svapls: an R package to correct for hidden factors of variability in gene expression studies.

abstract：BACKGROUND:In two-channel competitive genomic hybridization microarray experiments, the ratio of the two fluorescent signal intensities at each spot on the microarray is commonly used to infer the relative amounts of the test and reference sample DNA levels. This ratio may be influenced by systematic measurement effect...

journal_title：BMC bioinformatics

authors： Khojasteh M,Lam WL,Ward RK,MacAulay C

更新日期：2005-11-18 00:00:00

abstract：BACKGROUND:We present a model for tagging gene and protein mentions from text using the probabilistic sequence tagging framework of conditional random fields (CRFs). Conditional random fields model the probability P(t/o) of a tag sequence given an observation sequence directly, and have previously been employed success...

journal_title：BMC bioinformatics

authors： McDonald R,Pereira F

更新日期：2005-01-01 00:00:00

abstract：:Identifying segments in the genome of different individuals that are identical-by-descent (IBD) is a fundamental element of genetics. IBD data is used for numerous applications including demographic inference, heritability estimation, and mapping disease loci. Simultaneous detection of IBD over multiple haplotypes has...

journal_title：BMC bioinformatics

authors： Park DS,Baran Y,Hormozdiari F,Eng C,Torgerson DG,Burchard EG,Zaitlen N

更新日期：2015-01-01 00:00:00

abstract：BACKGROUND:Leishmania and other members of the Trypanosomatidae family diverged early on in eukaryotic evolution and consequently display unique cellular properties. Their apparent lack of transcriptional regulation is compensated by complex post-transcriptional control mechanisms, including the processing of polycistr...

journal_title：BMC bioinformatics

authors： Smith M,Blanchette M,Papadopoulou B

更新日期：2008-03-20 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:Gene expression experiments are common in molecular biology, for example in order to identify genes which play a certain role in a specified biological framework. For that purpose expression levels of several thousand genes are measured simultaneously using DNA microarrays. Comparing two distinct groups of t...

journal_title：BMC bioinformatics

authors： Jung K,Friede T,Beissbarth T

更新日期：2011-07-15 00:00:00

abstract：BACKGROUND:Single nucleotide polymorphisms (SNPs) are the most abundant genetic variant found in vertebrates and invertebrates. SNP discovery has become a highly automated, robust and relatively inexpensive process allowing the identification of many thousands of mutations for model and non-model organisms. Annotating ...

journal_title：BMC bioinformatics

authors： Doran AG,Creevey CJ

更新日期：2013-02-08 00:00:00

abstract：BACKGROUND:While researchers have utilized versions of the Affymetrix human GeneChip for the assessment of expression patterns in non human primate (NHP) samples, there has been no comprehensive sequence analysis study undertaken to demonstrate that the probe sequences designed to detect human transcripts are reliably ...

journal_title：BMC bioinformatics

authors： Wang Z,Lewis MG,Nau ME,Arnold A,Vahey MT

更新日期：2004-10-26 00:00:00

abstract：BACKGROUND:In mass spectrometry (MS) based proteomic data analysis, peak detection is an essential step for subsequent analysis. Recently, there has been significant progress in the development of various peak detection algorithms. However, neither a comprehensive survey nor an experimental comparison of these algorith...

journal_title：BMC bioinformatics

authors： Yang C,He Z,Yu W

更新日期：2009-01-06 00:00:00

abstract：BACKGROUND:The binding of regulatory proteins to their specific DNA targets determines the accurate expression of the neighboring genes. The in silico prediction of new binding sites in completely sequenced genomes is a key aspect in the deeper understanding of gene regulatory networks. Several algorithms have been des...

journal_title：BMC bioinformatics

authors： Oberto J

更新日期：2010-11-11 00:00:00

abstract：BACKGROUND:We aim to solve the problem of determining word senses for ambiguous biomedical terms with minimal human effort. METHODS:We build a fully automated system for Word Sense Disambiguation by designing a system that does not require manually-constructed external resources or manually-labeled training examples e...

journal_title：BMC bioinformatics

authors： Duan W,Song M,Yates A

更新日期：2009-03-19 00:00:00

abstract：BACKGROUND:High-throughput Next-Generation Sequencing (NGS) techniques are advancing genomics and molecular biology research. This technology generates substantially large data which puts up a major challenge to the scientists for an efficient, cost and time effective solution to analyse such data. Further, for the dif...

journal_title：BMC bioinformatics

authors： Maji RK,Sarkar A,Khatua S,Dasgupta S,Ghosh Z

更新日期：2014-06-04 00:00:00

abstract：BACKGROUND:Protein-structure alignment is a fundamental tool to study protein function, evolution and model building. In the last decade several methods for structure alignment were introduced, but most of them ignore that structurally similar proteins can share the same spatial arrangement of secondary structure eleme...

journal_title：BMC bioinformatics

authors： Kolbeck B,May P,Schmidt-Goenner T,Steinke T,Knapp EW

更新日期：2006-11-21 00:00:00

abstract：BACKGROUND:Microarray experiments enable simultaneous measurement of the expression levels of virtually all transcripts present in cells, thereby providing a 'molecular picture' of the cell state. On the other hand, the genomic responses to a pharmacological or hormonal stimulus are dynamic molecular processes, where t...

journal_title：BMC bioinformatics

authors： Mutarelli M,Cicatiello L,Ferraro L,Grober OM,Ravo M,Facchiano AM,Angelini C,Weisz A

更新日期：2008-03-26 00:00:00

abstract：BACKGROUND:For successful protein structure prediction by comparative modeling, in addition to identifying a good template protein with known structure, obtaining an accurate sequence alignment between a query protein and a template protein is critical. It has been known that the alignment accuracy can vary significant...

