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

Page 9 of 9

  1. Ultra-fast pseudo-alignment approaches are the tool of choice in transcript-level RNA sequencing (RNA-seq) analyses. Unfortunately, these methods couple the tasks of pseudo-alignment and transcript quantificat...

    Authors: Mohamed K Gunady, Stephen M Mount and Héctor Corrada Bravo
    Citation: BMC Bioinformatics 2019 20:421
    Content type: Methodology article Published on:

  2. Accurate prediction of inter-residue contacts of a protein is important to calculating its tertiary structure. Analysis of co-evolutionary events among residues has been proved effective in inferring inter-res...

    Authors: Haicang Zhang, Qi Zhang, Fusong Ju, Jianwei Zhu, Yujuan Gao, Ziwei Xie, Minghua Deng, Shiwei Sun, Wei-Mou Zheng and Dongbo Bu
    Citation: BMC Bioinformatics 2019 20:537
    Content type: Methodology Article Published on:

    The Correction to this article has been published in BMC Bioinformatics 2019 20:616

  3. Translational and post-translational control mechanisms in the cell result in widely observable differences between measured gene transcription and protein abundances. Herein, protein complexes are among the m...

    Authors: Morteza H. Chalabi, Vasileios Tsiamis, Lukas Käll, Fabio Vandin and Veit Schwämmle
    Citation: BMC Bioinformatics 2019 20:17
    Content type: Software Published on:

  5. Sequencing technologies allow the sequencing of microbial communities directly from the environment without prior culturing. Because assembly typically produces only genome fragments, also known as contigs, it...

    Authors: Jia Qian and Matteo Comin
    Citation: BMC Bioinformatics 2019 20(Suppl 9):367
    Content type: Research Published on:

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

  6. c-Myc plays an important role in cell proliferation, cell growth and in differentiation, making it a key regulator for carcinogenesis and pluripotency. Tight control of c-myc turnover is required by ubiquitin-...

    Authors: Debangana Chakravorty, Krishnendu Banerjee, Tarunendu Mapder and Sudipto Saha
    Citation: BMC Bioinformatics 2019 20:230
    Content type: Research article Published on:

  7. Blood pressure diseases have increasingly been identified as among the main factors threatening human health. How to accurately and conveniently measure blood pressure is the key to the implementation of effec...

    Authors: Bing Zhang, Huihui Ren, Guoyan Huang, Yongqiang Cheng and Changzhen Hu
    Citation: BMC Bioinformatics 2019 20:109
    Content type: Research article Published on:

  8. Accurate prediction of anticancer drug responses in cell lines is a crucial step to accomplish the precision medicine in oncology. Although many popular computational models have been proposed towards this non...

    Authors: Dong Wei, Chuanying Liu, Xiaoqi Zheng and Yushuang Li
    Citation: BMC Bioinformatics 2019 20:44
    Content type: Research article Published on:

  9. Ribosome profiling brings insight to the process of translation. A basic step in profile construction at transcript level is to map Ribo-seq data to transcripts, and then assign a huge number of multiple-mappe...

    Authors: Hongfei Cui, Hailin Hu, Jianyang Zeng and Ting Chen
    Citation: BMC Bioinformatics 2019 20(Suppl 24):678
    Content type: Research Published on:

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

  10. The biological network is highly dynamic. Functional relations between genes can be activated or deactivated depending on the biological conditions. On the genome-scale network, subnetworks that gain or lose l...

    Authors: Jianwei Lu, Yao Lu, Yusheng Ding, Qingyang Xiao, Linqing Liu, Qingpo Cai, Yunchuan Kong, Yun Bai and Tianwei Yu
    Citation: BMC Bioinformatics 2019 20(Suppl 15):489
    Content type: Methodology Published on:

    This article is part of a Supplement: Volume 20 Supplement 15

  11. Parametric feature selection methods for machine learning and association studies based on genetic data are not robust with respect to outliers or influential observations. While rank-based, distribution-free ...

    Authors: Jiaxing Lin, Alexander Sibley, Ivo Shterev, Andrew Nixon, Federico Innocenti, Cliburn Chan and Kouros Owzar
    Citation: BMC Bioinformatics 2019 20:333
    Content type: Software Published on:

  12. Next-generation sequencing technologies can produce tens of millions of reads, often paired-end, from transcripts or genomes. But few programs can align RNA on the genome and accurately discover introns, espec...

