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  1. Software

    QueryOR: a comprehensive web platform for genetic variant analysis and prioritization

    Whole genome and exome sequencing are contributing to the extraordinary progress in the study of human genetic variants. In this fast developing field, appropriate and easily accessible tools are required to f...

    Loris Bertoldi, Claudio Forcato, Nicola Vitulo, Giovanni Birolo, Fabio De Pascale, Erika Feltrin, Riccardo Schiavon, Franca Anglani, Susanna Negrisolo, Alessandra Zanetti, Francesca D’Avanzo, Rosella Tomanin, Georgine Faulkner, Alessandro Vezzi and Giorgio Valle

    BMC Bioinformatics 2017 18:225

    Published on: 28 April 2017

  2. Database

    MYCbase: a database of functional sites and biochemical properties of Myc in both normal and cancer cells

    Myc is an essential gene having multiple functions such as in cell growth, differentiation, apoptosis, genomic stability, angiogenesis, and disease biology. A large number of researchers dedicated to Myc biolo...

    Debangana Chakravorty, Tanmoy Jana, Sukhen Das Mandal, Anuradha Seth, Anubrata Bhattacharya and Sudipto Saha

    BMC Bioinformatics 2017 18:224

    Published on: 28 April 2017

  3. Methodology Article

    De novo assembly of highly polymorphic metagenomic data using in situ generated reference sequences and a novel BLAST-based assembly pipeline

    The accuracy of metagenomic assembly is usually compromised by high levels of polymorphism due to divergent reads from the same genomic region recognized as different loci when sequenced and assembled together...

    You-Yu Lin, Chia-Hung Hsieh, Jiun-Hong Chen, Xuemei Lu, Jia-Horng Kao, Pei-Jer Chen, Ding-Shinn Chen and Hurng-Yi Wang

    BMC Bioinformatics 2017 18:223

    Published on: 26 April 2017

  4. Software

    An auditory display tool for DNA sequence analysis

    DNA Sonification refers to the use of an auditory display to convey the information content of DNA sequence data. Six sonification algorithms are presented that each produce an auditory display. These algorith...

    Mark D. Temple

    BMC Bioinformatics 2017 18:221

    Published on: 24 April 2017

  5. Research Article

    AnkPlex: algorithmic structure for refinement of near-native ankyrin-protein docking

    Computational analysis of protein-protein interaction provided the crucial information to increase the binding affinity without a change in basic conformation. Several docking programs were used to predict the...

    Tanchanok Wisitponchai, Watshara Shoombuatong, Vannajan Sanghiran Lee, Kuntida Kitidee and Chatchai Tayapiwatana

    BMC Bioinformatics 2017 18:220

    Published on: 19 April 2017

  6. Research Article

    On the association analysis of CNV data: a fast and robust family-based association method

    Copy number variation (CNV) is known to play an important role in the genetics of complex diseases and several methods have been proposed to detect association of CNV with phenotypes of interest. Statistical m...

    Meiling Liu, Sanghoon Moon, Longfei Wang, Sulgi Kim, Yeon-Jung Kim, Mi Yeong Hwang, Young Jin Kim, Robert C. Elston, Bong-Jo Kim and Sungho Won

    BMC Bioinformatics 2017 18:217

    Published on: 18 April 2017

  7. Research article

    Comparison of different cell type correction methods for genome-scale epigenetics studies

    Whole blood is frequently utilized in genome-wide association studies of DNA methylation patterns in relation to environmental exposures or clinical outcomes. These associations can be confounded by cellular h...

    Akhilesh Kaushal, Hongmei Zhang, Wilfried J. J. Karmaus, Meredith Ray, Mylin A. Torres, Alicia K. Smith and Shu-Li Wang

    BMC Bioinformatics 2017 18:216

    Published on: 14 April 2017

  8. Software

    Segmentum: a tool for copy number analysis of cancer genomes

    Somatic alterations, including loss of heterozygosity, can affect the expression of oncogenes and tumor suppressor genes. Whole genome sequencing enables detailed characterization of such aberrations. However,...

    Ebrahim Afyounian, Matti Annala and Matti Nykter

    BMC Bioinformatics 2017 18:215

    Published on: 13 April 2017

  9. Research Article

    Meta-analysis approach as a gene selection method in class prediction: does it improve model performance? A case study in acute myeloid leukemia

    Aggregating gene expression data across experiments via meta-analysis is expected to increase the precision of the effect estimates and to increase the statistical power to detect a certain fold change. This s...

    Putri W. Novianti, Victor L. Jong, Kit C. B. Roes and Marinus J. C. Eijkemans

    BMC Bioinformatics 2017 18:210

    Published on: 11 April 2017

  10. Research Article

    Multi-scale structural community organisation of the human genome

    Structural interaction frequency matrices between all genome loci are now experimentally achievable thanks to high-throughput chromosome conformation capture technologies. This ensues a new methodological chal...

    Rasha E. Boulos, Nicolas Tremblay, Alain Arneodo, Pierre Borgnat and Benjamin Audit

    BMC Bioinformatics 2017 18:209

    Published on: 11 April 2017

  11. Research Article

    A machine learning approach for viral genome classification

    Advances in cloning and sequencing technology are yielding a massive number of viral genomes. The classification and annotation of these genomes constitute important assets in the discovery of genomic variabil...

    Mohamed Amine Remita, Ahmed Halioui, Abou Abdallah Malick Diouara, Bruno Daigle, Golrokh Kiani and Abdoulaye Baniré Diallo

    BMC Bioinformatics 2017 18:208

    Published on: 11 April 2017

  12. Database

    DisBind: A database of classified functional binding sites in disordered and structured regions of intrinsically disordered proteins

    Intrinsically unstructured or disordered proteins function via interacting with other molecules. Annotation of these binding sites is the first step for mapping functional impact of genetic variants in coding ...

    Jia-Feng Yu, Xiang-Hua Dou, Yu-Jie Sha, Chun-Ling Wang, Hong-Bo Wang, Yi-Ting Chen, Feng Zhang, Yaoqi Zhou and Ji-Hua Wang

    BMC Bioinformatics 2017 18:206

    Published on: 5 April 2017

  13. Software

    HALC: High throughput algorithm for long read error correction

    The third generation PacBio SMRT long reads can effectively address the read length issue of the second generation sequencing technology, but contain approximately 15% sequencing errors. Several error correcti...

    Ergude Bao and Lingxiao Lan

    BMC Bioinformatics 2017 18:204

    Published on: 5 April 2017

  14. Software

    The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism

    Modeling of microbial metabolism is a topic of growing importance in biotechnology. Mathematical modeling helps provide a mechanistic understanding for the studied process, separating the main drivers from the...

    Garrett W. Birkel, Amit Ghosh, Vinay S. Kumar, Daniel Weaver, David Ando, Tyler W. H. Backman, Adam P. Arkin, Jay D. Keasling and Héctor García Martín

    BMC Bioinformatics 2017 18:205

    Published on: 5 April 2017

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