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  2. Next-generation sequencing of individuals with genetic diseases often detects candidate rare variants in numerous genes, but determining which are causal remains challenging. We hypothesized that the spatial d...

    Authors: R. Michael Sivley, Jonathan H. Sheehan, Jonathan A. Kropski, Joy Cogan, Timothy S. Blackwell, John A. Phillips, William S. Bush, Jens Meiler and John A. Capra
    Citation: BMC Bioinformatics 2018 19:18
    Content type: Research Article Published on:

  4. The subcellular localization of a protein is an important aspect of its function. However, the experimental annotation of locations is not even complete for well-studied model organisms. Text mining might aid ...

    Authors: Juan Miguel Cejuela, Shrikant Vinchurkar, Tatyana Goldberg, Madhukar Sollepura Prabhu Shankar, Ashish Baghudana, Aleksandar Bojchevski, Carsten Uhlig, André Ofner, Pandu Raharja-Liu, Lars Juhl Jensen and Burkhard Rost
    Citation: BMC Bioinformatics 2018 19:15
    Content type: Research Article Published on:

  5. Hot spots are interface residues that contribute most binding affinity to protein-protein interaction. A compact and relevant feature subset is important for building machine learning methods to predict hot sp...

    Authors: Yanhua Qiao, Yi Xiong, Hongyun Gao, Xiaolei Zhu and Peng Chen
    Citation: BMC Bioinformatics 2018 19:14
    Content type: Research Article Published on:

  10. Cluster analysis is the most common unsupervised method for finding hidden groups in data. Clustering presents two main challenges: (1) finding the optimal number of clusters, and (2) removing “outliers” among...

    Authors: Min Wang, Zachary B. Abrams, Steven M. Kornblau and Kevin R. Coombes
    Citation: BMC Bioinformatics 2018 19:9
    Content type: Methodology article Published on:

  11. Genomic imprinting is one of the well-known epigenetic factors causing the association between traits and genes, and has generally been examined by detecting parent-of-origin effects of alleles. A lot of metho...

    Authors: Qi-Lei Zou, Xiao-Ping You, Jian-Long Li, Wing Kam Fung and Ji-Yuan Zhou
    Citation: BMC Bioinformatics 2018 19:8
    Content type: Research Article Published on:

  12. Ontologies are representations of a conceptualization of a domain. Traditionally, ontologies in biology were represented as directed acyclic graphs (DAG) which represent the backbone taxonomy and additional re...

    Authors: Miguel Ángel Rodríguez-García and Robert Hoehndorf
    Citation: BMC Bioinformatics 2018 19:7
    Content type: Methodology article Published on:

  13. Many R packages have been developed for transcriptome analysis but their use often requires familiarity with R and integrating results of different packages requires scripts to wrangle the datatypes. Furthermo...

    Authors: Qin Zhu, Stephen A. Fisher, Hannah Dueck, Sarah Middleton, Mugdha Khaladkar and Junhyong Kim
    Citation: BMC Bioinformatics 2018 19:6
    Content type: Software Published on:

  14. ‘Next-generation’ (NGS) sequencing has wide application in medical genetics, including the detection of somatic variation in cancer. The Ion Torrent-based (IONT) platform is among NGS technologies employed in ...

    Authors: Aditya Deshpande, Wenhua Lang, Tina McDowell, Smruthy Sivakumar, Jiexin Zhang, Jing Wang, F. Anthony San Lucas, Jerry Fowler, Humam Kadara and Paul Scheet
    Citation: BMC Bioinformatics 2018 19:5
    Content type: Methodology Article Published on:

  16. De novo prediction of Transcription Factor Binding Sites (TFBS) using computational methods is a difficult task and it is an important problem in Bioinformatics. The correct recognition of TFBS plays an important...

    Authors: Jader M. Caldonazzo Garbelini, André Y. Kashiwabara and Danilo S. Sanches
    Citation: BMC Bioinformatics 2018 19:4
    Content type: Software Published on:

  17. Running multiple-chain Markov Chain Monte Carlo (MCMC) provides an efficient parallel computing method for complex Bayesian models, although the efficiency of the approach critically depends on the length of t...

