Learning by aggregating experts and filtering novices: a solution to crowdsourcing problems in bioinformatics.

abstract：BACKGROUND:Reliability and Reproducibility of differentially expressed genes (DEGs) are essential for the biological interpretation of microarray data. The microarray quality control (MAQC) project launched by US Food and Drug Administration (FDA) elucidated that the lists of DEGs generated by intra- and inter-platform...

journal_title：BMC bioinformatics

authors： Zhang L,Zhang J,Yang G,Wu D,Jiang L,Wen Z,Li M

更新日期：2013-04-29 00:00:00

abstract：BACKGROUND:Biological molecules are often asymmetric with respect to stereochemistry, and correct stereochemistry is essential to their function. Molecular dynamics simulations of biomolecules have increasingly become an integral part of biophysical research. However, stereochemical errors in biomolecular structures ca...

journal_title：BMC bioinformatics

authors： Schreiner E,Trabuco LG,Freddolino PL,Schulten K

更新日期：2011-05-23 00:00:00

abstract：BACKGROUND:Atomic details of protein-DNA complexes can provide insightful information for better understanding of the function and binding specificity of DNA binding proteins. In addition to experimental methods for solving protein-DNA complex structures, protein-DNA docking can be used to predict native or near-native...

journal_title：BMC bioinformatics

authors： Corona RI,Sudarshan S,Aluru S,Guo JT

更新日期：2018-12-21 00:00:00

abstract：BACKGROUND:As a rule, peptides are more flexible and unstructured than proteins with their substantial stabilizing hydrophobic cores. Nevertheless, a few stably folding peptides have been discovered. This raises the question whether there may be more such peptides that are unknown as yet. These molecules could be helpf...

journal_title：BMC bioinformatics

authors： Gronwald W,Hohm T,Hoffmann D

更新日期：2008-02-19 00:00:00

abstract：BACKGROUND:The imputation of missing values is necessary for the efficient use of DNA microarray data, because many clustering algorithms and some statistical analysis require a complete data set. A few imputation methods for DNA microarray data have been introduced, but the efficiency of the methods was low and the va...

journal_title：BMC bioinformatics

authors： Kim KY,Kim BJ,Yi GS

更新日期：2004-10-26 00:00:00

abstract：BACKGROUND:Protein subcellular localization is crucial for genome annotation, protein function prediction, and drug discovery. Determination of subcellular localization using experimental approaches is time-consuming; thus, computational approaches become highly desirable. Extensive studies of localization prediction h...

journal_title：BMC bioinformatics

authors： Su EC,Chiu HS,Lo A,Hwang JK,Sung TY,Hsu WL

更新日期：2007-09-08 00:00:00

abstract：BACKGROUND:Many structural properties such as solvent accessibility, dihedral angles and helix-helix contacts can be assigned to each residue in a membrane protein. Independent studies exist on the analysis and sequence-based prediction of some of these so-called one-dimensional features. However, there is little expla...

journal_title：BMC bioinformatics

authors： Ahmad S,Singh YH,Paudel Y,Mori T,Sugita Y,Mizuguchi K

更新日期：2010-10-27 00:00:00

abstract：BACKGROUND:Evolutionary trees are central to a wide range of biological studies. In many of these studies, tree nodes and branches need to be associated (or annotated) with various attributes. For example, in studies concerned with organismal relationships, tree nodes are associated with taxonomic names, whereas tree b...

journal_title：BMC bioinformatics

authors： Han MV,Zmasek CM

更新日期：2009-10-27 00:00:00

abstract：BACKGROUND:The evolutionary history of genes serves as a cornerstone of contemporary biology. Most conserved sequences in mammalian genomes don't code for proteins, yielding a need to infer evolutionary history of sequences irrespective of what kind of functional element they may encode. Thus, sequence-, as opposed to ...

journal_title：BMC bioinformatics

authors： Gao K,Miller J

更新日期：2020-02-06 00:00:00

abstract：:Environmental shotgun sequencing (ESS) has potential to give greater insight into microbial communities than targeted sequencing of 16S regions, but requires much higher sequence coverage. The advent of next-generation sequencing has made it feasible for the Human Microbiome Project and other initiatives to generate E...

