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  1. This paper presents a novel approach for Generative Anatomy Modeling Language (GAML). This approach automatically detects the geometric partitions in 3D anatomy that in turn speeds up integrated non-linear opt...

    Authors: Doga Demirel, Berk Cetinsaya, Tansel Halic, Sinan Kockara and Shahryar Ahmadi
    Citation: BMC Bioinformatics 2019 20(Suppl 2):105
    Content type: Research Published on:

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

  2. 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
    Content type: Research Published on:

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

  3. Reference genome selection is a prerequisite for successful analysis of next generation sequencing (NGS) data. Current practice employs one of the two most recent human reference genome versions: HG19 or HG38....

    Authors: Bohu Pan, Rebecca Kusko, Wenming Xiao, Yuanting Zheng, Zhichao Liu, Chunlin Xiao, Sugunadevi Sakkiah, Wenjing Guo, Ping Gong, Chaoyang Zhang, Weigong Ge, Leming Shi, Weida Tong and Huixiao Hong
    Citation: BMC Bioinformatics 2019 20(Suppl 2):101
    Content type: Research Published on:

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

    The Correction to this article has been published in BMC Bioinformatics 2019 20:252

  4. Gene families are sets of structurally and evolutionarily related genes – in one or multiple species – that typically share a conserved biological function. As such, the identification and subsequent analyses ...

    Authors: Norbert Bokros, Sorina C. Popescu and George V. Popescu
    Citation: BMC Bioinformatics 2019 20(Suppl 2):99
    Content type: Research Published on:

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

  5. The number of publicly available metagenomic experiments in various environments has been rapidly growing, empowering the potential to identify similar shifts in species abundance between different experiments...

    Authors: Aleksandra I. Perz, Cory B. Giles, Chase A. Brown, Hunter Porter, Xiavan Roopnarinesingh and Jonathan D. Wren
    Citation: BMC Bioinformatics 2019 20(Suppl 2):96
    Content type: Research Published on:

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

  7. A revolutionary diversion from classical vaccinology to reverse vaccinology approach has been observed in the last decade. The ever-increasing genomic and proteomic data has greatly facilitated the vaccine des...

    Authors: Kanwal Naz, Anam Naz, Shifa Tariq Ashraf, Muhammad Rizwan, Jamil Ahmad, Jan Baumbach and Amjad Ali
    Citation: BMC Bioinformatics 2019 20:123
    Content type: Software Published on:

  9. Next-generation sequencing (NGS) technologies have produced large volumes of genomic data. One common operation on heterogeneous genomic data is genomic interval intersection. Most of the existing tools impose...

    Authors: Burçak Otlu and Tolga Can
    Citation: BMC Bioinformatics 2019 20:121
    Content type: Methodology article Published on:

  10. In bacterial genomes, there are two mechanisms to terminate the DNA transcription: the “intrinsic” or Rho-independent termination and the Rho-dependent termination. Intrinsic terminators are characterized by a...

    Authors: Marco Di Salvo, Simone Puccio, Clelia Peano, Stephan Lacour and Pietro Alifano
    Citation: BMC Bioinformatics 2019 20:117
    Content type: Software Published on:

  13. The standard genetic code is a recipe for assigning unambiguously 21 labels, i.e. amino acids and stop translation signal, to 64 codons. However, at early stages of the translational machinery development, the...

    Authors: Paweł BłaŻej, Małgorzata Wnetrzak, Dorota Mackiewicz and Paweł Mackiewicz
    Citation: BMC Bioinformatics 2019 20:114
    Content type: Research article Published on:

  14. High-throughput sequencing often provides a foundation for experimental analyses in the life sciences. For many such methods, an intermediate layer of bioinformatics data analysis is the genomic signal track c...

    Authors: Artyom A. Egorov, Ekaterina A. Sakharova, Aleksandra S. Anisimova, Sergey E. Dmitriev, Vadim N. Gladyshev and Ivan V. Kulakovskiy
    Citation: BMC Bioinformatics 2019 20:113
    Content type: Software Published on:

  15. As an important type of post-translational modification (PTM), protein glycosylation plays a crucial role in protein stability and protein function. The abundance and ubiquity of protein glycosylation across t...

    Authors: Fuyi Li, Yang Zhang, Anthony W. Purcell, Geoffrey I. Webb, Kuo-Chen Chou, Trevor Lithgow, Chen Li and Jiangning Song
    Citation: BMC Bioinformatics 2019 20:112
    Content type: Research article Published on:

  16. Cell direct reprogramming technology has been rapidly developed with its low risk of tumor risk and avoidance of ethical issues caused by stem cells, but it is still limited to specific cell types. Direct repr...

