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CASTIN: a system for comprehensive analysis of cancer-stromal interactome
Background Cancer microenvironment plays a vital role in cancer development and progression, and cancer-stromal interactions have been recognized as important targets for cancer... -
Qualitative dynamics semantics for SBGN process description
Background Qualitative dynamics semantics provide a coarse-grain modeling of networks dynamics by abstracting away kinetic parameters. They allow to capture general features of... -
A multi-animal tracker for studying complex behaviors
Background Animals exhibit astonishingly complex behaviors. Studying the subtle features of these behaviors requires quantitative, high-throughput, and accurate systems that can... -
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... -
Development of a central nervous system axonal myelination assay for high thr...
Background Regeneration of new myelin is impaired in persistent multiple sclerosis (MS) lesions, leaving neurons unable to function properly and subject to further degeneration.... -
PHENOS: a high-throughput and flexible tool for microorganism growth phenotyp...
ABSTRACTBACKGROUNDMicrobial arrays, with a large number of different strains on a single plate printed with robotic precision, underpin an increasing number of genetic and... -
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... -
Risk-conscious correction of batch effects: maximising information extraction...
Background Batch effects are a persistent and pervasive form of measurement noise which undermine the scientific utility of high-throughput genomic datasets. At their most... -
Mosaic autosomal aneuploidies are detectable from single-cell RNAseq data.
Background Aneuploidies are copy number variants that affect entire chromosomes. They are seen commonly in cancer, embryonic stem cells, human embryos, and in various trisomic... -
High-sensitivity HLA typing by Saturated Tiling Capture Sequencing (STC-Seq)
Background Highly polymorphic human leukocyte antigen (HLA) genes are responsible for fine-tuning the adaptive immune system. High-resolution HLA typing is important for the... -
A powerful score-based test statistic for detecting gene-gene co-association
Background The genetic variants identified by Genome-wide association study (GWAS) can only account for a small proportion of the total heritability for complex disease. The... -
A Support Vector Machine based method to distinguish long non-coding RNAs fro...
Background In recent years, a rapidly increasing number of RNA transcripts has been generated by thousands of sequencing projects around the world, creating enormous volumes of... -
Patterns of cross-contamination in a multispecies population genomic project:...
Background Contamination is a well-known but often neglected problem in molecular biology. Here, we investigated the prevalence of cross-contamination among 446 samples from 116... -
Tilting the Lasso by Knowledge-Based Post-Processing
Background It is useful to incorporate biological knowledge on the role of genetic determinants in predicting an outcome. It is, however, not always feasible to fully elicit... -
Fast dimension reduction and integrative clustering of multi-omics data using...
Background One major goal of large-scale cancer omics study is to identify molecular subtypes for more accurate cancer diagnoses and treatments. To deal with high-dimensional... -
A method for culturing Gram-negative skin microbiota
Background Commensal Gram-negative (CGN) microbiota have been identified on human skin by DNA sequencing; however, methods to reliably culture viable Gram-negative skin... -
Quality filtering of Illumina index reads mitigates sample cross-talk
Background Multiplexing multiple samples during Illumina sequencing is a common practice and is rapidly growing in importance as the throughput of the platform increases.... -
Benefits And Limitations Of Three-Dimensional Printing Technology For Ecologi...
BACKGROUND: Ecological research often involves sampling and manipulating non-model organisms that reside in heterogeneous environments. As such, ecologists often adapt... -
"EventPointer: an effective identification of alternative splicing events usi...
Background Alternative splicing (AS) is a major source of variability in the transcriptome of eukaryotes. There is an increasing interest in its role in different pathologies.... -
Nebulized heparin for patients under mechanical ventilation: an individual pa...
Pulmonary coagulopathy is a characteristic feature of lung injury including ventilator-induced lung injury. The aim of this individual patient data meta-analysis is to assess...
