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  1. Although rapid developed sequencing technologies make it possible for genotype data to be used in clinical diagnosis, it is still challenging for clinicians to understand the results of sequencing and make cor...

    Authors: Xiaofeng Gong, Jianping Jiang, Zhongqu Duan and Hui Lu
    Citation: BMC Bioinformatics 2018 19(Suppl 4):162
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 4

  2. A new emerged cancer treatment utilizes intrinsic immune surveillance mechanism that is silenced by those malicious cells. Hence, studies of tumor infiltrating lymphocyte populations (TILs) are key to the succ...

    Authors: Shu-Hwa Chen, Wen-Yu Kuo, Sheng-Yao Su, Wei-Chun Chung, Jen-Ming Ho, Henry Horng-Shing Lu and Chung-Yen Lin
    Citation: BMC Bioinformatics 2018 19(Suppl 4):154
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 4

  3. Evolutionary histories can be discordant across the genome, and such discordances need to be considered in reconstructing the species phylogeny. ASTRAL is one of the leading methods for inferring species trees...

    Authors: Chao Zhang, Maryam Rabiee, Erfan Sayyari and Siavash Mirarab
    Citation: BMC Bioinformatics 2018 19(Suppl 6):153
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 6

  4. The genomic similarity is a large-scale measure for comparing two given genomes. In this work we study the (NP-hard) problem of computing the genomic similarity under the DCJ model in a setting that does not a...

    Authors: Diego P. Rubert, Edna A. Hoshino, Marília D. V. Braga, Jens Stoye and Fábio V. Martinez
    Citation: BMC Bioinformatics 2018 19(Suppl 6):152
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 6

  5. Recently, Pereira Zanetti, Biller and Meidanis have proposed a new definition of a rearrangement distance between genomes. In this formulation, each genome is represented as a matrix, and the distance d is the ra...

    Authors: Leonid Chindelevitch, João Paulo Pereira Zanetti and João Meidanis
    Citation: BMC Bioinformatics 2018 19(Suppl 6):142
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 6

  6. Synthetic virology is an important multidisciplinary scientific field, with emerging applications in biotechnology and medicine, aiming at developing methods to generate and engineer synthetic viruses. In part...

    Authors: Eli Goz, Yael Tsalenchuck, Rony Oren Benaroya, Zohar Zafrir, Shimshi Atar, Tahel Altman, Justin Julander and Tamir Tuller
    Citation: BMC Bioinformatics 2018 19(Suppl 6):140
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 6

  7. Protein dihedral angles provide a detailed description of protein local conformation. Predicted dihedral angles can be used to narrow down the conformational space of the whole polypeptide chain significantly,...

    Authors: Yujuan Gao, Sheng Wang, Minghua Deng and Jinbo Xu
    Citation: BMC Bioinformatics 2018 19(Suppl 4):100
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 4

  8. Even though coexistence of multiple phenotypes sharing the same genomic background is interesting, it remains incompletely understood. Epigenomic profiles may represent key factors, with unknown contributions ...

    Authors: Y.-H. Taguchi
    Citation: BMC Bioinformatics 2018 19(Suppl 4):99
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 4

  9. Frequent subgraphs mining is a significant problem in many practical domains. The solution of this kind of problem can particularly used in some large-scale drug molecular or biological libraries to help us fi...

    Authors: Shunyun Yang, Runxin Guo, Rui Liu, Xiangke Liao, Quan Zou, Benyun Shi and Shaoliang Peng
    Citation: BMC Bioinformatics 2018 19(Suppl 4):98
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 4

  10. Comprehensively understanding the dynamics of biological systems is among the biggest current challenges in biology and medicine. To acquire this understanding, researchers have measured the time-series expres...

    Authors: Yoichi Takenaka, Kazuma Mikami, Shigeto Seno and Hideo Matsuda
    Citation: BMC Bioinformatics 2018 19(Suppl 4):89
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 4

  11. As one possible solution to the “missing heritability” problem, many methods have been proposed that apply pathway-based analyses, using rare variants that are detected by next generation sequencing technology...

    Authors: Sungyoung Lee, Yongkang Kim, Sungkyoung Choi, Heungsun Hwang and Taesung Park
    Citation: BMC Bioinformatics 2018 19(Suppl 4):79
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 4

  12. Identification of multi-markers is one of the most challenging issues in personalized medicine era. Nowadays, many different types of omics data are generated from the same subject. Although many methods endea...

    Authors: Yongkang Kim, Sungyoung Lee, Sungkyoung Choi, Jin-Young Jang and Taesung Park
    Citation: BMC Bioinformatics 2018 19(Suppl 4):75
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 4

  13. Protein-protein interactions (PPIs) play several roles in living cells, and computational PPI prediction is a major focus of many researchers. The three-dimensional (3D) structure and binding surface are impor...

