IDconverter and IDClight: conversion and annotation of gene and protein IDs.

abstract：BACKGROUND:Although metatranscriptomics-the study of diverse microbial population activity based on RNA-seq data-is rapidly growing in popularity, there are limited options for biologists to analyze this type of data. Current approaches for processing metatranscriptomes rely on restricted databases and a dedicated comp...

journal_title：BMC bioinformatics

authors： Westreich ST,Korf I,Mills DA,Lemay DG

更新日期：2016-09-29 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：BACKGROUND:Pattern recognition receptors of the immune system have key roles in the regulation of pathways after the recognition of microbial- and danger-associated molecular patterns in vertebrates. Members of NOD-like receptor (NLR) family typically function intracellularly. The NOD-like receptor family CARD domain c...

journal_title：BMC bioinformatics

authors： Mótyán JA,Bagossi P,Benkő S,Tőzsér J

更新日期：2013-09-17 00:00:00

abstract：BACKGROUND:Finishing is the process of improving the quality and utility of draft genome sequences generated by shotgun sequencing and computational assembly. Finishing can involve targeted sequencing. Finishing reads may be incorporated by manual or automated means. One automated method uses targeted addition by local...

journal_title：BMC bioinformatics

authors： Koren S,Miller JR,Walenz BP,Sutton G

更新日期：2010-09-10 00:00:00

abstract：BACKGROUND:With the growing availability of full-text articles online, scientists and other consumers of the life sciences literature now have the ability to go beyond searching bibliographic records (title, abstract, metadata) to directly access full-text content. Motivated by this emerging trend, I posed the followin...

journal_title：BMC bioinformatics

authors： Lin J

更新日期：2009-02-03 00:00:00

abstract：BACKGROUND:Tumors have been hypothesized to be the result of a mixture of oncogenic events, some of which will be reflected in the gene expression of the tumor. Based on this hypothesis a variety of data-driven methods have been employed to decompose tumor expression profiles into component profiles, hypothetically lin...

journal_title：BMC bioinformatics

authors： van Vliet MH,Wessels LF,Reinders MJ

更新日期：2009-01-30 00:00:00

abstract：BACKGROUND:Eukaryotic whole genome sequences are accumulating at an impressive rate. Effective methods for comparing multiple whole eukaryotic genomes on a large scale are needed. Most attempted solutions involve the production of large scale alignments, and many of these require a high stringency pre-screen for putati...

journal_title：BMC bioinformatics

authors： Stuart GW,Berry MW

更新日期：2004-12-17 00:00:00

abstract：BACKGROUND:Many statistical algorithms combine microarray expression data and genome sequence data to identify transcription factor binding motifs in the low eukaryotic genomes. Finding cis-regulatory elements in higher eukaryote genomes, however, remains a challenge, as searching in the promoter regions of genes with ...

journal_title：BMC bioinformatics

authors： Kim RS,Ji H,Wong WH

更新日期：2006-01-26 00:00:00

abstract：BACKGROUND:MLPA method is a potentially useful semi-quantitative method to detect copy number alterations in targeted regions. In this paper, we propose a method for the normalization procedure based on a non-linear mixed-model, as well as a new approach for determining the statistical significance of altered probes ba...

journal_title：BMC bioinformatics

authors： González JR,Carrasco JL,Armengol L,Villatoro S,Jover L,Yasui Y,Estivill X

更新日期：2008-06-04 00:00:00

abstract：BACKGROUND:Common existing phylogenetic tree visualisation tools are not able to display readable trees with more than a few thousand nodes. These existing methodologies are based in two dimensional space. RESULTS:We introduce the idea of visualising phylogenetic trees in three dimensional hyperbolic space with the Wa...

journal_title：BMC bioinformatics

authors： Hughes T,Hyun Y,Liberles DA

更新日期：2004-04-29 00:00:00

abstract：BACKGROUND:Different human responses to the same vaccine were frequently observed. For example, independent studies identified overlapping but different transcriptomic gene expression profiles in Yellow Fever vaccine 17D (YF-17D) immunized human subjects. Different experimental and analysis conditions were likely contr...

