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  1. Software

    VISMapper: ultra-fast exhaustive cartography of viral insertion sites for gene therapy

    The possibility of integrating viral vectors to become a persistent part of the host genome makes them a crucial element of clinical gene therapy. However, viral integration has associated risks, such as the u...

    José M. Juanes, Asunción Gallego, Joaquín Tárraga, Felipe J. Chaves, Pablo Marín-Garcia, Ignacio Medina, Vicente Arnau and Joaquín Dopazo

    BMC Bioinformatics 2017 18:421

    Published on: 20 September 2017

  2. Methodology Article

    Deep learning methods for protein torsion angle prediction

    Deep learning is one of the most powerful machine learning methods that has achieved the state-of-the-art performance in many domains. Since deep learning was introduced to the field of bioinformatics in 2012,...

    Haiou Li, Jie Hou, Badri Adhikari, Qiang Lyu and Jianlin Cheng

    BMC Bioinformatics 2017 18:417

    Published on: 18 September 2017

  3. Research Article

    Segmentation and classification of two-channel C. elegans nucleus-labeled fluorescence images

    Aging is characterized by a gradual breakdown of cellular structures. Nuclear abnormality is a hallmark of progeria in human. Analysis of age-dependent nuclear morphological changes in Caenorhabditis elegans is o...

    Mengdi Zhao, Jie An, Haiwen Li, Jiazhi Zhang, Shang-Tong Li, Xue-Mei Li, Meng-Qiu Dong, Heng Mao and Louis Tao

    BMC Bioinformatics 2017 18:412

    Published on: 15 September 2017

  4. Software

    mmquant: how to count multi-mapping reads?

    RNA-Seq is currently used routinely, and it provides accurate information on gene transcription. However, the method cannot accurately estimate duplicated genes expression. Several strategies have been previou...

    Matthias Zytnicki

    BMC Bioinformatics 2017 18:411

    Published on: 15 September 2017

  5. Research

    Vermont: a multi-perspective visual interactive platform for mutational analysis

    A huge amount of data about genomes and sequence variation is available and continues to grow on a large scale, which makes experimentally characterizing these mutations infeasible regarding disease associatio...

    Alexandre V. Fassio, Pedro M. Martins, Samuel da S. Guimarães, Sócrates S. A. Junior, Vagner S. Ribeiro, Raquel C. de Melo-Minardi and Sabrina de A. Silveira

    BMC Bioinformatics 2017 18(Suppl 10):403

    Published on: 13 September 2017

    This article is part of a Supplement: Volume 18 Supplement 10

  6. Research

    C-State: an interactive web app for simultaneous multi-gene visualization and comparative epigenetic pattern search

    Comparative epigenomic analysis across multiple genes presents a bottleneck for bench biologists working with NGS data. Despite the development of standardized peak analysis algorithms, the identification of n...

    Divya Tej Sowpati, Surabhi Srivastava, Jyotsna Dhawan and Rakesh K Mishra

    BMC Bioinformatics 2017 18(Suppl 10):392

    Published on: 13 September 2017

    This article is part of a Supplement: Volume 18 Supplement 10

  7. Research

    Reconstruction and visualization of large-scale volumetric models of neocortical circuits for physically-plausible in silico optical studies

    We present a software workflow capable of building large scale, highly detailed and realistic volumetric models of neocortical circuits from the morphological skeletons of their digitally reconstructed neurons...

    Marwan Abdellah, Juan Hernando, Nicolas Antille, Stefan Eilemann, Henry Markram and Felix Schürmann

    BMC Bioinformatics 2017 18(Suppl 10):402

    Published on: 13 September 2017

    This article is part of a Supplement: Volume 18 Supplement 10

  8. Research

    MediSyn: uncertainty-aware visualization of multiple biomedical datasets to support drug treatment selection

    Dispersed biomedical databases limit user exploration to generate structured knowledge. Linked Data unifies data structures and makes the dispersed data easy to search across resources, but it lacks supporting hu...

    Chen He, Luana Micallef, Zia-ur-Rehman Tanoli, Samuel Kaski, Tero Aittokallio and Giulio Jacucci

    BMC Bioinformatics 2017 18(Suppl 10):393

    Published on: 13 September 2017

    This article is part of a Supplement: Volume 18 Supplement 10

  9. Software

    CellNetVis: a web tool for visualization of biological networks using force-directed layout constrained by cellular components

    The advent of “omics” science has brought new perspectives in contemporary biology through the high-throughput analyses of molecular interactions, providing new clues in protein/gene function and in the organi...

