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  1. Following publication of the original article [1], the author requested changes to the figures 4, 7, 8, 9, 12 and 14 to align these with the text. The corrected figures are supplied below.

    Authors: Nauman Ahmed, Jonathan Lévy, Shanshan Ren, Hamid Mushtaq, Koen Bertels and Zaid Al-Ars

    Citation: BMC Bioinformatics 2019 20:597

    Content type: Correction

    Published on:

    The original article was published in BMC Bioinformatics 2019 20:520

  2. Researchers commonly analyze lists of differentially expressed entities (DEEs), such as differentially expressed genes (DEGs), differentially expressed proteins (DEPs), and differentially methylated positions/...

    Authors: Stanislav A. Listopad and Trina M. Norden-Krichmar

    Citation: BMC Bioinformatics 2019 20:595

    Content type: Software

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  3. To increase the accuracy of microbiome data analysis, solving the technical limitations of the existing sequencing machines is required. Quality trimming is suggested to reduce the effect of the progressive de...

    Authors: Attayeb Mohsen, Jonguk Park, Yi-An Chen, Hitoshi Kawashima and Kenji Mizuguchi

    Citation: BMC Bioinformatics 2019 20:581

    Content type: Methodology article

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  4. Differential abundance analysis is widely used with high-throughput sequencing data to compare gene abundance or expression between groups of samples. Many software packages exist for this purpose, but each us...

    Authors: Daniel J. Giguere, Jean M. Macklaim, Brandon Y. Lieng and Gregory B. Gloor

    Citation: BMC Bioinformatics 2019 20:580

    Content type: Software

    Published on:

  5. Lung cancer is one of the most common types of cancer, among which lung adenocarcinoma accounts for the largest proportion. Currently, accurate staging is a prerequisite for effective diagnosis and treatment o...

    Authors: Yunyun Dong, Wenkai Yang, Jiawen Wang, Juanjuan Zhao, Yan Qiang, Zijuan Zhao, Ntikurako Guy Fernand Kazihise, Yanfen Cui, Xiaotong Yang and Siyuan Liu

    Citation: BMC Bioinformatics 2019 20:578

    Content type: Research article

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  6. De novo drug discovery is a time-consuming and expensive process. Nowadays, drug repositioning is utilized as a common strategy to discover a new drug indication for existing drugs. This strategy is mostly use...

    Authors: Mahroo Moridi, Marzieh Ghadirinia, Ali Sharifi-Zarchi and Fatemeh Zare-Mirakabad

    Citation: BMC Bioinformatics 2019 20:577

    Content type: Research article

    Published on:

  7. The recent advances in human disease network have provided insights into establishing the relationships between the genotypes and phenotypes of diseases. In spite of the great progress, it yet remains as only a m...

    Authors: Yonghyun Nam, Dong-gi Lee, Sunjoo Bang, Ju Han Kim, Jae-Hoon Kim and Hyunjung Shin

    Citation: BMC Bioinformatics 2019 20:576

    Content type: Methodology article

    Published on:

  8. Biologically data-driven networks have become powerful analytical tools that handle massive, heterogeneous datasets generated from biomedical fields. Protein-protein interaction networks can identify the most ...

    Authors: Milagros Marín, Francisco J. Esteban, Hilario Ramírez-Rodrigo, Eduardo Ros and María José Sáez-Lara

    Citation: BMC Bioinformatics 2019 20:565

    Content type: Methodology article

    Published on:

  9. 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:

  10. The MG-RAST API provides search capabilities and delivers organism and function data as well as raw or annotated sequence data via the web interface and its RESTful API. For casual users, however, RESTful APIs...

    Authors: Tobias Paczian, William L. Trimble, Wolfgang Gerlach, Travis Harrison, Andreas Wilke and Folker Meyer

    Citation: BMC Bioinformatics 2019 20:561

    Content type: Software

    Published on:

  11. Use of the Genome Analysis Toolkit (GATK) continues to be the standard practice in genomic variant calling in both research and the clinic. Recently the toolkit has been rapidly evolving. Significant computati...

    Authors: Jacob R Heldenbrand, Saurabh Baheti, Matthew A Bockol, Travis M Drucker, Steven N Hart, Matthew E Hudson, Ravishankar K Iyer, Michael T Kalmbach, Katherine I Kendig, Eric W Klee, Nathan R Mattson, Eric D Wieben, Mathieu Wiepert, Derek E Wildman and Liudmila S Mainzer

    Citation: BMC Bioinformatics 2019 20:557

    Content type: Software

    Published on:

  12. 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

    Content type: Research article

    Published on:

  13. 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

    Content type: Methodology Article

    Published on:

  14. Tea is the oldest and among the world’s most popular non-alcoholic beverages, which has important economic, health and cultural values. Tea is commonly produced from the leaves of tea plants (Camellia sinensis), ...

    Authors: Fang-Dong Li, Wei Tong, En-Hua Xia and Chao-Ling Wei

    Citation: BMC Bioinformatics 2019 20:553

    Content type: Research article

    Published on:

  15. Long read sequencing technologies such as Oxford Nanopore can greatly decrease the complexity of de novo genome assembly and large structural variation identification. Currently Nanopore reads have high error ...

    Authors: Nathan LaPierre, Rob Egan, Wei Wang and Zhong Wang

    Citation: BMC Bioinformatics 2019 20:552

    Content type: Software

    Published on:

  16. 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

    Content type: Software

    Published on:

  17. 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:

  18. 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:

  19. 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:

  20. 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:

  21. 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:

  22. 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:

  23. 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:

  24. 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:

  25. 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:

  26. 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:

  27. 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:

  28. 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:

  29. 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:

  30. 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:

  31. 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:

  32. 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

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