Josh L Espinoza
San Diego, California, United States
575 followers
500+ connections
About
A doctorate-level Lead Bioinformatics Scientist with over a decade of experience building…
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575 followers
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Josh L Espinoza reposted thisJosh L Espinoza reposted thisWOW! Ten projects spanning blue carbon ecosystems and marine microbes will receive $3.4 million to demonstrate the use of genetic rescue as a tool for climate adaptation and mitigation. https://lnkd.in/gfUVp2sGRevive & Restore Announces Inaugural Climate Resilience Fund CohortRevive & Restore Announces Inaugural Climate Resilience Fund Cohort
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Josh L Espinoza reposted thisJosh L Espinoza reposted thisThe Founder and CEO of our J. Craig Venter Institute, where I am a professor, died yesterday. The world knows J. Craig Venter as the titan who decoded the human genome. I knew him as a "doer," a car lover, a data lover, a dog lover, a surfer, a medic in the military, a mechanic, a pilot, and a friend who changed the trajectory of my career. In addition to being a living genius, he was also a man of action who loved flying- recently, he was proud of the Cirrus SR22 Turbo G6. At the JCVI, he built a culture of humanity where every employee could bring their dog to work. He sequenced the first bacteria, Drosophila, the dog... He loved that I sequenced the human NETOME ( just trying to make him proud). In 2019, I organized the IADR conference here at JCVI, La Jolla. But the speaker got stuck in immigration for a 200-scientist conference. Craig stepped in for me as a keynote. With just two slides, he delivered a brilliant lecture on predicting craniofacial features through sequencing. His dog Darwin was there. He even shared that his first faculty position was at the University at Buffalo, where he sequenced the DNA of salivary glands. I believe he was working on ATP. In another event, this time on the East Coast, I had just arrived at his house in Nantucket, where we had planned a fundraising event. Minutes before I was set to give a talk, he asked for my help. “Can you help me fix this car?” I never imagined being elbow-deep in a motor with a man of his caliber with oil in my hands. I said, "Not really. No, I don't want to. But, for you, anything." After getting out of the car and then fixing the parts, he asked me to try to start the car, but it would not work, and then it did. He told me, “You have to deconstruct to know how to construct.” While in the past, multiple team members were intimidated by him, I did enjoy his directness. We both bonded over big data. While he initially had other ideas for what I was investigating in my laboratory, he listened—truly listened—to why and what I believed, and he would engage in the next steps and what to do. He was not political about things; he wanted things to be done well. He was never afraid to be curious about the "why." There were insane moments, such as high-stakes pool games in which we were very competitive or building and cofounding companies -Craig was unapologetically himself. He skipped the introductions and went straight to the data and facts. That kid from the sugar cane fields (me) never imagined working so closely with someone who changed the face of modern science globally. Craig, thank you for the unique moments we saw eye to eye, for the challenges, and for your friendship. You are immortal just as your legacy ; ) #CraigVenter #Science #Innovation #Mentorship #Genomics #JCVI https://lnkd.in/g7C4b5JU
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Josh L Espinoza shared thisOur next 20 years: AI, capitalism, and fractal minds | Judah Anttila | TEDxOUOur next 20 years: AI, capitalism, and fractal minds | Judah Anttila | TEDxOU
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Josh L Espinoza reposted thisJosh L Espinoza reposted thisIn 2022, we proposed the term and concept of “Microbiome Stewardship” https://lnkd.in/e3we2fAu To “underscore that organismal and ecosystem health can be more effectively managed and maintained by monitoring and suitably manipulating the microbiome.” If needed. “Accordingly, the term also encompasses the sum of all approaches, methodologies and technologies to understand and, consequently, manipulate microbiome function, with stewardship emphasizing the advocacy and support for science-based management” The paper takes a deep dive into the several aspects and tools that can be used to monitor, preserve and - if needed - manipulate the microbiome to preserve or recover ecosystems and organismal health. Our