Peipei Huo

Gene set enrichment (GSE) analysis plays an essential role in extracting biological insight from genome-scale experiments. ORA (overrepresentation analysis), FCS (functional class scoring), and PT (pathway topology) approaches are three generations of GSE methods along the timeline of development. Previous versions of KOBAS provided services based on just the ORA method. Here we presented version 3.0 of KOBAS, which is named KOBAS-i (short for KOBAS intelligent version). It introduced a novel machine learning-based method we published earlier, CGPS, which incorporates seven FCS tools and two PT tools into a single ensemble score and intelligently prioritizes the relevant biological pathways. In addition, KOBAS has expanded the downstream exploratory visualization for selecting and understanding the enriched results. The tool constructs a novel view of cirFunMap, which presents different enriched terms and their correlations in a landscape. Finally, based on the previous version's framework, KOBAS increased the number of supported species from 1327 to 5944. For an easier local run, it also provides a prebuilt Docker image that requires no installation, as a supplementary to the source code version. KOBAS can be freely accessed at http://kobas.cbi.pku.edu.cn, and a mirror site is available at http://bioinfo.org/kobas.

Pharmacotranscriptomics has become a powerful approach for evaluating the therapeutic efficacy of drugs and discovering new drug targets. Recently, studies of traditional Chinese medicine (TCM) have increasingly turned to high-throughput transcriptomic screens for molecular effects of herbs/ingredients. And numerous studies have examined gene targets for herbs/ingredients, and link herbs/ingredients to various modern diseases. However, there is currently no systematic database organizing these data for TCM. Therefore, we built HERB, a high-throughput experiment- and reference-guided database of TCM, with its Chinese name as BenCaoZuJian. We re-analyzed 6164 gene expression profiles from 1037 high-throughput experiments evaluating TCM herbs/ingredients, and generated connections between TCM herbs/ingredients and 2837 modern drugs by mapping the comprehensive pharmacotranscriptomics dataset in HERB to CMap, the largest such dataset for modern drugs. Moreover, we manually curated 1241 gene targets and 494 modern diseases for 473 herbs/ingredients from 1966 references published recently, and cross-referenced this novel information to databases containing such data for drugs. Together with database mining and statistical inference, we linked 12 933 targets and 28 212 diseases to 7263 herbs and 49 258 ingredients and provided six pairwise relationships among them in HERB. In summary, HERB will intensively support the modernization of TCM and guide rational modern drug discovery efforts. And it is accessible through http://herb.ac.cn/.

Bacteria mediated infections may cause various acute or chronic illnesses and antibiotic resistance in pathogenic bacteria has become a serious health problem around the world due to their excessive use or misuse. Replacement of existing antibacterial agents with a novel and efficient alternative is the immediate demand to alleviate this problem. Graphene-based materials have been exquisitely studied because of their remarkable bactericidal activity on a wide range of bacteria. Graphene-based materials provide advantages of easy preparation, renewable, unique catalytic properties, and exceptional physical properties such as a large specific surface area and mechanical strength. However, several queries related to the mechanism of action, significance of size and composition toward bacterial activity, toxicity criteria, and other issues are needed to be addressed. This review summarizes the recent efforts that have been made so far toward the development of graphene-based antibacterial materials to face current challenges to combat against the bacterial targets. This review describes the inherent antibacterial activity of graphene-family and recent advances that have been made on graphene-based antibacterial materials covering the functionalization with silver nanoparticles, other metal ions/oxides nanoparticles, polymers, antibiotics, and enzymes along with their multicomponent functionalization. Furthermore, the review describes the biosafety of the graphene-based antibacterial materials. It is hoped that this review will provide valuable current insight and excite new ideas for the further development of safe and efficient graphene-based antibacterial materials.

Many types of polymer nanofibers have been introduced as artificial extracellular matrices. Their controllable properties, such as wettability, surface charge, transparency, elasticity, porosity and surface to volume proportion, have attracted much attention. Moreover, functionalizing polymers with other bioactive components could enable the engineering of microenvironments to host cells for regenerative medical applications. In the current brief review, we focus on the most recently cited electrospun nanofibrous polymeric scaffolds and divide them into five main categories: natural polymer-natural polymer composite, natural polymer-synthetic polymer composite, synthetic polymer-synthetic polymer composite, crosslinked polymers and reinforced polymers with inorganic materials. Then, we focus on their physiochemical, biological and mechanical features and discussed the capability and efficiency of the nanofibrous scaffolds to function as the extracellular matrix to support cellular function.