BMC Bioinformatics

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A new protein-ligand binding sites prediction method based on the integration of protein sequence conservation information
BMC Bioinformatics - Tập 12 - Trang 1-7 - 2011
Tianli Dai, Qi Liu, Jun Gao, Zhiwei Cao, Ruixin Zhu
Prediction of protein-ligand binding sites is an important issue for protein function annotation and structure-based drug design. Nowadays, although many computational methods for ligand-binding prediction have been developed, there is still a demanding to improve the prediction accuracy and efficiency. In addition, most of these methods are purely geometry-based, if the prediction methods improve...... hiện toàn bộ
Identifying microRNA targets in different gene regions
BMC Bioinformatics - Tập 15 - Trang 1-11 - 2014
Wenlong Xu, Anthony San Lucas, Zixing Wang, Yin Liu
Currently available microRNA (miRNA) target prediction algorithms require the presence of a conserved seed match to the 5' end of the miRNA and limit the target sites to the 3' untranslated regions of mRNAs. However, it has been noted that these requirements may be too stringent, leading to a substantial number of missing targets. We have developed TargetS, a novel computational approach for predi...... hiện toàn bộ
Correlating overrepresented upstream motifs to gene expression: a computational approach to regulatory element discovery in eukaryotes
BMC Bioinformatics - Tập 3 - Trang 1-10 - 2002
Michele Caselle, Ferdinando Di Cunto, Paolo Provero
Gene regulation in eukaryotes is mainly effected through transcription factors binding to rather short recognition motifs generally located upstream of the coding region. We present a novel computational method to identify regulatory elements in the upstream region of eukaryotic genes. The genes are grouped in sets sharing an overrepresented short motif in their upstream sequence. For each set, th...... hiện toàn bộ
Modular prediction of protein structural classes from sequences of twilight-zone identity with predicting sequences
BMC Bioinformatics - Tập 10 - Trang 1-24 - 2009
Marcin J Mizianty, Lukasz Kurgan
Knowledge of structural class is used by numerous methods for identification of structural/functional characteristics of proteins and could be used for the detection of remote homologues, particularly for chains that share twilight-zone similarity. In contrast to existing sequence-based structural class predictors, which target four major classes and which are designed for high identity sequences,...... hiện toàn bộ
BioWord: A sequence manipulation suite for Microsoft Word
BMC Bioinformatics - Tập 13 - Trang 1-7 - 2012
Laura J Anzaldi, Daniel Muñoz-Fernández, Ivan Erill
The ability to manipulate, edit and process DNA and protein sequences has rapidly become a necessary skill for practicing biologists across a wide swath of disciplines. In spite of this, most everyday sequence manipulation tools are distributed across several programs and web servers, sometimes requiring installation and typically involving frequent switching between applications. To address this ...... hiện toàn bộ
Computing expectation values for RNA motifs using discrete convolutions
BMC Bioinformatics -
André Lambert, Matthieu Legendre, Jean-Fred Fontaine, Daniel Gautheret
Abstract Background Computational biologists use Expectation values (E-values) to estimate the number of solutions that can be expected by chance during a database scan. Here we focus on computing Expectation values for RNA motifs defined by single-strand and helix lod-score profiles with variable h...... hiện toàn bộ
scAnnotatR: framework to accurately classify cell types in single-cell RNA-sequencing data
BMC Bioinformatics - Tập 23 - Trang 1-13 - 2022
Vy Nguyen, Johannes Griss
Automatic cell type identification is essential to alleviate a key bottleneck in scRNA-seq data analysis. While most existing classification tools show good sensitivity and specificity, they often fail to adequately not-classify cells that are missing in the used reference. Additionally, many tools do not scale to the continuously increasing size of current scRNA-seq datasets. Therefore, additiona...... hiện toàn bộ
The exploration of disease-specific gene regulatory networks in esophageal carcinoma and stomach adenocarcinoma
BMC Bioinformatics - Tập 20 Số S22 - 2019
Guimin Qin, Luqiong Yang, Yan Ma, Jiayan Liu, Qiuyan Huo
Abstract Background Feed-forward loops (FFLs), consisting of miRNAs, transcription factors (TFs) and their common target genes, have been validated to be important for the initialization and development of complex diseases, including cancer. Esophageal Carcinoma (ESCA) and Stomach Adenocarcinoma (STAD) are two types of malignant t...... hiện toàn bộ
Highlights from the Third International Society for Computational Biology Student Council Symposium at the Fifteenth Annual International Conference on Intelligent Systems for Molecular Biology
BMC Bioinformatics - - 2007
Nils Gehlenborg, Manuel Corpas, Sarath Chandra Janga
In this meeting report we give an overview of the 3rd International Society for Computational Biology Student Council Symposium. Furthermore, we explain the role of the Student Council and the symposium series in the context of large, international conferences.
Erratum to: eSTGt: a programming and simulation environment for population dynamics
BMC Bioinformatics - Tập 17 - Trang 1-1 - 2016
Adam Spiro, Ehud Shapiro
Tổng số: 8,323   
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