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

Page 7 of 9

  1. Current NGS techniques are becoming exponentially cheaper. As a result, there is an exponential growth of genomic data unfortunately not followed by an exponential growth of storage, leading to the necessity o...

    Authors: Yoshihiro Shibuya and Matteo Comin
    Citation: BMC Bioinformatics 2019 20(Suppl 9):302

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

  2. Obesity is a complex disorder associated with an increased risk of developing several comorbid chronic diseases, including postmenopausal breast cancer. Although many studies have investigated this issue, the ...

    Authors: Ilaria Granata, Enrico Troiano, Mara Sangiovanni and Mario Rosario Guarracino
    Citation: BMC Bioinformatics 2019 20(Suppl 4):162

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

  3. In order to fully characterize the genome of an individual, the reconstruction of the two distinct copies of each chromosome, called haplotypes, is essential. The computational problem of inferring the full ha...

    Authors: Andrea Tangherloni, Simone Spolaor, Leonardo Rundo, Marco S. Nobile, Paolo Cazzaniga, Giancarlo Mauri, Pietro Liò, Ivan Merelli and Daniela Besozzi
    Citation: BMC Bioinformatics 2019 20(Suppl 4):172

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

  4. Molecule identification is a crucial step in metabolomics and environmental sciences. Besides in silico fragmentation, as performed by MetFrag, also machine learning and statistical methods evolved, showing an...

    Authors: Christoph Ruttkies, Steffen Neumann and Stefan Posch
    Citation: BMC Bioinformatics 2019 20:376
  5. A microRNA (miRNA) sponge is an RNA molecule with multiple tandem miRNA response elements that can sequester miRNAs from their target mRNAs. Despite growing appreciation of the importance of miRNA sponges, our...

    Authors: Junpeng Zhang, Lin Liu, Taosheng Xu, Yong Xie, Chunwen Zhao, Jiuyong Li and Thuc Duy Le
    Citation: BMC Bioinformatics 2019 20:235
  6. Human papillomavirus (HPV) is a common sexually transmitted infection associated with cervical cancer that frequently occurs as a coinfection of types and subtypes. Highly similar sublineages that show over 10...

    Authors: Eric T. Dawson, Sarah Wagner, David Roberson, Meredith Yeager, Joseph Boland, Erik Garrison, Stephen Chanock, Mark Schiffman, Tina Raine-Bennett, Thomas Lorey, Phillip E. Castle, Lisa Mirabello and Richard Durbin
    Citation: BMC Bioinformatics 2019 20:389
  7. Expression in H-sapiens plays a remarkable role when it comes to social communication. The identification of this expression by human beings is relatively easy and accurate. However, achieving the same result in ...

    Authors: Olalekan Agbolade, Azree Nazri, Razali Yaakob, Abdul Azim Ghani and Yoke Kqueen Cheah
    Citation: BMC Bioinformatics 2019 20:619
  8. Ordinary differential equation systems are frequently utilized to model biological systems and to infer knowledge about underlying properties. For instance, the development of drugs requires the knowledge to w...

    Authors: Pascal Dolejsch, Helge Hass and Jens Timmer
    Citation: BMC Bioinformatics 2019 20:395
  9. Next-generation sequencing is revolutionising diagnosis and treatment of rare diseases, however its application to understanding common disease aetiology is limited. Rare disease applications binarily attribut...

    Authors: E. Mossotto, J. J. Ashton, L. O’Gorman, R. J. Pengelly, R. M. Beattie, B. D. MacArthur and S. Ennis
    Citation: BMC Bioinformatics 2019 20:254
  10. Unsupervised machine learning methods (deep learning) have shown their usefulness with noisy single cell mRNA-sequencing data (scRNA-seq), where the models generalize well, despite the zero-inflation of the da...

    Authors: Savvas Kinalis, Finn Cilius Nielsen, Ole Winther and Frederik Otzen Bagger
    Citation: BMC Bioinformatics 2019 20:379
  11. Prioritization of variants in personal genomic data is a major challenge. Recently, computational methods that rely on comparing phenotype similarity have shown to be useful to identify causative variants. In ...

    Authors: Imane Boudellioua, Maxat Kulmanov, Paul N. Schofield, Georgios V. Gkoutos and Robert Hoehndorf
    Citation: BMC Bioinformatics 2019 20:65
  12. 5′-end sequencing assays, and Cap Analysis of Gene Expression (CAGE) in particular, have been instrumental in studying transcriptional regulation. 5′-end methods provide genome-wide maps of transcription start...

    Authors: Malte Thodberg, Axel Thieffry, Kristoffer Vitting-Seerup, Robin Andersson and Albin Sandelin
    Citation: BMC Bioinformatics 2019 20:487
  13. Mass Spectrometry (MS) is a widely used technique in biology research, and has become key in proteomics and metabolomics analyses. As a result, the amount of MS data has significantly increased in recent years...

