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  1. Content type: Research article

    In the rational drug design process, an ensemble of conformations obtained from a molecular dynamics simulation plays a crucial role in docking experiments. Some studies have found that Fully-Flexible Receptor...

    Authors: Renata De Paris, Christian Vahl Quevedo, Duncan D. Ruiz, Furia Gargano and Osmar Norberto de Souza

    Citation: BMC Bioinformatics 2018 19:235

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  2. Content type: Methodology article

    Current normalization methods for RNA-sequencing data allow either for intersample comparison to identify differentially expressed (DE) genes or for intrasample comparison for the discovery and validation of g...

    Authors: Marcel Smid, Robert R. J. Coebergh van den Braak, Harmen J. G. van de Werken, Job van Riet, Anne van Galen, Vanja de Weerd, Michelle van der Vlugt-Daane, Sandra I. Bril, Zarina S. Lalmahomed, Wigard P. Kloosterman, Saskia M. Wilting, John A. Foekens, Jan N. M. IJzermans, John W. M. Martens and Anieta M. Sieuwerts

    Citation: BMC Bioinformatics 2018 19:236

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  3. Content type: Methodology article

    Spastic cerebral palsy (CP) is a leading cause of physical disability. Most people with spastic CP are born with it, but early diagnosis is challenging, and no current biomarker platform readily identifies aff...

    Authors: Erin L. Crowgey, Adam G. Marsh, Karyn G. Robinson, Stephanie K. Yeager and Robert E. Akins

    Citation: BMC Bioinformatics 2018 19:225

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  4. Content type: Software

    The long-range sequencing information captured by linked reads, such as those available from 10× Genomics (10xG), helps resolve genome sequence repeats, and yields accurate and contiguous draft genome assembli...

    Authors: Lauren Coombe, Jessica Zhang, Benjamin P. Vandervalk, Justin Chu, Shaun D. Jackman, Inanc Birol and René L. Warren

    Citation: BMC Bioinformatics 2018 19:234

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  5. Content type: Research article

    Drug-disease associations provide important information for the drug discovery. Wet experiments that identify drug-disease associations are time-consuming and expensive. However, many drug-disease associations...

    Authors: Wen Zhang, Xiang Yue, Weiran Lin, Wenjian Wu, Ruoqi Liu, Feng Huang and Feng Liu

    Citation: BMC Bioinformatics 2018 19:233

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  6. Content type: Research Article

    A fundamental fact in biology states that genes do not operate in isolation, and yet, methods that infer regulatory networks for single cell gene expression data have been slow to emerge. With single cell sequ...

    Authors: Shuonan Chen and Jessica C. Mar

    Citation: BMC Bioinformatics 2018 19:232

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  7. Content type: Research article

    Given a set of t n-length DNA sequences, q satisfying 0 < q ≤ 1, and l and d satisfying 0 ≤ d < l < n, the quorum planted motif search (qPMS) finds l-length strings that occur in at least qt input sequences with ...

    Authors: Qiang Yu, Dingbang Wei and Hongwei Huo

    Citation: BMC Bioinformatics 2018 19:228

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  8. Content type: Research article

    Part of the missing heritability in Genome Wide Association Studies (GWAS) is expected to be explained by interactions between genetic variants, also called epistasis. Various statistical methods have been dev...

    Authors: Clément Chatelain, Guillermo Durand, Vincent Thuillier and Franck Augé

    Citation: BMC Bioinformatics 2018 19:231

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  10. Content type: Methodology article

    With the reduction of gene sequencing cost and demand for emerging technologies such as precision medical treatment and deep learning in genome, it is an era of gene data outbreaks today. How to store, transmi...

    Authors: Qiuming Luo, Chao Guo, Yi Jun Zhang, Ye Cai and Gang Liu

    Citation: BMC Bioinformatics 2018 19:230

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  12. Content type: Research article

    Third generation sequencing technologies generate long reads that exhibit high error rates, in particular for insertions and deletions which are usually the most difficult errors to cope with. The only exact a...

    Authors: Jean-François Gibrat

    Citation: BMC Bioinformatics 2018 19:226

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  13. Content type: Software

    Mutational signatures have been proved as a valuable pattern in somatic genomics, mainly regarding cancer, with a potential application as a biomarker in clinical practice. Up to now, several bioinformatic pac...

