The EnzymeTracker: an open-source laboratory information management system for sample tracking.

abstract：BACKGROUND:Bistability and ability to switch between two stable states is the hallmark of cellular responses. Cellular signaling pathways often contain bistable switches that regulate the transmission of the extracellular information to the nucleus where important biological functions are executed. RESULTS:In this wor...

journal_title：BMC bioinformatics

authors： Arkun Y

更新日期：2019-11-28 00:00:00

abstract：BACKGROUND:Despite marked recent improvements in long-read sequencing technology, the assembly of diploid genomes remains a difficult task. A major obstacle is distinguishing between alternative contigs that represent highly heterozygous regions. If primary and secondary contigs are not properly identified, the primary...

journal_title：BMC bioinformatics

authors： Solares EA,Tao Y,Long AD,Gaut BS

更新日期：2021-01-06 00:00:00

abstract：BACKGROUND:The application of high-throughput sequencing in a broad range of quantitative genomic assays (e.g., DNA-seq, ChIP-seq) has created a high demand for the analysis of large-scale read-count data. Typically, the genome is divided into tiling windows and windowed read-count data is generated for the entire geno...

journal_title：BMC bioinformatics

authors： Wang W,Sun W,Wang W,Szatkiewicz J

更新日期：2018-03-01 00:00:00

abstract：BACKGROUND:High throughput DNA/RNA sequencing has revolutionized biological and clinical research. Sequencing is widely used, and generates very large amounts of data, mainly due to reduced cost and advanced technologies. Quickly assessing the quality of giga-to-tera base levels of sequencing data has become a routine ...

journal_title：BMC bioinformatics

authors： Chanumolu SK,Albahrani M,Otu HH

更新日期：2019-08-15 00:00:00

abstract：BACKGROUND:The analysis of DNA copy number variants (CNV) has increasing impact in the field of genetic diagnostics and research. However, the interpretation of CNV data derived from high resolution array CGH or NGS platforms is complicated by the considerable variability of the human genome. Therefore, tools for multi...

journal_title：BMC bioinformatics

authors： Tebel K,Boldt V,Steininger A,Port M,Ebert G,Ullmann R

更新日期：2017-01-06 00:00:00

abstract：BACKGROUND:It has been proposed that future reference genomes should be graph structures in order to better represent the sequence diversity present in a species. However, there is currently no standard method to represent genomic intervals, such as the positions of genes or transcription factor binding sites, on graph...

journal_title：BMC bioinformatics

authors： Rand KD,Grytten I,Nederbragt AJ,Storvik GO,Glad IK,Sandve GK

更新日期：2017-05-18 00:00:00

abstract：BACKGROUND:The knowledge base-driven pathway analysis is becoming the first choice for many investigators, in that it not only can reduce the complexity of functional analysis by grouping thousands of genes into just several hundred pathways, but also can increase the explanatory power for the experiment by identifying...

journal_title：BMC bioinformatics

authors： Du J,Li M,Yuan Z,Guo M,Song J,Xie X,Chen Y

更新日期：2016-10-06 00:00:00

abstract：BACKGROUND:RNA-Seq is revolutionizing the way transcript abundances are measured. A key challenge in transcript quantification from RNA-Seq data is the handling of reads that map to multiple genes or isoforms. This issue is particularly important for quantification with de novo transcriptome assemblies in the absence o...

journal_title：BMC bioinformatics

authors： Li B,Dewey CN

更新日期：2011-08-04 00:00:00

abstract：BACKGROUND:The BioCreative text mining evaluation investigated the application of text mining methods to the task of automatically extracting information from text in biomedical research articles. We participated in Task 2 of the evaluation. For this task, we built a system to automatically annotate a given protein wit...

journal_title：BMC bioinformatics

authors： Ray S,Craven M

更新日期：2005-01-01 00:00:00

abstract：BACKGROUND:We carried out an analysis of intron length conservation across a diverse group of nineteen mammalian species. Motivated by recent research suggesting a role for time delays associated with intron transcription in gene expression oscillations required for early embryonic patterning, we searched for examples ...

