Created with Sketch.
Micro binfie podcast
44 minutes | Sep 29, 2022
90 Public health bioinformatics on the cloud with WDL + Terra.bio
90 Public health bioinformatics on the cloud with WDL + Terra.bio by Microbial Bioinformatics
26 minutes | Sep 15, 2022
89 What do we do with WDL?
Today on the @microbinfie podcast, we talk about WDL with @sevinsky and @DannyJPark. We learn what widdle means to Andrew and his kids. Joel takes a shot at Lyve-SET and you'll never guess what happens next.
53 minutes | Aug 4, 2022
88 - Sepia directors cut
This is an extended directors cut of our chat with Dr Henk den Bakker about Sepia. Its a summer holiday bonus. Some URLs Get Sepia here: https://github.com/hcdenbakker/sepia Some information on the food safety informatics group at UGA: https://www.denglab.site/ Rust: https://www.rust-lang.org/ Kalamari: https://github.com/lskatz/kalamari CAMI: https://www.nature.com/articles/nmeth.4458
28 minutes | Jul 21, 2022
87 Nextstrain, SARSCOV2 and dealing with a data deluge
87 Nextstrain, SARSCOV2 and dealing with a data deluge by Microbial Bioinformatics
23 minutes | Jul 7, 2022
86 What's next for nextstrain?
86 What's next for nextstrain? by Microbial Bioinformatics
27 minutes | Jun 23, 2022
85 Breaking the dogma with bioinformatics
We are joined again by Prof Mark Pallen who takes us through his early experiences in high-throughput microbial genomics. Mark was pleased that he persuaded Nick Loman to join him in Birmingham. Mark tells us how they worked with George Weinstock to perform the first genome sequence analyses of Gram-negatives for genomic epidemiology—in this case of multi-drug resistant Acinetobacter baumannii. After winning an Ion Torrent sequencer in a competition, Mark and Nick then contributed some pioneering genomic analyses of the German STEC outbreak. One of their studies involved crowd sourced approaches, primed by Twitter and was published in the New England Journal of Medicine; the other provided a performance comparison of newly launched bench top sequencing platforms. Mark, Lee and Nabil discuss how this outbreak overturned dogmas concerning the archetypal status of pathotypes of E. coli. The conversation then moves on to the need for evidence trails and challenging assumptions, whether annotating proteins or quoting Darwin (see https://colinpurrington.com/2012/02/darwin-on-the-floor-lhao/). Nabil recalls the excitement of realtime analysis of an epidemic and acknowledges the legacy of Mark and Nick's work in 2011 to current approaches to the Covid pandemic. Mark describes his exciting experiences exploiting metagenomics in clinical and ancient DNA contexts, including analysis of disease-associated stool samples and of 200-year TB genomes in Hungarian mummies. Yet again this led to overturning of assumptions--in this case that people only get infected with a single strain of M. tuberculosis. It turns out that multiple infections were the norm 200 years ago. Shortly afterwards, Pallen helped assemble a team that analysed undersea sediments shedding light on the Neolithic transition in England and culminating in a Science paper. Mark then takes us through his recent metagenomics analyses of critically ill patients and of the chicken gut, emphasising the excitement of finding hundreds of new species in such a commonplace setting. Mark finishes off by sharing his excitement that there is still so much of the microbial world left for us to discover using sequencing and bioinformatics analyses. We are just 2% of the way there!
