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This page shows you the 20 most read items in the past 30 days within this specialty in the MedWorm directory.

Classification of breast tissues using Moran's index and Geary's coefficient as texture signatures and SVMEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: Female breast cancer is the major cause of cancer-related deaths in western countries. Efforts in computer vision have been made in order to help improving the diagnostic accuracy by radiologists. In this paper, we present a methodology that uses Moran's index and Geary's coefficient measures in breast tissues extracted from mammogram images. These measures are used as input features for a support vector machine classifier with the purpose of distinguishing tissues between normal and abnormal cases as well as classifying them into benign and malignant cancerous cases. The use of both proposed techniques showed to...
Source: Computers in Biology and Medicine - November 16, 2009 Category: Bioinformatics Authors: Geraldo Braz Junior, Anselmo Cardoso de Paiva, Aristófanes Corrêa Silva, Alexandre Cesar Muniz de Oliveira Source Type: journals

ISOLATE: a computational strategy for identifying the primary origin of cancers using high-throughput sequencingEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We present ISOLATE, a new statistical method that simultaneously predicts the primary site of origin of cancers and addresses sample heterogeneity, while taking advantage of new high-throughput sequencing technology that promises to bring higher accuracy and reproducibility to gene expression profiling experiments. ISOLATE makes predictions de novo, without having seen any training expression profiles of cancers with identified origin. Compared with previous methods, ISOLATE is able to predict the primary site of origin, de-convolve and remove the effect of sample heterogeneity and identify differentially expressed genes w...
Source: Bioinformatics - October 23, 2009 Category: Bioinformatics Authors: Quon, G., Morris, Q. Tags: GENE EXPRESSION Source Type: journals

Statistical methods for gene set co-expression analysisEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Motivation: The power of a microarray experiment derives from the identification of genes differentially regulated across biological conditions. To date, differential regulation is most often taken to mean differential expression, and a number of useful methods for identifying differentially expressed (DE) genes or gene sets are available. However, such methods are not able to identify many relevant classes of differentially regulated genes. One important example concerns differentially co-expressed (DC) genes. Results: We propose an approach, gene set co-expression analysis (GSCA), to identify DC gene sets. The GSCA appro...
Source: Bioinformatics - October 23, 2009 Category: Bioinformatics Authors: Choi, Y., Kendziorski, C. Tags: GENE EXPRESSION Source Type: journals

Bioinformatics approaches for genomics and post genomics applications of next-generation sequencing.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Technical advances such as the development of molecular cloning, Sanger sequencing, PCR and oligonucleotide microarrays are key to our current capacity to sequence, annotate and study complete organismal genomes. Recent years have seen the development of a variety of so-called 'next-generation' sequencing platforms, with several others anticipated to become available shortly. The previously unimaginable scale and economy of these methods, coupled with their enthusiastic uptake by the scientific community and the potential for further improvements in accuracy and read length, suggest that these technologies are destined...
Source: Briefings in Bioinformatics - October 27, 2009 Category: Bioinformatics Authors: Horner DS, Pavesi G, Castrignanò T, De Meo PD, Liuni S, Sammeth M, Picardi E, Pesole G Tags: Brief Bioinform Source Type: journals

Integrative clustering of multiple genomic data types using a joint latent variable model with application to breast and lung cancer subtype analysisEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Motivation: The molecular complexity of a tumor manifests itself at the genomic, epigenomic, transcriptomic and proteomic levels. Genomic profiling at these multiple levels should allow an integrated characterization of tumor etiology. However, there is a shortage of effective statistical and bioinformatic tools for truly integrative data analysis. The standard approach to integrative clustering is separate clustering followed by manual integration. A more statistically powerful approach would incorporate all data types simultaneously and generate a single integrated cluster assignment. Methods: We developed a joint latent...
Source: Bioinformatics - November 4, 2009 Category: Bioinformatics Authors: Shen, R., Olshen, A. B., Ladanyi, M. Tags: GENOME ANALYSIS Source Type: journals

De novo transcriptome assembly with ABySSEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Motivation: Whole transcriptome shotgun sequencing data from non-normalized samples offer unique opportunities to study the metabolic states of organisms. One can deduce gene expression levels using sequence coverage as a surrogate, identify coding changes or discover novel isoforms or transcripts. Especially for discovery of novel events, de novo assembly of transcriptomes is desirable. Results: Transcriptome from tumor tissue of a patient with follicular lymphoma was sequenced with 36 base pair (bp) single- and paired-end reads on the Illumina Genome Analyzer II platform. We assembled ~194 million reads using ABySS into ...
Source: Bioinformatics - October 23, 2009 Category: Bioinformatics Authors: Birol, I., Jackman, S. D., Nielsen, C. B., Qian, J. Q., Varhol, R., Stazyk, G., Morin, R. D., Zhao, Y., Hirst, M., Schein, J. E., Horsman, D. E., Connors, J. M., Gascoyne, R. D., Marra, M. A., Jones, S. J. M. Tags: SEQUENCE ANALYSIS Source Type: journals

