A simple and robust method for connecting small-molecule drugs using gene-expression signatures.

abstract：BACKGROUND:Antibodies revolutionized cancer treatment over the past decades. Despite their successfully application, there are still challenges to overcome to improve efficacy, such as the heterogeneous distribution of antibodies within tumors. Tumor microenvironment features, such as the distribution of tumor and othe...

journal_title：BMC bioinformatics

authors： Cartaxo AL,Almeida J,Gualda EJ,Marsal M,Loza-Alvarez P,Brito C,Isidro IA

更新日期：2020-11-17 00:00:00

abstract：BACKGROUND:Current development of sequencing technologies is towards generating longer and noisier reads. Evidently, accurate alignment of these reads play an important role in any downstream analysis. Similarly, reducing the overall cost of sequencing is related to the time consumption of the aligner. The tradeoff bet...

journal_title：BMC bioinformatics

authors： Nashta-Ali D,Aliyari A,Ahmadian Moghadam A,Edrisi MA,Motahari SA,Hossein Khalaj B

更新日期：2017-02-23 00:00:00

abstract：BACKGROUND:Kernel-based learning algorithms are among the most advanced machine learning methods and have been successfully applied to a variety of sequence classification tasks within the field of bioinformatics. Conventional kernels utilized so far do not provide an easy interpretation of the learnt representations i...

journal_title：BMC bioinformatics

authors： Meinicke P,Tech M,Morgenstern B,Merkl R

更新日期：2004-10-28 00:00:00

abstract：BACKGROUND:SNP genotyping microarrays have revolutionized the study of complex disease. The current range of commercially available genotyping products contain extensive catalogues of low frequency and rare variants. Existing SNP calling algorithms have difficulty dealing with these low frequency variants, as the under...

journal_title：BMC bioinformatics

authors： Liu R,Dai Z,Yeager M,Irizarry RA,Ritchie ME

更新日期：2014-05-23 00:00:00

abstract：BACKGROUND:Identifying the interactions between proteins and long non-coding RNAs (lncRNAs) is of great importance to decipher the functional mechanisms of lncRNAs. However, current experimental techniques for detection of lncRNA-protein interactions are limited and inefficient. Many methods have been proposed to predi...

journal_title：BMC bioinformatics

authors： Deng L,Wang J,Xiao Y,Wang Z,Liu H

更新日期：2018-10-11 00:00:00

abstract：BACKGROUND:The wide use of high-throughput DNA microarray technology provide an increasingly detailed view of human transcriptome from hundreds to thousands of genes. Although biomedical researchers typically design microarray experiments to explore specific biological contexts, the relationships between genes are hard...

journal_title：BMC bioinformatics

authors： Kong W,Mou X,Hu X

更新日期：2011-01-01 00:00:00

abstract：BACKGROUND:With the ever increasing use of computational models in the biosciences, the need to share models and reproduce the results of published studies efficiently and easily is becoming more important. To this end, various standards have been proposed that can be used to describe models, simulations, data or other...

journal_title：BMC bioinformatics

authors： Bergmann FT,Adams R,Moodie S,Cooper J,Glont M,Golebiewski M,Hucka M,Laibe C,Miller AK,Nickerson DP,Olivier BG,Rodriguez N,Sauro HM,Scharm M,Soiland-Reyes S,Waltemath D,Yvon F,Le Novère N

更新日期：2014-12-14 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:Data extraction and integration methods are becoming essential to effectively access and take advantage of the huge amounts of heterogeneous genomics and clinical data increasingly available. In this work, we focus on The Cancer Genome Atlas, a comprehensive archive of tumoral data containing the results of ...

journal_title：BMC bioinformatics

authors： Cumbo F,Fiscon G,Ceri S,Masseroli M,Weitschek E

更新日期：2017-01-03 00:00:00

abstract：BACKGROUND:A metagenomic sample is a set of DNA fragments, randomly extracted from multiple cells in an environment, belonging to distinct, often unknown species. Unsupervised metagenomic clustering aims at partitioning a metagenomic sample into sets that approximate taxonomic units, without using reference genomes. Si...