    Authors: Takanori Hayashi, Yuri Matsuzaki, Keisuke Yanagisawa, Masahito Ohue and Yutaka Akiyama
    Citation: BMC Bioinformatics 2018 19(Suppl 4):62
    Content type: Database Published on:

    This article is part of a Supplement: Volume 19 Supplement 4

  14. Protein secondary structure is the three dimensional form of local segments of proteins and its prediction is an important problem in protein tertiary structure prediction. Developing computational approaches ...

    Authors: Jiyun Zhou, Hongpeng Wang, Zhishan Zhao, Ruifeng Xu and Qin Lu
    Citation: BMC Bioinformatics 2018 19(Suppl 4):60
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 4

  15. Learning accurate models from ‘omics data is bringing many challenges due to their inherent high-dimensionality, e.g. the number of gene expression variables, and comparatively lower sample sizes, which leads ...

    Authors: Marta B. Lopes, André Veríssimo, Eunice Carrasquinha, Sandra Casimiro, Niko Beerenwinkel and Susana Vinga
    Citation: BMC Bioinformatics 2018 19:168
    Content type: Research article Published on:

  17. The development of new ortholog detection algorithms and the improvement of existing ones are of major importance in functional genomics. We have previously introduced a successful supervised pairwise ortholog...

    Authors: Deborah Galpert, Alberto Fernández, Francisco Herrera, Agostinho Antunes, Reinaldo Molina-Ruiz and Guillermin Agüero-Chapin
    Citation: BMC Bioinformatics 2018 19:166
    Content type: Research article Published on:

  19. Large sequence datasets are difficult to visualize and handle. Additionally, they often do not represent a random subset of the natural diversity, but the result of uncoordinated and convenience sampling. Cons...

    Authors: Fabrizio Menardo, Chloé Loiseau, Daniela Brites, Mireia Coscolla, Sebastian M. Gygli, Liliana K. Rutaihwa, Andrej Trauner, Christian Beisel, Sonia Borrell and Sebastien Gagneux
    Citation: BMC Bioinformatics 2018 19:164
    Content type: Software Published on:

  20. Activation induced deaminase (AID) and apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3 (APOBEC3) are deaminases that mutate C to U on single-stranded DNA (ssDNA). AID is expressed primarily ...

    Authors: Maxwell Shapiro, Stephen Meier and Thomas MacCarthy
    Citation: BMC Bioinformatics 2018 19:163
    Content type: Methodology article Published on:

    The Correction to this article has been published in BMC Bioinformatics 2018 19:256

  21. Comparing and classifying functions of gene products are important in today’s biomedical research. The semantic similarity derived from the Gene Ontology (GO) annotation has been regarded as one of the most wi...

    Authors: Jiongmin Zhang, Ke Jia, Jinmeng Jia and Ying Qian
    Citation: BMC Bioinformatics 2018 19:161
    Content type: Methodology article Published on:

  22. PDZ-containing proteins comprise one of the most widely distributed protein families playing major role in localization and membrane receptor clustering. They are hence important regulators of signal transduct...

    Authors: Jitesh Doshi, Raja Reddy Kuppili, Siddharth Gurdasani, Navneet Venkatakrishnan, Amit Saxena and Kakoli Bose
    Citation: BMC Bioinformatics 2018 19:160
    Content type: Database Published on:

  24. In the last decade and a half it has been firmly established that a large number of proteins do not adopt a well-defined (ordered) structure under physiological conditions. Such intrinsically disordered protei...

    Authors: Nenad S. Mitić, Saša N. Malkov, Jovana J. Kovačević, Gordana M. Pavlović-Lažetić and Miloš V. Beljanski
    Citation: BMC Bioinformatics 2018 19:158
    Content type: Research article Published on:

  25. Somatic copy number alterations (CNAs) contribute to the clinically targetable aberrations in the tumor genome. For both routine diagnostics and biomarkers research, CNA analysis in a single assay together wit...

    Authors: Jan Budczies, Nicole Pfarr, Eva Romanovsky, Volker Endris, Albrecht Stenzinger and Carsten Denkert
    Citation: BMC Bioinformatics 2018 19:157
    Content type: Software Published on:

  26. Recent cancer genome studies on many human cancer types have relied on multiple molecular high-throughput technologies. Given the vast amount of data that has been generated, there are surprisingly few databas...

