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  1. Content type: Software

    The automated prediction of the enzymatic functions of uncharacterized proteins is a crucial topic in bioinformatics. Although several methods and tools have been proposed to classify enzymes, most of these st...

    Authors: Alperen Dalkiran, Ahmet Sureyya Rifaioglu, Maria Jesus Martin, Rengul Cetin-Atalay, Volkan Atalay and Tunca Doğan

    Citation: BMC Bioinformatics 2018 19:334

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  2. Content type: Methodology article

    The development of a disease is a complex process that may result from joint effects of multiple genes. In this article, we propose the overlapping group screening (OGS) approach to determining active genes an...

    Authors: Jie-Huei Wang and Yi-Hau Chen

    Citation: BMC Bioinformatics 2018 19:335

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  3. Content type: Research article

    Protein complexes are one of the keys to deciphering the behavior of a cell system. During the past decade, most computational approaches used to identify protein complexes have been based on discovering dense...

    Authors: Xiaoxia Liu, Zhihao Yang, Shengtian Sang, Ziwei Zhou, Lei Wang, Yin Zhang, Hongfei Lin, Jian Wang and Bo Xu

    Citation: BMC Bioinformatics 2018 19:332

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  4. Content type: Methodology article

    Sequence alignment is crucial in genomics studies. However, optimal multiple sequence alignment (MSA) is NP-hard. Thus, modern MSA methods employ progressive heuristics, breaking the problem into a series of p...

    Authors: Massimo Maiolo, Xiaolei Zhang, Manuel Gil and Maria Anisimova

    Citation: BMC Bioinformatics 2018 19:331

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  5. Content type: Methodology article

    Data-driven methods that automatically learn relations between attributes from given data are a popular tool for building mathematical models in computational biology. Since measurements are prone to errors, a...

    Authors: Lidija Magdevska, Miha Mraz, Nikolaj Zimic and Miha Moškon

    Citation: BMC Bioinformatics 2018 19:333

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  6. Content type: Research article

    Spanins are phage lysis proteins required to disrupt the outer membrane. Phages employ either two-component spanins or unimolecular spanins in this final step of Gram-negative host lysis. Two-component spanins...

    Authors: Rohit Kongari, Manoj Rajaure, Jesse Cahill, Eric Rasche, Eleni Mijalis, Joel Berry and Ry Young

    Citation: BMC Bioinformatics 2018 19:326

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  7. Content type: Methodology article

    Conventional phylogenetic clustering approaches rely on arbitrary cutpoints applied a posteriori to phylogenetic estimates. Although in practice, Bayesian and bootstrap-based clustering tend to lead to similar...

    Authors: Luc Villandré, Aurélie Labbe, Bluma Brenner, Michel Roger and David A Stephens

    Citation: BMC Bioinformatics 2018 19:324

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  8. Content type: Methodology article

    Procedures for controlling the false discovery rate (FDR) are widely applied as a solution to the multiple comparisons problem of high-dimensional statistics. Current FDR-controlling procedures require accurat...

    Authors: Matthew M. Parks, Benjamin J. Raphael and Charles E. Lawrence

    Citation: BMC Bioinformatics 2018 19:323

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  9. Content type: Research article

    Constraint-based metabolic flux analysis of knockout strategies is an efficient method to simulate the production of useful metabolites in microbes. Owing to the recent development of technologies for artifici...

    Authors: Takeyuki Tamura

    Citation: BMC Bioinformatics 2018 19:325

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  10. Content type: Methodology article

    The inclusion of high-dimensional omics data in prediction models has become a well-studied topic in the last decades. Although most of these methods do not account for possibly different types of variables in...

    Authors: Simon Klau, Vindi Jurinovic, Roman Hornung, Tobias Herold and Anne-Laure Boulesteix

    Citation: BMC Bioinformatics 2018 19:322

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  11. Content type: Methodology article

    Advancements in biophysical experimental techniques have pushed the limits in terms of the types of phenomena that can be characterized, the amount of data that can be produced and the resolution at which we c...

    Authors: Sandhya P. Tiwari, Florence Tama and Osamu Miyashita

    Citation: BMC Bioinformatics 2018 19:320

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  12. Content type: Software

    Networks whose nodes have labels can seem complex. Fortunately, many have substructures that occur often (“motifs”). A societal example of a motif might be a household. Replacing such motifs by named supernode...

    Authors: Danilo Dessì, Jacopo Cirrone, Diego Reforgiato Recupero and Dennis Shasha

    Citation: BMC Bioinformatics 2018 19:318

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  13. Content type: Research article

    Transcription factor binding site (TFBS) loss, gain, and reshuffling within the sequence of a regulatory element could alter the function of that regulatory element. Some of the changes will be detrimental to ...

