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  1. Content type: Software

    RNA-Seq technology is routinely used to characterize the transcriptome, and to detect gene expression differences among cell types, genotypes and conditions. Advances in short-read sequencing instruments such ...

    Authors: Refael Kohen, Jonathan Barlev, Gil Hornung, Gil Stelzer, Ester Feldmesser, Kiril Kogan, Marilyn Safran and Dena Leshkowitz

    Citation: BMC Bioinformatics 2019 20:154

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  2. Content type: Methodology article

    Whole exome sequencing (WES) has been widely used in human genetics research. BGISEQ-500 is a recently established next-generation sequencing platform. However, the performance of BGISEQ-500 on WES is not well...

    Authors: Yu Xu, Zhe Lin, Chong Tang, Yujing Tang, Yue Cai, Hongbin Zhong, Xuebin Wang, Wenwei Zhang, Chongjun Xu, Jingjing Wang, Jian Wang, Huanming Yang, Linfeng Yang and Qiang Gao

    Citation: BMC Bioinformatics 2019 20:153

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  3. Content type: Research article

    Long non-coding RNAs (lncRNAs) play an important role in regulating gene expression and are thus important for determining phenotypes. Most attempts to measure selection in lncRNAs have focused on the primary ...

    Authors: Maria Beatriz Walter Costa, Christian Höner zu Siederdissen, Marko Dunjić, Peter F. Stadler and Katja Nowick

    Citation: BMC Bioinformatics 2019 20:151

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  4. Content type: Methodology article

    Gene duplications are a major source of raw material for evolution and a likely contributor to the diversity of life on earth. Duplicate genes (i.e., homeologs, in the case of a whole genome duplication) may r...

    Authors: Ronald D. Smith, Taliesin J. Kinser, Gregory D. Conradi Smith and Joshua R. Puzey

    Citation: BMC Bioinformatics 2019 20:149

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  5. Content type: Software

    Genetic studies in tetraploids are lagging behind in comparison with studies of diploids as the complex genetics of tetraploids require much more elaborated computational methodologies. Recent advancements in ...

    Authors: Konrad Zych, Gerrit Gort, Chris A. Maliepaard, Ritsert C. Jansen and Roeland E. Voorrips

    Citation: BMC Bioinformatics 2019 20:148

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  6. Content type: Methodology article

    Thanks to the recent advancements in next-generation sequencing (NGS) technologies, large amount of genomic data, which are short DNA sequences known as reads, has been accumulating. Diverse assemblers have be...

    Authors: Daehong Kwon, Jongin Lee and Jaebum Kim

    Citation: BMC Bioinformatics 2019 20:147

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  7. Content type: Methodology article

    Gene Set Enrichment Analysis (GSEA) is a powerful tool to identify enriched functional categories of informative biomarkers. Canonical GSEA takes one-dimensional feature scores derived from the data of one pla...

    Authors: Khong-Loon Tiong and Chen-Hsiang Yeang

    Citation: BMC Bioinformatics 2019 20:145

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  8. Content type: Methodology article

    Using meta-analysis, high-dimensional transcriptome expression data from public repositories can be merged to make group comparisons that have not been considered in the original studies. Merging of high-dimen...

    Authors: Christine Winter, Robin Kosch, Martin Ludlow, Albert D. M. E. Osterhaus and Klaus Jung

    Citation: BMC Bioinformatics 2019 20:144

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  9. Content type: Research article

    microRNAs (miRNAs) regulate gene expression at the post-transcriptional level and they play an important role in various biological processes in the human body. Therefore, identifying their regulation mechanis...

    Authors: Vu VH Pham, Junpeng Zhang, Lin Liu, Buu Truong, Taosheng Xu, Trung T. Nguyen, Jiuyong Li and Thuc D. Le

    Citation: BMC Bioinformatics 2019 20:143

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  10. Content type: Software

    The segmentation of a 3D image is a task that can hardly be automatized in certain situations, notably when the contrast is low and/or the distance between elements is small. The existing supervised methods re...

