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  2. Transcriptomic data is often used to build statistical models which are predictive of a given phenotype, such as disease status. Genes work together in pathways and it is widely thought that pathway representa...

    Authors: Marcelo P. Segura-Lepe, Hector C. Keun and Timothy M. D. Ebbels
    Citation: BMC Bioinformatics 2019 20:543
    Content type: Research article Published on:

  3. In biological experiments, comprehensive experimental metadata tracking – which comprises experiment, reagent, and protocol annotation with controlled vocabulary from established ontologies – remains a challen...

    Authors: Elmar Bucher, Cheryl J. Claunch, Derrick Hee, Rebecca L. Smith, Kaylyn Devlin, Wallace Thompson, James E. Korkola and Laura M. Heiser
    Citation: BMC Bioinformatics 2019 20:542
    Content type: Software Published on:

  4. An increasing number of biological and clinical evidences have indicated that the microorganisms significantly get involved in the pathological mechanism of extensive varieties of complex human diseases. Infer...

    Authors: Yahui Long and Jiawei Luo
    Citation: BMC Bioinformatics 2019 20:541
    Content type: Research Article Published on:

  5. Knowledge of phase, the specific allele sequence on each copy of homologous chromosomes, is increasingly recognized as critical for detecting certain classes of disease-associated mutations. One approach for d...

    Authors: Ziad Al Bkhetan, Justin Zobel, Adam Kowalczyk, Karin Verspoor and Benjamin Goudey
    Citation: BMC Bioinformatics 2019 20:540
    Content type: Research Article Published on:

  6. Scaffolding is an important step in genome assembly that orders and orients the contigs produced by assemblers. However, repetitive regions in contigs usually prevent scaffolding from producing accurate result...

    Authors: Junwei Luo, Mengna Lyu, Ranran Chen, Xiaohong Zhang, Huimin Luo and Chaokun Yan
    Citation: BMC Bioinformatics 2019 20:539
    Content type: Methodology Article Published on:

    The Correction to this article has been published in BMC Bioinformatics 2020 21:50

  7. 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

  8. Analysis of high-throughput multi-’omics interactions across the hierarchy of expression has wide interest in making inferences with regard to biological function and biomarker discovery. Expression levels acr...

    Authors: Gregory M. Parkes and Mahesan Niranjan
    Citation: BMC Bioinformatics 2019 20:536
    Content type: Research Article Published on:

  10. Chromatin immunoprecipitation coupled to next generation sequencing (ChIP-Seq) is a widely-used molecular method to investigate the function of chromatin-related proteins by identifying their associated DNA se...

    Authors: Alejandro Saettone, Marcelo Ponce, Syed Nabeel-Shah and Jeffrey Fillingham
    Citation: BMC Bioinformatics 2019 20:533
    Content type: Methodology Article Published on:

  11. High-throughput sequencing experiments, which can determine allele origins, have been used to assess genome-wide allele-specific expression. Despite the amount of data generated from high-throughput experiment...

    Authors: Jing Xie, Tieming Ji, Marco A. R. Ferreira, Yahan Li, Bhaumik N. Patel and Rocio M. Rivera
    Citation: BMC Bioinformatics 2019 20:530
    Content type: Methodology Article Published on:

  14. 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:

  15. Our current understanding of archaic admixture in humans relies on statistical methods with large biases, whose magnitudes depend on the sizes and separation times of ancestral populations. To avoid these bias...

    Authors: Alan R. Rogers
    Citation: BMC Bioinformatics 2019 20:526
    Content type: Software Published on:

  16. Network inference is crucial for biomedicine and systems biology. Biological entities and their associations are often modeled as interaction networks. Examples include drug protein interaction or gene regulat...

    Authors: Konstantinos Pliakos and Celine Vens
    Citation: BMC Bioinformatics 2019 20:525
    Content type: Research Article Published on:

  18. Orthology inference is normally based on full-length protein sequences. However, most proteins contain independently folding and recurring regions, domains. The domain architecture of a protein is vital for it...

