Podcasts about Proteomics

On this special episode of Translating Proteomics, Parag and Andreas break down the basics of proteomics — perfect for anyone with a background in molecular biology looking to get started in the field.Seasoned experts: We hope you can share this episode as a teaching tool or to inspire others to explore proteomics.Parag and Andreas cover the following questions in the episode, and links to additional Nautilus resources can be found below each question.What is proteomics?Blog post – What is proteomics? Techniques, applications, and methodsWhat are key questions proteomics can answer?Blog category – Applications of proteomicsWhy is it important to measure the proteome?FAQ on the Nautilus Resources pageBlog post – Genomics vs. proteomics: Two complementary perspectives on lifeWhat can and can't you do with proteomics?Translating Proteomics episode – Plasma Proteomics: The Dream and the NightmareLearn how the Nautilus Platform is designed to enable comprehensive broadscale proteomics and targeted proteoform studiesWhat are key proteomics methods and techniques?Blog series – Traditional protein analysis methodsBlog series – Next-generation proteomics technologiesWhat are the major pitfalls when doing proteomics?What are the challenges in proteomic data analysis?Translating Proteomics episode – Biology in Space and TimeBlog post – What is multiomics?What are people excited about in proteomics?Translating Proteomics episode – Poised for a Proteomics BreakthroughTranslating Proteomics episode - US HUPO 2025 – Key Takeaways, Trends, and Future Directions for ProteomicsTranslating Proteomics episode –

If you listened to our episode focused on science communication featuring proteomics leaders Ben Orsburn Ph.D. and Ben Neely Ph.D., then you've already heard about their excellent podcast, The Proteomics Show. On The Proteomics Show, they interview researchers in the proteomics community to learn about their motivations, their backstories, and their work. Today, we're sharing an episode of The Proteomics Show where the Bens interview Translating Proteomics host Parag Mallick. Check it out to learn about Parag's journey to proteomics, his efforts advocating for open data sharing, and his work as a professional magician.After listening, be sure to check out more episodes of The Proteomics Show on their feed where you'll find over 70 interviews with many, many interesting people in the proteomics community. Find their feed here:https://us-hupo.org/Podcasts

On this episode of Translating Proteomics, hosts Parag Mallick and Andreas Huhmer discuss their recent experience at the 2025 US Human Proteome Organization conference or US HUPO. Their conversation covers:· The rising use of multiple proteomics platforms· Advances in multiomicsAnd· What they hope to see at the next US HUPOChapters:00:00 – Introduction01:47 – Things Parag and Andreas were most excited about going into US HUPO06:19 - Trends Parag observed at US HUPO· A bifurcation between studies that focused on measuring many proteins and those that focused on a specific biological process· People increasingly using multiomics to wholistically understanding biology as opposed to a means of comparing the different omes· A shift to researchers using multiple proteomics platforms11:44 – The rising prominence of proteoforms at US HUPO15:50 – The future of proteomics as informed by US HUPO18:06 – What Parag and Andreas hope to see at the next US HUPO19:57 - Outro

As part of the non-sponsored sporadic "B-sides" series*, Ben and Ben sit down with Parag Mallick, Nautilus Biotechnology. Actually this is a crossover from February where Parag had us on his podcast, Translating Proteomics. Find the original here.(* this series is where we put guests we want to talk to but who do not fit within any sponsored series, but is still proteomics.... mostly)

In this episode of the Cognitive Revolution, we hear from Siyu He, a postdoc at Stanford specializing in biomedical data science. Siyu discusses the implications and methods behind their recent AI-driven biological research papers, Squidiff and CORAL. The conversation explores the use of AI models to analyze complex cellular systems and disease mechanisms, focusing on transcriptome and tissue sample analyses. Squidiff aims to simulate cellular transcriptomes to predict outcomes of various conditions, significantly expediting traditionally lengthy and expensive biological experiments. CORAL Project extends this by integrating different levels of biological data, enabling a more comprehensive understanding of tissue structures and cellular interactions. The discussion also delves into the challenges of using synthetic data for validating AI models and the potential acceleration of scientific discoveries through AI in biomedical research. The episode encapsulates the interplay between AI and biology, highlighting the future possibilities and current limitations of this innovative research front. Squidiff: https://www.biorxiv.org/content/10.1101/2024.11.16.623974v1.full.pdf CORAL: https://www.biorxiv.org/content/10.1101/2025.02.01.636038v1.full.pdf SPONSORS: Oracle Cloud Infrastructure (OCI): Oracle's next-generation cloud platform delivers blazing-fast AI and ML performance with 50% less for compute and 80% less for outbound networking compared to other cloud providers. OCI powers industry leaders like Vodafone and Thomson Reuters with secure infrastructure and application development capabilities. New U.S. customers can get their cloud bill cut in half by switching to OCI before March 31, 2024 at https://oracle.com/cognitive Shopify: Shopify is revolutionizing online selling with its market-leading checkout system and robust API ecosystem. Its exclusive library of cutting-edge AI apps empowers e-commerce businesses to thrive in a competitive market. Cognitive Revolution listeners can try Shopify for just $1 per month at https://shopify.com/cognitive NetSuite: Over 41,000 businesses trust NetSuite by Oracle, the #1 cloud ERP, to future-proof their operations. With a unified platform for accounting, financial management, inventory, and HR, NetSuite provides real-time insights and forecasting to help you make quick, informed decisions. Whether you're earning millions or hundreds of millions, NetSuite empowers you to tackle challenges and seize opportunities. Download the free CFO's guide to AI and machine learning at https://netsuite.com/cognitive PRODUCED BY: https://aipodcast.ing CHAPTERS: (00:00) About the Episode (03:37) Introduction and Guest Welcome (04:00) Setting the Big Picture Context (04:37) Exploring the Squidiff and CORAL Papers (08:31) Understanding Transcriptomes (11:17) Single Cell RNA Sequencing Technology (15:32) Motivation Behind Squidiff (Part 1) (17:14) Sponsors: Oracle Cloud Infrastructure (OCI) | Shopify (19:41) Motivation Behind Squidiff (Part 2) (25:56) Training Data and Model Architecture (Part 1) (31:38) Sponsors: NetSuite (33:11) Training Data and Model Architecture (Part 2) (37:18) Diffusion Models in Biology (46:07) In Silico Experiments and Applications (54:25) Clarifying the Validation Process (55:36) Validation Strategies and Real Data (58:26) Challenges in Modeling and Predictions (01:02:14) Accelerating Research with AI Models (01:07:31) Future Directions and Collaboration (01:10:46) Introduction to CORAL Paper (01:13:09) Spatial Transcriptomics and Proteomics (01:17:10) Challenges in Integrating Spatial Data (01:31:53) Synthetic Data and Model Validation (01:36:42) The Future of AI in Healthcare (01:43:31) Outro SOCIAL LINKS: Website: https://www.cognitiverevolution.ai Twitter (Podcast): https://x.com/cogrev_podcast Twitter (Nathan): https://x.com/labenz LinkedIn: https://linkedin.com/in/nathanlabenz/ Youtube: https://youtube.com/@CognitiveRevolutionPodcast

Peter Cimermančič is the Co-Founder and CEO of Tesorai.

Milad Dagher is the Co-Founder and CEO of Nomic Bio.

Description: Dr. Evan Noch interviews Drs. Cecile Riviere-Cazaux and Terry Burns about their recent manuscript entitled: "A field resource for the glioma cerebrospinal fluid proteome: impacts of resection and location on biomarker discovery", published online in Neuro-Oncology in December 2024.   Link: https://doi.org/10.1093/neuonc/noae277  

Matters Microbial #80: Do Microbes Make the Best Chemists? February 27, 2025 Today, Dr. Marc Chevrette, Assistant Professor of Microbiology and Cell Science at the University of Florida, joins the #QualityQuorum to discuss how his research group can study novel metabolites and even interactions via study of microbial genomes! Dr. Chevrette reminds us all that microbes are the best chemists! Host: Mark O. Martin Guest: Marc Chevrette Subscribe: Apple Podcasts, Spotify Become a patron of Matters Microbial! Links for this episode  An overview of how quickly the field of microbial genomics has advanced. How secondary metabolites can be important to antibiosis, cell signaling, and even communication. An overview of genome mining, along with another review. The program antiSMASH that analyzes genomes for genes involved with secondary metabolites. A video describing how antiSMASH can be used to search for possible biosynthetic gene clusters. An essay about Dr. Julian Davies. An article by Dr. Davies' group suggesting that antibiotics can serve as chemical signals between microbes. The idea of “parvomics,” studying the role of small molecules in how microbes communicate and interact. A great article from Dr. Chevrette and colleagues about how to look for biosynthetic diversity using genome mining. An article by Dr. Chevrette and colleagues exploring how groups of microbes can interact in remarkable ways. Dr. Chevrette's faculty website. Dr. Chevrette's research website. Intro music is by Reber Clark Send your questions and comments to mattersmicrobial@gmail.com

