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  1. A range of rare and common genetic variants have been discovered to be potentially associated with mental diseases, but many more have not been uncovered. Powerful integrative methods are needed to systematica...

    Authors: Atlas Khan, Qian Liu and Kai Wang
    Citation: BMC Bioinformatics 2018 19(Suppl 17):501
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 17

  2. Systems approaches in studying disease relationship have wide applications in biomedical discovery, such as disease mechanism understanding and drug discovery. The FDA Adverse Event Reporting System (FAERS) co...

    Authors: Chunlei Zheng and Rong Xu
    Citation: BMC Bioinformatics 2018 19(Suppl 17):500
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 17

  3. Electronic Medical Record (EMR) comprises patients’ medical information gathered by medical stuff for providing better health care. Named Entity Recognition (NER) is a sub-field of information extraction aimed...

    Authors: Shanta Chowdhury, Xishuang Dong, Lijun Qian, Xiangfang Li, Yi Guan, Jinfeng Yang and Qiubin Yu
    Citation: BMC Bioinformatics 2018 19(Suppl 17):499
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 17

  4. Identifying local recurrences in breast cancer from patient data sets is important for clinical research and practice. Developing a model using natural language processing and machine learning to identify loca...

    Authors: Zexian Zeng, Sasa Espino, Ankita Roy, Xiaoyu Li, Seema A. Khan, Susan E. Clare, Xia Jiang, Richard Neapolitan and Yuan Luo
    Citation: BMC Bioinformatics 2018 19(Suppl 17):498
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 17

  5. In precision medicine, scarcity of suitable biological data often hinders the design of an appropriate predictive model. In this regard, large scale pharmacogenomics studies, like CCLE and GDSC hold the promis...

    Authors: Saugato Rahman Dhruba, Raziur Rahman, Kevin Matlock, Souparno Ghosh and Ranadip Pal
    Citation: BMC Bioinformatics 2018 19(Suppl 17):497
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 17

  6. Hi-C data have been widely used to reconstruct chromosomal three-dimensional (3D) structures. One of the key limitations of Hi-C is the unclear relationship between spatial distance and the number of Hi-C cont...

    Authors: Tong Liu and Zheng Wang
    Citation: BMC Bioinformatics 2018 19(Suppl 17):496
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 17

  7. Due to recent technology advancements, disease related knowledge is growing rapidly. It becomes nontrivial to go through all published literature to identify associations between human diseases and genetic, en...

    Authors: Junhui Shen, Suhas Vasaikar and Bing Zhang
    Citation: BMC Bioinformatics 2018 19(Suppl 17):495
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 17

  8. Top-down mass spectrometry has unique advantages in identifying proteoforms with multiple post-translational modifications and/or unknown alterations. Most software tools in this area search top-down mass spec...

    Authors: Ziwei Li, Bo He, Qiang Kou, Zhe Wang, Si Wu, Yunlong Liu, Weixing Feng and Xiaowen Liu
    Citation: BMC Bioinformatics 2018 19(Suppl 17):494
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 17

  9. In genomic studies, to investigate how the structure of a genetic network differs between two experiment conditions is a very interesting but challenging problem, especially in high-dimensional setting. Existi...

    Authors: Yong He, Jiadong Ji, Lei Xie, Xinsheng Zhang and Fuzhong Xue
    Citation: BMC Bioinformatics 2018 19(Suppl 17):493
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 17

  10. The 2018 International Conference on Intelligent Biology and Medicine (ICIBM 2018) was held on June 10–12, 2018, in Los Angeles, California, USA. The conference consisted of a total of eleven scientific sessio...

    Authors: Xiaoming Liu, Lei Xie, Zhijin Wu, Kai Wang, Zhongming Zhao, Jianhua Ruan and Degui Zhi
    Citation: BMC Bioinformatics 2018 19(Suppl 17):492
    Content type: Introduction Published on:

    This article is part of a Supplement: Volume 19 Supplement 17

  11. Adverse drug reactions (ADRs) are unintended and harmful reactions caused by normal uses of drugs. Predicting and preventing ADRs in the early stage of the drug development pipeline can help to enhance drug sa...

    Authors: Sanjoy Dey, Heng Luo, Achille Fokoue, Jianying Hu and Ping Zhang
    Citation: BMC Bioinformatics 2018 19(Suppl 21):476
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 21

  13. The neutral theory of Motoo Kimura stipulates that evolution is mostly driven by neutral mutations. However adaptive pressure eventually leads to changes in phenotype that involve non-neutral mutations. The re...

