Conversations with scientists

Pipelines are basically a series of steps. Algorithms are linked to one another, the output of one algorithm is the input to another. Pipelines can be simple and pretty complex. And maintenance of pipelines also ranges from simple to complex. They can run like a dream, they can get stuck, they can break. To talk about trends in this area, I sat down, virtually that is, with two scientists at DNAnexus: John Ellithorpe who is DNAnexus executive vice president and chief product officer and George Asimenos chief technology officer at DNAnexus.

Part I of the annual meeting of the American Association for Cancer Research—it was all virtual—had 61,000 attendees. Part II is about to start. Here’s a sneak peek about the meeting, its hundreds of talks and thousands of posters. Virtual conferences mean less of a carbon footprint, maybe a broader reach and a chance for attendees who cannot typically travel to AACR to attend virtually. Commenting on AACR II and about virtual conferences more generally: Dr. Elaine Mardis: the current president of the American Association for Cancer Research. She is co-Executive Director of the Institute for Genomic Medicine at Nationwide Children’s Hospital and the Nationwide Foundation Endowed Chair in Genomic Medicine. And Dr. Antoni Ribas, the incoming AACR president. He is at the University of California Los Angeles. He directs the Tumor Immunology Program at the Jonsson Comprehensive Cancer Center and is director of the Parker Institute for Cancer Immunotherapy Center at UCLA.

Part I of the annual meeting of the American Association for Cancer Research was all virtual. There were 61,000 attendees, including some job-hunters. I wonder how this year’s conference that is about to get underway will affect job-hunting. This episode is with scientists talking about their hopes and allergic points as they job-hunt. It’s based on conversations with job-hunters last year and this year. The guests on this episode are: Dr. Antonio Ward of the University of South Alabama, Melat Gebru from Penn State University, Paul Tran from Augusta University and Dr. Sadr-ul Shaheed from the University of Bradford.

Today’s episode is with and about Hui Yang. Dr. Yang is a researcher at the Institute of Neuroscience at Shanghai Institutes for Biological Sciences, which is part of the Chinese Academy of Sciences. He has developed new base-editor variants. Base-editing is a kind of gene-editing. Overall the result led to base-editors with fewer off-targets, high on-target efficiency and a narrowed editing window, fewer indels and fewer off-targets, he says. Yang sees a lot of promise for these base editors for both DNA and RNA base editing. Yang is a die-hard Manchester United. Among other aspects, he talks about how he organizes his lab for open communication. He is modeling the the culture of the Jaenisch lab at The Whitehead Institute. That's where Yang was a postdoctoral fellow.

Proteins in a cell don't tend to practice social distancing. They have many associates but capturing all of the associates in one experiment is difficult. Dr. Carol Robinson and her team developed a way to be able to dissociate such complexes in a mass spectrometer and look at them in one experiment. It's a new kind of mass spectrometer and one she and her team co-developed with Thermo Fisher Scientific. Robinson is the first female professor of the University of Oxford, previously the first female professor of the University of Cambridge and she was appointed Dame Commander of the Order of the British Empire. This is a story about her by Vivien Marx.