Bioinformatics » MedWorm.com http://bioinformatics.me BioData make sense! Thu, 18 Aug 2011 12:47:42 +0000 http://wordpress.org/?v=2.9.2 en hourly 1 PrePrint: Inferring the Number of Contributors to Mixed DNA Profiles http://bioinformatics.me/preprint-inferring-the-number-of-contributors-to-mixed-dna-profiles/ http://bioinformatics.me/preprint-inferring-the-number-of-contributors-to-mixed-dna-profiles/#comments Tue, 26 Apr 2011 16:43:41 +0000 Waleed Ghalwash http://bioinformatics.me/preprint-inferring-the-number-of-contributors-to-mixed-dna-profiles/ Determining the number of contributors to a genetic sample is usually a necessary step towards accurately using the information experimentally. This determination is often made using naive approaches. An error in this determination may cast doubt on the accuracy of the final conclusion. Nowhere is the importance of this issue more obvious than in the forensic testing of human DNA. In forensic testing, a misinterpretation of the number of contributors to a genetic mixture may make the difference between justice and injustice. Computational methods may take into account not only naive features (such as the number and magnitude of genetic markers), but also the frequency of occurrence of these markers in the general population. Use of this additional information allows the determination of li…

]]> http://bioinformatics.me/preprint-inferring-the-number-of-contributors-to-mixed-dna-profiles/feed/ 0 PrePrint: Identification of Relevant Properties for Epitopes Detection Using a Regression Model http://bioinformatics.me/preprint-identification-of-relevant-properties-for-epitopes-detection-using-a-regression-model/ http://bioinformatics.me/preprint-identification-of-relevant-properties-for-epitopes-detection-using-a-regression-model/#comments Tue, 26 Apr 2011 16:43:41 +0000 Waleed Ghalwash http://bioinformatics.me/preprint-identification-of-relevant-properties-for-epitopes-detection-using-a-regression-model/ A B-cell epitope is a part of an antigen that is recognized by a specific antibody or B-cell receptor. Detecting the immunogenic region of the antigen is useful in numerous immunodetection and immunotherapeutics applications. The aim of this paper is to find relevant properties to discriminate the location of potential epitopes from the rest of the protein surface. The most relevant properties, identified using two evaluation approaches, are the geometric properties, followed by the conservation score and some chemical properties, such as the proportion of glycine. The selected properties are used in a patch based epitope localization method including a Single Layer Perceptron for regression. The output of this Single Layer Perceptron is used to construct a probability map on the antigen s…

]]> http://bioinformatics.me/preprint-identification-of-relevant-properties-for-epitopes-detection-using-a-regression-model/feed/ 0 PrePrint: Protein Classification with Extended-Sequence Coding by Sliding Window http://bioinformatics.me/preprint-protein-classification-with-extended-sequence-coding-by-sliding-window/ http://bioinformatics.me/preprint-protein-classification-with-extended-sequence-coding-by-sliding-window/#comments Tue, 26 Apr 2011 16:43:41 +0000 Waleed Ghalwash http://bioinformatics.me/preprint-protein-classification-with-extended-sequence-coding-by-sliding-window/ A large numberof unclassified sequences is still found in public databases, which suggests that there is still need for new investigations in the area. In this contribution, we present a methodology based on Artificial Neural Networks for protein functional classification. A new protein coding scheme, called here Extended-Sequence Coding by Sliding Windows, is presented with the goal of overcoming some of the difficulties of the well method Sequence Coding by Sliding Window. The new protein coding scheme uses more than one sliding window length with a weight factor that is proportional to the window length, avoiding the ambiguity problem without ignoring the identity of small subsequences Accuracy for Sequence Coding by Sliding Windows ranged from 60.1% to 77.7% for the first bacterium pro…