    Authors: Rasmus Krempel, Pranav Kulkarni, Annie Yim, Ulrich Lang, Bianca Habermann and Peter Frommolt
    Citation: BMC Bioinformatics 2018 19:156
    Content type: Research article Published on:

  27. Mutations in the FMS-like tyrosine kinase 3 (FLT3) are associated with uncontrolled cellular functions that contribute to the development of acute myeloid leukaemia (AML). We performed computer simulations of ...

    Authors: Antoine Buetti-Dinh and Ran Friedman
    Citation: BMC Bioinformatics 2018 19:155
    Content type: Research article Published on:

  28. Metabolomics has the promise to transform the area of personalized medicine with the rapid development of high throughput technology for untargeted analysis of metabolites. Open access, easy to use, analytic t...

    Authors: Alexander S. Kirpich, Miguel Ibarra, Oleksandr Moskalenko, Justin M. Fear, Joseph Gerken, Xinlei Mi, Ali Ashrafi, Alison M. Morse and Lauren M. McIntyre
    Citation: BMC Bioinformatics 2018 19:151
    Content type: Software Published on:

  30. Bioactive peptides, including biological sources-derived peptides with different biological activities, are protein fragments that influence the functions or conditions of organisms, in particular humans and a...

    Authors: Krittima Anekthanakul, Apiradee Hongsthong, Jittisak Senachak and Marasri Ruengjitchatchawalya
    Citation: BMC Bioinformatics 2018 19:149
    Content type: Database Published on:

  31. Over the last two decades, an innovative technology called Tissue Microarray (TMA), which combines multi-tissue and DNA microarray concepts, has been widely used in the field of histology. It consists of a col...

    Authors: Hoai Nam Nguyen, Vincent Paveau, Cyril Cauchois and Charles Kervrann
    Citation: BMC Bioinformatics 2018 19:148
    Content type: Methodology article Published on:

  32. Detailed modelling of the neutral mutational process in cancer cells is crucial for identifying driver mutations and understanding the mutational mechanisms that act during cancer development. The neutral muta...

    Authors: Johanna Bertl, Qianyun Guo, Malene Juul, Søren Besenbacher, Morten Muhlig Nielsen, Henrik Hornshøj, Jakob Skou Pedersen and Asger Hobolth
    Citation: BMC Bioinformatics 2018 19:147
    Content type: Research article Published on:

  33. Despite the rapid progress of protein residue contact prediction, predicted residue contact maps frequently contain many errors. However, information of residue pairing in β strands could be extracted from a n...

    Authors: Wenzhi Mao, Tong Wang, Wenxuan Zhang and Haipeng Gong
    Citation: BMC Bioinformatics 2018 19:146
    Content type: Methodology article Published on:

  35. The study of the huge diversity of immune receptors, often referred to as immune repertoire profiling, is a prerequisite for diagnosis, prognostication and monitoring of hematological disorders. In the era of ...

    Authors: Christos Maramis, Athanasios Gkoufas, Anna Vardi, Evangelia Stalika, Kostas Stamatopoulos, Anastasia Hatzidimitriou, Nicos Maglaveras and Ioanna Chouvarda
    Citation: BMC Bioinformatics 2018 19:144
    Content type: Software Published on:

  36. Morphological features are widely used in the study of neuronal function and pathology. Invertebrate neurons are often structurally stereotypical, showing little variance in gross spatial features but larger v...

    Authors: Ajayrama Kumaraswamy, Kazuki Kai, Hiroyuki Ai, Hidetoshi Ikeno and Thomas Wachtler
    Citation: BMC Bioinformatics 2018 19:143
    Content type: Methodology article Published on:

  37. Recently, numerous laboratory studies have indicated that many microRNAs (miRNAs) are involved in and associated with human diseases and can serve as potential biomarkers and drug targets. Therefore, developin...

    Authors: Haochen Zhao, Linai Kuang, Lei Wang, Pengyao Ping, Zhanwei Xuan, Tingrui Pei and Zhelun Wu
    Citation: BMC Bioinformatics 2018 19:141
    Content type: Research article Published on:

  38. After decades of identifying risk factors using array-based genome-wide association studies (GWAS), genetic research of complex diseases has shifted to sequencing-based rare variants discovery. This requires l...

    Authors: Yingxue Ren, Joseph S. Reddy, Cyril Pottier, Vivekananda Sarangi, Shulan Tian, Jason P. Sinnwell, Shannon K. McDonnell, Joanna M. Biernacka, Minerva M. Carrasquillo, Owen A. Ross, Nilüfer Ertekin-Taner, Rosa Rademakers, Matthew Hudson, Liudmila Sergeevna Mainzer and Yan W. Asmann
    Citation: BMC Bioinformatics 2018 19:139
    Content type: Research article Published on:

  39. Conventional de novo drug design is costly and time consuming, making it accessible to only the best resourced research organizations. An emergent approach to new drug development is drug repurposing, in which...

