Proceedings of the 2018 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) conference.

abstract：BACKGROUND:Elucidating gene regulatory networks is crucial for understanding normal cell physiology and complex pathologic phenotypes. Existing computational methods for the genome-wide "reverse engineering" of such networks have been successful only for lower eukaryotes with simple genomes. Here we present ARACNE, a n...

journal_title：BMC bioinformatics

authors： Margolin AA,Nemenman I,Basso K,Wiggins C,Stolovitzky G,Dalla Favera R,Califano A

更新日期：2006-03-20 00:00:00

abstract：BACKGROUND:One of the important goals in the post-genomic era is to determine the regulatory elements within the non-coding DNA of a given organism's genome. The identification of functional cis-regulatory modules has proven difficult since the component factor binding sites are small and the rules governing their arra...

journal_title：BMC bioinformatics

authors： Emberly E,Rajewsky N,Siggia ED

更新日期：2003-11-20 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:Alternative splicing isoforms have been reported as a new and robust class of diagnostic biomarkers. Over 95% of human genes are estimated to be alternatively spliced as a powerful means of producing functionally diverse proteins from a single gene. The emergence of next-generation sequencing technologies, e...

journal_title：BMC bioinformatics

authors： Zhang F,Deng CK,Wang M,Deng B,Barber R,Huang G

更新日期：2020-12-03 00:00:00

abstract：BACKGROUND:Observed levels of gene expression strongly depend on both activity of DNA binding transcription factors (TFs) and chromatin state through different histone modifications (HMs). In order to recover the functional relationship between local chromatin state, TF binding and observed levels of gene expression, r...

journal_title：BMC bioinformatics

authors： Aflakparast M,Geeven G,de Gunst MCM

更新日期：2020-01-02 00:00:00

abstract：BACKGROUND:Because loops connect regular secondary structures, analysis of the former depends directly on the definition of the latter. The numerous assignment methods, however, can offer different definitions. In a previous study, we defined a structural alphabet composed of 16 average protein fragments, which we call...

journal_title：BMC bioinformatics

authors： Fourrier L,Benros C,de Brevern AG

更新日期：2004-05-12 00:00:00

abstract：BACKGROUND:In the last few years high-throughput analysis methods have become state-of-the-art in the life sciences. One of the latest developments is automated greenhouse systems for high-throughput plant phenotyping. Such systems allow the non-destructive screening of plants over a period of time by means of image ac...

journal_title：BMC bioinformatics

authors： Hartmann A,Czauderna T,Hoffmann R,Stein N,Schreiber F

更新日期：2011-05-12 00:00:00

abstract：BACKGROUND:Mass spectrometry is an essential analytical technique for high-throughput analysis in proteomics and metabolomics. The development of new separation techniques, precise mass analyzers and experimental protocols is a very active field of research. This leads to more complex experimental setups yielding ever ...

journal_title：BMC bioinformatics

authors： Sturm M,Bertsch A,Gröpl C,Hildebrandt A,Hussong R,Lange E,Pfeifer N,Schulz-Trieglaff O,Zerck A,Reinert K,Kohlbacher O

更新日期：2008-03-26 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

abstract：BACKGROUND:Microarray has been widely used to measure the gene expression level on the genome scale in the current decade. Many algorithms have been developed to reconstruct gene regulatory networks based on microarray data. Unfortunately, most of these models and algorithms focus on global properties of the expression...

journal_title：BMC bioinformatics

authors： Liu W,Li D,Liu Q,Zhu Y,He F

更新日期：2010-12-14 00:00:00

abstract：BACKGROUND:Recent technological advances in DNA sequencing and genotyping have led to the accumulation of a remarkable quantity of data on genetic polymorphisms. However, the development of new statistical and computational tools for effective processing of these data has not been equally as fast. In particular, Machin...

journal_title：BMC bioinformatics

authors： Lagani V,Montesanto A,Di Cianni F,Moreno V,Landi S,Conforti D,Rose G,Passarino G

