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  3. Natural products are the source of various functional materials such as medicines, and understanding their biosynthetic pathways can provide information that is helpful for their effective production through t...

    Authors: Kohei Amano, Tsubasa Matsumoto, Kenichi Tanaka, Kimito Funatsu and Masaaki Kotera

    Citation: BMC Bioinformatics 2019 20:728

    Content type: Methodology article

    Published on:

  4. The Drug Ontology (DrOn) is a modular, extensible ontology of drug products, their ingredients, and their biological activity created to enable comparative effectiveness and health services researchers to quer...

    Authors: Jonathan P. Bona, Mathias Brochhausen and William R. Hogan

    Citation: BMC Bioinformatics 2019 20(Suppl 21):708

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 21

  5. Use of medication can cause adverse drug reactions (ADRs), unwanted or unexpected events, which are a major safety concern. Drug labels, or prescribing information or package inserts, describe ADRs. Therefore,...

    Authors: Mert Tiftikci, Arzucan Özgür, Yongqun He and Junguk Hur

    Citation: BMC Bioinformatics 2019 20(Suppl 21):707

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 21

  6. In the United States and parts of the world, the human papillomavirus vaccine uptake is below the prescribed coverage rate for the population. Some research have noted that dialogue that communicates the risks...

    Authors: Muhammad Amith, Kirk Roberts and Cui Tao

    Citation: BMC Bioinformatics 2019 20(Suppl 21):706

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 21

  7. This Editorial first introduces the background of the vaccine and drug relations and how biomedical terminologies and ontologies have been used to support their studies. The history of the seven workshops, ini...

    Authors: Junguk Hur, Cui Tao and Yongqun He

    Citation: BMC Bioinformatics 2019 20(Suppl 21):705

    Content type: Introduction

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 21

  8. Different human responses to the same vaccine were frequently observed. For example, independent studies identified overlapping but different transcriptomic gene expression profiles in Yellow Fever vaccine 17D...

    Authors: Edison Ong, Peter Sun, Kimberly Berke, Jie Zheng, Guanming Wu and Yongqun He

    Citation: BMC Bioinformatics 2019 20(Suppl 21):704

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 21

  9. Adenosine-to-inosine RNA editing can markedly diversify the transcriptome, leading to a variety of critical molecular and biological processes in mammals. Over the past several years, researchers have develope...

    Authors: Xikang Feng, Zishuai Wang, Hechen Li and Shuai Cheng Li

    Citation: BMC Bioinformatics 2019 20(Suppl 24):596

    Content type: Research

    Published on:

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

  10. Following publication of the original article [1], the author reported that an incorrect figure has been published as Figure 2. The correct Figure 2 is shown below.

    Authors: Maria Littmann, Tatyana Goldberg, Sebastian Seitz, Mikael Bodén and Burkhard Rost

    Citation: BMC Bioinformatics 2019 20:727

    Content type: Correction

    Published on:

    The original article was published in BMC Bioinformatics 2019 20:205

  11. Emerging evidence suggests retroviruses play a role in the pathophysiology of amyotrophic lateral sclerosis (ALS). Specifically, activation of ancient viral genes embedded in the human genome is theorized to l...

    Authors: Jon P. Klein, Zhifu Sun and Nathan P. Staff

    Citation: BMC Bioinformatics 2019 20(Suppl 24):680

    Content type: Research

    Published on:

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

  12. RNA sequencing technologies have allowed researchers to gain a better understanding of how the transcriptome affects disease. However, sequencing technologies often unintentionally introduce experimental error...

    Authors: Zachary B. Abrams, Travis S. Johnson, Kun Huang, Philip R. O. Payne and Kevin Coombes

    Citation: BMC Bioinformatics 2019 20(Suppl 24):679

    Content type: Research

    Published on:

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

  13. 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

  14. Signal peptides play an important role in protein sorting, which is the mechanism whereby proteins are transported to their destination. Recognition of signal peptides is an important first step in determining...

