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  1. Content type: Research Article

    MicroRNAs (miRNAs) are noncoding RNA molecules heavily involved in human tumors, in which few of them circulating the human body. Finding a tumor-associated signature of miRNA, that is, the minimum miRNA entit...

    Authors: Alejandro Lopez-Rincon, Marlet Martinez-Archundia, Gustavo U. Martinez-Ruiz, Alexander Schoenhuth and Alberto Tonda

    Citation: BMC Bioinformatics 2019 20:480

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  2. Content type: Research Article

    The adverse reactions that are caused by drugs are potentially life-threatening problems. Comprehensive knowledge of adverse drug reactions (ADRs) can reduce their detrimental impacts on patients. Detecting AD...

    Authors: Tongxuan Zhang, Hongfei Lin, Yuqi Ren, Liang Yang, Bo Xu, Zhihao Yang, Jian Wang and Yijia Zhang

    Citation: BMC Bioinformatics 2019 20:479

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  3. Content type: Methodology Article

    Binding sites are the pockets of proteins that can bind drugs; the discovery of these pockets is a critical step in drug design. With the help of computers, protein pockets prediction can save manpower and fin...

    Authors: Mingjian Jiang, Zhen Li, Yujie Bian and Zhiqiang Wei

    Citation: BMC Bioinformatics 2019 20:478

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  4. Content type: Research article

    In most mammals, a vast array of genes coding for chemosensory receptors mediates olfaction. Odorant receptor (OR) genes generally constitute the largest multifamily (> 1100 intact members in the mouse). From ...

    Authors: Andrea Degl’Innocenti, Gabriella Meloni, Barbara Mazzolai and Gianni Ciofani

    Citation: BMC Bioinformatics 2019 20:474

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  5. Content type: Software

    HH-suite is a widely used open source software suite for sensitive sequence similarity searches and protein fold recognition. It is based on pairwise alignment of profile Hidden Markov models (HMMs), which rep...

    Authors: Martin Steinegger, Markus Meier, Milot Mirdita, Harald Vöhringer, Stephan J. Haunsberger and Johannes Söding

    Citation: BMC Bioinformatics 2019 20:473

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  6. Content type: Research Article

    Nucleus is a fundamental task in microscopy image analysis and supports many other quantitative studies such as object counting, segmentation, tracking, etc. Deep neural networks are emerging as a powerful too...

    Authors: Fuyong Xing, Yuanpu Xie, Xiaoshuang Shi, Pingjun Chen, Zizhao Zhang and Lin Yang

    Citation: BMC Bioinformatics 2019 20:472

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  8. Content type: Research article

    Neurogenesis in the murine cerebral cortex involves the coordinated divisions of two main types of progenitor cells, whose numbers, division modes and cell cycle durations set up the final neuronal output. To ...

    Authors: Marie Postel, Alice Karam, Guillaume Pézeron, Sylvie Schneider-Maunoury and Frédérique Clément

    Citation: BMC Bioinformatics 2019 20:470

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  9. Content type: Methodology article

    Long-chain non-coding RNA (lncRNA) is closely related to many biological activities. Since its sequence structure is similar to that of messenger RNA (mRNA), it is difficult to distinguish between the two base...

    Authors: Jianghui Wen, Yeshu Liu, Yu Shi, Haoran Huang, Bing Deng and Xinping Xiao

    Citation: BMC Bioinformatics 2019 20:469

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  10. Content type: Research article

    MiRNAs play significant roles in many fundamental and important biological processes, and predicting potential miRNA-disease associations makes contributions to understanding the molecular mechanism of human d...

    Authors: Yuchong Gong, Yanqing Niu, Wen Zhang and Xiaohong Li

    Citation: BMC Bioinformatics 2019 20:468

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  12. Content type: Research Article

    Although many of the genic features in Mycobacterium abscessus have been fully validated, a comprehensive understanding of the regulatory elements remains lacking. Moreover, there is little understanding of how t...

    Authors: Patrick M. Staunton, Aleksandra A. Miranda-CasoLuengo, Brendan J. Loftus and Isobel Claire Gormley

    Citation: BMC Bioinformatics 2019 20:466

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  13. Content type: Methodology article

    Atomic force microscopy (AFM) allows the mechanical characterization of single cells and live tissue by quantifying force-distance (FD) data in nano-indentation experiments. One of the main problems when deali...

    Authors: Paul Müller, Shada Abuhattum, Stephanie Möllmert, Elke Ulbricht, Anna V. Taubenberger and Jochen Guck

    Citation: BMC Bioinformatics 2019 20:465

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  14. Content type: Research article

    The function of oligomeric proteins is inherently linked to their quaternary structure. In the absence of high-resolution data, low-resolution information in the form of spatial restraints can significantly co...

    Authors: Aljaž Gaber, Gregor Gunčar and Miha Pavšič

    Citation: BMC Bioinformatics 2019 20:464

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  15. Content type: Software

    The Human Protein Atlas (HPA) aims to map human proteins via multiple technologies including imaging, proteomics and transcriptomics. Access of the HPA data is mainly via web-based interface allowing views of ...