journal_title：BMC bioinformatics

authors： Lee M,Jeong CS,Kim D

更新日期：2007-12-03 00:00:00

abstract：BACKGROUND:Linkage disequilibrium (LD)-the non-random association of alleles at different loci-defines population-specific haplotypes which vary by genomic ancestry. Assessment of allelic frequencies and LD patterns from a variety of ancestral populations enables researchers to better understand population histories as...

journal_title：BMC bioinformatics

authors： Alexander TA,Machiela MJ

更新日期：2020-01-10 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:Internal ribosomal entry sites (IRESs) provide alternative, cap-independent translation initiation sites in eukaryotic cells. IRES elements are important factors in viral genomes and are also useful tools for bi-cistronic expression vectors. Most existing RNA structure prediction programs are unable to deal ...

journal_title：BMC bioinformatics

authors： Wu TY,Hsieh CC,Hong JJ,Chen CY,Tsai YS

更新日期：2009-05-27 00:00:00

abstract：BACKGROUND:The traditional phylogeny analysis within gene family is mainly based on DNA or amino acid sequence homologies. However, these phylogenetic tree analyses are not suitable for those "non-traditional" gene families like microRNA with very short sequences. For the normal protein-coding gene families, low bootst...

journal_title：BMC bioinformatics

authors： Cai B,Yang X,Tuskan GA,Cheng ZM

更新日期：2011-03-18 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:The program InDeVal was originally developed to help researchers find known regions of insertion/deletion activity (with the exception of isolated single-base indels) in newly determined Poaceae trnL-F sequences and compare them with 533 previously determined sequences. It is supplied with input files design...

journal_title：BMC bioinformatics

authors： Stoneberg Holt SD,Holt JA

更新日期：2004-10-29 00:00:00

abstract：BACKGROUND:Interpretation of quantitative metagenomics data is important for our understanding of ecosystem functioning and assessing differences between various environmental samples. There is a need for an easy to use tool to explore the often complex metagenomics data in taxonomic and functional context. RESULTS:He...

journal_title：BMC bioinformatics

authors： Sanli K,Karlsson FH,Nookaew I,Nielsen J

更新日期：2013-02-01 00:00:00

abstract：BACKGROUND:The UNO/RIC Nanopore Detector provides a new way to study the binding and conformational changes of individual antibodies. Many critical questions regarding antibody function are still unresolved, questions that can be approached in a new way with the nanopore detector. RESULTS:We present evidence that diff...

journal_title：BMC bioinformatics

authors： Winters-Hilt S,Morales E,Amin I,Stoyanov A

更新日期：2007-11-01 00:00:00

abstract：BACKGROUND:The distance matrix computed from multiple alignments of homologous sequences is widely used by distance-based phylogenetic methods to provide information on the evolution of protein families. This matrix can also be visualized in a low dimensional space by metric multidimensional scaling (MDS). Applied to p...

journal_title：BMC bioinformatics

authors： Pelé J,Bécu JM,Abdi H,Chabbert M

更新日期：2012-06-15 00:00:00

abstract：BACKGROUND:Expression profiles obtained from multiple perturbation experiments are increasingly used to reconstruct transcriptional regulatory networks, from well studied, simple organisms up to higher eukaryotes. Admittedly, a key ingredient in developing a reconstruction method is its ability to integrate heterogeneo...

journal_title：BMC bioinformatics

authors： Veber P,Guziolowski C,Le Borgne M,Radulescu O,Siegel A

更新日期：2008-05-06 00:00:00

abstract：BACKGROUND:The 5'-terminal cap structure plays an important role in many aspects of mRNA metabolism. Capping enzymes encoded by viruses and pathogenic fungi are attractive targets for specific inhibitors. There is a large body of experimental data on viral and cellular methyltransferases (MTases) that carry out guanine...

journal_title：BMC bioinformatics

authors： Bujnicki JM,Feder M,Radlinska M,Rychlewski L

更新日期：2001-01-01 00:00:00

abstract：BACKGROUND:A standardized and cost-effective molecular identification system is now an urgent need for Fungi owing to their wide involvement in human life quality. In particular the potential use of mitochondrial DNA species markers has been taken in account. Unfortunately, a serious difficulty in the PCR and bioinform...

journal_title：BMC bioinformatics

authors： Santamaria M,Vicario S,Pappadà G,Scioscia G,Scazzocchio C,Saccone C

更新日期：2009-06-16 00:00:00

abstract：BACKGROUND:The protein-coding regions (coding exons) of a DNA sequence exhibit a triplet periodicity (TP) due to fact that coding exons contain a series of three nucleotide codons that encode specific amino acid residues. Such periodicity is usually not observed in introns and intergenic regions. If a DNA sequence is d...

journal_title：BMC bioinformatics

authors： Wang L,Stein LD

更新日期：2010-11-08 00:00:00

abstract：BACKGROUND:Peptidases are proteolytic enzymes responsible for fundamental cellular activities in all organisms. Apparently about 2-5% of the genes encode for peptidases, irrespectively of the organism source. The basic peptidase function is "protein digestion" and this can be potentially dangerous in living organisms w...

journal_title：BMC bioinformatics

authors： Bartoli L,Calabrese R,Fariselli P,Mita DG,Casadio R

更新日期：2007-03-08 00:00:00

abstract：BACKGROUND:High-throughput experiments, such as with DNA microarrays, typically result in hundreds of genes potentially relevant to the process under study, rendering the interpretation of these experiments problematic. Here, we propose and evaluate an approach to find functional associations between large numbers of g...

journal_title：BMC bioinformatics

authors： Jelier R,Jenster G,Dorssers LC,Wouters BJ,Hendriksen PJ,Mons B,Delwel R,Kors JA

更新日期：2007-01-18 00:00:00