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abstract：BACKGROUND:The ability to confidently predict health outcomes from gene expression would catalyze a revolution in molecular diagnostics. Yet, the goal of developing actionable, robust, and reproducible predictive signatures of phenotypes such as clinical outcome has not been attained in almost any disease area. Here, w...

journal_title：BMC bioinformatics

authors： Smith AM,Walsh JR,Long J,Davis CB,Henstock P,Hodge MR,Maciejewski M,Mu XJ,Ra S,Zhao S,Ziemek D,Fisher CK

更新日期：2020-03-20 00:00:00

abstract：BACKGROUND:Microarray devices permit a genome-scale evaluation of gene function. This technology has catalyzed biomedical research and development in recent years. As many important diseases can be traced down to the gene level, a long-standing research problem is to identify specific gene expression patterns linking t...

journal_title：BMC bioinformatics

authors： Fu LM,Fu-Liu CS

更新日期：2005-03-22 00:00:00

abstract：BACKGROUND:The field of protein sequence analysis is dominated by tools rooted in substitution matrices and alignments. A complementary approach is provided by methods of quantitative characterization. A major advantage of the approach is that quantitative properties defines a multidimensional solution space, where seq...

journal_title：BMC bioinformatics

authors： Konopka BM,Marciniak M,Dyrka W

更新日期：2017-07-17 00:00:00

abstract：BACKGROUND:Complex networks are studied across many fields of science and are particularly important to understand biological processes. Motifs in networks are small connected sub-graphs that occur significantly in higher frequencies than in random networks. They have recently gathered much attention as a useful concep...

journal_title：BMC bioinformatics

authors： Kashani ZR,Ahrabian H,Elahi E,Nowzari-Dalini A,Ansari ES,Asadi S,Mohammadi S,Schreiber F,Masoudi-Nejad A

更新日期：2009-10-04 00:00:00

abstract：BACKGROUND:Caspases are a family of proteases that have central functions in programmed cell death (apoptosis) and inflammation. Caspases mediate their effects through aspartate-specific cleavage of their target proteins, and at present almost 400 caspase substrates are known. There are several methods developed to pre...

journal_title：BMC bioinformatics

authors： Piippo M,Lietzén N,Nevalainen OS,Salmi J,Nyman TA

更新日期：2010-06-15 00:00:00

abstract：BACKGROUND:When constructing new biomarker or gene signature scores for time-to-event outcomes, the underlying aims are to develop a discrimination model that helps to predict whether patients have a poor or good prognosis and to identify the most influential variables for this task. In practice, this is often done fit...

journal_title：BMC bioinformatics

authors： Mayr A,Hofner B,Schmid M

更新日期：2016-07-22 00:00:00

abstract：BACKGROUND:High-throughput "omics" based data analysis play emerging roles in life sciences and molecular diagnostics. This emphasizes the urgent need for user-friendly windows-based software interfaces that could process the diversity of large tab-delimited raw data files generated by these methods. Depending on the s...

journal_title：BMC bioinformatics

authors： Schwager C,Wirkner U,Abdollahi A,Huber PE

更新日期：2009-07-29 00:00:00

abstract：BACKGROUND:Genome scale data on protein interactions are generally represented as large networks, or graphs, where hundreds or thousands of proteins are linked to one another. Since proteins tend to function in groups, or complexes, an important goal has been to reliably identify protein complexes from these graphs. Th...

journal_title：BMC bioinformatics

authors： Vlasblom J,Wodak SJ

更新日期：2009-03-30 00:00:00

abstract：BACKGROUND:In Gene Ontology, the "Molecular Function" (MF) categorization is a widely used knowledge framework for gene function comparison and prediction. Its structure and annotation provide a convenient way to compare gene functional similarities at the molecular level. The existing gene similarity measures, however...

journal_title：BMC bioinformatics

authors： Peng J,Wang Y,Chen J

更新日期：2014-01-01 00:00:00

abstract：BACKGROUND:Leishmaniasis is a virulent parasitic infection that causes a worldwide disease burden. Most treatments have toxic side-effects and efficacy has decreased due to the emergence of resistant strains. The outlook is worsened by the absence of promising drug targets for this disease. We have taken a computationa...

journal_title：BMC bioinformatics

authors： Flórez AF,Park D,Bhak J,Kim BC,Kuchinsky A,Morris JH,Espinosa J,Muskus C