journal_title：BMC bioinformatics

authors： Alanko J,Cunial F,Belazzougui D,Mäkinen V

更新日期：2017-03-14 00:00:00

abstract：BACKGROUND:The generation of multiple sequence alignments (MSAs) is a crucial step for many bioinformatic analyses. Thus improving MSA accuracy and identifying potential errors in MSAs is important for a wide range of post-genomic research. We present a novel method called MergeAlign which constructs consensus MSAs fro...

journal_title：BMC bioinformatics

authors： Collingridge PW,Kelly S

更新日期：2012-05-30 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:As a consequence of the evolutionary process, data collected from related species tend to be similar. This similarity by descent can obscure subtler signals in the data such as the evidence of constraint on variation due to shared selective pressures. In comparative sequence analysis, for example, sequence s...

journal_title：BMC bioinformatics

authors： Stone EA,Sidow A

更新日期：2007-06-26 00:00:00

abstract：BACKGROUND:Protein-protein interactions (PPIs) are of great importance in cellular systems of organisms, since they are the basis of cellular structure and function and many essential cellular processes are related to that. Most proteins perform their functions by interacting with other proteins, so predicting PPIs acc...

journal_title：BMC bioinformatics

authors： Liu L,Zhu X,Ma Y,Piao H,Yang Y,Hao X,Fu Y,Wang L,Peng J

更新日期：2020-12-16 00:00:00

abstract：BACKGROUND:Glycation is a one of the post-translational modifications (PTM) where sugar molecules and residues in protein sequences are covalently bonded. It has become one of the clinically important PTM in recent times attributed to many chronic and age related complications. Being a non-enzymatic reaction, it is a g...

journal_title：BMC bioinformatics

authors： Reddy HM,Sharma A,Dehzangi A,Shigemizu D,Chandra AA,Tsunoda T

更新日期：2019-02-04 00:00:00

abstract：BACKGROUND:Biological sequences play a major role in molecular and computational biology. They are studied as information-bearing entities that make up DNA, RNA or proteins. The Sequence Ontology, which is part of the OBO Foundry, contains descriptions and definitions of sequences and their properties. Yet the most bas...

journal_title：BMC bioinformatics

authors： Hoehndorf R,Kelso J,Herre H

更新日期：2009-11-18 00:00:00

abstract：BACKGROUND:Coalescent simulations have proven very useful in many population genetics studies. In order to arrive to meaningful conclusions, it is important that these simulations resemble the process of molecular evolution as much as possible. To date, no single coalescent program is able to simulate codon sequences s...

journal_title：BMC bioinformatics

authors： Arenas M,Posada D

更新日期：2007-11-20 00:00:00

abstract：:Transcript quantification is a long-standing problem in genomics and estimating the relative abundance of alternatively-spliced isoforms from the same transcript is an important special case. Both problems have recently been illuminated by high-throughput RNA sequencing experiments which are quickly generating large a...

journal_title：BMC bioinformatics

authors： Kakaradov B,Xiong HY,Lee LJ,Jojic N,Frey BJ

更新日期：2012-04-19 00:00:00

abstract：BACKGROUND:Two-dimensional electrophoresis (2DE) is one of the most widely applied techniques in comparative proteomics. The basic task of 2DE is to identify differential protein expression by quantitative analysis of 2DE images. To reduce the errors of spot quantification in 2DE images, a novel brightness correction m...

journal_title：BMC bioinformatics

authors： Ou Q,Xiao J,Yu L,Wu K,Xiong B

更新日期：2020-03-19 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:As phenotypic features derived from heritable characters, the topologies of metabolic pathways contain both phylogenetic and phenetic components. In the post-genomic era, it is possible to measure the "phylophenetic" contents of different pathways topologies from a global perspective. RESULTS:We reconstruct...

