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  1. Advances in next-generation sequencing (NGS) of antibody repertoires have led to an explosion in B cell receptor sequence data from donors with many different disease states. These data have the potential to d...

    Authors: Alexander M. Sevy, Cinque Soto, Robin G. Bombardi, Jens Meiler and James E. Crowe Jr

    Citation: BMC Bioinformatics 2019 20:629

    Content type: Methodology article

    Published on:

  2. The Bacteria Biotope (BB) task is a biomedical relation extraction (RE) that aims to study the interaction between bacteria and their locations. This task is considered to pertain to fundamental knowledge in a...

    Authors: Amarin Jettakul, Duangdao Wichadakul and Peerapon Vateekul

    Citation: BMC Bioinformatics 2019 20:627

    Content type: Research Article

    Published on:

  3. In recent years, lncRNAs (long-non-coding RNAs) have been proved to be closely related to the occurrence and development of many serious diseases that are seriously harmful to human health. However, most of th...

    Authors: Jiechen Li, Xueyong Li, Xiang Feng, Bing Wang, Bihai Zhao and Lei Wang

    Citation: BMC Bioinformatics 2019 20:626

    Content type: Research article

    Published on:

  4. Transcriptome analysis aims at gaining insight into cellular processes through discovering gene expression patterns across various experimental conditions. Biclustering is a standard approach to discover genes su...

    Authors: Vincent Branders, Pierre Schaus and Pierre Dupont

    Citation: BMC Bioinformatics 2019 20:625

    Content type: Research Article

    Published on:

  5. Comparative genomics has seen the development of many software performing the clustering, polymorphism and gene content analysis of genomes at different phylogenetic levels (isolates, species). These tools rel...

    Authors: Hatice Akarsu, Lisandra Aguilar-Bultet and Laurent Falquet

    Citation: BMC Bioinformatics 2019 20:621

    Content type: Software

    Published on:

  6. Cancer arises through accumulation of somatically acquired genetic mutations. An important question is to delineate the temporal order of somatic mutations during carcinogenesis, which contributes to better un...

    Authors: Menghan Wang, Tianxin Yu, Jinpeng Liu, Li Chen, Arnold J. Stromberg, John L. Villano, Susanne M. Arnold, Chunming Liu and Chi Wang

    Citation: BMC Bioinformatics 2019 20:620

    Content type: Methodology Article

    Published on:

  7. Expression in H-sapiens plays a remarkable role when it comes to social communication. The identification of this expression by human beings is relatively easy and accurate. However, achieving the same result in ...

    Authors: Olalekan Agbolade, Azree Nazri, Razali Yaakob, Abdul Azim Ghani and Yoke Kqueen Cheah

    Citation: BMC Bioinformatics 2019 20:619

    Content type: Research article

    Published on:

  8. Viruses are closely related to bacteria and human diseases. It is of great significance to predict associations between viruses and hosts for understanding the dynamics and complex functional networks in micro...

    Authors: Dan Liu, Yingjun Ma, Xingpeng Jiang and Tingting He

    Citation: BMC Bioinformatics 2019 20(Suppl 16):594

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 16

  9. A fundamental problem in RNA-seq data analysis is to identify genes or exons that are differentially expressed with varying experimental conditions based on the read counts. The relativeness of RNA-seq measure...

    Authors: Kefei Liu, Li Shen and Hui Jiang

    Citation: BMC Bioinformatics 2019 20(Suppl 16):593

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 16

  10. Topologically associating domains (TADs) are genomic regions with varying lengths. The interactions within TADs are more frequent than those between different TADs. TADs or sub-TADs are considered the structur...

    Authors: Tong Liu and Zheng Wang

    Citation: BMC Bioinformatics 2019 20(Suppl 16):592

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 16

  11. Supercomputers have become indispensable infrastructures in science and industries. In particular, most state-of-the-art scientific results utilize massively parallel supercomputers ranked in TOP500. However, ...

    Authors: Satoshi Ito, Masaaki Yadome, Tatsuo Nishiki, Shigeru Ishiduki, Hikaru Inoue, Rui Yamaguchi and Satoru Miyano

    Citation: BMC Bioinformatics 2019 20(Suppl 16):591

    Content type: Software

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 16

  12. The number of biomedical research articles have increased exponentially with the advancement of biomedicine in recent years. These articles have thus brought a great difficulty in obtaining the needed informat...

