121 K-mers, Sourmash, And Open Source Software - More Conversations With Titus Brown Micro Binfie podcast

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コンテンツは Micro Binfie Podcast and Microbial Bioinformatics によって提供されます。エピソード、グラフィック、ポッドキャストの説明を含むすべてのポッドキャストコンテンツは、Micro Binfie Podcast and Microbial Bioinformatics またはそのポッドキャストプラットフォームパートナーによって直接アップロードされ、提供されます。誰かがあなたの著作物をあなたの許可なく使用していると思われる場合は、ここで概説されているプロセスに従うことができますhttps://ja.player.fm/legal。

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Re-Recruiting and Other New HR Strategies You Can’t Ignore 18:09

約 19 日前18:09

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18:09

HR is no longer just about managing people—it’s about shaping the future of work. Jens Baier, BCG’s HR transformation expert, discusses how AI and shifting employee expectations are forcing companies to rethink talent strategies. From re-recruiting to upskilling employees, HR must adapt to a rapidly changing landscape. Learn More: Jens Baier: https://on.bcg.com/41ca7Gv BCG on People Strategy: https://on.bcg.com/3QtAjro Decoding Global Talent: https://on.bcg.com/4gUC4IT…

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121 K-mers, Sourmash, and Open Source Software - More Conversations with Titus Brown

約 1 年前 20:03

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コンテンツは Micro Binfie Podcast and Microbial Bioinformatics によって提供されます。エピソード、グラフィック、ポッドキャストの説明を含むすべてのポッドキャストコンテンツは、Micro Binfie Podcast and Microbial Bioinformatics またはそのポッドキャストプラットフォームパートナーによって直接アップロードされ、提供されます。誰かがあなたの著作物をあなたの許可なく使用していると思われる場合は、ここで概説されているプロセスに従うことができますhttps://ja.player.fm/legal。

In this episode, Andrew Page and Lee Katz continue their conversation with Titus Brown, diving deeper into his work on k-mers, Sourmash, and open source software development: Topics discussed: K-mers for analyzing sequencing data, and how Sourmash builds on MinHash How Sourmash handles k-mers for metagenomic comparisons vs. MASH The modhash and bottom sketch approaches used in Sourmash Dealing with sequencing errors and noise in k-mer data Sourmash as a reference-based method, and applications for metagenomics Titus' focus on building reusable libraries and APIs vs one-off tools Recruiting collaborators through "nerd sniping" with interesting problems The open source philosophy that motivates Titus' software work Overall, the conversation provides insight into Titus' approach to bioinformatics software through iterating quickly, focusing on usability, and building open source tools. Papers: Spacegraphcats - https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02066-4 Sourmash - https://www.biorxiv.org/content/10.1101/2022.01.11.475838v2 IBD exploration - https://dib-lab.github.io/2021-paper-ibd/

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141 つのエピソード

#Science #Micro Binfie #Microbial Bioinformatics

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121 K-mers, Sourmash, and Open Source Software - More Conversations with Titus Brown

Micro binfie podcast

published 約 1 年前

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MP3•エピソードのホーム

コンテンツは Micro Binfie Podcast and Microbial Bioinformatics によって提供されます。エピソード、グラフィック、ポッドキャストの説明を含むすべてのポッドキャストコンテンツは、Micro Binfie Podcast and Microbial Bioinformatics またはそのポッドキャストプラットフォームパートナーによって直接アップロードされ、提供されます。誰かがあなたの著作物をあなたの許可なく使用していると思われる場合は、ここで概説されているプロセスに従うことができますhttps://ja.player.fm/legal。

In this episode, Andrew Page and Lee Katz continue their conversation with Titus Brown, diving deeper into his work on k-mers, Sourmash, and open source software development: Topics discussed: K-mers for analyzing sequencing data, and how Sourmash builds on MinHash How Sourmash handles k-mers for metagenomic comparisons vs. MASH The modhash and bottom sketch approaches used in Sourmash Dealing with sequencing errors and noise in k-mer data Sourmash as a reference-based method, and applications for metagenomics Titus' focus on building reusable libraries and APIs vs one-off tools Recruiting collaborators through "nerd sniping" with interesting problems The open source philosophy that motivates Titus' software work Overall, the conversation provides insight into Titus' approach to bioinformatics software through iterating quickly, focusing on usability, and building open source tools. Papers: Spacegraphcats - https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02066-4 Sourmash - https://www.biorxiv.org/content/10.1101/2022.01.11.475838v2 IBD exploration - https://dib-lab.github.io/2021-paper-ibd/

