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  1. As the terminal products of cellular regulatory process, functional related metabolites have a close relationship with complex diseases, and are often associated with the same or similar diseases. Therefore, i...

    Authors: Yongtian Wang, Liran Juan, Jiajie Peng, Tianyi Zang and Yadong Wang
    Citation: BMC Bioinformatics 2019 20(Suppl 18):574
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 18

  2. During procedures for conducting multiple sequence alignment, that is so essential to use the substitution score of pairwise alignment. To compute adaptive scores for alignment, researchers usually use Hidden ...

    Authors: Qing Zhan, Nan Wang, Shuilin Jin, Renjie Tan, Qinghua Jiang and Yadong Wang
    Citation: BMC Bioinformatics 2019 20(Suppl 18):573
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 18

  3. There is evidence to suggest that lncRNAs are associated with distinct and diverse biological processes. The dysfunction or mutation of lncRNAs are implicated in a wide range of diseases. An accurate computati...

    Authors: Jialu Hu, Yiqun Gao, Jing Li, Yan Zheng, Jingru Wang and Xuequn Shang
    Citation: BMC Bioinformatics 2019 20(Suppl 18):569
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 18

  4. It’s a very urgent task to identify cancer genes that enables us to understand the mechanisms of biochemical processes at a biomolecular level and facilitates the development of bioinformatics. Although a larg...

    Authors: Wenxiang Zhang, Xiujuan Lei (IEEE member) and Chen Bian
    Citation: BMC Bioinformatics 2019 20(Suppl 18):518
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 18

  5. This preface introduces the content of the BioMed Central Bioinformatics journal Supplement related to the 15th annual meeting of the Bioinformatics Italian Society, BITS2018. The Conference was held in Torino...

    Authors: Francesca Cordero, Raffaele A. Calogero and Michele Caselle
    Citation: BMC Bioinformatics 2019 20(Suppl 9):562
    Content type: Introduction Published on:

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

  6. Transposable elements (TEs) are DNA sequences able to mobilize themselves and to increase their copy-number in the host genome. In the past, they have been considered mainly selfish DNA without evident functions....

    Authors: Giovanni Spirito, Damiano Mangoni, Remo Sanges and Stefano Gustincich
    Citation: BMC Bioinformatics 2019 20(Suppl 9):495
    Content type: Research Published on:

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

  7. Transposable Elements (TE) are mobile sequences that make up large portions of eukaryote genomes. The functions they play within the complex cellular architecture are still not clearly understood, but it is be...

    Authors: Federico Ansaloni, Margherita Scarpato, Elia Di Schiavi, Stefano Gustincich and Remo Sanges
    Citation: BMC Bioinformatics 2019 20(Suppl 9):484
    Content type: Research Published on:

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

  8. In the last few years, 16S rRNA gene sequencing (16S rDNA-seq) has seen a surprisingly rapid increase in election rate as a methodology to perform microbial community studies. Despite the considerable populari...

    Authors: Ilaria Patuzzi, Giacomo Baruzzo, Carmen Losasso, Antonia Ricci and Barbara Di Camillo
    Citation: BMC Bioinformatics 2019 20(Suppl 9):416
    Content type: Methodology Published on:

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

  9. Humans have adapted to widespread changes during the past 2 million years in both environmental and lifestyle factors. This is evident in overall body alterations such as average height and brain size. Althoug...

    Authors: Mainá Bitar, Stefanie Kuiper, Elizabeth A. O’Brien and Guy Barry
    Citation: BMC Bioinformatics 2019 20(Suppl 9):406
    Content type: Research Published on:

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

  10. Logic Learning Machine (LLM) is an innovative method of supervised analysis capable of constructing models based on simple and intelligible rules.

    Authors: Damiano Verda, Stefano Parodi, Enrico Ferrari and Marco Muselli
    Citation: BMC Bioinformatics 2019 20(Suppl 9):390
    Content type: Research Published on:

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

  11. Sequencing technologies allow the sequencing of microbial communities directly from the environment without prior culturing. Because assembly typically produces only genome fragments, also known as contigs, it...