    Authors: Grzegorz M. Boratyn, Jean Thierry-Mieg, Danielle Thierry-Mieg, Ben Busby and Thomas L. Madden
    Citation: BMC Bioinformatics 2019 20:405
    Content type: Software Published on:

  13. Neural network based embedding models are receiving significant attention in the field of natural language processing due to their capability to effectively capture semantic information representing words, sen...

    Authors: Kathrin Blagec, Hong Xu, Asan Agibetov and Matthias Samwald
    Citation: BMC Bioinformatics 2019 20:178
    Content type: Research article Published on:

  14. Real biological and social data is increasingly being represented as graphs. Pattern-mining-based graph learning and analysis techniques report meaningful biological subnetworks that elucidate important intera...

    Authors: Mohammed Alokshiya, Saeed Salem and Fidaa Abed
    Citation: BMC Bioinformatics 2019 20(Suppl 12):319
    Content type: Research Published on:

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

  15. Genome-wide Association Studies (GWAS) have contributed to unraveling associations between genetic variants in the human genome and complex traits for more than a decade. While many works have been invented as...

    Authors: Haohan Wang, Tianwei Yue, Jingkang Yang, Wei Wu and Eric P. Xing
    Citation: BMC Bioinformatics 2019 20(Suppl 23):656
    Content type: Methodology Published on:

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

  16. Harmonization techniques make different gene expression profiles and their sets compatible and ready for comparisons. Here we present a new bioinformatic tool termed Shambhala for harmonization of multiple hum...

    Authors: Nicolas Borisov, Irina Shabalina, Victor Tkachev, Maxim Sorokin, Andrew Garazha, Andrey Pulin, Ilya I. Eremin and Anton Buzdin
    Citation: BMC Bioinformatics 2019 20:66
    Content type: Research article Published on:

  18. Graphlets are useful for bioinformatics network analysis. Based on the structure of Hočevar and Demšar’s ORCA algorithm, we have created an orbit counting algorithm, named Jesse. This algorithm, like ORCA, use...

    Authors: Ine Melckenbeeck, Pieter Audenaert, Thomas Van Parys, Yves Van De Peer, Didier Colle and Mario Pickavet
    Citation: BMC Bioinformatics 2019 20:27
    Content type: Software Published on:

  19. In bacterial genomes, there are two mechanisms to terminate the DNA transcription: the “intrinsic” or Rho-independent termination and the Rho-dependent termination. Intrinsic terminators are characterized by a...

    Authors: Marco Di Salvo, Simone Puccio, Clelia Peano, Stephan Lacour and Pietro Alifano
    Citation: BMC Bioinformatics 2019 20:117
    Content type: Software Published on:

  20. One of the main issues in the automated protein function prediction (AFP) problem is the integration of multiple networked data sources. The UNIPred algorithm was thereby proposed to efficiently integrate —in ...

    Authors: Paolo Perlasca, Marco Frasca, Cheick Tidiane Ba, Marco Notaro, Alessandro Petrini, Elena Casiraghi, Giuliano Grossi, Jessica Gliozzo, Giorgio Valentini and Marco Mesiti
    Citation: BMC Bioinformatics 2019 20:422
    Content type: Software Published on:

  21. The genetic bases of many complex phenotypes are still largely unknown, mostly due to the polygenic nature of the traits and the small effect of each associated mutation. An alternative approach to classic ass...

    Authors: Luis Torada, Lucrezia Lorenzon, Alice Beddis, Ulas Isildak, Linda Pattini, Sara Mathieson and Matteo Fumagalli
    Citation: BMC Bioinformatics 2019 20(Suppl 9):337
    Content type: Software Published on:

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

  22. Antimicrobial resistance (AMR) is a major threat to global public health because it makes standard treatments ineffective and contributes to the spread of infections. It is important to understand AMR’s biolog...

    Authors: Jinhong Shi, Yan Yan, Matthew G. Links, Longhai Li, Jo-Anne R. Dillon, Michael Horsch and Anthony Kusalik
    Citation: BMC Bioinformatics 2019 20(Suppl 15):535
    Content type: Methodology Published on:

    This article is part of a Supplement: Volume 20 Supplement 15

  23. Due the computational complexity of sequence alignment algorithms, various accelerated solutions have been proposed to speedup this analysis. NVBIO is the only available GPU library that accelerates sequence a...