On this episode of Translating Proteomics, host Parag Mallick speaks with special guests doctors Ben Neely and Ben Orsburn, leaders in the proteomics community and hosts of “The Proteomics Show” podcast. Their insightful conversation focuses on the role of communication in proteomics and covers:· Impactful things they've learned while hosting The Proteomics Show· How their communication efforts have changed their research· Barriers to proteomics becoming more popular in the life sciences and in the broader publicChapters:00:00 – 03:04 – Intro03:04 – 07:23 – Why the Bens created "The Proteomics Show"07:23 – 10:42 – Ways the proteomics show has impacted the Bens' research10:42 – 16:44 – Every scientist is interesting!16:44 – 20:36 – Ways the Bens' communication efforts have changed their research20:36 – 25:08 – Trends in proteomics25:08 – 35:34 – Barriers to communication between the proteomics community and others in the life science34:34-48:34 - Barriers to communication between the proteomics community and the broader public48:34 - End - OutroResourcesThe Proteomics Show - Ben Neely and Ben Orsburn host this podcast sponsored by the Human Proteomics Organization. On it, they interview proteomics researchers in a “fireside chat” format. Their conversations cover not just the latest research, but also their guests' motivations, hobbies, and histories. Definitely check it out!News in Proteomics Research - Ben Orsburn's blog on the latest developments in proteomics.Proteomics, the next truly massive investment opportunity - Forbes article on the potential of proteomics.The Magic School Bus Rides Again - Recently rebooted version of The Magic School Bus. Will we see an episode featuring proteomics?

In this second entry in the JACC-Baran Japanese language series, JACC Executive Associate Editor Mitsuaki Sawano, MD, Shun Kohsaka, MD, FACC, and Yuichi Shimada, MD, MPH, speak on topics ranging from all things Super Bowl to Dr. Shimada's recently published JACC paper, Comprehensive Proteomic Profiling of Human Myocardium Reveals Signaling Pathways Dysregulated in Hypertrophic Cardiomyopathy.

As part of the US HUPO sponsored "Philly Express" series highlighting speakers at the upcoming 2025 US HUPO meeting in Philadelphia, Ben and Ben sit down to talk with Dr. Ileana Cristea, Princeton University, winner of the 2025 Catherine E. Costello Award for Exemplary Achievements in Proteomics.

On this episode of Translating Proteomics, hosts Parag Mallick and Andreas Huhmer discuss the many ways proteomics can impact our interactions with food. Some of the topics they touch upon in this wide-ranging conversation include:· Proteomics and food quality· Proteomics and food safety· Developing new kinds of food with proteomicsChapters00:00 – 01:23 – Introduction01:23 – 03:27 – Proteomics and alcohol fermentation03:27 – 05:24 – Food properties and their relationship with molecular composition05:24 – 07: 42 – How can we use proteoforms to improve food quality?07:42 – 11:49 – Proteomics to aid plant and animal breeding11:49 – 14:35 – Proteomics, Food Safety, and Food Security14:35 – 17:05 – Proteomics and food authenticity17:05 – 20:36 – Proteomics and terroir20:36 – 22:48 – Proteomics, the microbiome, and health22:48 – 24:29 – A fun party trick24:29 – 30:24 – Creating new foods and flavors30:24 – 34:33 – Designing food for space34:33 – End – OutroResourcesThe post-translational modification landscape of commercial beers (Kerr et al. 2021)· Paper looking at the ways post-translational modification differ between different beers and how protein content relates to the properties of foamHeat shock and structural proteins associated with meat tenderness in Nellore beef cattle, a Bos indicus breed (Carvalho et al. 2024)· Paper looking at the relationship between proteins and meat tendernessComprehensive proteome analysis of bread dicphering the allergenic potential of bread wheat, spelt and rye (Zimmermann et al. 2021)· Research measuring the levels of allergens in different kinds of breadDifferential proteomic analysis by SWATH-MS unravels the most dominant mechanisms underlying yeast adaptation to non-optimal temperatures under anaerobic conditions· Study using proteomics to reveal how yeast adapt to growth at different temperatures

Welcome to the Olink® Proteomics in Proximity podcast!  Below are some useful resources mentioned in this episode:  Olink® Reveal, accessible NGS-based proteomics for every lab: https://olink.com/products/olink-revealOlink tools and software·       Olink® Explore 3072, the platform utilized by the UK Biobank to measure ~3000 proteins in plasma: https://olink.com/products-services/explore/·       Olink® Explore HT, Olink's most advanced solution for high-throughput biomarker discovery, measuring 5400+ proteins simultaneously with a streamlined workflow and industry-leading specificity: https://olink.com/products-services/exploreht/  UK Biobank Pharma Proteomics Project (UKB-PPP), one of the world's largest scientific studies of blood protein biomarkers conducted to date, https://www.ukbiobank.ac.uk/learn-more-about-uk-biobank/news/uk-biobank-launches-one-of-the-largest-scientific-studies   Subscribe to the podcast on your favorite player or app:Apple Podcasts: https://apple.co/3T0YbSm   Spotify Podcasts: https://open.spotify.com/show/2sZ2wxO...   Google Podcasts: https://podcasts.google.com/feed/aHR0...   Amazon Music: https://music.amazon.com/podcasts/d97...   Podcast Addict: https://podcastaddict.com/podcast/409...   Deezer: https://www.deezer.com/show/5178787   Player FM: https://player.fm/series/series-3396598   In case you were wondering, Proteomics in Proximity refers to the principle underlying Olink technology called the Proximity Extension Assay (PEA). More information about the assay and how it works can be found here: https://bit.ly/3Rt7YiY  For any questions regarding information Olink Proteomics, please email us ...

On this episode of Translating Proteomics, co-hosts Parag Mallick and Andreas Huhmer of Nautilus Biotechnology discuss the reproducibility crisis in biology and specifically focus on how we can enhance reproducibility in computational proteomics. Key topics they cover include:• What the reproducibility crisis is• Factors that make it difficult to replicate multiomics research• Steps we can take to make biology research more reproducibleChapters 00:00 – 01:20 – Introduction01:20– 03:10 – What is reproducibility in research and why is it important?03:10 – 05:42 – Recent work from the Mallick Lab focused on computational proteomics reproducibility05:42 – 09:32 – Ways to help improve reproducibility in computational proteomics – More detailed documentation, moving beyond papers as our main form of documentation, and ensuring computational workflows are available,09:32 – 11:30 – Why Parag got interested reproducibility – Attempts to build AI layers on top of current workflows11:30 – 14:00 – The need to create repositories of analytical workflows codified in a structured way that AI can learn from14:00 – 15:24 – A role for dedicated data curators15:24 – 18:31 – Moving beyond the idea of study endpoints and recognizing data as part of a larger whole18:31 – 21:32 – How does AI fit into the continuous analysis and incorporation of new datasets21:32 – 23:36 – The role of AI in helping researchers design experiments23:36 – 27:25 – Three things we can do today to increase the reproducibility of computational proteomics experiments:· Be clear about the stated hypothesis· Document analyses through workflow engines and containerized workflows· Advocate for support for funding for reproducibility and reproducibility tools27:25 – End – OutroResourcesParag's Gilbert S. Omenn Computational Proteomics Award Lectureo In this lecture, Parag describes his vision for a more reproducible future in proteomicsNature Special on “Challenges in irreproducible research”o A list of articles and perspective pieces discussing the “reproducibility crisis” in researchWhy Most Published Research Findings Are False (Ioannidis 2005)o Article outlining many of the issues that make it difficult to reproduce research findingsReproducibility Project: Cancer Biologyo eLife initiative investigating reproducibility in preclinical cancer researchCenter for Open Science Preregistration Initiativeo Resources for preregistering a hypothesis as part of a studyNational Institute of Standards and Technology (NIST)o US government agency that aims to...

Darshan H. Brahmbhatt, Podcast Editor of JACC: Advances, discusses a recently published original research paper on Proteomics-Based Soluble Urokinase Plasminogen Activator Receptor Levels Are Associated With Incident Heart Failure Risk.

Commentary by Dr. Jan Leerink.