    Authors: Leijie Li, Dongxue Che, Xiaodan Wang, Peng Zhang, Siddiq Ur Rahman, Jianbang Zhao, Jiantao Yu, Shiheng Tao, Hui Lu and Mingzhi Liao
    Citation: BMC Bioinformatics 2019 20:111
    Content type: Software Published on:

  17. Existing tools for the aggregation and visualization of differential expression data have discrete functionality and require that end-users rely on multiple software packages with complex dependencies or manua...

    Authors: Adam Price, Adrian Caciula, Cheng Guo, Bohyun Lee, Juliet Morrison, Angela Rasmussen, W. Ian Lipkin and Komal Jain
    Citation: BMC Bioinformatics 2019 20:110
    Content type: Software Published on:

  18. Blood pressure diseases have increasingly been identified as among the main factors threatening human health. How to accurately and conveniently measure blood pressure is the key to the implementation of effec...

    Authors: Bing Zhang, Huihui Ren, Guoyan Huang, Yongqiang Cheng and Changzhen Hu
    Citation: BMC Bioinformatics 2019 20:109
    Content type: Research article Published on:

  19. The accurate determination of parent-progeny relationships within both in situ natural populations and ex situ genetic resource collections can greatly enhance plant breeding/domestication efforts and support ...

    Authors: Arthur T. O. Melo and Iago Hale
    Citation: BMC Bioinformatics 2019 20:108
    Content type: Software Published on:

  20. Recent comparative studies have brought to our attention how somatic mutation detection from next-generation sequencing data is still an open issue in bioinformatics, because different pipelines result in a lo...

    Authors: Noemi Di Nanni, Marco Moscatelli, Matteo Gnocchi, Luciano Milanesi and Ettore Mosca
    Citation: BMC Bioinformatics 2019 20:107
    Content type: Software Published on:

  21. A large fraction of human and mouse autosomal genes are subject to random monoallelic expression (MAE), an epigenetic mechanism characterized by allele-specific gene expression that varies between clonal cell ...

    Authors: Svetlana Vinogradova, Sachit D. Saksena, Henry N. Ward, Sébastien Vigneau and Alexander A. Gimelbrant
    Citation: BMC Bioinformatics 2019 20:106
    Content type: Software Published on:

  22. Group structures among genes encoded in functional relationships or biological pathways are valuable and unique features in large-scale molecular data for survival analysis. However, most of previous approache...

    Authors: Zaixiang Tang, Shufeng Lei, Xinyan Zhang, Zixuan Yi, Boyi Guo, Jake Y. Chen, Yueping Shen and Nengjun Yi
    Citation: BMC Bioinformatics 2019 20:94
    Content type: Methodology article Published on:

  25. Next-Generation Sequencing (NGS) is now widely used in biomedical research for various applications. Processing of NGS data requires multiple programs and customization of the processing pipelines according to...

    Authors: Taewoon Joo, Ji-Hye Choi, Ji-Hye Lee, So Eun Park, Youngsic Jeon, Sae Hoon Jung and Hyun Goo Woo
    Citation: BMC Bioinformatics 2019 20:90
    Content type: Software Published on:

  26. The investigation of intracellular metabolism is the mainstay in the biotechnology and physiology settings. Intracellular metabolic rates are commonly evaluated using labeling pattern of the identified metabol...

    Authors: Di Du, Lin Tan, Yumeng Wang, Bo Peng, John N. Weinstein, Fredric E. Wondisford, Xiaoyang Su and Philip L. Lorenzi
    Citation: BMC Bioinformatics 2019 20:89
    Content type: Research article Published on:

  27. High-throughput amplicon sequencing of environmental DNA (eDNA metabarcoding) has become a routine tool for biodiversity survey and ecological studies. By including sample-specific tags in the primers prior PC...

    Authors: Yoann Dufresne, Franck Lejzerowicz, Laure Apotheloz Perret-Gentil, Jan Pawlowski and Tristan Cordier
    Citation: BMC Bioinformatics 2019 20:88
    Content type: Software Published on:

  28. Long non-coding RNAs play an important role in human complex diseases. Identification of lncRNA-disease associations will gain insight into disease-related lncRNAs and benefit disease diagnoses and treatment. ...

    Authors: Xiao-Nan Fan, Shao-Wu Zhang, Song-Yao Zhang, Kunju Zhu and Songjian Lu
    Citation: BMC Bioinformatics 2019 20:87
    Content type: Research article Published on:

  30. The identification of prognostic genes that can distinguish the prognostic risks of cancer patients remains a significant challenge. Previous works have proven that functional gene sets were more reliable for ...

