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  1. Drug-drug interaction extraction (DDI) needs assistance from automated methods to address the explosively increasing biomedical texts. In recent years, deep neural network based models have been developed to a...

    Authors: Wei Wang, Xi Yang, Canqun Yang, Xiaowei Guo, Xiang Zhang and Chengkun Wu
    Citation: BMC Bioinformatics 2017 18(Suppl 16):578
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 16

  2. The β-Lactamase (BL) enzyme family is an important class of enzymes that plays a key role in bacterial resistance to antibiotics. As the newly identified number of BL enzymes is increasing daily, it is imperat...

    Authors: Clarence White, Hamid D. Ismail, Hiroto Saigo and Dukka B. KC
    Citation: BMC Bioinformatics 2017 18(Suppl 16):577
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 16

  3. Cancer constitutes a momentous health burden in our society. Critical information on cancer may be hidden in its signaling pathways. However, even though a large amount of money has been spent on cancer resear...

    Authors: Yahui Sun, Chenkai Ma and Saman Halgamuge
    Citation: BMC Bioinformatics 2017 18(Suppl 16):551
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 16

  4. Biological data comprises various topologies or a mixture of forms, which makes its analysis extremely complicated. With this data increasing in a daily basis, the design and development of efficient and accur...

    Authors: Alok Sharma, Yosvany López and Tatsuhiko Tsunoda
    Citation: BMC Bioinformatics 2017 18(Suppl 16):546
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 16

  5. Accumulating biological and clinical reports have indicated that imbalance of microbial community is closely associated with occurrence and development of various complex human diseases. Identifying potential ...

    Authors: Wenzheng Bao, Zhichao Jiang and De-Shuang Huang
    Citation: BMC Bioinformatics 2017 18(Suppl 16):543
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 16

  6. Small noncoding regulatory RNAs (sRNAs) are post-transcriptional regulators, regulating mRNAs, proteins, and DNA in bacteria. One class of sRNAs, trans-acting sRNAs, are the most abundant sRNAs transcribed from t...

    Authors: Ethan C. Rath, Stephanie Pitman, Kyu Hong Cho and Yongsheng Bai
    Citation: BMC Bioinformatics 2017 18(Suppl 14):540
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 14

  7. NCBI’s Gene Expression Omnibus (GEO) is a rich community resource containing millions of gene expression experiments from human, mouse, rat, and other model organisms. However, information about each experimen...

    Authors: Cory B. Giles, Chase A. Brown, Michael Ripperger, Zane Dennis, Xiavan Roopnarinesingh, Hunter Porter, Aleksandra Perz and Jonathan D. Wren
    Citation: BMC Bioinformatics 2017 18(Suppl 14):509
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 14

  8. Functional modules in biological networks consist of numerous biomolecules and their complicated interactions. Recent studies have shown that biomolecules in a functional module tend to have similar interactio...

    Authors: Hyundoo Jeong, Xiaoning Qian and Byung-Jun Yoon
    Citation: BMC Bioinformatics 2017 18(Suppl 14):500
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 14

  9. Blockage of some ion channels and in particular, the hERG (human Ether-a’-go-go-Related Gene) cardiac potassium channel delays cardiac repolarization and can induce arrhythmia. In some cases it leads to a pote...

    Authors: Mohsen Sharifi, Dan Buzatu, Stephen Harris and Jon Wilkes
    Citation: BMC Bioinformatics 2017 18(Suppl 14):497
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 14

  10. Abruptness of pigment patterns at the periphery of a skin lesion is one of the most important dermoscopic features for detection of malignancy. In current clinical setting, abrupt cutoff of a skin lesion deter...

    Authors: Recep Erol, Mustafa Bayraktar, Sinan Kockara, Sertan Kaya and Tansel Halic
    Citation: BMC Bioinformatics 2017 18(Suppl 14):484
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 14

  11. Knowledge of catalytic residues can play an essential role in elucidating mechanistic details of an enzyme. However, experimental identification of catalytic residues is a tedious and time-consuming task, whic...

