FIGENIX: intelligent automation of genomic annotation: expertise integration in a new software platform.

abstract：BACKGROUND:The third edition of the BioNLP Shared Task was held with the grand theme "knowledge base construction (KB)". The Genia Event (GE) task was re-designed and implemented in light of this theme. For its final report, the participating systems were evaluated from a perspective of annotation. To further explore t...

journal_title：BMC bioinformatics

authors： Kim JD,Kim JJ,Han X,Rebholz-Schuhmann D

更新日期：2015-01-01 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：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：BACKGROUND:Annotations of the phylogenetic tree of the human kinome is an intuitive way to visualize compound profiling data, structural features of kinases or functional relationships within this important class of proteins. The increasing volume and complexity of kinase-related data underlines the need for a tool tha...

journal_title：BMC bioinformatics

authors： Eid S,Turk S,Volkamer A,Rippmann F,Fulle S

更新日期：2017-01-05 00:00:00

abstract：BACKGROUND:Direct in vivo investigation of human metabolism is complicated by the distinct metabolic functions of various sub-cellular organelles. Diverse micro-environments in different organelles may lead to distinct functions of the same protein and the use of different enzymes for the same metabolic reaction. To be...

journal_title：BMC bioinformatics

authors： Hao T,Ma HW,Zhao XM,Goryanin I

更新日期：2010-07-22 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:Eisenia fetida, commonly known as red wiggler or compost worm, belongs to the Lumbricidae family of the Annelida phylum. Little is known about its genome sequence although it has been extensively used as a test organism in terrestrial ecotoxicology. In order to understand its gene expression response to envi...

journal_title：BMC bioinformatics

authors： Pirooznia M,Gong P,Guan X,Inouye LS,Yang K,Perkins EJ,Deng Y

更新日期：2007-11-01 00:00:00

abstract：BACKGROUND:While technological advances have made it possible to profile the immune system at high resolution, translating high-throughput data into knowledge of immune mechanisms has been challenged by the complexity of the interactions underlying immune processes. Tools to explore the immune network are critical for ...

journal_title：BMC bioinformatics

authors： Atallah MB,Tandon V,Hiam KJ,Boyce H,Hori M,Atallah W,Spitzer MH,Engleman E,Mallick P

更新日期：2020-08-10 00:00:00

abstract：BACKGROUND:Journal articles and databases are two major modes of communication in the biological sciences, and thus integrating these critical resources is of urgent importance to increase the pace of discovery. Projects focused on bridging the gap between journals and databases have been on the rise over the last five...

journal_title：BMC bioinformatics

authors： Rangarajan A,Schedl T,Yook K,Chan J,Haenel S,Otis L,Faelten S,DePellegrin-Connelly T,Isaacson R,Skrzypek MS,Marygold SJ,Stefancsik R,Cherry JM,Sternberg PW,Müller HM

更新日期：2011-05-19 00:00:00

abstract：BACKGROUND:The field of protein sequence analysis is dominated by tools rooted in substitution matrices and alignments. A complementary approach is provided by methods of quantitative characterization. A major advantage of the approach is that quantitative properties defines a multidimensional solution space, where seq...

journal_title：BMC bioinformatics

authors： Konopka BM,Marciniak M,Dyrka W

更新日期：2017-07-17 00:00:00

abstract：BACKGROUND:Evolutionary trees are central to a wide range of biological studies. In many of these studies, tree nodes and branches need to be associated (or annotated) with various attributes. For example, in studies concerned with organismal relationships, tree nodes are associated with taxonomic names, whereas tree b...

journal_title：BMC bioinformatics

authors： Han MV,Zmasek CM

更新日期：2009-10-27 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: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: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:Alternative splicing is the critical process in a single gene coding, which removes introns and joins exons, and splicing branchpoints are indicators for the alternative splicing. Wet experiments have identified a great number of human splicing branchpoints, but many branchpoints are still unknown. In order ...

journal_title：BMC bioinformatics

authors： Zhang W,Zhu X,Fu Y,Tsuji J,Weng Z

更新日期：2017-12-01 00:00:00

abstract：BACKGROUND:Several studies demonstrated the feasibility of predicting bacterial antibiotic resistance phenotypes from whole-genome sequences, the prediction process usually amounting to detecting the presence of genes involved in antibiotic resistance mechanisms, or of specific mutations, previously identified from a t...

journal_title：BMC bioinformatics

authors： Mahé P,Tournoud M

更新日期：2018-10-17 00:00:00

abstract：BACKGROUND:Microarray technology can acquire information about thousands of genes simultaneously. We analyzed published breast cancer microarray databases to predict five-year recurrence and compared the performance of three data mining algorithms of artificial neural networks (ANN), decision trees (DT) and logistic re...

journal_title：BMC bioinformatics

authors： Chou HL,Yao CT,Su SL,Lee CY,Hu KY,Terng HJ,Shih YW,Chang YT,Lu YF,Chang CW,Wahlqvist ML,Wetter T,Chu CM

更新日期：2013-03-19 00:00:00

abstract：BACKGROUND:Chemical cross-linking is used for protein-protein contacts mapping and for structural analysis. One of the difficulties in cross-linking studies is the analysis of mass-spectrometry data and the assignment of the site of cross-link incorporation. The difficulties are due to higher charges of fragment ions, ...