    Authors: Jhe-Ming Wu, Yu-Chen Liu and Darby Tien-Hao Chang

    Citation: BMC Bioinformatics 2019 20(Suppl 24):677

    Content type: Research

    Published on:

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

  15. Between June 9–11, 2019, the International Conference on Intelligent Biology and Medicine (ICIBM 2019) was held in Columbus, Ohio, USA. The conference included 12 scientific sessions, five tutorials or worksho...

    Authors: Zhongming Zhao, Yulin Dai, Chi Zhang, Ewy Mathé, Lai Wei and Kai Wang

    Citation: BMC Bioinformatics 2019 20(Suppl 24):676

    Content type: Introduction

    Published on:

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

  16. Gene expression profiling experiments with few replicates lead to great variability in the estimates of gene variances. Toward this end, several moderated t-test methods have been developed to reduce this vari...

    Authors: Lianbo Yu, Jianying Zhang, Guy Brock and Soledad Fernandez

    Citation: BMC Bioinformatics 2019 20(Suppl 24):675

    Content type: Methodology

    Published on:

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

  17. Computational prediction of a phenotypic response upon the chemical perturbation on a biological system plays an important role in drug discovery, and many other applications. Chemical fingerprints are a widel...

    Authors: Mohamed Ayed, Hansaim Lim and Lei Xie

    Citation: BMC Bioinformatics 2019 20(Suppl 24):674

    Content type: Research

    Published on:

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

  18. With the rise of metabolomics, the development of methods to address analytical challenges in the analysis of metabolomics data is of great importance. Missing values (MVs) are pervasive, yet the treatment of ...

    Authors: Jasmit Shah, Guy N. Brock and Jeremy Gaskins

    Citation: BMC Bioinformatics 2019 20(Suppl 24):673

    Content type: Research

    Published on:

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

  19. Various statistical models have been developed to model the single cell RNA-seq expression profiles, capture its multimodality, and conduct differential gene expression test. However, for expression data gener...

    Authors: Yu Zhang, Changlin Wan, Pengcheng Wang, Wennan Chang, Yan Huo, Jian Chen, Qin Ma, Sha Cao and Chi Zhang

    Citation: BMC Bioinformatics 2019 20(Suppl 24):672

    Content type: Research

    Published on:

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

  20. 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

    Content type: Methodology

    Published on:

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

  21. RNA sequencing has become an increasingly affordable way to profile gene expression patterns. Here we introduce a workflow implementing several open-source softwares that can be run on a high performance compu...

    Authors: Venkat Sundar Gadepalli, Hatice Gulcin Ozer, Ayse Selen Yilmaz, Maciej Pietrzak and Amy Webb

    Citation: BMC Bioinformatics 2019 20(Suppl 24):670

    Content type: Research

    Published on:

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

  22. Proteomic measurements, which closely reflect phenotypes, provide insights into gene expression regulations and mechanisms underlying altered phenotypes. Further, integration of data on proteome and transcript...

    Authors: Tara Eicher, Andrew Patt, Esko Kautto, Raghu Machiraju, Ewy Mathé and Yan Zhang

    Citation: BMC Bioinformatics 2019 20(Suppl 24):669

    Content type: Case Study

    Published on:

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

  23. Skewness is an under-utilized statistical measure that captures the degree of asymmetry in the distribution of any dataset. This study applied a new metric based on skewness to identify regulators or genes tha...

    Authors: Benjamin V. Church, Henry T. Williams and Jessica C. Mar

    Citation: BMC Bioinformatics 2019 20(Suppl 24):668

    Content type: Research

    Published on:

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

  24. Current approaches to identifying drug-drug interactions (DDIs), include safety studies during drug development and post-marketing surveillance after approval, offer important opportunities to identify potenti...

    Authors: Remzi Celebi, Huseyin Uyar, Erkan Yasar, Ozgur Gumus, Oguz Dikenelli and Michel Dumontier

    Citation: BMC Bioinformatics 2019 20:726

    Content type: Research Article

    Published on:

  25. 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

    Content type: Research article

    Published on:

  26. Quantitative areas is of great measurement of wound significance in clinical trials, wound pathological analysis, and daily patient care. 2D methods cannot solve the problems caused by human body curvatures an...