    Henry Heberle, Marcelo Falsarella Carazzolle, Guilherme P. Telles, Gabriela Vaz Meirelles and Rosane Minghim

    BMC Bioinformatics 2017 18(Suppl 10):395

    Published on: 13 September 2017

    This article is part of a Supplement: Volume 18 Supplement 10

  10. Research

    Bayesian Unidimensional Scaling for visualizing uncertainty in high dimensional datasets with latent ordering of observations

    Detecting patterns in high-dimensional multivariate datasets is non-trivial. Clustering and dimensionality reduction techniques often help in discerning inherent structures. In biological datasets such as micr...

    Lan Huong Nguyen and Susan Holmes

    BMC Bioinformatics 2017 18(Suppl 10):394

    Published on: 13 September 2017

    This article is part of a Supplement: Volume 18 Supplement 10

  11. Software

    Interactive visual exploration and refinement of cluster assignments

    With ever-increasing amounts of data produced in biology research, scientists are in need of efficient data analysis methods. Cluster analysis, combined with visualization of the results, is one such method th...

    Michael Kern, Alexander Lex, Nils Gehlenborg and Chris R. Johnson

    BMC Bioinformatics 2017 18:406

    Published on: 12 September 2017

  12. Research Article

    Statistical classifiers for diagnosing disease from immune repertoires: a case study using multiple sclerosis

    Deep sequencing of lymphocyte receptor repertoires has made it possible to comprehensively profile the clonal composition of lymphocyte populations. This opens the door for novel approaches to diagnose and pro...

    Jared Ostmeyer, Scott Christley, William H. Rounds, Inimary Toby, Benjamin M. Greenberg, Nancy L. Monson and Lindsay G. Cowell

    BMC Bioinformatics 2017 18:401

    Published on: 7 September 2017

  13. Software

    High-throughput PCR assay design for targeted resequencing using primerXL

    Although the sequencing landscape is rapidly evolving and sequencing costs are continuously decreasing, whole genome sequencing is still too expensive for use on a routine basis. Targeted resequencing of only ...

    Steve Lefever, Filip Pattyn, Bram De Wilde, Frauke Coppieters, Sarah De Keulenaer, Jan Hellemans and Jo Vandesompele

    BMC Bioinformatics 2017 18:400

    Published on: 6 September 2017

  14. Software

    BUFET: boosting the unbiased miRNA functional enrichment analysis using bitsets

    A group of miRNAs can regulate a biological process by targeting genes involved in the process. The unbiased miRNA functional enrichment analysis is the most precise in silico approach to predict the biological p...

    Konstantinos Zagganas, Thanasis Vergoulis, Maria D. Paraskevopoulou, Ioannis S. Vlachos, Spiros Skiadopoulos and Theodore Dalamagas

    BMC Bioinformatics 2017 18:399

    Published on: 6 September 2017

  15. Software

    Phylo_dCor: distance correlation as a novel metric for phylogenetic profiling

    Elaboration of powerful methods to predict functional and/or physical protein-protein interactions from genome sequence is one of the main tasks in the post-genomic era. Phylogenetic profiling allows the predi...

    Gabriella Sferra, Federica Fratini, Marta Ponzi and Elisabetta Pizzi

    BMC Bioinformatics 2017 18:396

    Published on: 5 September 2017

  16. Research Article

    Investigating MicroRNA and transcription factor co-regulatory networks in colorectal cancer

    Colorectal cancer (CRC) is one of the most common malignancies worldwide with poor prognosis. Studies have showed that abnormal microRNA (miRNA) expression can affect CRC pathogenesis and development through t...

    Hao Wang, Jiamao Luo, Chun Liu, Huilin Niu, Jing Wang, Qi Liu, Zhongming Zhao, Hua Xu, Yanqing Ding, Jingchun Sun and Qingling Zhang

    BMC Bioinformatics 2017 18:388

    Published on: 2 September 2017

  17. Database

    A new and updated resource for codon usage tables

    Due to the degeneracy of the genetic code, most amino acids can be encoded by multiple synonymous codons. Synonymous codons naturally occur with different frequencies in different organisms. The choice of codo...

    John Athey, Aikaterini Alexaki, Ekaterina Osipova, Alexandre Rostovtsev, Luis V. Santana-Quintero, Upendra Katneni, Vahan Simonyan and Chava Kimchi-Sarfaty

    BMC Bioinformatics 2017 18:391

    Published on: 2 September 2017

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