更新日期：2010-09-27 00:00:00

abstract：BACKGROUND:As part of its broad and ambitious mission, the MicroArray Quality Control (MAQC) project reported the results of experiments using External RNA Controls (ERCs) on five microarray platforms. For most platforms, several different methods of data processing were considered. However, there was no similar consid...

journal_title：BMC bioinformatics

authors： Kerr KF

更新日期：2007-10-03 00:00:00

abstract：BACKGROUND:The toxic effects of many simple organic compounds stem from their biotransformation to chemically reactive metabolites which bind covalently to cellular proteins. To understand the mechanisms of cytotoxic responses it may be important to know which proteins become adducted and whether some may be common tar...

journal_title：BMC bioinformatics

authors： Hanzlik RP,Koen YM,Theertham B,Dong Y,Fang J

更新日期：2007-03-16 00:00:00

abstract：BACKGROUND:Modern high throughput experimental techniques such as DNA microarrays often result in large lists of genes. Computational biology tools such as clustering are then used to group together genes based on their similarity in expression profiles. Genes in each group are probably functionally related. The functi...

journal_title：BMC bioinformatics

authors： Tchagang AB,Gawronski A,Bérubé H,Phan S,Famili F,Pan Y

更新日期：2010-05-06 00:00:00

abstract：BACKGROUND:A large effort to discover microRNAs (miRNAs) has been under way. Currently miRBase is their primary repository, providing annotations of primary sequences, precursors and probable genomic loci. In many cases miRNAs are identical or very similar between related (or in some cases more distant) species. Howeve...

journal_title：BMC bioinformatics

authors： Guerra-Assunção JA,Enright AJ

更新日期：2010-03-16 00:00:00

abstract：BACKGROUND:A rapidly increasing flow of genomic data requires the development of efficient methods for obtaining its compact representation. Feature extraction facilitates classification, clustering and model analysis for testing and refining biological hypotheses. "Shotgun" metagenome is an analytically challenging ty...

journal_title：BMC bioinformatics

authors： Dubinkina VB,Ischenko DS,Ulyantsev VI,Tyakht AV,Alexeev DG

更新日期：2016-01-16 00:00:00

abstract：BACKGROUND:Cryo-electron microscopy (Cryo-EM) is widely used in the determination of the three-dimensional (3D) structures of macromolecules. Particle picking from 2D micrographs remains a challenging early step in the Cryo-EM pipeline due to the diversity of particle shapes and the extremely low signal-to-noise ratio ...

journal_title：BMC bioinformatics

authors： Al-Azzawi A,Ouadou A,Max H,Duan Y,Tanner JJ,Cheng J

更新日期：2020-11-09 00:00:00

abstract：BACKGROUND:In addition to single-locus (main) effects of disease variants, there is a growing consensus that gene-gene and gene-environment interactions may play important roles in disease etiology. However, for the very large numbers of genetic markers currently in use, it has proven difficult to develop suitable and ...

journal_title：BMC bioinformatics

authors： Long Q,Zhang Q,Ott J

更新日期：2009-01-30 00:00:00

abstract：BACKGROUND:The Immunoglobulins (IG) and the T cell receptors (TR) play the key role in antigen recognition during the adaptive immune response. Recent progress in next-generation sequencing technologies has provided an opportunity for the deep T cell receptor repertoire profiling. However, a specialised software is req...

journal_title：BMC bioinformatics

authors： Nazarov VI,Pogorelyy MV,Komech EA,Zvyagin IV,Bolotin DA,Shugay M,Chudakov DM,Lebedev YB,Mamedov IZ

更新日期：2015-05-28 00:00:00

abstract：BACKGROUND:Although metatranscriptomics-the study of diverse microbial population activity based on RNA-seq data-is rapidly growing in popularity, there are limited options for biologists to analyze this type of data. Current approaches for processing metatranscriptomes rely on restricted databases and a dedicated comp...

journal_title：BMC bioinformatics

authors： Westreich ST,Korf I,Mills DA,Lemay DG

更新日期：2016-09-29 00:00:00

abstract：BACKGROUND:The process of horizontal gene transfer (HGT) is believed to be widespread in Bacteria and Archaea, but little comparative data is available addressing its occurrence in complete microbial genomes. Collection of high-quality, automated HGT prediction data based on phylogenetic evidence has previously been im...

journal_title：BMC bioinformatics

authors： Podell S,Gaasterland T,Allen EE

更新日期：2008-10-07 00:00:00

abstract：BACKGROUND:The exponential growth of gigantic biological data from various sources, such as protein-protein interaction (PPI), genome sequences scaffolding, Mass spectrometry (MS) molecular networking and metabolic flux, demands an efficient way for better visualization and interpretation beyond the conventional, two-d...

