Taking U out, with two nucleases?

abstract：BACKGROUND:Chemical named entities represent an important facet of biomedical text. RESULTS:We have developed a system to use character-based n-grams, Maximum Entropy Markov Models and rescoring to recognise chemical names and other such entities, and to make confidence estimates for the extracted entities. An adjusta...

journal_title：BMC bioinformatics

authors： Corbett P,Copestake A

更新日期：2008-11-19 00:00:00

abstract：BACKGROUND:Structural interaction frequency matrices between all genome loci are now experimentally achievable thanks to high-throughput chromosome conformation capture technologies. This ensues a new methodological challenge for computational biology which consists in objectively extracting from these data the structu...

journal_title：BMC bioinformatics

authors： Boulos RE,Tremblay N,Arneodo A,Borgnat P,Audit B

更新日期：2017-04-11 00:00:00

abstract：BACKGROUND:Microarray technology has become very popular for globally evaluating gene expression in biological samples. However, non-linear variation associated with the technology can make data interpretation unreliable. Therefore, methods to correct this kind of technical variation are critical. Here we consider a me...

journal_title：BMC bioinformatics

authors： Pelz CR,Kulesz-Martin M,Bagby G,Sears RC

更新日期：2008-12-04 00:00:00

abstract：BACKGROUND:Gas chromatography coupled with mass spectrometry (GC-MS) is one of the technologies widely used for qualitative and quantitative analysis of small molecules. In particular, GC coupled to single quadrupole MS can be utilized for targeted analysis by selected ion monitoring (SIM). However, to our knowledge, t...

journal_title：BMC bioinformatics

authors： Ranjbar MR,Di Poto C,Wang Y,Ressom HW

更新日期：2015-08-19 00:00:00

abstract：BACKGROUND:Functional genomics involves the parallel experimentation with large sets of proteins. This requires management of large sets of open reading frames as a prerequisite of the cloning and recombinant expression of these proteins. RESULTS:A Java program was developed for retrieval of protein and nucleic acid s...

journal_title：BMC bioinformatics

authors： Büssow K,Hoffmann S,Sievert V

更新日期：2002-12-19 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 spatial configuration of chromosomes is essential to various cellular processes, notably gene regulation, while architecture related alterations, such as translocations and gene fusions, are often cancer drivers. Thus, eliciting chromatin conformation is important, yet challenging due to compaction, dyna...

journal_title：BMC bioinformatics

authors： Segal MR,Fletez-Brant K

更新日期：2020-02-24 00:00:00

abstract：BACKGROUND:Ensemble predictors such as the random forest are known to have superior accuracy but their black-box predictions are difficult to interpret. In contrast, a generalized linear model (GLM) is very interpretable especially when forward feature selection is used to construct the model. However, forward feature ...

journal_title：BMC bioinformatics

authors： Song L,Langfelder P,Horvath S

更新日期：2013-01-16 00:00:00

abstract：BACKGROUND:The molecular recognition based on the complementary base pairing of deoxyribonucleic acid (DNA) is the fundamental principle in the fields of genetics, DNA nanotechnology and DNA computing. We present an exhaustive DNA sequence design algorithm that allows to generate sets containing a maximum number of seq...

journal_title：BMC bioinformatics

authors： Kick A,Bönsch M,Mertig M

更新日期：2012-06-20 00:00:00

abstract：BACKGROUND:Sequence alignment is crucial in genomics studies. However, optimal multiple sequence alignment (MSA) is NP-hard. Thus, modern MSA methods employ progressive heuristics, breaking the problem into a series of pairwise alignments guided by a phylogeny. Changes between homologous characters are typically modell...

journal_title：BMC bioinformatics

authors： Maiolo M,Zhang X,Gil M,Anisimova M

更新日期：2018-09-21 00:00:00

abstract：BACKGROUND:Identifying similarities between datasets is a fundamental task in data mining and has become an integral part of modern scientific investigation. Whether the task is to identify co-expressed genes in large-scale expression surveys or to predict combinations of gene knockouts which would elicit a similar phe...

