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  1. As a machine learning method with high performance and excellent generalization ability, extreme learning machine (ELM) is gaining popularity in various studies. Various ELM-based methods for different fields ...

    Authors: Liang-Rui Ren, Ying-Lian Gao, Jin-Xing Liu, Junliang Shang and Chun-Hou Zheng
    Citation: BMC Bioinformatics 2020 21:445
    Content type: Methodology article Published on:

  4. Identification of genes responsible for anatomical entities is a major requirement in many fields including developmental biology, medicine, and agriculture. Current wet lab techniques used for this purpose, s...

    Authors: Pasan C. Fernando, Paula M. Mabee and Erliang Zeng
    Citation: BMC Bioinformatics 2020 21:442
    Content type: Methodology article Published on:

  6. Mass spectrometry (MS) has become a promising analytical technique to acquire proteomics information for the characterization of biological samples. Nevertheless, most studies focus on the final proteins ident...

    Authors: Shisheng Wang, Hongwen Zhu, Hu Zhou, Jingqiu Cheng and Hao Yang
    Citation: BMC Bioinformatics 2020 21:439
    Content type: Software Published on:

  7. In epigenetics, the change of the combination of histone modifications at the same genomic location during cell differentiation is of great interest for understanding the function of these modifications and th...

    Authors: Dirk Zeckzer, Alrik Hausdorf, Nicole Hinzmann, Lydia Müller and Daniel Wiegreffe
    Citation: BMC Bioinformatics 2020 21:437
    Content type: Software Published on:

  8. Discoveries in cellular dynamics and tissue development constantly reshape our understanding of fundamental biological processes such as embryogenesis, wound-healing, and tumorigenesis. High-quality microscopy...

    Authors: Marco Berghoff, Jakob Rosenbauer, Felix Hoffmann and Alexander Schug
    Citation: BMC Bioinformatics 2020 21:436
    Content type: Software Published on:

  10. Precise disease module is conducive to understanding the molecular mechanism of disease causation and identifying drug targets. However, due to the fragmentization of disease module in incomplete human interac...

    Authors: Bingbo Wang, Jie Hu, Yajun Wang, Chenxing Zhang, Yuanjun Zhou, Liang Yu, Xingli Guo, Lin Gao and Yunru Chen
    Citation: BMC Bioinformatics 2020 21:433
    Content type: Methodology article Published on:

  11. In systems biology, it is of great interest to identify previously unreported associations between genes. Recently, biomedical literature has been considered as a valuable resource for this purpose. While clas...

    Authors: Jin Hyun Nam, Daniel Couch, Willian A. da Silveira, Zhenning Yu and Dongjun Chung
    Citation: BMC Bioinformatics 2020 21:432
    Content type: Methodology article Published on:

  13. A typical task in bioinformatics consists of identifying which features are associated with a target outcome of interest and building a predictive model. Automated machine learning (AutoML) systems such as the...

    Authors: Elisabetta Manduchi, Weixuan Fu, Joseph D. Romano, Stefano Ruberto and Jason H. Moore
    Citation: BMC Bioinformatics 2020 21:430
    Content type: Methodology article Published on:

  15. Second messengers, c-di-GMP and (p)ppGpp, are vital regulatory molecules in bacteria, influencing cellular processes such as biofilm formation, transcription, virulence, quorum sensing, and proliferation. Whil...

    Authors: Chunrui Xu, Bronson R. Weston, John J. Tyson and Yang Cao
    Citation: BMC Bioinformatics 2020 21(Suppl 14):408
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 14

  16. Chromosome conformation capture-based methods, especially Hi-C, enable scientists to detect genome-wide chromatin interactions and study the spatial organization of chromatin, which plays important roles in ge...

    Authors: Chanaka Bulathsinghalage and Lu Liu
    Citation: BMC Bioinformatics 2020 21(Suppl 14):369
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 14

  17. Lung cancer is the leading cause of the largest number of deaths worldwide and lung adenocarcinoma is the most common form of lung cancer. In order to understand the molecular basis of lung adenocarcinoma, int...

    Authors: Talip Zengin and Tuğba Önal-Süzek
    Citation: BMC Bioinformatics 2020 21(Suppl 14):368
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 14

  18. Essential genes are those genes that are critical for the survival of an organism. The prediction of essential genes in bacteria can provide targets for the design of novel antibiotic compounds or antimicrobia...

    Authors: Md Abid Hasan and Stefano Lonardi
    Citation: BMC Bioinformatics 2020 21(Suppl 14):367
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 14

  19. Machine learning has been utilized to predict cancer drug response from multi-omics data generated from sensitivities of cancer cell lines to different therapeutic compounds. Here, we build machine learning mo...

    Authors: Evan A. Clayton, Toyya A. Pujol, John F. McDonald and Peng Qiu
    Citation: BMC Bioinformatics 2020 21(Suppl 14):364
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 14

  20. The abundance of molecular profiling of breast cancer tissues entailed active research on molecular marker-based early diagnosis of metastasis. Recently there is a surging interest in combining gene expression...