journal_title：BMC bioinformatics

authors： Seoighe C,Korir PK

更新日期：2011-10-05 00:00:00

abstract：BACKGROUND:With the growing availability of entire genome sequences, an increasing number of scientists can exploit oligonucleotide microarrays for genome-scale expression studies. While probe-design is a major research area, relatively little work has been reported on the optimization of microarray protocols. RESULTS...

journal_title：BMC bioinformatics

authors： Sykacek P,Kreil DP,Meadows LA,Auburn RP,Fischer B,Russell S,Micklem G

更新日期：2011-03-14 00:00:00

abstract：BACKGROUND:The analysis of sequence-structure relations of RNA is based on a specific notion and folding of RNA structure. The notion of coarse grained structure employed here is that of canonical RNA pseudoknot contact-structures with at most two mutually crossing bonds (3-noncrossing). These structures are folded by ...

journal_title：BMC bioinformatics

authors： Huang FW,Li LY,Reidys CM

更新日期：2009-01-30 00:00:00

abstract：BACKGROUND:Pattern matching is the core of bioinformatics; it is used in database searching, restriction enzyme mapping, and finding open reading frames. It is done repeatedly over increasingly long sequences, thus codes must be efficient and insensitive to sequence length. Such patterns of interest include simple moti...

journal_title：BMC bioinformatics

authors： Mangalam HJ

更新日期：2002-01-01 00:00:00

abstract：BACKGROUND:Biological data that are well-organized by an ontology, such as Gene Ontology, enables high-throughput availability of the semantic web. It can also be used to facilitate high throughput classification of biomedical information. However, to our knowledge, no evaluation has been published on automating classi...

journal_title：BMC bioinformatics

authors： Chen JL,Liu Y,Sam LT,Li J,Lussier YA

更新日期：2007-05-09 00:00:00

abstract：BACKGROUND:With continuing identification of novel structured noncoding RNAs, there is an increasing need to create schematic diagrams showing the consensus features of these molecules. RNA structural diagrams are typically made either with general-purpose drawing programs like Adobe Illustrator, or with automated or i...

journal_title：BMC bioinformatics

authors： Weinberg Z,Breaker RR

更新日期：2011-01-04 00:00:00

abstract：BACKGROUND:Enrichment analysis is a popular approach to identify pathways or sets of genes which are significantly enriched in the context of differentially expressed genes. The traditional gene set enrichment approach considers a pathway as a simple gene list disregarding any knowledge of gene or protein interactions....

journal_title：BMC bioinformatics

authors： Bayerlová M,Jung K,Kramer F,Klemm F,Bleckmann A,Beißbarth T

更新日期：2015-10-22 00:00:00

abstract：BACKGROUND:Membrane transport proteins (transporters) play an essential role in every living cell by transporting hydrophilic molecules across the hydrophobic membranes. While the sequences of many membrane proteins are known, their structure and function is still not well characterized and understood, owing to the imm...

journal_title：BMC bioinformatics

authors： Alballa M,Butler G

更新日期：2020-04-23 00:00:00

abstract：BACKGROUND:The creation of a complete genome-wide map of transcription factor binding sites is essential for understanding gene regulatory networks in vivo. However, current prediction methods generally rely on statistical models that imperfectly model transcription factor binding. Generation of new prediction methods ...

journal_title：BMC bioinformatics

authors： Hill JT,Anderson KR,Mastracci TL,Kaestner KH,Sussel L

更新日期：2011-02-25 00:00:00

abstract：BACKGROUND:Whole exome sequencing (WES) has become the strategy of choice to identify a coding allelic variant for a rare human monogenic disorder. This approach is a revolution in medical genetics history, impacting both fundamental research, and diagnostic methods leading to personalized medicine. A plethora of effic...

journal_title：BMC bioinformatics

authors： Coutant S,Cabot C,Lefebvre A,Léonard M,Prieur-Gaston E,Campion D,Lecroq T,Dauchel H

更新日期：2012-01-01 00:00:00

abstract：BACKGROUND:Parsimony and maximum likelihood methods of phylogenetic tree estimation and parsimony methods for genome rearrangements are central to the study of genome evolution yet to date they have largely been pursued in isolation. RESULTS:We present a data structure called a history graph that offers a practical ba...