… continue reading

141 つのエピソード

#Science #Micro Binfie #Microbial Bioinformatics

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138 Decoding Tetracycline Resistance in MRSA 11:24

9 weeks前11:24

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11:24

In this episode of the Micro Binfie Podcast, host Andrew Page takes listeners to the heart of the microbial genomics hackathon in Bethesda, Maryland, for an engaging conversation with special guest Megan Phillips, a PhD student from Emory University. Megan delves into her research on Staphylococcus aureus (MRSA), highlighting its fascinating dual nature as both a harmless and potentially serious pathogen. Megan discusses the complexities of tetracycline resistance, particularly focusing on plasmid-mediated mechanisms involving the pt181 plasmid. She explains how this plasmid’s efflux pump, encoded by the gene tetK, contributes to variable resistance levels and the factors influencing MIC (Minimum Inhibitory Concentration) variability. Listeners will learn about the intricacies of plasmid copy numbers, their global spread across clonal complexes, and the occurrence of horizontal and vertical gene transfer. Throughout the episode, Megan shares insights on working with short-read sequencing data and the strategies she employs to detect plasmid presence using tools like BLAST. She also touches on the challenges and fascinating discoveries of tracking historical sample data and integrating findings from older research papers, showcasing her appreciation for the poetic style of scientific writing from the 1940s. For those interested in antimicrobial resistance, evolutionary microbiology, and the subtleties of bacterial genome analysis, this episode offers a compelling blend of technical details and engaging storytelling. Tune in to hear more about Megan’s upcoming publications, her experiences navigating complex genomic data, and her thoughts on antimicrobial stewardship and historical perspectives on drug resistance.…

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137 Contagion part 2 32:26

11 weeks前32:26

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32:26

In a two-part discussion, the hosts analyze the movie Contagion from their expert perspectives, focusing on the film's portrayal of epidemiology and genomics. They note that the movie compresses timelines for dramatic effect, speeding up the virus's spread and the response to it, and that decisions about managing a crisis are based on societal values, not just science. In part one, the hosts discuss the movie's depiction of the R0 value. They note that while this explanation is useful for the audience, it is unlikely that an epidemiologist would need to explain this concept to other epidemiologists. The group notes that the MEV1 virus is modeled on the real-life Nipah virus and comment on a scene where the genome of the virus is described as being 15 to 19 kilobases in length with 6 to 10 genes. They also discuss the movie's depiction of virus isolation and the unrealistic speed with which the initial assessment of the virus occurs. The podcasters touch upon the BSL4 lab and how the film depicts how the scientists behave. They also discuss the character of Matt Damon, who is exposed to the virus but does not get sick, and is an example of an asymptomatic carrier. In part two, the bioinformaticians examine the "genome dashboard" scene, noting the software's informative interface, which includes an alignment panel, protein structure, and a recombination map. They also discuss a scene where a phylogenetic tree is used to determine a change in the R0 value. They find this unrealistic because the tree is just a picture that doesn't accurately represent how a virus spreads. The group discusses how the bioinformatician is depicted in the film as moving in and out of the lab, which may have been realistic in 2011 but is less so in the present day. They discuss how the CDC is portrayed in the film, noting scenes that were filmed at the actual CDC, as well as their experiences at the CDC. The podcasters note the movie is very US-centric and that many international partners would be involved in solving a global pandemic.…

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135 Assembling ATCC bacterial strains 13:35

12 weeks前13:35

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13:35

In this episode of the Micro Binfie podcast, host Andrew Page is joined by Nikhita Puthuveetil, Senior Bioinformatician at the American Type Culture Collection (ATCC). They delve into ATCC's ambitious project of sequencing a vast array of organisms from their renowned collection, tackling the challenges of assembling complex genomes from bacteria, viruses, fungi, and more. Discover how Nikhita and her team navigate through genomic roadblocks, leverage cutting-edge sequencing technologies, and work to ensure accurate data provenance. Whether it's large viral genomes or evolving taxonomy, this episode offers a deep dive into the fascinating world of microbial bioinformatics and genomic curation.…

