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  1. Content type: Research article

    In this study, we compared four models for predicting rice blast disease, two operational process-based models (Yoshino and Water Accounting Rice Model (WARM)) and two approaches based on machine learning algo...

    Authors: David F. Nettleton, Dimitrios Katsantonis, Argyris Kalaitzidis, Natasa Sarafijanovic-Djukic, Pau Puigdollers and Roberto Confalonieri

    Citation: BMC Bioinformatics 2019 20:514

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  4. Content type: Research Article

    One of the challenges in large-scale information retrieval (IR) is developing fine-grained and domain-specific methods to answer natural language questions. Despite the availability of numerous sources and dat...

    Authors: Asma Ben Abacha and Dina Demner-Fushman

    Citation: BMC Bioinformatics 2019 20:511

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  7. Content type: Software

    At the molecular level, nonlinear networks of heterogeneous molecules control many biological processes, so that systems biology provides a valuable approach in this field, building on the integration of exper...

    Authors: S. Ha, E. Dimitrova, S. Hoops, D. Altarawy, M. Ansariola, D. Deb, J. Glazebrook, R. Hillmer, H. Shahin, F. Katagiri, J. McDowell, M. Megraw, J. Setubal, B. M. Tyler and R. Laubenbacher

    Citation: BMC Bioinformatics 2019 20:508

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  8. Content type: Research article

    Human tumor is a complex tissue with multiple heterogeneous hypoxic regions and significant cell-to-cell variability. Due to the complexity of the disease, the explanation of why anticancer therapies fail cann...

    Authors: Emile P. Chen, Roy S. Song and Xueer Chen

    Citation: BMC Bioinformatics 2019 20:507

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  9. Content type: Methodology Article

    Identifying differentially abundant features between different experimental groups is a common goal for many metabolomics and proteomics studies. However, analyzing data from mass spectrometry (MS) is difficul...

    Authors: Yuntong Li, Teresa W.M. Fan, Andrew N. Lane, Woo-Young Kang, Susanne M. Arnold, Arnold J. Stromberg, Chi Wang and Li Chen

    Citation: BMC Bioinformatics 2019 20:501

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  10. Content type: Publisher Correction

    Following publication of the original article [1], the authors noticed that the following errors were introduced by pdf/html formatting issues.

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

    Citation: BMC Bioinformatics 2019 20:500

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    The original article was published in BMC Bioinformatics 2019 20:442

  11. Content type: Research Article

    Metabolic networks reflect the relationships between metabolites (biomolecules) and the enzymes (proteins), and are of particular interest since they describe all chemical reactions of an organism. The metabol...

    Authors: Adèle Weber Zendrera, Nataliya Sokolovska and Hédi A. Soula

    Citation: BMC Bioinformatics 2019 20:499

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  12. Content type: Methodology article

    Selecting the proper parameter settings for bioinformatic software tools is challenging. Not only will each parameter have an individual effect on the outcome, but there are also potential interaction effects ...

    Authors: Daniel Svensson, Rickard Sjögren, David Sundell, Andreas Sjödin and Johan Trygg

    Citation: BMC Bioinformatics 2019 20:498

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  13. Content type: Research article

    It is widely believed that tertiary nucleotide-nucleotide interactions are essential in determining RNA structure and function. Currently, direct coupling analysis (DCA) infers nucleotide contacts in a sequenc...

    Authors: Yiren Jian, Xiaonan Wang, Jaidi Qiu, Huiwen Wang, Zhichao Liu, Yunjie Zhao and Chen Zeng

    Citation: BMC Bioinformatics 2019 20:497

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  14. Content type: Research Article

    When applying genomic medicine to a rare disease patient, the primary goal is to identify one or more genomic variants that may explain the patient’s phenotypes. Typically, this is done through annotation, fil...

