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438 result(s) for 'Software' within Volume 20 of BMC Bioinformatics

Page 8 of 9

  2. Recurrent neural network(RNN) is a good way to process sequential data, but the capability of RNN to compute long sequence data is inefficient. As a variant of RNN, long short term memory(LSTM) solved the prob...

    Authors: Jiale Liu and Xinqi Gong
    Citation: BMC Bioinformatics 2019 20:609
    Content type: Methodology Article Published on:

  3. Bioinformatics methods are helpful to identify new molecules for diagnostic or therapeutic applications. For example, the use of peptides capable of mimicking binding sites has several benefits in replacing a ...

    Authors: Vincent Demolombe, Alexandre G. de Brevern, Liza Felicori, Christophe NGuyen, Ricardo Andrez Machado de Avila, Lionel Valera, Bénédicte Jardin-Watelet, Géraldine Lavigne, Aurélien Lebreton, Franck Molina and Violaine Moreau
    Citation: BMC Bioinformatics 2019 20:387
    Content type: Methodology article Published on:

  4. Cryo-electron tomography (Cryo-ET) is an imaging technique used to generate three-dimensional structures of cellular macromolecule complexes in their native environment. Due to developing cryo-electron microsc...

    Authors: Yongchun Lü, Xiangrui Zeng, Xiaofang Zhao, Shirui Li, Hua Li, Xin Gao and Min Xu
    Citation: BMC Bioinformatics 2019 20:443
    Content type: Methodology article Published on:

  5. Transposable Elements (TE) are mobile sequences that make up large portions of eukaryote genomes. The functions they play within the complex cellular architecture are still not clearly understood, but it is be...

    Authors: Federico Ansaloni, Margherita Scarpato, Elia Di Schiavi, Stefano Gustincich and Remo Sanges
    Citation: BMC Bioinformatics 2019 20(Suppl 9):484
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 9

  7. Identifying splice sites is a necessary step to analyze the location and structure of genes. Two dinucleotides, GT and AG, are highly frequent on splice sites, and many other patterns are also on splice sites ...

    Authors: Ruohan Wang, Zishuai Wang, Jianping Wang and Shuaicheng Li
    Citation: BMC Bioinformatics 2019 20(Suppl 23):652
    Content type: Methodology Published on:

    This article is part of a Supplement: Volume 20 Supplement 23

  8. Although a few comparison methods based on the biological meaning of gene lists have been developed, the goProfiles approach is one of the few that are being used for that purpose. It consists of projecting li...

    Authors: Alex Sánchez-Pla, Miquel Salicrú and Jordi Ocaña
    Citation: BMC Bioinformatics 2019 20:441
    Content type: Methodology article Published on:

  9. The recognition of protein interaction sites is of great significance in many biological processes, signaling pathways and drug designs. However, most sites on protein sequences cannot be defined as interface ...

    Authors: Ye Wang, Changqing Mei, Yuming Zhou, Yan Wang, Chunhou Zheng, Xiao Zhen, Yan Xiong, Peng Chen, Jun Zhang and Bing Wang
    Citation: BMC Bioinformatics 2019 20(Suppl 25):699
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 25

  12. In silico experiments, with the aid of computer simulation, speed up the process of in vitro or in vivo experiments. Cancer therapy design is often based on signalling pathway. MicroRNAs (miRNA) are small non-...

    Authors: Valeria Boscaino, Antonino Fiannaca, Laura La Paglia, Massimo La Rosa, Riccardo Rizzo and Alfonso Urso
    Citation: BMC Bioinformatics 2019 20(Suppl 9):344
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 9

  13. Transcriptome analysis aims at gaining insight into cellular processes through discovering gene expression patterns across various experimental conditions. Biclustering is a standard approach to discover genes su...

    Authors: Vincent Branders, Pierre Schaus and Pierre Dupont
    Citation: BMC Bioinformatics 2019 20:625
    Content type: Research Article Published on:

  14. Lung adenocarcinoma is the most common type of lung cancer, with high mortality worldwide. Its occurrence and development were thoroughly studied by high-throughput expression microarray, which produced abunda...

    Authors: Xuemeng Fan, Yaolai Wang and Xu-Qing Tang
    Citation: BMC Bioinformatics 2019 20(Suppl 7):197
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 7

  15. In recent years, the study of immune response behaviour using bottom up approach, Agent Based Modeling (ABM), has attracted considerable efforts. The ABM approach is a very common technique in the biological d...

    Authors: Mozhgan Kabiri Chimeh, Peter Heywood, Marzio Pennisi, Francesco Pappalardo and Paul Richmond
    Citation: BMC Bioinformatics 2019 20(Suppl 6):579
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 6

  16. Over one hundred different types of post-transcriptional RNA modifications have been identified in human. Researchers discovered that RNA modifications can regulate various biological processes, and RNA methyl...

    Authors: Xiangyu Wu, Zhen Wei, Kunqi Chen, Qing Zhang, Jionglong Su, Hui Liu, Lin Zhang and Jia Meng
    Citation: BMC Bioinformatics 2019 20:223
    Content type: Research article Published on:

  17. Next-generation sequencing (NGS) technologies have produced large volumes of genomic data. One common operation on heterogeneous genomic data is genomic interval intersection. Most of the existing tools impose...

