ProLego: tool for extracting and visualizing topological modules in protein structures.

abstract：BACKGROUND:RNA-Sequencing (RNA-seq) experiments have been popularly applied to transcriptome studies in recent years. Such experiments are still relatively costly. As a result, RNA-seq experiments often employ a small number of replicates. Power analysis and sample size calculation are challenging in the context of dif...

journal_title：BMC bioinformatics

authors： Bi R,Liu P

更新日期：2016-03-31 00:00:00

abstract：BACKGROUND:S-glutathionylation is the formation of disulfide bonds between the tripeptide glutathione and cysteine residues of the protein, protecting them from irreversible oxidation and in some cases causing change in their functions. Regulatory glutathionylation of proteins is a controllable and reversible process a...

journal_title：BMC bioinformatics

authors： Anashkina AA,Poluektov YM,Dmitriev VA,Kuznetsov EN,Mitkevich VA,Makarov AA,Petrushanko IY

更新日期：2020-09-14 00:00:00

abstract：BACKGROUND:A common method for presenting and studying biological interaction networks is visualization. Software tools can enhance our ability to explore network visualizations and improve our understanding of biological systems, particularly when these tools offer analysis capabilities. However, most published networ...

journal_title：BMC bioinformatics

authors： Macpherson JI,Pinney JW,Robertson DL

更新日期：2009-03-26 00:00:00

abstract：BACKGROUND:Microorganisms display vast diversity, and each one has its own set of genes, cell components and metabolic reactions. To assess their huge unexploited metabolic potential in different ecosystems, we need high throughput tools, such as functional microarrays, that allow the simultaneous analysis of thousands...

journal_title：BMC bioinformatics

authors： Terrat S,Peyretaillade E,Gonçalves O,Dugat-Bony E,Gravelat F,Moné A,Biderre-Petit C,Boucher D,Troquet J,Peyret P

更新日期：2010-09-23 00:00:00

abstract：BACKGROUND:Transposable elements (TE) are mobile genetic entities present in nearly all genomes. Previous work has shown that TEs tend to have a different nucleotide composition than the host genes, either considering codon usage bias or dinucleotide frequencies. We show here how these compositional differences can be ...

journal_title：BMC bioinformatics

authors： Andrieu O,Fiston AS,Anxolabéhère D,Quesneville H

更新日期：2004-07-13 00:00:00

abstract：BACKGROUND:RNA sequencing has become an increasingly affordable way to profile gene expression patterns. Here we introduce a workflow implementing several open-source softwares that can be run on a high performance computing environment. RESULTS:Developed as a tool by the Bioinformatics Shared Resource Group (BISR) at...

journal_title：BMC bioinformatics

authors： Gadepalli VS,Ozer HG,Yilmaz AS,Pietrzak M,Webb A

更新日期：2019-12-20 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:The scientific literature contains millions of microbial gene identifiers within the full text and tables, but these annotations rarely get incorporated into public sequence databases. We propose to utilize the Open Access (OA) subset of PubMed Central (PMC) as a gene annotation database and have developed a...

journal_title：BMC bioinformatics

authors： Stubben CJ,Challacombe JF

更新日期：2014-02-05 00:00:00

abstract：BACKGROUND:Numerous functional genomics approaches have been developed to study the model organism yeast, Saccharomyces cerevisiae, with the aim of systematically understanding the biology of the cell. Some of these techniques are based on yeast growth differences under different conditions, such as those generated by ...

journal_title：BMC bioinformatics

authors： Memarian N,Jessulat M,Alirezaie J,Mir-Rashed N,Xu J,Zareie M,Smith M,Golshani A

更新日期：2007-04-04 00:00:00

abstract：BACKGROUND:Microarrays permit biologists to simultaneously measure the mRNA abundance of thousands of genes. An important issue facing investigators planning microarray experiments is how to estimate the sample size required for good statistical power. What is the projected sample size or number of replicate chips need...

journal_title：BMC bioinformatics

authors： Page GP,Edwards JW,Gadbury GL,Yelisetti P,Wang J,Trivedi P,Allison DB

更新日期：2006-02-22 00:00:00

abstract：BACKGROUND:Accurate annotation of translation initiation sites (TISs) is essential for understanding the translation initiation mechanism. However, the reliability of TIS annotation in widely used databases such as RefSeq is uncertain due to the lack of experimental benchmarks. RESULTS:Based on a homogeneity assumptio...

journal_title：BMC bioinformatics

authors： Hu GQ,Zheng X,Ju LN,Zhu H,She ZS

更新日期：2008-03-25 00:00:00

abstract：BACKGROUND:Biomedical research projects deal with data management requirements from multiple sources like funding agencies' guidelines, publisher policies, discipline best practices, and their own users' needs. We describe functional and quality requirements based on many years of experience implementing data managemen...

journal_title：BMC bioinformatics

authors： Suhr M,Lehmann C,Bauer CR,Bender T,Knopp C,Freckmann L,Öst Hansen B,Henke C,Aschenbrandt G,Kühlborn LK,Rheinländer S,Weber L,Marzec B,Hellkamp M,Wieder P,Sax U,Kusch H,Nussbeck SY

更新日期：2020-12-17 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: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:Mecp2 null mice model Rett syndrome (RTT) a human neurological disorder affecting females after apparent normal pre- and peri-natal developmental periods. Neuroanatomical studies in cerebral cortex of RTT mouse models revealed delayed maturation of neuronal morphology and autonomous as well as non-cell auton...