    Authors: Emma Persson, Mateusz Kaduk, Sofia K. Forslund and Erik L. L. Sonnhammer
    Citation: BMC Bioinformatics 2019 20:523
    Content type: Research article Published on:

  19. 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
    Content type: Research article Published on:

  20. Quantitative structure-activity relationship (QSAR) is a computational modeling method for revealing relationships between structural properties of chemical compounds and biological activities. QSAR modeling i...

    Authors: Sunyoung Kwon, Ho Bae, Jeonghee Jo and Sungroh Yoon
    Citation: BMC Bioinformatics 2019 20:521
    Content type: Methodology Article Published on:

  21. 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

  24. 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
    Content type: Research article Published on:

  27. One of the challenges in large-scale information retrieval (IR) is developing fine-grained and domain-specific methods to answer natural language questions. Despite the availability of numerous sources and dat...

    Authors: Asma Ben Abacha and Dina Demner-Fushman
    Citation: BMC Bioinformatics 2019 20:511
    Content type: Research Article Published on:

  30. At the molecular level, nonlinear networks of heterogeneous molecules control many biological processes, so that systems biology provides a valuable approach in this field, building on the integration of exper...

    Authors: S. Ha, E. Dimitrova, S. Hoops, D. Altarawy, M. Ansariola, D. Deb, J. Glazebrook, R. Hillmer, H. Shahin, F. Katagiri, J. McDowell, M. Megraw, J. Setubal, B. M. Tyler and R. Laubenbacher
    Citation: BMC Bioinformatics 2019 20:508
    Content type: Software Published on:

  31. Human tumor is a complex tissue with multiple heterogeneous hypoxic regions and significant cell-to-cell variability. Due to the complexity of the disease, the explanation of why anticancer therapies fail cann...

    Authors: Emile P. Chen, Roy S. Song and Xueer Chen
    Citation: BMC Bioinformatics 2019 20:507
    Content type: Research article Published on:

  32. Identifying differentially abundant features between different experimental groups is a common goal for many metabolomics and proteomics studies. However, analyzing data from mass spectrometry (MS) is difficul...

    Authors: Yuntong Li, Teresa W.M. Fan, Andrew N. Lane, Woo-Young Kang, Susanne M. Arnold, Arnold J. Stromberg, Chi Wang and Li Chen
    Citation: BMC Bioinformatics 2019 20:501
    Content type: Methodology Article Published on:

  33. Following publication of the original article [1], the authors noticed that the following errors were introduced by pdf/html formatting issues.

    Authors: Markos Antonopoulos, Dimitra Dionysiou, Georgios Stamatakos and Nikolaos Uzunoglu
    Citation: BMC Bioinformatics 2019 20:500
    Content type: Publisher Correction Published on:

    The original article was published in BMC Bioinformatics 2019 20:442

  34. Metabolic networks reflect the relationships between metabolites (biomolecules) and the enzymes (proteins), and are of particular interest since they describe all chemical reactions of an organism. The metabol...

    Authors: Adèle Weber Zendrera, Nataliya Sokolovska and Hédi A. Soula
    Citation: BMC Bioinformatics 2019 20:499
    Content type: Research Article Published on:

  35. Selecting the proper parameter settings for bioinformatic software tools is challenging. Not only will each parameter have an individual effect on the outcome, but there are also potential interaction effects ...

    Authors: Daniel Svensson, Rickard Sjögren, David Sundell, Andreas Sjödin and Johan Trygg
    Citation: BMC Bioinformatics 2019 20:498
    Content type: Methodology article Published on:

  36. It is widely believed that tertiary nucleotide-nucleotide interactions are essential in determining RNA structure and function. Currently, direct coupling analysis (DCA) infers nucleotide contacts in a sequenc...