journal_title：BMC bioinformatics

authors： Wang Q,Tang B,Song L,Ren B,Liang Q,Xie F,Zhuo Y,Liu X,Zhang L

更新日期：2013-11-14 00:00:00

abstract：BACKGROUND:There are a number of different methods for generation of trees and algorithms for phylogenetic analysis in the study of bacterial taxonomy. Genotypic information, such as SSU rRNA gene sequences, now plays a more prominent role in microbial systematics than does phenotypic information. However, the integrat...

journal_title：BMC bioinformatics

authors： Tanaka N,Uchino M,Miyazaki S,Sugawara H

更新日期：2007-08-02 00:00:00

abstract：BACKGROUND:A survey of presences and absences of specific species across multiple biogeographic units (or bioregions) are used in a broad area of biological studies from ecology to microbiology. Using binary presence-absence data, we evaluate species co-occurrences that help elucidate relationships among organisms and ...

journal_title：BMC bioinformatics

authors： Chung NC,Miasojedow B,Startek M,Gambin A

更新日期：2019-12-24 00:00:00

abstract：BACKGROUND:Quadruplexes are specific structure motifs occurring, e.g., in telomeres and transcriptional regulatory regions. Recent discoveries confirmed their importance in biomedicine and led to an intensified examination of their properties. So far, the study of these motifs has focused mainly on the sequence and the...

journal_title：BMC bioinformatics

authors： Zok T,Popenda M,Szachniuk M

更新日期：2020-01-31 00:00:00

abstract：BACKGROUND:Progress in genome sequencing is proceeding at an exponential pace, and several new algal genomes are becoming available every year. One of the challenges facing the community is the association of protein sequences encoded in the genomes with biological function. While most genome assembly projects generate...

journal_title：BMC bioinformatics

authors： Lopez D,Casero D,Cokus SJ,Merchant SS,Pellegrini M

更新日期：2011-07-12 00:00:00

abstract：BACKGROUND:A drug-drug interaction (DDI) occurs when one drug influences the level or activity of another drug. The increasing volume of the scientific literature overwhelms health care professionals trying to be kept up-to-date with all published studies on DDI. METHODS:This paper describes a hybrid linguistic approa...

journal_title：BMC bioinformatics

authors： Segura-Bedmar I,Martínez P,de Pablo-Sánchez C

更新日期：2011-03-29 00:00:00

abstract：BACKGROUND:Various computer-based methods exist for the detection and quantification of protein spots in two dimensional gel electrophoresis images. Area-based methods are commonly used for spot quantification: an area is assigned to each spot and the sum of the pixel intensities in that area, the so-called volume, is ...

journal_title：BMC bioinformatics

authors： Brauner JM,Groemer TW,Stroebel A,Grosse-Holz S,Oberstein T,Wiltfang J,Kornhuber J,Maler JM

更新日期：2014-06-11 00:00:00

abstract：BACKGROUND:Testing the dependence of two variables is one of the fundamental tasks in statistics. In this work, we developed an open-source R package (knnAUC) for detecting nonlinear dependence between one continuous variable X and one binary dependent variables Y (0 or 1). RESULTS:We addressed this problem by using k...

journal_title：BMC bioinformatics

authors： Li Y,Liu X,Ma Y,Wang Y,Zhou W,Hao M,Yuan Z,Liu J,Xiong M,Shugart YY,Wang J,Jin L

更新日期：2018-11-22 00:00:00

abstract：BACKGROUND:Bioinformatics tools for automatic processing of biomedical literature are invaluable for both the design and interpretation of large-scale experiments. Many information extraction (IE) systems that incorporate natural language processing (NLP) techniques have thus been developed for use in the biomedical fi...

journal_title：BMC bioinformatics

authors： Tsai RT,Chou WC,Su YS,Lin YC,Sung CL,Dai HJ,Yeh IT,Ku W,Sung TY,Hsu WL

更新日期：2007-09-01 00:00:00

abstract：BACKGROUND:The development of high-throughput technologies has produced several large scale protein interaction data sets for multiple species, and significant efforts have been made to analyze the data sets in order to understand protein activities. Considering that the basic units of protein interactions are domain i...

journal_title：BMC bioinformatics

authors： Lee H,Deng M,Sun F,Chen T

更新日期：2006-05-25 00:00:00