CoMI: consensus mutual information for tissue-specific gene signatures.

Background: The gene signatures have been considered as a promising early diagnosis and prognostic analysis to identify disease subtypes and to determine subsequent treatments. Tissue-specific gene signatures of a specific disease are an emergency requirement for precision medicine to improve the accuracy and reduce the side effects. Currently, many approaches have been proposed for identifying gene signatures for diagnosis and prognostic.

Whole-Blood 3-Gene Signature as a Decision Aid for Rifapentine-based Tuberculosis Preventive Therapy.

Background: Systemic drug reaction (SDR) is a major safety concern with weekly rifapentine plus isoniazid for 12 doses (3HP) for latent tuberculosis infection (LTBI). Identifying SDR predictors and at-risk participants before treatment can improve cost-effectiveness of the LTBI program.

Methods: We prospectively recruited 187 cases receiving 3HP (44 SDRs and 143 non-SDRs).

Transcriptomic and Proteomic Profiling of Human Mesenchymal Stem Cell Derived from Umbilical Cord in the Study of Preterm Birth.

Objective: Mesenchymal stem cells (MSCs) hold great therapeutic potential in morbidities associated with preterm birth. However, the molecular expressions of MSCs in preterm birth infants are not systematically evaluated. In this study, the dual-omics analyses of umbilical-cord (UC)-derived MSCs to identify the dysregulated cellular functions are presented.

A homologous mapping method for three-dimensional reconstruction of protein networks reveals disease-associated mutations.

Background: One of the crucial steps toward understanding the associations among molecular interactions, pathways, and diseases in a cell is to investigate detailed atomic protein-protein interactions (PPIs) in the structural interactome. Despite the availability of large-scale methods for analyzing PPI networks, these methods often focused on PPI networks using genome-scale data and/or known experimental PPIs. However, these methods are unable to provide structurally resolved interaction residues and their conservations in PPI networks.

A genome-wide comparison of mesenchymal stem cells derived from human placenta and umbilical cord.

Objective: The human umbilical cord and placenta have been considered as attractive alternative sources for noninvasive isolation of human mesenchymal stem cells (hMSCs). Different sources of MSC may have individual differentiation potential and phenotype. In this study, we compared the genome-wide expression data of umbilical cord and placenta derived hMSCs to identify specific differential expression genes (DEGs) and corresponding functions.

Module organization and variance in protein-protein interaction networks.

A module is a group of closely related proteins that act in concert to perform specific biological functions through protein-protein interactions (PPIs) that occur in time and space. However, the underlying module organization and variance remain unclear. In this study, we collected module templates to infer respective module families, including 58,041 homologous modules in 1,678 species, and PPI families using searches of complete genomic database.

Reconstructing genome-wide protein-protein interaction networks using multiple strategies with homologous mapping.

Background: One of the crucial steps toward understanding the biological functions of a cellular system is to investigate protein-protein interaction (PPI) networks. As an increasing number of reliable PPIs become available, there is a growing need for discovering PPIs to reconstruct PPI networks of interesting organisms. Some interolog-based methods and homologous PPI families have been proposed for predicting PPIs from the known PPIs of source organisms.

Genome-wide structural modelling of TCR-pMHC interactions.

Background: The adaptive immune response is antigen-specific and triggered by pathogen recognition through T cells. Although the interactions and mechanisms of TCR-peptide-MHC (TCR-pMHC) have been studied over three decades, the biological basis for these processes remains controversial. As an increasing number of high-throughput binding epitopes and available TCR-pMHC complex structures, a fast genome-wide structural modelling of TCR-pMHC interactions is an emergent task for understanding immune interactions and developing peptide vaccines.

Template-based scoring functions for visualising biological insights of H-2Kb-peptide-TCR complexes.

Major Histocompatibility Complex (MHC), peptide and T-Cell Receptor (TCR) play an essential role of adaptive immune responses. Many prediction servers are available for identification of peptides that bind to MHC class I molecules but often lack detailed interacting residues for analysing MHC-peptide-TCR interaction mechanisms. This study considers both the interface similarity and the interacting force for identifying binding models.