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136 Contagion part 1 30:43

13 weeks前30:43

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30:43

In a two-part discussion, the hosts analyze the movie Contagion from their expert perspectives, focusing on the film's portrayal of epidemiology and genomics. They note that the movie compresses timelines for dramatic effect, speeding up the virus's spread and the response to it, and that decisions about managing a crisis are based on societal values, not just science. In part one, the hosts discuss the movie's depiction of the R0 value. They note that while this explanation is useful for the audience, it is unlikely that an epidemiologist would need to explain this concept to other epidemiologists. The group notes that the MEV1 virus is modeled on the real-life Nipah virus and comment on a scene where the genome of the virus is described as being 15 to 19 kilobases in length with 6 to 10 genes. They also discuss the movie's depiction of virus isolation and the unrealistic speed with which the initial assessment of the virus occurs. The podcasters touch upon the BSL4 lab and how the film depicts how the scientists behave. They also discuss the character of Matt Damon, who is exposed to the virus but does not get sick, and is an example of an asymptomatic carrier. In part two, the bioinformaticians examine the "genome dashboard" scene, noting the software's informative interface, which includes an alignment panel, protein structure, and a recombination map. They also discuss a scene where a phylogenetic tree is used to determine a change in the R0 value. They find this unrealistic because the tree is just a picture that doesn't accurately represent how a virus spreads. The group discusses how the bioinformatician is depicted in the film as moving in and out of the lab, which may have been realistic in 2011 but is less so in the present day. They discuss how the CDC is portrayed in the film, noting scenes that were filmed at the actual CDC, as well as their experiences at the CDC. The podcasters note the movie is very US-centric and that many international partners would be involved in solving a global pandemic.…

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133 The Role of Bioinformatics in Public Health and Disease Outbreaks 12:36

14 weeks前12:36

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12:36

In this episode of the Micro Binfie podcast, host Andrew Page talks with Dr. Erin Young, a bioinformatician at the Utah Public Health Laboratory, recorded during the 10th Microbial Bioinformatics Hackathon in Bethesda, Maryland. Erin shares her journey from researching hereditary cancer predisposition to her current role in public health bioinformatics, which she entered through a prestigious CDC and APHL fellowship. The conversation delves into her work with bacterial pathogens, particularly in tracking antimicrobial resistance in organisms like Klebsiella. Erin discusses the tools she uses for genome typing, such as MASH, FastANI, and SKA, and her innovative research on the accuracy of long-read sequencing technologies like Nanopore for detecting antimicrobial resistance genes. She also provides a preview of her upcoming poster for ASM, where she examines how Nanopore reads can be used effectively in public health microbiology. This episode offers a fascinating look at how bioinformatics and genomics are advancing the fight against infectious diseases.…

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134 Diving into MRSA, Genomics, and Public Health 13:27

14 weeks前13:27

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13:27

In this episode of the Micro Binfie Podcast, host Andrew Page speaks with Dr. Brooke Talbot, a recent PhD graduate from Emory University, about her research on Staphylococcus aureus, with a focus on MRSA and antibiotic resistance. Brooke shares insights into her molecular epidemiology work, discussing the complexities of tracking resistant bacterial strains in clinical settings and the significance of genomic epidemiology in public health. From honeybees to foodborne outbreaks, Brooke’s diverse research background offers listeners a fascinating journey through science, microbiology, and epidemiology.…

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132 Unlocking the Secrets of Antimicrobial Resistance in Metagenomes 11:02

16 weeks前11:02

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11:02

In this episode of the Micro Binfie podcast, host Andrew Page is live from the 10th Microbial Bioinformatics Hackathon in Bethesda, Maryland. He sits down with David Mahoney, a PhD student from Dalhousie University in Halifax, Nova Scotia. David shares his research on characterizing antimicrobial resistance (AMR) genes and their transfer within metagenomes, focusing on metagenomic assembly graphs. They delve into David’s background in food safety microbiology and his interest in the public health implications of genomics. He explains his exciting work on analyzing how AMR genes transfer across different environments, such as food production plants and clinical settings, using both new and existing data from Canada’s Genomics Research and Development Initiative. David also highlights his use of innovative methods like assembly graphs and graph-based approaches to uncover AMR gene flow and lateral gene transfers, including the potential of machine learning techniques such as graph convolutional neural networks.…

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131 Bioinformatics Evolution: Torsten Seemann on Snippy, Open-Source Support, and Global Genomics 12:47