    Authors: Ruochen Yang, Xi Chen and Idoia Ochoa
    Citation: BMC Bioinformatics 2019 20:368
  14. Maximum parsimony reconciliation in the duplication-transfer-loss model is widely used in studying the evolutionary histories of genes and species and in studying coevolution of parasites and their hosts and p...

    Authors: Santi Santichaivekin, Ross Mawhorter and Ran Libeskind-Hadas
    Citation: BMC Bioinformatics 2019 20(Suppl 20):636

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

  15. The number of publicly available metagenomic experiments in various environments has been rapidly growing, empowering the potential to identify similar shifts in species abundance between different experiments...

    Authors: Aleksandra I. Perz, Cory B. Giles, Chase A. Brown, Hunter Porter, Xiavan Roopnarinesingh and Jonathan D. Wren
    Citation: BMC Bioinformatics 2019 20(Suppl 2):96

    This article is part of a Supplement: Volume 20 Supplement 2

  16. The accurate determination of parent-progeny relationships within both in situ natural populations and ex situ genetic resource collections can greatly enhance plant breeding/domestication efforts and support ...

    Authors: Arthur T. O. Melo and Iago Hale
    Citation: BMC Bioinformatics 2019 20:108
  17. Cancer arises through accumulation of somatically acquired genetic mutations. An important question is to delineate the temporal order of somatic mutations during carcinogenesis, which contributes to better un...

    Authors: Menghan Wang, Tianxin Yu, Jinpeng Liu, Li Chen, Arnold J. Stromberg, John L. Villano, Susanne M. Arnold, Chunming Liu and Chi Wang
    Citation: BMC Bioinformatics 2019 20:620
  18. Short tandem repeats (STRs) serve as genetic markers in forensic scenes due to their high polymorphism in eukaryotic genomes. A variety of STRs profiling systems have been developed for species including human...

    Authors: Yilin Liu, Jiao Xu, Miaoxia Chen, Changfa Wang and Shuaicheng Li
    Citation: BMC Bioinformatics 2019 20(Suppl 24):671

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

  19. The rapid increase in High-throughput sequencing of RNA (RNA-seq) has led to tremendous improvements in the detection and reconstruction of both expressed coding and non-coding RNA transcripts. Yet, the comple...

    Authors: Thomas Gatter and Peter F Stadler
    Citation: BMC Bioinformatics 2019 20:190
  20. Recent studies have proposed deep learning techniques, namely recurrent neural networks, to improve biomedical text mining tasks. However, these techniques rarely take advantage of existing domain-specific res...

    Authors: Andre Lamurias, Diana Sousa, Luka A. Clarke and Francisco M. Couto
    Citation: BMC Bioinformatics 2019 20:10
  21. Ontology has attracted substantial attention from both academia and industry. Handling uncertainty reasoning is important in researching ontology. For example, when a patient is suffering from cirrhosis, the a...

    Authors: Ying Shen, Yaliang Li, Hai-Tao Zheng, Buzhou Tang and Min Yang
    Citation: BMC Bioinformatics 2019 20:330
  22. The detection of weak signals and selection of single particles from low-contrast micrographs of frozen hydrated biomolecules by cryo-electron microscopy (cryo-EM) represents a major practical bottleneck in cr...

    Authors: Wei Li Wang, Zhou Yu, Luis R. Castillo-Menendez, Joseph Sodroski and Youdong Mao
    Citation: BMC Bioinformatics 2019 20:169
  23. In this study, we compared four models for predicting rice blast disease, two operational process-based models (Yoshino and Water Accounting Rice Model (WARM)) and two approaches based on machine learning algo...

    Authors: David F. Nettleton, Dimitrios Katsantonis, Argyris Kalaitzidis, Natasa Sarafijanovic-Djukic, Pau Puigdollers and Roberto Confalonieri
    Citation: BMC Bioinformatics 2019 20:514
  24. Understanding the genetic networks and their role in chronic diseases (e.g., cancer) is one of the important objectives of biological researchers. In this work, we present a text mining system that constructs ...

    Authors: Amira Al-Aamri, Kamal Taha, Yousof Al-Hammadi, Maher Maalouf and Dirar Homouz
    Citation: BMC Bioinformatics 2019 20:70
  25. Although several studies have provided insights into the role of long non-coding RNAs (lncRNAs), the majority of them have unknown function. Recent evidence has shown the importance of both lncRNAs and chromat...

    Authors: Denise Thiel, Nataša Djurdjevac Conrad, Evgenia Ntini, Ria X. Peschutter, Heike Siebert and Annalisa Marsico
    Citation: BMC Bioinformatics 2019 20:292
  26. Although targeted drugs have contributed to impressive advances in the treatment of cancer patients, their clinical benefits on tumor therapies are greatly limited due to intrinsic and acquired resistance of c...

