A topological algorithm for identification of structural domains of proteins
BMC Bioinformatics 2007, 8:237 (3 July 2007)
The non-dosage compensated Lsp1 α gene of Drosophila melanogaster escapes acetylation by MOF in larval fat body nuclei, but is flanked by two dosage compensated genes
BMC Molecular Biology 2007, 8:35 (19 May 2007)
The Genopolis Microarray Database
BMC Bioinformatics 2007, 8(Suppl 1):S21 (8 March 2007)
Characterization of the minimum domain required for targeting budding yeast myosin II to the site of cell division
BMC Biology 2006, 4:19 (26 June 2006)
The budding yeast myosin II protein Myo1 is likely to exist as a trimer and within the Myo1 minimum localization domain as now defined, the hinge region is required for contraction of the contractile ring during cytokinesis.
Similarity searches in genome-wide numerical data sets
Biology Direct 2006, 1:13 (30 May 2006)
Histone H4 lysine 16 acetylation breaks the genome's silence
Genome Biology 2006, 7:217 (10 May 2006)
The acetylation of histone H4 on lysine 16 is a crucial event in switching chromatin from a repressive to a transcriptionally active state.
CBF β is a facultative Runx partner in the sea urchin embryo
BMC Biology 2006, 4:4 (9 February 2006)
Like its mammalian homologs, sea urchin Core Binding Factor beta binds to a Runx partner, but although Runt-1 deficiency affects embryonic differentiation and cell survival, CBFbeta knockdown affects only differentiation.
Identification of significant periodic genes in microarray gene expression data
BMC Bioinformatics 2005, 6:286 (30 November 2005)
An approach using both Bartlett's C-statistic and Fisher's G-statistic can successfully identity genes which are significantly periodic in microarray time series data.
Chromatin dynamics rule the genome
Genome Biology 2005, 6:355 (31 October 2005)
A report on the FASEB Summer Research Conference 'Chromatin and Transcription', Snowmass, USA, 9-14 July 2005.
Natural history of S-adenosylmethionine-binding proteins
BMC Structural Biology 2005, 5:19 (14 October 2005)
Analysis of the phyletic distribution and structural similarities of S-adenosylmethionine-binding proteins indicate that two widespread folds, the Rossman fold and TIM barrel, have repeatedly evolved for diverse types of reactions that require S-adenosylmethionine.
Runx-dependent expression of PKC is critical for cell survival in the sea urchin embryo
BMC Biology 2005, 3:18 (2 August 2005)
Sea urchin embryonic knockdown of either Runx protein or protein kinase C causes extensive apoptosis, while Runx deficiency is rescued by inhibition of caspase-3 and by PKC mRNA injection, providing evidence that Runx maintains PKC levels to ensure cell survival.
Use of adenoviral E1A protein to analyze K18 promoter deregulation in colon carcinoma cells discloses a role for CtBP1 and BRCA1
BMC Molecular Biology 2005, 6:8 (14 April 2005)
Sea urchin vault structure, composition, and differential localization during development
BMC Developmental Biology 2005, 5:3 (14 February 2005)
Histones: should I stay or should I go?
Genome Biology 2005, 6:306 (14 January 2005)
A report on the American Society for Biochemistry and Molecular Biology symposium 'Transcriptional Regulation by Chromatin and RNA polymerase II', Lake Tahoe, USA, 29 October-1 November 2004.
Evaluation of the chicken transcriptome by SAGE of B cells and the DT40 cell line
BMC Genomics 2004, 5:98 (21 December 2004)
Two Drosophila suppressors of cytokine signaling (SOCS) differentially regulate JAK and EGFR pathway activities
BMC Cell Biology 2004, 5:38 (15 October 2004)
Global nucleosome distribution and the regulation of transcription in yeast
Genome Biology 2004, 5:243 (30 September 2004)
Recent studies show that active regulatory regions of the yeast genome have a lower density of nucleosomes than other regions, and that there is an inverse correlation between nucleosome density and the transcription rate of a gene.
Evaluation of developmental phenotypes produced by morpholino antisense targeting of a sea urchin Runx gene
BMC Biology 2004, 2:6 (7 May 2004)
The sea urchin's Runx transcription factor is crucial both for embryonic development and for cell proliferation and differentiation, according to a study using `morpholino' antisense oligonucleotides to knock down gene expression.
Detection of evolutionarily stable fragments of cellular pathways by hierarchical clustering of phyletic patterns
Genome Biology 2004, 5:R32 (27 April 2004)
A hierarchy of 3,688 phyletic patterns was characterized encompassing more than 5,000 known protein-coding genes from 66 complete microbial genomes. The results indicate that gene loss and displacement has occurred in the evolution of most pathways.
The evolution of Runx genes I. A comparative study of sequences from phylogenetically diverse model organisms
BMC Evolutionary Biology 2003, 3:4 (24 March 2003)
Quod erat demonstrandum? The mystery of experimental validation of apparently erroneous computational analyses of protein sequences
Genome Biology 2001, 2:research0051-research0051.11 (13 November 2001)
Six cases where application of novel or conventional computational methods for protein sequence and structure analysis led to non-trivial predictions that were subsequently supported by direct experiments were analyzed. On all occasions, the original prediction seemed unjustified, and in at least three cases an alternative, well-supported computational prediction, incompatible with the original one, could be derived.