In my view, it’s time to slow down and or even “pause” AI development. The tech has progressed exponentially in just the last year, and shows no sign of slowing down or reaching a plateau. As a result, it is outpacing our ability to understand, align, and adapt to it. I signed the Future of Life Institute letter six months ago. This editorial in the Hill.com makes the case: Six months later, our call to slow AI development is more crucial than ever Right now, tens of thousands of brand-new cutting-edge chips are humming away in massive river-cooled data centers, growing the next generation ..read more

Introduction Genomics is the study of an organism’s complete set of genetic material, including its DNA sequence, genes, and regulation of gene expression. Other “omics” techniques, such as proteomics and metabolomics, focus on the study of proteins and metabolites, respectively. By analyzing these different types of data together, researchers can generate new insights into the inner workings of an organism and how it responds to its environment. For example, by combining genomics data with proteomics and metabolomics data, researchers can gain a more complete understanding of an organism’s ge ..read more

Spatial single cell RNA-seq data are essentially regular single-cell RNA-seq data that have spatial coordinates associated through localization on a special capture slide. I had previously used so-called “perturbation” analysis successfully with 10X single-cell data and I wanted to apply the technique to spatial single cell to understand how a treatment affects the spatially-resolved clusters. Here, I want to briefly describe the steps I went through to perform ‘augur’ perturbation analysis of 10X Visium Spatial single cell RNA-seq data. augur works as follows: Augur is an R package to priori ..read more

From our IIHG Bioinformatics Workshop series: The post Video tutorial: Bioconductor and NCBI GEO data access appeared first on Michael's Bioinformatics Blog ..read more

The post New video: Beyond the DE gene list appeared first on Michael's Bioinformatics Blog ..read more

My colleague, Diana Kolbe, just created this great presentation on ACMG variant classification for our Institute. I have published it to our YouTube channel so more people can learn this complex material. The post New video tutorial on ACMG variant classification appeared first on Michael's Bioinformatics Blog ..read more

A few best practices for ATAC-seq assays are suggested as follows: Digest away background DNA (medium/dead cells) using DNase I22 Use fresh/cyropreserved cells/tissues to isolate nuclei7,9 Reduce mitochondrial/chloroplast DNA contamination as much as possible by using the Omni-ATAC protocol or other methods22–25 Optimize the ratio of the amount of Tn5 enzyme to the number of nuclei Optimize the number of PCR cycles19 Perform Paired-end (PE) sequencing, e.g., 2 x 50 to 100 bp Sequence > 50 M PE reads (~200 M for footprinting analysis)7 A few best practices for ATAC-seq data analysis are s ..read more

Machine-learning (ML) and neural networks are transforming data science and life sciences. They are being applied to deal with the challenges of making sense of piles of ‘big data’ that are growing bigger all the time. Now, these same tools are now being applied to searching the gigantic scientific literature databases (PubMed contains > 30M citations) in order to bring more relevant results to researchers. A simple PubMed search proceeds by matching terms like the following: …if you enter child rearing in the search box, PubMed will translate this search to: “child rearing ..read more

I’m thrilled to report that I’ve been promoted to the position of Director of our bioinformatics group here at the University of Iowa. We are within the Iowa Institute of Human Genetics (IIHG) and we support clinical activities in the institute, but also a wide array of research collaborations across the University. I have a lot of goals and ideas for the group and look forward to working to implement those going forward. I may not be able to write posts here as often, but I’ll try to keep up with it. We also have a new twitter account: @iowabioinfo. Please follow us there. The pos ..read more

I just returned from another great experience at Great Lakes Bio 2019 (#GLBIO2019), a regional meeting of the International Society of Computational Biologists (ISCB). Below I’ll summarize briefly a few of the talks that I found most interesting to me personally (there were several parallel tracks, so I did not attend all talks). Docker workshop taught by Sara Stevens On Sunday of the conference, I attended a 3-hour workshop introducing Docker technology held in the beautiful and very modern Wisconsin Institutes of Discovery building. The course was taught by Sara Stevens, an expert in ..read more