Open Access. Powered by Scholars. Published by Universities.®

Life Sciences Commons™

Open Access. Powered by Scholars. Published by Universities.®

Bioinformatics

PDF

Selected Works

2009

Articles 1 - 8 of 8

Full-Text Articles in Life Sciences

Genetic Effect Of The Dwarfing Genes On Some Culm Characteristics Associatcd With Lodging Resistance In Bread Wheat, Md. Mahbub Hasan Dec 2009

Genetic Effect Of The Dwarfing Genes On Some Culm Characteristics Associatcd With Lodging Resistance In Bread Wheat, Md. Mahbub Hasan

Md. Mahbub Hasan

Due to the challenge of screening traits related to lodging resistance under natural field conditions, selection for lodging resistant varieties in wheat breeding programs is difficult. The identification of easily measurable culm anatomical traits related to lodging resistance would simplify the selection process. The present study was conducted to determine the effect of dwarfing genes on culm anatomical traits related to lodging resistance in our of basal internode 1. Field and laboratory study was conducted in Shahjalal University of Science and Technology, Sylhet, Bangladesh with eight wheat genotypes having Rhr1, Rht2 dwarfing genes in them and a local land race …

Go to article

Integrative Analysis Of Cancer Genomic Data, Shuangge Ma Sep 2009

Integrative Analysis Of Cancer Genomic Data, Shuangge Ma

Shuangge Ma

In the past decade, we have witnessed a period of unparallel development in the field of cancer genomics. To address the same or similar biomedical questions, multiple cancer genomic studies have been independently designed and conducted. Cancer gene signatures identified from analysis of individual datasets often have low reproducibility. A cost-effective way of improving reproducibility is to conduct integrative analysis of datasets from multiple studies with comparable designs. To properly integrate multiple studies and conduct integrative analysis, we need to access various public data warehouses, retrieve experiment protocols and raw data, evaluate individual studies and select those with comparable designs, …

Go to article

Triangle Network Motifs Predict Complexes By Complementing High-Error Interactomes With Structural Information, Bill Andreopoulos, Christof Winter, Dirk Labudde, Michael Schroeder Jun 2009

Triangle Network Motifs Predict Complexes By Complementing High-Error Interactomes With Structural Information, Bill Andreopoulos, Christof Winter, Dirk Labudde, Michael Schroeder

William B. Andreopoulos

Background
A lot of high-throughput studies produce protein-protein interaction networks (PPINs) with many errors and missing information. Even for genome-wide approaches, there is often a low overlap between PPINs produced by different studies. Second-level neighbors separated by two protein-protein interactions (PPIs) were previously used for predicting protein function and finding complexes in high-error PPINs. We retrieve second level neighbors in PPINs, and complement these with structural domain-domain interactions (SDDIs) representing binding evidence on proteins, forming PPI-SDDI-PPI triangles.

Results
We find low overlap between PPINs, SDDIs and known complexes, all well below 10%. We evaluate the overlap of PPI-SDDI-PPI triangles with …

Go to article

A Tale Of Two Streets: Incorporating Grouping Structure In High Dimensional Data Mining, Shuangge Ma Jun 2009

A Tale Of Two Streets: Incorporating Grouping Structure In High Dimensional Data Mining, Shuangge Ma

Shuangge Ma

No abstract provided.

Go to article

Catena-Poly[[(Pyridine-Κn)Copper(Ii)]-Μ3-Pyridine-2,6-Dicarboxylato-Κ3o2:O2′,N,O6:O6′], Manoj Trivedi, Daya Shankar Pandey, Nigam P. Rath Mar 2009

Catena-Poly[[(Pyridine-Κn)Copper(Ii)]-Μ3-Pyridine-2,6-Dicarboxylato-Κ3o2:O2′,N,O6:O6′], Manoj Trivedi, Daya Shankar Pandey, Nigam P. Rath