journal_title：BMC bioinformatics

authors： Lee JY,Fujimoto GM,Wilson R,Wiley HS,Payne SH

更新日期：2018-06-11 00:00:00

abstract：BACKGROUND:Identifying diagnosis and prognosis biomarkers from expression profiling data is of great significance for achieving personalized medicine and designing therapeutic strategy in complex diseases. However, the reproducibility of identified biomarkers across tissues and experiments is still a challenge for this...

journal_title：BMC bioinformatics

authors： Zhang X,Gao L,Liu ZP,Chen L

更新日期：2015-03-18 00:00:00

abstract：BACKGROUND:The annotation of protein post-translational modifications (PTMs) is an important task of UniProtKB curators and, with continuing improvements in experimental methodology, an ever greater number of articles are being published on this topic. To help curators cope with this growing body of information we have...

journal_title：BMC bioinformatics

authors： Veuthey AL,Bridge A,Gobeill J,Ruch P,McEntyre JR,Bougueleret L,Xenarios I

更新日期：2013-03-22 00:00:00

abstract：BACKGROUND:Copy number alterations (CNAs), due to their large impact on the genome, have been an important contributing factor to oncogenesis and metastasis. Detecting genomic alterations from the shallow-sequencing data of a low-purity tumor sample remains a challenging task. RESULTS:We introduce Accucopy, a method t...

journal_title：BMC bioinformatics

authors： Fan X,Luo G,Huang YS

更新日期：2021-01-15 00:00:00

abstract：BACKGROUND:An important application of high dimensional gene expression measurements is the risk prediction and the interpretation of the variables in the resulting survival models. A major problem in this context is the typically large number of genes compared to the number of observations (individuals). Feature selec...

journal_title：BMC bioinformatics

authors： Kammers K,Lang M,Hengstler JG,Schmidt M,Rahnenführer J

更新日期：2011-12-16 00:00:00

abstract：BACKGROUND:Vast progress in sequencing projects has called for annotation on a large scale. A Number of methods have been developed to address this challenging task. These methods, however, either apply to specific subsets, or their predictions are not formalised, or they do not provide precise confidence values for th...

journal_title：BMC bioinformatics

authors： Vinayagam A,del Val C,Schubert F,Eils R,Glatting KH,Suhai S,König R

更新日期：2006-03-20 00:00:00

abstract：BACKGROUND:MicroRNAs (miRNAs) are small ~22 nucleotide non-coding RNAs that function as post-transcriptional regulators of messenger RNA (mRNA) through base-pairing to 6-8 nucleotide long target sites, usually located within the mRNA 3' untranslated region. A common approach to validate and probe microRNA-mRNA interact...

journal_title：BMC bioinformatics

authors： Ryan BC,Werner TS,Howard PL,Chow RL

更新日期：2016-04-27 00:00:00

abstract：BACKGROUND:To infer the tree of life requires knowledge of the common characteristics of each species descended from a common ancestor as the measuring criteria and a method to calculate the distance between the resulting values of each measure. Conventional phylogenetic analysis based on genomic sequences provides inf...

journal_title：BMC bioinformatics

authors： Oh SJ,Joung JG,Chang JH,Zhang BT

更新日期：2006-06-06 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:Human triosephosphate isomerase (HsTIM) deficiency is a genetic disease caused often by the pathogenic mutation E104D. This mutation, located at the side of an abnormally large cluster of water in the inter-subunit interface, reduces the thermostability of the enzyme. Why and how these water molecules are di...

journal_title：BMC bioinformatics

authors： Li Z,He Y,Liu Q,Zhao L,Wong L,Kwoh CK,Nguyen H,Li J

更新日期：2013-01-01 00:00:00

abstract：BACKGROUND:Somatic copy number alternation (SCNA) is a common feature of the cancer genome and is associated with cancer etiology and prognosis. The allele-specific SCNA analysis of a tumor sample aims to identify the allele-specific copy numbers of both alleles, adjusting for the ploidy and the tumor purity. Next gene...