    Authors: Bo Xu, Hongfei Lin, Liang Yang, Kan Xu, Yijia Zhang, Dongyu Zhang, Zhihao Yang, Jian Wang, Yuan Lin and Fuliang Yin

    Citation: BMC Bioinformatics 2019 20(Suppl 16):590

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 16

  13. Predicting disease-related genes is helpful for understanding the disease pathology and the molecular mechanisms during the disease progression. However, traditional methods are not suitable for screening gene...

    Authors: Han Zhang, Xueting Huo, Xia Guo, Xin Su, Xiongwen Quan and Chen Jin

    Citation: BMC Bioinformatics 2019 20(Suppl 16):589

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 16

  14. Integrated analysis that uses multiple sample gene expression data measured under the same stress can detect stress response genes more accurately than analysis of individual sample data. However, the integrat...

    Authors: Hongryul Ahn, Inuk Jung, Heejoon Chae, Dongwon Kang, Woosuk Jung and Sun Kim

    Citation: BMC Bioinformatics 2019 20(Suppl 16):588

    Content type: Methodology

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 16

  15. Malignant liver tumor is one of the main causes of human death. In order to help physician better diagnose and make personalized treatment schemes, in clinical practice, it is often necessary to segment and vi...

    Authors: Lei Chen, Hong Song, Chi Wang, Yutao Cui, Jian Yang, Xiaohua Hu and Le Zhang

    Citation: BMC Bioinformatics 2019 20(Suppl 16):587

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 16

  16. Sleep is a complex and dynamic biological process characterized by different sleep patterns. Comprehensive sleep monitoring and analysis using multivariate polysomnography (PSG) records has achieved significan...

    Authors: Ye Yuan, Kebin Jia, Fenglong Ma, Guangxu Xun, Yaqing Wang, Lu Su and Aidong Zhang

    Citation: BMC Bioinformatics 2019 20(Suppl 16):586

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 16

  17. Low diversity of the gut microbiome, often progressing to the point of intestinal domination by a single species, has been linked to poor outcomes in patients undergoing hematopoietic cell transplantation (HCT...

    Authors: Joyce B. Kang, Benjamin A. Siranosian, Eli L. Moss, Niaz Banaei, Tessa M. Andermann and Ami S. Bhatt

    Citation: BMC Bioinformatics 2019 20(Suppl 16):585

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 16

  18. In order to isolate an individual’s genotype from a sample of biological material, most laboratories use PCR and Capillary Electrophoresis (CE) to construct a genetic profile based on polymorphic loci known as...

    Authors: Slim Karkar, Lauren E. Alfonse, Catherine M. Grgicak and Desmond S. Lun

    Citation: BMC Bioinformatics 2019 20(Suppl 16):584

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 16

  19. Microbes have been shown to play a crucial role in various ecosystems. Many human diseases have been proved to be associated with bacteria, so it is essential to extract the interaction between bacteria for me...

    Authors: Xusheng Li, Chengcheng Fu, Ran Zhong, Duo Zhong, Tingting He and Xingpeng Jiang

    Citation: BMC Bioinformatics 2019 20(Suppl 16):583

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 16

  20. Over the past decades, a large number of long non-coding RNAs (lncRNAs) have been identified. Growing evidence has indicated that the mutation and dysregulation of lncRNAs play a critical role in the developme...

    Authors: Yongtian Wang, Liran Juan, Jiajie Peng, Tianyi Zang and Yadong Wang

    Citation: BMC Bioinformatics 2019 20(Suppl 16):582

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 16

  21. Protein-protein interactions(PPIs) engage in dynamic pathological and biological procedures constantly in our life. Thus, it is crucial to comprehend the PPIs thoroughly such that we are able to illuminate the...

    Authors: Da Zhang and Mansur Kabuka

    Citation: BMC Bioinformatics 2019 20(Suppl 16):531

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 16

  22. Essential proteins are crucial for cellular life and thus, identification of essential proteins is an important topic and a challenging problem for researchers. Recently lots of computational approaches have b...

    Authors: Min Zeng, Min Li, Fang-Xiang Wu, Yaohang Li and Yi Pan

    Citation: BMC Bioinformatics 2019 20(Suppl 16):506

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 16

  23. Understanding cellular responses via signal transduction is a core focus in systems biology. Tools to automatically reconstruct signaling pathways from protein-protein interactions (PPIs) can help biologists g...

    Authors: Ibrahim Youssef, Jeffrey Law and Anna Ritz

    Citation: BMC Bioinformatics 2019 20(Suppl 16):505

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 16

  24. In recent years, deep learning methods have been applied to many natural language processing tasks to achieve state-of-the-art performance. However, in the biomedical domain, they have not out-performed superv...