    Authors: Peng Guo, Bo Zhu, Hong Niu, Zezhao Wang, Yonghu Liang, Yan Chen, Lupei Zhang, Hemin Ni, Yong Guo, El Hamidi A. Hay, Xue Gao, Huijiang Gao, Xiaolin Wu, Lingyang Xu and Junya Li
    Citation: BMC Bioinformatics 2018 19:3
    Content type: Research article Published on:

  19. Bioinformatic tools for the enrichment of ‘omics’ datasets facilitate interpretation and understanding of data. To date few are suitable for metabolomics datasets. The main objective of this work is to give a ...

    Authors: Anna Marco-Ramell, Magali Palau-Rodriguez, Ania Alay, Sara Tulipani, Mireia Urpi-Sarda, Alex Sanchez-Pla and Cristina Andres-Lacueva
    Citation: BMC Bioinformatics 2018 19:1
    Content type: Research article Published on:

  20. Genotyping-by-sequencing (GBS), a method to identify genetic variants and quickly genotype samples, reduces genome complexity by using restriction enzymes to divide the genome into fragments whose ends are seq...

    Authors: Daniel P. Wickland, Gopal Battu, Karen A. Hudson, Brian W. Diers and Matthew E. Hudson
    Citation: BMC Bioinformatics 2017 18:586
    Content type: Methodology article Published on:

  22. Prediction in high dimensional settings is difficult due to the large number of variables relative to the sample size. We demonstrate how auxiliary ‘co-data’ can be used to improve the performance of a Random ...

    Authors: Dennis E. te Beest, Steven W. Mes, Saskia M. Wilting, Ruud H. Brakenhoff and Mark A. van de Wiel
    Citation: BMC Bioinformatics 2017 18:584
    Content type: Methodology Article Published on:

  23. Differential co-expression (DCX) signifies change in degree of co-expression of a set of genes among different biological conditions. It has been used to identify differential co-expression networks or interac...

    Authors: Herty Liany, Jagath C. Rajapakse and R. Krishna Murthy Karuturi
    Citation: BMC Bioinformatics 2017 18(Suppl 16):576
    Content type: Research Published on:

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

  24. In current statistical methods for calling differentially expressed genes in RNA-Seq experiments, the assumption is that an adjusted observed gene count represents an unknown true gene count. This adjustment u...

    Authors: Joel Z. B. Low, Tsung Fei Khang and Martti T. Tammi
    Citation: BMC Bioinformatics 2017 18(Suppl 16):575
    Content type: Research Published on:

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

  25. RNA molecules have been known to play a variety of significant roles in cells. In principle, the functions of RNAs are largely determined by their three-dimensional (3D) structures. As more and more RNA 3D str...

    Authors: Ching-Yu Yen, Jian-Cheng Lin, Kun-Tze Chen and Chin Lung Lu
    Citation: BMC Bioinformatics 2017 18(Suppl 16):574
    Content type: Research Published on:

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

  26. The Gene Ontology (GO) is a community-based bioinformatics resource that employs ontologies to represent biological knowledge and describes information about gene and gene product function. GO includes three i...

    Authors: Jiajie Peng, Honggang Wang, Junya Lu, Weiwei Hui, Yadong Wang and Xuequn Shang
    Citation: BMC Bioinformatics 2017 18(Suppl 16):573
    Content type: Research Published on:

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

  27. (-)-Balanol is an ATP mimic that inhibits protein kinase C (PKC) isozymes and cAMP-dependent protein kinase (PKA) with limited selectivity. While PKA is a tumour promoter, PKC isozymes act as tumour promoters ...

    Authors: Ari Hardianto, Muhammad Yusuf, Fei Liu and Shoba Ranganathan
    Citation: BMC Bioinformatics 2017 18(Suppl 16):572
    Content type: Research Published on:

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

  28. In metagenomics, the separation of nucleotide sequences belonging to an individual or closely matched populations is termed binning. Binning helps the evaluation of underlying microbial population structure as...

    Authors: Damayanthi Herath, Sen-Lin Tang, Kshitij Tandon, David Ackland and Saman Kumara Halgamuge
    Citation: BMC Bioinformatics 2017 18(Suppl 16):571
    Content type: Research Published on:

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

  29. Plankton, including phytoplankton and zooplankton, are the main source of food for organisms in the ocean and form the base of marine food chain. As the fundamental components of marine ecosystems, plankton is...

