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  1. 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

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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:

  9. 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:

  10. 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:

  11. 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:

  12. 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:

  13. 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:

  14. 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:

  15. 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:

  16. 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:

  17. 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:

  18. 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:

  19. 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:

  20. An important task of macromolecular structure determination by cryo-electron microscopy (cryo-EM) is the identification of single particles in micrographs (particle picking). Due to the necessity of human invo...

    Authors: Adil Al-Azzawi, Anes Ouadou, John J. Tanner and Jianlin Cheng

    Citation: BMC Bioinformatics 2019 20:326

    Content type: Methodology article

    Published on:

  21. 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:

  22. 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:

  23. Mathematical and computational models are widely used to study the transmission, pathogenicity, and propagation of infectious diseases. Unfortunately, complex mathematical models are difficult to define, reuse...

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

    Citation: BMC Bioinformatics 2019 20:312

    Content type: Software

    Published on:

    The Correction to this article has been published in BMC Bioinformatics 2019 20:439

  24. Although various machine learning-based predictors have been developed for estimating protein–protein interactions, their performances vary with dataset and species, and are affected by two primary aspects: ch...

    Authors: Kuan-Hsi Chen, Tsai-Feng Wang and Yuh-Jyh Hu

    Citation: BMC Bioinformatics 2019 20:308

    Content type: Methodology article

    Published on:

  25. The maturation of the female germ cell, the oocyte, requires the synthesis and storing of all the necessary metabolites to support multiple divisions after fertilization. Oocyte maturation is only possible in ...

    Authors: Beatriz Peñalver Bernabé, Ines Thiele, Eugene Galdones, Anaar Siletz, Sriram Chandrasekaran, Teresa K. Woodruff, Linda J. Broadbelt and Lonnie D. Shea

    Citation: BMC Bioinformatics 2019 20:307

    Content type: Research article

    Published on:

  26. Representation learning provides new and powerful graph analytical approaches and tools for the highly valued data science challenge of mining knowledge graphs. Since previous graph analytical methods have mos...

    Authors: Zheng Gao, Gang Fu, Chunping Ouyang, Satoshi Tsutsui, Xiaozhong Liu, Jeremy Yang, Christopher Gessner, Brian Foote, David Wild, Ying Ding and Qi Yu

    Citation: BMC Bioinformatics 2019 20:306

    Content type: Methodology article

    Published on:

  27. Antimicrobial peptides (AMPs) are essential components of the innate immune system and can protect the host from various pathogenic bacteria. The marine environment is known to be one of the richest sources fo...

    Authors: Yuan Lin, Yinyin Cai, Juan Liu, Chen Lin and Xiangrong Liu

    Citation: BMC Bioinformatics 2019 20(Suppl 8):291

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 8

  28. It is of great clinical significance to develop an accurate computer aided system to accurately diagnose the breast cancer. In this study, an enhanced machine learning framework is established to diagnose the ...

    Authors: Hui Huang, Xi’an Feng, Suying Zhou, Jionghui Jiang, Huiling Chen, Yuping Li and Chengye Li

    Citation: BMC Bioinformatics 2019 20(Suppl 8):290

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 8

  29. Gene selection is one of the critical steps in the course of the classification of microarray data. Since particle swarm optimization has no complicated evolutionary operators and fewer parameters need to be a...

    Authors: Fei Han, Di Tang, Yu-Wen-Tian Sun, Zhun Cheng, Jing Jiang and Qiu-Wei Li

    Citation: BMC Bioinformatics 2019 20(Suppl 8):289

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 8

  30. Avian influenza virus can directly cross species barriers and infect humans with high fatality. As antigen novelty for human host, the public health is being challenged seriously. The pandemic risk of avian in...

    Authors: Xiaoli Qiang and Zheng Kou

    Citation: BMC Bioinformatics 2019 20(Suppl 8):288

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 8

  31. Predicting drug-target interactions is time-consuming and expensive. It is important to present the accuracy of the calculation method. There are many algorithms to predict global interactions, some of which u...

    Authors: Zhen Cui, Ying-Lian Gao, Jin-Xing Liu, Ling-Yun Dai and Sha-Sha Yuan

    Citation: BMC Bioinformatics 2019 20(Suppl 8):287

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 8

  32. DNA is a promising candidate for the construction of biological devices due to its unique properties, including structural simplicity, convenient synthesis, high flexibility, and predictable behavior. And DNA ...

    Authors: Yanan Wang, Qi Lv, Yingying Zhang, Luhui Wang and Yafei Dong

    Citation: BMC Bioinformatics 2019 20(Suppl 8):285

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 8

  33. Single cell RNA sequencing (scRNA-seq) is applied to assay the individual transcriptomes of large numbers of cells. The gene expression at single-cell level provides an opportunity for better understanding of ...

    Authors: Jiajie Peng, Xiaoyu Wang and Xuequn Shang

    Citation: BMC Bioinformatics 2019 20(Suppl 8):284

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 8

  34. Numerous essential algorithms and methods, including entropy-based quantitative methods, have been developed to analyze complex DNA sequences since the last decade. Exons and introns are the most notable compo...

    Authors: Junyi Li, Li Zhang, Huinian Li, Yuan Ping, Qingzhe Xu, Rongjie Wang, Renjie Tan, Zhen Wang, Bo Liu and Yadong Wang

    Citation: BMC Bioinformatics 2019 20(Suppl 8):283

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 8

  35. Nearly all cellular processes involve proteins structurally rearranging to accommodate molecular partners. The energy landscape underscores the inherent nature of proteins as dynamic molecules interconverting ...

    Authors: David Morris, Tatiana Maximova, Erion Plaku and Amarda Shehu

    Citation: BMC Bioinformatics 2019 20(Suppl 11):280

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 11

  36. Recent advances in whole-genome sequencing and SNP array technology have led to the generation of a large amount of genotype data. Large volumes of genotype data will require faster and more efficient methods ...

    Authors: Ardalan Naseri, Degui Zhi and Shaojie Zhang

    Citation: BMC Bioinformatics 2019 20(Suppl 11):279

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 11

  37. Computing centrality is a foundational concept in social networking that involves finding the most “central” or important nodes. In some biological networks defining importance is difficult, which then creates ch...

    Authors: Trevor Cickovski, Vanessa Aguiar-Pulido and Giri Narasimhan

    Citation: BMC Bioinformatics 2019 20(Suppl 11):278

    Content type: Methodology

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 11

  38. The advent of single cell RNA sequencing (scRNA-seq) enabled researchers to study transcriptomic activity within individual cells and identify inherent cell types in the sample. Although numerous computational...

    Authors: Douglas Abrams, Parveen Kumar, R. Krishna Murthy Karuturi and Joshy George

    Citation: BMC Bioinformatics 2019 20(Suppl 11):275

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 11

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