Information extraction from full text scientific articles: where are the keywords?

abstract：BACKGROUND:Elucidating gene regulatory networks is crucial for understanding normal cell physiology and complex pathologic phenotypes. Existing computational methods for the genome-wide "reverse engineering" of such networks have been successful only for lower eukaryotes with simple genomes. Here we present ARACNE, a n...

journal_title：BMC bioinformatics

authors： Margolin AA,Nemenman I,Basso K,Wiggins C,Stolovitzky G,Dalla Favera R,Califano A

更新日期：2006-03-20 00:00:00

abstract：BACKGROUND:Clustering of protein sequences is of key importance in predicting the structure and function of newly sequenced proteins and is also of use for their annotation. With the advent of multiple high-throughput sequencing technologies, new protein sequences are becoming available at an extraordinary rate. The ra...

journal_title：BMC bioinformatics

authors： Abnousi A,Broschat SL,Kalyanaraman A

更新日期：2018-03-05 00:00:00

abstract：BACKGROUND:A phylogeny is the evolutionary history of a group of organisms. To date, sequence data is still the most used data type for phylogenetic reconstruction. Before any sequences can be used for phylogeny reconstruction, they must be aligned, and the quality of the multiple sequence alignment has been shown to a...

journal_title：BMC bioinformatics

authors： Yue F,Shi J,Tang J

更新日期：2009-01-30 00:00:00

abstract：BACKGROUND:Visualization tools for deep learning models typically focus on discovering key input features without considering how such low level features are combined in intermediate layers to make decisions. Moreover, many of these methods examine a network's response to specific input examples that may be insufficien...

journal_title：BMC bioinformatics

authors： Liu G,Zeng H,Gifford DK

更新日期：2019-07-19 00:00:00

abstract：:Time course gene expression experiments are a popular means to infer co-expression. Many methods have been proposed to cluster genes or to build networks based on similarity measures of their expression dynamics. In this paper we apply a correlation based approach to network reconstruction to three datasets of time se...

journal_title：BMC bioinformatics

authors： Neretti N,Remondini D,Tatar M,Sedivy JM,Pierini M,Mazzatti D,Powell J,Franceschi C,Castellani GC

更新日期：2007-03-08 00:00:00

abstract：BACKGROUND:Metabolomics, petroleum and biodiesel chemistry, biomarker discovery, and other fields which rely on high-resolution profiling of complex chemical mixtures generate datasets which contain millions of detector intensity readings, each uniquely addressed along dimensions of time (e.g., retention time of chemic...

journal_title：BMC bioinformatics

authors： Chae M,Shmookler Reis RJ,Thaden JJ

更新日期：2008-08-12 00:00:00

abstract：BACKGROUND:Adapter trimming is a prerequisite step for analyzing next-generation sequencing (NGS) data when the reads are longer than the target DNA/RNA fragments. Although typically used in small RNA sequencing, adapter trimming is also used widely in other applications, such as genome DNA sequencing and transcriptome...

journal_title：BMC bioinformatics

authors： Jiang H,Lei R,Ding SW,Zhu S

更新日期：2014-06-12 00:00:00

abstract：BACKGROUND:Gene function annotations, which are associations between a gene and a term of a controlled vocabulary describing gene functional features, are of paramount importance in modern biology. Datasets of these annotations, such as the ones provided by the Gene Ontology Consortium, are used to design novel biologi...

journal_title：BMC bioinformatics

authors： Pinoli P,Chicco D,Masseroli M

更新日期：2015-01-01 00:00:00

abstract：BACKGROUND:Identifying key components in biological processes and their associations is critical for deciphering cellular functions. Recently, numerous gene expression and molecular interaction experiments have been reported in Saccharomyces cerevisiae, and these have enabled systematic studies. Although a number of ap...

journal_title：BMC bioinformatics

authors： Hsu JT,Peng CH,Hsieh WP,Lan CY,Tang CY

更新日期：2011-07-12 00:00:00

abstract：BACKGROUND:DNA microarrays offer motivation and hope for the simultaneous study of variations in multiple genes. Gene expression is a temporal process that allows variations in expression levels with a characterized gene function over a period of time. Temporal gene expression curves can be treated as functional data s...

journal_title：BMC bioinformatics

authors： Kim J,Kim H

更新日期：2017-10-12 00:00:00

abstract：BACKGROUND:Time-lapse analysis of cellular images is an important and growing need in biology. Algorithms for cell tracking are widely available; what researchers have been missing is a single open-source software package to visualize standard tracking output (from software like CellProfiler) in a way that allows conve...

journal_title：BMC bioinformatics

authors： Bray MA,Carpenter AE

更新日期：2015-11-04 00:00:00

abstract：BACKGROUND:Linkage disequilibrium (LD)-the non-random association of alleles at different loci-defines population-specific haplotypes which vary by genomic ancestry. Assessment of allelic frequencies and LD patterns from a variety of ancestral populations enables researchers to better understand population histories as...

journal_title：BMC bioinformatics

authors： Alexander TA,Machiela MJ

更新日期：2020-01-10 00:00:00

abstract：BACKGROUND:A massive amount of proteomic data is generated on a daily basis, nonetheless annotating all sequences is costly and often unfeasible. As a countermeasure, machine learning methods have been used to automatically annotate new protein functions. More specifically, many studies have investigated hierarchical m...