    Authors: Nahim Adnan, Chengwei Lei and Jianhua Ruan
    Citation: BMC Bioinformatics 2020 21(Suppl 14):359
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 14

  23. Multi-gene expression assays are an attractive tool in revealing complex regulatory mechanisms in living organisms. Normalization is an indispensable step of data analysis in all those studies, since it remove...

    Authors: Szymon Grabia, Urszula Smyczynska, Konrad Pagacz and Wojciech Fendler
    Citation: BMC Bioinformatics 2020 21:425
    Content type: Software Published on:

  25. Quantitative polymerase chain reaction (qPCR) is the technique of choice for quantifying gene expression. While the technique itself is well established, approaches for the analysis of qPCR data continue to im...

    Authors: Michael T. Ganger, Geoffrey D. Dietz, Patrick Headley and Sarah J. Ewing
    Citation: BMC Bioinformatics 2020 21:423
    Content type: Methodology article Published on:

  26. Antigen receptors are characterized by an extreme diversity of specificities, which poses major computational and analytical challenges, particularly in the era of high-throughput immunoprofiling by next gener...

    Authors: Maria Th. Kotouza, Katerina Gemenetzi, Chrysi Galigalidou, Elisavet Vlachonikola, Nikolaos Pechlivanis, Andreas Agathangelidis, Raphael Sandaltzopoulos, Pericles A. Mitkas, Kostas Stamatopoulos, Anastasia Chatzidimitriou and Fotis E. Psomopoulos
    Citation: BMC Bioinformatics 2020 21:422
    Content type: Software Published on:

  27. The treatment of complex diseases by taking multiple drugs becomes increasingly popular. However, drug-drug interactions (DDIs) may give rise to the risk of unanticipated adverse effects and even unknown toxic...

    Authors: Yue-Hua Feng, Shao-Wu Zhang and Jian-Yu Shi
    Citation: BMC Bioinformatics 2020 21:419
    Content type: Methodology article Published on:

  29. Strand cross-correlation profiles are used for both peak calling pre-analysis and quality control (QC) in chromatin immunoprecipitation followed by sequencing (ChIP-seq) analysis. Despite its potential for rob...

    Authors: Hayato Anzawa, Hitoshi Yamagata and Kengo Kinoshita
    Citation: BMC Bioinformatics 2020 21:417
    Content type: Research article Published on:

  34. Protein microarray is a well-established approach for characterizing activity levels of thousands of proteins in a parallel manner. Analysis of protein microarray data is complex and time-consuming, while exis...

    Authors: Dmytro Fishman, Ivan Kuzmin, Priit Adler, Jaak Vilo and Hedi Peterson
    Citation: BMC Bioinformatics 2020 21:411
    Content type: Software Published on:

  35. Drug-target interaction prediction is of great significance for narrowing down the scope of candidate medications, and thus is a vital step in drug discovery. Because of the particularity of biochemical experi...

    Authors: Jiajie Peng, Jingyi Li and Xuequn Shang
    Citation: BMC Bioinformatics 2020 21(Suppl 13):394
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 13

  36. High-dimensional flow cytometry and mass cytometry allow systemic-level characterization of more than 10 protein profiles at single-cell resolution and provide a much broader landscape in many biological appli...

    Authors: Ko Abe, Kodai Minoura, Yuka Maeda, Hiroyoshi Nishikawa and Teppei Shimamura
    Citation: BMC Bioinformatics 2020 21(Suppl 13):393
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 13

  37. In recent years, the rapid development of single-cell RNA-sequencing (scRNA-seq) techniques enables the quantitative characterization of cell types at a single-cell resolution. With the explosive growth of the...

    Authors: Xiaoyang Chen, Shengquan Chen and Rui Jiang
    Citation: BMC Bioinformatics 2020 21(Suppl 13):392
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 13

  38. Resolution estimation is the main evaluation criteria for the reconstruction of macromolecular 3D structure in the field of cryoelectron microscopy (cryo-EM). At present, there are many methods to evaluate the...

    Authors: Yongchun Lü, Xiangrui Zeng, Xinhui Tian, Xiao Shi, Hui Wang, Xiaohui Zheng, Xiaodong Liu, Xiaofang Zhao, Xin Gao and Min Xu
    Citation: BMC Bioinformatics 2020 21(Suppl 13):391
    Content type: Methodology Published on:

    This article is part of a Supplement: Volume 21 Supplement 13

  39. Advances in mobile sequencing devices and laptop performance make metagenomic sequencing and analysis in the field a technologically feasible prospect. However, metagenomic analysis pipelines are usually desig...

