Browsing Harvard Medical School by Keyword "bioinformatics"
Now showing items 1-20 of 32
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Aging and Environmental Exposures Alter Tissue-Specific DNA Methylation Dependent upon CpG Island Context
(Public Library of Science, 2009)Epigenetic control of gene transcription is critical for normal human development and cellular differentiation. While alterations of epigenetic marks such as DNA methylation have been linked to cancers and many other human ... -
Allele-Specific Amplification in Cancer Revealed by SNP Array Analysis
(Public Library of Science, 2005)Amplification, deletion, and loss of heterozygosity of genomic DNA are hallmarks of cancer. In recent years a variety of studies have emerged measuring total chromosomal copy number at increasingly high resolution. Similarly, ... -
Amino-Acid Co-Variation in HIV-1 Gag Subtype C: HLA-Mediated Selection Pressure and Compensatory Dynamics
(Public Library of Science, 2010)Background: Despite high potential for HIV-1 genetic variation, the emergence of some mutations is constrained by fitness costs, and may be associated with compensatory amino acid (AA) co-variation. To characterize the ... -
Analysis of Multiple Sarcoma Expression Datasets: Implications for Classification, Oncogenic Pathway Activation and Chemotherapy Resistance
(Public Library of Science, 2010)Background: Diagnosis of soft tissue sarcomas (STS) is challenging. Many remain unclassified (not-otherwise-specified, NOS) or grouped in controversial categories such as malignant fibrous histiocytoma (MFH), with unclear ... -
The Bioconductor channel in F1000Research
(F1000Research, 2015)Bioconductor ( bioconductor.org) is a rich source of software and know-how for the integrative analysis of genomic data. The Bioconductor channel in F1000Research provides a forum for task-oriented workflows that each cover ... -
Bioinformatics Workflow for Clinical Whole Genome Sequencing at Partners HealthCare Personalized Medicine
(MDPI, 2016)Effective implementation of precision medicine will be enhanced by a thorough understanding of each patient’s genetic composition to better treat his or her presenting symptoms or mitigate the onset of disease. This ideally ... -
Comparative Genomic Characterization of Francisella tularensis Strains Belonging to Low and High Virulence Subspecies
(Public Library of Science, 2009)Tularemia is a geographically widespread, severely debilitating, and occasionally lethal disease in humans. It is caused by infection by a gram-negative bacterium, Francisella tularensis. In order to better understand its ... -
Comparative ICE Genomics: Insights into the Evolution of the SXT/R391 Family of ICEs
(Public Library of Science, 2009)Integrating and conjugative elements (ICEs) are one of the three principal types of self-transmissible mobile genetic elements in bacteria. ICEs, like plasmids, transfer via conjugation; but unlike plasmids and similar to ... -
A computational method for identification of vaccine targets from protein regions of conserved human leukocyte antigen binding
(BioMed Central, 2015)Background: Computational methods for T cell-based vaccine target discovery focus on selection of highly conserved peptides identified across pathogen variants, followed by prediction of their binding of human leukocyte ... -
Discovering Causal Signaling Pathways Through Gene-Expression Patterns
(Oxford University Press, 2010)High-throughput gene-expression studies result in lists of differentially expressed genes. Most current meta-analyses of these gene lists include searching for significant membership of the translated proteins in various ... -
Evidence of Molecular Evolution Driven by Recombination Events Influencing Tropism in a Novel Human Adenovirus that Causes Epidemic Keratoconjunctivitis
(Public Library of Science, 2009)In 2005, a human adenovirus strain (formerly known as HAdV-D22/H8 but renamed here HAdV-D53) was isolated from an outbreak of epidemic keratoconjunctititis (EKC), a disease that is usually caused by HAdV-D8, -D19, or -D37, ... -
Functional Copy-Number Alterations in Cancer
(Public Library of Science, 2008)Understanding the molecular basis of cancer requires characterization of its genetic defects. DNA microarray technologies can provide detailed raw data about chromosomal aberrations in tumor samples. Computational analysis ... -
A Functional Selection Model Explains Evolutionary Robustness Despite Plasticity in Regulatory Networks
(Nature Publishing Group, 2012)Evolutionary rewiring of regulatory networks is an important source of diversity among species. Previous evidence suggested substantial divergence of regulatory networks across species. However, systematically assessing ... -
Genes to Diseases (G2D) Computational Method to Identify Asthma Candidate Genes
(Public Library of Science, 2008)Asthma is a complex trait for which different strategies have been used to identify its environmental and genetic predisposing factors. Here, we describe a novel methodological approach to select candidate genes for asthma ... -
High-Throughput, Kingdom-Wide Prediction and Annotation of Bacterial Non-Coding RNAs
(Public Library of Science, 2008)Background: Diverse bacterial genomes encode numerous small non-coding RNAs (sRNAs) that regulate myriad biological processes. While bioinformatic algorithms have proven effective in identifying sRNA-encoding loci, the ... -
Hypermutable Non-Synonymous Sites are Under Stronger Negative Selection
(Public Library of Science, 2008)Mutation rate varies greatly between nucleotide sites of the human genome and depends both on the global genomic location and the local sequence context of a site. In particular, CpG context elevates the mutation rate by ... -
Identification and Rational Redesign of Peptide Ligands to CRIP1, A Novel Biomarker for Cancers
(Public Library of Science, 2008)Cysteine-rich intestinal protein 1 (CRIP1) has been identified as a novel marker for early detection of cancers. Here we report on the use of phage display in combination with molecular modeling to identify a high-affinity ... -
Individual Retinal Progenitor Cells Display Extensive Heterogeneity of Gene Expression
(Public Library of Science, 2008)The development of complex tissues requires that mitotic progenitor cells integrate information from the environment. The highly varied outcomes of such integration processes undoubtedly depend at least in part upon ... -
An Integrated Strategy for Analyzing the Unique Developmental Programs of Different Myoblast Subtypes
(Public Library of Science, 2006)An important but largely unmet challenge in understanding the mechanisms that govern the formation of specific organs is to decipher the complex and dynamic genetic programs exhibited by the diversity of cell types within ... -
An Integration of Genome-Wide Association Study and Gene Expression Profiling to Prioritize the Discovery of Novel Susceptibility Loci for Osteoporosis-Related Traits
(Public Library of Science, 2010)Osteoporosis is a complex disorder and commonly leads to fractures in elderly persons. Genome-wide association studies (GWAS) have become an unbiased approach to identify variations in the genome that potentially affect ...