    Authors: Reza Rezazadegan and Christian Reidys
    Citation: BMC Bioinformatics 2018 19:543
    Content type: Research article Published on:

  14. As a result of its simplicity and high efficiency, the CRISPR-Cas system has been widely used as a genome editing tool. Recently, CRISPR base editors, which consist of deactivated Cas9 (dCas9) or Cas9 nickase ...

    Authors: Gue-Ho Hwang, Jeongbin Park, Kayeong Lim, Sunghyun Kim, Jihyeon Yu, Eunchong Yu, Sang-Tae Kim, Roland Eils, Jin-Soo Kim and Sangsu Bae
    Citation: BMC Bioinformatics 2018 19:542
    Content type: Software Published on:

  16. DNA methylation of CpG dinucleotides is an essential epigenetic modification that plays a key role in transcription. Widely used DNA enrichment-based methods offer high coverage for measuring methylated CpG di...

    Authors: Jingting Xu, Shimeng Liu, Ping Yin, Serdar Bulun and Yang Dai
    Citation: BMC Bioinformatics 2018 19:540
    Content type: Methodology article Published on:

  18. Pathway enrichment techniques are useful for understanding experimental metabolomics data. Their purpose is to give context to the affected metabolites in terms of the prior knowledge contained in metabolic pa...

    Authors: Sergio Picart-Armada, Francesc Fernández-Albert, Maria Vinaixa, Oscar Yanes and Alexandre Perera-Lluna
    Citation: BMC Bioinformatics 2018 19:538
    Content type: Software Published on:

  19. Sequencing highly-variable 16S regions is a common and often effective approach to the study of microbial communities, and next-generation sequencing (NGS) technologies provide abundant quantities of data for ...

    Authors: Timothy Chappell, Shlomo Geva, James M. Hogan, Flavia Huygens, Irani U. Rathnayake, Stephen Rudd, Wayne Kelly and Dimitri Perrin
    Citation: BMC Bioinformatics 2018 19(Suppl 20):509
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 20

  20. With applications in cancer, drug metabolism, and disease etiology, understanding structural variation in the human genome is critical in advancing the thrusts of individualized medicine. However, structural v...

    Authors: Zachary Stephens, Chen Wang, Ravishankar K. Iyer and Jean-Pierre Kocher
    Citation: BMC Bioinformatics 2018 19(Suppl 20):508
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 20

  21. In biomedical information extraction, event extraction plays a crucial role. Biological events are used to describe the dynamic effects or relationships between biological entities such as proteins and genes. ...

    Authors: Yan Wang, Jian Wang, Hongfei Lin, Xiwei Tang, Shaowu Zhang and Lishuang Li
    Citation: BMC Bioinformatics 2018 19(Suppl 20):507
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 20

  22. Atomic details of protein-DNA complexes can provide insightful information for better understanding of the function and binding specificity of DNA binding proteins. In addition to experimental methods for solv...

    Authors: Rosario I. Corona, Sanjana Sudarshan, Srinivas Aluru and Jun-tao Guo
    Citation: BMC Bioinformatics 2018 19(Suppl 20):506
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 20

  23. The traditional methods of visualizing high-dimensional data objects in low-dimensional metric spaces are subject to the basic limitations of metric space. These limitations result in multidimensional scaling ...

    Authors: Xianchao Zhu, Xianjun Shen, Xingpeng Jiang, Kaiping Wei, Tingting He, Yuanyuan Ma, Jiaqi Liu and Xiaohua Hu
    Citation: BMC Bioinformatics 2018 19(Suppl 20):505
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 20

  24. The majority of cancer-related deaths are due to lung cancer, and there is a need for reliable diagnostic biomarkers to predict stages in non-small cell lung cancer cases. Recently, microRNAs were found to hav...

    Authors: Nhat Tran, Vinay Abhyankar, KyTai Nguyen, Jon Weidanz and Jean Gao
    Citation: BMC Bioinformatics 2018 19(Suppl 20):504
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 20

  25. Bacterial small non-coding RNAs (sRNAs) have emerged as important elements in diverse physiological processes, including growth, development, cell proliferation, differentiation, metabolic reactions and carbon...