    Authors: Preeti Choudhary, Shailesh Kumar, Anand Kumar Bachhawat and Shashi Bhushan Pandit
    Citation: BMC Bioinformatics 2017 18:583
    Content type: Methodology Article Published on:

  13. Gene expression connectivity mapping has gained much popularity in recent years with a number of successful applications in biomedical research testifying its utility and promise. A major application of connec...

    Authors: Gayathri Thillaiyampalam, Fabio Liberante, Liam Murray, Chris Cardwell, Ken Mills and Shu-Dong Zhang
    Citation: BMC Bioinformatics 2017 18:581
    Content type: Research Article Published on:

  14. Cell lines and cell types are extensively studied in biomedical research yielding to a significant amount of publications each year. Identifying cell lines and cell types precisely in publications is crucial f...

    Authors: Åženay Kafkas, Sirarat Sarntivijai and Robert Hoehndorf
    Citation: BMC Bioinformatics 2017 18(Suppl 17):561
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 17

  15. Cell cultures used in biomedical experiments come in the form of both sample biopsy primary cells, and maintainable immortalised cell lineages. The rise of bioinformatics and high-throughput technologies has l...

    Authors: Sirarat Sarntivijai, Alexander D. Diehl and Yongqun He
    Citation: BMC Bioinformatics 2017 18(Suppl 17):560
    Content type: Introduction Published on:

    This article is part of a Supplement: Volume 18 Supplement 17

  16. A fundamental characteristic of multicellular organisms is the specialization of functional cell types through the process of differentiation. These specialized cell types not only characterize the normal func...

    Authors: Trygve Bakken, Lindsay Cowell, Brian D. Aevermann, Mark Novotny, Rebecca Hodge, Jeremy A. Miller, Alexandra Lee, Ivan Chang, Jamison McCorrison, Bali Pulendran, Yu Qian, Nicholas J. Schork, Roger S. Lasken, Ed S. Lein and Richard H. Scheuermann
    Citation: BMC Bioinformatics 2017 18(Suppl 17):559
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 17

  18. The Experimental Factor Ontology (EFO) is an application ontology driven by experimental variables including cell lines to organize and describe the diverse experimental variables and data resided in the EMBL-...

    Authors: Edison Ong, Sirarat Sarntivijai, Simon Jupp, Helen Parkinson and Yongqun He
    Citation: BMC Bioinformatics 2017 18(Suppl 17):557
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 17

  19. Aiming to understand cellular responses to different perturbations, the NIH Common Fund Library of Integrated Network-based Cellular Signatures (LINCS) program involves many institutes and laboratories working...

    Authors: Edison Ong, Jiangan Xie, Zhaohui Ni, Qingping Liu, Sirarat Sarntivijai, Yu Lin, Daniel Cooper, Raymond Terryn, Vasileios Stathias, Caty Chung, Stephan Schürer and Yongqun He
    Citation: BMC Bioinformatics 2017 18(Suppl 17):556
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 17

  20. Alzheimer’s disease (AD) is a chronic neuro-degenerative disruption of the brain which involves in large scale transcriptomic variation. The disease does not impact every regions of the brain at the same time,...

    Authors: Sumanta Ray, Sk Md Mosaddek Hossain, Lutfunnesa Khatun and Anirban Mukhopadhyay
    Citation: BMC Bioinformatics 2017 18:579
    Content type: Methodology Article Published on:

  21. Stratification of patient subpopulations that respond favorably to treatment or experience and adverse reaction is an essential step toward development of new personalized therapies and diagnostics. It is curr...

    Authors: Tianyu Kang, Wei Ding, Luoyan Zhang, Daniel Ziemek and Kourosh Zarringhalam
    Citation: BMC Bioinformatics 2017 18:565
    Content type: Research Article Published on:

  22. The next generation sequencing (NGS) techniques have been around for over a decade. Many of their fundamental applications rely on the ability to compute good genome assemblies. As the technology evolves, the ...

    Authors: Nilesh Khiste and Lucian Ilie
    Citation: BMC Bioinformatics 2017 18:564
    Content type: Research Article Published on:

  23. Genetic association studies (GAS) aims to evaluate the association between genetic variants and phenotypes. In the last few years, the number of this type of study has increased exponentially, but the results ...