    Authors: Jia Qian and Matteo Comin
    Citation: BMC Bioinformatics 2019 20(Suppl 9):367
    Content type: Research Published on:

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

  12. Several large public repositories of microarray datasets and RNA-seq data are available. Two prominent examples include ArrayExpress and NCBI GEO. Unfortunately, there is no easy way to import and manipulate d...

    Authors: Salvatore Alaimo, Antonio Di Maria, Dennis Shasha, Alfredo Ferro and Alfredo Pulvirenti
    Citation: BMC Bioinformatics 2019 20(Suppl 9):366
    Content type: Software Published on:

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

  13. Multi-locus sequence typing (MLST) is a standard typing technique used to associate a sequence type (ST) to a bacterial isolate. When the output of whole genome sequencing (WGS) of a sample is available the ST...

    Authors: Mattia Dalsass, Margherita Bodini, Christophe Lambert, Marie-Cécile Mortier, Marco Romanelli, Duccio Medini, Alessandro Muzzi and Alessandro Brozzi
    Citation: BMC Bioinformatics 2019 20(Suppl 9):347
    Content type: Software Published on:

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

  14. In silico experiments, with the aid of computer simulation, speed up the process of in vitro or in vivo experiments. Cancer therapy design is often based on signalling pathway. MicroRNAs (miRNA) are small non-...

    Authors: Valeria Boscaino, Antonino Fiannaca, Laura La Paglia, Massimo La Rosa, Riccardo Rizzo and Alfonso Urso
    Citation: BMC Bioinformatics 2019 20(Suppl 9):344
    Content type: Research Published on:

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

  15. The genetic bases of many complex phenotypes are still largely unknown, mostly due to the polygenic nature of the traits and the small effect of each associated mutation. An alternative approach to classic ass...

    Authors: Luis Torada, Lucrezia Lorenzon, Alice Beddis, Ulas Isildak, Linda Pattini, Sara Mathieson and Matteo Fumagalli
    Citation: BMC Bioinformatics 2019 20(Suppl 9):337
    Content type: Software Published on:

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

  16. 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
    Content type: Research Published on:

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

  18. Deep sequencing of transposon mutant libraries (or TnSeq) is a powerful method for probing essentiality of genomic loci under different environmental conditions. Various analytical methods have been described ...

    Authors: Siddharth Subramaniyam, Michael A. DeJesus, Anisha Zaveri, Clare M. Smith, Richard E. Baker, Sabine Ehrt, Dirk Schnappinger, Christopher M. Sassetti and Thomas R. Ioerger
    Citation: BMC Bioinformatics 2019 20:603
    Content type: Methodology Article Published on:

  19. 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
    Content type: Software Published on:

  20. High-throughput gene expression profiles have allowed discovery of potential biomarkers enabling early diagnosis, prognosis and developing individualized treatment. However, it remains a challenge to identify ...

    Authors: Ling Zhang, Ishwor Thapa, Christian Haas and Dhundy Bastola
    Citation: BMC Bioinformatics 2019 20:601
    Content type: Methodology Article Published on:

  21. Following publication of the original article [1], the authors requested to update a link in the article. There was a server update and the hosted applications needed to move to a new web location.

    Authors: Bhusan K. Kuntal, Anirban Dutta and Sharmila S. Mande
    Citation: BMC Bioinformatics 2019 20:600
    Content type: Correction Published on:

    The original article was published in BMC Bioinformatics 2016 17:185

  23. 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

  24. 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 Published on:

  25. 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 Published on:

  26. 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:

  27. 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 Published on:

  28. 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:

  29. 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:

  31. 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:

  33. 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:

  34. 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:

  38. 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:

    The Correction to this article has been published in BMC Bioinformatics 2019 20:722

  39. 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:

  40. 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:

  43. 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:

  44. 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:

  48. 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:

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