The Experts below are selected from a list of 277542 Experts worldwide ranked by ideXlab platform
Amy M Hauth - One of the best experts on this subject based on the ideXlab platform.
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ISMB - Beyond tandem repeats: Complex Pattern structures and distant regions of similarity.
2002Co-Authors: Amy M Hauth, Deborah JosephAbstract:Motivation: Tandem repeats (TRs) are associated with human disease, play a role in evolution and are important in regulatory processes. Despite their importance, locating and characterizing these Patterns within anonymous DNA sequences remains a challenge. In part, the difficulty is due to imperfect conservation of Patterns and Complex Pattern structures. We study recognition algorithms for two Complex Pattern structures: variable length tandem repeats (VLTRs) and multi-period tandem repeats (MPTRs). Results: We extend previous algorithmic research to a class of regular tandem repeats (RegTRs). We formally define RegTRs, as well as two important subclasses: VLTRs and MPTRs. We present algorithms for identification of TRs in these classes. Furthermore, our algorithms identify degenerate VLTRs and MPTRs: repeats containing substitutions, insertions and deletions. To illustrate our work, we present results of our analysis for two difficult regions in cattle and human data which reflect practical occurrences of these subclasses in GenBank sequence data. In addition, we show the applicability of our algorithmic techniques for identifying Alu sequences, gene clusters and other distant regions of similarity. We illustrate this with an example from yeast chromosome I. Availability: Algorithms can be accessed at http://www.cs.
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Beyond tandem repeats: Complex Pattern structures and distant regions of similarity.
Bioinformatics (Oxford England), 2002Co-Authors: Amy M Hauth, Deborah A JosephAbstract:Tandem repeats (TRs) are associated with human disease, play a role in evolution and are important in regulatory processes. Despite their importance, locating and characterizing these Patterns within anonymous DNA sequences remains a challenge. In part, the difficulty is due to imperfect conservation of Patterns and Complex Pattern structures. We study recognition algorithms for two Complex Pattern structures: variable length tandem repeats (VLTRs) and multi-period tandem repeats (MPTRs). We extend previous algorithmic research to a class of regular tandem repeats (RegTRs). We formally define RegTRs, as well as two important subclasses: VLTRs and MPTRs. We present algorithms for identification of TRs in these classes. Furthermore, our algorithms identify degenerate VLTRs and MPTRs: repeats containing substitutions, insertions and deletions. To illustrate our work, we present results of our analysis for two difficult regions in cattle and human data which reflect practical occurrences of these subclasses in GenBank sequence data. In addition, we show the applicability of our algorithmic techniques for identifying Alu sequences, gene clusters and other distant regions of similarity. We illustrate this with an example from yeast chromosome I.
Jorge R Oksenberg - One of the best experts on this subject based on the ideXlab platform.
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transcriptional analysis of multiple sclerosis brain lesions reveals a Complex Pattern of cytokine expression
Journal of Immunology, 2000Co-Authors: Sergio E Baranzini, Carita Maria San Francisco Elfstrom, Shengyung Chang, Catalin Butunoi, Ronald S Murray, Russell Higuchi, Jorge R OksenbergAbstract:Multiple sclerosis (MS) is a common and severe neurological disorder associated with an autoimmune response directed against myelin components within the CNS. Lymphocyte activation, extravasation, and recruitment, as well as effector function, involves the turning on and off of a number of genes, thus triggering specific transcriptional pathways. The characterization of the transcriptome in MS lesions should provide a better understanding of the mechanisms that generate and sustain the pathogenic immune response in this disease. Here we performed transcriptional profiling of 56 relevant genes in brain specimens from eight MS patients and eight normal controls by kinetic RT-PCR. Results showed a high transcriptional activity for the gene coding for myelin basic protein (MBP); however, it was not differentially expressed in MS samples, suggesting that remyelination is an active process also in the noninflammatory brain. CD4 and HLA-DRα transcripts were dramatically increased in MS as compared with controls. This reveals a robust MHC class II up-regulation and suggests that Ag is being presented locally to activated T cells. Although analysis of cytokine and cytokine receptor genes expression showed predominantly increased levels of several Th1 molecules (TGF-β, RANTES, and macrophage-inflammatory protein (MIP)-1α) in MS samples, some Th2 genes (IL-3, IL-5, and IL-6/IL-6R) were found to be up-regulated as well. Similarly, both proinflammatory type (CCR1, CCR5) and immunomodulatory type (CCR4, CCR8) chemokine receptors were differentially expressed in the MS brain. Overall, our data suggest a Complex regulation of the inflammatory response in human autoimmune demyelination.
Deborah Joseph - One of the best experts on this subject based on the ideXlab platform.
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ISMB - Beyond tandem repeats: Complex Pattern structures and distant regions of similarity.
2002Co-Authors: Amy M Hauth, Deborah JosephAbstract:Motivation: Tandem repeats (TRs) are associated with human disease, play a role in evolution and are important in regulatory processes. Despite their importance, locating and characterizing these Patterns within anonymous DNA sequences remains a challenge. In part, the difficulty is due to imperfect conservation of Patterns and Complex Pattern structures. We study recognition algorithms for two Complex Pattern structures: variable length tandem repeats (VLTRs) and multi-period tandem repeats (MPTRs). Results: We extend previous algorithmic research to a class of regular tandem repeats (RegTRs). We formally define RegTRs, as well as two important subclasses: VLTRs and MPTRs. We present algorithms for identification of TRs in these classes. Furthermore, our algorithms identify degenerate VLTRs and MPTRs: repeats containing substitutions, insertions and deletions. To illustrate our work, we present results of our analysis for two difficult regions in cattle and human data which reflect practical occurrences of these subclasses in GenBank sequence data. In addition, we show the applicability of our algorithmic techniques for identifying Alu sequences, gene clusters and other distant regions of similarity. We illustrate this with an example from yeast chromosome I. Availability: Algorithms can be accessed at http://www.cs.
Ikuko T. Smith - One of the best experts on this subject based on the ideXlab platform.
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The influence of a single neuron on its network
Nature, 2019Co-Authors: Ikuko T. SmithAbstract:The contribution of a single neuron to brain function might seem negligible. But a map of the influence of single neurons reveals a Complex Pattern that prevents redundancy and enables clear messaging. Inhibitory and activating effects of a neuron on its neighbours
Deborah A Joseph - One of the best experts on this subject based on the ideXlab platform.
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Beyond tandem repeats: Complex Pattern structures and distant regions of similarity.
Bioinformatics (Oxford England), 2002Co-Authors: Amy M Hauth, Deborah A JosephAbstract:Tandem repeats (TRs) are associated with human disease, play a role in evolution and are important in regulatory processes. Despite their importance, locating and characterizing these Patterns within anonymous DNA sequences remains a challenge. In part, the difficulty is due to imperfect conservation of Patterns and Complex Pattern structures. We study recognition algorithms for two Complex Pattern structures: variable length tandem repeats (VLTRs) and multi-period tandem repeats (MPTRs). We extend previous algorithmic research to a class of regular tandem repeats (RegTRs). We formally define RegTRs, as well as two important subclasses: VLTRs and MPTRs. We present algorithms for identification of TRs in these classes. Furthermore, our algorithms identify degenerate VLTRs and MPTRs: repeats containing substitutions, insertions and deletions. To illustrate our work, we present results of our analysis for two difficult regions in cattle and human data which reflect practical occurrences of these subclasses in GenBank sequence data. In addition, we show the applicability of our algorithmic techniques for identifying Alu sequences, gene clusters and other distant regions of similarity. We illustrate this with an example from yeast chromosome I.