Welcome to the Olink® Proteomics in Proximity podcast!   Below are some useful resources mentioned in this episode:  Olink tools and software·       Olink® Explore 3072, the platform utilized by the UK Biobank to measure ~3000 proteins in plasma: https://olink.com/products-services/explore/·       Olink® Explore HT, Olink's most advanced solution for high-throughput biomarker discovery, measuring 5400+ proteins simultaneously with a streamlined workflow and industry-leading specificity: https://olink.com/products-services/exploreht/  UK Biobank Pharma Proteomics Project (UKB-PPP), one of the world's largest scientific studies of blood protein biomarkers conducted to date, https://www.ukbiobank.ac.uk/learn-more-about-uk-biobank/news/uk-biobank-launches-one-of-the-largest-scientific-studies  Press release and news story from UK Biobank:https://www.ukbiobank.ac.uk/learn-more-about-uk-biobank/news/launch-of-world-s-most-significant-protein-study-set-to-usher-in-new-understanding-for-medicine https://www.ukbiobank.ac.uk/learn-more-about-uk-biobank/news/dataset-of-thousands-of-proteins-marks-landmark-step-for-research-into-human-health https://www.ukbiobank.ac.uk/learn-more-about-uk-biobank/news/uk-biobank-launches-one-of-the-largest-scientific-studies News stories:Today Programme – Professor Rory Collins live on programme, timestamp 02:36:37   Times – ‘Game-changing' study of blood proteins will help fight disease Independent – World's largest proteins study ‘invaluable' for understanding disease – experts Daily Mail – How Alzheimer's could be diagnosed a DECADE earlier following huge study of blood proteins Mirror – New blood test reveals risk of developing different diseases in 'new frontier of science' Science – Seeking disease insights, UK Biobank launches largest study of human proteinsTechnology Networks – UK Biobank Launches Largest Proteomics Study for Disease Research Chemical and Engineering News – Pharma firms team up to study UK proteomics data  Links to referred episodes:  • Evan – Episode 20:     https://share.transistor.fm/s/f795811e    https://open.spotify.com/episode/6lv5GA8hZCgDvujlBltS9f?si=36a29e6cfa4b4fae     https://podcasts.apple.com/us/podcast/how-proteomics-is-shaping-pharma-strategies/id1645900688?i=1000635040581 • Chris – Episode 16:     https://share.transistor.fm/s/255ad207     https://open.spotify.com/episode/0oe0S6zI8cryUtgZTjGlRq?si=8a7b0323b1364b96     https://podcasts.apple.com/us/podcast/interview-about-the-uk-biobank-with-dr-christopher-whelan/id1645900688?i=1000622521524  Subscribe to the podcast on your favorite player or app:Apple Podcasts: https://apple.co/3T0YbSm   Spotify Podcasts: https://open.spotify.com/show/2sZ2wxO...   Google Podcasts: https://podcasts.google.com/feed/aHR0...   Amazon Music:

In this episode of “Answers From the Lab,” host Bobbi Pritt, M.D., chair of the Division of Clinical Microbiology at Mayo Clinic, is joined by William Morice II, M.D., Ph.D., CEO and president of Mayo Clinic Laboratories. They discuss Dr. Morice's recent article in Becker's Hospital Review, “Nine Developments Predicted to Shape Laboratory Medicine and Diagnostics in 2025,” and go deeper into conversation about: The rapid evolution of artificial intelligence and large language models.Digital pathology.Proteomics, metabolomics, and mass spectrometry.