    Authors: Chunhui Liu, Xingyu Fan, Zhizhi Guo, Zhongjun Mo, Eric I-Chao Chang and Yan Xu

    Citation: BMC Bioinformatics 2019 20:724

    Content type: Methodology Article

    Published on:

  27. Predicting protein function and structure from sequence is one important challenge for computational biology. For 26 years, most state-of-the-art approaches combined machine learning and evolutionary informati...

    Authors: Michael Heinzinger, Ahmed Elnaggar, Yu Wang, Christian Dallago, Dmitrii Nechaev, Florian Matthes and Burkhard Rost

    Citation: BMC Bioinformatics 2019 20:723

    Content type: Research article

    Published on:

  28. Following publication of the original article [1], the author explained that Table 2 is displayed incorrectly. The correct Table 2 is given below. The original article has been corrected.

    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 20:722

    Content type: Correction

    Published on:

    The original article was published in BMC Bioinformatics 2019 20:557

  29. Galled trees are studied as a recombination model in theoretical population genetics. This class of phylogenetic networks has been generalized to tree-child networks and other network classes by relaxing a str...

    Authors: Louxin Zhang

    Citation: BMC Bioinformatics 2019 20(Suppl 20):642

    Content type: Research

    Published on:

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

  30. Many cancer genomes are extensively rearranged with highly aberrant chromosomal karyotypes. Structural and copy number variations in cancer genomes can be determined via abnormal mapping of sequenced reads to ...

    Authors: Sergey Aganezov, Ilya Zban, Vitaly Aksenov, Nikita Alexeev and Michael C. Schatz

    Citation: BMC Bioinformatics 2019 20(Suppl 20):641

    Content type: Research

    Published on:

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

  31. It is now well established that eukaryotic coding genes have the ability to produce more than one type of transcript thanks to the mechanisms of alternative splicing and alternative transcription. Because of t...

    Authors: Esaie Kuitche, Safa Jammali and Aïda Ouangraoua

    Citation: BMC Bioinformatics 2019 20(Suppl 20):640

    Content type: Research

    Published on:

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

  32. Reconciliation methods are widely used to explain incongruence between a gene tree and species tree. However, the common approach of inferring maximum parsimony reconciliations (MPRs) relies on user-defined co...

    Authors: Ross Mawhorter, Nuo Liu, Ran Libeskind-Hadas and Yi-Chieh Wu

    Citation: BMC Bioinformatics 2019 20(Suppl 20):639

    Content type: Methodology

    Published on:

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

  33. In many fields of biomedical research, it is important to estimate phylogenetic distances between taxa based on low-coverage sequencing reads. Major applications are, for example, phylogeny reconstruction, spe...

    Authors: Anna-Katharina Lau, Svenja Dörrer, Chris-André Leimeister, Christoph Bleidorn and Burkhard Morgenstern

    Citation: BMC Bioinformatics 2019 20(Suppl 20):638

    Content type: Research

    Published on:

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

  34. Bacterial pathogens exhibit an impressive amount of genomic diversity. This diversity can be informative of evolutionary adaptations, host-pathogen interactions, and disease transmission patterns. However, cap...

    Authors: Guo Liang Gan, Elijah Willie, Cedric Chauve and Leonid Chindelevitch

    Citation: BMC Bioinformatics 2019 20(Suppl 20):637

    Content type: Research

    Published on:

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

  35. 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

    Content type: Methodology

    Published on:

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

  36. A basic tool for studying the polyploidization history of a genome, especially in plants, is the distribution of duplicate gene similarities in syntenically aligned regions of a genome. This distribution can u...

    Authors: Yue Zhang, Chunfang Zheng and David Sankoff

    Citation: BMC Bioinformatics 2019 20(Suppl 20):635

    Content type: Research

    Published on:

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

  37. High-throughput technologies have brought tremendous changes to biological domains, and the resulting high-dimensional data has also posed enormous challenges to computational science. A Bayesian network is a ...

    Authors: Jiajin Chen, Ruyang Zhang, Xuesi Dong, Lijuan Lin, Ying Zhu, Jieyu He, David C. Christiani, Yongyue Wei and Feng Chen

    Citation: BMC Bioinformatics 2019 20:711

    Content type: Software

    Published on:

  38. High throughput sequence data has provided in depth means of molecular characterization of populations. When recorded at numerous time steps, such data can reveal the evolutionary dynamics of the population un...