    Authors: Jordi Martorell-Marugan, Daniel Toro-Dominguez, Marta E. Alarcon-Riquelme and Pedro Carmona-Saez
    Citation: BMC Bioinformatics 2017 18:563
    Content type: Software Published on:

  24. The spatial Principal Component Analysis (sPCA, Jombart (Heredity 101:92-103, 2008) is designed to investigate non-random spatial distributions of genetic variation. Unfortunately, the associated tests used fo...

    Authors: V. Montano and T. Jombart
    Citation: BMC Bioinformatics 2017 18:562
    Content type: Methodology Article Published on:

  25. High throughput sequencing requires bioinformatics pipelines to process large volumes of data into meaningful variants that can be translated into a clinical report. These pipelines often suffer from a number ...

    Authors: Kenneth D. Doig, Jason Ellul, Andrew Fellowes, Ella R. Thompson, Georgina Ryland, Piers Blombery, Anthony T. Papenfuss and Stephen B. Fox
    Citation: BMC Bioinformatics 2017 18:555
    Content type: Software Published on:

  26. Haloplex targeted resequencing is a popular method to analyze both germline and somatic variants in gene panels. However, involved wet-lab procedures may introduce false positives that need to be considered in...

    Authors: Matthias Beyens, Nele Boeckx, Guy Van Camp, Ken Op de Beeck and Geert Vandeweyer
    Citation: BMC Bioinformatics 2017 18:554
    Content type: Software Published on:

  28. As one of the most successful knowledge-based energy functions, the distance-dependent atom-pair potential is widely used in all aspects of protein structure prediction, including conformational search, model ...

    Authors: Yuangen Yao, Rong Gui, Quan Liu, Ming Yi and Haiyou Deng
    Citation: BMC Bioinformatics 2017 18:542
    Content type: Research Article Published on:

  30. High-throughput sequencing data are widely collected and analyzed in the study of complex diseases in quest of improving human health. Well-studied algorithms mostly deal with single data source, and cannot fu...

    Authors: Kang K. Yan, Hongyu Zhao and Herbert Pang
    Citation: BMC Bioinformatics 2017 18:539
    Content type: Research Article Published on:

  31. One of the most crucial steps in high-throughput sequence-based microbiome studies is the taxonomic assignment of sequences belonging to operational taxonomic units (OTUs). Without taxonomic classification, fu...

    Authors: Kristi Gdanetz, Gian Maria Niccolò Benucci, Natalie Vande Pol and Gregory Bonito
    Citation: BMC Bioinformatics 2017 18:538
    Content type: Methodology Article Published on:

  32. Chromosome structure is a very limited model of the genome including the information about its chromosomes such as their linear or circular organization, the order of genes on them, and the DNA strand encoding...

    Authors: Vassily Lyubetsky, Roman Gershgorin and Konstantin Gorbunov
    Citation: BMC Bioinformatics 2017 18:537
    Content type: Research Article Published on:

  33. An RNA folding/RNA secondary structure prediction algorithm determines the non-nested/pseudoknot-free structure by maximizing the number of complementary base pairs and minimizing the energy. Several implement...

    Authors: Chunchun Zhao and Sartaj Sahni
    Citation: BMC Bioinformatics 2017 18(Suppl 15):518
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 15

  34. The inference of species divergence time is a key step in most phylogenetic studies. Methods have been available for the last ten years to perform the inference, but the performance of the methods does not yet...

    Authors: Ralph W. Crosby and Tiffani L. Williams
    Citation: BMC Bioinformatics 2017 18(Suppl 15):514
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 15

  35. RNA sequencing technique (RNA-seq) enables scientists to develop novel data-driven methods for discovering more unidentified lincRNAs. Meantime, knowledge-based technologies are experiencing a potential revolu...

    Authors: Ning Yu, Zeng Yu and Yi Pan
    Citation: BMC Bioinformatics 2017 18(Suppl 15):511
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 15

  36. Understanding protein structure and dynamics is essential for understanding their function. This is a challenging task due to the high complexity of the conformational landscapes of proteins and their rugged e...