    Authors: Hui Liu, Wenhao Zhang, Lixia Nie, Xiancheng Ding, Judong Luo and Ling Zou
    Citation: BMC Bioinformatics 2019 20:645
  27. Computational methods provide approaches to identify epitopes in protein Ags to help characterizing potential biomarkers identified by high-throughput genomic or proteomic experiments. PEPOP version 1.0 was de...

    Authors: Vincent Demolombe, Alexandre G. de Brevern, Franck Molina, Géraldine Lavigne, Claude Granier and Violaine Moreau
    Citation: BMC Bioinformatics 2019 20:738
  28. Biochemical networks are often described through static or time-averaged measurements of the component macromolecules. Temporal variation in these components plays an important role in both describing the dyna...

    Authors: Maryam Masnadi-Shirazi, Mano R. Maurya, Gerald Pao, Eugene Ke, Inder M. Verma and Shankar Subramaniam
    Citation: BMC Bioinformatics 2019 20:294
  29. The data deluge can leverage sophisticated ML techniques for functionally annotating the regulatory non-coding genome. The challenge lies in selecting the appropriate classifier for the specific functional ann...

    Authors: Chih-Hao Fang, Nawanol Theera-Ampornpunt, Michael A. Roth, Ananth Grama and Somali Chaterji
    Citation: BMC Bioinformatics 2019 20:488
  30. Alkaloids, a class of organic compounds that contain nitrogen bases, are mainly synthesized as secondary metabolites in plants and fungi, and they have a wide range of bioactivities. Although there are thousan...

    Authors: Ryohei Eguchi, Naoaki Ono, Aki Hirai Morita, Tetsuo Katsuragi, Satoshi Nakamura, Ming Huang, Md. Altaf-Ul-Amin and Shigehiko Kanaya
    Citation: BMC Bioinformatics 2019 20:380
  31. Group structures among genes encoded in functional relationships or biological pathways are valuable and unique features in large-scale molecular data for survival analysis. However, most of previous approache...

    Authors: Zaixiang Tang, Shufeng Lei, Xinyan Zhang, Zixuan Yi, Boyi Guo, Jake Y. Chen, Yueping Shen and Nengjun Yi
    Citation: BMC Bioinformatics 2019 20:94
  32. Protein subcellular localization plays a crucial role in understanding cell function. Proteins need to be in the right place at the right time, and combine with the corresponding molecules to fulfill their fun...

    Authors: Fan Yang, Yang Liu, Yanbin Wang, Zhijian Yin and Zhen Yang
    Citation: BMC Bioinformatics 2019 20:522
  33. As whole-genome sequencing is becoming a routine technique, it is important to identify a cost-effective depth of sequencing for such studies. However, the relationship between sequencing depth and biological ...

    Authors: Yifan Jiang, Yao Jiang, Sheng Wang, Qin Zhang and Xiangdong Ding
    Citation: BMC Bioinformatics 2019 20:556
  34. Cell counting from cell cultures is required in multiple biological and biomedical research applications. Especially, accurate brightfield-based cell counting methods are needed for cell growth analysis. With ...

    Authors: Kaisa Liimatainen, Lauri Kananen, Leena Latonen and Pekka Ruusuvuori
    Citation: BMC Bioinformatics 2019 20:80
  35. A folding RNA molecule encounters multiple opportunities to form non-native yet energetically favorable pairings of nucleotide sequences. Given this forbidding free-energy landscape, mechanisms have evolved th...

    Authors: Guangyao Zhou, Jackson Loper and Stuart Geman
    Citation: BMC Bioinformatics 2019 20:666
  36. We have developed a novel automatic adaptive LASSO (AUTALASSO) based on the alternating direction method of multipliers (ADMM) optimization algorithm. The two major hyper-parameters of ADMM are the learning rate ...

    Authors: Patrik Waldmann, Maja Ferenčaković, Gábor Mészáros, Negar Khayatzadeh, Ino Curik and Johann Sölkner
    Citation: BMC Bioinformatics 2019 20:167
  37. There are many different types of microRNAs (miRNAs) and elucidating their functions is still under intensive research. A fundamental step in functional annotation of a new miRNA is to classify it into charact...

    Authors: Xubo Tang and Yanni Sun
    Citation: BMC Bioinformatics 2019 20(Suppl 23):646

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

  38. The present LSC method will not only provide an initial-stage docking approach for post-docking processes but also have a general implementation for accurate representation of other energy terms on grids in prote...

    Authors: Yumeng Yan and Sheng-You Huang
    Citation: BMC Bioinformatics 2019 20(Suppl 25):696

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

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