    Authors: Bastien Kovac, Jérôme Fehrenbach, Ludivine Guillaume and Pierre Weiss

    Citation: BMC Bioinformatics 2019 20:142

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  11. Content type: Methodology article

    Functional antibody genes are often assembled by VDJ recombination and then diversified by somatic hypermutation. Identifying the combination of sourcing germline genes is critical to understand the process of...

    Authors: Qingchen Zhang, Lu Zhang, Chen Zhou, Yiyan Yang, Zuojing Yin, Dingfeng Wu, Kailin Tang and Zhiwei Cao

    Citation: BMC Bioinformatics 2019 20:137

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  12. Content type: Research

    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

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

  13. Content type: Research

    Gene co-expression studies can provide important insights into molecular and cellular signaling pathways. The GeneNetwork database is a unique resource for co-expression analysis using data from a variety of t...

    Authors: Sujoy Roy, Kazi I. Zaman, Robert W. Williams and Ramin Homayouni

    Citation: BMC Bioinformatics 2019 20(Suppl 2):104

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

  14. Content type: Software

    One of the main challenges when analyzing complex metagenomics data is the fact that large amounts of information need to be presented in a comprehensive and easy-to-navigate way. In the process of analyzing F...

    Authors: Adam Thrash, Mark Arick II, Robyn A. Barbato, Robert M. Jones, Thomas A. Douglas, Julie Esdale, Edward J. Perkins and Natàlia Garcia-Reyero

    Citation: BMC Bioinformatics 2019 20(Suppl 2):103

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

  15. Content type: Research

    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

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

  16. Content type: Research

    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

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

  17. Content type: Research

    The ability to predict which pairs of amino acid residues in a protein are in contact with each other offers many advantages for various areas of research that focus on proteins. For example, contact predictio...

    Authors: Joseph Luttrell IV, Tong Liu, Chaoyang Zhang and Zheng Wang

    Citation: BMC Bioinformatics 2019 20(Suppl 2):100

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

  18. Content type: Research

    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

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

  19. Content type: Research

    Barrett’s esophagus (BE) is most commonly seen as the condition in which the normal squamous epithelium lining of the esophagus is replaced by goblet cells. Many studies show that BE is a predisposing factor f...

    Authors: Visanu Wanchai, Jing Jin, Emine Bircan, Charis Eng and Mohammed Orloff

    Citation: BMC Bioinformatics 2019 20(Suppl 2):98

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

  20. Content type: Research

    Adverse Drug Reactions (ADRs) are of great public health concern. FDA-approved drug labeling summarizes ADRs of a drug product mainly in three sections, i.e., Boxed Warning (BW), Warnings and Precautions (WP),...

    Authors: Leihong Wu, Taylor Ingle, Zhichao Liu, Anna Zhao-Wong, Stephen Harris, Shraddha Thakkar, Guangxu Zhou, Junshuang Yang, Joshua Xu, Darshan Mehta, Weigong Ge, Weida Tong and Hong Fang

    Citation: BMC Bioinformatics 2019 20(Suppl 2):97

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

  21. Content type: Research

    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

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

  22. Content type: Research

    Dermoscopy is one of the common and effective imaging techniques in diagnosis of skin cancer, especially for pigmented lesions. Accurate skin lesion border detection is the key to extract important dermoscopic...

    Authors: Mustafa Bayraktar, Sinan Kockara, Tansel Halic, Mutlu Mete, Henry K. Wong and Kamran Iqbal

    Citation: BMC Bioinformatics 2019 20(Suppl 2):91

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

  23. Content type: Software

    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

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  24. Content type: Methodology article

    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

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  25. Content type: Software

    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

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  26. Content type: Research article

    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

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  27. Content type: Software

    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

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  28. Content type: Research article

    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

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  29. Content type: Software

    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

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  30. Content type: Software

    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

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  31. Content type: Research article

    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

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  32. Content type: Software

    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

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  33. Content type: Software

    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

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  34. Content type: Software

    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

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  35. Content type: Methodology article

    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

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  36. Content type: Software

    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

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  37. Content type: Research article

    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

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  38. Content type: Software

    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

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  39. Content type: Research article

    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

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