    Authors: Guifeng Tang, Jingwen Shi, Wenjian Wu, Xiang Yue and Wen Zhang
    Citation: BMC Bioinformatics 2018 19(Suppl 20):503
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 20

  26. Biomedical semantic indexing is important for information retrieval and many other research fields in bioinformatics. It annotates biomedical citations with Medical Subject Headings. In face of unbalanced cate...

    Authors: Yongping Du, Yunpeng Pan, Chencheng Wang and Junzhong Ji
    Citation: BMC Bioinformatics 2018 19(Suppl 20):502
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 20

  27. Current multi-petaflop supercomputers are powerful systems, but present challenges when faced with problems requiring large machine learning workflows. Complex algorithms running at system scale, often with di...

    Authors: Justin M. Wozniak, Rajeev Jain, Prasanna Balaprakash, Jonathan Ozik, Nicholson T. Collier, John Bauer, Fangfang Xia, Thomas Brettin, Rick Stevens, Jamaludin Mohd-Yusof, Cristina Garcia Cardona, Brian Van Essen and Matthew Baughman
    Citation: BMC Bioinformatics 2018 19(Suppl 18):491
    Content type: Methodology Published on:

    This article is part of a Supplement: Volume 19 Supplement 18

  28. Real-time analysis of patient data during medical procedures can provide vital diagnostic feedback that significantly improves chances of success. With sensors becoming increasingly fast, frameworks such as De...

    Authors: Ahmed Sanaullah, Chen Yang, Yuri Alexeev, Kazutomo Yoshii and Martin C. Herbordt
    Citation: BMC Bioinformatics 2018 19(Suppl 18):490
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 18

  29. Histopathology images of tumor biopsies present unique challenges for applying machine learning to the diagnosis and treatment of cancer. The pathology slides are high resolution, often exceeding 1GB, have non...

    Authors: Will Fischer, Sanketh S. Moudgalya, Judith D. Cohn, Nga T. T. Nguyen and Garrett T. Kenyon
    Citation: BMC Bioinformatics 2018 19(Suppl 18):489
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 18

  30. Deep Learning (DL) has advanced the state-of-the-art capabilities in bioinformatics applications which has resulted in trends of increasingly sophisticated and computationally demanding models trained by large...

    Authors: John X. Qiu, Hong-Jun Yoon, Kshitij Srivastava, Thomas P. Watson, J. Blair Christian, Arvind Ramanathan, Xiao C. Wu, Paul A. Fearn and Georgia D. Tourassi
    Citation: BMC Bioinformatics 2018 19(Suppl 18):488
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 18

  32. The National Cancer Institute drug pair screening effort against 60 well-characterized human tumor cell lines (NCI-60) presents an unprecedented resource for modeling combinational drug activity.

    Authors: Fangfang Xia, Maulik Shukla, Thomas Brettin, Cristina Garcia-Cardona, Judith Cohn, Jonathan E. Allen, Sergei Maslov, Susan L. Holbeck, James H. Doroshow, Yvonne A. Evrard, Eric A. Stahlberg and Rick L. Stevens
    Citation: BMC Bioinformatics 2018 19(Suppl 18):486
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 18

  33. Manual extraction of information from electronic pathology (epath) reports to populate the Surveillance, Epidemiology, and End Result (SEER) database is labor intensive. Systematizing the data extraction autom...

    Authors: Nicolas Hengartner, Leticia Cuellar, Xiao-Cheng Wu, Georgia Tourassi, John Qiu, Blair Christian and Tanmoy Bhattacharya
    Citation: BMC Bioinformatics 2018 19(Suppl 18):485
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 18

  34. We examine the problem of clustering biomolecular simulations using deep learning techniques. Since biomolecular simulation datasets are inherently high dimensional, it is often necessary to build low dimensio...

    Authors: Debsindhu Bhowmik, Shang Gao, Michael T. Young and Arvind Ramanathan
    Citation: BMC Bioinformatics 2018 19(Suppl 18):484
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 18

  35. Cancer is a complex, multiscale dynamical system, with interactions between tumor cells and non-cancerous host systems. Therapies act on this combined cancer-host system, sometimes with unexpected results. Sys...

