Hotspot Hunter: a computational system for large-scale screening and selection of candidate immunological hotspots in pathogen proteomes.

abstract：BACKGROUND:Drug resistance testing is mandatory in antiretroviral therapy in human immunodeficiency virus (HIV) infected patients for successful treatment. The emergence of resistances against antiretroviral agents remains the major obstacle in inhibition of viral replication and thus to control infection. Due to the h...

journal_title：BMC bioinformatics

authors： Riemenschneider M,Hummel T,Heider D

更新日期：2016-08-22 00:00:00

abstract：BACKGROUND:Non-negative matrix factorisation (NMF), a machine learning algorithm, has been applied to the analysis of microarray data. A key feature of NMF is the ability to identify patterns that together explain the data as a linear combination of expression signatures. Microarray data generally includes individual e...

journal_title：BMC bioinformatics

authors： Wang G,Kossenkov AV,Ochs MF

更新日期：2006-03-28 00:00:00

abstract：BACKGROUND:We previously developed GoMiner, an application that organizes lists of 'interesting' genes (for example, under-and overexpressed genes from a microarray experiment) for biological interpretation in the context of the Gene Ontology. The original version of GoMiner was oriented toward visualization and interp...

journal_title：BMC bioinformatics

authors： Zeeberg BR,Qin H,Narasimhan S,Sunshine M,Cao H,Kane DW,Reimers M,Stephens RM,Bryant D,Burt SK,Elnekave E,Hari DM,Wynn TA,Cunningham-Rundles C,Stewart DM,Nelson D,Weinstein JN

更新日期：2005-07-05 00:00:00

abstract：BACKGROUND:The majority of experimentally verified molecular interaction and biological pathway data are present in the unstructured text of biomedical journal articles where they are inaccessible to computational methods. The Biomolecular interaction network database (BIND) seeks to capture these data in a machine-rea...

journal_title：BMC bioinformatics

authors： Donaldson I,Martin J,de Bruijn B,Wolting C,Lay V,Tuekam B,Zhang S,Baskin B,Bader GD,Michalickova K,Pawson T,Hogue CW

更新日期：2003-03-27 00:00:00

abstract：BACKGROUND:Since their first commercialization, the diversity of taxa and the genetic composition of transgene sequences in genetically modified plants (GMOs) are constantly increasing. To date, the detection of GMOs and derived products is commonly performed by PCR-based methods targeting specific DNA sequences introd...

journal_title：BMC bioinformatics

authors： Block A,Debode F,Grohmann L,Hulin J,Taverniers I,Kluga L,Barbau-Piednoir E,Broeders S,Huber I,Van den Bulcke M,Heinze P,Berben G,Busch U,Roosens N,Janssen E,Žel J,Gruden K,Morisset D

更新日期：2013-08-22 00:00:00

abstract：BACKGROUND:Frequent pattern mining analysis applied on microarray dataset appears to be a promising strategy for identifying relationships between gene expression levels. Unfortunately, too many itemsets (co-expressed genes) are identified by this analysis method since it does not consider the importance of each gene w...

journal_title：BMC bioinformatics

authors： Liu YC,Cheng CP,Tseng VS

更新日期：2013-07-21 00:00:00

abstract：BACKGROUND:Intracellular signal transduction is achieved by networks of proteins and small molecules that transmit information from the cell surface to the nucleus, where they ultimately effect transcriptional changes. Understanding the mechanisms cells use to accomplish this important process requires a detailed molec...

journal_title：BMC bioinformatics

authors： Steffen M,Petti A,Aach J,D'haeseleer P,Church G

更新日期：2002-11-01 00:00:00

abstract：BACKGROUND:Comparative genomics has become an essential approach for identifying homologous gene candidates and their functions, and for studying genome evolution. There are many tools available for genome comparisons. Unfortunately, most of them are not applicable for the identification of unique genes and the inferen...