    Authors: Nauman Ahmed, Jonathan Lévy, Shanshan Ren, Hamid Mushtaq, Koen Bertels and Zaid Al-Ars
    Citation: BMC Bioinformatics 2019 20:520
    Content type: Software Published on:

    The Correction to this article has been published in BMC Bioinformatics 2019 20:597

  26. The development of high throughput sequencing techniques provides us with the possibilities to obtain large data sets, which capture the effect of dynamic perturbations on cellular processes. However, because ...

    Authors: T. J. M. Kuijpers, J. E. J. Wolters, J. C. S. Kleinjans and D. G. J. Jennen
    Citation: BMC Bioinformatics 2019 20:417
    Content type: Software Published on:

  28. In short-read DNA sequencing experiments, the read coverage is a key parameter to successfully assemble the reads and reconstruct the sequence of the input DNA. When coverage is very low, the original sequence...

    Authors: Louis Ranjard, Thomas K. F. Wong and Allen G. Rodrigo
    Citation: BMC Bioinformatics 2019 20:654
    Content type: Research Article Published on:

    The Correction to this article has been published in BMC Bioinformatics 2020 21:24

  30. How can we obtain fast and high-quality clusters in genome scale bio-networks? Graph clustering is a powerful tool applied on bio-networks to solve various biological problems such as protein complexes detecti...

    Authors: Yongsub Lim, Injae Yu, Dongmin Seo, U Kang and Lee Sael
    Citation: BMC Bioinformatics 2019 20(Suppl 13):381
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 13

  31. Malaria is a major global health problem, with the Plasmodium falciparum protozoan parasite causing the most severe form of the disease. Prevalence of drug-resistant P. falciparum highlights the need to understan...

    Authors: Ana M. Untaroiu, Maureen A. Carey, Jennifer L. Guler and Jason A. Papin
    Citation: BMC Bioinformatics 2019 20:186
    Content type: Research article Published on:

  32. Benefiting from big data, powerful computation and new algorithmic techniques, we have been witnessing the renaissance of deep learning, particularly the combination of natural language processing (NLP) and de...

    Authors: Xiaozheng Li, Huazhen Wang, Huixin He, Jixiang Du, Jian Chen and Jinzhun Wu
    Citation: BMC Bioinformatics 2019 20:62
    Content type: Research article Published on:

  33. Cancer subtype classification attains the great importance for accurate diagnosis and personalized treatment of cancer. Latest developments in high-throughput sequencing technologies have rapidly produced mult...

    Authors: Jing Xu, Peng Wu, Yuehui Chen, Qingfang Meng, Hussain Dawood and Hassan Dawood
    Citation: BMC Bioinformatics 2019 20:527
    Content type: Methodology Article Published on:

  34. Calling genetic variations from sequence reads is an important problem in genomics. There are many existing methods for calling various types of variations. Recently, Google developed a method for calling sing...

    Authors: Lei Cai, Yufeng Wu and Jingyang Gao
    Citation: BMC Bioinformatics 2019 20:665
    Content type: Research article Published on:

  35. Protein interaction databases often provide confidence scores for each recorded interaction based on the available experimental evidence. Protein interaction networks (PINs) are then built by thresholding on t...

    Authors: Lyuba V. Bozhilova, Alan V. Whitmore, Jonny Wray, Gesine Reinert and Charlotte M. Deane
    Citation: BMC Bioinformatics 2019 20:446
    Content type: Research article Published on:

  37. Sub-nuclear structures or locations are associated with various nuclear processes. Proteins localized in these substructures are important to understand the interior nuclear mechanisms. Despite advances in hig...

    Authors: Maria Littmann, Tatyana Goldberg, Sebastian Seitz, Mikael Bodén and Burkhard Rost
    Citation: BMC Bioinformatics 2019 20:205
    Content type: Methodology article Published on:

    The Correction to this article has been published in BMC Bioinformatics 2019 20:727

  38. Quorum sensing drives biofilm formation in bacteria in order to ensure that biofilm formation only occurs when colonies are of a sufficient size and density. This spatial behaviour is achieved by the broadcast...

    Authors: David Gilbert, Monika Heiner, Leila Ghanbar and Jacek Chodak
    Citation: BMC Bioinformatics 2019 20(Suppl 4):173
    Content type: Methodology Published on:

    This article is part of a Supplement: Volume 20 Supplement 4

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