    Authors: Benjamin Albrecht, Caner Bağcı and Daniel H. Huson
    Citation: BMC Bioinformatics 2020 21(Suppl 13):390
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 13

  40. MicroRNAs (miRNAs) play a key role in mediating the action of insulin on cell growth and the development of diabetes. However, few studies have been conducted to provide a comprehensive overview of the miRNA-m...

    Authors: Yang-Chi-Dung Lin, Hsi-Yuan Huang, Sirjana Shrestha, Chih-Hung Chou, Yen-Hua Chen, Chi-Ru Chen, Hsiao-Chin Hong, Jing Li, Yi-An Chang, Men-Yee Chiew, Ya-Rong Huang, Siang-Jyun Tu, Ting-Hsuan Sun, Shun-Long Weng, Ching-Ping Tseng and Hsien-Da Huang
    Citation: BMC Bioinformatics 2020 21(Suppl 13):389
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 13

  41. In Overlap-Layout-Consensus (OLC) based de novo assembly, all reads must be compared with every other read to find overlaps. This makes the process rather slow and limits the practicality of using de novo asse...

    Authors: Nauman Ahmed, Tong Dong Qiu, Koen Bertels and Zaid Al-Ars
    Citation: BMC Bioinformatics 2020 21(Suppl 13):388
    Content type: Software Published on:

    This article is part of a Supplement: Volume 21 Supplement 13

  42. Drug discovery is known for the large amount of money and time it consumes and the high risk it takes. Drug repositioning has, therefore, become a popular approach to save time and cost by finding novel indica...

    Authors: Renyi Zhou, Zhangli Lu, Huimin Luo, Ju Xiang, Min Zeng and Min Li
    Citation: BMC Bioinformatics 2020 21(Suppl 13):387
    Content type: Methodology Published on:

    This article is part of a Supplement: Volume 21 Supplement 13

  43. In the field of computational biology, analyzing complex data helps to extract relevant biological information. Sample classification of gene expression data is one such popular bio-data analysis technique. Ho...

    Authors: Sudipta Acharya, Laizhong Cui and Yi Pan
    Citation: BMC Bioinformatics 2020 21(Suppl 13):386
    Content type: Methodology Published on:

    This article is part of a Supplement: Volume 21 Supplement 13

  44. Network alignment is an efficient computational framework in the prediction of protein function and phylogenetic relationships in systems biology. However, most of existing alignment methods focus on aligning ...

    Authors: Yuanke Zhong, Jing Li, Junhao He, Yiqun Gao, Jie Liu, Jingru Wang, Xuequn Shang and Jialu Hu
    Citation: BMC Bioinformatics 2020 21(Suppl 13):385
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 13

  45. Protein-DNA interaction governs a large number of cellular processes, and it can be altered by a small fraction of interface residues, i.e., the so-called hot spots, which account for most of the interface bindin...

    Authors: Yuliang Pan, Shuigeng Zhou and Jihong Guan
    Citation: BMC Bioinformatics 2020 21(Suppl 13):384
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 13

  46. Glioblastoma multiforme (GBM) is one of the most common malignant brain tumors and its average survival time is less than 1 year after diagnosis.

    Authors: Yujie You, Xufang Ru, Wanjing Lei, Tingting Li, Ming Xiao, Huiru Zheng, Yujie Chen and Le Zhang
    Citation: BMC Bioinformatics 2020 21(Suppl 13):383
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 13

  47. Introducing deep learning approach to medical images has rendered a large amount of un-decoded information into usage in clinical research. But mostly, it has been focusing on the performance of the prediction...

    Authors: Sangwoo Lee, Eun Kyung Choe, So Yeon Kim, Hua Sun Kim, Kyu Joo Park and Dokyoon Kim
    Citation: BMC Bioinformatics 2020 21(Suppl 13):382
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 13

  48. Identification of hot spots in protein-DNA interfaces provides crucial information for the research on protein-DNA interaction and drug design. As experimental methods for determining hot spots are time-consum...

    Authors: Ke Li, Sijia Zhang, Di Yan, Yannan Bin and Junfeng Xia
    Citation: BMC Bioinformatics 2020 21(Suppl 13):381
    Content type: Methodology Published on:

    This article is part of a Supplement: Volume 21 Supplement 13

  49. Biomedical document triage is the foundation of biomedical information extraction, which is important to precision medicine. Recently, some neural networks-based methods have been proposed to classify biomedic...

    Authors: Jian Wang, Mengying Li, Qishuai Diao, Hongfei Lin, Zhihao Yang and YiJia Zhang
    Citation: BMC Bioinformatics 2020 21(Suppl 13):380
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 13

  50. Protein phosphorylation networks play an important role in cell signaling. In these networks, phosphorylation of a protein kinase usually leads to its activation, which in turn will phosphorylate its downstrea...

    Authors: Jinling Liu, Xiaojun Ma, Gregory F. Cooper and Xinghua Lu
    Citation: BMC Bioinformatics 2020 21(Suppl 13):379
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 13

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