    Authors: James M. Holt, Brandon Wilk, Camille L. Birch, Donna M. Brown, Manavalan Gajapathy, Alexander C. Moss, Nadiya Sosonkina, Melissa A. Wilk, Julie A. Anderson, Jeremy M. Harris, Jacob M. Kelly, Fariba Shaterferdosian, Angelina E. Uno-Antonison, Arthur Weborg and Elizabeth A. Worthey

    Citation: BMC Bioinformatics 2019 20:496

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  15. Content type: Methodology article

    Literature derived knowledge assemblies have been used as an effective way of representing biological phenomenon and understanding disease etiology in systems biology. These include canonical pathway databases...

    Authors: Reagon Karki, Alpha Tom Kodamullil, Charles Tapley Hoyt and Martin Hofmann-Apitius

    Citation: BMC Bioinformatics 2019 20:494

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  17. Content type: Research article

    LC-MS technology makes it possible to measure the relative abundance of numerous molecular features of a sample in single analysis. However, especially non-targeted metabolite profiling approaches generate vas...

    Authors: Marietta Kokla, Jyrki Virtanen, Marjukka Kolehmainen, Jussi Paananen and Kati Hanhineva

    Citation: BMC Bioinformatics 2019 20:492

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  18. Content type: Methodology Article

    The analysis of health and medical data is crucial for improving the diagnosis precision, treatments and prevention. In this field, machine learning techniques play a key role. However, the amount of health da...

    Authors: Josefa Díaz Álvarez, Jordi A. Matias-Guiu, María Nieves Cabrera-Martín, José L. Risco-Martín and José L. Ayala

    Citation: BMC Bioinformatics 2019 20:491

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  19. Content type: Methodology article

    The development of accurate epitope prediction tools is important in facilitating disease diagnostics, treatment and vaccine development. The advent of new approaches making use of antibody and TCR sequence in...

    Authors: Swapnil Mahajan, Zhen Yan, Martin Closter Jespersen, Kamilla Kjærgaard Jensen, Paolo Marcatili, Morten Nielsen, Alessandro Sette and Bjoern Peters

    Citation: BMC Bioinformatics 2019 20:490

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  20. Content type: Research Article

    The data deluge can leverage sophisticated ML techniques for functionally annotating the regulatory non-coding genome. The challenge lies in selecting the appropriate classifier for the specific functional ann...

    Authors: Chih-Hao Fang, Nawanol Theera-Ampornpunt, Michael A. Roth, Ananth Grama and Somali Chaterji

    Citation: BMC Bioinformatics 2019 20:488

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  21. Content type: Software

    5′-end sequencing assays, and Cap Analysis of Gene Expression (CAGE) in particular, have been instrumental in studying transcriptional regulation. 5′-end methods provide genome-wide maps of transcription start...

    Authors: Malte Thodberg, Axel Thieffry, Kristoffer Vitting-Seerup, Robin Andersson and Albin Sandelin

    Citation: BMC Bioinformatics 2019 20:487

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  22. Content type: Database

    Recent advances in high-volume sequencing technology and mining of genomes from metagenomic samples call for rapid and reliable genome quality evaluation. The current release of the PATRIC database contains ov...

    Authors: Bruce Parrello, Rory Butler, Philippe Chlenski, Robert Olson, Jamie Overbeek, Gordon D. Pusch, Veronika Vonstein and Ross Overbeek

    Citation: BMC Bioinformatics 2019 20:486

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  24. 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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  25. 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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  26. 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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  27. 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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  28. 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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  29. 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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  31. 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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  32. 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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  33. 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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  35. 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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  36. 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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  37. 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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  38. 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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  39. 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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  40. 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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  43. 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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  44. 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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  45. 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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  47. 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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  48. 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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  49. 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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  50. 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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  • Citation Impact
    2.511 - 2-year Impact Factor
    2.970 - 5-year Impact Factor
    0.855 - Source Normalized Impact per Paper (SNIP)
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ISSN: 1471-2105

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