JCO PO author Dr. David R. Gandara at UC Davis Comprehensive Cancer Center, shares insights into his JCO PO article, “Plasma Proteome–Based Test for First-Line Treatment Selection in Metastatic Non–Small Cell Lung Cancer,” one of the Top Articles of 2024. Host Dr. Rafeh Naqash and Dr. Gandara discuss how the PROphet® blood test supports first-line immunotherapy treatment decisions for metastatic NSCLC patients. TRANSCRIPT  Dr. Rafeh Naqash: Hello and welcome to JCO Precision Oncology Conversations where we bring you engaging conversations with authors of clinically relevant and highly significant JCOPO articles. I'm your host, Dr. Rafeh Naqash, Podcast Editor for JCO Precision Oncology and Assistant Professor at the OU Health Stephenson Cancer Center at the University of Oklahoma.  Today, we are absolutely thrilled to be joined by Dr. David R. Gandara, Professor of Medicine Emeritus, Co-Director of the Center for Experimental Therapeutics and Cancer and Senior Advisor to the Director at UC Davis Comprehensive Cancer Center and also the senior author of the JCO Precision Oncology article entitled “Plasma Proteome–Based Test for First-Line Treatment Selection in Metastatic Non–Small Cell Lung Cancer.” This was one of the top performing articles of 2024, which is one of the reasons why we wanted to bring it in for a podcast discussion. At the time of this recording, our guest's disclosures will be linked in the transcript.  David, it is an absolute pleasure to have you today. For somebody like you who's led the field of lung cancer over the years, I'm really excited that you are going to be talking to us about this very interesting article, especially given that I think you're one of the big proponents of liquid biopsies and plasma-based testing. So, for the sake of our listeners - which comprises of academic oncologists, community oncologists, trainees - could you tell us where the biomarker landscape for non-small cell lung cancer is currently, and then we can try to take a deeper dive into this article. Dr. David Gandar: Okay. Well, thank you, Rafeh. It's a pleasure to be with you here today. And I think the current landscape for biomarkers for immunotherapy in non-small cell lung cancer is a mess. There's no better way to describe it. That makes this paper describing a new plasma proteomic assay even more important. So I'll just give you a perspective. There are 14 trials, phase three trials, that were done in first line non-small cell lung cancer advanced stage of immunotherapy versus chemotherapy and some other aspects, although they vary tremendously. Some of them were checkpoint monotherapy, some combined with chemotherapy, some combined with CTLA-4 inhibitors and so forth. 12 out of the 14 were positive, 12 got FDA approval. So there are 12 different options that an oncologist could use. Some of them were squamous cell only, some non-squamous, some used PD-L1 as a biomarker driven part of the study. Some used TMB, tumor mutational burden, some were agnostic. So when you put all of this together, an oncologist can pick and choose among all these various regimens. And by and large, it's PD-L1 that is the therapeutic decision maker.  ASCO actually, I think, has done the very best job of making a guideline, and it's, as you well know, called a living guideline, it's dynamic. And it is much easier to interpret, for me and I think for oncologists, than some of the other guidelines. It's got a green light and a red light, it may be kind of orange. And so the green light means this is a strong recommendation by the guideline committee. The orange means it's weak. For this purpose, non-small cell lung cancer, advanced stage, only a very few of the recommendations were green. It's mainly monotherapy and patients with cancers with a PD-L1 over 50%. In our surveys, at our meetings, less than 50% of oncologists in the United States are following these guidelines. Why? Because they don't trust the biomarker. And TMB has the same sort of limitations. They're not bad biomarkers, they're incomplete. They're only looking at a part of the story. So that means we need a new biomarker. And this is one that, I think, the data are quite impressive and we'll discuss it more. Dr. Rafeh Naqash: Absolutely. Like you said, abundance of many therapy options, but not necessarily everything works the same in different subsets of PD-L1 positivity or different subsets of patients with different levels of tumor burden. And like you said, again, difficulty in trying to identify the right biomarker. And that's a nice segue to this PROphet test that you guys ran. So can you tell us a little bit about the plasma proteomic assay? Because to the best of my knowledge, there's not a lot of validated plasma proteomic assays. A lot has been done on the tumor tissue side as far as biomarkers are concerned, but not much on the blood side, except for maybe ctDNA MRD testing. So what was the background for trying to develop a plasma-based proteomic test? And then how did this idea of testing it in the lung cancer setting come into play? And then we can go into the patient population specifics, the cohort that you guys have. Dr. David Gandara: Okay. Well, of course there's a company behind this assay, it's called OncoHost, and I'm a consultant for them. And they came to me two years ago and they said, “We have something different from anyone else.” And they explained the science to me, as well as some other lung cancer experts here in the United States. I'm not a proteomic expert, of course, but they developed an AI machine learning platform to assess plasma proteins in normal people and in people with cancer, and specifically then in people with non-small cell lung cancer. They identified over 7,000 proteins that had cancer implications for therapy, for resistance, for prognosis, etc., and they categorized them based on the literature, TCGA data, etc., and used this machine learning process to figure out which proteins might be most specific for non-small cell lung cancer. And that's where they started. And so out of that 7,000 proteins, where they've identified which ones are angiogenic, which ones are involved with EMT or cell cycle or whatever it might be, they distilled it down to 388 proteins which they thought were worth testing in non-small cell lung cancer. And that's when I became involved.  They had a retrospective cohort of patients that had been treated with various immunotherapies. They looked at the analytic validation first, then applied it to this cohort. It looked good. Then they had a very large cohort, which they split, as you usually do with an assay, into a test set and then a validation set. For the test set, they wanted something more than a response. They wanted some indicator of long term benefit because that's where immunotherapy differentiates itself from chemotherapy and even targeted therapy. And so they picked PFS at 12 months. And I became involved at that point and it looked really good. I mean, if you look at the figures in the manuscript, the AUC is superb about their prediction and then what actually happened in the patient. And then in this paper, we applied it to a validation set of over 500 patients in a prospective trial, not randomized, it's called an observational trial. The investigator got to pick what they thought was the best therapy for that patient. And then in a blinded fashion, the proteomic assay experts did the analysis and applied it to the group.  And so what that means is some of the patients got chemotherapy alone, some got checkpoint immunotherapy monotherapy, some got in combination with chemotherapy. None of the patients in this study got a CTLA-4 inhibitor. That work is ongoing now. But what the study showed was that this assay can be used together with PD-L1 as what I would call a composite biomarker. You take the two together and it informs the oncologist about the meaning of that PD-L1. I'll give you an example. If that patient has a PD-L1 over 50% in their cancer and yet the PROphet test is negative, meaning less than 5 - it's a 0 to 10 scale - that patient for survival is better served by getting chemotherapy and immunotherapy. However, if the PROphet test is positive and the PD-L1 is over 50%, then the survival curves really look equivalent. As I said earlier, even in that group of patients, a lot of oncologists are reluctant to give them monotherapy. So if you have a test and the same sort of example is true for PD-L1 0, that you can differentiate. So this can really help inform the oncologist about what direction to go. And of course then you use your clinical judgment, you look at what you think of as the aggressiveness of the tumor or their liver metastases, etc. So again, that's how this test is being used for non-small cell lung cancer. And maybe I'll stop there and then I'll come back and add some other points. Dr. Rafeh Naqash: I definitely like your analogy of this therapy de-escalation strategy. Like you mentioned for PD-L1 high where the PROphet test is negative, then perhaps you could just go with immunotherapy alone. In fact, interestingly enough, I was invited to a talk at SITC a couple of weeks back and this exact figure that you're referring to was one of the figures in my slide deck. And it happened by chance that I realized that we were doing a podcast on the same paper today.  So I guess from a provocative question standpoint, when you look at the PD-L1 high cohort in the subset where you didn't see a survival difference for chemo plus immunotherapy versus immunotherapy alone, do you think any element of that could have been influenced by the degree of PD-L1 positivity above 50%? Meaning could there have been a cohort that is, let's say PD-L1 75 and above, and that kind of skews the data because I know you've published on this yourself also where the higher the PD-L1 above 50%, like 90% PD-L1 positivity survival curves are much better than 50% to 89%. So could that have somehow played a role? Dr. David Gandara: The first thing to say is that PD-L1 and the PROphet score, there's very little overlap. I know that sounds surprising, but it's also true for tumor mutational burden. There's very little overlap. They're measuring different things. The PD-L1 is measuring a specific regulatory protein that is applicable to some patients, but not all. That's why even in almost all of the studies, people with PD-L1 0 could still have some survival benefit. But in this case they're independent. And not in this paper, but in other work done by this group, the PROphet group, they've shown that the PROphet score does not seem to correlate with super high PD-L1. So it's not like the cemiplimab data where if you have a PD-L1 of greater than 90%, then of course the patient does spectacularly with monotherapy. The other thing that's important here is they had a group of around a little less than 100 patients that got chemotherapy alone. The PROphet score is agnostic to chemotherapy. And so that means that you're not just looking at some prognostic factor. It's actually clinical utility on a predictive basis. Dr. Rafeh Naqash: I think those are very important points. I was on a podcast a couple of days back. I think there's a theme these days we're trying to do for JCO Precision Oncology, we're trying to do a few biomarker based podcasts, and the most recent one that we did was using a tissue transcriptome with ctDNA MRD and you mentioned the composite of the PD-L1 and the PROphet test and they use a composite of the tissue transcriptome. I believe they called it the VIGex test as well as MRD ctDNA. And when your ctDNA was negative at, I believe, the three month mark, those individuals had the highest inflamed VIGex test or highest infiltration of T cells, STING pathway, etc. So are there any thoughts of trying to add or correlate tissue based biomarkers or ctDNA based correlations as a further validation in this research with the company? Dr. David Gandara: Right. So there are many things that are being looked at, various composites looking at the commutations that might affect the efficacy of immunotherapy and how they correlate with profit positivity or negativity. And I'll just give the examples of STK11 and KEAP1. As you know, there's some controversy about whether these are for immunotherapy, whether they're more prognostic or predictive. I'm one of the co-authors among many in the recently published Nature paper by Dr. Skoulidis and the group at MD Anderson which report that for KEAP1 positive especially, but also SDK11 mutated getting immunotherapy, that that's where the CTLA-4 inhibitors actually play the greatest role. So realizing that this is still controversial, there are preliminary data, not published yet, that'll be presented at an upcoming meeting, looking at many of these other aspects, P53, SCK11, KEAP1, other aspects, TMB, that's actually already published, I think in one of their papers. So yes, there's lots of opportunities.  The other cool thing is that this isn't a test, it's a platform. And so that means that the OncoHost scientists have already said, “What if we look at this test, the assay in a group of patients with small cell lung cancer?” And so I just presented this as a poster at the world conference in San Diego. And it turns out if you look at the biology of small cell, where neither PD-L1 nor TMB seem to be very important, if you look at the biology of small cell and you form an assay, it only shares 44 proteins out of the 388 with non-small cell. It's a different biology. And when we applied that to a group of patients with small cell lung cancer, again it had really pretty impressive results, although still a fairly small number of patients. So we have a big phase three study that we're doing with a pharmaceutical company developing immunotherapy where we are prospectively placing the PROphet test in a small cell trial.  The platform can also be altered for other cancer types. And at AACR, Dr. Jarushka Naidoo presented really impressive data that you can modify the proteins and you can predict immunotherapy side effects. So this is not like a company that says, “We have one test that's great for everything.” You know how some companies say, “Our test, you can use it for everything.” This company is saying we can alter the protein structures using AI machine learning assisted process to do it and we can have a very informed assay in different tumor types and different situations. So to me, it's really exciting. Dr. Rafeh Naqash: Definitely to me, I think, combining the AI machine learning aspect with the possibility of finding or trying to find a composite biomarker using less invasive approaches such as plasma or blood, definitely checks a lot of boxes. And as you mentioned, trying to get it to prospective trials as an integral biomarker perhaps would be likely the next step. And hopefully we see some interesting, exciting results where we can try to match or stratify patients into optimal combination therapies based on this test.  So now to the next aspect of this discussion, David, which I'm really excited about. You've been a leader and a mentor to many. You've led ISLC and several other corporate group organizations, et cetera. Can you tell us, for the sake of all the listeners, junior investigators, trainees, what being a mentor has meant for you? How your career has started many years back and how it's evolved? And what are some of the things that you want to tell people for a successful and a more exciting career as you've led over the years? Dr. David Gandara: Well, thank you for the question. Mentoring is a very important part of my own career. I didn't have an institutional mentor when I was a junior investigator, but I had a lot of senior collaborators, very famous people that kind of took me under their wing and guided me. And I thought when I basically establish myself, I want to give back by being a mentor to other people. And you wouldn't believe the number of people that I'm even mentoring today. And some of them are not medical oncologists, they're surgeons, they're radiation oncologists, they're basic scientists. Because you don't have to be an expert in that person's field to be a mentor. It helps, but in other words, you can guide somebody in what are the decision making processes in your career. When is it time to move from this institution onward because you can't grow in the institution you're in, either because it's too big or it's too small? So I established a leadership academy in the Southwest Oncology Group, SWOG. I've led many mentoring courses, for instance, for ISLC, now for International Society Liquid Biopsy, where I'm the executive committee liaison for what's called The Young Committee. So ISLB Society, totally devoted to liquid biopsy, six years old now, we have a Young Committee that has a budget. They develop projects, they publish articles on their own, they do podcasts. So what I'm saying is those are all things that I think opens up opportunities. They're not waiting behind senior people, they are leading themselves.  We just, at our International Lung Cancer Congress, reestablished a fellows program where a group of fellows are invited to that Huntington beach meeting. It's now in its 25th year and we spend a day and a half with them, mentoring them on career building. I'll just give you my first, I have the “Letterman Top 10”. So my first recommendation is if all you have is lemons, make lemonade. And what I'm meaning is find what you can do at your institution if you're a junior person, what you can claim to be your own and make the very best of it. But then as you get further along in my recommendations, one of them is learn when to say ‘no'. Because as a junior investigator the biggest threat to your career is saying ‘yes' to everybody and then you become overwhelmed and you can't concentrate. So I'll stop there. But anyway, yes, mentoring is a big part of my life. Dr. Rafeh Naqash: Well, thank you, David. This is definitely something that I'm going to try to apply to my career as well. And this has been an absolute pleasure, especially with all the insights that you provided, not just on the scientific side but also on the personal career side and the mentorship side. And hopefully we'll see more of this work that you and other investigators have led and collaborated on. perhaps more interesting plasma based biomarkers. And hopefully some of that work will find its home in JCO Precision Oncology. Thank you again for joining us today. Dr. David Gandara: My pleasure. Dr. Rafeh Naqash: And thank you for listening to JCO Precision Oncology Conversations. Don't forget to give us a rating or review and be sure to subscribe so you never miss an episode. You can find all ASCO shows at asco.org/podcasts.   The purpose of this podcast is to educate and to inform. This is not a substitute for professional medical care and is not intended for use in the diagnosis or treatment of individual conditions.  Guests on this podcast express their own opinions, experience and conclusions. Guest statements on the podcast do not express the opinions of ASCO. The mention of any product, service organization, activity or therapy should not be construed as an ASCO endorsement.   Dr. David Gandara Disclosures: Consulting or Advisory Role Company: Henlius USA, Foundation Medicine, Janssen Pharma, Merck & Co, Mirati Therapeutics, Regeneron, AstraZeneca, Guardant Health, Genentech, Exact Sciences  Research Funding Company: Amgen, Genentech, Astex Pharma  