22 minutes | Jun 9, 2022
84 Bioinformatics in the noughties with Mark Pallen
Mark Pallen explains how exciting it was to be in microbial bioinformatics around the turn of the millennium, as we gained genomes for the first time from model organisms and fearsome pathogens. He recounts working with his hero David Relman on the genome sequencing of the strange slow-growing organism called Tropheryma whipplei in competition with a French team. Mark moved to Belfast in late 1999 collaborating with another Englishman working on the island of Ireland, Tim Foster in Dublin. Pallen describes the addictive exhilaration of using PSI-BLAST to find new sortases and sortase substrates across a range of new genomes—for him this was the bioinformatics equivalent of crack cocaine. He quotes the philosopher Alfred North Whitehead in saying that the goal of every scientist is to seek simplicity but distrust it. What Mark found was that in most organisms sortases were behaving quite differently from the rather simple scenario seen in Staphylococcus aureus. He made similar observations on the WXG100 proteins and type VII secretion, which he found in many new contexts quite different from the original context of ESAT-6 as an antigen in Mycobacterium tuberculosis. Mark makes clear that we still don't really fully understand the role of ESAT-6 twenty years on. The focus of Pallen's work then shifted to E. coli, where he described vestigial gene clusters for non-functional type III secretion systems in this model organism. He came to realize that E. coli K-12 was not handed to microbiologist by God as a model organism but was just another strain of E. coli and nothing special. Many of the earliest genomes to be sequenced came from worn-out lab strains. To counter this problem, Gordon Dougan at the Wellcome Trust Sanger Institute moved the focus to genome-sequencing freshly isolated minimally passaged isolates. With Brendan Wren, Pallen wrote a review article for nature, emphasizing the importance of adopting an eco-evo perspective when trying to interpret bacterial genomes. Around that time, Scott Beatson joined Pallen's group. Mark managed to persuade Scott to work on type III secretion in E. coli rather than Pseudomonas aeruginosa. The result was the discovery of dozens of new type III secretion effectors, tying together bioinformatics and lab work to culminate in a PNAS paper. References - https://microbinfie.github.io/2022/06/09/bioinformatics-in-the-noughties.html
18 minutes | May 26, 2022
83 A short journey into mobile genetic elements
We discuss mobile genetic elements in bacteria and find, its really hard. Its just a short chat as Lee lost power, but we will be back with a part 2 sometime soon.
40 minutes | May 12, 2022
82 Bioinformatics moments before the millennium
In this episode we talk to Professor Mark Pallen, who discusses the highlights from his long career as a medical microbiologist turned bioinformatician. His bioinformatics journey began in 1977, the year Fred Sanger invented DNA sequencing-as-we know-it, when Mark was tasked with assembling some amino acid sequences under exam conditions. Mark explains how little was know about sequences at the time. Luckily he managed to gain a grasp of molecular biology and joined a group in the late 1908s at Barts Hospital in London, where he met Brendan Wren. Mark's first eureka moment followed shortly afterwards, when he analysed sequences encoding the key enzyme urease from Helicobacter pylori. He also got very excited when he analysed genes from a clostridial butanol fermentation pathway, which he explains, played a central role in the formation of the state of Israel. His next big break came when he got the chance to do a PhD under Gordon Dougan. During this time, Mark not only improved his lab and bioinformatics skills, but captained a winning team in University Challenge and introduced the medical profession to the Internet. He recalls with excitement the moment when he first heard the news that a bacterial genome had been sequenced. Shortly afterwards he recruited an 18-year old gap year student, Nick Loman, to come and work with him analysing the very first Campylobacter jejuni genome. We close this episode just as the new millennium begins, with much more excitement to follow in the next episode. Relevant links: Butanol - https://academic.oup.com/femsle/article/124/1/61/486499 Tree-like thinking for genes, languages and gospel manuscripts - https://www.youtube.com/watch?v=8Ykj5wQs7vU Further references - https://microbinfie.github.io/2022/05/12/bioinformatics-moments-before-the-millennium.html
9 minutes | Apr 29, 2022
81 The people behind the benchmark datasets for SARS-CoV-2