concept was adopted and very well received and applied, supported and highlighted by several colleagues (e.g., https://lnkd.in/ewEa5Y4Z). In our paper, we also propose a science-based framework for policy/decision makers for the proper use of these approaches, from observing to managing/preserving and, ultimately, actively acting when needed. This idea is more timely than ever and a core aspect of the new IUCN microbial conservation specialist group; to use science, risk assessment tools and ecological concepts to guide the preservation - and, if needed, restoration or rehabilitation - of the Earth microbes and microbiomes. It is a big challenge and we hope to have a lot of transparency, collaboration and support to get it done! Some key resources: https://lnkd.in/e3we2fAu https://lnkd.in/eD2k5749 https://lnkd.in/dm4PNbQX https://lnkd.in/eY2PiZbT https://lnkd.in/eJGXxXBN Jack Gilbert Chris Greening Christian R Voolstra Berg Gabriele Amber Hartman Scholz, Ph.D. Diego J. Jiménez Avella PhD. Alexandre Soares Rosado Applied Microbiology International ISME | International Society for Microbial Ecology Linda Scholten Lucy Harper PhD MBA Kent Redford Brajesh Singh, FAA Blake Ushijima Prof. Michael J Sweet Rodrigo Costa Tina Keller-Costa Helena Villela Suzanne Ishaq Jonathan Eisen Gerard Muyzer Seth Bordenstein Emily Kunselman and all other co-authors of the cited papers and/or involved with the MCSG! #microbiomestewardship #microbialconservationspecialistgroup #iucn #mcsg #microbiomes
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Josh L Espinoza reposted thisJosh L Espinoza reposted thisWhat happens when you train a transformer on 123 million bacterial proteins Bacteria have been fighting viruses for billions of years. To do it, they have evolved a remarkable diversity of antiphage defense systems — molecular immune machines that detect and destroy invading phages. Yet fewer than 250 such systems had been experimentally validated. A new study in Science suggests we've barely scratched the surface. Mordret and coauthors asked a simple but powerful question: can language models trained on protein sequences and genomic context learn the "grammar" of bacterial immunity well enough to predict entirely unknown defense systems at scale? They developed three complementary deep learning models. ALBERTDF adapts the ALBERT transformer architecture to treat genes as words and genome neighborhoods as sentences — learning defensiveness from genomic context alone, without any sequence information. ESMDF fine-tunes the ESM2 protein language model with LoRA adapters to classify proteins as defensive or non-defensive directly from amino acid sequence — trained on a dataset of 123 million proteins drawn from 32,000 bacterial genomes. GeneCLRDF combines both signals through contrastive learning: it teaches the model that a gene's identity can be inferred either from its sequence or from the genomic neighborhood where it lives. This joint embedding achieves 99% precision and 92% recall on held-out benchmarks — far outperforming each approach independently. The models aren't just impressive on paper. The authors experimentally validated 12 antiphage systems with no prior link to immunity, in both E. coli and Streptomyces albus. Some carry canonical defense domains; others involve proteins with no known association to antiphage function whatsoever. Applied to over 32,000 bacterial genomes, GeneCLRDF predicts 2.39 million antiphage proteins. Around 1.5% of a typical bacterial genome is devoted to defense — three times previous estimates — and more than 85% of predicted protein families have no prior link to immunity. The implications are immediate. The predicted atlas — including ~23,000 candidate operon families — is a ready-made discovery pipeline for novel nucleases, molecular effectors, and antimicrobial mechanisms directly relevant to phage therapy and programmable biologics. Language models are turning the bacterial pangenome into an actionable resource. Paper: Mordret et al., Science (2026) — Science license | https://lnkd.in/efZkdNb9 #ArtificialIntelligence #MachineLearning #DeepLearning #ProteinLanguageModels #Transformers #ContrastiveLearning #Bioinformatics #ComputationalBiology #Microbiology #SyntheticBiology #DrugDiscovery #Biotechnology #PhageTherapy #AIforScience #GenomicsAI