On this episode of Translating Proteomics, co-hosts Parag Mallick and Andreas Huhmer of Nautilus Biotechnology discuss how clinical researchers can leverage proteomics for drug development. Some of the themes covered in this episode include:· Proteomics and pre-clinical models· How proteomics can drive patient selection· Choosing the right end points in clinical trialsChapters00:00 – 01:06 – Introduction01:06 – 06:51 – Proteomics in pre-clinical studies06:51 – 11:40 – The importance of choosing the right model for preclinical work11:40 – 17:10 – How proteomics is used in Phase I/II clinical trials17:10 – 19:29 – Proteomics tools in patient selection19:29 – 24:33 – Useful information that we get from proteomics that we can't get from genomics or transcriptomics24:33 – 28:14 – Proteomics in Phase III clinical trials and picking the best indications of drug efficacy28:14 – 29:19 - Understanding why clinical trials fail29:19 – End - Outro ResourcesThe National Cancer Institute's webpage covering how clinical trials workPreprint on the miBrain model - An example of a new in vitro brain modelGeary et al., 2021 - Discovery and Evaluation of Protein Biomarkers as a Signature of Wellness in Late-Stage Cancer Patients in Early Phase Clinical TrialsWasko et al., 2024 - Tumour-selective activity of RAS-GTP inhibition in pancreatic cancerThe NCI-MATCH trail: Lessons for precision oncology – Report on a large-scale trial using genomic biomarkers to match cancer patients to treatmentsTumour-selective activity of RAS-GTP inhibition in pancreatic cancer – Study using proteomics to understand mechanisms of resistance to a cancer drug

On this special, year-end episode of Translating Proteomics, hosts Parag Mallick and Andreas Huhmer discuss three of their favorite proteomics publications from 2024. They'll cover one paper in each of the following topic areas:Proteomics in pre-clinical researchProteomics in basic researchTechnology development in proteomicsSynopses of each of the papers can be found below and you can find many more insights in the podcast.Decrypting the molecular basis of cellular drug phenotypes by dose-resolved expression proteomicsIn this work from Professor Bernhard Kuster's Lab at the Technical University of Munich, researchers assess protein abundance changes that result from treating Jurkat acute T cell leukemia cells with 144 drugs over five drug doses. The researchers use their proteomic data to generate millions of dose response curves for the thousands of proteins measured and discover that the drugs impact many more proteins and pathways than those identified as drug targets. In addition, they checked how 7 of the drug treatments impacted the transcriptome and found there was often discordance between impacts at the mRNA level and the protein level. This works highlights the many ways drugs can impact biological systems and suggests that similar studies will help researchers understand the effects of drug treatments and may even aid in the development of more effective or more specific therapies.Find the publication here.Natural proteome diversity links aneuploidy tolerance to protein turnoverAs we discussed on a previous episode of Translating Proteomics, genome alterations often fail to faithfully propagate to the proteome. In this work, researchers from the labs of Professor Judith Berman at Tel Aviv University and Professor Markus Ralser at the Charité - Universitätsmedizin Berlin, investigate the means through which yeast strains adapt chromosome gains or losses (aneuploidy). They assess the concordance between changes in mRNA and protein expression in aneuploid yeast that were either found in nature or generated in the lab. The researchers observed dosage compensation, a tendency to return to expression levels associated with normal chromosome numbers, for both mRNAs and proteins expressed on aneuploid chromosomes. However, dosage compensation was much stronger at the protein level than the mRNA level and even stronger at the protein level in naturally aneuploid strains compared to lab-generated strains. This work suggests that multiomics efforts are necessary to determine the effects of genomic alterations. In addition, the authors find that protein degradation, as observed through increased ubiquitination, increased turnover of proteins encoded in aneuploid chromosomes, and the up regulation of the proteasome complex, is a key means of dosage compensation. Finally, because the naturally aneuploid strains achieved a higher a level of dosage compensation than the lab-generated strains, the authors suggest there has been selection for natural aneuploid strains that down-regulate proteins causing detrimental effects.

Dr. Christoph Borchers is a Full Member in the McGill Centre for Translational Research in Cancer, Senior Investigator at the Lady Davis Institute for Medical Research, Director of the Segal Cancer Proteomics Centre, and Professor in the Department of Oncology at McGill University. In this episode, Christoph discusses his research in the area of proteomics and important applications of his work in anti-doping, including a PCC-funded research project examining quantitative proteomics longitudinally in blood to screen for blood doping. He also shares future directions for this line of research and his perspectives on important areas of opportunity in anti-doping science.

As part of the US HUPO sponsored "What is a proteomics?" series, Ben and Ben sit down to talk with Dorte Bekker-Jensen, Evosep.

As part of the US HUPO sponsored "What is a proteomics?" series, Ben and Ben sit down to talk with Dr. Ilaria Piazza, Max Delbrück Center for Molecular Medicine.

Welcome to the Olink® Proteomics in Proximity podcast! Below are some useful resources mentioned in this episode:  Olink tools and softwareOlink® Explore 3072, the platform utilized by the UK Biobank to measure ~3000 proteins in plasma: https://olink.com/products-services/explore/Olink® Explore HT, Olink's most advanced solution for high-throughput biomarker discovery, measuring 5400+ proteins simultaneously with a streamlined workflow and industry-leading specificity: https://olink.com/products-services/exploreht/  UK Biobank Pharma Proteomics Project (UKB-PPP), one of the world's largest scientific studies of blood protein biomarkers conducted to date, https://www.ukbiobank.ac.uk/learn-more-about-uk-biobank/news/uk-biobank-launches-one-of-the-largest-scientific-studies  Research articlesThe support of human genetic evidence for approved drug indicationsMatthew R Nelson et al,  Nature Genetics 2015https://www.nature.com/articles/ng.3314 Proteomic aging clock predicts mortality and risk of common age-related diseases in diverse populationsM. Austin Argentieri et al,  Nature Medicine 2024https://www.nature.com/articles/s41591-024-03164-7 Plasma protein-based organ-specific aging and mortality models unveil diseases as accelerated aging of organismal systemsLudger J.E. Goeminne et al, Cell Metabolism 2024, in presshttps://www.sciencedirect.com/science/article/abs/pii/S1550413124004017?via%3Dihub Plasma proteomic associations with genetics and health in the UK BiobankBenjamin B. Sun et, Nature 2023https://www.nature.com/articles/s41586-023-06592-6 Rare variant associations with plasma protein levels in the UK BiobankRyan S. Dhindsa; Nature 2023https://www.nature.com/articles/s41586-023-06547-x Disease prediction with multi-omics and biomarkers empowers case–control genetic discoveries in the UK BiobankManik Garg, Nature Genetics, 2024https://www.nature.com/articles/s41588-024-01898-1 China Kadoorie Biobank: https://www.ckbiobank.org/publicationsPublications: https://www.ckbiobank.org/publications Subscribe to the podcast on your favorite player or app:Apple Podcasts: https://apple.co/3T0YbSm  Spotify Podcasts: https://open.spotify.com/show/2sZ2wxO...  Google Podcasts: https://podcasts.google.com/feed/aHR0...   Amazon Music: https://music.amazon.com/podcasts/d97...   Podcast Addict:

As part of the US HUPO sponsored "What is a proteomics?" series, Ben and Ben sit down to talk with Dr. Winston Timp, Johns Hopkins University.