Nigam Rath

In the title compound, [Cu(C7H3NO4)(C5H5N)]n, the CuII atom is in a slightly distorted octa­hedral coordination environment. Each CuII atom is bound to two N atoms and one O atom of the pyridine­dicarboxyl­ate (PDA) ligand in a tridentate manner, one N atom of the pyridine mol­ecule and two bridging carboxyl­ate O atoms of adjacent PDA ligands, leading to a linear one-dimensional chain running along the c axis. These chains are further assembled via weak C-H...O and [pi]-[pi] inter­actions into a three-dimensional supra­molecular network structure. The centroid-centroid distance between the [pi]-[pi] inter­acting pyridine rings is 3.9104 (13) Å. The two N atoms …

Go to article

Biomedical Word Sense Disambiguation With Ontologies And Metadata: Automation Meets Accuracy, Dimitra Alexopoulou, Bill Andreopoulos, Heiko Dietze, Andreas Doms, Fabien Gandon, Jörg Hakenberg, Khaled Khelif, Michael Schroeder, Thomas Wächter Jan 2009

Biomedical Word Sense Disambiguation With Ontologies And Metadata: Automation Meets Accuracy, Dimitra Alexopoulou, Bill Andreopoulos, Heiko Dietze, Andreas Doms, Fabien Gandon, Jörg Hakenberg, Khaled Khelif, Michael Schroeder, Thomas Wächter

William B. Andreopoulos

Background
Ontology term labels can be ambiguous and have multiple senses. While this is no problem for human annotators, it is a challenge to automated methods, which identify ontology terms in text. Classical approaches to word sense disambiguation use co-occurring words or terms. However, most treat ontologies as simple terminologies, without making use of the ontology structure or the semantic similarity between terms. Another useful source of information for disambiguation are metadata. Here, we systematically compare three approaches to word sense disambiguation, which use ontologies and metadata, respectively.

Results
The 'Closest Sense' method assumes that the ontology defines multiple senses …

Go to article

Towards A New Paradigm In Mayfly Phylogeny (Ephemeroptera): Combined Analysis Of Morphological And Molecular Data, T. Heath Ogden Dec 2008

Towards A New Paradigm In Mayfly Phylogeny (Ephemeroptera): Combined Analysis Of Morphological And Molecular Data, T. Heath Ogden

T. Heath Ogden

This study represents the first formal morphological and combined (morphological and molecular) phylogenetic analyses of the order Ephemeroptera. Taxonomic sampling comprised 112 species in 107 genera, including 42 recognized families (all major lineages of Ephemeroptera). Morphological data consisted of 101 morphological characters. Molecular data were acquired from DNA sequences of the 12S, 16S, 18S, 28S and H3 genes. The Asian genus Siphluriscus (Siphluriscidae) was supported as sister to all other mayflies. The lineages Carapacea, Furcatergalia, Fossoriae, Pannota, Caenoidea and Ephemerelloidea were supported as monophyletic, as were many of the families. However, some recognized families (for example, Ameletopsidae and Coloburiscidae) and …

Go to article

Combined Morphological And Molecular Phylogeny Of Ephemerellidae (Ephemeroptera), T. Heath Ogden Dec 2008

Combined Morphological And Molecular Phylogeny Of Ephemerellidae (Ephemeroptera), T. Heath Ogden

T. Heath Ogden

This study represents the first combined molecular and morphological analysis for the mayfly family Ephemerellidae (Ephemeroptera), with a focus on the relationships of genera and species groups of the subfamily Ephemerellinae. The phylogeny was constructed based on DNA sequence data from 3 nuclear (18S rDNA, 28S rDNA, histone H3) and 2 mitochondrial (12S rDNA, 16S rDNA) genes, and 23 morphological characters. Taxon sampling for Ephemerellidae included exemplars from all 25 extant genus groups and additional representatives from those genera with the highest diversity. Ephemerellidae appears to consist of three major clades. Ephemerella, the largest genus of Ephemerellidae, and Serratella were …

Go to article