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  1. 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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  2. 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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  3. 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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  4. 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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  5. 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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  6. 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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  7. 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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  8. 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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  9. 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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  10. 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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  11. 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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  12. Content type: Methodology article

    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

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  13. Content type: Methodology article

    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

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  14. 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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  15. Content type: Software

    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

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  16. Content type: Methodology article

    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

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  17. Content type: Research article

    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

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  18. Content type: Methodology article

    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

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  19. Content type: Research

    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

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

  20. Content type: Research

    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

    Published on:

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

  21. Content type: Research

    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

    Published on:

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

  22. Content type: Research

    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

    Published on:

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

  23. Content type: Research

    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

    Published on:

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

  24. Content type: Research

    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

    Published on:

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

  25. Content type: Research

    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

    Published on:

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

  26. Content type: Research

    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

    Published on:

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

  27. Content type: Research

    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

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

  28. Content type: Research

    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

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

  29. Content type: Research

    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

    Published on:

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

  30. Content type: Research

    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

    Published on:

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

  31. Content type: Methodology

    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

    Published on:

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

  32. Content type: Research

    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

    Published on:

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

  33. Content type: Research

    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

    Published on:

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

  34. Content type: Methodology article

    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

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  35. Content type: Methodology article

    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

    Published on:

  36. Content type: Methodology article

    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

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  37. Content type: Research article

    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

    Published on:

  38. Content type: Research article

    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

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2018 Journal Metrics

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    2.970 - 5-year Impact Factor
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