On this episode of Translating Proteomics, hosts Parag Mallick and Andreas Huhmer of Nautilus Biotechnology discuss the challenges and opportunities of plasma proteomics. Their conversation focuses on:· Why blood plasma may be a good source of protein biomarkers· Current methodologies and pitfalls in plasma proteomics· The path forward for plasma proteomicsWhat is Plasma Proteomics?For those who are new to this topic, plasma is the liquid portion of the blood distinct from fractions containing red and white blood cells. Given the relatively non-invasive ways physicians can collect patient plasma, and the blood's intimate association with tissues throughout the body, plasma is potentially an excellent source of protein biomarkers. Yet, it is quite difficult to measure the levels of all plasma proteins because their concentrations span over 12 orders of magnitude. This episode features an in-depth discussion of the ways plasma proteomics efforts have and have not lived up to the promise of biomarker discovery and what we can do to advance plasma biomarker discovery efforts in the future.Chapters00:00 – 01:01 – Intro01:02 – 4:55 – What is the promise of plasma proteomics?04:55 – 07:23 – Is the plasma proteome really the best source of biomarkers?07:23 – 10:16 – How do proteins get into the blood and what are the implications for biomarker discovery?10:16 – 13:59 – Is it clear that proteins are the best candidates for blood biomarkers?13:59 – 19:57 – Advances in and the future of comprehensive plasma proteomics19:57 – 22:31 – Pros and cons of fractionating the plasma proteome to discover biomarkers22:31 – 28:14 – Progress in identifying multiomic plasma biomarkers and the path forward28:14 – End – OutroResourcesNano-omics: nanotechnology-based multidimensional harvesting of the blood-circulating cancerome (Gardner et al. 2022)o Review from focused on the development multiomics liquid biopsiesMulticompartment modeling of protein shedding kinetics during vascularized tumor growth (Machiraju et al. 2020)o Work from Parag's Lab investigating tumor protein sheddingSimulation of the Protein-Shedding Kinetics of a Fully Vascularized Tumor (Frieboes et al. 2015)o Tumor protein shedding work from Parag's LabMathematical model identifies blood biomarker-based early cancer detection strategies and limitations (Hori and Gambhir et al. 2011)o Study modeling how much protein could be shed and detected from different size tumorsThe human plasma proteome: history, character, and diagnostic prospects (Anderson and Anderson 2002)o Review discussing...

Bone mass declines with age, and the anabolic effects of skeletal loading decrease. While much research has focused on gene transcription, how bone ages and loses its mechanoresponsiveness at the protein level remains unclear. Researchers Christopher J. Chermside-Scabbo, John T. Shuster, Petra Erdmann-Gilmore, Eric Tycksen, Qiang Zhang, R. Reid Townsend, Matthew J. Silva from Washington University School of Medicine and Washington University in St. Louis, MO, share their findings which underscore the need for complementary protein-level assays in skeletal biology research. On October 12, 2024, their research paper was published as the cover of Aging (listed by MEDLINE/PubMed as “Aging (Albany NY)” and “Aging-US” by Web of Science), Volume 16, Issue 19, entitled, “A proteomics approach to study mouse long bones: examining baseline differences and mechanical loading-induced bone formation in young-adult and old mice.” Full blog - https://aging-us.org/2024/10/exploring-baseline-variations-and-mechanical-loading-induced-bone-formation-in-young-adult-and-aging-mice-through-proteomics/ Paper DOI - https://doi.org/10.18632/aging.206131 Corresponding author - Christopher J. Chermside-Scabbo - ccherms@wustl.edu Video short - https://www.youtube.com/watch?v=xm6o7gWH8p4 Sign up for free Altmetric alerts about this article - https://aging.altmetric.com/details/email_updates?id=10.18632%2Faging.206131 Subscribe for free publication alerts from Aging - https://www.aging-us.com/subscribe-to-toc-alerts Keywords - aging, bone, mechanical loading, proteomics, RNA-seq/transcriptomics About Aging-US The mission of the journal is to understand the mechanisms surrounding aging and age-related diseases, including cancer as the main cause of death in the modern aged population. The journal aims to promote 1) treatment of age-related diseases by slowing down aging, 2) validation of anti-aging drugs by treating age-related diseases, and 3) prevention of cancer by inhibiting aging. (Cancer and COVID-19 are age-related diseases.) Please visit our website at https://www.Aging-US.com​​ and connect with us: Facebook - https://www.facebook.com/AgingUS/ X - https://twitter.com/AgingJrnl Instagram - https://www.instagram.com/agingjrnl/ YouTube - https://www.youtube.com/@AgingJournal LinkedIn - https://www.linkedin.com/company/aging/ Pinterest - https://www.pinterest.com/AgingUS/ Spotify - https://open.spotify.com/show/1X4HQQgegjReaf6Mozn6Mc Media Contact 18009220957 MEDIA@IMPACTJOURNALS.COM

BUFFALO, NY- October 15, 2024 – A new #research paper was #published on the #cover of Aging (listed by MEDLINE/PubMed as "Aging (Albany NY)" and "Aging-US" by Web of Science), Volume 16, Issue 19 on October 12, 2024, entitled, “A proteomics approach to study mouse long bones: examining baseline differences and mechanical loading-induced bone formation in young-adult and old mice.” As noted in the abstract, bone mass declines with age, and the anabolic effects of skeletal loading decrease. While much research has focused on gene transcription, how bone ages and loses its mechanoresponsiveness at the protein level remains unclear. In their paper, researchers Christopher J. Chermside-Scabbo, John T. Shuster, Petra Erdmann-Gilmore, Eric Tycksen, Qiang Zhang, R. Reid Townsend, and Matthew J. Silva from Washington University School of Medicine and Washington University in St. Louis, Missouri, describe how they developed a novel proteomics approach and conducted paired mass spectrometry and RNA-seq analyses on tibias from young-adult (5-month) and old (22-month) mice. The researchers report the first correlation estimate between the bone proteome and transcriptome (Spearman ρ = 0.40). While this is consistent with findings from other tissues, it suggests that only a relatively low amount of variation in protein levels is explained by variation in transcript levels. Of the 71 shared targets that differed with age, eight were associated with bone mineral density in previous GWAS, including the understudied targets Asrgl1 and Timp2. Using complementary RNA in situ hybridization, the researchers confirmed that Asrgl1 and Timp2 showed reduced expression in osteoblasts/osteocytes in aged bones. Additionally, they found evidence of reduced TGF-beta signaling with aging, particularly Tgfb2. The researchers also identified proteomic changes following mechanical loading, noting that at the protein level, bone differed more with age than with loading, and aged bone exhibited fewer loading-induced changes. "Overall, our findings underscore the need for complementary protein-level assays in skeletal biology research.” DOI - https://doi.org/10.18632/aging.206131 Corresponding author - Christopher J. Chermside-Scabbo - ccherms@wustl.edu Video short - https://www.youtube.com/watch?v=xm6o7gWH8p4 Sign up for free Altmetric alerts about this article - https://aging.altmetric.com/details/email_updates?id=10.18632%2Faging.206131 Subscribe for free publication alerts from Aging - https://www.aging-us.com/subscribe-to-toc-alerts Keywords - aging, bone, mechanical loading, proteomics, RNA-seq/transcriptomics About Aging-US The mission of the journal is to understand the mechanisms surrounding aging and age-related diseases, including cancer as the main cause of death in the modern aged population. The journal aims to promote 1) treatment of age-related diseases by slowing down aging, 2) validation of anti-aging drugs by treating age-related diseases, and 3) prevention of cancer by inhibiting aging. (Cancer and COVID-19 are age-related diseases.) Please visit our website at https://www.Aging-US.com​​ and connect with us: Facebook - https://www.facebook.com/AgingUS/ X - https://twitter.com/AgingJrnl Instagram - https://www.instagram.com/agingjrnl/ YouTube - https://www.youtube.com/@AgingJournal LinkedIn - https://www.linkedin.com/company/aging/ Pinterest - https://www.pinterest.com/AgingUS/ Spotify - https://open.spotify.com/show/1X4HQQgegjReaf6Mozn6Mc MEDIA@IMPACTJOURNALS.COM

