mlDEEPre: Multi-Functional Enzyme Function Prediction With Hierarchical Multi-Label Deep Learning

As a great challenge in bioinformatics, enzyme function prediction is a significant step toward designing novel enzymes and diagnosing enzyme-related diseases. Existing studies mainly focus on the mono-functional enzyme function prediction. However, the number of multi-functional enzymes is growing rapidly, which requires novel computational methods to be developed. In this paper, following our previous work, DEEPre, which uses deep learning to annotate mono-functional enzyme's function, we propose a novel method, mlDEEPre, which is designed specifically for predicting the functionalities of multi-functional enzymes. By adopting a novel loss function, associated with the relationship between different labels, and a self-adapted label assigning threshold, mlDEEPre can accurately and efficiently perform multi-functional enzyme prediction. Extensive experiments also show that mlDEEPre can outperform the other methods in predicting whether an enzyme is a mono-functional or a multi-functional enzyme (mono-functional vs. multi-functional), as well as the main class prediction across different criteria. Furthermore, due to the flexibility of mlDEEPre and DEEPre, mlDEEPre can be incorporated into DEEPre seamlessly, which enables the updated DEEPre to handle both mono-functional and multi-functional predictions without human intervention

Up-to-date catalogues of yeast protein complexes

Gold standard datasets on protein complexes are key to inferring and validating protein–protein interactions. Despite much progress in characterizing protein complexes in the yeast Saccharomyces cerevisiae, numerous researchers still use as reference the manually curated complexes catalogued by the Munich Information Center of Protein Sequences database. Although this catalogue has served the community extremely well, it no longer reflects the current state of knowledge. Here, we report two catalogues of yeast protein complexes as results of systematic curation efforts. The first one, denoted as CYC2008, is a comprehensive catalogue of 408 manually curated heteromeric protein complexes reliably backed by small-scale experiments reported in the current literature. This catalogue represents an up-to-date reference set for biologists interested in discovering protein interactions and protein complexes. The second catalogue, denoted as YHTP2008, comprises 400 high-throughput complexes annotated with current literature evidence. Among them, 262 correspond, at least partially, to CYC2008 complexes. Evidence for interacting subunits is collected for 68 complexes that have only partial or no overlap with CYC2008 complexes, whereas no literature evidence was found for 100 complexes. Some of these partially supported and as yet unsupported complexes may be interesting candidates for experimental follow up. Both catalogues are freely available at: http://wodaklab.org/cyc2008/

Flexible Jobs Make Parents Happier:Evidence from Australia

Recent studies have found that self-reported life satisfaction drops during the transition into parenthood. This decline is often attributed to work-family conflict. This study investigates whether different forms of flexible employment can alleviate this drop in parental life satisfaction during this period. A fixed-effects analysis in an event study framework using Australian household survey data (HILDA) delivers convincing evidence that working flexibly indeed alleviates the drop in subjective well-being, suggesting that it relieves the stress related to work-family conflict. Moreover, we find substantial gender heterogeneity in the effects of different types of flexible employment on mothers' and fathers' life satisfaction. Mothers with short part-time jobs (0-20 hours per week) exhibit greater life satisfaction than mothers who work full-time, especially when their children are younger than four. Among fathers, self-scheduling and home-based work yield a significant increase in perceived happiness compared to fixed employment terms. This is especially true for fathers of one- and two-years-olds. These results are consistent with a typical intra-household time allocation of parents in Australia