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  1. Content type: Software

    Clustering methods are essential to partitioning biological samples being useful to minimize the information complexity in large datasets. Tools in this context usually generates data with greed algorithms tha...

    Authors: Bruno Thiago de Lima Nichio, Aryel Marlus Repula de Oliveira, Camilla Reginatto de Pierri, Leticia Graziela Costa Santos, Alexandre Quadros Lejambre, Ricardo Assunção Vialle, Nilson Antônio da Rocha Coimbra, Dieval Guizelini, Jeroniza Nunes Marchaukoski, Fabio de Oliveira Pedrosa and Roberto Tadeu Raittz

    Citation: BMC Bioinformatics 2019 20:392

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  2. Content type: Research article

    Asymmetry during cellular division, both in the uneven partitioning of damaged cellular components and of cell volume, is a cell biological phenomenon experienced by many unicellular organisms. Previous work b...

    Authors: Ruijie Song and Murat Acar

    Citation: BMC Bioinformatics 2019 20:391

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  3. Content type: Software

    Human papillomavirus (HPV) is a common sexually transmitted infection associated with cervical cancer that frequently occurs as a coinfection of types and subtypes. Highly similar sublineages that show over 10...

    Authors: Eric T. Dawson, Sarah Wagner, David Roberson, Meredith Yeager, Joseph Boland, Erik Garrison, Stephen Chanock, Mark Schiffman, Tina Raine-Bennett, Thomas Lorey, Phillip E. Castle, Lisa Mirabello and Richard Durbin

    Citation: BMC Bioinformatics 2019 20:389

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  4. Content type: Methodology article

    Bioinformatics methods are helpful to identify new molecules for diagnostic or therapeutic applications. For example, the use of peptides capable of mimicking binding sites has several benefits in replacing a ...

    Authors: Vincent Demolombe, Alexandre G. de Brevern, Liza Felicori, Christophe NGuyen, Ricardo Andrez Machado de Avila, Lionel Valera, Bénédicte Jardin-Watelet, Géraldine Lavigne, Aurélien Lebreton, Franck Molina and Violaine Moreau

    Citation: BMC Bioinformatics 2019 20:387

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  5. Content type: Research article

    Mathematical models of biological networks can provide important predictions and insights into complex disease. Constraint-based models of cellular metabolism and probabilistic models of gene regulatory networ...

    Authors: Han Yu and Rachael Hageman Blair

    Citation: BMC Bioinformatics 2019 20:386

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  6. Content type: Software

    In cancer research, robustness of a complex biochemical network is one of the most relevant properties to investigate for the development of novel targeted therapies. In cancer systems biology, biological netw...

    Authors: Fortunato Bianconi, Chiara Antonini, Lorenzo Tomassoni and Paolo Valigi

    Citation: BMC Bioinformatics 2019 20:385

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  7. Content type: Research article

    Alkaloids, a class of organic compounds that contain nitrogen bases, are mainly synthesized as secondary metabolites in plants and fungi, and they have a wide range of bioactivities. Although there are thousan...

    Authors: Ryohei Eguchi, Naoaki Ono, Aki Hirai Morita, Tetsuo Katsuragi, Satoshi Nakamura, Ming Huang, Md. Altaf-Ul-Amin and Shigehiko Kanaya

    Citation: BMC Bioinformatics 2019 20:380

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  8. Content type: Methodology article

    Unsupervised machine learning methods (deep learning) have shown their usefulness with noisy single cell mRNA-sequencing data (scRNA-seq), where the models generalize well, despite the zero-inflation of the da...

    Authors: Savvas Kinalis, Finn Cilius Nielsen, Ole Winther and Frederik Otzen Bagger

    Citation: BMC Bioinformatics 2019 20:379

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  9. Content type: Methodology article

    The QuantiGene® Plex 2.0 platform (ThermoFisher Scientific) combines bDNA with the Luminex/xMAP magnetic bead capturing technology to assess differential gene expression in a compound exposure setting. This te...