更新日期：2009-06-16 00:00:00

abstract：:Metabolic network alignment is a system scale comparative analysis that discovers important similarities and differences across different metabolisms and organisms. Although the problem of aligning metabolic networks has been considered in the past, the computational complexity of the existing solutions has so far lim...

journal_title：BMC bioinformatics

authors： Ay F,Dang M,Kahveci T

更新日期：2012-03-21 00:00:00

abstract：BACKGROUND:The amount of gene expression data available in public repositories has grown exponentially in the last years, now requiring new data mining tools to transform them in information easily accessible to biologists. RESULTS:By exploiting expression data publicly available in the Gene Expression Omnibus (GEO) d...

journal_title：BMC bioinformatics

authors： Cremaschi P,Rovida S,Sacchi L,Lisa A,Calvi F,Montecucco A,Biamonti G,Bione S,Sacchi G

更新日期：2014-01-01 00:00:00

abstract：BACKGROUND:The human immunodeficiency virus type 1 (HIV-1) aspartic protease is an important enzyme owing to its imperative part in viral development and a causative agent of deadliest disease known as acquired immune deficiency syndrome (AIDS). Development of HIV-1 protease inhibitors can help understand the specifici...

journal_title：BMC bioinformatics

authors： Singh O,Su EC

更新日期：2016-12-23 00:00:00

abstract：BACKGROUND:DNA methylation changes are associated with a wide array of biological processes. Bisulfite conversion of DNA followed by high-throughput sequencing is increasingly being used to assess genome-wide methylation at single-base resolution. The relative slowness of most commonly used aligners for processing such...

journal_title：BMC bioinformatics

authors： Ryan DP,Ehninger D

更新日期：2014-10-18 00:00:00

abstract：BACKGROUND:Correctly identifying genomic regions enriched with histone modifications and transcription factors is key to understanding their regulatory and developmental roles. Conceptually, these regions are divided into two categories, narrow peaks and broad domains, and different algorithms are used to identify each...

journal_title：BMC bioinformatics

authors： Starmer J,Magnuson T

更新日期：2016-03-24 00:00:00

abstract：BACKGROUND:Stable isotope tracing can follow individual atoms through metabolic transformations through the detection of the incorporation of stable isotope within metabolites. This resulting data can be interpreted in terms related to metabolic flux. However, detection of a stable isotope in metabolites by mass spectr...

journal_title：BMC bioinformatics

authors： Jin H,Moseley HNB

更新日期：2019-10-28 00:00:00

abstract：BACKGROUND:Next (second) generation sequencing is an increasingly important tool for many areas of molecular biology, however, care must be taken when interpreting its output. Even a low error rate can cause a large number of errors due to the high number of nucleotides being sequenced. Identifying sequencing errors fr...

journal_title：BMC bioinformatics

authors： Sleep JA,Schreiber AW,Baumann U

更新日期：2013-12-18 00:00:00

abstract：BACKGROUND:In template-based modeling when using a single template, inter-atomic distances of an unknown protein structure are assumed to be distributed by Gaussian probability density functions, whose center peaks are located at the distances between corresponding atoms in the template structure. The width of the Gaus...

journal_title：BMC bioinformatics

authors： Lee J,Lee K,Joung I,Joo K,Brooks BR,Lee J

更新日期：2015-03-21 00:00:00

abstract：BACKGROUND:High-throughput sequencing technologies, such as the Illumina Genome Analyzer, are powerful new tools for investigating a wide range of biological and medical questions. Statistical and computational methods are key for drawing meaningful and accurate conclusions from the massive and complex datasets generat...

journal_title：BMC bioinformatics

authors： Bullard JH,Purdom E,Hansen KD,Dudoit S

更新日期：2010-02-18 00:00:00

abstract：BACKGROUND:N-linked protein glycosylation plays an important role in various biological processes, including protein folding and trafficking, and cell adhesion and signaling. The acquisition of a novel N-glycosylation site may have significant effect on protein structure and function, and therefore, on the phenotype. ...