    Authors: Canlin Zhang, Daniel Biś, Xiuwen Liu and Zhe He

    Citation: BMC Bioinformatics 2019 20(Suppl 16):502

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 16

  25. The kinase pocket structural information is important for drug discovery targeting cancer or other diseases. Although some kinase sequence, structure or drug databases have been developed, the databases cannot...

    Authors: Huiwen Wang, Jiadi Qiu, Haoquan Liu, Ying Xu, Ya Jia and Yunjie Zhao

    Citation: BMC Bioinformatics 2019 20:617

    Content type: Database

    Published on:

  26. Following publication of the original article [1], the author explained that there are several errors in the original article

    Authors: Haicang Zhang, Qi Zhang, Fusong Ju, Jianwei Zhu, Yujuan Gao, Ziwei Xie, Minghua Deng, Shiwei Sun, Wei-Mou Zheng and Dongbo Bu

    Citation: BMC Bioinformatics 2019 20:616

    Content type: Correction

    Published on:

    The original article was published in BMC Bioinformatics 2019 20:537

  27. Untargeted metabolomics of host-associated samples has yielded insights into mechanisms by which microbes modulate health. However, data interpretation is challenged by the complexity of origins of the small m...

    Authors: M. Shaffer, K. Thurimella, K. Quinn, K. Doenges, X. Zhang, S. Bokatzian, N. Reisdorph and C. A. Lozupone

    Citation: BMC Bioinformatics 2019 20:614

    Content type: Methodology article

    Published on:

  28. Maximum parsimony reconciliation in the duplication-transfer-loss model is a widely-used method for analyzing the evolutionary histories of pairs of entities such as hosts and parasites, symbiont species, and ...

    Authors: Ross Mawhorter and Ran Libeskind-Hadas

    Citation: BMC Bioinformatics 2019 20:612

    Content type: Methodology Article

    Published on:

  29. Over the last 10 years, there have been over 3300 genome-wide association studies (GWAS). Almost every GWAS study provides a Manhattan plot either as a main figure or in the supplement. Several software packag...

    Authors: Christopher Grace, Martin Farrall, Hugh Watkins and Anuj Goel

    Citation: BMC Bioinformatics 2019 20:610

    Content type: Software

    Published on:

  30. Recurrent neural network(RNN) is a good way to process sequential data, but the capability of RNN to compute long sequence data is inefficient. As a variant of RNN, long short term memory(LSTM) solved the prob...

    Authors: Jiale Liu and Xinqi Gong

    Citation: BMC Bioinformatics 2019 20:609

    Content type: Methodology Article

    Published on:

  31. Microarray datasets consist of complex and high-dimensional samples and genes, and generally the number of samples is much smaller than the number of genes. Due to this data imbalance, gene selection is a dema...

    Authors: Russul Alanni, Jingyu Hou, Hasseeb Azzawi and Yong Xiang

    Citation: BMC Bioinformatics 2019 20:608

    Content type: Research article

    Published on:

  32. To study cell biological phenomena which depend on diffusion, active transport processes, or the locations of species, modeling and simulation studies need to take space into account. To describe the system as...

    Authors: Till Köster, Philipp Henning and Adelinde M. Uhrmacher

    Citation: BMC Bioinformatics 2019 20:607

    Content type: Methodology Article

    Published on:

  33. Influenza is an infectious respiratory disease that can cause serious public health hazard. Due to its huge threat to the society, precise real-time forecasting of influenza outbreaks is of great value to our ...

    Authors: Xianglei Zhu, Bofeng Fu, Yaodong Yang, Yu Ma, Jianye Hao, Siqi Chen, Shuang Liu, Tiegang Li, Sen Liu, Weiming Guo and Zhenyu Liao

    Citation: BMC Bioinformatics 2019 20(Suppl 18):575

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 18

  34. As the terminal products of cellular regulatory process, functional related metabolites have a close relationship with complex diseases, and are often associated with the same or similar diseases. Therefore, i...

    Authors: Yongtian Wang, Liran Juan, Jiajie Peng, Tianyi Zang and Yadong Wang

    Citation: BMC Bioinformatics 2019 20(Suppl 18):574

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 18

  35. During procedures for conducting multiple sequence alignment, that is so essential to use the substitution score of pairwise alignment. To compute adaptive scores for alignment, researchers usually use Hidden ...

