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- The Gene Set Builder: Collation, Curation, and Distribution of Sets of Genes
- In bioinformatics and genomics, there are many applications designed to investigate the common properties for a set of genes. While tremendous effort has been invested in developing tools that can analyze a set of genes, minimal effort has been invested in developing tools that can help researchers compile, store, and...
- White papers 2005-12-21
- Human Cytomegalovirus Plasmid-Based Amplicon Vector System for Gene Therapy
- The paper deals with the construction and evaluation of the utility of a helper-dependent virus vector system that is derived from Human Cytomegalovirus HCMV. This vector is based on the herpes simplex virus HSV amplicon system and contains the HCMV orthologs of the two cis-acting functions required for replication and...
- White papers 2005-01-26
- cAMP Response Element Binding Protein (CREB) Activates Transcription via Two Distinct Genetic Elements of the Human Glucose-6-Phosphatase Gene
- The enzyme glucose-6-phosphatase catalyzes the dephosphorylation of glucose-6-phosphatase to glucose, the final step in the gluconeogenic and glycogenolytic pathways. Expression of the glucose-6-phosphatase gene is induced by glucocorticoids and elevated levels of intracellular cAMP. The effect of cAMP in regulating glucose-6-phosphatase gene transcription was corroborated by the identification of two...
- White papers 2005-01-19
- Selection and Characterization of a Promoter for Expression of Single-Copy Recombinant Genes in Gram-Positive Bacteria
- This white paper reports about a genetic system based on suicide vectors on conjugative transposons allowing stable integration of recombinant DNA into the chromosome of transformable and non-transformable Gram-positive bacteria. The aim of this work was to select a strong chromosomal promoter from Streptococcus gordonii to improve this genetic system...
- White papers 2005-01-14
- A Minor Alternative Transcript of the Fumarylacetoacetate Hydrolase Gene Produces a Protein despite Being Likely Subjected to Nonsense-Mediated mRNA Decay
- Coupling of alternative splicing with nonsense-mediated mRNA decay NMD may regulate gene expression. The paper reports the identification of nonsense alternative transcript of the fumarylacetoacetate hydrolase gene, which produces a protein despite the fact that it is subject to NMD. This system, termed RUST for Regulated Unproductive Splicing and Translation,...
- White papers 2005-01-07
- An Empirical Analysis of Training Protocols for Probabilistic Gene Finders
- Generalized hidden Markov models GHMMs appear to be approaching acceptance as a de facto standard for state-of-the-art ab initio gene finding, as evidenced by the recent proliferation of GHMM implementations. While prevailing methods for modeling and parsing genes using GHMMs have been described in the literature, little attention has been...
- White papers 2004-12-21
- A Power Law Global Error Model for the Identification of Differentially Expressed Genes in Microarray Data
- High-density oligonucleotide microarray technology enables the discovery of genes that are transcriptionally modulated in different biological samples due to physiology, disease or intervention. Methods for the identification of these so-called "differentially expressed genes" DEG would largely benefit from a deeper knowledge of the intrinsic measurement variability. The aim of this...
- White papers 2004-12-17
- Comparing Functional Annotation Analyses With Catmap
- Ranked gene lists from microarray experiments are usually analyzed by assigning significance to predefined gene categories, e.g., based on functional annotations. Tools performing such analyses are often restricted to a category score based on a cutoff in the ranked list and a significance calculation based on random gene permutations as...
- White papers 2004-12-09
- RNA Interference: Learning Gene Knock-Down From Cell Physiology
- Over the past decade RNA interference RNAi has emerged as a natural mechanism for silencing gene expression. This ancient cellular antiviral response can be exploited to allow specific inhibition of the function of any chosen target gene. RNAi is proving to be an invaluable research tool, allowing much more rapid...
- White papers 2004-11-22
- On the Optimal Ratio of Heavy to Light Chain Genes for Efficient Recombinant Antibody Production by CHO Cells
- The data given in this paper suggests that the optimal ratio of hc: lc genes used for transient and stable expression of Mab differ. In the case of the latter, the paper infers that optimal Mab production by stably transfected cells represents a compromise between HC abundance limiting productivity and...