    Authors: Mario A. Flores and Ivan Ovcharenko

    Citation: BMC Bioinformatics 2018 19:316

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  14. Content type: Research article

    Target identification is necessary for the comprehensive inference of the mechanism of action of a compound. The application of computational methods to predict the targets of bioactive compounds saves cost an...

    Authors: Hao Sun, Yiting Shen, Guangwen Luo, Yuepiao Cai and Zheng Xiang

    Citation: BMC Bioinformatics 2018 19:315

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  15. Content type: Methodology article

    Normalization is essential to ensure accurate analysis and proper interpretation of sequencing data, and chromosome conformation capture data such as Hi-C have particular challenges. Although several methods h...

    Authors: Nicolas Servant, Nelle Varoquaux, Edith Heard, Emmanuel Barillot and Jean-Philippe Vert

    Citation: BMC Bioinformatics 2018 19:313

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  16. Content type: Methodology article

    To address high-dimensional genomic data, most of the proposed prediction methods make use of genomic data alone without considering clinical data, which are often available and known to have predictive value....

    Authors: Caroline Bazzoli and Sophie Lambert-Lacroix

    Citation: BMC Bioinformatics 2018 19:314

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  17. Content type: Research article

    Viral infection by dengue virus is a major public health problem in tropical countries. Early diagnosis and detection are increasingly based on quantitative reverse transcriptase real-time polymerase chain rea...

    Authors: Kevin Vanneste, Linda Garlant, Sylvia Broeders, Steven Van Gucht and Nancy H. Roosens

    Citation: BMC Bioinformatics 2018 19:312

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  18. Content type: Software

    Metagenomic approaches have revealed the complexity of environmental microbiomes with the advancement in whole genome sequencing displaying a significant level of genetic heterogeneity on the species level. It...

    Authors: Adeola M. Rotimi, Rian Pierneef and Oleg N. Reva

    Citation: BMC Bioinformatics 2018 19:309

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  19. Content type: Research article

    Biomedical knowledge grows in complexity, and becomes encoded in network-based repositories, which include focused, expert-drawn diagrams, networks of evidence-based associations and established ontologies. Co...

    Authors: Marek Ostaszewski, Emmanuel Kieffer, Grégoire Danoy, Reinhard Schneider and Pascal Bouvry

    Citation: BMC Bioinformatics 2018 19:308

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  20. Content type: Methodology article

    In recent decades, detecting protein complexes (PCs) from protein-protein interaction networks (PPINs) has been an active area of research. There are a large number of excellent graph clustering methods that w...

    Authors: Rongquan Wang, Guixia Liu, Caixia Wang, Lingtao Su and Liyan Sun

    Citation: BMC Bioinformatics 2018 19:305

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  21. Content type: Software

    Computational RNA 3D structure prediction and modeling are rising as complementary approaches to high-resolution experimental techniques for structure determination. They often apply to substitute or complemen...

    Authors: Maciej Antczak, Tomasz Zok, Maciej Osowiecki, Mariusz Popenda, Ryszard W. Adamiak and Marta Szachniuk

    Citation: BMC Bioinformatics 2018 19:304

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  22. Content type: Software

    Computational biology requires the reading and comprehension of biological data files. Plain-text formats such as SAM, VCF, GTF, PDB and FASTA, often contain critical information which is obfuscated by the dat...

    Authors: Artem Babaian, Anicet Ebou, Alyssa Fegen, Ho Yin Kam, German E. Novakovsky, Jasper Wong, Dylan Aïssi and Li Yao

    Citation: BMC Bioinformatics 2018 19:303

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  23. Content type: Methodology article

    Reproducibility of hits from independent CRISPR or siRNA screens is poor. This is partly due to data normalization primarily addressing technical variability within independent screens, and not the technical d...

    Authors: Costa Bachas, Jasmina Hodzic, Johannes C. van der Mijn, Chantal Stoepker, Henk M. W. Verheul, Rob M. F. Wolthuis, Emanuela Felley-Bosco, Wessel N. van Wieringen, Victor W. van Beusechem, Ruud H. Brakenhoff and Renée X. de Menezes

    Citation: BMC Bioinformatics 2018 19:301

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  24. Content type: Methodology article

    Targeted resequencing with high-throughput sequencing (HTS) platforms can be used to efficiently interrogate the genomes of large numbers of individuals. A critical issue for research and applications using HT...

    Authors: Felix Francis, Michael D. Dumas, Scott B. Davis and Randall J. Wisser

    Citation: BMC Bioinformatics 2018 19:302

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  25. Content type: Software

    Here, we present an R package for entropy/variability analysis that facilitates prompt and convenient data extraction, manipulation and visualization of protein features from multiple sequence alignments. BALC...