journal_title：BMC bioinformatics

authors： Ander C,Schulz-Trieglaff OB,Stoye J,Cox AJ

更新日期：2013-01-01 00:00:00

abstract：:Semantic Web technologies offer a promising framework for integration of disparate biomedical data. In this paper we present the semantic information integration platform under development at the Center for Clinical and Translational Sciences (CCTS) at the University of Texas Health Science Center at Houston (UTHSC-H)...

journal_title：BMC bioinformatics

authors： Mirhaji P,Zhu M,Vagnoni M,Bernstam EV,Zhang J,Smith JW

更新日期：2009-02-05 00:00:00

abstract：BACKGROUND:The topology of a biological pathway provides clues as to how a pathway operates, but rationally using this topology information with observed gene expression data remains a challenge. RESULTS:We introduce a new general-purpose analytic method called Mechanistic Bayesian Networks (MBNs) that allows for the ...

journal_title：BMC bioinformatics

authors： Shah A,Tenzen T,McMahon AP,Woolf PJ

更新日期：2009-12-18 00:00:00

abstract：BACKGROUND:Emerging and re-emerging infectious diseases such as Zika, SARS, ncovid19 and Pertussis, pose a compelling challenge for epidemiologists due to their significant impact on global public health. In this context, computational models and computer simulations are one of the available research tools that epidemi...

journal_title：BMC bioinformatics

authors： Castagno P,Pernice S,Ghetti G,Povero M,Pradelli L,Paolotti D,Balbo G,Sereno M,Beccuti M

更新日期：2020-09-16 00:00:00

abstract：BACKGROUND:Cancer is caused through a multistep process, in which a succession of genetic changes, each conferring a competitive advantage for growth and proliferation, leads to the progressive conversion of normal human cells into malignant cancer cells. Interrogation of cancer genomes holds the promise of understandi...

journal_title：BMC bioinformatics

authors： Sanchez-Garcia F,Akavia UD,Mozes E,Pe'er D

更新日期：2010-04-14 00:00:00

abstract：BACKGROUND:Inferring gene regulatory network (GRN) has been an important topic in Bioinformatics. Many computational methods infer the GRN from high-throughput expression data. Due to the presence of time delays in the regulatory relationships, High-Order Dynamic Bayesian Network (HO-DBN) is a good model of GRN. Howeve...

journal_title：BMC bioinformatics

authors： Lo LY,Wong ML,Lee KH,Leung KS

更新日期：2015-11-25 00:00:00

abstract：BACKGROUND:Cross-platform analysis of gene express data requires multiple, intricate processes at different layers with various platforms. However, existing tools handle only a single platform and are not flexible enough to support custom changes, which arise from the new statistical methods, updated versions of refere...

journal_title：BMC bioinformatics

authors： Kim J,Patel K,Jung H,Kuo WP,Ohno-Machado L

更新日期：2011-03-17 00:00:00

abstract：BACKGROUND:The large gap between the number of protein sequences in databases and the number of functionally characterized proteins calls for the development of a fast computational tool for the prediction of subnuclear and subcellular localizations generally applicable to protein sequences. The information on localiza...

journal_title：BMC bioinformatics

authors： Lei Z,Dai Y

更新日期：2005-12-07 00:00:00

abstract：BACKGROUND:Deep mutational scanning is a technique to estimate the impacts of mutations on a gene by using deep sequencing to count mutations in a library of variants before and after imposing a functional selection. The impacts of mutations must be inferred from changes in their counts after selection. RESULTS:I desc...

journal_title：BMC bioinformatics

authors： Bloom JD

更新日期：2015-05-20 00:00:00

abstract：BACKGROUND:Microsatellite (simple sequence repeat - SSR) and single nucleotide polymorphism (SNP) markers are two types of important genetic markers useful in genetic mapping and genotyping. Often, large-scale genomic research projects require high-throughput computer-assisted primer design. Numerous such web-based or ...

journal_title：BMC bioinformatics

authors： You FM,Huo N,Gu YQ,Luo MC,Ma Y,Hane D,Lazo GR,Dvorak J,Anderson OD

更新日期：2008-05-29 00:00:00

abstract：BACKGROUND:Identification of homologous genes is fundamental to comparative genomics, functional genomics and phylogenomics. Extensive public homology databases are of great value for investigating homology but need to be continually updated to incorporate new sequences. As new sequences are rapidly being generated, th...