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Josh L Espinoza reposted thisJosh L Espinoza reposted this‼️ Transformative Manuscript Alert!! https://lnkd.in/eym9m3VX What if restoring microbes could protect entire ecosystems - not just individual hosts? We’re excited to share our new preprint showing the first evidence that: 😁 Coral microbiome restoration can scale from the organism to the ecosystem. In this study, we applied coral probiotics to corals in the Red Sea over 18 months - right through a record marine heatwave during the fourth global bleaching event. The result? - Not only did treated corals perform better… - Entire surrounding reef communities were buffered. What we observed: Compared to untreated areas, probiotic-treated reef patches showed: Higher cryptobenthic biodiversity More stable and connected microbial networks Continued positive calcification (vs. dissolution) Greater overall ecosystem stability under extreme heat Meanwhile, control reefs experienced: ❌ Biodiversity collapse ❌ Microbial network breakdown ❌ Net reef erosion Why this matters This is the first long-term in situ evidence that: - Not only do Coral Probiotics not seem to cause any harm to off-target organisms, but targeting the microbiome of a key species can actually cascade into ecosystem-level PROTECTION. - Importantly, differences emerged without detectable off-target effects prior to the heatwave (aligned with the results by Dr. Nathalia Delgadillo Ordoñez and colleagues https://lnkd.in/dyhkRKDJ in HEALTHY conditions). Treatment-dependent trajectories after the heatwave reflect, in fact, the reduced deterioration in probiotic patches, which IS a beneficial off-target STRESS-dependent effect. This shifts the paradigm from: ❌ Protecting species in isolation to ✅ Engineering resilience across entire ecosystems A new frontier: Microbiome-driven ecosystem restoration As climate change accelerates, traditional conservation alone is not enough. Kudos to the AMAZING Scientists doing this work (***very hard 18month field work + lots of lab and computational analyses, lots of samples and lots of love and dedication) led by Yusuf Christian E. and the team Francisca C. Garcia Erika Santoro Neus Garcias Bonet Matteo Monti Marcos Teixeira Micaela Justo Gloria Juan Glafira Laura BeenhamGustavo Duarte Duarte Anthony Torsten and Susana Carvalho. You guys are the best! International Coral Reef Initiative (ICRI)International Coral Reef Society Christian R Voolstra Jack Gilbert ISME | International Society for Microbial Ecology Applied Microbiology International Lucy Harper PhD MBA Jonathan Eisen Alexandre Soares Rosado Mashael AlShalan Great Barrier Reef Foundation David Suggett Tali Vardi, Ph.D. Blake Ushijima Sean M. Gibbons Seth Bordenstein Maximilian P. David Feary Chico Birrell General Organization for Conservation of Coral Reefs and Turtles in the Red Sea - shams Dr Edward Oldmeadow Red Sea Global Thomas W. Crowther Bronwyn Wake Clare Davis Emily White Gerard Muyzer
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Josh L Espinoza reposted thisThrilled to release our report on biological approaches to atmospheric methane removal! The report consists of 22 problem statements describing actionable problems for advancing four prospective methane removal pathways, which we coauthored with 35 international contributors. It all stemmed from a workshop we co-hosted with Spark Climate Solutions. These problem statements have already driven $750k of grants to support new research. See funded projects led by: Carlos G. Acevedo-Rocha: https://lnkd.in/g25jvX9W Carol Baumbauer: https://lnkd.in/gkb_iXQP Doug Call: https://lnkd.in/g6m-VgMi Hendrik Schäfer and Vincent Gauci: https://lnkd.in/gYsrRSia Michael Konopka and Loren Looger: https://lnkd.in/geKZmuhY Hinsby Cadillo-Quiroz: https://lnkd.in/gWGfrfUA Huge appreciation to Spark and all of the amazing researchers who contributed to the report.Josh L Espinoza reposted this📣 Homeworld Releases Biological Methane Removal Report - https://lnkd.in/emsGAf3p Methane is responsible for roughly 30% of global warming to date, and it's an 80x more potent greenhouse gas than CO₂ over a 20-year period. Even with full deployment of known mitigation strategies, a significant emissions gap is expected to persist through 2050—driven in part by rising natural emissions feedbacks that we can't simply regulate away. Biological methane removal (bioMR) is one of the most promising frontiers for closing that gap, but the field is early, and the key technical bottlenecks haven't been systematically mapped. In Fall 2024, Homeworld Collective and Spark Climate Solutions convened 30 expert researchers from around the world for a two-day workshop, with the goal of surfacing the highest-leverage open problems across four bioMR pathways: engineered methane-removing plants, methanotroph-based bioreactors, and enhanced methane uptake in forests and soils. Workshop participants drafted 22 problem statements, which Homeworld polished and published to guide future efforts by researchers and funders. The report is a collection of those problem statements. Notably, Homeworld has already helped deploy $750k in funding across 5 research teams working on problems addressed in the report. 🔗 Read our blog and full report here: https://lnkd.in/eG_ZTdQW #HomeworldCollective #ClimateBiotech #BioMethaneRemovalBiological Methane Removal: Open Problems and Research OpportunitiesBiological Methane Removal: Open Problems and Research Opportunities
