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Modifications to the core histones are thought to contribute to ESC pluripotency by priming tissue-specific promoters and enhancers for later activation. However, it is unclear how these marks are targeted in ESCs and maintained during differentiation. Her ...
Numerous methods have been developed for inference of gene regulatory networks from expression data, however, their strengths and weaknesses remain poorly understood. Accurate and systematic evaluation of these methods is hampered by the difficulty of cons ...
Differences in gene expression may play a major role in speciation and phenotypic diversity. We examined genome-wide differences in transcription factor (TF) binding in several humans and a single chimpanzee by using chromatin immunoprecipitation followed ...
American Association for the Advancement of Science2010
A dominant mutation in the gene coding for the vesicle-associated membrane protein-associated protein B (VAPB) was associated with amyotrophic lateral sclerosis, a fatal paralytic disorder characterized by the selective loss of motoneurons in the brain and ...
GermOnline 4.0 is a cross-species database portal focusing on high-throughput expression data relevant for germline development, the meiotic cell cycle and mitosis in healthy versus malignant cells. It is thus a source of information for life scientists as ...
Hox genes are central to the specification of structures along the anterior-posterior body axis, and modifications in their expression have paralleled the emergence of diversity in vertebrate body plans. Here we describe the genomic organization of Hox clu ...
We consider the problem of learning dynamical models of genetic regulatory networks from time-lapse measurements of gene expression. In our previous work [Porreca et al,Bioinformatics,2010], we described a method for the structural and parametric identific ...
This master project describes computational analysis of nucleosomes positioning in four yeast species: S. cerevisiae, S. kudriavzevii, S. bayanus (three relatively close species, ~75% of sequence similarity) and C. glabrata (more distant, ~57% of sequence ...
The segmentation of Drosophila is a prime model to study spatial patterning during embryogenesis. The spatial expression of segment polarity genes results from a complex network of interacting proteins whose expression products are maintained after success ...
Numerous methods have been developed for inferring gene regulatory networks from expression data, however, both their absolute and comparative performance remain poorly understood. In this paper, we introduce a framework for critical performance assessment ...