journal_title：BMC bioinformatics

authors： Ong E,Sun P,Berke K,Zheng J,Wu G,He Y

更新日期：2019-12-23 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：BACKGROUND:The number of protein structures from structural genomics centers dramatically increases in the Protein Data Bank (PDB). Many of these structures are functionally unannotated because they have no sequence similarity to proteins of known function. However, it is possible to successfully infer function using o...

journal_title：BMC bioinformatics

authors： von Grotthuss M,Plewczynski D,Ginalski K,Rychlewski L,Shakhnovich EI

更新日期：2006-02-06 00:00:00

abstract：BACKGROUND:Systems biology modeling from microarray data requires the most contemporary structural and functional array annotation. However, microarray annotations, especially for non-commercial, non-traditional biomedical model organisms, are often dated. In addition, most microarray analysis tools do not readily acce...

journal_title：BMC bioinformatics

authors： van den Berg BH,Konieczka JH,McCarthy FM,Burgess SC

更新日期：2009-01-23 00:00:00

abstract：BACKGROUND:Domain fusion analysis is a useful method to predict functionally linked proteins that may be involved in direct protein-protein interactions or in the same metabolic or signaling pathway. As separate domain databases like BLOCKS, PROSITE, Pfam, SMART, PRINTS-S, ProDom, TIGRFAMs, and amalgamated domain datab...

journal_title：BMC bioinformatics

authors： Truong K,Ikura M

更新日期：2003-05-06 00:00:00

abstract：BACKGROUND:Extant genomes share regions where genes have the same order and orientation, which are thought to arise from the conservation of an ancestral order of genes during evolution. Such regions of so-called conserved synteny, or synteny blocks, must be precisely identified and quantified, as a prerequisite to bet...

journal_title：BMC bioinformatics

authors： Lucas JM,Muffato M,Roest Crollius H

更新日期：2014-08-08 00:00:00

abstract：BACKGROUND:MicroRNAs (miRNAs) are a class of endogenous regulatory small RNAs which play an important role in posttranscriptional regulations by targeting mRNAs for cleavage or translational repression. The base-pairing between the 5'-end of miRNA and the target mRNA 3'-UTRs is essential for the miRNA:mRNA recognition....

journal_title：BMC bioinformatics

authors： Gu J,Fu H,Zhang X,Li Y

更新日期：2007-11-08 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：BACKGROUND:Molecular docking is a widely-employed method in structure-based drug design. An essential component of molecular docking programs is a scoring function (SF) that can be used to identify the most stable binding pose of a ligand, when bound to a receptor protein, from among a large set of candidate poses. Des...

journal_title：BMC bioinformatics

authors： Ashtawy HM,Mahapatra NR

更新日期：2015-01-01 00:00:00

abstract：BACKGROUND:Microbial electrosynthesis and electro fermentation are techniques that aim to optimize microbial production of chemicals and fuels by regulating the cellular redox balance via interaction with electrodes. While the concept is known for decades major knowledge gaps remain, which make it hard to evaluate its ...

journal_title：BMC bioinformatics

authors： Kracke F,Krömer JO

更新日期：2014-12-30 00:00:00

abstract：BACKGROUND:The advance of next generation sequencing enables higher throughput with lower price, and as the basic of high-throughput sequencing data analysis, variant calling is widely used in disease research, clinical treatment and medicine research. However, current mainstream variant caller tools have a serious pro...

journal_title：BMC bioinformatics

authors： Xiao A,Wu Z,Dong S

更新日期：2019-02-14 00:00:00

abstract：BACKGROUND:Prostate carcinoma is among the most common types of cancer affecting hundreds of thousands people every year. Once the metastatic form of prostate carcinoma is documented, the majority of patients die from their tumors as opposed to other causes. The key to successful treatment is in the earliest possible d...