journal_title：BMC bioinformatics

authors： Kim DS,Hahn Y

更新日期：2015-01-28 00:00:00

abstract：BACKGROUND:Systems biology modeling from microarray data requires the most contemporary structural and functional array annotation. However, microarray annotations, especially for non-commercial, non-traditional biomedical model organisms, are often dated. In addition, most microarray analysis tools do not readily acce...

journal_title：BMC bioinformatics

authors： van den Berg BH,Konieczka JH,McCarthy FM,Burgess SC

更新日期：2009-01-23 00:00:00

abstract：BACKGROUND:In many biomedical applications, there is a need for developing classification models based on noisy annotations. Recently, various methods addressed this scenario by relaying on unreliable annotations obtained from multiple sources. RESULTS:We proposed a probabilistic classification algorithm based on labe...

journal_title：BMC bioinformatics

authors： Zhang P,Cao W,Obradovic Z

更新日期：2013-01-01 00:00:00

abstract：BACKGROUND:Protein-protein interactions play a key role in biological processes of proteins within a cell. Recent high-throughput techniques have generated protein-protein interaction data in a genome-scale. A wide range of computational approaches have been applied to interactome network analysis for uncovering functi...

journal_title：BMC bioinformatics

authors： Cho YR,Zhang A

更新日期：2010-04-29 00:00:00

abstract：BACKGROUND:As numerous diseases involve errors in signal transduction, modern therapeutics often target proteins involved in cellular signaling. Interpretation of the activity of signaling pathways during disease development or therapeutic intervention would assist in drug development, design of therapy, and target ide...

journal_title：BMC bioinformatics

authors： Bidaut G,Suhre K,Claverie JM,Ochs MF

更新日期：2006-02-28 00:00:00

abstract：BACKGROUND:An important step in understanding the conditions that specify gene expression is the recognition of gene regulatory elements. Due to high diversity of different types of transcription factors and their DNA binding preferences, it is a challenging problem to establish an accurate model for recognition of fun...

journal_title：BMC bioinformatics

authors： Stepanova M,Lin F,Lin VC

更新日期：2006-12-12 00:00:00

abstract：BACKGROUND:High throughput experiments have generated a significantly large amount of protein interaction data, which is being used to study protein networks. Studying complete protein networks can reveal more insight about healthy/disease states than studying proteins in isolation. Similarly, a comparative study of pr...

journal_title：BMC bioinformatics

authors： Ayub U,Haider I,Naveed H

更新日期：2020-11-04 00:00:00

abstract：BACKGROUND:Evolutionary genomics requires management and filtering of large numbers of diverse genomic sequences for accurate analysis and inference on evolutionary processes of genomic and functional change. We developed Evolutionary Genomics and Biodiversity (EGenBio; http://egenbio.lsu.edu) to begin to address this....

journal_title：BMC bioinformatics

authors： Nahum LA,Reynolds MT,Wang ZO,Faith JJ,Jonna R,Jiang ZJ,Meyer TJ,Pollock DD

更新日期：2006-09-06 00:00:00

abstract：BACKGROUND:Recently differential variability has been showed to be valuable in evaluating the association of DNA methylation to the risks of complex human diseases. The statistical tests based on both differential methylation level and differential variability can be more powerful than those based only on differential ...

journal_title：BMC bioinformatics

authors： Li X,Fu Y,Wang X,Qiu W

更新日期：2018-05-18 00:00:00

abstract：BACKGROUND:The Damerau-Levenshtein (DL) distance metric has been widely used in the biological science. It tries to identify the similar region of DNA,RNA and protein sequences by transforming one sequence to the another using the substitution, insertion, deletion and transposition operations. Lowrance and Wagner have ...

journal_title：BMC bioinformatics

authors： Zhao C,Sahni S

更新日期：2020-12-09 00:00:00