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Article
Open AccessHuman Bronchial Epithelial Cell Transcriptome Changes in Response to Serum from Patients with Different Status of Inflammation
To investigate the transcriptome of human bronchial epithelial cells (HBEC) in response to serum from patients with different degrees of inflammation.
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Article
Open AccessA comparison of curated gene sets versus transcriptomics-derived gene signatures for detecting pathway activation in immune cells
Despite the significant contribution of transcriptomics to the fields of biological and biomedical research, interpreting long lists of significantly differentially expressed genes remains a challenging step i...
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Article
Open AccessMolecular profiling of rheumatoid arthritis patients reveals an association between innate and adaptive cell populations and response to anti-tumor necrosis factor
The goal of this study is to use comprehensive molecular profiling to characterize clinical response to anti-TNF therapy in a real-world setting and identify reproducible markers differentiating good responder...
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Article
Correction: Corrigendum: Comparative analysis of RNA sequencing methods for degraded or low-input samples
Nat. Methods 10, 623–629 (2013); published online 19 May 2013; corrected after 2 December 2013 In the version of this article initially published, in the Online Methods “RNase H libraries” section, the sentenc...
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Article
Comparative analysis of RNA sequencing methods for degraded or low-input samples
This comparison of five RNA-seq library preparation methods highlights metrics for assessing the suitability of the methods for samples with low amounts of RNA and/or those with low-quality RNA.
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Article
Open AccessPB1-F2 Finder: scanning influenza sequences for PB1-F2 encoding RNA segments
PB1-F2 is a major virulence factor of influenza A. This protein is a product of an alternative reading frame in the PB1-encoding RNA segment 2. Its presence of is dictated by the presence or absence of prematu...
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Protocol
Data Processing and Analysis for Protein Microarrays
Protein microarrays are a high-throughput technology capable of generating large quantities of proteomics data. They can be used for general research or for clinical diagnostics. Bioinformatics and statistical...
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Protocol
Database Resources for Proteomics-Based Analysis of Cancer
Biological/bioinformatics databases are essential for medical and biological studies. They integrate and organize biologically related information in a structured format and provide researchers with easy acces...
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Article
Amino acid 95 causes strong alteration of peptide position PΩ in HLA-B*41 variants
There have been several attempts over the years to identify positions in the peptide-binding region (PBR) of human leukocyte antigens (HLA) that influence the specificity of bound amino acids (AAs) at each pos...
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Protocol
Implementing the Modular MHC Model for Predicting Peptide Binding
The challenge of predicting which peptide sequences bind to which major histocompatibility complex (MHC) molecules has been met with various computational techniques. Scoring matrices, hidden Markov models, an...
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Protocol
HistoCheck
The HistoCheck webtool provides clinicians and researchers with a way of visualizing and understanding the structural differences among related major histocompatibility complex (MHC) molecules. In the clinical...
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Article
A modular concept of HLA for comprehensive peptide binding prediction
A variety of algorithms have been successful in predicting human leukocyte antigen (HLA)-peptide binding for HLA variants for which plentiful experimental binding data exist. Although predicting binding for on...