    Authors: Bie Verbist, Eva Adriaensen, Vikki Keersmaekers, Dea Putri, Marjolein Crabbe, Maarten Derks, Rytis Bagdziunas, Griet Laenen and Hans De Wolf

    Citation: BMC Bioinformatics 2019 20:378

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  10. Content type: Research article

    Molecule identification is a crucial step in metabolomics and environmental sciences. Besides in silico fragmentation, as performed by MetFrag, also machine learning and statistical methods evolved, showing an...

    Authors: Christoph Ruttkies, Steffen Neumann and Stefan Posch

    Citation: BMC Bioinformatics 2019 20:376

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  11. Content type: Software

    One of the major challenges facing investigators in the microbiome field is turning large numbers of reads generated by next-generation sequencing (NGS) platforms into biological knowledge. Effective analytica...

    Authors: Teresia M. Buza, Triza Tonui, Francesca Stomeo, Christian Tiambo, Robab Katani, Megan Schilling, Beatus Lyimo, Paul Gwakisa, Isabella M. Cattadori, Joram Buza and Vivek Kapur

    Citation: BMC Bioinformatics 2019 20:374

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  12. Content type: Research article

    RNA molecules play many crucial roles in living systems. The spatial complexity that exists in RNA structures determines their cellular functions. Therefore, understanding RNA folding conformations, in particu...

    Authors: Congzhe Su, Jeffery D. Weir, Fei Zhang, Hao Yan and Teresa Wu

    Citation: BMC Bioinformatics 2019 20:373

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  13. Content type: Research

    Predicting the effect of single point variations on protein stability constitutes a crucial step toward understanding the relationship between protein structure and function. To this end, several methods have ...

    Authors: Ludovica Montanucci, Emidio Capriotti, Yotam Frank, Nir Ben-Tal and Piero Fariselli

    Citation: BMC Bioinformatics 2019 20(Suppl 14):335

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    This article is part of a Supplement: Volume 20 Supplement 14

  14. Content type: Software

    The studies of functions of circular RNAs (circRNAs) are heavily focused on the regulation of gene expression through interactions with multiple miRNAs. However, the number of predicted target genes is typical...

    Authors: Ya-Chi Lin, Yueh-Chun Lee, Kai-Li Chang and Kuei-Yang Hsiao

    Citation: BMC Bioinformatics 2019 20:372

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  15. Content type: Research article

    In spite of the abundance of genomic data, predictive models that describe phenotypes as a function of gene expression or mutations are difficult to obtain because they are affected by the curse of dimensional...

    Authors: Marina Esteban-Medina, María Peña-Chilet, Carlos Loucera and Joaquín Dopazo

    Citation: BMC Bioinformatics 2019 20:370

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  16. Content type: Methodology article

    Single cell RNA sequencing (scRNA-seq) brings unprecedented opportunities for mapping the heterogeneity of complex cellular environments such as bone marrow, and provides insight into many cellular processes. ...

    Authors: Sergii Domanskyi, Anthony Szedlak, Nathaniel T Hawkins, Jiayin Wang, Giovanni Paternostro and Carlo Piermarocchi

    Citation: BMC Bioinformatics 2019 20:369

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  17. Content type: Methodology article

    Mass Spectrometry (MS) is a widely used technique in biology research, and has become key in proteomics and metabolomics analyses. As a result, the amount of MS data has significantly increased in recent years...

    Authors: Ruochen Yang, Xi Chen and Idoia Ochoa

    Citation: BMC Bioinformatics 2019 20:368

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  18. Content type: Research article

    Missense mutations in the first five exons of F9, which encodes factor FIX, represent 40% of all mutations that cause hemophilia B. To address the ongoing debate regarding in silico identification of disease-caus...

