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Biomedical subjects

Christopher Lee

Publications and source records attributed to Christopher Lee.

10 recordsLinked to original sources
PubMed2003

POAVIZ: a Partial order multiple sequence alignment visualizer.

SUMMARY: POAVIZ creates a visualization of a multiple sequence alignment that makes clear the overall structure of how sequences match and diverge in the alignment. POAVIZ can construct visualizations from any multiple sequence alignment source (e.g. PIR and CLUSTAL formats), and is valuable for revealing complex branching structure (such as domains, large-scale insertions / deletions or recombinations), especially in partnership with the Partial Order Alignment (POA) multiple sequence alignment program. AVAILABILITY: The Partial Order multiple sequence Alignment Visualizer (POAVIZ) program is available at http://www.bioinformatics.ucla.edu/poa

Algorithms↗
PubMed2003

Generating consensus sequences from partial order multiple sequence alignment graphs.

MOTIVATION: Consensus sequence generation is important in many kinds of sequence analysis ranging from sequence assembly to profile-based iterative search methods. However, how can a consensus be constructed when its inherent assumption-that the aligned sequences form a single linear consensus-is not true? RESULTS: Partial Order Alignment (POA) enables construction and analysis of multiple sequence alignments as directed acyclic graphs containing complex branching structure. Here we present a dynamic programming algorithm (heaviest_bundle) for generating multiple consensus sequences from such complex alignments. The number and relationships of these consensus sequences reveals the degree of structural complexity of the source alignment. This is a powerful and general approach for analyzing and visualizing complex alignment structures, and can be applied to any alignment. We illustrate its value for analyzing expressed sequence alignments to detect alternative splicing, reconstruct full length mRNA isoform sequences from EST fragments, and separate paralog mixtures that can cause incorrect SNP predictions. AVAILABILITY: The heaviest_bundle source code is available at http://www.bioinformatics.ucla.edu/poa

Algorithms↗
PubMed2003

Motor cortex organization after stroke is related to side of stroke and level of recovery.

BACKGROUND AND PURPOSE: The present study hypothesized that side of stroke and level of recovery influence motor system organization after stroke. METHODS: Functional MRI was performed on 14 control subjects and 21 patients with chronic stroke during index finger tapping (control subjects, right; patients, recovered side). RESULTS: On functional MRI, stroke patients with right arm involvement showed (1) significantly smaller activation in contralateral motor cortexes compared with control subjects; (2) smaller ipsilateral (nonstroke) premotor and larger contralateral (stroke-side) sensorimotor activation compared with patients with left arm involvement, although electromyogram across groups was similar; and (3) 2.7-fold-larger contralateral sensorimotor cortex activation, ventrally, in those with full recovery compared with those with partial recovery, despite similar tapping force, frequency, range of motion, and electromyogram between groups. Supplementary motor area activation was unrelated to level of recovery. CONCLUSIONS: After stroke that causes mild to moderate initial impairment and mild residual hand weakness, cortical organization varies with side of injury and with final motor status. The findings may have implications for treatment after stroke.

Arm↗
PubMed2003

ASAP: the Alternative Splicing Annotation Project.

Recently, genomics analyses have demonstrated that alternative splicing is widespread in mammalian genomes (30-60% of genes reported to have multiple isoforms), and may be one of their most important mechanisms of functional regulation. However, by comparison with other genomics data such as genome annotation, SNPs, or gene expression, there exists relatively little database infrastructure for the study of alternative splicing. We have constructed an online database ASAP (the Alternative Splicing Annotation Project) for biologists to access and mine the enormous wealth of alternative splicing information coming from genomics and proteomics. ASAP is based on genome-wide analyses of alternative splicing in human (30 793 alternative splice relationships found) from detailed alignment of expressed sequences onto the genomic sequence. ASAP provides precise gene exon-intron structure, alternative splicing, tissue specificity of alternative splice forms, and protein isoform sequences resulting from alternative splicing. Moreover, it can help biologists design probe sequences for distinguishing specific mRNA isoforms. ASAP is intended to be a community resource for collaborative annotation of alternative splice forms, their regulation, and biological functions. The URL for ASAP is http://www.bioinformatics.ucla.edu/ASAP.

Alternative Splicing↗
PubMed2002

Genome-wide detection of tissue-specific alternative splicing in the human transcriptome.

