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  1. 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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  2. 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

  3. 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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  4. 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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  5. 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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  6. 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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  7. 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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  8. 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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  9. 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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  10. 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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  11. 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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  12. 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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  13. 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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  14. 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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  15. 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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  16. 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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  17. 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

  18. 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

  19. 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

  20. 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

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

  21. 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

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

  22. 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

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

  23. 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

  24. 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

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

  25. 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

  26. Content type: Research article

    Acetylation on lysine is a widespread post-translational modification which is reversible and plays a crucial role in some biological activities. To better understand the mechanism, it is necessary to identify...

    Authors: Qiao Ning, Miao Yu, Jinchao Ji, Zhiqiang Ma and Xiaowei Zhao

    Citation: BMC Bioinformatics 2019 20:346

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  27. Content type: Software

    Next-generation sequencing technology is developing rapidly and the vast amount of data that is generated needs to be preprocessed for downstream analyses. However, until now, software that can efficiently mak...

    Authors: Xiaoshuang Liu, Zhenhe Yan, Chao Wu, Yang Yang, Xiaomin Li and Guangxin Zhang

    Citation: BMC Bioinformatics 2019 20:345

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  28. Content type: Research article

    Whole exome sequencing (WES) is a cost-effective method that identifies clinical variants but it demands accurate variant caller tools. Currently available tools have variable accuracy in predicting specific c...

    Authors: Manojkumar Kumaran, Umadevi Subramanian and Bharanidharan Devarajan

    Citation: BMC Bioinformatics 2019 20:342

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  29. Content type: Research article

    Protein secondary structure (PSS) is critical to further predict the tertiary structure, understand protein function and design drugs. However, experimental techniques of PSS are time consuming and expensive, ...

    Authors: Yanbu Guo, Weihua Li, Bingyi Wang, Huiqing Liu and Dongming Zhou

    Citation: BMC Bioinformatics 2019 20:341

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  30. 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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  31. Content type: Software

    The advent of high-throughput experimental techniques paved the way to genome-wide computational analysis and predictive annotation studies. When considering the joint annotation of a large set of related enti...

    Authors: Stefano Teso, Luca Masera, Michelangelo Diligenti and Andrea Passerini

    Citation: BMC Bioinformatics 2019 20:338

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  32. Content type: Software

    Numerical chromosomal variation is a hallmark of populations of malignant cells. Identifying the factors that promote numerical chromosomal variation is important for understanding mechanisms of carcinogenesis...

    Authors: Daniel G. Piqué, Grasiella A. Andriani, Elaine Maggi, Samuel E. Zimmerman, John M. Greally, Cristina Montagna and Jessica C. Mar

    Citation: BMC Bioinformatics 2019 20:336

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  33. Content type: Methodology article

    Untargeted metabolomics datasets contain large proportions of uninformative features that can impede subsequent statistical analysis such as biomarker discovery and metabolic pathway analysis. Thus, there is a...

    Authors: Courtney Schiffman, Lauren Petrick, Kelsi Perttula, Yukiko Yano, Henrik Carlsson, Todd Whitehead, Catherine Metayer, Josie Hayes, Stephen Rappaport and Sandrine Dudoit

    Citation: BMC Bioinformatics 2019 20:334

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  34. Content type: Software

    Parametric feature selection methods for machine learning and association studies based on genetic data are not robust with respect to outliers or influential observations. While rank-based, distribution-free ...

    Authors: Jiaxing Lin, Alexander Sibley, Ivo Shterev, Andrew Nixon, Federico Innocenti, Cliburn Chan and Kouros Owzar

    Citation: BMC Bioinformatics 2019 20:333

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  35. Content type: Research article

    Ontology has attracted substantial attention from both academia and industry. Handling uncertainty reasoning is important in researching ontology. For example, when a patient is suffering from cirrhosis, the a...

    Authors: Ying Shen, Yaliang Li, Hai-Tao Zheng, Buzhou Tang and Min Yang

    Citation: BMC Bioinformatics 2019 20:330

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  36. Content type: Research article

    Detection of central nodes in asymmetrically directed biological networks depends on centrality metrics quantifying individual nodes’ importance in a network. In topological analyses on metabolic networks, var...

    Authors: Eun-Youn Kim, Daniel Ashlock and Sung Ho Yoon

    Citation: BMC Bioinformatics 2019 20:328

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  37. Content type: Research article

    The gap gene system controls the early cascade of the segmentation pathway in Drosophila melanogaster as well as other insects. Owing to its tractability and key role in embryo patterning, this system has been th...

    Authors: Asif Zubair, I. Gary Rosen, Sergey V. Nuzhdin and Paul Marjoram

    Citation: BMC Bioinformatics 2019 20:327

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  38. Content type: Software

    Deep learning techniques have been successfully applied to bioimaging problems; however, these methods are highly data demanding. An approach to deal with the lack of data and avoid overfitting is the applicat...

    Authors: Ángela Casado-García, César Domínguez, Manuel García-Domínguez, Jónathan Heras, Adrián Inés, Eloy Mata and Vico Pascual

    Citation: BMC Bioinformatics 2019 20:323

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2018 Journal Metrics

  • 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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