Inferring homologous protein-protein interactions through pair position specific scoring matrix.

Background: The protein-protein interaction (PPI) is one of the most important features to understand biological processes. For a PPI, the physical domain-domain interaction (DDI) plays the key role for biology functions. In the post-genomic era, to rapidly identify homologous PPIs for analyzing the contact residue pairs of their interfaces within DDIs on a genomic scale is essential to determine PPI networks and the PPI interface evolution across multiple species.

MoNetFamily: a web server to infer homologous modules and module-module interaction networks in vertebrates.

A module is a fundamental unit forming with highly connected proteins and performs a certain kind of biological functions. Modules and module-module interaction (MMI) network are essential for understanding cellular processes and functions. The MoNetFamily web server can identify the modules, homologous modules (called module family) and MMI networks across multiple species for the query protein(s).

Steric recognition of T-cell receptor contact residues is required to map mutant epitopes by immunoinformatical programmes.

MHC class I-restricted CD8 T-lymphocyte epitopes comprise anchor motifs, T-cell receptor (TCR) contact residues and the peptide backbone. Serial variant epitopes with substitution of amino acids at either anchor motifs or TCR contact residues have been synthesized for specific interferon-γ responses to clarify the TCR recognition mechanism as well as to assess the epitope prediction capacity of immunoinformatical programmes. CD8 T lymphocytes recognise the steric configuration of functional groups at the TCR contact side chain with a parallel observation that peptide backbones of various epitopes adapt to the conserved conformation upon binding to the same MHC class I molecule.

PAComplex: a web server to infer peptide antigen families and binding models from TCR-pMHC complexes.

One of the most adaptive immune responses is triggered by specific T-cell receptors (TCR) binding to peptide-major histocompatibility complexes (pMHC). Despite the availability of many prediction servers to identify peptides binding to MHC, these servers are often lacking in peptide-TCR interactions and detailed atomic interacting models. PAComplex is the first web server investigating both pMHC and peptide-TCR interfaces to infer peptide antigens and homologous peptide antigens of a query.

3D-interologs: an evolution database of physical protein- protein interactions across multiple genomes.

Background: Comprehensive exploration of protein-protein interactions is a challenging route to understand biological processes. For efficiently enlarging protein interactions annotated with residue-based binding models, we proposed a new concept "3D-domain interolog mapping" with a scoring system to explore all possible protein pairs between the two homolog families, derived from a known 3D-structure dimmer (template), across multiple species. Each family consists of homologous proteins which have interacting domains of the template for studying domain interface evolution of two interacting homolog families.

PCFamily: a web server for searching homologous protein complexes.

The proteins in a cell often assemble into complexes to carry out their functions and play an essential role of biological processes. The PCFamily server identifies template-based homologous protein complexes [called protein complex family (PCF)] and infers functional modules of the query proteins. This server first finds homologous structure complexes of the query using BLASTP to search the structural template database (11,263 complexes).

PPISearch: a web server for searching homologous protein-protein interactions across multiple species.

As an increasing number of reliable protein-protein interactions (PPIs) become available and high-throughput experimental methods provide systematic identification of PPIs, there is a growing need for fast and accurate methods for discovering homologous PPIs of a newly determined PPI. PPISearch is a web server that rapidly identifies homologous PPIs (called PPI family) and infers transferability of interacting domains and functions of a query protein pair. This server first identifies two homologous families of the query, respectively, by using BLASTP to scan an annotated PPIs database (290 137 PPIs in 576 species), which is a collection of five public databases.

3D-partner: a web server to infer interacting partners and binding models.

The 3D-partner is a web tool to predict interacting partners and binding models of a query protein sequence through structure complexes and a new scoring function. 3D-partner first utilizes IMPALA to identify homologous structures (templates) of a query from a heterodimer profile library. The interacting-partner sequence profiles of these templates are then used to search interacting candidates of the query from protein sequence databases (e.