    Authors: Burçak Otlu and Tolga Can
    Citation: BMC Bioinformatics 2019 20:121
    Content type: Methodology article Published on:

  19. Signal peptides play an important role in protein sorting, which is the mechanism whereby proteins are transported to their destination. Recognition of signal peptides is an important first step in determining...

    Authors: Jhe-Ming Wu, Yu-Chen Liu and Darby Tien-Hao Chang
    Citation: BMC Bioinformatics 2019 20(Suppl 24):677
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 24

  20. As genome sequencing projects grow rapidly, the diversity of organisms with recently assembled genome sequences peaks at an unprecedented scale, thereby highlighting the need to make gene functional annotation...

    Authors: Fernando Cruz, Davide Lagoa, João Mendes, Isabel Rocha, Eugénio C. Ferreira, Miguel Rocha and Oscar Dias
    Citation: BMC Bioinformatics 2019 20:454
    Content type: Methodology article Published on:

  21. Data from discovery proteomic and phosphoproteomic experiments typically include missing values that correspond to proteins that have not been identified in the analyzed sample. Replacing the missing values wi...

    Authors: Matúš Medo, Daniel M. Aebersold and Michaela Medová
    Citation: BMC Bioinformatics 2019 20:563
    Content type: Methodology Article Published on:

  23. Along with the development of precision medicine, individual heterogeneity is attracting more and more attentions in clinical research and application. Although the biomolecular reaction seems to be some vario...

    Authors: Shaoyan Sun, Xiangtian Yu, Fengnan Sun, Ying Tang, Juan Zhao and Tao Zeng
    Citation: BMC Bioinformatics 2019 20(Suppl 25):697
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 25

  24. A key problem in systems biology is the determination of the regulatory mechanism corresponding to a phenotype. An empirical approach in this regard is to compare the expression profiles of cells under two con...

    Authors: Yance Feng, Sheng Zhang, Liang Li and Lei M. Li
    Citation: BMC Bioinformatics 2019 20(Suppl 7):201
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 7

  27. The interactions among proteins act as crucial roles in most cellular processes. Despite enormous effort put for identifying protein-protein interactions (PPIs) from a large number of organisms, existing first...

    Authors: Zhengwei Li, Ru Nie, Zhuhong You, Chen Cao and Jiashu Li
    Citation: BMC Bioinformatics 2019 20(Suppl 25):694
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 25

  28. The function of oligomeric proteins is inherently linked to their quaternary structure. In the absence of high-resolution data, low-resolution information in the form of spatial restraints can significantly co...

    Authors: Aljaž Gaber, Gregor Gunčar and Miha Pavšič
    Citation: BMC Bioinformatics 2019 20:464
    Content type: Research article Published on:

  29. The hybrid stochastic simulation algorithm, proposed by Haseltine and Rawlings (HR), is a combination of differential equations for traditional deterministic models and Gillespie’s algorithm (SSA) for stochast...

    Authors: Minghan Chen and Yang Cao
    Citation: BMC Bioinformatics 2019 20(Suppl 12):315
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 12

  30. Pairwise alignment of short DNA sequences with affine-gap scoring is a common processing step performed in a range of bioinformatics analyses. Dynamic programming (i.e. Smith-Waterman algorithm) is widely used...

    Authors: Arash Bayat, Bruno Gaëta, Aleksandar Ignjatovic and Sri Parameswaran
    Citation: BMC Bioinformatics 2019 20:261
    Content type: Methodology article Published on:

  31. Many cancer genomes are extensively rearranged with highly aberrant chromosomal karyotypes. Structural and copy number variations in cancer genomes can be determined via abnormal mapping of sequenced reads to ...

    Authors: Sergey Aganezov, Ilya Zban, Vitaly Aksenov, Nikita Alexeev and Michael C. Schatz
    Citation: BMC Bioinformatics 2019 20(Suppl 20):641
    Content type: Research Published on:

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

  32. RNAs can interact and form complexes, which have various biological roles. The secondary structure prediction of those complexes is a first step towards the identification of their 3D structure. We propose an ...

    Authors: Audrey Legendre, Eric Angel and Fariza Tahi
    Citation: BMC Bioinformatics 2019 20(Suppl 3):128
    Content type: Research Published on:

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

  33. Hypothetical proteins [HP] are those that are predicted to be expressed in an organism, but no evidence of their existence is known. In the recent past, annotation and curation efforts have helped overcome the...

    Authors: Johny Ijaq, Girik Malik, Anuj Kumar, Partha Sarathi Das, Narendra Meena, Neeraja Bethi, Vijayaraghava Seshadri Sundararajan and Prashanth Suravajhala
    Citation: BMC Bioinformatics 2019 20:14
    Content type: Methodology article Published on:

  34. Modern plant taxonomy reflects phylogenetic relationships among taxa based on proposed morphological and genetic similarities. However, taxonomical relation is not necessarily reflected by close overall resemb...

