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

Page 6 of 9

  1. Differences in average signature size were observed with different methods applied. The gene signatures identified by the Latent Effect Adjustment after Primary Projection (LEAPP) method and the methods fitted...

    Authors: Wei Zhou, Karel K. M. Koudijs and Stefan Böhringer
    Citation: BMC Bioinformatics 2019 20:437
  2. Computational approaches for the determination of biologically-active/native three-dimensional structures of proteins with novel sequences have to handle several challenges. The (conformation) space of possibl...

    Authors: Ahmed Bin Zaman and Amarda Shehu
    Citation: BMC Bioinformatics 2019 20:211
  3. Reconstruction of protein-protein interaction networks (PPIN) has been riddled with controversy for decades. Particularly, false-negative and -positive interactions make this progress even more complicated. Al...

    Authors: Minoo Ashtiani, Payman Nickchi, Soheil Jahangiri-Tazehkand, Abdollah Safari, Mehdi Mirzaie and Mohieddin Jafari
    Citation: BMC Bioinformatics 2019 20:73
  4. Mining epistatic loci which affects specific phenotypic traits is an important research issue in the field of biology. Bayesian network (BN) is a graphical model which can express the relationship between gene...

    Authors: Yang Guo, Zhiman Zhong, Chen Yang, Jiangfeng Hu, Yaling Jiang, Zizhen Liang, Hui Gao and Jianxiao Liu
    Citation: BMC Bioinformatics 2019 20:444
  5. S-sulphenylation is a ubiquitous protein post-translational modification (PTM) where an S-hydroxyl (−SOH) bond is formed via the reversible oxidation on the Sulfhydryl group of cysteine (C). Recent experimenta...

    Authors: Xiaochuan Wang, Chen Li, Fuyi Li, Varun S. Sharma, Jiangning Song and Geoffrey I. Webb
    Citation: BMC Bioinformatics 2019 20:602
  6. Although many of the genic features in Mycobacterium abscessus have been fully validated, a comprehensive understanding of the regulatory elements remains lacking. Moreover, there is little understanding of how t...

    Authors: Patrick M. Staunton, Aleksandra A. Miranda-CasoLuengo, Brendan J. Loftus and Isobel Claire Gormley
    Citation: BMC Bioinformatics 2019 20:466
  7. Several methods to handle data generated from bottom-up proteomics via liquid chromatography-mass spectrometry, particularly for peptide-centric quantification dealing with post-translational modification (PTM...

    Authors: Philip Berg, Evan W. McConnell, Leslie M. Hicks, Sorina C. Popescu and George V. Popescu
    Citation: BMC Bioinformatics 2019 20(Suppl 2):102

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

  8. The proposed method was applied to 10 disease pathways. In total, thirty candidate genes were suggested. The result was validated with gene set enrichment analysis software, PubMed literature review and de facto ...

    Authors: Sunjoo Bang, Sangjoon Son, Sooyoung Kim and Hyunjung Shin
    Citation: BMC Bioinformatics 2019 20:74
  9. 2′-O-methylation (2′-O-me or Nm) is a post-transcriptional RNA methylation modified at 2′-hydroxy, which is common in mRNAs and various non-coding RNAs. Previous studies revealed the significance of Nm in mult...

    Authors: Yiran Zhou, Qinghua Cui and Yuan Zhou
    Citation: BMC Bioinformatics 2019 20(Suppl 25):690

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

  10. Lineage rate heterogeneity can be a major source of bias, especially in multi-gene phylogeny inference. We had previously tackled this issue by developing LS3, a data subselection algorithm that, by removing fast...

    Authors: Carlos J. Rivera-Rivera and Juan I. Montoya-Burgos
    Citation: BMC Bioinformatics 2019 20:420
  11. Macrophages show versatile functions in innate immunity, infectious diseases, and progression of cancers and cardiovascular diseases. These versatile functions of macrophages are conducted by different macroph...

    Authors: Ricardo Ramirez, Allen Michael Herrera, Joshua Ramirez, Chunjiang Qian, David W. Melton, Paula K. Shireman and Yu-Fang Jin
    Citation: BMC Bioinformatics 2019 20:725
  12. In systems biology, there is an acute need for integrative approaches in heterogeneous network mining in order to exploit the continuous flux of genomic data. Simultaneous analysis of the metabolic pathways an...

    Authors: Alexandra Zaharia, Bernard Labedan, Christine Froidevaux and Alain Denise
    Citation: BMC Bioinformatics 2019 20:19
  13. When applying genomic medicine to a rare disease patient, the primary goal is to identify one or more genomic variants that may explain the patient’s phenotypes. Typically, this is done through annotation, fil...

    Authors: James M. Holt, Brandon Wilk, Camille L. Birch, Donna M. Brown, Manavalan Gajapathy, Alexander C. Moss, Nadiya Sosonkina, Melissa A. Wilk, Julie A. Anderson, Jeremy M. Harris, Jacob M. Kelly, Fariba Shaterferdosian, Angelina E. Uno-Antonison, Arthur Weborg and Elizabeth A. Worthey
    Citation: BMC Bioinformatics 2019 20:496
  14. Data from genome-wide association studies (GWASs) have been used to estimate the heritability of human complex traits in recent years. Existing methods are based on the linear mixed model, with the assumption ...