]]> http://bioinformatics.me/preprint-protein-classification-with-extended-sequence-coding-by-sliding-window/feed/ 0 PrePrint: Molecular Pattern Discovery based on Penalized Matrix Decomposition http://bioinformatics.me/preprint-molecular-pattern-discovery-based-on-penalized-matrix-decomposition/ http://bioinformatics.me/preprint-molecular-pattern-discovery-based-on-penalized-matrix-decomposition/#comments Tue, 26 Apr 2011 16:43:41 +0000 Waleed Ghalwash http://bioinformatics.me/preprint-molecular-pattern-discovery-based-on-penalized-matrix-decomposition/ A reliable and precise identification of the type of tumors is crucial to the effective treatment of cancer. With the rapid development of microarray technologies, tumor clustering based on gene expression data is becoming a powerful approach to cancer class discovery. In this paper, we apply the penalized matrix decomposition (PMD) to gene expression data to extract metasamples for clustering. The extracted metasamples capture the inherent structures of samples belong to the same class. At the same time, the PMD factors of a sample over the metasamples can be used as its class indicator in return. Compared with the conventional methods such as hierarchical clustering (HC), self-organizing maps (SOM), affinity propagation (AP) and non-negative matrix factorization (NMF), the proposed metho…

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]]> http://bioinformatics.me/preprint-molecular-pattern-discovery-based-on-penalized-matrix-decomposition/feed/ 0 PrePrint: Mutual Information Optimization for Mass Spectra Data Alignment http://bioinformatics.me/preprint-mutual-information-optimization-for-mass-spectra-data-alignment/ http://bioinformatics.me/preprint-mutual-information-optimization-for-mass-spectra-data-alignment/#comments Tue, 26 Apr 2011 16:43:41 +0000 Waleed Ghalwash http://bioinformatics.me/preprint-mutual-information-optimization-for-mass-spectra-data-alignment/ We present the results of a competitive analysis of our method against other approaches. The analysis was conducted on data from plasma/ethylenediaminetetraacetic acid (EDTA) of “control” and Alzheimer patients collected from three different hospitals. The results point to a significant performance advantage of our method with respect to the competing ones tested. (Source: IEEE/ACM Transactions on Computational Biology and Bioinformatics)

]]> http://bioinformatics.me/preprint-mutual-information-optimization-for-mass-spectra-data-alignment/feed/ 0 The Proteogenomic Mapping Tool http://bioinformatics.me/the-proteogenomic-mapping-tool/ http://bioinformatics.me/the-proteogenomic-mapping-tool/#comments Tue, 26 Apr 2011 16:43:41 +0000 Waleed Ghalwash http://bioinformatics.me/the-proteogenomic-mapping-tool/ Conclusions:
The Proteogenomic Mapping Tool provides a standalone application for mapping peptides back to their source genome on a number of operating system platforms with standard desktop computer hardware and executes very rapidly for a variety of datasets. Allowing the selection of different genetic codes for different organisms allows researchers to easily customize the tool to their own research interests and is recommended for anyone working to structurally annotate genomes using MS derived proteomics data. (Source: BMC Bioinformatics – Latest articles)

]]> http://bioinformatics.me/the-proteogenomic-mapping-tool/feed/ 0 Ultra-fast sequence clustering from similarity networks with SiLiX http://bioinformatics.me/ultra-fast-sequence-clustering-from-similarity-networks-with-silix/ http://bioinformatics.me/ultra-fast-sequence-clustering-from-similarity-networks-with-silix/#comments Tue, 26 Apr 2011 16:43:41 +0000 Waleed Ghalwash http://bioinformatics.me/ultra-fast-sequence-clustering-from-similarity-networks-with-silix/ Conclusions:
Comparing state-of-the-art software, SiLiX presents the best up-to-date capabilities to face the problem of clustering large collections of sequences. SiLiX is freely available at http://lbbe.univ-lyon1.fr/silix. (Source: BMC Bioinformatics – Latest articles)