    Authors: Lennon Meléndez-Aranda, Ana Rebeca Jaloma-Cruz, Nina Pastor and Marina María de Jesús Romero-Prado

    Citation: BMC Bioinformatics 2019 20:363

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  19. Content type: Research article

    Accurate detection of polymorphisms with a next generation sequencer data is an important element of current genetic analysis. However, there is still no detection pipeline that is completely reliable.

    Authors: Akio Miyao, Jianyu Song Kiyomiya, Keiko Iida, Koji Doi and Hiroshi Yasue

    Citation: BMC Bioinformatics 2019 20:362

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  20. Content type: Software

    Exploration and processing of FASTQ files are the first steps in state-of-the-art data analysis workflows of Next Generation Sequencing (NGS) platforms. The large amount of data generated by these technologies...

    Authors: Leandro Gabriel Roser, Fernán Agüero and Daniel Oscar Sánchez

    Citation: BMC Bioinformatics 2019 20:361

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  21. Content type: Methodology article

    Because of its non-destructive nature, label-free imaging is an important strategy for studying biological processes. However, routine microscopic techniques like phase contrast or DIC suffer from shadow-cast ...

    Authors: Tomas Vicar, Jan Balvan, Josef Jaros, Florian Jug, Radim Kolar, Michal Masarik and Jaromir Gumulec

    Citation: BMC Bioinformatics 2019 20:360

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  22. Content type: Research article

    Essential proteins are distinctly important for an organism’s survival and development and crucial to disease analysis and drug design as well. Large-scale protein-protein interaction (PPI) data sets exist in Sac...

    Authors: Bihai Zhao, Yulin Zhao, Xiaoxia Zhang, Zhihong Zhang, Fan Zhang and Lei Wang

    Citation: BMC Bioinformatics 2019 20:355

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  23. Content type: Research article

    Helitron is a rolling-circle DNA transposon; it plays an important role in plant evolution. However, Helitron distribution and contribution to evolution at the family level have not been previously investigated.

    Authors: Kaining Hu, Kai Xu, Jing Wen, Bin Yi, Jinxiong Shen, Chaozhi Ma, Tingdong Fu, Yidan Ouyang and Jinxing Tu

    Citation: BMC Bioinformatics 2019 20:354

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  24. Content type: Methodology article

    Predicting meaningful miRNA-disease associations (MDAs) is costly. Therefore, an increasing number of researchers are beginning to focus on methods to predict potential MDAs. Thus, prediction methods with impr...

    Authors: Ying-Lian Gao, Zhen Cui, Jin-Xing Liu, Juan Wang and Chun-Hou Zheng

    Citation: BMC Bioinformatics 2019 20:353

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  25. Content type: Software

    Third-generation sequencing platforms, such as PacBio sequencing, have been developed rapidly in recent years. PacBio sequencing generates much longer reads than the second-generation sequencing (or the next g...

    Authors: Wenmin Zhang, Ben Jia and Chaochun Wei

    Citation: BMC Bioinformatics 2019 20:352

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  26. Content type: Methodology article

    Protein feature extraction plays an important role in the areas of similarity analysis of protein sequences and prediction of protein structures, functions and interactions. The feature extraction based on gra...

    Authors: Zengchao Mu, Ting Yu, Enfeng Qi, Juntao Liu and Guojun Li

    Citation: BMC Bioinformatics 2019 20:351

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  27. Content type: Methodology article

    Testing model adequacy is important before a DNA substitution model is chosen for phylogenetic inference. Using a mis-specified model can negatively impact phylogenetic inference, for example, the maximum like...

    Authors: Wei Chen, Toby Kenney, Joseph Bielawski and Hong Gu

    Citation: BMC Bioinformatics 2019 20:349

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  28. Content type: Research

    Cell size is a key characteristic that significantly affects many aspects of cellular physiology. There are specific control mechanisms during cell cycle that maintain the cell size within a range from generat...