    Authors: Marco Seeland, Michael Rzanny, David Boho, Jana Wäldchen and Patrick Mäder
    Citation: BMC Bioinformatics 2019 20:4
    Content type: Research article Published on:

  35. Gene Set Enrichment Analysis (GSEA) is a powerful tool to identify enriched functional categories of informative biomarkers. Canonical GSEA takes one-dimensional feature scores derived from the data of one pla...

    Authors: Khong-Loon Tiong and Chen-Hsiang Yeang
    Citation: BMC Bioinformatics 2019 20:145
    Content type: Methodology article Published on:

  37. Natural products are the source of various functional materials such as medicines, and understanding their biosynthetic pathways can provide information that is helpful for their effective production through t...

    Authors: Kohei Amano, Tsubasa Matsumoto, Kenichi Tanaka, Kimito Funatsu and Masaaki Kotera
    Citation: BMC Bioinformatics 2019 20:728
    Content type: Methodology article Published on:

  39. Single-cell RNA-sequencing (scRNA-seq) technologies have advanced rapidly in recent years and enabled the quantitative characterization at a microscopic resolution. With the exponential growth of the number of...

    Authors: Shengquan Chen, Kui Hua, Hongfei Cui and Rui Jiang
    Citation: BMC Bioinformatics 2019 20(Suppl 7):0
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 7

  40. Biological pathways represent chains of molecular interactions in biological systems that jointly form complex dynamic networks. The network structure changes from the significance of biological experiments an...

    Authors: Hsiang-Yun Wu, Martin Nöllenburg, Filipa L. Sousa and Ivan Viola
    Citation: BMC Bioinformatics 2019 20:187
    Content type: Research article Published on:

  41. Computational prediction of a phenotypic response upon the chemical perturbation on a biological system plays an important role in drug discovery, and many other applications. Chemical fingerprints are a widel...

    Authors: Mohamed Ayed, Hansaim Lim and Lei Xie
    Citation: BMC Bioinformatics 2019 20(Suppl 24):674
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 24

  42. Reconciliation methods are widely used to explain incongruence between a gene tree and species tree. However, the common approach of inferring maximum parsimony reconciliations (MPRs) relies on user-defined co...

    Authors: Ross Mawhorter, Nuo Liu, Ran Libeskind-Hadas and Yi-Chieh Wu
    Citation: BMC Bioinformatics 2019 20(Suppl 20):639
    Content type: Methodology Published on:

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

  44. Metagenomics caused a quantum leap in microbial ecology. However, the inherent size and complexity of metagenomic data limit its interpretation. The quantification of metagenomic traits in metagenomic analysis...

    Authors: Emiliano Pereira-Flores, Frank Oliver Glöckner and Antonio Fernandez-Guerra
    Citation: BMC Bioinformatics 2019 20:453
    Content type: Software Published on:

  45. Imbalanced datasets are commonly encountered in bioinformatics classification problems, that is, the number of negative samples is much larger than that of positive samples. Particularly, the data imbalance ph...

    Authors: Yongqing Zhang, Shaojie Qiao, Rongzhao Lu, Nan Han, Dingxiang Liu and Jiliu Zhou
    Citation: BMC Bioinformatics 2019 20(Suppl 25):695
    Content type: Methodology Published on:

    This article is part of a Supplement: Volume 20 Supplement 25

  46. Background Consisting of dictated free-text documents such as discharge summaries, medical narratives are widely used in medical natural language processing. Relationships between anatomical entities and human...

    Authors: Yipei Wang, Xingyu Fan, Luoxin Chen, Eric I-Chao Chang, Sophia Ananiadou, Junichi Tsujii and Yan Xu
    Citation: BMC Bioinformatics 2019 20:430
    Content type: Methodology article Published on:

  47. Integrated analysis that uses multiple sample gene expression data measured under the same stress can detect stress response genes more accurately than analysis of individual sample data. However, the integrat...

    Authors: Hongryul Ahn, Inuk Jung, Heejoon Chae, Dongwon Kang, Woosuk Jung and Sun Kim
    Citation: BMC Bioinformatics 2019 20(Suppl 16):588
    Content type: Methodology Published on:

    This article is part of a Supplement: Volume 20 Supplement 16

  48. Predicting protein function and structure from sequence is one important challenge for computational biology. For 26 years, most state-of-the-art approaches combined machine learning and evolutionary informati...

    Authors: Michael Heinzinger, Ahmed Elnaggar, Yu Wang, Christian Dallago, Dmitrii Nechaev, Florian Matthes and Burkhard Rost
    Citation: BMC Bioinformatics 2019 20:723
    Content type: Research article Published on:

  49. Neurogenesis in the murine cerebral cortex involves the coordinated divisions of two main types of progenitor cells, whose numbers, division modes and cell cycle durations set up the final neuronal output. To ...

    Authors: Marie Postel, Alice Karam, Guillaume Pézeron, Sylvie Schneider-Maunoury and Frédérique Clément
    Citation: BMC Bioinformatics 2019 20:470
    Content type: Research Article Published on:

  50. 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:

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