journal_title：BMC bioinformatics

authors： Ptitsyn A

更新日期：2009-10-08 00:00:00

abstract：BACKGROUND:Protein-protein docking is a valuable computational approach for investigating protein-protein interactions. Shape complementarity is the most basic component of a scoring function and plays an important role in protein-protein docking. Despite significant progresses, shape representation remains an open que...

journal_title：BMC bioinformatics

authors： Yan Y,Huang SY

更新日期：2019-12-24 00:00:00

abstract：BACKGROUND:Dynamic programming algorithms provide exact solutions to many problems in computational biology, such as sequence alignment, RNA folding, hidden Markov models (HMMs), and scoring of phylogenetic trees. Structurally analogous algorithms compute optimal solutions, evaluate score distributions, and perform sto...

journal_title：BMC bioinformatics

authors： zu Siederdissen CH,Prohaska SJ,Stadler PF

更新日期：2015-01-01 00:00:00

abstract：BACKGROUND:Reliable prediction of antibody, or B-cell, epitopes remains challenging yet highly desirable for the design of vaccines and immunodiagnostics. A correlation between antigenicity, solvent accessibility, and flexibility in proteins was demonstrated. Subsequently, Thornton and colleagues proposed a method for ...

journal_title：BMC bioinformatics

authors： Ponomarenko J,Bui HH,Li W,Fusseder N,Bourne PE,Sette A,Peters B

更新日期：2008-12-02 00:00:00

abstract：BACKGROUND:The ability to detect nuclei in embryos is essential for studying the development of multicellular organisms. A system of automated nuclear detection has already been tested on a set of four-dimensional (4D) Nomarski differential interference contrast (DIC) microscope images of Caenorhabditis elegans embryos...

journal_title：BMC bioinformatics

authors： Hamahashi S,Onami S,Kitano H

更新日期：2005-05-24 00:00:00

abstract：BACKGROUND:Aiming to understand cellular responses to different perturbations, the NIH Common Fund Library of Integrated Network-based Cellular Signatures (LINCS) program involves many institutes and laboratories working on over a thousand cell lines. The community-based Cell Line Ontology (CLO) is selected as the defa...

journal_title：BMC bioinformatics

authors： Ong E,Xie J,Ni Z,Liu Q,Sarntivijai S,Lin Y,Cooper D,Terryn R,Stathias V,Chung C,Schürer S,He Y

更新日期：2017-12-21 00:00:00

abstract：BACKGROUND:Large-scale genomic studies often identify large gene lists, for example, the genes sharing the same expression patterns. The interpretation of these gene lists is generally achieved by extracting concepts overrepresented in the gene lists. This analysis often depends on manual annotation of genes based on c...

journal_title：BMC bioinformatics

authors： He X,Sarma MS,Ling X,Chee B,Zhai C,Schatz B

更新日期：2010-05-20 00:00:00

abstract：BACKGROUND:Study on long non-coding RNAs (lncRNAs) has been promoted by high-throughput RNA sequencing (RNA-Seq). However, it is still not trivial to identify lncRNAs from the RNA-Seq data and it remains a challenge to uncover their functions. RESULTS:We present a computational pipeline for detecting novel lncRNAs fro...

journal_title：BMC bioinformatics

authors： Sun L,Zhang Z,Bailey TL,Perkins AC,Tallack MR,Xu Z,Liu H

更新日期：2012-12-13 00:00:00

abstract：BACKGROUND:In the post-genomic era, systems-level studies are being performed that seek to explain complex biological systems by integrating diverse resources from fields such as genomics, proteomics or transcriptomics. New information management systems are now needed for the collection, validation and analysis of the...

journal_title：BMC bioinformatics

authors： Thompson JD,Muller A,Waterhouse A,Procter J,Barton GJ,Plewniak F,Poch O

更新日期：2006-06-23 00:00:00