    Authors: Haiyong Zheng, Ruchen Wang, Zhibin Yu, Nan Wang, Zhaorui Gu and Bing Zheng
    Citation: BMC Bioinformatics 2017 18(Suppl 16):570
    Content type: Research Published on:

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

  30. Direct prediction of the three-dimensional (3D) structures of proteins from one-dimensional (1D) sequences is a challenging problem. Significant structural characteristics such as solvent accessibility and con...

    Authors: Lei Deng, Chao Fan and Zhiwen Zeng
    Citation: BMC Bioinformatics 2017 18(Suppl 16):569
    Content type: Research Published on:

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

  31. Pathogen detection in clinical samples based on 16S metagenomic sequencing technology in microbiology laboratories is an important strategy for clinical diagnosis, public health surveillance, and investigation...

    Authors: Jiaojiao Miao, Na Han, Yujun Qiang, Tingting Zhang, Xiuwen Li and Wen Zhang
    Citation: BMC Bioinformatics 2017 18(Suppl 16):568
    Content type: Research Published on:

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

  32. The identification of target molecules is important for understanding the mechanism of “target deconvolution” in phenotypic screening and “polypharmacology” of drugs. Because conventional methods of identifyin...

    Authors: Kyoungyeul Lee, Minho Lee and Dongsup Kim
    Citation: BMC Bioinformatics 2017 18(Suppl 16):567
    Content type: Research Published on:

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

  33. Cell division (mitosis) results in the equal segregation of chromosomes between two daughter cells. The mitotic spindle plays a pivotal role in chromosome alignment and segregation during metaphase and anaphas...

    Authors: Matloob Khushi, Imraan M. Dean, Erdahl T. Teber, Megan Chircop, Jonathan W. Arthur and Neftali Flores-Rodriguez
    Citation: BMC Bioinformatics 2017 18(Suppl 16):566
    Content type: Research Published on:

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

  34. Phenotypic classification is problematic because small samples are ubiquitous; and, for these, use of prior knowledge is critical. If knowledge concerning the feature-label distribution – for instance, genetic...

    Authors: Shahin Boluki, Mohammad Shahrokh Esfahani, Xiaoning Qian and Edward R Dougherty
    Citation: BMC Bioinformatics 2017 18(Suppl 14):552
    Content type: Research Published on:

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

  35. In recent years, biological interaction networks have become the basis of some essential study and achieved success in many applications. Some typical networks such as protein-protein interaction networks have...

    Authors: Zhen Tian, Maozu Guo, Chunyu Wang, Xiaoyan Liu and Shiming Wang
    Citation: BMC Bioinformatics 2017 18(Suppl 16):550
    Content type: Research Published on:

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

  36. The dramatic development of DNA sequencing technology is generating real big data, craving for more storage and bandwidth. To speed up data sharing and bring data to computing resource faster and cheaper, it i...

    Authors: Yuting Xing, Gen Li, Zhenguo Wang, Bolun Feng, Zhuo Song and Chengkun Wu
    Citation: BMC Bioinformatics 2017 18(Suppl 16):549
    Content type: Research Published on:

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

  37. Viruses of the flaviviridae family are responsible for some of the major infectious viral diseases around the world and there is an urgent need for drug development for these diseases. Most of the virtual screeni...

    Authors: Nikhil Pathak, Mei-Ling Lai, Wen-Yu Chen, Betty-Wu Hsieh, Guann-Yi Yu and Jinn-Moon Yang
    Citation: BMC Bioinformatics 2017 18(Suppl 16):548
    Content type: Research Published on:

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

  38. Clustering methods are becoming widely utilized in biomedical research where the volume and complexity of data is rapidly increasing. Unsupervised clustering of patient information can reveal distinct phenotyp...

    Authors: Alok Sharma, Piotr J. Kamola and Tatsuhiko Tsunoda
    Citation: BMC Bioinformatics 2017 18(Suppl 16):547
    Content type: Research Published on:

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

  39. Common spatial pattern (CSP) has been an effective technique for feature extraction in electroencephalography (EEG) based brain computer interfaces (BCIs). However, motor imagery EEG signal feature extraction ...

    Authors: Shiu Kumar, Alok Sharma and Tatsuhiko Tsunoda
    Citation: BMC Bioinformatics 2017 18(Suppl 16):545
    Content type: Research Published on:

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

  40. Human papillomavirus infection is a global social burden that, every year, leads to thousands new diagnosis of cancer. The introduction of a protocol of immunization, with Gardasil and Cervarix vaccines, has r...