In this episode of FYI, Brett Winton, ARK's Chief Futurist, and Nemo Marjanovic, ARK's Multiomics Analyst, have an in-depth discussion with Professor Nikolai Slavov from Northeastern University. Professor Slalov is the Director of Parallel Squared Technology Institute (PTI). Together they explore the fascinating and complex world of multiomics, focusing on the importance of proteomics in understanding biological processes. Professor Slavov shares his insights on the technological advancements in single-cell proteomics, the challenges in measuring protein interactions, and the critical role of proteomics in drug development. The conversation also delves into the underfunded nature of proteomics research and its potential to revolutionize biopharma R&D and diagnostics.Key Points From This Episode:Introduction to multi-omics and its relevance in modern biology.Explanation of the central dogma of molecular biology: DNA, RNA, and proteins.Overview of Professor Slavov's research on single-cell proteomics and its implications.Challenges in measuring the dynamic and complex nature of the proteome.The role of advanced technologies like mass spectrometry in proteomic analysis.Importance of protein interactions and modifications in cellular functions.Discussion on the underfunding of proteomics research and its impact on scientific progress.The potential of proteomics to improve drug development and diagnostic precision.Advances in AI and data analysis techniques for better understanding protein structures and functions.Future frontiers in proteomics, including improved technology access and dynamic protein measurements.References:MacCoss, M.J., Alfaro, J.A., Faivre, D.A. et al. Sampling the proteome by emerging single-molecule and mass spectrometry methods. Nat Methods 20, 339–346 (2023). https://doi.org/10.1038/s41592-023-01802-5 Derks J, Jonson T, Leduc A, Khan S, Khoury L, Rafiee M, Slavov N Single-nucleus proteomics identifies regulators of protein transportbioRxiv  doi: 10.1101/2024.06.17.599449 (2024)

As part of the US HUPO sponsored "What is a proteomics?" series, Ben and Ben sit down to talk with Dr. Rob Moritz, Institute for Systems Biology.

As part of the US HUPO sponsored "What is a proteomics?" series, Ben and Ben sit down to talk about "What is Proteomics?" with Dr. Marc Wilkins, University of New South Wales. This episode was released on 5 September 2024, the 30th anniversary of the coining of the term proteomics.

Send us a textAbout the guest: Austin Argentieri, PhD is a researcher in the Analytic & Translational Genetics Unit at the Massachusetts General Hospital with academic appointments at Harvard & the Broad Institute. His research focuses on large-scale analyses to to understand human aging.Episode summary: Nick and Dr. Argentieri discuss: chronological vs. biological age; DNA methylation and aging clocks; proteomics and protein measurements in aging research; health, longevity, and human healthspan; and more.Related episodes:Aging, mTOR, Sirtuins, Rapamycin, Metformin, the Truth of Resveratrol & Longevity Supplements, David Sinclair & Anti-Aging Myths | Matt Kaeberlein | #151Cellular Aging, Taurine, Nutrition, Senescence, Longevity, Mitochondria, Metabolism | Vijay Yadav | #122*This content is never meant to serve as medical advice.Support the Show.All episodes (audio & video), show notes, transcripts, and more at the M&M Substack Try Athletic Greens: Comprehensive & convenient daily nutrition. Free 1-year supply of vitamin D with purchase.Try SiPhox Health—Affordable, at-home bloodwork w/ a comprehensive set of key health marker. Use code TRIKOMES for a 10% discount.Try the Lumen device to optimize your metabolism for weight loss or athletic performance. Use code MIND for 10% off.Learn all the ways you can support my efforts

As part of the US HUPO sponsored "What is a proteomics?" series, Ben and Ben sit down to talk with Dr. Lindsay Pino, Talus Bio, in an episode that is really just us talking about what Season 5 could be. Enjoy?

Episodi 127 i Buchi Podcast Shqip sjell një intervistë me Mirea Mema, e cila ka përfunduar studimet për Bioteknologji në Universitetin Politeknik të Berlinit dhe aktualisht është në përfundim të studimeve master me specializim në bioteknologji mjekësore. Përveç angazhimit të saj akademik, Mirea ka punuar për tre vite si asistente në kërkim shkencor në fushën e "Proteomics", duke kontribuar në avancimin e kërkimeve të rëndësishme shkencore. Në këtë episod, Mirea ndan përvojën e saj në fushën e bioteknologjisë dhe përpjekjet e saj për të balancuar studimet me karrierën kërkimore.

Azra Raza, Professor of Medicine and Director of the Myelodysplastic Syndrome (MDS) Center at Columbia University in New York, joins Jonathan Sackier to discuss her mission to shift the field of oncology, ensuring it focuses on eliminating the first cancer cell rather than chasing after the last.     Timestamps:   (00:00)-Introduction  (02:37)-Poetry  (08:50)-Raza's journey into oncology  (14:41)-Myelodysplastic syndrome and Raza's tissue bank  (21:16)-The First Cell    (28:18)-The cancer Questions Project  (38:20)-Goals for the future  (44:40)-The most pressing issues in cancer care  (48:14)-Financially incentivising early detection  (57:00)-3 Quarks Daily  (59:10)-Three wishes for healthcare   

Sujal Patel, co-founder and CEO of Nautilus Biotechnology, discusses their innovative work in proteomics and its impact on drug development. Sujal shares his transition from tech to biotech, the formation of Nautilus with Parag Mallick, and their revolutionary approach using multi-affinity probes. The conversation highlights the importance of proteomics in drug discovery, the broad applications of their technology, and the significance of product-market fit and fiscal discipline in building a sustainable business. Biography: Sujal Patel is the co-founder of Nautilus Biotechnology, a life sciences company working to create a platform technology for quantifying and unlocking the complexity of the proteome. Nautilus' mission is to democratize access to the proteome and, in doing so, enable fundamental advancements across human health and medicine. Sujal founded Isilon Systems in 2001, a storage company built for the future of unstructured, file-based data. In 2006, Isilon completed one of the most successful initial public offerings of the year. EMC (since acquired by Dell) acquired Isilon in December 2010 for $2.6 Billion, the largest acquisition in EMC's history. Sujal served as the president of EMC's Isilon Storage Division from the acquisition until November 2012, driving significant revenue growth, market expansion, and organizational scale. Prior to EMC and Isilon, Sujal served in various engineering roles at RealNetworks, Inc., in part as the chief architect behind the company's second-generation core media delivery system. Sujal holds nineteen patents in the areas of storage, networking, and media delivery and five patents for innovations related to the development of Nautilus Biotechnology's technology. He is a well-known speaker on entrepreneurship and has received a variety of industry awards. Currently, Sujal serves on the board of directors at Qumulo and Rainier Scholars and helps direct the philanthropic efforts of his family's foundation. He graduated from the University of Maryland College Park in 1996 with a degree in computer science.

Despite incredible leaps in our understanding of molecular biology, the majority of drug development efforts still fail, and those that succeed often fail to return investment dollars. Proteomics has the potential to change that by providing high-resolution views of the biochemical drivers of biological function - proteins. In this episode of Translating Proteomics, Parag and Andreas discuss how proteomics can help researchers identify good drug targets, personalize drug development, and advance precision medicine.Chapters:00:00 - How do we define good drug targets and "druggable" in the age of proteomics08:16 - Advancing personalized medicine through proteomics10:58 - How proteomics technologies have changed drug development15:13 - New abilities next-generation proteomics technologies give us in drug developmentLearn about proteomics and biomarker discovery:https://youtu.be/8rcAxHSRGYs?si=kZ0UX42TJ8tWIaSNLearn more about proteomics and precision medicine:https://youtu.be/bzRlM45agBY?si=eop2XcGLc_oLeiVc

Proteomics is an emerging field in cancer care and research. The National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium (CPTAC) aims to get to the heart of cancer by studying its molecular basis across different cancers. The group believes expanding open-source resources and other data can lead to new treatments in cancer and expand precision medicine. Dr. Henry Rodriguez, the founding director of the Office of Cancer Clinical Proteomics Research at NCI, discusses the program and how the related International Cancer Proteogenome Consortium (ICPC) is helping researchers pull together resources necessary to innovate cancer care.