    Authors: Alicja Płuciennik, Michał Stolarczyk, Maria Bzówka, Agata Raczyńska, Tomasz Magdziarz and Artur Góra

    Citation: BMC Bioinformatics 2018 19:300

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  26. Content type: Research

    The risk factors of diabetic retinopathy (DR) were investigated extensively in the past studies, but it remains unknown which risk factors were more associated with the DR than others. If we can detect the DR ...

    Authors: Hsin-Yi Tsao, Pei-Ying Chan and Emily Chia-Yu Su

    Citation: BMC Bioinformatics 2018 19(Suppl 9):2277

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    This article is part of a Supplement: Volume 19 Supplement 9

  27. Content type: Research

    Human Microbiome Project reveals the significant mutualistic influence between human body and microbes living in it. Such an influence lead to an interesting phenomenon that many noninfectious diseases are clo...

    Authors: Jian-Yu Shi, Hua Huang, Yan-Ning Zhang, Jiang-Bo Cao and Siu-Ming Yiu

    Citation: BMC Bioinformatics 2018 19(Suppl 9):2274

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    This article is part of a Supplement: Volume 19 Supplement 9

  28. Content type: Research

    In bioinformatics, network alignment algorithms have been applied to protein-protein interaction (PPI) networks to discover evolutionary conserved substructures at the system level. However, most previous meth...

    Authors: Jianliang Gao, Bo Song, Xiaohua Hu, Fengxia Yan and Jianxin Wang

    Citation: BMC Bioinformatics 2018 19(Suppl 9):2271

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    This article is part of a Supplement: Volume 19 Supplement 9

  29. Content type: Research

    Biomedical event extraction is a crucial task in biomedical text mining. As the primary forum for international evaluation of different biomedical event extraction technologies, BioNLP Shared Task represents a...

    Authors: Lishuang Li, Jia Wan, Jieqiong Zheng and Jian Wang

    Citation: BMC Bioinformatics 2018 19(Suppl 9):2275

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    This article is part of a Supplement: Volume 19 Supplement 9

  30. Content type: Research

    Global maritime trade plays an important role in the modern transportation industry. It brings significant economic profit along with bioinvasion risk. Species translocate and establish in a non-native area th...

    Authors: Shengling Wang, Chenyu Wang, Shenling Wang and Liran Ma

    Citation: BMC Bioinformatics 2018 19(Suppl 9):2272

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    This article is part of a Supplement: Volume 19 Supplement 9

  31. Content type: Software

    The knowledge of miRNAs regulating the expression of sets of mRNAs has led to novel insights into numerous and diverse cellular mechanisms. While a single miRNA may regulate many genes, one gene can be regulat...

    Authors: Luqman Hakim Abdul Hadi, Quy Xiao Xuan Lin, Tri Tran Minh, Marie Loh, Hong Kiat Ng, Agus Salim, Richie Soong and Touati Benoukraf

    Citation: BMC Bioinformatics 2018 19:299

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  32. Content type: Software

    Taxonomic identification of plants and insects is a hard process that demands expert taxonomists and time, and it’s often difficult to distinguish on morphology only. DNA barcodes allow a rapid species discove...

    Authors: Renato Renison Moreira Oliveira, Gisele Lopes Nunes, Talvâne Glauber Lopes de Lima, Guilherme Oliveira and Ronnie Alves

    Citation: BMC Bioinformatics 2018 19:297

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  33. Content type: Software

    Microarray experiments comprise more than half of all series in the Gene Expression Omnibus (GEO). However, downloading and analyzing raw or semi-processed microarray data from GEO is not intuitive and require...

    Authors: Maria Luisa Amaral, Galina A. Erikson and Maxim N. Shokhirev

    Citation: BMC Bioinformatics 2018 19:296

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  34. Content type: Software

    Polygenic risk scores (PRS) describe the genomic contribution to complex phenotypes and consistently account for a larger proportion of variance in outcome than single nucleotide polymorphisms (SNPs) alone. Ho...

    Authors: Lawrence M. Chen, Nelson Yao, Elika Garg, Yuecai Zhu, Thao T. T. Nguyen, Irina Pokhvisneva, Shantala A. Hari Dass, Eva Unternaehrer, Hélène Gaudreau, Marie Forest, Lisa M. McEwen, Julia L. MacIsaac, Michael S. Kobor, Celia M. T. Greenwood, Patricia P. Silveira, Michael J. Meaney…

    Citation: BMC Bioinformatics 2018 19:295

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  35. Content type: Software

    Since circular RNAs (circRNAs) post-transcriptionally regulate gene expression, they have attracted increasing attention. However, there is no existing tool to annotate and extract spliced sequences for circRN...

    Authors: Shanliang Zhong, Jinyan Wang, Qian Zhang, Hanzi Xu and Jifeng Feng

    Citation: BMC Bioinformatics 2018 19:292

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