    Authors: Marcos Díaz-Gay, Maria Vila-Casadesús, Sebastià Franch-Expósito, Eva Hernández-Illán, Juan José Lozano and Sergi Castellví-Bel

    Citation: BMC Bioinformatics 2018 19:224

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  14. Content type: Research

    Finding common molecular interactions from different samples is essential work to understanding diseases and other biological processes. Coexpression networks and their modules directly reflect sample-specific...

    Authors: Yousang Jo, Sanghyeon Kim and Doheon Lee

    Citation: BMC Bioinformatics 2018 19(Suppl 8):213

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 8

  15. Content type: Research

    Deep Neural Networks (DNN), in particular, Convolutional Neural Networks (CNN), has recently achieved state-of-art results for the task of Drug-Drug Interaction (DDI) extraction. Most CNN architectures incorpo...

    Authors: Víctor Suárez-Paniagua and Isabel Segura-Bedmar

    Citation: BMC Bioinformatics 2018 19(Suppl 8):209

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 8

  16. Content type: Research

    Systems biology is an important field for understanding whole biological mechanisms composed of interactions between biological components. One approach for understanding complex and diverse mechanisms is to a...

    Authors: Munui Kim, Seung Han Baek and Min Song

    Citation: BMC Bioinformatics 2018 19(Suppl 8):206

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 8

  17. Content type: Research

    Suicide is an alarming public health problem accounting for a considerable number of deaths each year worldwide. Many more individuals contemplate suicide. Understanding the attributes, characteristics, and ex...

    Authors: Reilly N. Grant, David Kucher, Ana M. León, Jonathan F. Gemmell, Daniela S. Raicu and Samah J. Fodeh

    Citation: BMC Bioinformatics 2018 19(Suppl 8):211

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 8

  18. Content type: Research

    Administered drugs are often converted into an ineffective or activated form by enzymes in our body. Conventional in silico prediction approaches focused on therapeutically important enzymes such as CYP450. Ho...

    Authors: Myeong-Sang Yu, Hyang-Mi Lee, Aaron Park, Chungoo Park, Hyithaek Ceong, Ki-Hyeong Rhee and Dokyun Na

    Citation: BMC Bioinformatics 2018 19(Suppl 8):207

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 8

  19. Content type: Research

    Natural products have been widely investigated in the drug development field. Their traditional use cases as medicinal agents and their resemblance of our endogenous compounds show the possibility of new drug ...

    Authors: Kyungrin Noh, Sunyong Yoo and Doheon Lee

    Citation: BMC Bioinformatics 2018 19(Suppl 8):205

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 8

  20. Content type: Research

    As Twitter has become an active data source for health surveillance research, it is important that efficient and effective methods are developed to identify tweets related to personal health experience. Conven...

    Authors: Keyuan Jiang, Shichao Feng, Qunhao Song, Ricardo A. Calix, Matrika Gupta and Gordon R. Bernard

    Citation: BMC Bioinformatics 2018 19(Suppl 8):210

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 8

  21. Content type: Research

    Social media is a useful platform to share health-related information due to its vast reach. This makes it a good candidate for public-health monitoring tasks, specifically for pharmacovigilance. We study the ...

    Authors: Shashank Gupta, Sachin Pawar, Nitin Ramrakhiyani, Girish Keshav Palshikar and Vasudeva Varma

    Citation: BMC Bioinformatics 2018 19(Suppl 8):212

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 8

  22. Content type: Research

    Identification of drug-target interactions acts as a key role in drug discovery. However, identifying drug-target interactions via in-vitro, in-vivo experiments are very laborious, time-consuming. Thus, predic...

    Authors: Ingoo Lee and Hojung Nam

    Citation: BMC Bioinformatics 2018 19(Suppl 8):208

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 8

  23. Content type: Software

    Targeted PCR amplicon sequencing (TAS) techniques provide a sensitive, scalable, and cost-effective way to query and identify closely related bacterial species and strains. Typically, this is accomplished by t...

    Authors: Tara N. Furstenau, Jill H. Cocking, Jason W. Sahl and Viacheslav Y. Fofanov

    Citation: BMC Bioinformatics 2018 19:222

    Published on:

  25. Content type: Methodology article

    Discovering over-represented approximate motifs in DNA sequences is an essential part of bioinformatics. This topic has been studied extensively because of the increasing number of potential applications. Howe...

    Authors: Chadi Saad, Laurent Noé, Hugues Richard, Julie Leclerc, Marie-Pierre Buisine, Hélène Touzet and Martin Figeac

    Citation: BMC Bioinformatics 2018 19:223

    Published on:

Page 1 of 354

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