]]> http://bioinformatics.me/ultra-fast-sequence-clustering-from-similarity-networks-with-silix/feed/ 0 MI-GWAS: a SAS platform for the analysis of inherited and maternal genetic effects in genome-wide association studies using log-linear models http://bioinformatics.me/mi-gwas-a-sas-platform-for-the-analysis-of-inherited-and-maternal-genetic-effects-in-genome-wide-association-studies-using-log-linear-models/ http://bioinformatics.me/mi-gwas-a-sas-platform-for-the-analysis-of-inherited-and-maternal-genetic-effects-in-genome-wide-association-studies-using-log-linear-models/#comments Tue, 26 Apr 2011 16:43:41 +0000 Waleed Ghalwash http://bioinformatics.me/mi-gwas-a-sas-platform-for-the-analysis-of-inherited-and-maternal-genetic-effects-in-genome-wide-association-studies-using-log-linear-models/ Conclusions:
The MI-GWAS platform provides a valuable tool for the analysis of association of a phenotype or condition with maternal and inherited genotypes using genome-wide data from case-parent triads. The source code for this platform is freely available at http://www.sph.uth.tmc.edu/sbrr/mi-gwas.htm. (Source: BMC Bioinformatics – Latest articles)

]]> http://bioinformatics.me/mi-gwas-a-sas-platform-for-the-analysis-of-inherited-and-maternal-genetic-effects-in-genome-wide-association-studies-using-log-linear-models/feed/ 0 Modulation of hepatitis B virus replication and hepatocyte differentiation by MicroRNA‐1 http://bioinformatics.me/modulation-of-hepatitis-b-virus-replication-and-hepatocyte-differentiation-by-microrna%e2%80%901/ http://bioinformatics.me/modulation-of-hepatitis-b-virus-replication-and-hepatocyte-differentiation-by-microrna%e2%80%901/#comments Tue, 26 Apr 2011 16:43:41 +0000 Waleed Ghalwash http://bioinformatics.me/modulation-of-hepatitis-b-virus-replication-and-hepatocyte-differentiation-by-microrna%e2%80%901/ Conclusion: MiR‐1 regulates the expression of several host genes to enhance HBV replication and reverse cancer cell phenotype, which is apparently beneficial for HBV replication. Our findings provide a novel perspective on the role of miRNAs in host‐virus interactions in HBV infection. (HEPATOLOGY 2011;) (Source: Hepatology)

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]]> http://bioinformatics.me/modulation-of-hepatitis-b-virus-replication-and-hepatocyte-differentiation-by-microrna%e2%80%901/feed/ 0 A novel bioinformatics strategy for searching industrially useful genome resources from metagenomic sequence libraries. http://bioinformatics.me/a-novel-bioinformatics-strategy-for-searching-industrially-useful-genome-resources-from-metagenomic-sequence-libraries/ http://bioinformatics.me/a-novel-bioinformatics-strategy-for-searching-industrially-useful-genome-resources-from-metagenomic-sequence-libraries/#comments Tue, 26 Apr 2011 16:43:41 +0000 Waleed Ghalwash http://bioinformatics.me/a-novel-bioinformatics-strategy-for-searching-industrially-useful-genome-resources-from-metagenomic-sequence-libraries/ Authors: Uehara H, Iwasaki Y, Wada C, Ikemura T, Abe T
Although remarkable progress in metagenomic sequencing of various environmental samples has been made, large numbers of fragment sequences have been registered in the international DNA databanks, primarily without information on gene function and phylotype, and thus with limited usefulness. Industrial useful biological activity is often carried out by a set of genes, such as those constituting an operon. In this connection, metagenomic approaches have a weakness because sets of the genes are usually split up, since the sequences obtained by metagenome analyses are fragmented into 1-kb or much shorter segments. Therefore, even when a set of genes responsible for an industrially useful function is found in one metagenome library, it …