journal_title：BMC bioinformatics

authors： Lu G,Jiang L,Helikar RM,Rowley TW,Zhang L,Chen X,Moriyama EN

更新日期：2006-12-12 00:00:00

abstract：BACKGROUND:Protein-protein interactions (PPIs) play crucial roles in virtually every aspect of cellular function within an organism. Over the last decade, the development of novel high-throughput techniques has resulted in enormous amounts of data and provided valuable resources for studying protein interactions. Howev...

journal_title：BMC bioinformatics

authors： Lei YK,You ZH,Ji Z,Zhu L,Huang DS

更新日期：2012-05-08 00:00:00

abstract：BACKGROUND:Over the course of the last few years there has been a significant amount of research performed on ontology-based formalization of phenotype descriptions. In order to fully capture the intrinsic value and knowledge expressed within them, we need to take advantage of their inner structure, which implicitly co...

journal_title：BMC bioinformatics

authors： Groza T,Hunter J,Zankl A

更新日期：2012-10-15 00:00:00

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: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:Recently, revealing the function of proteins with protein-protein interaction (PPI) networks is regarded as one of important issues in bioinformatics. With the development of experimental methods such as the yeast two-hybrid method, the data of protein interaction have been increasing extremely. Many databas...

journal_title：BMC bioinformatics

authors： Monji H,Koizumi S,Ozaki T,Ohkawa T

更新日期：2011-02-15 00:00:00

abstract：BACKGROUND:Primer design for highly variable DNA sequences is difficult, and experimental success requires attention to many interacting constraints. The advent of next-generation sequencing methods allows the investigation of rare variants otherwise hidden deep in large populations, but requires attention to populatio...

journal_title：BMC bioinformatics

authors： Brodin J,Krishnamoorthy M,Athreya G,Fischer W,Hraber P,Gleasner C,Green L,Korber B,Leitner T

更新日期：2013-08-21 00:00:00

abstract：BACKGROUND:To understand biological processes and diseases, it is crucial to unravel the concerted interplay of transcription factors (TFs), microRNAs (miRNAs) and their targets within regulatory networks and fundamental sub-networks. An integrative computational resource generating a comprehensive view of these regula...

journal_title：BMC bioinformatics

authors： Le Béchec A,Portales-Casamar E,Vetter G,Moes M,Zindy PJ,Saumet A,Arenillas D,Theillet C,Wasserman WW,Lecellier CH,Friederich E

更新日期：2011-03-04 00:00:00

abstract：BACKGROUND:Phenotype prediction problems are usually considered ill-posed, as the amount of samples is very limited with respect to the scrutinized genetic probes. This fact complicates the sampling of the defective genetic pathways due to the high number of possible discriminatory genetic networks involved. In this re...

journal_title：BMC bioinformatics

authors： Cernea A,Fernández-Martínez JL,deAndrés-Galiana EJ,Fernández-Ovies FJ,Alvarez-Machancoses O,Fernández-Muñiz Z,Saligan LN,Sonis ST

更新日期：2020-03-11 00:00:00

abstract：BACKGROUND:Human immunology studies often rely on the isolation and quantification of cell populations from an input sample based on flow cytometry and related techniques. Such techniques classify cells into populations based on the detection of a pattern of markers. The description of the cell populations targeted in ...

journal_title：BMC bioinformatics

authors： Overton JA,Vita R,Dunn P,Burel JG,Bukhari SAC,Cheung KH,Kleinstein SH,Diehl AD,Peters B

更新日期：2019-04-25 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:Many proteins contain conserved sequence patterns (motifs) that contribute to their functionality. The process of experimentally identifying and validating novel protein motifs can be difficult, expensive, and time consuming. A means for helping to identify in advance the possible function of a novel motif i...

journal_title：BMC bioinformatics

authors： Bristow F,He R,Van Domselaar G

更新日期：2011-09-26 00:00:00

abstract：BACKGROUND:The signal peptide plays an important role in protein targeting and protein translocation in both prokaryotic and eukaryotic cells. This transient, short peptide sequence functions like a postal address on an envelope by targeting proteins for secretion or for transfer to specific organelles for further proc...