journal_title：BMC bioinformatics

authors： Paten B,Zerbino DR,Hickey G,Haussler D

更新日期：2014-06-19 00:00:00

abstract：BACKGROUND:In recent years, substantial effort has been applied to de novo regulatory motif discovery. At this time, more than 150 software tools exist to detect regulatory binding sites given a set of genomic sequences. As the number of software packages increases, it becomes more important to identify the tools with ...

journal_title：BMC bioinformatics

authors： Quest D,Dempsey K,Shafiullah M,Bastola D,Ali H

更新日期：2008-08-12 00:00:00

abstract：BACKGROUND:Mass spectrometry based peptide mass fingerprints (PMFs) offer a fast, efficient, and robust method for protein identification. A protein is digested (usually by trypsin) and its mass spectrum is compared to simulated spectra for protein sequences in a database. However, existing tools for analyzing PMFs oft...

journal_title：BMC bioinformatics

authors： Kaltenbach HM,Wilke A,Böcker S

更新日期：2007-03-26 00:00:00

abstract：BACKGROUND:The amount of gene expression data available in public repositories has grown exponentially in the last years, now requiring new data mining tools to transform them in information easily accessible to biologists. RESULTS:By exploiting expression data publicly available in the Gene Expression Omnibus (GEO) d...

journal_title：BMC bioinformatics

authors： Cremaschi P,Rovida S,Sacchi L,Lisa A,Calvi F,Montecucco A,Biamonti G,Bione S,Sacchi G

更新日期：2014-01-01 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:The goal of class prediction studies is to develop rules to accurately predict the class membership of new samples. The rules are derived using the values of the variables available for each subject: the main characteristic of high-dimensional data is that the number of variables greatly exceeds the number o...

journal_title：BMC bioinformatics

authors： Blagus R,Lusa L

更新日期：2010-10-20 00:00:00

abstract：BACKGROUND:Protein-protein interactions (PPIs) can offer compelling evidence for protein function, especially when viewed in the context of proteome-wide interactomes. Bacteria have been popular subjects of interactome studies: more than six different bacterial species have been the subjects of comprehensive interactom...

journal_title：BMC bioinformatics

authors： Caufield JH,Wimble C,Shary S,Wuchty S,Uetz P

更新日期：2017-03-16 00:00:00

abstract：BACKGROUND:Mouse xenografts from (patient-derived) tumors (PDX) or tumor cell lines are widely used as models to study various biological and preclinical aspects of cancer. However, analyses of their RNA and DNA profiles are challenging, because they comprise reads not only from the grafted human cancer but also from t...

journal_title：BMC bioinformatics

authors： Kluin RJC,Kemper K,Kuilman T,de Ruiter JR,Iyer V,Forment JV,Cornelissen-Steijger P,de Rink I,Ter Brugge P,Song JY,Klarenbeek S,McDermott U,Jonkers J,Velds A,Adams DJ,Peeper DS,Krijgsman O

更新日期：2018-10-04 00:00:00

abstract：BACKGROUND:Regulation of gene expression, protein synthesis, replication and assembly of many viruses involve RNA-protein interactions. Although some successful computational tools have been reported to recognize RNA binding sites in proteins, the problem of specificity remains poorly investigated. After the nucleotide...

journal_title：BMC bioinformatics

authors： Fernandez M,Kumagai Y,Standley DM,Sarai A,Mizuguchi K,Ahmad S

更新日期：2011-01-01 00:00:00

abstract：BACKGROUND:In the analysis of networks we frequently require the statistical significance of some network statistic, such as measures of similarity for the properties of interacting nodes. The structure of the network may introduce dependencies among the nodes and it will in general be necessary to account for these de...

journal_title：BMC bioinformatics

authors： Thorne T,Stumpf MP

更新日期：2007-11-30 00:00:00

abstract：BACKGROUND:Microarray technology allows the analysis of genomic aberrations at an ever increasing resolution, making functional interpretation of these vast amounts of data the main bottleneck in routine implementation of high resolution array platforms, and emphasising the need for a centralised and easy to use CNV da...

journal_title：BMC bioinformatics

authors： Vandeweyer G,Reyniers E,Wuyts W,Rooms L,Kooy RF

更新日期：2011-01-05 00:00:00