    Authors: Xiong-Hui Zhou, Xin-Yi Chu, Gang Xue, Jiang-Hui Xiong and Hong-Yu Zhang
    Citation: BMC Bioinformatics 2019 20:85
    Content type: Research article Published on:

  31. Prioritisation of gene ontology terms from differential gene expression analyses in a two-dimensional format remains a challenge with exponentially growing data volumes. Typically, gene ontology terms are repr...

    Authors: Irina Kuznetsova, Artur Lugmayr, Stefan J. Siira, Oliver Rackham and Aleksandra Filipovska
    Citation: BMC Bioinformatics 2019 20:84
    Content type: Software Published on:

  32. Drug combinations have the potential to improve efficacy while limiting toxicity. To robustly identify synergistic combinations, high-throughput screens using full dose-response surface are desirable but requi...

    Authors: Arnaud Amzallag, Sridhar Ramaswamy and Cyril H. Benes
    Citation: BMC Bioinformatics 2019 20:83
    Content type: Methodology article Published on:

  34. Life science research is moving quickly towards large-scale experimental designs that are comprised of multiple tissues, time points, and samples. Omic time-series experiments offer answers to three big questi...

    Authors: Joshua R. Williams, Ruoting Yang, John L. Clifford, Daniel Watson, Ross Campbell, Derese Getnet, Raina Kumar, Rasha Hammamieh and Marti Jett
    Citation: BMC Bioinformatics 2019 20:81
    Content type: Software Published on:

  35. Cell counting from cell cultures is required in multiple biological and biomedical research applications. Especially, accurate brightfield-based cell counting methods are needed for cell growth analysis. With ...

    Authors: Kaisa Liimatainen, Lauri Kananen, Leena Latonen and Pekka Ruusuvuori
    Citation: BMC Bioinformatics 2019 20:80
    Content type: Methodology article Published on:

  36. Functional annotation of genes is an essential step in omics data analysis. Multiple databases and methods are currently available to summarize the functions of sets of genes into higher level representations,...

    Authors: Giovanni Scala, Angela Serra, Veer Singh Marwah, Laura Aliisa Saarimäki and Dario Greco
    Citation: BMC Bioinformatics 2019 20:79
    Content type: Software Published on:

  40. With the availability of well-assembled genomes of a growing number of organisms, identifying the bioinformatic basis of whole genome duplication (WGD) is a growing field of genomics. The most extant software ...

    Authors: Yongzhi Yang, Ying Li, Qiao Chen, Yongshuai Sun and Zhiqiang Lu
    Citation: BMC Bioinformatics 2019 20:75
    Content type: Software Published on:

  41. Biomarker discovery studies have been moving the focus from a single target gene to a set of target genes. However, the number of target genes in a drug should be minimum to avoid drug side-effect or toxicity....

    Authors: Sunjoo Bang, Sangjoon Son, Sooyoung Kim and Hyunjung Shin
    Citation: BMC Bioinformatics 2019 20:74
    Content type: Methodology article Published on:

  42. 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
    Content type: Software Published on:

  45. Understanding the genetic networks and their role in chronic diseases (e.g., cancer) is one of the important objectives of biological researchers. In this work, we present a text mining system that constructs ...

    Authors: Amira Al-Aamri, Kamal Taha, Yousof Al-Hammadi, Maher Maalouf and Dirar Homouz
    Citation: BMC Bioinformatics 2019 20:70
    Content type: Methodology article Published on:

  48. Non-coding RNAs (ncRNAs) are emerging as key regulators and play critical roles in a wide range of tumorigenesis. Recent studies have suggested that long non-coding RNAs (lncRNAs) could interact with microRNAs...

    Authors: Qiu Xiao, Jiawei Luo, Cheng Liang, Jie Cai, Guanghui Li and Buwen Cao
    Citation: BMC Bioinformatics 2019 20:67
    Content type: Research article Published on:

  49. Harmonization techniques make different gene expression profiles and their sets compatible and ready for comparisons. Here we present a new bioinformatic tool termed Shambhala for harmonization of multiple hum...

    Authors: Nicolas Borisov, Irina Shabalina, Victor Tkachev, Maxim Sorokin, Andrew Garazha, Andrey Pulin, Ilya I. Eremin and Anton Buzdin
    Citation: BMC Bioinformatics 2019 20:66
    Content type: Research article Published on:

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