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  2. 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:

  3. 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

  7. 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:

  8. 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:

  9. 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:

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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

  16. 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

  17. 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

  18. 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

  19. Intra-tumor heterogeneity is known to contribute to cancer complexity and drug resistance. Understanding the number of distinct subclones and the evolutionary relationships between them is scientifically and c...

    Authors: Hosein Toosi, Ali Moeini and Iman Hajirasouliha
    Citation: BMC Bioinformatics 2019 20(Suppl 11):282
    Content type: Research Published on:

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

  20. The limitations of traditional computer-aided detection (CAD) systems for mammography, the extreme importance of early detection of breast cancer and the high impact of the false diagnosis of patients drive re...

    Authors: Dina Abdelhafiz, Clifford Yang, Reda Ammar and Sheida Nabavi
    Citation: BMC Bioinformatics 2019 20(Suppl 11):281
    Content type: Research Published on:

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

  21. 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

  22. 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

  23. 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

  25. A crucial task in metagenomic analysis is to annotate the function and taxonomy of the sequencing reads generated from a microbiome sample. In general, the reads can either be assembled into contigs and search...

    Authors: Cuncong Zhong, Youngik Yang and Shibu Yooseph
    Citation: BMC Bioinformatics 2019 20(Suppl 11):276
    Content type: Research Published on:

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

  26. 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

  28. Pharmacological treatment of complex diseases using more than two drugs is commonplace in the clinic due to better efficacy, decreased toxicity and reduced risk for developing resistance. However, many of thes...

    Authors: Efthymia Chantzi, Malin Jarvius, Mia Niklasson, Anna Segerman and Mats G. Gustafsson
    Citation: BMC Bioinformatics 2019 20:304
    Content type: Methodology article Published on:

  29. The spatial distribution and colocalization of functionally related metabolites is analysed in order to investigate the spatial (and functional) aspects of molecular networks. We propose to consider community ...

    Authors: Karsten Wüllems, Jan Kölling, Hanna Bednarz, Karsten Niehaus, Volkmar H. Hans and Tim W. Nattkemper
    Citation: BMC Bioinformatics 2019 20:303
    Content type: Methodology article Published on:

  30. elPrep is an established multi-threaded framework for preparing SAM and BAM files in sequencing pipelines. To achieve good performance, its software architecture makes only a single pass through a SAM/BAM file...

    Authors: Pascal Costanza, Charlotte Herzeel and Wilfried Verachtert
    Citation: BMC Bioinformatics 2019 20:301
    Content type: Methodology article Published on:

  32. The knowledge-based statistical potential has been widely used in protein structure modeling and model quality assessment. They are commonly evaluated based on their abilities of native recognition as well as ...

    Authors: Zhongwang Yu, Yuangen Yao, Haiyou Deng and Ming Yi
    Citation: BMC Bioinformatics 2019 20:299
    Content type: Methodology article Published on:

  33. Several standalone error correction tools have been proposed to correct sequencing errors in Illumina data in order to facilitate de novo genome assembly. However, in a recent survey, we showed that state-of-t...

    Authors: Mahdi Heydari, Giles Miclotte, Yves Van de Peer and Jan Fostier
    Citation: BMC Bioinformatics 2019 20:298
    Content type: Research article Published on:

  34. Host factors of influenza virus replication are often found in key topological positions within protein-protein interaction networks. This work explores how protein states can be manipulated through controllab...

    Authors: Emily E. Ackerman, John F. Alcorn, Takeshi Hase and Jason E. Shoemaker
    Citation: BMC Bioinformatics 2019 20:297
    Content type: Research article Published on:

  35. Gene regulatory networks can be modelled in various ways depending on the level of detail required and biological questions addressed. One of the earliest formalisms used for modeling is a Boolean network, alt...

    Authors: Dace Ruklisa, Alvis Brazma, Karlis Cerans, Thomas Schlitt and Juris Viksna
    Citation: BMC Bioinformatics 2019 20:296
    Content type: Research article Published on:

  36. The real-time quantitative polymerase chain reaction (qPCR) is routinely used for quantification of nucleic acids and is considered the gold standard in the field of relative nucleic acid measurements. The eff...

    Authors: Yulia Panina, Arno Germond, Brit G. David and Tomonobu M. Watanabe
    Citation: BMC Bioinformatics 2019 20:295
    Content type: Methodology article Published on:

  37. Biochemical networks are often described through static or time-averaged measurements of the component macromolecules. Temporal variation in these components plays an important role in both describing the dyna...

