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  1. 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
    Content type: Research article Published on:

  2. 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
    Content type: Methodology article Published on:

  3. 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
    Content type: Methodology article Published on:

  6. 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
    Content type: Research article Published on:

  7. 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
    Content type: Research article Published on:

  8. 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
    Content type: Software Published on:

  9. 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
    Content type: Methodology article Published on:

  14. 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
    Content type: Research article Published on:

  15. 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
    Content type: Research article Published on:

  16. 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
    Content type: Methodology article Published on:

  17. 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
    Content type: Software Published on:

  18. 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
    Content type: Methodology article Published on:

  20. 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
    Content type: Methodology article Published on:

  21. 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
    Content type: Research Published on:

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

  22. 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
    Content type: Research Published on:

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

  23. 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
    Content type: Research Published on:

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

  24. 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
    Content type: Research Published on:

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

  25. 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
    Content type: Research Published on:

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

  26. 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
    Content type: Research Published on:

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

  28. 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
    Content type: Research Published on:

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

  29. 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
    Content type: Research Published on:

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

  30. 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
    Content type: Research Published on:

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

  32. 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
    Content type: Research article Published on:

  33. 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
    Content type: Software Published on:

  35. 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
    Content type: Research article Published on:

  36. 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
    Content type: Research article Published on:

  38. 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
    Content type: Research article Published on:

  39. 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
    Content type: Software Published on:

  40. 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
    Content type: Software Published on:

  41. 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
    Content type: Methodology article Published on:

  42. 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
    Content type: Software Published on:

  44. 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
    Content type: Research article Published on:

  46. 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
    Content type: Research article Published on:

  47. 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
    Content type: Research article Published on:

  48. Modern genomic and proteomic profiling methods produce large amounts of data from tissue and blood-based samples that are of potential utility for improving patient care. However, the design of precision medic...

    Authors: Joanna Roder, Carlos Oliveira, Lelia Net, Maxim Tsypin, Benjamin Linstid and Heinrich Roder
    Citation: BMC Bioinformatics 2019 20:325
    Content type: Methodology article Published on:

  50. 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
    Content type: Software Published on:

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