    Authors: Matthew D. King, Thomas Long, Daniel L. Pfalmer, Timothy L. Andersen and Owen M. McDougal
    Citation: BMC Bioinformatics 2018 19:138
    Content type: Research article Published on:

  41. Drug repositioning is the process of identifying new targets for known drugs. It can be used to overcome problems associated with traditional drug discovery by adapting existing drugs to treat new discovered d...

    Authors: Makbule Guclin Ozsoy, Tansel Özyer, Faruk Polat and Reda Alhajj
    Citation: BMC Bioinformatics 2018 19:136
    Content type: Research article Published on:

    The Correction to this article has been published in BMC Bioinformatics 2018 19:250

  42. RNA sequencing has become a ubiquitous technology used throughout life sciences as an effective method of measuring RNA abundance quantitatively in tissues and cells. The increase in use of RNA-seq technology ...

    Authors: MacIntosh Cornwell, Mahesh Vangala, Len Taing, Zachary Herbert, Johannes Köster, Bo Li, Hanfei Sun, Taiwen Li, Jian Zhang, Xintao Qiu, Matthew Pun, Rinath Jeselsohn, Myles Brown, X. Shirley Liu and Henry W. Long
    Citation: BMC Bioinformatics 2018 19:135
    Content type: Software Published on:

  43. Systems biologists study interaction data to understand the behaviour of whole cell systems, and their environment, at a molecular level. In order to effectively achieve this goal, it is critical that research...

    Authors: M. Sivade (Dumousseau), D. Alonso-López, M. Ammari, G. Bradley, N. H. Campbell, A. Ceol, G. Cesareni, C. Combe, J. De Las Rivas, N. del-Toro, J. Heimbach, H. Hermjakob, I. Jurisica, M. Koch, L. Licata, R. C. Lovering…
    Citation: BMC Bioinformatics 2018 19:134
    Content type: Software Published on:

  44. A number of different molecular interactions data download formats now exist, designed to allow access to these valuable data by diverse user groups. These formats include the PSI-XML and MITAB standard interc...

    Authors: M. Sivade (Dumousseau), M. Koch, A. Shrivastava, D. Alonso-López, J. De Las Rivas, N. del-Toro, C. W. Combe, B. H. M. Meldal, J. Heimbach, J. Rappsilber, J. Sullivan, Y. Yehudi and S. Orchard
    Citation: BMC Bioinformatics 2018 19:133
    Content type: Software Published on:

  45. In-depth study of the intron retention levels of transcripts provide insights on the mechanisms regulating pre-mRNA splicing efficiency. Additionally, detailed analysis of retained introns can link these intro...

    Authors: Ali Oghabian, Dario Greco and Mikko J. Frilander
    Citation: BMC Bioinformatics 2018 19:130
    Content type: Software Published on:

  46. Making accurate patient care decision, as early as possible, is a constant challenge, especially for physicians in the emergency department. The increasing volumes of electronic medical records (EMRs) open new...

    Authors: Huaixiao Tou, Lu Yao, Zhongyu Wei, Xiahai Zhuang and Bo Zhang
    Citation: BMC Bioinformatics 2018 19(Suppl 5):117
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 5

  47. Metabolites disrupted by abnormal state of human body are deemed as the effect of diseases. In comparison with the cause of diseases like genes, these markers are easier to be captured for the prevention and d...

    Authors: Yang Hu, Tianyi Zhao, Ningyi Zhang, Tianyi Zang, Jun Zhang and Liang Cheng
    Citation: BMC Bioinformatics 2018 19(Suppl 5):116
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 5

  48. DNA methylation has been identified to be widely associated to complex diseases. Among biological platforms to profile DNA methylation in human, the Illumina Infinium HumanMethylation450 BeadChip (450K) has be...

    Authors: Zhenxing Wang, XiaoLiang Wu and Yadong Wang
    Citation: BMC Bioinformatics 2018 19(Suppl 5):115
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 5

  49. Extensive studies have shown that gene expression levels are strongly affected by chromatin mark combinations via at least two mechanisms, i.e., activation or repression. But their combinatorial patterns are s...

    Authors: Shiquan Sun, Xifang Sun and Yan Zheng
    Citation: BMC Bioinformatics 2018 19(Suppl 5):113
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 5

  50. Somatic copy number alternations (SCNAs) can be utilized to infer tumor subclonal populations in whole genome seuqncing studies, where usually their read count ratios between tumor-normal paired samples serve ...

    Authors: Yanshuo Chu, Mingxiang Teng and Yadong Wang
    Citation: BMC Bioinformatics 2018 19(Suppl 5):112
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 5

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