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Motivation Dimensionality reduction is a key step in the analysis of single-cell RNA-sequencing data. It produces a low-dimensional embedding for visualization and as a calculation base for downstream analysis. Nonlinear techniques are most suitable to handle the intrinsic complexity of large, heterogeneous single-cell data. However, with no linear relation between gene and embedding coordinate, there is no way to extract the identity of genes driving any cell's position in the low-dimensional embedding, making it difficult to characterize the underlying biological processes. Results In this article, we introduce the concepts of local and global gene relevance to compute an equivalent of principal component analysis loadings for non-linear low-dimensional embeddings. Global gene relevance identifies drivers of the overall embedding, while local gene relevance identifies those of a defined sub-region. We apply our method to single-cell RNA-seq datasets from different experimental protocols and to different low-dimensional embedding techniques. This shows our method's versatility to identify key genes for a variety of biological processes. Availability and implementation To ensure reproducibility and ease of use, our method is released as part of destiny 3.0, a popular R package for building diffusion maps from single-cell transcriptomic data. It is readily available through Bioconductor. Supplementary information Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]

Summary: Diffusion maps are a spectral method for non-linear dimension reduction and have recently been adapted for the visualization of single-cell expression data. Here we present destiny, an efficient R implementation of the diffusion map algorithm. Our package includes a single-cell specific noise model allowing for missing and censored values. In contrast to previous implementations, we further present an efficient nearest-neighbour approximation that allows for the processing of hundreds of thousands of cells and a functionality for projecting new data on existing diffusion maps. We exemplarily apply destiny to a recent time-resolved mass cytometry dataset of cellular reprogramming. Availability and implementation: destiny is an open-source R/Bioconductor package "bioconductor.org/packages/destiny" also available at www.helmholtz-muenchen.de/icb/destiny. A detailed vignette describing functions and workflows is provided with the package. [ABSTRACT FROM AUTHOR]

Shares the experience of a PhD student in biotechnology at the Swiss Federal Institute of Technology in Zurich, Switzerland. Job opportunities in academia and industry; Limitations on future job choices.

Presents a first-person narrative of a scientist making a tough decision to abandon a research project on a biophysical problem. Indication that the problem remained elusive even after two years of research; Observation that a new project means the opportunity to dive into a subject in which more knowledge and experience is available.

Relates the accounts of the author on his supervision job to a student. Admiration of the student on his job as a supervisor; Importance of learning how to supervise; Challenges in training young scientists.

This article presents the views of author on choosing an academic computer after completing doctorate Universities have their attractions but the grey zone between completing a Ph.D. and becoming a full professor makes the author hesitate. The author feels that there are risks in the early stages of an academic career. It might as well take an even bigger chance and try to start a company. If that doesn't work out, he could consider a job with an established biotech or life-sciences firm. The author might not be tied to an academic future but it nevertheless dominates his present.

The article presents information on the experiences of Zhenan Bao, a distinguished member of the technical staff of Bell Laboratories Inc. Before she obtained her first set of business cards, she considered them to be accessories only for business people or perhaps the overly career savvy - certainly not necessary for a graduate student like herself. But she changed her mind when she became involved in the student association during her studies and realized then that cards were an essential way to market the organization.

Describes the working environment in a biotechnology laboratory at the Swiss Federal Institute of Technology in Zurich, Switzerland. Attitude of laboratory staff; Author's views on the importance of a working environment on the performance of employees; Advice on how to determine the working condition in a laboratory.

Describes a more formalized mentoring approach for college students considering their career options. Experience in mentoring with a professional adviser; Role of international student organizations in promoting mentoring.