]]> http://bioinformatics.me/a-novel-bioinformatics-strategy-for-searching-industrially-useful-genome-resources-from-metagenomic-sequence-libraries/feed/ 0 PrePrint: An Algebraic Spline Model of Molecular Surfaces for Energetic Computations http://bioinformatics.me/preprint-an-algebraic-spline-model-of-molecular-surfaces-for-energetic-computations/ http://bioinformatics.me/preprint-an-algebraic-spline-model-of-molecular-surfaces-for-energetic-computations/#comments Tue, 26 Apr 2011 16:43:41 +0000 Waleed Ghalwash http://bioinformatics.me/preprint-an-algebraic-spline-model-of-molecular-surfaces-for-energetic-computations/ We describe a new method to generate a smooth algebraic spline (AS) approximation of the molecular surface (MS) based on an initial coarse linear triangulation derived from the atomic coordinate information of biomolecules, present in the PDB (Protein Data Bank). Our method first constructs a triangular prism scaffold covering the MS triangulation, and then generates a piecewise polynomial function F in the Bernstein-Bezier (BB) basis within the scaffold. An ASMS (algebraic spline molecular surface) of the molecular surface is extracted as the zero contours of F which is almost C 1 everywhere, and has dual implicit and parametric representations. The dual representations allow us to easily construct Gaussian quadrature point and normal samplings of the ASMS and apply it to the accurate est…

]]> http://bioinformatics.me/preprint-an-algebraic-spline-model-of-molecular-surfaces-for-energetic-computations/feed/ 0 Retinoic acid induces HL-60 cell differentiation via the upregulation of miR-663 http://bioinformatics.me/retinoic-acid-induces-hl-60-cell-differentiation-via-the-upregulation-of-mir-663/ http://bioinformatics.me/retinoic-acid-induces-hl-60-cell-differentiation-via-the-upregulation-of-mir-663/#comments Tue, 26 Apr 2011 16:43:41 +0000 Waleed Ghalwash http://bioinformatics.me/retinoic-acid-induces-hl-60-cell-differentiation-via-the-upregulation-of-mir-663/ Conclusions: Our results show miR-663 may play an important role in ATRA induced HL-60 cell differentiation. Lentivirus delivery of miR-663 could potentially be used directly as an anticancer treatment in hematological malignancies. (Source: Journal of Hematology and Oncology)

]]> http://bioinformatics.me/retinoic-acid-induces-hl-60-cell-differentiation-via-the-upregulation-of-mir-663/feed/ 0 Fungal proteomics: from identification to function http://bioinformatics.me/fungal-proteomics-from-identification-to-function/ http://bioinformatics.me/fungal-proteomics-from-identification-to-function/#comments Tue, 26 Apr 2011 16:43:41 +0000 Waleed Ghalwash http://bioinformatics.me/fungal-proteomics-from-identification-to-function/ AbstractSome fungi cause disease in humans and plants, while others have demonstrable potential for the control of insect pests. In addition, fungi are also a rich reservoir of therapeutic metabolites and industrially‐useful enzymes. Detailed analysis of fungal biochemistry is now enabled by multiple technologies including protein mass spectrometry, genome and transcriptome sequencing and advances in bioinformatics. Yet, the assignment of function to fungal proteins, encoded either by in silico annotated, or unannotated genes, remains problematic. The purpose of this review is to describe the strategies used by many researchers to reveal protein function in fungi, and more importantly, to consolidate the nomenclature of ‘unknown function protein’, or UFP, as opposed to ‘hypothetica…

]]> http://bioinformatics.me/fungal-proteomics-from-identification-to-function/feed/ 0 A structural bioinformatics approach to explore the interactions of P53 and BRCA1 gene products on ovarian and breast cancer. http://bioinformatics.me/a-structural-bioinformatics-approach-to-explore-the-interactions-of-p53-and-brca1-gene-products-on-ovarian-and-breast-cancer/ http://bioinformatics.me/a-structural-bioinformatics-approach-to-explore-the-interactions-of-p53-and-brca1-gene-products-on-ovarian-and-breast-cancer/#comments Tue, 26 Apr 2011 16:43:41 +0000 Waleed Ghalwash http://bioinformatics.me/a-structural-bioinformatics-approach-to-explore-the-interactions-of-p53-and-brca1-gene-products-on-ovarian-and-breast-cancer/ This study sets out to check similar pattern, domain and residue-specific mutation, which may interact with expressions of P53 and BRCA1.
PMID: 21441093 [PubMed - in process] (Source: International Journal of Bioinformatics Research and Applications)