journal_title：BMC bioinformatics

authors： Zhang Y,Li S,Skogerbø G,Zhang Z,Zhu X,Zhang Z,Sun S,Lu H,Shi B,Chen R

更新日期：2006-05-09 00:00:00

abstract：BACKGROUND:The importance of biodiversity conservation has been increasing steadily due to its benefits to human beings. Recently, producing and managing biodiversity databases have become much easier because of the information technology (IT) advancement. This made the general public's participation in biodiversity co...

journal_title：BMC bioinformatics

authors： Paik IH,Lim J,Chun BS,Jin SD,Yu JP,Lee JW,Bhak J,Paek WK

更新日期：2009-12-03 00:00:00

abstract：BACKGROUND:Microarray technology is commonly used as a simple screening tool with a focus on selecting genes that exhibit extremely large differential expressions between different phenotypes. It lacks the ability to select genes that change their relationships with other genes in different biological conditions (diffe...

journal_title：BMC bioinformatics

authors： Hu R,Qiu X,Glazko G,Klebanov L,Yakovlev A

更新日期：2009-01-15 00:00:00

abstract：BACKGROUND:High-throughput sequencing has rapidly become an essential part of precision cancer medicine. But validating results obtained from analyzing and interpreting genomic data remains a rate-limiting factor. The gold standard, of course, remains manual validation by expert panels, which is not without its weaknes...

journal_title：BMC bioinformatics

authors： Bian X,Zhu B,Wang M,Hu Y,Chen Q,Nguyen C,Hicks B,Meerzaman D

更新日期：2018-11-19 00:00:00

abstract：BACKGROUND:New "next generation" DNA sequencing technologies offer individual researchers the ability to rapidly generate large amounts of genome sequence data at dramatically reduced costs. As a result, a need has arisen for new software tools for storage, management and analysis of genome sequence data. Although bioi...

journal_title：BMC bioinformatics

authors： Duncan S,Sirkanungo R,Miller L,Phillips GJ

更新日期：2010-02-22 00:00:00

abstract：BACKGROUND:Improvements in protein sequence annotation and an increase in the number of annotated protein databases has fueled development of an increasing number of software tools to predict secreted proteins. Six software programs capable of high throughput and employing a wide range of prediction methods, SignalP 3....

journal_title：BMC bioinformatics

authors： Klee EW,Ellis LB

更新日期：2005-10-14 00:00:00

abstract：BACKGROUND:As high-throughput sequencing applications continue to evolve, the rapid growth in quantity and variety of sequence-based data calls for the development of new software libraries and tools for data analysis and visualization. Often, effective use of these tools requires computational skills beyond those of m...

journal_title：BMC bioinformatics

authors： Yousif A,Drou N,Rowe J,Khalfan M,Gunsalus KC

更新日期：2020-06-29 00:00:00

abstract：BACKGROUND:Circular RNAs (circRNAs) are a newly appreciated class of non-coding RNA molecules. Numerous tools have been developed for the detection of circRNAs, however computational tools to perform downstream functional analysis of circRNAs are scarce. RESULTS:We present circRNAprofiler, an R-based computational fra...

journal_title：BMC bioinformatics

authors： Aufiero S,Reckman YJ,Tijsen AJ,Pinto YM,Creemers EE

更新日期：2020-04-29 00:00:00

abstract：BACKGROUND:A wide variety of short-read alignment programmes have been published recently to tackle the problem of mapping millions of short reads to a reference genome, focusing on different aspects of the procedure such as time and memory efficiency, sensitivity, and accuracy. These tools allow for a small number of ...

journal_title：BMC bioinformatics

authors： Alachiotis N,Berger S,Flouri T,Pissis SP,Stamatakis A

更新日期：2013-01-01 00:00:00

abstract：BACKGROUND:Viral infection by dengue virus is a major public health problem in tropical countries. Early diagnosis and detection are increasingly based on quantitative reverse transcriptase real-time polymerase chain reaction (RT-qPCR) directed against genomic regions conserved between different isolates. Genetic varia...

journal_title：BMC bioinformatics

authors： Vanneste K,Garlant L,Broeders S,Van Gucht S,Roosens NH

更新日期：2018-09-04 00:00:00