IEEE/ACM Transactions on Computational Biology and Bioinformatics - October-December 2009 (Vol. 6, No. 4)Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
IEEE/ACM Transactions on Computational Biology and Bioinformatics (Source: IEEE/ACM Transactions on Computational Biology and Bioinformatics)
Source: IEEE/ACM Transactions on Computational Biology and Bioinformatics - October 30, 2009 Category: Bioinformatics Source Type: journals

General Model of Inflammation.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Dysfunctions in the immune system, due to genetics, disease or environmental factors, can cause bacterial colonization and chronic inflammation. In cystic fibrosis and chronic obstructive pulmonary disease, respiratory infections can initiate inflammation of the airway. We propose a system of nonlinear ordinary differential equations to describe interactions between macrophages, both inflammatory and anti-inflammatory cytokines, and bacteria. Small changes in parameters governing inflammatory cytokine production and macrophage sensitivity to cytokines result in dramatically different model behaviors. When the immune sy...
Source: Bulletin of Mathematical Biology - October 23, 2009 Category: Bioinformatics Authors: Herald MC Tags: Bull Math Biol Source Type: journals

TagDust--a program to eliminate artifacts from next generation sequencing dataEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Motivation: Next-generation parallel sequencing technologies produce large quantities of short sequence reads. Due to experimental procedures various types of artifacts are commonly sequenced alongside the targeted RNA or DNA sequences. Identification of such artifacts is important during the development of novel sequencing assays and for the downstream analysis of the sequenced libraries. Results: Here we present TagDust, a program identifying artifactual sequences in large sequencing runs. Given a user-defined cutoff for the false discovery rate, TagDust identifies all reads explainable by combinations and partial matche...
Source: Bioinformatics - October 23, 2009 Category: Bioinformatics Authors: Lassmann, T., Hayashizaki, Y., Daub, C. O. Tags: GENOME ANALYSIS Source Type: journals

A novel R-package graphic user interface for the analysis of metabonomic profilesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: We made complex multivariate analysis user-friendly for both experienced and novice users, which could help to expand the use of NMR-based metabonomics. (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - October 29, 2009 Category: Bioinformatics Authors: Jose Izquierdo-GarciaIgnacio RodriguezAngelos KyriazisPalmira VillaPilar BarreiroManuel DescoJesus Ruiz-Cabello Source Type: journals

Prediction of hot spot residues at protein-protein interfaces by combining machine learning and energy-based methodsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: We have developed an hybrid scheme in which energy terms are used as input features of machine learning models. This strategy combines the strengths of machine learning and energy-based methods. Although so far these two types of approaches have mainly been applied separately to biomolecular problems, the results of our investigation indicate that there are substantial benefits to be gained by their integration. (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - October 30, 2009 Category: Bioinformatics Authors: Stefano LiseCedric ArchambeauMassimiliano PontilDavid Jones Source Type: journals

integrOmics: an R package to unravel relationships between two omics datasetsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Motivation: With the availability of many ‘omics’ data, such as transcriptomics, proteomics or metabolomics, the integrative or joint analysis of multiple datasets from different technology platforms is becoming crucial to unravel the relationships between different biological functional levels. However, the development of such an analysis is a major computational and technical challenge as most approaches suffer from high data dimensionality. New methodologies need to be developed and validated. Results: integrOmics efficiently performs integrative analyses of two types of ‘omics’ variables that ar...
Source: Bioinformatics - October 23, 2009 Category: Bioinformatics Authors: Le Cao, K.-A., Gonzalez, I., Dejean, S. Tags: SYSTEMS BIOLOGY Source Type: journals

Arabidopsis gene co-expression network and its functional modulesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: This study reveals new insight into the topological properties of biological networks. The preferential hub-hub connections might be necessary for the formation of modular structure in gene co-expression networks. The study also reveals new insight into the organization of gene functional modules. (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - October 20, 2009 Category: Bioinformatics Authors: Linyong MaoJohn Van HemertSudhansu DashJulie Dickerson Source Type: journals

Analysis and comparison of very large metagenomes with fast clustering and functional annotationEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conclusions: RAMMCAP is a very fast method that can cluster and annotate one million metagenomic reads in only hundreds of CPU hours. It is available from http://tools.camera.calit2.net/camera/rammcap/. (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - October 28, 2009 Category: Bioinformatics Authors: Weizhong Li Source Type: journals

