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  1. Methodology Article

    A weighted string kernel for protein fold recognition

    Alignment-free methods for comparing protein sequences have proved to be viable alternatives to approaches that first rely on an alignment of the sequences to be compared. Much work however need to be done bef...

    Saghi Nojoomi and Patrice Koehl

    BMC Bioinformatics 2017 18:378

    Published on: 25 August 2017

  2. Methodology Article

    Identifying pleiotropic genes in genome-wide association studies from related subjects using the linear mixed model and Fisher combination function

    A multivariate genome-wide association test is proposed for analyzing data on multivariate quantitative phenotypes collected from related subjects. The proposed method is a two-step approach. The first step mo...

    James J. Yang, L Keoki Williams and Anne Buu

    BMC Bioinformatics 2017 18:376

    Published on: 24 August 2017

  3. Research Article

    Coreference annotation and resolution in the Colorado Richly Annotated Full Text (CRAFT) corpus of biomedical journal articles

    Coreference resolution is the task of finding strings in text that have the same referent as other strings. Failures of coreference resolution are a common cause of false negatives in information extraction fr...

    K. Bretonnel Cohen, Arrick Lanfranchi, Miji Joo-young Choi, Michael Bada, William A. Baumgartner Jr., Natalya Panteleyeva, Karin Verspoor, Martha Palmer and Lawrence E. Hunter

    BMC Bioinformatics 2017 18:372

    Published on: 17 August 2017

  4. Software

    eccCL: parallelized GPU implementation of Ensemble Classifier Chains

    Multi-label classification has recently gained great attention in diverse fields of research, e.g., in biomedical application such as protein function prediction or drug resistance testing in HIV. In this cont...

    Mona Riemenschneider, Alexander Herbst, Ari Rasch, Sergei Gorlatch and Dominik Heider

    BMC Bioinformatics 2017 18:371

    Published on: 17 August 2017

  5. Research Article

    Cancerouspdomains: comprehensive analysis of cancer type-specific recurrent somatic mutations in proteins and domains

    Discriminating driver mutations from the ones that play no role in cancer is a severe bottleneck in elucidating molecular mechanisms underlying cancer development. Since protein domains are representatives of ...

    Seirana Hashemi, Abbas Nowzari Dalini, Adrin Jalali, Ali Mohammad Banaei-Moghaddam and Zahra Razaghi-Moghadam

    BMC Bioinformatics 2017 18:370

    Published on: 16 August 2017

  6. Research Article

    Improving fold resistance prediction of HIV-1 against protease and reverse transcriptase inhibitors using artificial neural networks

    Drug resistance in HIV treatment is still a worldwide problem. Predicting resistance to antiretrovirals (ARVs) before starting any treatment is important. Prediction accuracy is essential, as low-accuracy pred...

    Olivier Sheik Amamuddy, Nigel T. Bishop and Özlem Tastan Bishop

    BMC Bioinformatics 2017 18:369

    Published on: 15 August 2017

  7. Research Article

    Full L1-regularized Traction Force Microscopy over whole cells

    Traction Force Microscopy (TFM) is a widespread technique to estimate the tractions that cells exert on the surrounding substrate. To recover the tractions, it is necessary to solve an inverse problem, which i...

    Alejandro Suñé-Auñón, Alvaro Jorge-Peñas, Rocío Aguilar-Cuenca, Miguel Vicente-Manzanares, Hans Van Oosterwyck and Arrate Muñoz-Barrutia

    BMC Bioinformatics 2017 18:365

    Published on: 10 August 2017

  8. Research Article

    Network design and analysis for multi-enzyme biocatalysis

    As more and more biological reaction data become available, the full exploration of the enzymatic potential for the synthesis of valuable products opens up exciting new opportunities but is becoming increasing...

    Lisa Katharina Blaß, Christian Weyler and Elmar Heinzle

    BMC Bioinformatics 2017 18:366

    Published on: 10 August 2017

  9. Software

    ODG: Omics database generator - a tool for generating, querying, and analyzing multi-omics comparative databases to facilitate biological understanding

    Rapid generation of omics data in recent years have resulted in vast amounts of disconnected datasets without systemic integration and knowledge building, while individual groups have made customized, annotate...