18 weeks前12:47

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12:47

In this episode of the Micro Binfie Podcast, host Andrew Page catches up with Torsten Seemann at the 10th Microbial Bioinformatics Hackathon in Bethesda, Maryland. They discuss the rapid evolution of bioinformatics, the challenges faced by labs worldwide, and the explosion of tools post-COVID. Torsten shares insights into his work at Melbourne’s Microbiological Diagnostic Unit (MDU), the development of platforms like OzTracker for bacterial genomics, and how his lab plays a national and international role in data sharing. The conversation dives into the future of the widely-used variant calling tool Snippy, as Torsten reveals exciting updates funded by the Chan Zuckerberg Initiative, including nanopore read support and the ability to process pre-assembled genomes. They also explore the importance of maintaining open-source bioinformatics tools to prevent them from becoming obsolete. Tune in for an in-depth discussion on the state of genomics, software development, and the challenges and rewards of open-source collaboration.…

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130 Exploring Genomic Innovation and Machine Learning in Public Health 12:35

20 weeks前12:35

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12:35

In this episode of the Micro binfie Podcast, host Andrew Page sits down with Tim Dallman at the 10th Bioinformatics Hackathon in Bethesda, Maryland. Tim shares insights from his work at Utrecht University in the Netherlands, where he focuses on genomic surveillance and machine learning models to predict disease risk and severity. They discuss the challenges of integrating genomic variation into predictive models, the importance of high-quality metadata, and the complexities of working with pathogens like Shiga toxin-producing E. coli. Tim also talks about his role at the WHO Pandemic and Epidemic Intelligence Hub and how global collaboration can drive innovation in public health genomics. Tune in to hear about cutting-edge research, the importance of interdisciplinary teamwork, and how genomic data can be harnessed for future pandemic preparedness.…

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129 Genomics on the Frontier: Bactopia, Bioinformatics, and Pathogen Surveillance with Robert Petit 14:58

22 weeks前14:58

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14:58

Host Andrew Page is joined by Robert Petit from the Wyoming Public Health Laboratory. Robert, a key developer of the Bactopia pipeline, shares insights into how this end-to-end tool is transforming bacterial genomic surveillance. They dive into the origins of Bactopia, its applications in public health, and Robert's experience leading genomic projects in a rural setting. Discover how Bactopia streamlines pathogen detection, improves documentation, and integrates with other tools to deliver fast and accurate results. Listen in as they discuss new innovations in bioinformatics, including visualizations and human-read filtering, and explore future projects like CamelHUMP, designed to simplify sequence-based typing. Recorded live at the Microbial Bioinformatics Hackathon in Bethesda, Maryland, this episode brings you the latest in pathogen genomics and the challenges and rewards of working on the frontier of public health.…

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128 Haiti cholera outbreak with Christine Lee and Cynney Walters 21:57

26 weeks前21:57

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21:57

Andrew and Lee talk with Christine and Cynney about the Haiti cholera outbreak Cynney Walters: https://www.linkedin.com/in/cynney-walters-763111190 Walters et al, "Genome sequences from a reemergence of Vibrio cholerae in Haiti, 2022 reveal relatedness to previously circulating strains" https://journals.asm.org/doi/abs/10.1128/jcm.00142-23…

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127 Minimum spanning trees 15:49

28 weeks前15:49

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15:49

Nabil and Lee have a quick chat about minimum spanning trees (MST). Eburst paper: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-10-152

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126 Tree viz 21:21

29 weeks前21:21

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21:21

We go over tree visualizations! * Microreact https://microreact.org/,https://www.phylocanvas.gl/ * grapetree https://github.com/achtman-lab/GrapeTree * Auspice/NextStrain https://nextstrain.org/ * Taxonium https://taxonium.org/ * Itol: https://itol.embl.de/ * PhyloViz https://online.phyloviz.net/index * Phandango https://jameshadfield.github.io/phandango/#/main…

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125 Kostas Konstantinidis returns to talk to us about ANI and metagenomics 22:07

41 weeks前22:07

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22:07

125 Kostas Konstantinidis returns to talk to us about ANI and metagenomics by Microbial Bioinformatics

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124 Kostas Konstantinidis talks to us about ANI and metagenomics 22:58

43 weeks前22:58

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22:58

We talk with Kostas! For more information please visit https://enve-omics.gatech.edu/

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