journal_title：BMC bioinformatics

authors： Nakano FK,Lietaert M,Vens C

更新日期：2019-09-23 00:00:00

abstract：BACKGROUND:Amino acids in proteins are not used equally. Some of the differences in the amino acid composition of proteins are between species (mainly due to nucleotide composition and lifestyle) and some are between proteins from the same species (related to protein function, expression or subcellular localization, fo...

journal_title：BMC bioinformatics

authors： Pasamontes A,Garcia-Vallve S

更新日期：2006-05-18 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: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:Human breast cancer resistance protein (BCRP) is an ATP-binding cassette (ABC) efflux transporter that confers multidrug resistance in cancers and also plays an important role in the absorption, distribution and elimination of drugs. Prediction as to if drugs or new molecular entities are BCRP substrates sho...

journal_title：BMC bioinformatics

authors： Hazai E,Hazai I,Ragueneau-Majlessi I,Chung SP,Bikadi Z,Mao Q

更新日期：2013-04-15 00:00:00

abstract：BACKGROUND:A large effort to discover microRNAs (miRNAs) has been under way. Currently miRBase is their primary repository, providing annotations of primary sequences, precursors and probable genomic loci. In many cases miRNAs are identical or very similar between related (or in some cases more distant) species. Howeve...

journal_title：BMC bioinformatics

authors： Guerra-Assunção JA,Enright AJ

更新日期：2010-03-16 00:00:00

abstract：BACKGROUND:Genome and metagenome studies have identified thousands of protein families whose functions are poorly understood and for which techniques for functional characterization provide only partial information. For such proteins, the genome context can give further information about their functional context. RESU...

journal_title：BMC bioinformatics

authors： Konietzny SG,Dietz L,McHardy AC

更新日期：2011-05-09 00:00:00

abstract：BACKGROUND:Protein subcellular localization is an important determinant of protein function and hence, reliable methods for prediction of localization are needed. A number of prediction algorithms have been developed based on amino acid compositions or on the N-terminal characteristics (signal peptides) of proteins. Ho...

journal_title：BMC bioinformatics

authors： Sarda D,Chua GH,Li KB,Krishnan A

更新日期：2005-06-17 00:00:00

abstract：BACKGROUND:Nearly all cellular processes involve proteins structurally rearranging to accommodate molecular partners. The energy landscape underscores the inherent nature of proteins as dynamic molecules interconverting between structures with varying energies. In principle, reconstructing a protein's energy landscape ...

journal_title：BMC bioinformatics

authors： Morris D,Maximova T,Plaku E,Shehu A

更新日期：2019-06-06 00:00:00

abstract：BACKGROUND:Accurate somatic mutation-calling is essential for insightful mutation analyses in cancer studies. Several mutation-callers are publicly available and more are likely to appear. Nonetheless, mutation-calling is still challenging and there is unlikely to be one established caller that systematically outperfor...

journal_title：BMC bioinformatics

authors： Kim SY,Jacob L,Speed TP

更新日期：2014-05-21 00:00:00

abstract：BACKGROUND:Time course microarray profiles examine the expression of genes over a time domain. They are necessary in order to determine the complete set of genes that are dynamically expressed under given conditions, and to determine the interaction between these genes. Because of cost and resource issues, most time se...

journal_title：BMC bioinformatics

authors： Sinha A,Markatou M

更新日期：2011-01-11 00:00:00

abstract：BACKGROUND:Protein domains coordinate to perform multifaceted cellular functions, and domain combinations serve as the functional building blocks of the cell. The available methods to identify functional domain combinations are limited in their scope, e.g. to the identification of combinations falling within individual...

journal_title：BMC bioinformatics

authors： McLaughlin WA,Chen K,Hou T,Wang W

更新日期：2007-10-16 00:00:00

abstract：BACKGROUND:This study addresses a recurrent biological problem, that is to define a formal clustering structure for a set of tissues on the basis of the relative abundance of multiple alternatively spliced isoforms mRNAs generated by the same gene. To this aim, we have used a model-based clustering approach, based on a...

journal_title：BMC bioinformatics

authors： Pelosi M,Alfò M,Martella F,Pappalardo E,Musarò A

更新日期：2015-09-15 00:00:00

abstract：BACKGROUND:Ontology term labels can be ambiguous and have multiple senses. While this is no problem for human annotators, it is a challenge to automated methods, which identify ontology terms in text. Classical approaches to word sense disambiguation use co-occurring words or terms. However, most treat ontologies as si...

journal_title：BMC bioinformatics

authors： Alexopoulou D,Andreopoulos B,Dietze H,Doms A,Gandon F,Hakenberg J,Khelif K,Schroeder M,Wächter T

更新日期：2009-01-21 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:One approach to improving the personalized treatment of cancer is to understand the cellular signaling transduction pathways that cause cancer at the level of the individual patient. In this study, we used unsupervised deep learning to learn the hierarchical structure within cancer gene expression data. Deep...

journal_title：BMC bioinformatics

authors： Young JD,Cai C,Lu X

更新日期：2017-10-03 00:00:00

abstract：BACKGROUND:Periodogram analysis of time-series is widespread in biology. A new challenge for analyzing the microarray time series data is to identify genes that are periodically expressed. Such challenge occurs due to the fact that the observed time series usually exhibit non-idealities, such as noise, short length, an...

journal_title：BMC bioinformatics

authors： Liew AW,Xian J,Wu S,Smith D,Yan H

更新日期：2007-04-24 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