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]]> http://bioinformatics.me/a-structural-bioinformatics-approach-to-explore-the-interactions-of-p53-and-brca1-gene-products-on-ovarian-and-breast-cancer/feed/ 0 Genotypic prediction of resistant mutation in HIV-1 pol gene towards the antiretroviral drugs. http://bioinformatics.me/genotypic-prediction-of-resistant-mutation-in-hiv-1-pol-gene-towards-the-antiretroviral-drugs/ http://bioinformatics.me/genotypic-prediction-of-resistant-mutation-in-hiv-1-pol-gene-towards-the-antiretroviral-drugs/#comments Tue, 26 Apr 2011 16:43:41 +0000 Waleed Ghalwash http://bioinformatics.me/genotypic-prediction-of-resistant-mutation-in-hiv-1-pol-gene-towards-the-antiretroviral-drugs/ This study is useful in making more accurate prediction of results with better combination Highly Active Antiretroviral Therapy (HAART) and important mutations.
PMID: 21441094 [PubMed - in process] (Source: International Journal of Bioinformatics Research and Applications)

]]> http://bioinformatics.me/genotypic-prediction-of-resistant-mutation-in-hiv-1-pol-gene-towards-the-antiretroviral-drugs/feed/ 0 Unique marker finder algorithm generates molecular diagnostic markers. http://bioinformatics.me/unique-marker-finder-algorithm-generates-molecular-diagnostic-markers/ http://bioinformatics.me/unique-marker-finder-algorithm-generates-molecular-diagnostic-markers/#comments Tue, 26 Apr 2011 16:43:41 +0000 Waleed Ghalwash http://bioinformatics.me/unique-marker-finder-algorithm-generates-molecular-diagnostic-markers/ Authors: Chiu SK, Hsieh MH, Tzeng CM
By taking advantage of the power of comparative genomics, we devised an algorithm, Unique Marker Finder (U-MarFin), to generate a collection of unique DNA sequences from a target organism. The whole target genome is partitioned into a scoring pool of less 4000 base-pair fragments, which are then subjected to elimination of homologous sequences in other bacterial genomes by BLAST alignment, and looked for all open reading frames as they may be applied as unique markers. Through regular, nested, multiplex and real time PCR and microarray technology, we empirically demonstrated that the sequences discovered were highly specific to the species that they are derived from, and they can serve as molecular biomarkers for diagnostic purpose.
PMID: 214410…

]]> http://bioinformatics.me/unique-marker-finder-algorithm-generates-molecular-diagnostic-markers/feed/ 0 SyDiG: uncovering Synteny in Distant Genomes. http://bioinformatics.me/sydig-uncovering-synteny-in-distant-genomes/ http://bioinformatics.me/sydig-uncovering-synteny-in-distant-genomes/#comments Tue, 26 Apr 2011 16:43:41 +0000 Waleed Ghalwash http://bioinformatics.me/sydig-uncovering-synteny-in-distant-genomes/ Authors: Jean G, Nikolski M
Current methods for detecting synteny work well for genomes with high degrees of inter- and intra-species chromosomal homology, such as mammals. This paper presents a new algorithm for synteny computation that is well suited to genomes covering a large evolutionary span. It is based on a three-step process: identification of initial microsyntenic homologous regions, extension of homologous boundaries and reconstruction of syntenic blocks by identification of groups of homologous genomic segments that are conserved in every subject genome. Our method performs as well as GRIMM-Synteny on mammalian genomes, and outperforms it for clades with much greater evolutionary distances such as the Hemiascomycetous yeasts.
PMID: 21441096 [PubMed - in process] (Source…