    Authors: Chandler D. Gatenbee, Ryan O. Schenck, Rafael R. Bravo and Alexander R. A. Anderson

    Citation: BMC Bioinformatics 2019 20:710

    Content type: Software

    Published on:

  39. Late-Onset Alzheimer’s Disease (LOAD) is a leading form of dementia. There is no effective cure for LOAD, leaving the treatment efforts to depend on preventive cognitive therapies, which stand to benefit from ...

    Authors: Javier De Velasco Oriol, Edgar E. Vallejo, Karol Estrada, José Gerardo Taméz Peña and The Alzheimer’s Disease Neuroimaging Initiative

    Citation: BMC Bioinformatics 2019 20:709

    Content type: Research Article

    Published on:

  40. Development of new drugs is a time-consuming and costly process, and the cost is still increasing in recent years. However, the number of drugs approved by FDA every year per dollar spent on development is dec...

    Authors: Ran Wang, Shuai Li, Lixin Cheng, Man Hon Wong and Kwong Sak Leung

    Citation: BMC Bioinformatics 2019 20(Suppl 26):628

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 26

  41. 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

    Content type: Research Article

    Published on:

  42. 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:

  43. A lack of reproducibility has been repeatedly criticized in computational research. High throughput sequencing (HTS) data analysis is a complex multi-step process. For most of the steps a range of bioinformati...

    Authors: Christoph Kämpf, Michael Specht, Alexander Scholz, Sven-Holger Puppel, Gero Doose, Kristin Reiche, Jana Schor and Jörg Hackermüller

    Citation: BMC Bioinformatics 2019 20:664

    Content type: Software

    Published on:

  44. Circular DNA has recently been identified across different species including human normal and cancerous tissue, but short-read mappers are unable to align many of the reads crossing circle junctions hence limi...

    Authors: Iñigo Prada-Luengo, Anders Krogh, Lasse Maretty and Birgitte Regenberg

    Citation: BMC Bioinformatics 2019 20:663

    Content type: Software

    Published on:

  45. Next generation sequencing instruments are providing new opportunities for comprehensive analyses of cancer genomes. The increasing availability of tumor data allows to research the complexity of cancer diseas...

    Authors: Martin Palazzo, Pierre Beauseroy and Patricio Yankilevich

    Citation: BMC Bioinformatics 2019 20:655

    Content type: Methodology Article

    Published on:

  46. 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

  47. Computational compound repositioning has the potential for identifying new uses for existing drugs, and new algorithms and data source aggregation strategies provide ever-improving results via in silico metric...

    Authors: Michael Mayers, Tong Shu Li, Núria Queralt-Rosinach and Andrew I. Su

    Citation: BMC Bioinformatics 2019 20:653

    Content type: Research article

    Published on:

  48. Multiple Sclerosis (MS) is an immune-mediated inflammatory disease of the Central Nervous System (CNS) which damages the myelin sheath enveloping nerve cells thus causing severe physical disability in patients...

    Authors: Simone Pernice, Marzio Pennisi, Greta Romano, Alessandro Maglione, Santina Cutrupi, Francesco Pappalardo, Gianfranco Balbo, Marco Beccuti, Francesca Cordero and Raffaele A. Calogero

    Citation: BMC Bioinformatics 2019 20(Suppl 6):623

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 6

  49. The 2nd Computational Methods for the Immune System function Workshop has been held in Madrid in conjunction with the IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2018) in Madrid, Spai...

    Authors: Francesco Pappalardo, Marzio Pennisi, Pedro A. Reche and Giulia Russo

    Citation: BMC Bioinformatics 2019 20(Suppl 6):622

    Content type: Introduction

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 6

  50. Neutrophils are one of the key players in the human innate immune system (HIIS). In the event of an insult where the body is exposed to inflammation triggering moieties (ITMs), neutrophils are mobilized toward...

    Authors: Alva Presbitero, Emiliano Mancini, Filippo Castiglione, Valeria V. Krzhizhanovskaya and Rick Quax

    Citation: BMC Bioinformatics 2019 20(Suppl 6):475

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 6

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