    Joseph Guhlin, Kevin A. T. Silverstein, Peng Zhou, Peter Tiffin and Nevin D. Young

    BMC Bioinformatics 2017 18:367

    Published on: 10 August 2017

  10. Research Article

    Local sequence and sequencing depth dependent accuracy of RNA-seq reads

    Many biases and spurious effects are inherent in RNA-seq technology, resulting in a non-uniform distribution of sequencing read counts for each base position in a gene. Therefore, a base-level strategy is requ...

    Guoshuai Cai, Shoudan Liang, Xiaofeng Zheng and Feifei Xiao

    BMC Bioinformatics 2017 18:364

    Published on: 9 August 2017

  11. Software

    Repliscan: a tool for classifying replication timing regions

    Replication timing experiments that use label incorporation and high throughput sequencing produce peaked data similar to ChIP-Seq experiments. However, the differences in experimental design, coverage density...

    Gregory J. Zynda, Jawon Song, Lorenzo Concia, Emily E. Wear, Linda Hanley-Bowdoin, William F. Thompson and Matthew W. Vaughn

    BMC Bioinformatics 2017 18:362

    Published on: 7 August 2017

  12. Methodology Article

    A nonparametric Bayesian method of translating machine learning scores to probabilities in clinical decision support

    Probabilistic assessments of clinical care are essential for quality care. Yet, machine learning, which supports this care process has been limited to categorical results. To maximize its usefulness, it is imp...

    Brian Connolly, K. Bretonnel Cohen, Daniel Santel, Ulya Bayram and John Pestian

    BMC Bioinformatics 2017 18:361

    Published on: 7 August 2017

  13. Research Article

    Parallel multiple instance learning for extremely large histopathology image analysis

    Histopathology images are critical for medical diagnosis, e.g., cancer and its treatment. A standard histopathology slice can be easily scanned at a high resolution of, say, 200,000×200,000 pixels. These high ...

    Yan Xu, Yeshu Li, Zhengyang Shen, Ziwei Wu, Teng Gao, Yubo Fan, Maode Lai and Eric I-Chao Chang

    BMC Bioinformatics 2017 18:360

    Published on: 3 August 2017

  14. Methodology Article

    Correcting nucleotide-specific biases in high-throughput sequencing data

    High-throughput sequence (HTS) data exhibit position-specific nucleotide biases that obscure the intended signal and reduce the effectiveness of these data for downstream analyses. These biases are particularl...

    Jeremy R. Wang, Bryan Quach and Terrence S. Furey

    BMC Bioinformatics 2017 18:357

    Published on: 1 August 2017

  15. Research Article

    Assessing the model transferability for prediction of transcription factor binding sites based on chromatin accessibility

    Computational prediction of transcription factor (TF) binding sites in different cell types is challenging. Recent technology development allows us to determine the genome-wide chromatin accessibility in vario...

    Sheng Liu, Cristina Zibetti, Jun Wan, Guohua Wang, Seth Blackshaw and Jiang Qian

    BMC Bioinformatics 2017 18:355

    Published on: 27 July 2017

  16. Methodology Article

    Quantification of tumour evolution and heterogeneity via Bayesian epiallele detection

    Epigenetic heterogeneity within a tumour can play an important role in tumour evolution and the emergence of resistance to treatment. It is increasingly recognised that the study of DNA methylation (DNAm) patt...

    James E. Barrett, Andrew Feber, Javier Herrero, Miljana Tanic, Gareth A. Wilson, Charles Swanton and Stephan Beck

    BMC Bioinformatics 2017 18:354

    Published on: 25 July 2017

  17. Research Article

    An extended model of vesicle fusion at the plasma membrane to estimate protein lateral diffusion from TIRF microscopy images

    Characterizing membrane dynamics is a key issue to understand cell exchanges with the extra-cellular medium. Total internal reflection fluorescence microscopy (TIRFM) is well suited to focus on the late steps ...

    Antoine Basset, Patrick Bouthemy, Jérôme Boulanger, François Waharte, Jean Salamero and Charles Kervrann

    BMC Bioinformatics 2017 18:352

    Published on: 24 July 2017

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