Browsing Harvard Medical School by Keyword "computational biology"
Now showing items 1-20 of 89
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Adaptive Mutations in the JC Virus Protein Capsid Are Associated with Progressive Multifocal Leukoencephalopathy (PML)
(Public Library of Science, 2009)PML is a progressive and mostly fatal demyelinating disease caused by JC virus infection and destruction of infected oligodendrocytes in multiple brain foci of susceptible individuals. While JC virus is highly prevalent ... -
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, ... -
Allelic Selection of Amplicons in Glioblastoma Revealed by Combining Somatic and Germline Analysis
(Public Library of Science, 2010)Cancer is a disease driven by a combination of inherited risk alleles coupled with the acquisition of somatic mutations, including amplification and deletion of genomic DNA. Potential relationships between the inherited ... -
Analysis Method and Experimental Conditions Affect Computed Circadian Phase from Melatonin Data
(Public Library of Science, 2012)Accurate determination of circadian phase is necessary for research and clinical purposes because of the influence of the master circadian pacemaker on multiple physiologic functions. Melatonin is presently the most accurate ... -
Analysis of Sequence Conservation at Nucleotide Resolution
(Public Library of Science, 2007)One of the major goals of comparative genomics is to understand the evolutionary history of each nucleotide in the human genome sequence, and the degree to which it is under selective pressure. Ascertainment of selective ... -
Angiogenic mRNA and microRNA Gene Expression Signature Predicts a Novel Subtype of Serous Ovarian Cancer
(Public Library of Science, 2012)Ovarian cancer is the fifth leading cause of cancer death for women in the U.S. and the seventh most fatal worldwide. Although ovarian cancer is notable for its initial sensitivity to platinum-based therapies, the vast ... -
Automated Discovery of Functional Generality of Human Gene Expression Programs
(Public Library of Science, 2007)An important research problem in computational biology is the identification of expression programs, sets of co-expressed genes orchestrating normal or pathological processes, and the characterization of the functional ... -
canEvolve: A Web Portal for Integrative Oncogenomics
(Public Library of Science, 2013)Background & objective: Genome-wide profiles of tumors obtained using functional genomics platforms are being deposited to the public repositories at an astronomical scale, as a result of focused efforts by individual ... -
The Cis-regulatory Logic of the Mammalian Photoreceptor Transcriptional Network
(Public Library of Science, 2007)The photoreceptor cells of the retina are subject to a greater number of genetic diseases than any other cell type in the human body. The majority of more than 120 cloned human blindness genes are highly expressed in ... -
Clustering Heart Rate Dynamics Is Associated with β-Adrenergic Receptor Polymorphisms: Analysis by Information-Based Similarity Index
(Public Library of Science, 2011)Background: Genetic polymorphisms in the gene encoding the β-adrenergic receptors (β -AR) have a pivotal role in the functions of the autonomic nervous system. Using heart rate variability (HRV) as an indicator of autonomic ... -
Combinatorial Complexity and Compositional Drift in Protein Interaction Networks
(Public Library of Science, 2012)The assembly of molecular machines and transient signaling complexes does not typically occur under circumstances in which the appropriate proteins are isolated from all others present in the cell. Rather, assembly must ... -
Common Inherited Variation in Mitochondrial Genes Is Not Enriched for Associations with Type 2 Diabetes or Related Glycemic Traits
(Public Library of Science, 2010)Mitochondrial dysfunction has been observed in skeletal muscle of people with diabetes and insulin-resistant individuals. Furthermore, inherited mutations in mitochondrial DNA can cause a rare form of diabetes. However, ... -
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 ... -
Computational Analysis of Mouse piRNA Sequence and Biogenesis
(Public Library of Science, 2007)The recent discovery of a new class of 30-nucleotide long RNAs in mammalian testes, called PIWI-interacting RNA (piRNA), with similarities to microRNAs and repeat-associated small interfering RNAs (rasiRNAs), has raised ... -
Computational and Serologic Analysis of Novel and Known Viruses in Species Human Adenovirus D in Which Serology and Genomics Do Not Correlate
(Public Library of Science, 2012)In November of 2007 a human adenovirus (HAdV) was isolated from a bronchoalveolar lavage (BAL) sample recovered from a biopsy of an AIDS patient who presented with fever, cough, tachycardia, and expiratory wheezes. To ... -
A Computational Screen for Regulators of Oxidative Phosphorylation Implicates SLIRP in Mitochondrial RNA Homeostasis
(Public Library of Science, 2009)The human oxidative phosphorylation (OxPhos) system consists of approximately 90 proteins encoded by nuclear and mitochondrial genomes and serves as the primary cellular pathway for ATP biosynthesis. While the core protein ... -
Consequences of Cold-Ischemia Time on Primary Nonfunction and Patient and Graft Survival in Liver Transplantation: A Meta-Analysis
(Public Library of Science, 2008)Introduction: The ability to preserve organs prior to transplant is essential to the organ allocation process. Objective: The purpose of this study is to describe the functional relationship between cold-ischemia time (CIT) ... -
Dinosaur Peptides Suggest Mechanisms of Protein Survival
(Public Library of Science, 2011)Eleven collagen peptide sequences recovered from chemical extracts of dinosaur bones were mapped onto molecular models of the vertebrate collagen fibril derived from extant taxa. The dinosaur peptides localized to fibril ... -
Discrete States of a Protein Interaction Network Govern Interphase and Mitotic Microtubule Dynamics
(Public Library of Science, 2007)The cytoplasm of eukaryotic cells is thought to adopt discrete “states” corresponding to different steady states of protein networks that govern changes in subcellular organization. For example, in Xenopus eggs, the ... -
Dynamics of Envelope Evolution in Clade C SHIV-Infected Pig-Tailed Macaques during Disease Progression Analyzed by Ultra-Deep Pyrosequencing
(Public Library of Science, 2012)Understanding the evolution of the human immunodeficiency virus type 1 (HIV-1) envelope during disease progression can provide tremendous insights for vaccine development, and simian-human immunodeficiency virus (SHIV) ...