- White papers 2004-11-16
- The Evolution of Drug-Activated Nuclear Receptors: One Ancestral Gene Diverged Into Two Xenosensor Genes in Mammals
- This white paper deals with activating the pregnane X receptor PXR and constitutive androstane receptor CAR in mammals. In non-mammalian species, only one xenosensor gene has been found. Using chicken as a model organism, the aim of the study was to elucidate whether non-mammalian species only have one or two...
- White papers 2004-10-12
- Transcriptional Oscillation of Canonical Clock Genes in Mouse Peripheral Tissues
- The circadian rhythm of about 24 hours is a fundamental physiological function observed in almost all organisms from prokaryotes to humans. Identification of clock genes has allowed to study the molecular bases for circadian behaviors and temporal physiological processes such as hormonal secretion, and has prompted the idea that molecular...
- White papers 2004-10-09
- What Is the Impact of the ACE Gene Insertion/Deletion (I/D) Polymorphism on the Clinical Effectiveness and Adverse Events of ACE Inhibitors? - Protocol of a Systematic Review
- This white paper deals with a protocol that describes a strategy to quantify the effect modification of the ACE polymorphism on ACE inhibitors in relevant clinical domains using meta-epidemiological research methods. The results may provide evidence for the usefulness of pharmacogenetic testing for individualized ACE inhibitor therapy. The Angiotensin Converting...
- White papers 2004-09-10
- Co-Transcriptional Folding Is Encoded Within RNA Genes
- The main aim of this work is to study if and how co-transcriptional folding is encoded within the primary and secondary structure of RNA genes. In order to achieve this, the paper presents the known primary and secondary structures of a comprehensive data set of 361 RNA genes as well...
- White papers 2004-08-05
- A Multivariate Empirical Bayes Statistic for Replicated Microarray Time Course Data
- In this paper they derive a one-sample multivariate empirical Bayes statistic to rank genes in the order of differential expression from replicated microarray time course experiments. They do this by testing the null hypothesis that the expectation of a k-vector of a gene's expression levels is a multiple of 1k,...
- White papers 2004-08-04
- Modeling Periodic Oscillation of Biological Systems With Multiple Timescale Networks
- This paper, aims to develop a new methodology to model and design periodic oscillators of biological networks, in particular gene regulatory networks with multiple genes, proteins and time delays, by using multiple timescale networks MTN. Fast reactions constitute a positive feedback-loop network PFN, while slow reactions consist of a cyclic...
- White papers 2004-06-01
- Coupling of Importin Beta Binding Peptide on Plasmid DNA: Physico-Chemical Properties
- This white paper deals with Non-viral vectors for gene transfer are less immunogenic than viral vectors but also less efficient. Significant effort has focused on enhancing non-viral gene transfer efficiency by increasing nuclear import of plasmid DNA, particularly by coupling nuclear localization peptidic sequences to plasmid DNA. It reveals conclusion...
- White papers 2003-09-12
- Crystal Structure of T7 Gene 4 Ring Helicase Indicates a Mechanism for Sequential Hydrolysis of Nucleotides
- This paper determines the crystal structure of an active, hexameric fragment of the gene 4 helicase from bactewereriophage T7. The structure reveals how subunit contacts stabilize the hexamer. The structural consequences of the asymmetry suggest a "binding change" mechanism to explain how cooperative binding and hydrolysis of nucleotides are coupled...
- White papers 2003-03-17
- Antihypertensive Pharmacokinetics: Getting the Right Drug Into the Right Patient
- Pharmaco-genetic investigation seeks to identify genetic factors that contribute to interpatient and interdrug variation in responses to antihypertensive drug therapy. Classical studies have characterized single gene polymorphisms of drug metabolizing enzymes that are responsible for large inter-individual differences in pharmacokinetic responses to several antihypertensive drugs. Progress is being made using...
- White papers 2000-08-11
- Statistical Methods for Identifying Dierentially Expressed Genes in Replicated cDNA Microarray Experiments
- Microarrays are part of a new class of biotechnologies which allow the monitoring of expression levels for thousands of genes simultaneously. This paper describes statistical methods for the identification of differentially expressed genes in replicated cDNA microarray experiments. Although it is not the main focus of the paper, they stress...
- White papers 2000-08-01
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