesonline.org/treebrowseHelp.html]
no DOI — not checkedSwofford DL: PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4. 2003, Sunderland, MA: Sinauer Associates
no DOI — not checkedPHYLIP home page. [http://evolution.genetics.washington.edu/phylip.html]
no DOI — not checkedBailey TL, Elkan C: Unsupervised learning of multiple motifs in biopolymers using expectation maximization. Machine Learning. 1995, 21: 51-80.
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work were clean at the dated check: each resolved to a known work in a public registry, and none
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