journal_title：BMC bioinformatics

authors： Choo-Wosoba H,Albert PS,Zhu B

更新日期：2018-11-14 00:00:00

abstract：BACKGROUND:The aberrant expression of microRNAs is closely connected to the occurrence and development of a great deal of human diseases. To study human diseases, numerous effective computational models that are valuable and meaningful have been presented by researchers. RESULTS:Here, we present a computational framew...

journal_title：BMC bioinformatics

authors： Gao Z,Wang YT,Wu QW,Ni JC,Zheng CH

更新日期：2020-02-18 00:00:00

abstract：BACKGROUND:DNA methylation patterns have been shown to significantly correlate with different tissue types and disease states. High-throughput methylation arrays enable large-scale DNA methylation analysis to identify informative DNA methylation biomarkers. The identification of disease-specific methylation signatures ...

journal_title：BMC bioinformatics

authors： Meng H,Murrelle EL,Li G

更新日期：2008-10-27 00:00:00

abstract：BACKGROUND:Genetic interaction profiles are highly informative and helpful for understanding the functional linkages between genes, and therefore have been extensively exploited for annotating gene functions and dissecting specific pathway structures. However, our understanding is rather limited to the relationship bet...

journal_title：BMC bioinformatics

authors： You ZH,Yin Z,Han K,Huang DS,Zhou X

更新日期：2010-06-24 00:00:00

abstract：BACKGROUND:The explosive growth of biological data provides opportunities for new statistical and comparative analyses of large information sets, such as alignments comprising tens of thousands of sequences. In such studies, sequence annotations frequently play an essential role, and reliable results depend on metadata...

journal_title：BMC bioinformatics

authors： Miotto O,Tan TW,Brusic V

更新日期：2008-01-01 00:00:00

abstract：BACKGROUND:Genome-wide association studies (GWAS) of single nucleotide polymorphisms (SNPs) have been successful in identifying loci contributing genetic effects to a wide range of complex human diseases and quantitative traits. The traditional approach to GWAS analysis is to consider each phenotype separately, despite...

journal_title：BMC bioinformatics

authors： Mägi R,Suleimanov YV,Clarke GM,Kaakinen M,Fischer K,Prokopenko I,Morris AP

更新日期：2017-01-11 00:00:00

abstract：BACKGROUND:Short oligonucleotide arrays have several probes measuring the expression level of each target transcript. Therefore the selection of probes is a key component for the quality of measurements. However, once probes have been selected and synthesized on an array, it is still possible to re-evaluate the results...

journal_title：BMC bioinformatics

authors： Gautier L,Møller M,Friis-Hansen L,Knudsen S

更新日期：2004-08-14 00:00:00

abstract：BACKGROUND:Discovering patterns from gene expression levels is regarded as a classification problem when tissue classes of the samples are given and solved as a discrete-data problem by discretizing the expression levels of each gene into intervals maximizing the interdependence between that gene and the class labels. ...

journal_title：BMC bioinformatics

authors： Wu GP,Chan KC,Wong AK

更新日期：2011-01-01 00:00:00

abstract：BACKGROUND:Last generations of Single Nucleotide Polymorphism (SNP) arrays allow to study copy-number variations in addition to genotyping measures. RESULTS:MPAgenomics, standing for multi-patient analysis (MPA) of genomic markers, is an R-package devoted to: (i) efficient segmentation and (ii) selection of genomic ma...

journal_title：BMC bioinformatics

authors： Grimonprez Q,Celisse A,Blanck S,Cheok M,Figeac M,Marot G

更新日期：2014-12-14 00:00:00

abstract：BACKGROUND:Reverse transcription followed by real-time PCR is widely used for quantification of specific mRNA, and with the use of double-stranded DNA binding dyes it is becoming a standard for microarray data validation. Despite the kinetic information generated by real-time PCR, most popular analysis methods assume c...

journal_title：BMC bioinformatics

authors： Alvarez MJ,Vila-Ortiz GJ,Salibe MC,Podhajcer OL,Pitossi FJ

更新日期：2007-03-09 00:00:00