journal_title：BMC bioinformatics

authors： Vacca M,Tripathi KP,Speranza L,Aiese Cigliano R,Scalabrì F,Marracino F,Madonna M,Sanseverino W,Perrone-Capano C,Guarracino MR,D'Esposito M

更新日期：2016-01-20 00:00:00

abstract：BACKGROUND:Clustering techniques are routinely used in gene expression data analysis to organize the massive data. Clustering techniques arrange a large number of genes or assays into a few clusters while maximizing the intra-cluster similarity and inter-cluster separation. While clustering of genes facilitates learnin...

journal_title：BMC bioinformatics

authors： Jonnalagadda S,Srinivasan R

更新日期：2009-01-30 00:00:00

abstract：BACKGROUND:The abundant data available for protein interaction networks have not yet been fully understood. New types of analyses are needed to reveal organizational principles of these networks to investigate the details of functional and regulatory clusters of proteins. RESULTS:In the present work, individual cluste...

journal_title：BMC bioinformatics

authors： Sen TZ,Kloczkowski A,Jernigan RL

更新日期：2006-07-24 00:00:00

abstract：BACKGROUND:The identification of a consensus RNA motif often consists in finding a conserved secondary structure with minimum free energy in an ensemble of aligned sequences. However, an alignment is often difficult to obtain without prior structural information. Thus the need for tools to automate this process. RESUL...

journal_title：BMC bioinformatics

authors： Anwar M,Nguyen T,Turcotte M

更新日期：2006-05-05 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:The classification of cancer subtypes is of great importance to cancer disease diagnosis and therapy. Many supervised learning approaches have been applied to cancer subtype classification in the past few years, especially of deep learning based approaches. Recently, the deep forest model has been proposed a...

journal_title：BMC bioinformatics

authors： Guo Y,Liu S,Li Z,Shang X

更新日期：2018-04-11 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:Recently, mass spectrometry data have been mined using a genetic algorithm to produce discriminatory models that distinguish healthy individuals from those with cancer. This algorithm is the basis for claims of 100% sensitivity and specificity in two related publicly available datasets. To date, no detailed ...

journal_title：BMC bioinformatics

authors： Jeffries NO

更新日期：2004-11-19 00:00:00

abstract：:Complexes of physically interacting proteins are one of the fundamental functional units responsible for driving key biological mechanisms within the cell. With the advent of high-throughput techniques, significant amount of protein interaction (PPI) data has been catalogued for organisms such as yeast, which has in t...

journal_title：BMC bioinformatics

authors： Srihari S,Leong HW

更新日期：2012-01-01 00:00:00

abstract：BACKGROUND:Most state-of-the-art biomedical entity normalization systems, such as rule-based systems, merely rely on morphological information of entity mentions, but rarely consider their semantic information. In this paper, we introduce a novel convolutional neural network (CNN) architecture that regards biomedical e...

journal_title：BMC bioinformatics

authors： Li H,Chen Q,Tang B,Wang X,Xu H,Wang B,Huang D

更新日期：2017-10-03 00:00:00

abstract：BACKGROUND:In bioinformatics community, many tasks associate with matching a set of protein query sequences in large sequence datasets. To conduct multiple queries in the database, a common used method is to run BLAST on each original querey or on the concatenated queries. It is inefficient since it doesn't exploit the...

journal_title：BMC bioinformatics

authors： Ge H,Sun L,Yu J

更新日期：2017-11-21 00:00:00

abstract：BACKGROUND:The organization of the canonical code has intrigued researches since it was first described. If we consider all codes mapping the 64 codes into 20 amino acids and one stop codon, there are more than 1.51×10(84) possible genetic codes. The main question related to the organization of the genetic code is why ...

journal_title：BMC bioinformatics

authors： de Oliveira LL,de Oliveira PS,Tinós R

更新日期：2015-02-19 00:00:00

abstract：BACKGROUND:A relevant problem in drug design is the comparison and recognition of protein binding sites. Binding sites recognition is generally based on geometry often combined with physico-chemical properties of the site since the conformation, size and chemical composition of the protein surface are all relevant for ...

journal_title：BMC bioinformatics

authors： Bertolazzi P,Guerra C,Liuzzi G

更新日期：2010-09-29 00:00:00

abstract：BACKGROUND:Microarray technology provides an efficient means for globally exploring physiological processes governed by the coordinated expression of multiple genes. However, identification of genes differentially expressed in microarray experiments is challenging because of their potentially high type I error rate. Me...

journal_title：BMC bioinformatics

authors： Tan YD,Fornage M,Xu H

更新日期：2008-03-06 00:00:00

abstract：BACKGROUND:Selective pressures at the DNA level shape genes into profiles consisting of patterns of rapidly evolving sites and sites withstanding change. These profiles remain detectable even when protein sequences become extensively diverged. A common task in molecular biology is to infer functional, structural or evo...

journal_title：BMC bioinformatics

authors： Ndhlovu A,Hazelhurst S,Durand PM

更新日期：2015-08-14 00:00:00

abstract：BACKGROUND:The immune system is multifaceted, structured by diverse components that interconnect using multilayered dynamic cellular processes. Genomic technologies provide a means for investigating, at the molecular level, the adaptations of the immune system in host defense and its dysregulation in pathological condi...

journal_title：BMC bioinformatics

authors： Liu H,Liu J,Toups M,Soos T,Arendt C

更新日期：2016-04-18 00:00:00