    Authors: Anh Nhat Tran, Alex M. Dussaq, Timothy Kennell Jr, Christopher D. Willey and Anita B. Hjelmeland

    Citation: BMC Bioinformatics 2019 20:463

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  16. Content type: Research Article

    Determining the association between tumor sample and the gene is demanding because it requires a high cost for conducting genetic experiments. Thus, the discovered association between tumor sample and gene fur...

    Authors: Mohan Timilsina, Haixuan Yang, Ratnesh Sahay and Dietrich Rebholz-Schuhmann

    Citation: BMC Bioinformatics 2019 20:462

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  17. Content type: Software

    The efficient biological production of industrially and economically important compounds is a challenging problem. Brute-force determination of the optimal pathways to efficient production of a target chemical...

    Authors: Leanne S. Whitmore, Bernard Nguyen, Ali Pinar, Anthe George and Corey M. Hudson

    Citation: BMC Bioinformatics 2019 20:461

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  20. Content type: Methodology article

    Despite the availability of many ready-made testing software, reliable detection of differentially expressed genes in RNA-seq data is not a trivial task. Even though the data collection is considered high-thro...

    Authors: Lindsay Rutter, Adrienne N. Moran Lauter, Michelle A. Graham and Dianne Cook

    Citation: BMC Bioinformatics 2019 20:458

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  21. Content type: Methodology article

    Mathematics and Phy sics-based simulation models have the potential to help interpret and encapsulate biological phenomena in a computable and reproducible form. Similarly, comprehensive descriptions of such m...

    Authors: Dewan M. Sarwar, Reza Kalbasi, John H. Gennari, Brian E. Carlson, Maxwell L. Neal, Bernard de Bono, Koray Atalag, Peter J. Hunter and David P. Nickerson

    Citation: BMC Bioinformatics 2019 20:457

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  22. Content type: Methodology article

    Background In the search for therapeutic peptides for disease treatments, many efforts have been made to identify various functional peptides from large numbers of peptide sequence databases. In this paper, we...

    Authors: Chuanyan Wu, Rui Gao, Yusen Zhang and Yang De Marinis

    Citation: BMC Bioinformatics 2019 20:456

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  24. Content type: Methodology article

    As genome sequencing projects grow rapidly, the diversity of organisms with recently assembled genome sequences peaks at an unprecedented scale, thereby highlighting the need to make gene functional annotation...

    Authors: Fernando Cruz, Davide Lagoa, João Mendes, Isabel Rocha, Eugénio C. Ferreira, Miguel Rocha and Oscar Dias

    Citation: BMC Bioinformatics 2019 20:454

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  25. Content type: Software

    Metagenomics caused a quantum leap in microbial ecology. However, the inherent size and complexity of metagenomic data limit its interpretation. The quantification of metagenomic traits in metagenomic analysis...

    Authors: Emiliano Pereira-Flores, Frank Oliver Glöckner and Antonio Fernandez-Guerra

    Citation: BMC Bioinformatics 2019 20:453

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  26. Content type: Software

    Streptomycetes are filamentous microorganisms of high biotechnological relevance, especially for the production of antibiotics. In submerged cultures, the productivity of these microorganisms is closely linked...

    Authors: Christian Carsten Sachs, Joachim Koepff, Wolfgang Wiechert, Alexander Grünberger and Katharina Nöh

    Citation: BMC Bioinformatics 2019 20:452

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  27. Content type: Software

    High-throughput gene expression technologies provide complex datasets reflecting mechanisms perturbed in an experiment, typically in a treatment versus control design. Analysis of these information-rich data c...

    Authors: Florian Martin, Sylvain Gubian, Marja Talikka, Julia Hoeng and Manuel C. Peitsch

    Citation: BMC Bioinformatics 2019 20:451

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  28. Content type: Software

    Mutational signatures are specific patterns of somatic mutations introduced into the genome by oncogenic processes. Several mutational signatures have been identified and quantified from multiple cancer studie...

    Authors: Franziska Schumann, Eric Blanc, Clemens Messerschmidt, Thomas Blankenstein, Antonia Busse and Dieter Beule

    Citation: BMC Bioinformatics 2019 20:450

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  32. Content type: Research article

    Protein interaction databases often provide confidence scores for each recorded interaction based on the available experimental evidence. Protein interaction networks (PINs) are then built by thresholding on t...

    Authors: Lyuba V. Bozhilova, Alan V. Whitmore, Jonny Wray, Gesine Reinert and Charlotte M. Deane

    Citation: BMC Bioinformatics 2019 20:446

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  34. Content type: Methodology article

    Mining epistatic loci which affects specific phenotypic traits is an important research issue in the field of biology. Bayesian network (BN) is a graphical model which can express the relationship between gene...

    Authors: Yang Guo, Zhiman Zhong, Chen Yang, Jiangfeng Hu, Yaling Jiang, Zizhen Liang, Hui Gao and Jianxiao Liu

    Citation: BMC Bioinformatics 2019 20:444

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  35. Content type: Methodology article

    Cryo-electron tomography (Cryo-ET) is an imaging technique used to generate three-dimensional structures of cellular macromolecule complexes in their native environment. Due to developing cryo-electron microsc...