    Authors: Mansooreh Ahmadian, John J. Tyson and Yang Cao

    Citation: BMC Bioinformatics 2019 20(Suppl 12):322

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    This article is part of a Supplement: Volume 20 Supplement 12

  29. Content type: Research

    Missing values frequently arise in modern biomedical studies due to various reasons, including missing tests or complex profiling technologies for different omics measurements. Missing values can complicate th...

    Authors: Shahin Boluki, Siamak Zamani Dadaneh, Xiaoning Qian and Edward R. Dougherty

    Citation: BMC Bioinformatics 2019 20(Suppl 12):321

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    This article is part of a Supplement: Volume 20 Supplement 12

  30. Content type: Research

    As Genome-Wide Association Studies (GWAS) have been increasingly used with data from various populations, it has been observed that data from different populations reveal different sets of Single Nucleotide Po...

    Authors: Dalia Elmansy and Mehmet Koyutürk

    Citation: BMC Bioinformatics 2019 20(Suppl 12):320

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    This article is part of a Supplement: Volume 20 Supplement 12

  31. Content type: Research

    Real biological and social data is increasingly being represented as graphs. Pattern-mining-based graph learning and analysis techniques report meaningful biological subnetworks that elucidate important intera...

    Authors: Mohammed Alokshiya, Saeed Salem and Fidaa Abed

    Citation: BMC Bioinformatics 2019 20(Suppl 12):319

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 12

  32. Content type: Research

    Identification of motifs–recurrent and statistically significant patterns–in biological networks is the key to understand the design principles, and to infer governing mechanisms of biological systems. This, h...

    Authors: Yuanfang Ren, Ahmet Ay, Alin Dobra and Tamer Kahveci

    Citation: BMC Bioinformatics 2019 20(Suppl 12):318

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 12

  33. Content type: Research

    Clinical studies often track dose-response curves of subjects over time. One can easily model the dose-response curve at each time point with Hill equation, but such a model fails to capture the temporal evolu...

    Authors: Saugato Rahman Dhruba, Aminur Rahman, Raziur Rahman, Souparno Ghosh and Ranadip Pal

    Citation: BMC Bioinformatics 2019 20(Suppl 12):317

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 12

  34. Content type: Research

    The hybrid stochastic simulation algorithm, proposed by Haseltine and Rawlings (HR), is a combination of differential equations for traditional deterministic models and Gillespie’s algorithm (SSA) for stochast...

    Authors: Minghan Chen and Yang Cao

    Citation: BMC Bioinformatics 2019 20(Suppl 12):315

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    This article is part of a Supplement: Volume 20 Supplement 12

  35. Content type: Research

    Microbiome profiles in the human body and environment niches have become publicly available due to recent advances in high-throughput sequencing technologies. Indeed, recent studies have already identified dif...

    Authors: Chieh Lo and Radu Marculescu

    Citation: BMC Bioinformatics 2019 20(Suppl 12):314

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 12

  36. Content type: Research

    Schizophrenia and autism are examples of polygenic diseases caused by a multitude of genetic variants, many of which are still poorly understood. Recently, both diseases have been associated with disrupted neu...

    Authors: Miriam Bern, Alexander King, Derek A. Applewhite and Anna Ritz

    Citation: BMC Bioinformatics 2019 20(Suppl 12):313

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    This article is part of a Supplement: Volume 20 Supplement 12

  37. Content type: Research article

    In the era of precision oncology and publicly available datasets, the amount of information available for each patient case has dramatically increased. From clinical variables and PET-CT radiomics measures to ...

    Authors: Michael C. Rendleman, John M. Buatti, Terry A. Braun, Brian J. Smith, Chibuzo Nwakama, Reinhard R. Beichel, Bart Brown and Thomas L. Casavant

    Citation: BMC Bioinformatics 2019 20:339

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2018 Journal Metrics

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    2.970 - 5-year Impact Factor
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