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GOTA: GO term annotation of biomedical literature
Background Functional annotation of genes and gene products is a major challenge in the post-genomic era. Nowadays, gene function curation is largely based on manual assignment... -
Significance evaluation in factor graphs
Background Factor graphs provide a flexible and general framework for specifying probability distributions. They can capture a range of popular and recent models for analysis of... -
Visualizing histopathologic deep learning classification and anomaly detectio...
Background There is growing interest in utilizing artificial intelligence, and particularly deep learning, for computer vision in histopathology. While accumulating studies... -
Combining location-and-scale batch effect adjustment with data cleaning by la...
Background In the context of high-throughput molecular data analysis it is common that the observations included in a dataset form distinct groups; for example, measured at... -
Alternative empirical Bayes models for adjusting for batch effects in genomic...
Background Combining genomic data sets from multiple studies is advantageous to increase statistical power in studies where logistical considerations restrict sample size or... -
Parametric bootstrapping for biological sequence motifs
Background Biological sequence motifs drive the specific interactions of proteins and nucleic acids. Accordingly, the effective computational discovery and analysis of such... -
MetICA: independent component analysis for high-resolution mass-spectrometry ...
Background Interpreting non-targeted metabolomics data remains a challenging task. Signals from non-targeted metabolomics studies stem from a combination of biological causes,... -
An individualized predictor of health and disease using paired reference and ...
Background Consider the problem of designing a panel of complex biomarkers to predict a patient’s health or disease state when one can pair his or her current test sample,... -
NoLogo: a new statistical model highlights the diversity and suggests new cla...
Background Crm1-dependent Nuclear Export Signals (NESs) are clusters of alternating hydrophobic and non-hydrophobic amino acid residues between 10 to 15 amino acids in length.... -
Evaluation of logistic regression models and effect of covariates for case–co...
Background Next generation sequencing provides a count of RNA molecules in the form of short reads, yielding discrete, often highly non-normally distributed gene expression... -
Explaining the geographic spread of emerging epidemics: a framework for compa...
Phylogenetic analysis is now an important tool in the study of viral outbreaks. It can reconstruct epidemic history when surveillance epidemiology data are sparse, and can... -
Single sample scoring of molecular phenotypes.
Background Gene set scoring provides a useful approach for quantifying concordance between sample transcriptomes and selected molecular signatures. Most methods use information... -
A Bayesian active learning strategy for sequential experimental design in sys...
Background Dynamical models used in systems biology involve unknown kinetic parameters. Setting these parameters is a bottleneck in many modeling projects. This motivates the... -
McTwo: a two-step feature selection algorithm based on maximal information co...
Background High-throughput bio-OMIC technologies are producing high-dimension data from bio-samples at an ever increasing rate, whereas the training sample number in a... -
A random effects model for the identification of differential splicing (REIDS...
Background Alternative gene splicing is a common phenomenon in which a single gene gives rise to multiple transcript isoforms. The process is strictly guided and involves a... -
SW1PerS: Sliding windows and 1-persistence scoring; discovering periodicity i...
Background Identifying periodically expressed genes across different processes (e.g. the cell and metabolic cycles, circadian rhythms, etc) is a central problem in computational...