journal_title：BMC bioinformatics

authors： Choo KH,Tan TW,Ranganathan S

更新日期：2005-10-13 00:00:00

abstract：BACKGROUND:Next-generation sequencing allows the analysis of an unprecedented number of viral sequence variants from infected patients, presenting a novel opportunity for understanding virus evolution, drug resistance and immune escape. However, sequencing in bulk is error prone. Thus, the generated data require error ...

journal_title：BMC bioinformatics

authors： Skums P,Dimitrova Z,Campo DS,Vaughan G,Rossi L,Forbi JC,Yokosawa J,Zelikovsky A,Khudyakov Y

更新日期：2012-06-25 00:00:00

abstract：BACKGROUND:In current comparative proteomics studies, the large number of images generated by 2D gels is currently compared using spot matching algorithms. Unfortunately, differences in gel migration and sample variability make efficient spot alignment very difficult to obtain, and, as consequence most of the software ...

journal_title：BMC bioinformatics

authors： Pérès S,Molina L,Salvetat N,Granier C,Molina F

更新日期：2008-10-28 00:00:00

abstract：BACKGROUND:Guanine protein-coupled receptors (GPCRs) constitute a eukaryotic transmembrane protein family and function as "molecular switches" in the second messenger cascades and are found in all organisms between yeast and humans. They form the single, biggest drug-target family due to their versatility of action and...

journal_title：BMC bioinformatics

authors： Sarkar A,Kumar S,Sundar D

更新日期：2011-02-15 00:00:00

abstract：BACKGROUND:The rapid development of structural genomics has resulted in many "unknown function" proteins being deposited in Protein Data Bank (PDB), thus, the functional prediction of these proteins has become a challenge for structural bioinformatics. Several sequence-based and structure-based methods have been develo...

journal_title：BMC bioinformatics

authors： Li GH,Huang JF

更新日期：2010-08-27 00:00:00

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:Several large-scale gene co-expression networks have been constructed successfully for predicting gene functional modules and cis-regulatory elements in Arabidopsis (Arabidopsis thaliana). However, these networks are usually constructed and analyzed in an ad hoc manner. In this study, we propose a completely...

journal_title：BMC bioinformatics

authors： Ruan J,Perez J,Hernandez B,Lei C,Sunter G,Sponsel VM

更新日期：2011-11-24 00:00:00

abstract：BACKGROUND:Protein function is closely intertwined with protein structure. Discovery of meaningful structure-function relationships is of utmost importance in protein biochemistry and has led to creation of high-quality, manually curated classification databases, such as the gold-standard SCOP (Structural Classificatio...

journal_title：BMC bioinformatics

authors： Asarnow D,Singh R

更新日期：2014-01-01 00:00:00

abstract：BACKGROUND:The structure conservation in various α-helix subclasses reveals the sequence and context dependent factors causing distortions in the α-helix. The sequence-structure relationship in these subclasses can be used to predict structural variations in α-helix purely based on its sequence. We train support vector...

journal_title：BMC bioinformatics

authors： Tendulkar AV,Wangikar PP

更新日期：2011-02-15 00:00:00

abstract：BACKGROUND:Integrative network methods are commonly used for interpretation of high-throughput experimental biological data: transcriptomics, proteomics, metabolomics and others. One of the common approaches is finding a connected subnetwork of a global interaction network that best encompasses significant individual c...

journal_title：BMC bioinformatics

authors： Alexeev N,Isomurodov J,Sukhov V,Korotkevich G,Sergushichev A

更新日期：2020-11-18 00:00:00

abstract：BACKGROUND:In the last decade, techniques were established for the large scale genome-wide analysis of proteins, RNA, and metabolites, and database solutions have been developed to manage the generated data sets. The Golm Metabolome Database for metabolite data (GMD) represents one such effort to make these data broadl...

journal_title：BMC bioinformatics

authors： Hummel J,Niemann M,Wienkoop S,Schulze W,Steinhauser D,Selbig J,Walther D,Weckwerth W

更新日期：2007-06-23 00:00:00