    Authors: Maryam Masnadi-Shirazi, Mano R. Maurya, Gerald Pao, Eugene Ke, Inder M. Verma and Shankar Subramaniam
    Citation: BMC Bioinformatics 2019 20:294
    Content type: Research article Published on:

  39. Although several studies have provided insights into the role of long non-coding RNAs (lncRNAs), the majority of them have unknown function. Recent evidence has shown the importance of both lncRNAs and chromat...

    Authors: Denise Thiel, Nataša Djurdjevac Conrad, Evgenia Ntini, Ria X. Peschutter, Heike Siebert and Annalisa Marsico
    Citation: BMC Bioinformatics 2019 20:292
    Content type: Methodology article Published on:

  41. Drug candidates often cause an unwanted blockage of the potassium ion channel of the human ether-a-go-go-related gene (hERG). The blockage leads to long QT syndrome (LQTS), which is a severe life-threatening c...

    Authors: Hyang-Mi Lee, Myeong-Sang Yu, Sayada Reemsha Kazmi, Seong Yun Oh, Ki-Hyeong Rhee, Myung-Ae Bae, Byung Ho Lee, Dae-Seop Shin, Kwang-Seok Oh, Hyithaek Ceong, Donghyun Lee and Dokyun Na
    Citation: BMC Bioinformatics 2019 20(Suppl 10):250
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 10

  42. Finding biomedical named entities is one of the most essential tasks in biomedical text mining. Recently, deep learning-based approaches have been applied to biomedical named entity recognition (BioNER) and sh...

    Authors: Wonjin Yoon, Chan Ho So, Jinhyuk Lee and Jaewoo Kang
    Citation: BMC Bioinformatics 2019 20(Suppl 10):249
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 10

  43. Computational analysis of complex diseases involving multiple organs requires the integration of multiple different models into a unified model. Different models are often constructed in heterogeneous formats....

    Authors: Mijin Kwon, Soorin Yim, Gwangmin Kim, Saehwan Lee, Chungsun Jeong and Doheon Lee
    Citation: BMC Bioinformatics 2019 20(Suppl 10):248
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 10

  44. Drug repositioning, also known as drug repurposing, defines new indications for existing drugs and can be used as an alternative to drug development. In recent years, the accumulation of large volumes of infor...

    Authors: Eunyoung Kim, A-sol Choi and Hojung Nam
    Citation: BMC Bioinformatics 2019 20(Suppl 10):247
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 10

  45. Given the increasing amount of biomedical resources that are being annotated with concepts from more than one ontology and covering multiple domains of knowledge, it is important to devise mechanisms to compar...

    Authors: João D. Ferreira and Francisco M. Couto
    Citation: BMC Bioinformatics 2019 20(Suppl 10):246
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 10

  46. The selection of reference genes is essential for quantifying gene expression. Theoretically they should be expressed stably and not regulated by experimental or pathological conditions. However, identificatio...

    Authors: Jihoon Jo, Sunkyung Choi, Jooseong Oh, Sung-Gwon Lee, Song Yi Choi, Kee K. Kim and Chungoo Park
    Citation: BMC Bioinformatics 2019 20(Suppl 10):245
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 10

  47. Due to the advent of deep learning, the increasing number of studies in the biomedical domain has attracted much interest in feature extraction and classification tasks. In this research, we seek the best comb...

    Authors: Zolzaya Dashdorj and Min Song
    Citation: BMC Bioinformatics 2019 20(Suppl 10):244
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 10

  48. Modern molecular profiling techniques are yielding vast amounts of data from patient samples that could be utilized with machine learning methods to provide important biological insights and improvements in pa...

    Authors: Heinrich Roder, Carlos Oliveira, Lelia Net, Benjamin Linstid, Maxim Tsypin and Joanna Roder
    Citation: BMC Bioinformatics 2019 20:273
    Content type: Methodology article Published on:

  49. The recent success of immunotherapy in treating tumors has attracted increasing interest in research related to the adaptive immune system in the tumor microenvironment. Recent advances in next-generation sequ...

    Authors: Hiroki Konishi, Daisuke Komura, Hiroto Katoh, Shinichiro Atsumi, Hirotomo Koda, Asami Yamamoto, Yasuyuki Seto, Masashi Fukayama, Rui Yamaguchi, Seiya Imoto and Shumpei Ishikawa
    Citation: BMC Bioinformatics 2019 20:267
    Content type: Research article Published on:

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