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Browsing by Subject "Sequence Alignment"
Now showing items 1-20 of 27
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29 mammalian genomes reveal novel exaptations of mobile elements for likely regulatory functions in the human genome.
(PloS one, 2012-01)Recent research supports the view that changes in gene regulation, as opposed to changes in the genes themselves, play a significant role in morphological evolution. Gene regulation is largely dependent on transcription ... -
A flexible statistical model for alignment of label-free proteomics data--incorporating ion mobility and product ion information.
(BMC Bioinformatics, 2013-12-16)BACKGROUND: The goal of many proteomics experiments is to determine the abundance of proteins in biological samples, and the variation thereof in various physiological conditions. High-throughput quantitative proteomics, ... -
A high-resolution map of human evolutionary constraint using 29 mammals.
(Nature, 2011-10-12)The comparison of related genomes has emerged as a powerful lens for genome interpretation. Here we report the sequencing and comparative analysis of 29 eutherian genomes. We confirm that at least 5.5% of the human genome ... -
An enzyme that inactivates the inflammatory mediator leukotriene b4 restricts mycobacterial infection.
(PLoS One, 2013)While tuberculosis susceptibility has historically been ascribed to failed inflammation, it is now known that an excess of leukotriene A4 hydrolase (LTA4H), which catalyzes the final step in leukotriene B4 (LTB4) synthesis, ... -
Binding site on human immunoglobulin G for the affinity ligand HWRGWV.
(Journal of molecular recognition : JMR, 2010-05)Affinity ligand HWRGWV has demonstrated the ability to isolate human immunoglobulin G (hIgG) from mammalian cell culture media. The ligand specifically binds hIgG through its Fc portion. This work shows that deglycosylation ... -
Comparative genomics based on massive parallel transcriptome sequencing reveals patterns of substitution and selection across 10 bird species.
(Mol Ecol, 2010-03)Next-generation sequencing technology provides an attractive means to obtain large-scale sequence data necessary for comparative genomic analysis. To analyse the patterns of mutation rate variation and selection intensity ... -
Domain-oriented edge-based alignment of protein interaction networks.
(Bioinformatics, 2009-06-15)MOTIVATION: Recent advances in high-throughput experimental techniques have yielded a large amount of data on protein-protein interactions (PPIs). Since these interactions can be organized into networks, and since separate ... -
Evolution of networks and sequences in eukaryotic cell cycle control.
(Philos Trans R Soc Lond B Biol Sci, 2011-12-27)The molecular networks regulating the G1-S transition in budding yeast and mammals are strikingly similar in network structure. However, many of the individual proteins performing similar network roles appear to have unrelated ... -
Finding regulatory DNA motifs using alignment-free evolutionary conservation information.
(Nucleic Acids Res, 2010-04)As an increasing number of eukaryotic genomes are being sequenced, comparative studies aimed at detecting regulatory elements in intergenic sequences are becoming more prevalent. Most comparative methods for transcription ... -
Genetic signatures in the envelope glycoproteins of HIV-1 that associate with broadly neutralizing antibodies.
(PLoS Comput Biol, 2010-10-07)A steady increase in knowledge of the molecular and antigenic structure of the gp120 and gp41 HIV-1 envelope glycoproteins (Env) is yielding important new insights for vaccine design, but it has been difficult to translate ... -
Horsetails and ferns are a monophyletic group and the closest living relatives to seed plants.
(Nature, 2001-02)Most of the 470-million-year history of plants on land belongs to bryophytes, pteridophytes and gymnosperms, which eventually yielded to the ecological dominance by angiosperms 90 Myr ago. Our knowledge of angiosperm phylogeny, ... -
Identification of cis-suppression of human disease mutations by comparative genomics.
(Nature, 2015-08)Patterns of amino acid conservation have served as a tool for understanding protein evolution. The same principles have also found broad application in human genomics, driven by the need to interpret the pathogenic potential ... -
IGHV1-69 B cell chronic lymphocytic leukemia antibodies cross-react with HIV-1 and hepatitis C virus antigens as well as intestinal commensal bacteria.
(PLoS One, 2014)B-cell chronic lymphocytic leukemia (B-CLL) patients expressing unmutated immunoglobulin heavy variable regions (IGHVs) use the IGHV1-69 B cell receptor (BCR) in 25% of cases. Since HIV-1 envelope gp41 antibodies also frequently ... -
Incongruence between primary sequence data and the distribution of a mitochondrial atp1 group II intron among ferns and horsetails.
(Molecular phylogenetics and evolution, 2005-09)Using DNA sequence data from multiple genes (often from more than one genome compartment) to reconstruct phylogenetic relationships has become routine. Augmenting this approach with genomic structural characters (e.g., intron ... -
Interrogation of individual intratumoral B lymphocytes from lung cancer patients for molecular target discovery.
(Cancer Immunol Immunother, 2016-02)Intratumoral B lymphocytes are an integral part of the lung tumor microenvironment. Interrogation of the antibodies they express may improve our understanding of the host response to cancer and could be useful in elucidating ... -
Investigating deep phylogenetic relationships among cyanobacteria and plastids by small subunit rRNA sequence analysis.
(The Journal of eukaryotic microbiology, 1999-07)Small subunit rRNA sequence data were generated for 27 strains of cyanobacteria and incorporated into a phylogenetic analysis of 1,377 aligned sequence positions from a diverse sampling of 53 cyanobacteria and 10 photosynthetic ... -
Leveraging Fungal and Human Calcineurin-Inhibitor Structures, Biophysical Data, and Dynamics To Design Selective and Nonimmunosuppressive FK506 Analogs.
(mBio, 2021-12)Calcineurin is a critical enzyme in fungal pathogenesis and antifungal drug tolerance and, therefore, an attractive antifungal target. Current clinically accessible calcineurin inhibitors, such as FK506, are immunosuppressive ... -
Modeling the evolution of regulatory elements by simultaneous detection and alignment with phylogenetic pair HMMs.
(PLoS Comput Biol, 2010-12-16)The computational detection of regulatory elements in DNA is a difficult but important problem impacting our progress in understanding the complex nature of eukaryotic gene regulation. Attempts to utilize cross-species ... -
Phylogenomic analyses data of the avian phylogenomics project.
(Gigascience, 2015)BACKGROUND: Determining the evolutionary relationships among the major lineages of extant birds has been one of the biggest challenges in systematic biology. To address this challenge, we assembled or collected the genomes ... -
Screening the human exome: a comparison of whole genome and whole transcriptome sequencing.
(Genome Biol, 2010)BACKGROUND: There is considerable interest in the development of methods to efficiently identify all coding variants present in large sample sets of humans. There are three approaches possible: whole-genome sequencing, ...