PrePrint: GPD: A Graph Pattern Diffusion Kernel for Accurate Graph Classification with Applications in CheminformaticsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Graph data mining is an active research area. Graphs are general modeling tools to organize information from heterogenous sources and have been applied in many scientific, engineering, and business fields. With the fast accumulation of graph data, building highly accurate predictive models for graph data emerges as a new challenge that has not been fully explored in the data mining community. In this paper, we demonstrate a novel technique called graph pattern diffusion kernel (GPD) with applications in cheminformatics. Our idea is to leverage existing frequent pattern discovery methods and to explore the application of ke...
Source: IEEE/ACM Transactions on Computational Biology and Bioinformatics - November 4, 2009 Category: Bioinformatics Source Type: journals

A Structured Threshold Model for Mountain Pine Beetle Outbreak.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A vigor-structured model for mountain pine beetle outbreak dynamics within a forest stand is proposed and analyzed. This model explicitly tracks the changing vigor structure in the stand. All model parameters, other than beetle vigor preference, were determined by fitting model components to empirical data. An abrupt threshold for tree mortality to beetle densities allows for model simplification. Based on initial beetle density, model outcomes vary from decimation of the entire stand in a single year, to inability of the beetles to infect any trees. An intermediate outcome involves an initial infestation which subsequ...
Source: Bulletin of Mathematical Biology - October 24, 2009 Category: Bioinformatics Authors: Lewis MA, Nelson W, Xu C Tags: Bull Math Biol Source Type: journals

From Microscopic to Macroscopic Descriptions of Cell Migration on Growing Domains.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Cell migration and growth are essential components of the development of multicellular organisms. The role of various cues in directing cell migration is widespread, in particular, the role of signals in the environment in the control of cell motility and directional guidance. In many cases, especially in developmental biology, growth of the domain also plays a large role in the distribution of cells and, in some cases, cell or signal distribution may actually drive domain growth. There is an almost ubiquitous use of partial differential equations (PDEs) for modelling the time evolution of cellular density and environm...
Source: Bulletin of Mathematical Biology - October 28, 2009 Category: Bioinformatics Authors: Baker RE, Yates CA, Erban R Tags: Bull Math Biol Source Type: journals

Plasma and urine biomarkers in acute viral hepatitis EEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Background: Hepatitis E, caused by the hepatitis E virus (HEV), is endemic to developing countries where it manifests as waterborne outbreaks and sporadic cases. Though generally self-limited with a low mortality rate, some cases progress to fulminant hepatic failure (FHF) with high mortality. With no identified predictive or diagnostic markers, the events leading to disease exacerbation are not known. Our aim is to use proteomic tools to identify biomarkers of acute and fulminant hepatitis E. Results: We analyzed proteins in the plasma and urine of hepatitis E patients and healthy controls by two-dimensional Differential ...
Source: Proteome Science - October 27, 2009 Category: Bioinformatics Authors: Shikha TanejaSomdutta SenVijay GuptaRakesh AggarwalShahid Jameel Source Type: journals

iBioSim: a tool for the analysis and design of genetic circuitsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Summary: iBioSim is a tool that supports learning of genetic circuit models, efficient abstraction-based analysis of these models and the design of synthetic genetic circuits. iBioSim includes project management features and a graphical user interface that facilitate the development and maintenance of genetic circuit models as well as both experimental and simulation data records. Availability: iBioSim is available for download for Windows, Linux, and MacOS at http://www.async.ece.utah.edu/iBioSim/ Contact: myers@ece.utah.edu (Source: Bioinformatics)
Source: Bioinformatics - October 23, 2009 Category: Bioinformatics Authors: Myers, C. J., Barker, N., Jones, K., Kuwahara, H., Madsen, C., Nguyen, N.-P. D. Tags: SYSTEMS BIOLOGY Source Type: journals

A hypergraph-based learning algorithm for classifying gene expression and arrayCGH data with prior knowledgeEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Motivation: Incorporating biological prior knowledge into predictive models is a challenging data integration problem in analyzing high-dimensional genomic data. We introduce a hypergraph-based semi-supervised learning algorithm called HyperPrior to classify gene expression and array-based comparative genomic hybridization (arrayCGH) data using biological knowledge as constraints on graph-based learning. HyperPrior is a robust two-step iterative method that alternatively finds the optimal labeling of the samples and the optimal weighting of the features, guided by constraints encoding prior knowledge. The prior knowledge f...
Source: Bioinformatics - October 23, 2009 Category: Bioinformatics Authors: Tian, Z., Hwang, T., Kuang, R. Tags: SYSTEMS BIOLOGY Source Type: journals