We bring on Lingzi Xiaoli and Jill Hagey to talk about their benchmark datasets for SARS-CoV-2. Find out more at https://github.com/CDCgov/datasets-sars-cov-2. See our previous episode for part 1 of the conversation. * Previous paper for bacterial datasets can be found at https://peerj.com/articles/3893/ * Jill can be found on Twitter at @JillHagey and jvhagey.github.io * Lingzi can be found on LinkedIn at https://www.linkedin.com/in/lingzi-xiaoli-27b87174/
43 minutes | Apr 28, 2022
80 Benchmark datasets for SARS-CoV-2
We bring on Lingzi Xiaoli and Jill Hagey to talk about their benchmark datasets for SARS-CoV-2. Find out more at https://github.com/CDCgov/datasets-sars-cov-2 * Previous paper for bacterial datasets can be found at https://peerj.com/articles/3893/ * Jill can be found on Twitter at @JillHagey and jvhagey.github.io * Lingzi can be found on LinkedIn at https://www.linkedin.com/in/lingzi-xiaoli-27b87174/
28 minutes | Apr 14, 2022
79 StaPH-B: Stable containers for public health bioinformatics
Dr Erin Young from the Utah Department of Health and Dr Kelsey Florek from the Wisconsin State Laboratory of Hygiene join us to talk about StaPH-B containers for public health bioinformatics. Its basically how to make biology easier for everyone! Github: https://github.com/StaPH-B
26 minutes | Mar 31, 2022
78 StaPH-B: state public health bioinformatics
Dr. Erin Young and Dr Kelsey Florek join us to talk about StaPH-B, a US state public health bioinformatics group. They also give some insights into the popular SARS-CoV-2 pipeline cecret. Website: https://staphb.org/ Cecret Pipeline: https://github.com/CDCgov/SC2CLIA
38 minutes | Mar 17, 2022
77 Genomics for a new era
Today we’re talking about some exciting new developments in the area of comparative genomics. We are joined by Dr. Zamin Iqbal who is a Research Group Leader at the European Bioinformatics Institute and Dr. Grace Blackwell who is jointly at the European Bioinformatics Institute, in Zam’s group and Nick Thomson’s team at Wellcome Sanger Institute
41 minutes | Mar 3, 2022
76 What are the major challenges for getting AMR genomics into the clinic?
What are the major challenges for getting AMR genomics into the clinic? This was the question poised to a panel of experts at the 7th Microbial Bioinformatics hackathon run in conjunction with JPIAMR, PHA4GE and CLIMB. The panel were: Mark Pallen from the Quadram Institute Bioscience, UK, Finlay Maguire from Dalhousie University, Canada, Anthony Underwood from the Centre for genomic pathogen surveillance, UK and Clement Tsui from the Weill Cornell Medicine, Qatar. Andrew Page was the Chair, supported by Lee Katz.
38 minutes | Feb 3, 2022
74 SEPIA With Henk - Soup Or Salad Yes!
74 SEPIA With Henk - Soup Or Salad Yes! by Microbial Bioinformatics
29 minutes | Jan 20, 2022
73 Bactopia and using workflow managers in bioinformatics part 2
We are again joined by Dr Robert Petit from the Wyoming Public Health Laboratory who is talking to us about BACTOPIA, a bioinformatics workflow specifically for bacterial genomes. Docs: https://bactopia.github.io/ Repo: https://github.com/bactopia/bactopia/ Pub: https://doi.org/10.1128/mSystems.00190-20
35 minutes | Jan 6, 2022
72 Bactopia and using workflow managers in bioinformatics part 1
We are joined by Dr Robert Petit from the Wyoming Public Health Laboratory who is talking to us about BACTOPIA, a bioinformatics workflow specifically for bacterial genomes. Docs: https://bactopia.github.io/ Repo: https://github.com/bactopia/bactopia/ Pub: https://doi.org/10.1128/mSystems.00190-20
41 minutes | Dec 17, 2021
71 Bacterial taxonomy: Into the unknown, SeqCode, naming uncultured multitudes and renaming of phyla
We finish our discussion on bacterial taxonomy, this time looking at new approaches of naming the multitudes of unnamed uncultured organisms and the controversial renaming of phyla. With guests Professor Phil Hugenholtz, Professor Iain Sutcliffe and Professor Mark Pallen. Selective bibliography: https://github.com/MicroBinfie/MicroBinfie.github.io/blob/45db8eb57d732176449073065dbdacc88a288fe9/assets/Taxonomy_Selective_bibliography.pdf
29 minutes | Dec 17, 2021
70 Bacterial Taxonomy: the grand vista is ahead of us
We continue our discussion on bacterial taxonomy, this time looking at how genomics has changed taxonomy with: Professor Phil Hugenholtz, Professor Iain Sutcliffe and Professor Mark Pallen. Selective bibliography: https://github.com/MicroBinfie/MicroBinfie.github.io/blob/45db8eb57d732176449073065dbdacc88a288fe9/assets/Taxonomy_Selective_bibliography.pdf
Terms of Service
Do Not Sell My Personal Information
© Stitcher 2022