We have developed an automated method for discovering tissue-specific regulation of alternative splicing through a genome-wide analysis of expressed sequence tags (ESTs). Using this approach, we have identified 667 tissue-specific alternative splice forms of human genes. We validated our muscle-specific and brain-specific splice forms for known genes. A high fraction (8/10) were reported to have a matching tissue specificity by independent studies in the published literature. The number of tissue-specific alternative splice forms is highest in brain, while eye-retina, muscle, skin, testis and lymph have the greatest enrichment of tissue-specific splicing. Overall, 10-30% of human alternatively spliced genes in our data show evidence of tissue-specific splice forms. Seventy-eight percent of our tissue-specific alternative splices appear to be novel discoveries. We present bioinformatics analysis of several tissue-specific splice forms, including automated protein isoform sequence and domain prediction, showing how our data can provide valuable insights into gene function in different tissues. For example, we have discovered a novel kidney-specific alternative splice form of the WNK1 gene, which appears to specifically disrupt its N-terminal kinase domain and may play a role in PHAII hypertension. Our database greatly expands knowledge of tissue-specific alternative splicing and provides a comprehensive dataset for investigating its functional roles and regulation in different human tissues.

Alternative Splicing↗
PubMed2002

Treatment of PTSD: stress inoculation training with prolonged exposure compared to EMDR.

The effectiveness of Stress Inoculation Training with Prolonged Exposure (SITPE) was compared to Eye Movement Desensitization and Reprocessing (EMDR). Twenty-four participants who had a diagnosis of Post Traumatic Stress Disorder (PTSD) were randomly assigned to one of the treatment conditions. Participants were also their own wait-list control. Outcome measures included self-report and observer-rated measures of PTSD, and self-report measures of depression. On global PTSD measures, there were no significant differences between the treatments at the end of therapy. However on the subscale measures of the degree of intrusion symptoms, EMDR did significantly better than SITPE. At follow-up EMDR was found to lead to greater gains on all measures.

Adult↗
PubMed2002

A genomic view of alternative splicing.

Recent genome-wide analyses of alternative splicing indicate that 40-60% of human genes have alternative splice forms, suggesting that alternative splicing is one of the most significant components of the functional complexity of the human genome. Here we review these recent results from bioinformatics studies, assess their reliability and consider the impact of alternative splicing on biological functions. Although the 'big picture' of alternative splicing that is emerging from genomics is exciting, there are many challenges. High-throughput experimental verification of alternative splice forms, functional characterization, and regulation of alternative splicing are key directions for research. We recommend a community-based effort to discover and characterize alternative splice forms comprehensively throughout the human genome.

Alternative Splicing↗
PubMed2002

Multiple sequence alignment using partial order graphs.

MOTIVATION: Progressive Multiple Sequence Alignment (MSA) methods depend on reducing an MSA to a linear profile for each alignment step. However, this leads to loss of information needed for accurate alignment, and gap scoring artifacts. RESULTS: We present a graph representation of an MSA that can itself be aligned directly by pairwise dynamic programming, eliminating the need to reduce the MSA to a profile. This enables our algorithm (Partial Order Alignment (POA)) to guarantee that the optimal alignment of each new sequence versus each sequence in the MSA will be considered. Moreover, this algorithm introduces a new edit operator, homologous recombination, important for multidomain sequences. The algorithm has improved speed (linear time complexity) over existing MSA algorithms, enabling construction of massive and complex alignments (e.g. an alignment of 5000 sequences in 4 h on a Pentium II). We demonstrate the utility of this algorithm on a family of multidomain SH2 proteins, and on EST assemblies containing alternative splicing and polymorphism. AVAILABILITY: The partial order alignment program POA is available at http://www.bioinformatics.ucla.edu/poa.

Algorithms↗
PubMedDate not supplied

Use of a SCID mouse model to select for a more aggressive strain of prostate cancer.

BACKGROUND: Prostate cancer is the most common non-cutaneous malignancy to affect men and has a propensity for metastasizing to bone. To better mimic the biology of metastatic prostate cancer, we have developed a model that utilizes both human prostate cancer and human bone in the SCID mouse. MATERIALS AND METHODS: Injection of a xenograft of human prostate cancer, LAPC-4, near a human bone core that was previously implanted within the hindlimb of a SCID mouse allowed for the selection of a more aggressive subset of cells, known as LAPC-4(2) (read as "LAPC-4 squared"). RESULTS: As compared to LAPC-4 cells, these "bone-selected" LAPC-4(2) cells form tumors more rapidly, develop PSA-positive serum at an earlier time-point as well as with higher levels, develop androgen independence, and metastasize to human bone after orthotopic injection. CONCLUSION: The selection of a more aggressive subset of prostate cancer cells that have developed androgen independence and the propensity to metastasize is of paramount importance as these are the cellular characteristics that are clinically linked to morbidity. Analysis of these "bone-selected" cells may lead to a better understanding of the molecular basis behind the conversion of low-grade prostate carcinoma to its more deadly, metastatic form.

Adult↗