Methods for enhancing the reproducibility of biomedical research findings using electronic health records
The ability of external investigators to reproduce published scientific findings is critical for the evaluation and validation of biomedical research by the wider community. However, a substantial proportion o... (Source: BioData Mining)
Source: BioData Mining - September 11, 2017 Category: Bioinformatics Authors: Spiros Denaxas, Kenan Direk, Arturo Gonzalez-Izquierdo, Maria Pikoula, Aylin Cakiroglu, Jason Moore, Harry Hemingway and Liam Smeeth Tags: Review Source Type: research
RNA-sequence data normalization through in silico prediction of reference genes: the bacterial response to DNA damage as case study
Measuring how gene expression changes in the course of an experiment assesses how an organism responds on a molecular level. Sequencing of RNA molecules, and their subsequent quantification, aims to assess glo... (Source: BioData Mining)
Source: BioData Mining - September 5, 2017 Category: Bioinformatics Authors: Bork A. Berghoff, Torgny Karlsson, Thomas K ällman, E. Gerhart H. Wagner and Manfred G. Grabherr Tags: Research Source Type: research
Identifying time-delayed gene regulatory networks via an evolvable hierarchical recurrent neural network
The modeling of genetic interactions within a cell is crucial for a basic understanding of physiology and for applied areas such as drug design. Interactions in gene regulatory networks (GRNs) include effects ... (Source: BioData Mining)
Source: BioData Mining - August 3, 2017 Category: Bioinformatics Authors: Mina Moradi Kordmahalleh, Mohammad Gorji Sefidmazgi, Scott H. Harrison and Abdollah Homaifar Tags: Methodology Source Type: research
Genetically improved BarraCUDA
BarraCUDA is an open source C program which uses the BWA algorithm in parallel with nVidia CUDA to align short next generation DNA sequences against a reference genome. Recently its source code was optimised u... (Source: BioData Mining)
Source: BioData Mining - August 2, 2017 Category: Bioinformatics Authors: W. B. Langdon and Brian Yee Hong Lam Tags: Short Report Source Type: research
nRC: non-coding RNA Classifier based on structural features
Non-coding RNA (ncRNA) are small non-coding sequences involved in gene expression regulation of many biological processes and diseases. The recent discovery of a large set of different ncRNAs with biologically... (Source: BioData Mining)
Source: BioData Mining - August 1, 2017 Category: Bioinformatics Authors: Antonino Fiannaca, Massimo La Rosa, Laura La Paglia, Riccardo Rizzo and Alfonso Urso Tags: Research Source Type: research
Evolutionary computation: the next major transition of artificial intelligence?
(Source: BioData Mining)
Source: BioData Mining - July 29, 2017 Category: Bioinformatics Authors: Moshe Sipper, Randal S. Olson and Jason H. Moore Tags: Editorial Source Type: research
Discovery and replication of SNP-SNP interactions for quantitative lipid traits in over 60,000 individuals
The genetic etiology of human lipid quantitative traits is not fully elucidated, and interactions between variants may play a role. We performed a gene-centric interaction study for four different lipid traits... (Source: BioData Mining)
Source: BioData Mining - July 24, 2017 Category: Bioinformatics Authors: Emily R. Holzinger, Shefali S. Verma, Carrie B. Moore, Molly Hall, Rishika De, Diane Gilbert-Diamond, Matthew B. Lanktree, Nathan Pankratz, Antoinette Amuzu, Amber Burt, Caroline Dale, Scott Dudek, Clement E. Furlong, Tom R. Gaunt, Daniel Seung Kim, Helen Source Type: research
The Dark Proteome Database
Recently we surveyed the dark-proteome, i.e., regions of proteins never observed by experimental structure determination and inaccessible to homology modelling. Surprisingly, we found that most of the dark pro... (Source: BioData Mining)
Source: BioData Mining - July 20, 2017 Category: Bioinformatics Authors: Nelson Perdig ão, Agostinho C. Rosa and Seán I. O’Donoghue Source Type: research
Arete – candidate gene prioritization using biological network topology with additional evidence types
Refinement of candidate gene lists to select the most promising candidates for further experimental verification remains an essential step between high-throughput exploratory analysis and the discovery of spec... (Source: BioData Mining)
Source: BioData Mining - July 6, 2017 Category: Bioinformatics Authors: Artem Lysenko, Keith Anthony Boroevich and Tatsuhiko Tsunoda Source Type: research
epiACO - a method for identifying epistasis based on ant Colony optimization algorithm
Identifying epistasis or epistatic interactions, which refer to nonlinear interaction effects of single nucleotide polymorphisms (SNPs), is essential to understand disease susceptibility and to detect genetic ... (Source: BioData Mining)
Source: BioData Mining - July 6, 2017 Category: Bioinformatics Authors: Yingxia Sun, Junliang Shang, Jin-Xing Liu, Shengjun Li and Chun-Hou Zheng Source Type: research
EFS: an ensemble feature selection tool implemented as R-package and web-application
Feature selection methods aim at identifying a subset of features that improve the prediction performance of subsequent classification models and thereby also simplify their interpretability. Preceding studies... (Source: BioData Mining)
Source: BioData Mining - June 27, 2017 Category: Bioinformatics Authors: Ursula Neumann, Nikita Genze and Dominik Heider Source Type: research
Computational dynamic approaches for temporal omics data with applications to systems medicine
Modeling and predicting biological dynamic systems and simultaneously estimating the kinetic structural and functional parameters are extremely important in systems and computational biology. This is key for u... (Source: BioData Mining)
Source: BioData Mining - June 17, 2017 Category: Bioinformatics Authors: Yulan Liang and Arpad Kelemen Source Type: research
Grid-based stochastic search for hierarchical gene-gene interactions in population-based genetic studies of common human diseases
Large-scale genetic studies of common human diseases have focused almost exclusively on the independent main effects of single-nucleotide polymorphisms (SNPs) on disease susceptibility. These studies have had ... (Source: BioData Mining)
Source: BioData Mining - May 30, 2017 Category: Bioinformatics Authors: Jason H. Moore, Peter C. Andrews, Randal S. Olson, Sarah E. Carlson, Curt R. Larock, Mario J. Bulhoes, James P. O ’Connor, Ellen M. Greytak and Steven L. Armentrout Source Type: research
Gene Set Enrichment Analyses: lessons learned from the heart failure phenotype
Genetic studies for complex diseases have predominantly discovered main effects at individual loci, but have not focused on genomic and environmental contexts important for a phenotype. Gene Set Enrichment Ana... (Source: BioData Mining)
Source: BioData Mining - May 26, 2017 Category: Bioinformatics Authors: Vinicius Tragante, Johannes M. I. H. Gho, Janine F. Felix, Ramachandran S. Vasan, Nicholas L. Smith, Benjamin F. Voight, Colin Palmer, Pim van der Harst, Jason H. Moore and Folkert W. Asselbergs Source Type: research
Vinasse fertirrigation alters soil resistome dynamics: an analysis based on metagenomic profiles
Every year around 300 Gl of vinasse, a by-product of ethanol distillation in sugarcane mills, are flushed into more than 9 Mha of sugarcane cropland in Brazil. This practice links fermentation waste management... (Source: BioData Mining)
Source: BioData Mining - May 23, 2017 Category: Bioinformatics Authors: Lucas P. P. Braga, Rafael F. Alves, Marina T. F. Dellias, Acacio A. Navarrete, Thiago O. Basso and Siu M. Tsai Source Type: research