    Authors: Nurit Haspel, Dong Luo and Eduardo González
    Citation: BMC Bioinformatics 2017 18(Suppl 15):502
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 15

  37. Despite the recent progress in genome sequencing and assembly, many of the currently available assembled genomes come in a draft form. Such draft genomes consist of a large number of genomic fragments (scaffolds)...

    Authors: Sergey S. Aganezov and Max A. Alekseyev
    Citation: BMC Bioinformatics 2017 18(Suppl 15):496
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 15

  38. Protein-protein interactions (PPI) play a key role in an investigation of various biochemical processes, and their identification is thus of great importance. Although computational prediction of which amino a...

    Authors: Jan Jelínek, Petr Škoda and David Hoksza
    Citation: BMC Bioinformatics 2017 18(Suppl 15):492
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 15

  39. In recent years, protein-protein interaction (PPI) networks have been well recognized as important resources to elucidate various biological processes and cellular mechanisms. In this paper, we address the pro...

    Authors: Osamu Maruyama and Yuki Kuwahara
    Citation: BMC Bioinformatics 2017 18(Suppl 15):491
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 15

  41. In the search for novel causal mutations, public and/or private variant databases are nearly always used to facilitate the search as they result in a massive reduction of putative variants in one step. Practic...

    Authors: Bart J. G. Broeckx, Luc Peelman, Jimmy H. Saunders, Dieter Deforce and Lieven Clement
    Citation: BMC Bioinformatics 2017 18:535
    Content type: Methodology Article Published on:

  42. qPCR has established itself as the technique of choice for the quantification of gene expression. Procedures for conducting qPCR have received significant attention; however, more rigorous approaches to the st...

    Authors: Michael T. Ganger, Geoffrey D. Dietz and Sarah J. Ewing
    Citation: BMC Bioinformatics 2017 18:534
    Content type: Methodology Article Published on:

  43. High-throughput sequencing has made it theoretically possible to obtain high-quality de novo assembled genome sequences but in practice DNA extracts are often contaminated with sequences from other organisms. Cur...

    Authors: Janna L. Fierst and Duncan A. Murdock
    Citation: BMC Bioinformatics 2017 18:533
    Content type: Methodology Article Published on:

  44. With the rapid development of deep sequencing techniques in the recent years, enhancers have been systematically identified in such projects as FANTOM and ENCODE, forming genome-wide landscapes in a series of ...

    Authors: Xu Min, Wanwen Zeng, Shengquan Chen, Ning Chen, Ting Chen and Rui Jiang
    Citation: BMC Bioinformatics 2017 18(Suppl 13):478
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 13

  45. Essential proteins are indispensable to the survival and development process of living organisms. To understand the functional mechanisms of essential proteins, which can be applied to the analysis of disease ...

    Authors: Yetian Fan, Xiwei Tang, Xiaohua Hu, Wei Wu and Qing Ping
    Citation: BMC Bioinformatics 2017 18(Suppl 13):470
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 13

  46. RNA binding proteins play important roles in post-transcriptional RNA processing and transcriptional regulation. Distinguishing the RNA-binding residues in proteins is crucial for understanding how protein and...

    Authors: Yongjun Tang, Diwei Liu, Zixiang Wang, Ting Wen and Lei Deng
    Citation: BMC Bioinformatics 2017 18(Suppl 13):465
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 13

  47. Alternative splicing is the critical process in a single gene coding, which removes introns and joins exons, and splicing branchpoints are indicators for the alternative splicing. Wet experiments have identifi...

    Authors: Wen Zhang, Xiaopeng Zhu, Yu Fu, Junko Tsuji and Zhiping Weng
    Citation: BMC Bioinformatics 2017 18(Suppl 13):464
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 13

  48. The accurate identification of protein complexes is important for the understanding of cellular organization. Up to now, computational methods for protein complex detection are mostly focus on mining clusters ...

    Authors: Le Ou-Yang, Hong Yan and Xiao-Fei Zhang
    Citation: BMC Bioinformatics 2017 18(Suppl 13):463
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 13

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