    Authors: Xin Li, Dongya Wu, Yue Cui, Bing Liu, Henrik Walter, Gunter Schumann, Chong Li and Tianzi Jiang
    Citation: BMC Bioinformatics 2019 20:219
  15. Pharmacogenomics (PGx) studies how genomic variations impact variations in drug response phenotypes. Knowledge in pharmacogenomics is typically composed of units that have the form of ternary relationships gene v...

    Authors: Pierre Monnin, Joël Legrand, Graziella Husson, Patrice Ringot, Andon Tchechmedjiev, Clément Jonquet, Amedeo Napoli and Adrien Coulet
    Citation: BMC Bioinformatics 2019 20(Suppl 4):139

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

    The Data Descriptor to this article has been published in Scientific Data 2020 7:3

  16. The advent of high-throughput experimental techniques paved the way to genome-wide computational analysis and predictive annotation studies. When considering the joint annotation of a large set of related enti...

    Authors: Stefano Teso, Luca Masera, Michelangelo Diligenti and Andrea Passerini
    Citation: BMC Bioinformatics 2019 20:338
  17. Untargeted metabolomics of host-associated samples has yielded insights into mechanisms by which microbes modulate health. However, data interpretation is challenged by the complexity of origins of the small m...

    Authors: M. Shaffer, K. Thurimella, K. Quinn, K. Doenges, X. Zhang, S. Bokatzian, N. Reisdorph and C. A. Lozupone
    Citation: BMC Bioinformatics 2019 20:614
  18. Due to the challenging nature of contact prediction, it is beneficial to develop and benchmark a variety of different prediction methods. Our work has produced useful tools with a simple interface that can provid...

    Authors: Joseph Luttrell IV, Tong Liu, Chaoyang Zhang and Zheng Wang
    Citation: BMC Bioinformatics 2019 20(Suppl 2):100

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

  19. Genome graph is an emerging approach for representing structural variants on genomes with branches. For example, representing structural variants of cancer genomes as a genome graph is more natural than repres...

    Authors: Toshiyuki T. Yokoyama, Yoshitaka Sakamoto, Masahide Seki, Yutaka Suzuki and Masahiro Kasahara
    Citation: BMC Bioinformatics 2019 20:548
  20. Super-enhancers (SEs) are clusters of transcriptional active enhancers, which dictate the expression of genes defining cell identity and play an important role in the development and progression of tumors and ...

    Authors: Hongda Bu, Jiaqi Hao, Yanglan Gan, Shuigeng Zhou and Jihong Guan
    Citation: BMC Bioinformatics 2019 20(Suppl 15):598

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

  21. Protein feature extraction plays an important role in the areas of similarity analysis of protein sequences and prediction of protein structures, functions and interactions. The feature extraction based on gra...

    Authors: Zengchao Mu, Ting Yu, Enfeng Qi, Juntao Liu and Guojun Li
    Citation: BMC Bioinformatics 2019 20:351
  22. 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

  23. 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

  24. With advancements in high-throughput technologies, the cost of obtaining expression profiles of both mRNA and microRNA in the same individual has substantially decreased. Integrated analysis of these profiles ...

    Authors: Ti-Tai Wang, Chien-Yueh Lee, Liang-Chuan Lai, Mong-Hsun Tsai, Tzu-Pin Lu and Eric Y. Chuang
    Citation: BMC Bioinformatics 2019 20:239
  25. 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

  26. We previously introduced a random-effects model to analyze a set of patients, each of which has two distinct tumors. The goal is to estimate the proportion of patients for which one of the tumors is a metastas...

    Authors: Audrey Mauguen, Venkatraman E. Seshan, Irina Ostrovnaya and Colin B. Begg
    Citation: BMC Bioinformatics 2019 20:555
  27. 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
  28. The retrieval of plant-related information is a challenging task due to variations in species name mentions as well as spelling or typographical errors across data sources. Scalable solutions are needed for id...

    Authors: Vivekanand Sharma, Maria Isabel Restrepo and Indra Neil Sarkar
    Citation: BMC Bioinformatics 2019 20:263
  29. It has been shown that the deregulation of miRNAs is associated with the development and progression of many human diseases. To reduce time and cost of biological experiments, a number of algorithms have been ...

    Authors: Hailin Chen, Zuping Zhang and Dayi Feng
    Citation: BMC Bioinformatics 2019 20:404
  30. 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
  31. 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
  32. Third-generation sequencing platforms, such as PacBio sequencing, have been developed rapidly in recent years. PacBio sequencing generates much longer reads than the second-generation sequencing (or the next g...

    Authors: Wenmin Zhang, Ben Jia and Chaochun Wei
    Citation: BMC Bioinformatics 2019 20:352
  33. 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
  34. Recent advances in whole-genome sequencing and SNP array technology have led to the generation of a large amount of genotype data. Large volumes of genotype data will require faster and more efficient methods ...

    Authors: Ardalan Naseri, Degui Zhi and Shaojie Zhang
    Citation: BMC Bioinformatics 2019 20(Suppl 11):279

    This article is part of a Supplement: Volume 20 Supplement 11

  35. 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
  36. 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

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