    Authors: Marzio Pennisi, Giulia Russo, Silvia Ravalli and Francesco Pappalardo
    Citation: BMC Bioinformatics 2017 18(Suppl 16):544
    Content type: Research Published on:

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

  41. Much effort has been devoted to the discovery of specific mechanisms between drugs and single targets to date. However, as biological systems maintain homeostasis at the level of functional networks robustly c...

    Authors: Zongliang Yue, Itika Arora, Eric Y. Zhang, Vincent Laufer, S. Louis Bridges and Jake Y. Chen
    Citation: BMC Bioinformatics 2017 18(Suppl 14):532
    Content type: Research Published on:

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

  42. Multi-label classification of data remains to be a challenging problem. Because of the complexity of the data, it is sometimes difficult to infer information about classes that are not mutually exclusive. For ...

    Authors: Andrew Maxwell, Runzhi Li, Bei Yang, Heng Weng, Aihua Ou, Huixiao Hong, Zhaoxian Zhou, Ping Gong and Chaoyang Zhang
    Citation: BMC Bioinformatics 2017 18(Suppl 14):523
    Content type: Research Published on:

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

  43. Piwi-interacting RNAs (piRNAs) are a new class of small non-coding RNAs that are known to be associated with RNA silencing. The piRNAs play an important role in protecting the genome from invasive transposons ...

    Authors: Chun-Chi Chen, Xiaoning Qian and Byung-Jun Yoon
    Citation: BMC Bioinformatics 2017 18(Suppl 14):517
    Content type: Research Published on:

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

  44. Recent breakthroughs in molecular biology and next generation sequencing technologies have led to the expenential growh of the sequence databases. Researchrs use BLAST for processing these sequences. However t...

    Authors: Mike Mikailov, Fu-Jyh Luo, Stuart Barkley, Lohit Valleru, Stephen Whitney, Zhichao Liu, Shraddha Thakkar, Weida Tong and Nicholas Petrick
    Citation: BMC Bioinformatics 2017 18(Suppl 14):501
    Content type: Research Published on:

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

  45. Quantification and identification of microbial genomes based on next-generation sequencing data is a challenging problem in metagenomics. Although current methods have mostly focused on analyzing bacteria whos...

    Authors: Quang Tran, Diem-Trang Pham and Vinhthuy Phan
    Citation: BMC Bioinformatics 2017 18(Suppl 14):499
    Content type: Research Published on:

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

  47. Long noncoding RNAs (lncRNAs) are involved in diverse biological processes and play an essential role in various human diseases. The number of lncRNAs identified has increased rapidly in recent years owing to ...

    Authors: Dan Li and Mary Qu Yang
    Citation: BMC Bioinformatics 2017 18(Suppl 14):489
    Content type: RESEARCH Published on:

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

    The Correction to this article has been published in BMC Bioinformatics 2018 19:181

  48. It is well-known that genome sequencing technologies are becoming significantly cheaper and faster. As a result of this, the exponential growth in sequencing data in public databases allows us to explore ever ...

    Authors: Visanu Wanchai, Preecha Patumcharoenpol, Intawat Nookaew and David Ussery
    Citation: BMC Bioinformatics 2017 18(Suppl 14):483
    Content type: Database Published on:

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

  49. Endometrial cancers (ECs) are one of the most common types of malignant tumor in females. Substantial efforts had been made to identify significantly mutated genes (SMGs) in ECs and use them as biomarkers for ...

    Authors: Keqin Liu, Li He, Zhichao Liu, Junmei Xu, Yuan Liu, Qifan Kuang, Zhining Wen and Menglong Li
    Citation: BMC Bioinformatics 2017 18(Suppl 14):472
    Content type: Research Published on:

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

  50. Zika virus (ZIKV) is an emerging human pathogen. Since its arrival in the Western hemisphere, from Africa via Asia, it has become a serious threat to pregnant women, causing microcephaly and other neuropathies...

    Authors: Se-Ran Jun, Trudy M. Wassenaar, Visanu Wanchai, Preecha Patumcharoenpol, Intawat Nookaew and David W. Ussery
    Citation: BMC Bioinformatics 2017 18(Suppl 14):471
    Content type: Research Published on:

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

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