journal_title：BMC bioinformatics

authors： Sheikhizadeh Anari S,de Ridder D,Schranz ME,Smit S

更新日期：2018-09-26 00:00:00

abstract：BACKGROUND:Metabolic networks reflect the relationships between metabolites (biomolecules) and the enzymes (proteins), and are of particular interest since they describe all chemical reactions of an organism. The metabolic networks are constructed from the genome sequence of an organism, and the graphs can be used to s...

journal_title：BMC bioinformatics

authors： Weber Zendrera A,Sokolovska N,Soula HA

更新日期：2019-10-15 00:00:00

abstract：BACKGROUND:Orthologs inference is the starting point of most comparative genomics studies, and a plethora of methods have been designed in the last decade to address this challenging task. In this paper we focus on the problems of deciding consistency with a species tree (known or not) of a partial set of orthology/par...

journal_title：BMC bioinformatics

authors： Jones M,Paul C,Scornavacca C

更新日期：2016-11-11 00:00:00

abstract：BACKGROUND:The large increase in the size of patent collections has led to the need of efficient search strategies. But the development of advanced text-mining applications dedicated to patents of the biomedical field remains rare, in particular to address the needs of the pharmaceutical & biotech industry, which inten...

journal_title：BMC bioinformatics

authors： Pasche E,Gobeill J,Kreim O,Oezdemir-Zaech F,Vachon T,Lovis C,Ruch P

更新日期：2014-01-01 00:00:00

abstract：BACKGROUND:One of the most important goals of the mathematical modeling of gene regulatory networks is to alter their behavior toward desirable phenotypes. Therapeutic techniques are derived for intervention in terms of stationary control policies. In large networks, it becomes computationally burdensome to derive an o...

journal_title：BMC bioinformatics

authors： Ghaffari N,Ivanov I,Qian X,Dougherty ER

更新日期：2011-10-18 00:00:00

abstract：BACKGROUND:Copy number variants (CNVs) have been demonstrated to occur at a high frequency and are now widely believed to make a significant contribution to the phenotypic variation in human populations. Array-based comparative genomic hybridization (array-CGH) and newly developed read-depth approach through ultrahigh ...

journal_title：BMC bioinformatics

authors： Zhang ZD,Gerstein MB

更新日期：2010-10-31 00:00:00

abstract：BACKGROUND:Despite marked recent improvements in long-read sequencing technology, the assembly of diploid genomes remains a difficult task. A major obstacle is distinguishing between alternative contigs that represent highly heterozygous regions. If primary and secondary contigs are not properly identified, the primary...

journal_title：BMC bioinformatics

authors： Solares EA,Tao Y,Long AD,Gaut BS

更新日期：2021-01-06 00:00:00

abstract：BACKGROUND:Long-range interactions between regulatory DNA elements such as enhancers, insulators and promoters play an important role in regulating transcription. As chromatin contacts have been found throughout the human genome and in different cell types, spatial transcriptional control is now viewed as a general mec...

journal_title：BMC bioinformatics

authors： Rousseau M,Fraser J,Ferraiuolo MA,Dostie J,Blanchette M

更新日期：2011-10-25 00:00:00

abstract：BACKGROUND:Event sequences where different types of events often occur close together arise, e.g., when studying potential transcription factor binding sites (TFBS, events) of certain transcription factors (TF, types) in a DNA sequence. These events tend to occur in bursts: in some genomic regions there are more genes ...

journal_title：BMC bioinformatics

authors： Haiminen N,Mannila H,Terzi E

更新日期：2008-08-08 00:00:00

abstract：BACKGROUND:Cellular functions are coordinately carried out by groups of genes forming functional modules. Identifying such modules in the transcriptional regulatory network (TRN) of organisms is important for understanding the structure and function of these fundamental cellular networks and essential for the emerging ...

journal_title：BMC bioinformatics

authors： Ma HW,Buer J,Zeng AP

更新日期：2004-12-16 00:00:00

abstract：: ...

journal_title：BMC bioinformatics

authors： Wren JD,Doerkson RJ,Toby IT,Nanduri B,Homayouni R,Manda P,Thakkar S

更新日期：2019-03-14 00:00:00