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  1. In the field of drug repositioning, it is assumed that similar drugs may treat similar diseases, therefore many existing computational methods need to compute the similarities of drugs and diseases. However, t...

    Authors: Guangsheng Wu, Juan Liu and Xiang Yue

    Citation: BMC Bioinformatics 2019 20(Suppl 3):134

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 3

  2. In this paper, we study the problem of RNA motif search in long genomic sequences. This approach uses a combination of sequence and structure constraints to uncover new distant homologs of known functional RNA...

    Authors: Ladislav Rampášek, Randi M. Jimenez, Andrej Lupták, Tomáš Vinař and Broňa Brejová

    Citation: BMC Bioinformatics 2016 17:216

    Content type: Methodology Article

    Published on:

  3. Classifying cancers by gene selection is among the most important and challenging procedures in biomedicine. A major challenge is to design an effective method that eliminates irrelevant, redundant, or noisy g...

    Authors: Xiaoping Cheng, Hongmin Cai, Yue Zhang, Bo Xu and Weifeng Su

    Citation: BMC Bioinformatics 2015 16:219

    Content type: Methodology Article

    Published on:

  5. The accurate identification of protein complexes is important for the understanding of cellular organization. Up to now, computational methods for protein complex detection are mostly focus on mining clusters ...

    Authors: Le Ou-Yang, Hong Yan and Xiao-Fei Zhang

    Citation: BMC Bioinformatics 2017 18(Suppl 13):463

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 18 Supplement 13

  6. It is of great clinical significance to develop an accurate computer aided system to accurately diagnose the breast cancer. In this study, an enhanced machine learning framework is established to diagnose the ...

    Authors: Hui Huang, Xi’an Feng, Suying Zhou, Jionghui Jiang, Huiling Chen, Yuping Li and Chengye Li

    Citation: BMC Bioinformatics 2019 20(Suppl 8):290

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 8

  7. The recent pandemic of obesity and the metabolic syndrome (MetS) has led to the realisation that new drug targets are needed to either reduce obesity or the subsequent pathophysiological consequences associate...

    Authors: Animesh Acharjee, Zsuzsanna Ament, James A. West, Elizabeth Stanley and Julian L. Griffin

    Citation: BMC Bioinformatics 2016 17(Suppl 15):440

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 17 Supplement 15

  8. Recent years have witnessed an increasing interest in multi-omics data, because these data allow for better understanding complex diseases such as cancer on a molecular system level. In addition, multi-omics d...

    Authors: Amina Lemsara, Salima Ouadfel and Holger Fröhlich

    Citation: BMC Bioinformatics 2020 21:146

    Content type: Methodology article

    Published on:

  10. Molecular structures can be represented as strings of special characters using SMILES. Since each molecule is represented as a string, the similarity between compounds can be computed using SMILES-based string...

    Authors: Hakime Öztürk, Elif Ozkirimli and Arzucan Özgür

    Citation: BMC Bioinformatics 2016 17:128

    Content type: Research Article

    Published on:

  12. Maximum parsimony reconciliation in the duplication-transfer-loss model is a widely-used method for analyzing the evolutionary histories of pairs of entities such as hosts and parasites, symbiont species, and ...

    Authors: Ross Mawhorter and Ran Libeskind-Hadas

    Citation: BMC Bioinformatics 2019 20:612

    Content type: Methodology Article

    Published on:

  13. The abundance of biological data characterizing the genomics era is contributing to a comprehensive understanding of human mitochondrial genetics. Nevertheless, many aspects are still unclear, specifically abo...

    Authors: Maria Angela Diroma, Paolo Lubisco and Marcella Attimonelli

    Citation: BMC Bioinformatics 2016 17(Suppl 12):338

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 17 Supplement 12

  14. Despite the significant contribution of transcriptomics to the fields of biological and biomedical research, interpreting long lists of significantly differentially expressed genes remains a challenging step i...

    Authors: Bin Liu, Patrick Lindner, Adan Chari Jirmo, Ulrich Maus, Thomas Illig and David S. DeLuca

    Citation: BMC Bioinformatics 2020 21:28

    Content type: Methodology Article

    Published on:

  15. One of the main aims of phylogenomics is the reconstruction of objects defined in the leaves along the whole phylogenetic tree to minimize the specified functional, which may also include the phylogenetic tree...

    Authors: Vassily Lyubetsky, Roman Gershgorin, Alexander Seliverstov and Konstantin Gorbunov

    Citation: BMC Bioinformatics 2016 17:40

    Content type: Research article

    Published on:

  16. A visualization referred to as rainfall plot has recently gained popularity in genome data analysis. The plot is mostly used for illustrating the distribution of somatic cancer mutations along a reference geno...

    Authors: Diana Domanska, Daniel Vodák, Christin Lund-Andersen, Stefania Salvatore, Eivind Hovig and Geir Kjetil Sandve

    Citation: BMC Bioinformatics 2017 18:264

    Content type: Research Article

    Published on:

  18. The spatial distribution and colocalization of functionally related metabolites is analysed in order to investigate the spatial (and functional) aspects of molecular networks. We propose to consider community ...

    Authors: Karsten Wüllems, Jan Kölling, Hanna Bednarz, Karsten Niehaus, Volkmar H. Hans and Tim W. Nattkemper

    Citation: BMC Bioinformatics 2019 20:303

    Content type: Methodology article

    Published on:

  19. A rapidly increasing flow of genomic data requires the development of efficient methods for obtaining its compact representation. Feature extraction facilitates classification, clustering and model analysis fo...

    Authors: Veronika B. Dubinkina, Dmitry S. Ischenko, Vladimir I. Ulyantsev, Alexander V. Tyakht and Dmitry G. Alexeev

    Citation: BMC Bioinformatics 2016 17:38

    Content type: Research Article

    Published on:

  20. The deployment of Genome-wide association studies (GWASs) requires genomic information of a large population to produce reliable results. This raises significant privacy concerns, making people hesitate to con...

    Authors: Charlotte Bonte, Eleftheria Makri, Amin Ardeshirdavani, Jaak Simm, Yves Moreau and Frederik Vercauteren

    Citation: BMC Bioinformatics 2018 19:537

    Content type: Research article

    Published on:

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