Today I am speaking with Dr. Jin-Xiong She about all thing NAD+, we discuss what it is, how to measure your NAD+ levels, what impact your NAD+ levels have on your health and longevity, how to optimize your NAD+ levels and so much more! Use code KAYLA to save on all NAD+ optimization products ! About Dr. Dr. Jin-Xiong She Dr. Jin-Xiong She received his college education in China and PhD degree in France.  After a short postdoctoral training at the University of Florida (UF), he was quickly promoted to Assistant Professor, Associate Professor, Full and Endowed Professor.  He served as Division Chief of Experimental Pathology and Director of Research of the UF's world-class Diabetes Center.  Dr. She was recruited in 2002 to be the Georgia Research Alliance Eminent Scholar in Genomic Medicine at the Medical College of Georgia.  He was the founding Director of the Center for Biotechnology and Genomic Medicine, Professor of the Departments of Obstetrics and Gynecology and Department of Health Technologies as well as the director of two core research facilities for Augusta University (Genomics, Proteomics & Mass Spectrometry). In his long academic career, he has authored over 400-peer reviewed papers with an H-Index of 76 and over 19,000 citations, secured over $100 million in research grants, has been invited to speak globally.  He mentored a large number of doctoral students, post-docs and faculty members. Dr. She is one of the 20 “Georgia Top Medical Researchers”.  He served as President of the Chinese Geneticists in America and President of the American Diabetes Association's council on Immunology, transplantation and Immunogenetics among other honors.  Dr. She is a serial entrepreneur and has founded or co-founded multiple companies in the US and China. He is the founder and CEO of Jinfiniti Precision Medicine, a company dedicated to optimizing healthspan through biomarker testing and precision nutraceuticals. More information can be found on Jin-Xiong She' LinkedIn Profile and Jin-Xiong She's Google Scholar Profile. Boying DunPhD, co-Founder & Chief Innovation OfficerBob ThordarsonChief Technology OfficerMichael HeckPhD, CLIA Clinical Laboratory Director

We know that there are a billion people in the world with undiagnosed obstructive sleep apnea (OSA) and that it simply isn't practical to have every person undergo a sleep study. Are there other methods that might be more efficient identifying those at the highest risk of OSA? Dr. Laura Castillo is a chemist who has studied biological matrices to identify biomarkers for obstructive sleep apnea. Her research involves analyzing sweat and she has found that there are specific markers for those with severe OSA and those without any OSA. Dr. David Gozal has been working in this field for many years and has published extensively. He has also studied urine proteomics as a method to identify sleep disordered breathing in children.

Ivan Godinez Director of Product Management at Proteintech(2:00) What does Ivan do for Proteintech?(4:10) Importance of single-cell level resolution and getting diverse data to answer scientific questions with different approaches(6:10) How did Ivan get to where he wanted? (8:12) Ivan's entrance into biotech, and subsequently, product management.(13:30) What makes a great product manager?(22:07) The science behind Proteintech(34:57)  Proteomics compared to transcriptomics (RNA-seq) and the unique challenges of proteomics. (38:35) Advice to students regarding taking the leap from benchtop science to business in biotechnology companies.  Follow our Instagram @insidebiotech for updates about episodes and upcoming guests! To learn more about BCLA's events and consulting visit our website.Follow BCLA on LinkedIn

The idea to measure the proteome to get a clear understanding of healthy and diseased tissues at the molecular level has been around for many years but has not come to fruition in a broadly accessible and applicable way. In this episode we discuss:Why now is the time to make this goal a realityWhy past efforts to broadly leverage proteomics did not work outWhat we've learned from the pastWhat's changed in proteomics and science in general that makes a proteomics breakthrough possibleLearn more about proteomics

Sure, proteomics may revolutionize precision medicine and biomarker discovery, but did you know it can help make better cheese? Listen to the latest episode of our new series, "Translating Proteomics" featuring Nautilus Co-Founder and Chief Scientist, Parag Mallick, and Nautilus Senior Director of Scientific Affairs and Alliance Management, Andreas Huhmer to learn the many ways we can put the proteome to work as the proteomics revolution begins to bear fruit.Learn more about applications of proteomicsIn this episode, Parag mentions work from Matthias Selbach's Lab. Learn more about the Selbach Lab here.

Welcome to the Olink® Proteomics in Proximity podcast! Below are some useful resources mentioned in this episode:  UK Biobank Pharma Proteomics Project (UKB-PPP), one of the world's largest scientific studies of blood protein biomarkers conducted to date, https://www.ukbiobank.ac.uk/learn-more-about-uk-biobank/news/uk-biobank-launches-one-of-the-largest-scientific-studies  UKB-PPP online resources developed by Nick Lehner and Maria Wörheidehttps://metabolomips.org/ukbbpgwas/ Metabolomics and Proteomics Core in Munich:https://www.helmholtz-munich.de/en/core-facility-overview/metabolomics-and-proteomicshttps://www.helmholtz-munich.de/core-facilitiesStefanie.hauck@helmholtz-munich.de ClinspectM (https://clinspect-m.mscoresys.de/) consortium in the Munich area dedicated to move proteomics forward to clinical applicationMore joint initiatives towards Germany-wide benchmarking and standardized processes are in the making, follow the news on https://www.mscoresys.de/ Research articlesSun, B.B., Chiou, J., Traylor, M. et al.  Plasma proteomic associations with genetics and health in the UK Biobank. 2023 Nature, DOI: 10.1038/s41586-023-06592-6 https://www.nature.com/articles/s41586-023-06592-6Petrera A, von Toerne C, Behlr J, et al. Multiplatform Approach for Plasma Proteomics: Complementarity of Olink Proximity Extension Assay Technology to Mass Spectrometry-Based Protein Profiling. (2020) Journal of Proteome Researchhttps://pubs.acs.org/doi/pdf/10.1021/acs.jproteome.0c00641Multicenter Collaborative Study to Optimize Mass Spectrometry Workflows of Clinical Specimens. Kardell O, von Toerne C, Merl-Pham J, König AC, Blindert M, Barth TK, Mergner J, Ludwig C, Tüshaus J, Eckert S, Müller SA, Breimann S, Giesbertz P, Bernhardt AM, Schweizer L, Albrecht V, Teupser D, Imhof A, Kuster B, Lichtenthaler SF, Mann M, Cox J, Hauck SM. J Proteome Res. 2024 Jan 5;23(1):117-129. doi: 10.1021/acs.jproteome.3c00473. Epub 2023 Nov 28. PMID: 38015820 https://pubs.acs.org/doi/10.1021/acs.jproteome.3c00473 Olink tools and softwareOlink® Explore 3072, the platform utilized by the UK Biobank to measure ~3000 proteins in plasma: https://olink.com/products-services/explore/Olink® Explore HT, Olink's most advanced solution for high-throughput biomarker discovery, measuring 5400+ proteins simultaneously with a streamlined workflow and industry-leading specificity: https://olink.com/products-services/exploreht/  Subscribe to the podcast on your favorite player or app:Apple Podcasts: https://apple.co/3T0YbSm  Spotify Podcasts: https://open.spotify.com/show/2sZ2wxO...   Google Podcasts: https://podcasts.google.com/feed/aHR0...  Amazon Music:

Jan Spacek is an explorer both on Earth and beyond. He has worked in the fields of astrobiology, electrochemistry, nanoscience, genomics, and proteomics searching for life within our solar system. Jan is an astrobiologist working with renowned scientist Steven Benner on expanding the genetic alphabet.  In this episode of Casual Space, Jan discusses his transition to astrobiology, his work on projects related to the search for life on Mars and Venus, and the potential for private space missions. Jan explains the importance of planetary protection, the challenges of distinguishing between Earthly contamination and Martian life, and the implications of discovering life for future human missions.  When he's not looking for life on Mars, or why Venus is yellow, Jan is busy freediving or bicycling across Australia. (!)  Follow Jan's critical thinking about life in the universe at The Primordial Scoop https://primordialscoop.org/, a blog devoted to discussing questions related to synthetic biology and astrobiology and asking the big questions about where life began and how.  Jan has worked in the field of electrochemistry of modified and natural DNA at the Czech Academy of Sciences and the Central European Institute of Technology. He has also visited the Ege University (Izmir), the Interdisciplinary Nanoscience Center (Aarhus), the Department of NanoEngineering at UCSD, and the Foundation for Applied Molecular Evolution (Alachua). He presently develops life detection devices, from coronavirus to Venusians and Martians, at the Firebird Biomolecular Sciences LLC. Outside of science, Jan bicycled around the Baltic Sea and across the Australian continent, 7500 kilometers in all. Jan earned a Master's degree in Molecular Biology and Genetics and a Ph.D. in Genomics and Proteomics (both at Masaryk University in the Czech Republic).