    Authors: Qing Zhan, Nan Wang, Shuilin Jin, Renjie Tan, Qinghua Jiang and Yadong Wang

    Citation: BMC Bioinformatics 2019 20(Suppl 18):573

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 18

  36. The Gene Ontology (GO) knowledgebase is the world’s largest source of information on the functions of genes. Since the beginning of GO project, various tools have been developed to perform GO enrichment analys...

    Authors: Jiajie Peng, Guilin Lu, Hansheng Xue, Tao Wang and Xuequn Shang

    Citation: BMC Bioinformatics 2019 20(Suppl 18):572

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 18

  37. Collective cell migration is a significant and complex phenomenon that affects many basic biological processes. The coordination between leader cell and follower cell affects the rate of collective cell migrat...

    Authors: Hanxu Hou, Tian Gan, Yaodong Yang, Xianglei Zhu, Sen Liu, Weiming Guo and Jianye Hao

    Citation: BMC Bioinformatics 2019 20(Suppl 18):571

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 18

  38. Alzheimer’s disease (AD) imposes a heavy burden on society and every family. Therefore, diagnosing AD in advance and discovering new drug targets are crucial, while these could be achieved by identifying AD-re...

    Authors: Tianyi Zhao, Yang Hu, Tianyi Zang and Liang Cheng

    Citation: BMC Bioinformatics 2019 20(Suppl 18):570

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 18

  39. There is evidence to suggest that lncRNAs are associated with distinct and diverse biological processes. The dysfunction or mutation of lncRNAs are implicated in a wide range of diseases. An accurate computati...

    Authors: Jialu Hu, Yiqun Gao, Jing Li, Yan Zheng, Jingru Wang and Xuequn Shang

    Citation: BMC Bioinformatics 2019 20(Suppl 18):569

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 18

  40. Lung cancer is one of the most malignant tumors, causing over 1,000,000 deaths each year worldwide. Deep learning has brought success in many domains in recent years. DNA methylation, an epigenetic factor, is ...

    Authors: Zhenxing Wang and Yadong Wang

    Citation: BMC Bioinformatics 2019 20(Suppl 18):568

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 18

  41. With the development of e-Health, it plays a more and more important role in predicting whether a doctor’s answer can be accepted by a patient through online healthcare community. Unlike the previous work whic...

    Authors: Qianlong Liu, Kangenbei Liao, Kelvin Kam-fai Tsoi and Zhongyu Wei

    Citation: BMC Bioinformatics 2019 20(Suppl 18):567

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 18

  42. It’s a very urgent task to identify cancer genes that enables us to understand the mechanisms of biochemical processes at a biomolecular level and facilitates the development of bioinformatics. Although a larg...

    Authors: Wenxiang Zhang, Xiujuan Lei (IEEE member) and Chen Bian

    Citation: BMC Bioinformatics 2019 20(Suppl 18):518

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 18

  43. This preface introduces the content of the BioMed Central Bioinformatics journal Supplement related to the 15th annual meeting of the Bioinformatics Italian Society, BITS2018. The Conference was held in Torino...

    Authors: Francesca Cordero, Raffaele A. Calogero and Michele Caselle

    Citation: BMC Bioinformatics 2019 20(Suppl 9):562

    Content type: Introduction

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 9

  44. Logic Learning Machine (LLM) is an innovative method of supervised analysis capable of constructing models based on simple and intelligible rules.

    Authors: Damiano Verda, Stefano Parodi, Enrico Ferrari and Marco Muselli

    Citation: BMC Bioinformatics 2019 20(Suppl 9):390

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 9

  45. Several large public repositories of microarray datasets and RNA-seq data are available. Two prominent examples include ArrayExpress and NCBI GEO. Unfortunately, there is no easy way to import and manipulate d...

    Authors: Salvatore Alaimo, Antonio Di Maria, Dennis Shasha, Alfredo Ferro and Alfredo Pulvirenti

    Citation: BMC Bioinformatics 2019 20(Suppl 9):366

    Content type: Software

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 9

  46. Multi-locus sequence typing (MLST) is a standard typing technique used to associate a sequence type (ST) to a bacterial isolate. When the output of whole genome sequencing (WGS) of a sample is available the ST...

    Authors: Mattia Dalsass, Margherita Bodini, Christophe Lambert, Marie-Cécile Mortier, Marco Romanelli, Duccio Medini, Alessandro Muzzi and Alessandro Brozzi

    Citation: BMC Bioinformatics 2019 20(Suppl 9):347

    Content type: Software

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 9

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