    Authors: Jonathan Ozik, Nicholson Collier, Justin M. Wozniak, Charles Macal, Chase Cockrell, Samuel H. Friedman, Ahmadreza Ghaffarizadeh, Randy Heiland, Gary An and Paul Macklin
    Citation: BMC Bioinformatics 2018 19(Suppl 18):483
    Content type: Methodology Published on:

    This article is part of a Supplement: Volume 19 Supplement 18

  36. Resistance to chemotherapy and molecularly targeted therapies is a major factor in limiting the effectiveness of cancer treatment. In many cases, resistance can be linked to genetic changes in target proteins,...

    Authors: Jumana Dakka, Matteo Turilli, David W. Wright, Stefan J. Zasada, Vivek Balasubramanian, Shunzhou Wan, Peter V. Coveney and Shantenu Jha
    Citation: BMC Bioinformatics 2018 19(Suppl 18):482
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 18

  37. The deployment of Genome-wide association studies (GWASs) requires genomic information of a large population to produce reliable results. This raises significant privacy concerns, making people hesitate to con...

    Authors: Charlotte Bonte, Eleftheria Makri, Amin Ardeshirdavani, Jaak Simm, Yves Moreau and Frederik Vercauteren
    Citation: BMC Bioinformatics 2018 19:537
    Content type: Research article Published on:

  39. Identifying protein complexes from protein-protein interaction (PPI) network is one of the most important tasks in proteomics. Existing computational methods try to incorporate a variety of biological evidence...

    Authors: Bo Xu, Kun Li, Wei Zheng, Xiaoxia Liu, Yijia Zhang, Zhehuan Zhao and Zengyou He
    Citation: BMC Bioinformatics 2018 19:535
    Content type: Research article Published on:

  42. Virus genome sequences, generated in ever-higher volumes, can provide new scientific insights and inform our responses to epidemics and outbreaks. To facilitate interpretation, such data must be organised and ...

    Authors: Joshua B. Singer, Emma C. Thomson, John McLauchlan, Joseph Hughes and Robert J. Gifford
    Citation: BMC Bioinformatics 2018 19:532
    Content type: Software Published on:

  43. Various algorithms have been developed to predict fetal trisomies using cell-free DNA in non-invasive prenatal testing (NIPT). As basis for prediction, a control group of non-trisomy samples is needed. Predict...

    Authors: Lennart F. Johansson, Hendrik A. de Weerd, Eddy N. de Boer, Freerk van Dijk, Gerard J. te Meerman, Rolf H. Sijmons, Birgit Sikkema-Raddatz and Morris A. Swertz
    Citation: BMC Bioinformatics 2018 19:531
    Content type: Software Published on:

  44. After publication of the original article [1], it was noticed that the dagger symbol indicating equal contribution wasn’t added next to the names of all authors.

    Authors: Paolo Boldi, Marco Frasca and Dario Malchiodi
    Citation: BMC Bioinformatics 2018 19:530
    Content type: Correction Published on:

    The original article was published in BMC Bioinformatics 2018 19:417

  45. Selection for feed efficiency is crucial for overall profitability and sustainability in dairy cattle production. Key regulator genes and genetic markers derived from co-expression networks underlying feed eff...

    Authors: S. M. Salleh, G. Mazzoni, P. Løvendahl and H. N. Kadarmideen
    Citation: BMC Bioinformatics 2018 19:513
    Content type: Research article Published on:

  47. The challenge of classifying cortical interneurons is yet to be solved. Data-driven classification into established morphological types may provide insight and practical value.

    Authors: Bojan Mihaljević, Pedro Larrañaga, Ruth Benavides-Piccione, Sean Hill, Javier DeFelipe and Concha Bielza
    Citation: BMC Bioinformatics 2018 19:511
    Content type: Research article Published on:

    The Data Descriptor to this article has been published in Scientific Data 2019 6:221

  48. Predicting prognosis in patients from large-scale genomic data is a fundamentally challenging problem in genomic medicine. However, the prognosis still remains poor in many diseases. The poor prognosis may be ...

    Authors: Jie Hao, Youngsoon Kim, Tae-Kyung Kim and Mingon Kang
    Citation: BMC Bioinformatics 2018 19:510
    Content type: Methodology article Published on:

  49. The current versions of reference genome assemblies still contain gaps represented by stretches of Ns. Since high throughput sequencing reads cannot be mapped to those gap regions, the regions are depleted of ...

    Authors: Diana Domanska, Chakravarthi Kanduri, Boris Simovski and Geir Kjetil Sandve
    Citation: BMC Bioinformatics 2018 19:481
    Content type: Research article Published on:

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