]]> http://bioinformatics.me/sydig-uncovering-synteny-in-distant-genomes/feed/ 0 TRFolder: computational prediction of novel telomerase RNA structures in yeast genomes. http://bioinformatics.me/trfolder-computational-prediction-of-novel-telomerase-rna-structures-in-yeast-genomes/ http://bioinformatics.me/trfolder-computational-prediction-of-novel-telomerase-rna-structures-in-yeast-genomes/#comments Tue, 26 Apr 2011 16:43:41 +0000 Waleed Ghalwash http://bioinformatics.me/trfolder-computational-prediction-of-novel-telomerase-rna-structures-in-yeast-genomes/ We describe a novel approach to predict the structure of key TR features and to aid the identification of TRs in genomes, using a program we developed, TRFolder. We applied our method to confirm and improve previously studied core structures from Saccharomyces and Kluyveromyces TRs. We made novel structural predictions of core elements of the TRs from Schizosaccharomyces pombe, Candida albicans, and several other yeast species.
PMID: 21441097 [PubMed - in process] (Source: International Journal of Bioinformatics Research and Applications)

]]> http://bioinformatics.me/trfolder-computational-prediction-of-novel-telomerase-rna-structures-in-yeast-genomes/feed/ 0 Improvement in protein-coding region identification based on sliding window trigonometric fast transforms using singular value decomposition. http://bioinformatics.me/improvement-in-protein-coding-region-identification-based-on-sliding-window-trigonometric-fast-transforms-using-singular-value-decomposition/ http://bioinformatics.me/improvement-in-protein-coding-region-identification-based-on-sliding-window-trigonometric-fast-transforms-using-singular-value-decomposition/#comments Tue, 26 Apr 2011 16:43:41 +0000 Waleed Ghalwash http://bioinformatics.me/improvement-in-protein-coding-region-identification-based-on-sliding-window-trigonometric-fast-transforms-using-singular-value-decomposition/ Authors: Hota MK, Srivastava VK
In this paper, the performance of various sliding window trigonometric fast transforms for identification of protein coding regions has been analysed at the nucleotide level. It is found that, Short-Time Discrete Fourier Transform (ST-DFT) gives better identification accuracy in comparison with Short-Time Discrete Cosine Transform (ST-DCT), Short-Time Discrete Sine Transform (ST-DST) and Short-Time Discrete Hartley Transform (ST-DHT). In the proposed method, identification accuracy of protein coding regions has been improved by applying Singular Value Decomposition (SVD) on the DNA spectrum obtained using sliding window trigonometric fast transforms. The results show that, in proposed method all trigonometric fast transforms gives almost similar results …

]]> http://bioinformatics.me/improvement-in-protein-coding-region-identification-based-on-sliding-window-trigonometric-fast-transforms-using-singular-value-decomposition/feed/ 0 PrePrint: A Shape Descriptor for Fast Complementarity Matching in Molecular Docking http://bioinformatics.me/preprint-a-shape-descriptor-for-fast-complementarity-matching-in-molecular-docking/ http://bioinformatics.me/preprint-a-shape-descriptor-for-fast-complementarity-matching-in-molecular-docking/#comments Tue, 26 Apr 2011 16:43:40 +0000 Waleed Ghalwash http://bioinformatics.me/preprint-a-shape-descriptor-for-fast-complementarity-matching-in-molecular-docking/ This paper presents a novel approach for fast rigid docking of proteins based on geometric complementarity. After extraction of the 3D molecular surface, a set of local surface patches is generated based on the local surface curvature. The shape complementarity between a pair of patches is calculated using an efficient shape descriptor, the Shape Impact Descriptor. The key property of the Shape Impact Descriptor is its rotation invariance, which obviates the need for taking an exhaustive set of rotations for each pair of patches. Thus, complementarity matching between two patches is reduced to a simple histogram matching. Finally, a condensed set of almost complementary pairs of surface patches is supplied as input to the final scoring step, where each pose is evaluated using a 3D distance…

]]> http://bioinformatics.me/preprint-a-shape-descriptor-for-fast-complementarity-matching-in-molecular-docking/feed/ 0