    Authors: Yongchun Lü, Xiangrui Zeng, Xiaofang Zhao, Shirui Li, Hua Li, Xin Gao and Min Xu

    Citation: BMC Bioinformatics 2019 20:443

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  36. Content type: Research article

    Contemporary biological observations have revealed a large variety of mechanisms acting during the expansion of a tumor. However, there are still many qualitative and quantitative aspects of the phenomenon tha...

    Authors: Markos Antonopoulos, Dimitra Dionysiou, Georgios Stamatakos and Nikolaos Uzunoglu

    Citation: BMC Bioinformatics 2019 20:442

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  37. Content type: Methodology article

    Although a few comparison methods based on the biological meaning of gene lists have been developed, the goProfiles approach is one of the few that are being used for that purpose. It consists of projecting li...

    Authors: Alex Sánchez-Pla, Miquel Salicrú and Jordi Ocaña

    Citation: BMC Bioinformatics 2019 20:441

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  38. Content type: Software

    With every new genome that is sequenced, thousands of species-specific genes (orphans) are found, some originating from ultra-rapid mutations of existing genes, many others originating de novo from non-genic r...

    Authors: Zebulun Arendsee, Jing Li, Urminder Singh, Priyanka Bhandary, Arun Seetharam and Eve Syrkin Wurtele

    Citation: BMC Bioinformatics 2019 20:440

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  39. Content type: Correction

    Following publication of the original article [1], the author noticed that the following lines were missing from the published article. The original article has been corrected.

    Authors: Mai Anh BUI T, Nick Papoulias, Serge Stinckwich, Mikal Ziane and Benjamin Roche

    Citation: BMC Bioinformatics 2019 20:439

    Published on:

    The original article was published in BMC Bioinformatics 2019 20:312

  41. Content type: Methodology article

    Batch effects were not accounted for in most of the studies of computational drug repositioning based on gene expression signatures. It is unknown how batch effect removal methods impact the results of signatu...

    Authors: Wei Zhou, Karel K. M. Koudijs and Stefan Böhringer

    Citation: BMC Bioinformatics 2019 20:437

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  42. Content type: Research article

    Creating a scalable computational infrastructure to analyze the wealth of information contained in data repositories is difficult due to significant barriers in organizing, extracting and analyzing relevant da...

    Authors: Hamid Bagheri, Usha Muppirala, Rick E. Masonbrink, Andrew J. Severin and Hridesh Rajan

    Citation: BMC Bioinformatics 2019 20:436

    Published on:

  43. Content type: Research article

    Gene and protein interaction data are often represented as interaction networks, where nodes stand for genes or gene products and each edge stands for a relationship between a pair of gene nodes. Commonly, tha...

    Authors: Joëlle Barido-Sottani, Samuel D. Chapman, Evsey Kosman and Arcady R. Mushegian

    Citation: BMC Bioinformatics 2019 20:435

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  44. Content type: Research article

    The epidermal growth factor receptor (EGFR) is a major regulator of proliferation in tumor cells. Elevated expression levels of EGFR are associated with prognosis and clinical outcomes of patients in a variety...

    Authors: Claus Weinholdt, Henri Wichmann, Johanna Kotrba, David H. Ardell, Matthias Kappler, Alexander W. Eckert, Dirk Vordermark and Ivo Grosse

    Citation: BMC Bioinformatics 2019 20:434

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  45. Content type: Research article

    Host immune response is coordinated by a variety of different specialized cell types that vary in time and location. While host immune response can be studied using conventional low-dimensional approaches, adv...

    Authors: Arezo Torang, Paraag Gupta and David J. Klinke II

    Citation: BMC Bioinformatics 2019 20:433

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  46. Content type: Research article

    Relationships between specific microbes and proper immune system development, composition, and function have been reported in a number of studies. However, researchers have discovered only a fraction of the li...

    Authors: Janet C. Siebert, Charles Preston Neff, Jennifer M. Schneider, Emilie H. Regner, Neha Ohri, Kristine A. Kuhn, Brent E. Palmer, Catherine A. Lozupone and Carsten Görg

    Citation: BMC Bioinformatics 2019 20:432

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  48. Content type: Methodology article

    Background Consisting of dictated free-text documents such as discharge summaries, medical narratives are widely used in medical natural language processing. Relationships between anatomical entities and human...

    Authors: Yipei Wang, Xingyu Fan, Luoxin Chen, Eric I-Chao Chang, Sophia Ananiadou, Junichi Tsujii and Yan Xu

    Citation: BMC Bioinformatics 2019 20:430

    Published on:

  49. Content type: Methodology article

    With the advent of array-based techniques to measure methylation levels in primary tumor samples, systematic investigations of methylomes have widely been performed on a large number of tumor entities. Most of...

    Authors: Pascal David Johann, Natalie Jäger, Stefan M. Pfister and Martin Sill

    Citation: BMC Bioinformatics 2019 20:428

    Published on:

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