journal_title：BMC bioinformatics

authors： Jaiswal M,Crabtree N,Bauer MA,Hall R,Raney KD,Zybailov BL

更新日期：2014-01-01 00:00:00

abstract：BACKGROUND:The incorporation of biological knowledge can enhance the analysis of biomedical data. We present a novel method that uses a proteomic knowledge base to enhance the performance of a rule-learning algorithm in identifying putative biomarkers of disease from high-dimensional proteomic mass spectral data. In pa...

journal_title：BMC bioinformatics

authors： Lustgarten JL,Visweswaran S,Bowser RP,Hogan WR,Gopalakrishnan V

更新日期：2009-09-17 00:00:00

abstract：BACKGROUND:Text mining tools have gained popularity to process the vast amount of available research articles in the biomedical literature. It is crucial that such tools extract information with a sufficient level of detail to be applicable in real life scenarios. Studies of mining non-causal molecular relations attrib...

journal_title：BMC bioinformatics

authors： Van Landeghem S,Björne J,Abeel T,De Baets B,Salakoski T,Van de Peer Y

更新日期：2012-06-26 00:00:00

abstract：BACKGROUND:InterPro is a collection of protein signatures for the classification and automated annotation of proteins. Interproscan is a software tool that scans protein sequences against Interpro member databases using a variety of profile-based, hidden markov model and positional specific score matrix methods. It not...

journal_title：BMC bioinformatics

authors： Kelly RJ,Vincent DE,Friedberg I

更新日期：2010-12-21 00:00:00

abstract：BACKGROUND:Genes encoding transcription factors that constitute gene-regulatory networks and maternal factors accumulating in egg cytoplasm are two classes of essential genes that play crucial roles in developmental processes. Transcription factors control the expression of their downstream target genes by interacting ...

journal_title：BMC bioinformatics

authors： Wang K,Nishida H

更新日期：2015-04-10 00:00:00

abstract：BACKGROUND:This paper presents a novel approach for Generative Anatomy Modeling Language (GAML). This approach automatically detects the geometric partitions in 3D anatomy that in turn speeds up integrated non-linear optimization model in GAML for 3D anatomy modeling with constraints (e.g. joints). This integrated non-...

journal_title：BMC bioinformatics

authors： Demirel D,Cetinsaya B,Halic T,Kockara S,Ahmadi S

更新日期：2019-03-14 00:00:00

abstract：BACKGROUND:The information in large collections of phylogenetic trees is useful for many comparative genomic studies. Therefore, there is a need for flexible tools that allow exploration of such collections in order to retrieve relevant data as quickly as possible. RESULTS:In this paper, we present TPMS (Tree Pattern-...

journal_title：BMC bioinformatics

authors： Bigot T,Daubin V,Lassalle F,Perrière G

更新日期：2013-03-27 00:00:00

abstract：BACKGROUND:Our knowledge of global protein-protein interaction (PPI) networks in complex organisms such as humans is hindered by technical limitations of current methods. RESULTS:On the basis of short co-occurring polypeptide regions, we developed a tool called MP-PIPE capable of predicting a global human PPI network ...

journal_title：BMC bioinformatics

authors： Schoenrock A,Samanfar B,Pitre S,Hooshyar M,Jin K,Phillips CA,Wang H,Phanse S,Omidi K,Gui Y,Alamgir M,Wong A,Barrenäs F,Babu M,Benson M,Langston MA,Green JR,Dehne F,Golshani A

更新日期：2014-12-10 00:00:00

abstract：BACKGROUND:The behaviour of biological systems can be deduced from their mathematical models. However, multiple sources of data in diverse forms are required in the construction of a model in order to define its components and their biochemical reactions, and corresponding parameters. Automating the assembly and use of...

journal_title：BMC bioinformatics

authors： Li P,Dada JO,Jameson D,Spasic I,Swainston N,Carroll K,Dunn W,Khan F,Malys N,Messiha HL,Simeonidis E,Weichart D,Winder C,Wishart J,Broomhead DS,Goble CA,Gaskell SJ,Kell DB,Westerhoff HV,Mendes P,Paton NW

更新日期：2010-11-29 00:00:00

abstract：BACKGROUND:N-linked protein glycosylation plays an important role in various biological processes, including protein folding and trafficking, and cell adhesion and signaling. The acquisition of a novel N-glycosylation site may have significant effect on protein structure and function, and therefore, on the phenotype. ...

journal_title：BMC bioinformatics

authors： Kim DS,Hahn Y

更新日期：2015-01-28 00:00:00

abstract：BACKGROUND:Conservation and variation scores are used when evaluating sites in a multiple sequence alignment, in order to identify residues critical for structure or function. A variety of scores are available today but it is not clear how different scores relate to each other. RESULTS:We applied 25 conservation and v...

journal_title：BMC bioinformatics

authors： Johansson F,Toh H

更新日期：2010-07-21 00:00:00

abstract：BACKGROUND:Interpretation of gene expression microarray data in the light of external information on both columns and rows (experimental variables and gene annotations) facilitates the extraction of pertinent information hidden in these complex data. Biologists classically interpret genes of interest after retrieving f...

journal_title：BMC bioinformatics

authors： Baty F,Rüdiger J,Miglino N,Kern L,Borger P,Brutsche M

更新日期：2013-06-06 00:00:00

abstract：BACKGROUND:Interpretation of quantitative metagenomics data is important for our understanding of ecosystem functioning and assessing differences between various environmental samples. There is a need for an easy to use tool to explore the often complex metagenomics data in taxonomic and functional context. RESULTS:He...

journal_title：BMC bioinformatics

authors： Sanli K,Karlsson FH,Nookaew I,Nielsen J

更新日期：2013-02-01 00:00:00