    Authors: Yiren Jian, Xiaonan Wang, Jaidi Qiu, Huiwen Wang, Zhichao Liu, Yunjie Zhao and Chen Zeng
    Citation: BMC Bioinformatics 2019 20:497
    Content type: Research article Published on:

  37. 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
    Content type: Research Article Published on:

  38. Literature derived knowledge assemblies have been used as an effective way of representing biological phenomenon and understanding disease etiology in systems biology. These include canonical pathway databases...

    Authors: Reagon Karki, Alpha Tom Kodamullil, Charles Tapley Hoyt and Martin Hofmann-Apitius
    Citation: BMC Bioinformatics 2019 20:494
    Content type: Methodology article Published on:

  40. LC-MS technology makes it possible to measure the relative abundance of numerous molecular features of a sample in single analysis. However, especially non-targeted metabolite profiling approaches generate vas...

    Authors: Marietta Kokla, Jyrki Virtanen, Marjukka Kolehmainen, Jussi Paananen and Kati Hanhineva
    Citation: BMC Bioinformatics 2019 20:492
    Content type: Research article Published on:

  41. The analysis of health and medical data is crucial for improving the diagnosis precision, treatments and prevention. In this field, machine learning techniques play a key role. However, the amount of health da...

    Authors: Josefa Díaz Álvarez, Jordi A. Matias-Guiu, María Nieves Cabrera-Martín, José L. Risco-Martín and José L. Ayala
    Citation: BMC Bioinformatics 2019 20:491
    Content type: Methodology Article Published on:

  42. The development of accurate epitope prediction tools is important in facilitating disease diagnostics, treatment and vaccine development. The advent of new approaches making use of antibody and TCR sequence in...

    Authors: Swapnil Mahajan, Zhen Yan, Martin Closter Jespersen, Kamilla Kjærgaard Jensen, Paolo Marcatili, Morten Nielsen, Alessandro Sette and Bjoern Peters
    Citation: BMC Bioinformatics 2019 20:490
    Content type: Methodology article Published on:

  43. 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
    Content type: Research Article Published on:

  44. 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
    Content type: Software Published on:

  45. Recent advances in high-volume sequencing technology and mining of genomes from metagenomic samples call for rapid and reliable genome quality evaluation. The current release of the PATRIC database contains ov...

    Authors: Bruce Parrello, Rory Butler, Philippe Chlenski, Robert Olson, Jamie Overbeek, Gordon D. Pusch, Veronika Vonstein and Ross Overbeek
    Citation: BMC Bioinformatics 2019 20:486
    Content type: Database Published on:

  47. MicroRNAs (miRNAs) are noncoding RNA molecules heavily involved in human tumors, in which few of them circulating the human body. Finding a tumor-associated signature of miRNA, that is, the minimum miRNA entit...

    Authors: Alejandro Lopez-Rincon, Marlet Martinez-Archundia, Gustavo U. Martinez-Ruiz, Alexander Schoenhuth and Alberto Tonda
    Citation: BMC Bioinformatics 2019 20:480
    Content type: Research Article Published on:

  48. The adverse reactions that are caused by drugs are potentially life-threatening problems. Comprehensive knowledge of adverse drug reactions (ADRs) can reduce their detrimental impacts on patients. Detecting AD...

    Authors: Tongxuan Zhang, Hongfei Lin, Yuqi Ren, Liang Yang, Bo Xu, Zhihao Yang, Jian Wang and Yijia Zhang
    Citation: BMC Bioinformatics 2019 20:479
    Content type: Research Article Published on:

  49. Binding sites are the pockets of proteins that can bind drugs; the discovery of these pockets is a critical step in drug design. With the help of computers, protein pockets prediction can save manpower and fin...

    Authors: Mingjian Jiang, Zhen Li, Yujie Bian and Zhiqiang Wei
    Citation: BMC Bioinformatics 2019 20:478
    Content type: Methodology Article Published on:

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