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Josh L Espinoza reposted thisJosh L Espinoza reposted thisOur paper is now out in Nature Communications We found the smallest bacterial genomes known to date — just ~50 kilobases. For context, that's smaller than many viral genomes. These belong to Vidania, an ancient symbiont of planthoppers, and they evolved convergently in two lineages separated by over 260 million years of evolution. At this level of reduction, these bacteria have lost so many core cellular functions — including DNA replication initiation and most translation machinery — that they likely depend on host-encoded proteins to survive, much like mitochondria do. They retain barely enough genes to function as cells, blurring the line between free-living bacteria and organelles. This was a massive collaborative effort led by Anna Michalik and Piotr Łukasik, together with Junchen Deng, Monika Prus-Frankowska, and Adam Stroiński — involving metagenomic data from 149 planthopper species across 19 families. https://lnkd.in/euJ-4f9u #Symbiosis #Genomics #Metagenomics #EvolutionaryBiology #Microbiology
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Josh L Espinoza reposted thisThe biggest limit in CRISPR isn’t the guide RNA, it’s PAM recognition. Without the right DNA motif present, the Cas protein can’t edit that genomic site. In our new Nature Biotechnology paper, we introduce Protein2PAM, a machine learning tool that predicts PAM specificity from CRISPR-Cas proteins and guides engineering toward new PAMs. This expands the set of mutations we can target with CRISPR editors. Huge credit to Aadyot Bhatnagar for leading the ML work, and collaborators in Ben Kleinstiver’s lab for experimental validation. Paper: https://lnkd.in/g8ZGYt52 | Tool: https://lnkd.in/gsJQ2em7Josh L Espinoza reposted thisWe’re excited to share our latest work published today in Nature Biotechnology: Protein2PAM, an AI model that enables the rapid design of CRISPR editors with new PAM recognition. And we’re making the model freely available. CRISPR was promised as fully programmable: “Just change the guide RNA.” But in practice, editing is constrained by a short DNA sequence adjacent to a target site (the PAM). If the right PAM isn’t in the right place, your target simply can’t be accessed by a given CRISPR editor. Protein2PAM helps close this gap. Trained on 45,000+ natural CRISPR systems, the model learned rules of protein-DNA recognition: which amino acids in the Cas protein determine which DNA sequence it recognizes. As a proof of concept, we used it to engineer CRISPR editors toward new PAMs. In our wet lab experiments, 50% of the editors we engineered with Protein2PAM worked on the first try, and some were up to 50x more active than wild-type. Listen to our Head of Bioinformatics Stephen Nayfach describe the model and explore the tool (freely available for research and commercial use!): https://lnkd.in/e2vpPmch 📄 Read the full paper here: https://lnkd.in/ejkj7cPnNew: Protein2PAM model, published today in Nature BiotechnologyNew: Protein2PAM model, published today in Nature Biotechnology
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Josh L Espinoza liked thisJosh L Espinoza liked thisUnderstanding the Immune and Genetic Basis of VITT Post-COVID Vaccines - Jack Hadfield https://lnkd.in/dJYgyfrU #Covid #Health #Hematology #Hemostasis #HemostasisNews #HemostasisToday #Medicine #NEJM #Thrombosis #Vaccines #VITT
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Josh L Espinoza reacted on thisJosh L Espinoza reacted on thisSad to hear of the passing of J. Craig Venter (1946-2026) Polarizing, but an absolute science rock star who drove some of the most significant scientific accomplishments in my lifetime. Forever grateful and proud to have had the privilege of 5 formative years learning #bioinformatics while working for J. Craig Venter Institute. Presenting to him as part of my promotion process was one of the most intimidating moments of my career—and succeeding remains one of my proudest.
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Josh L Espinoza liked thisJosh L Espinoza liked thisWOW! Ten projects spanning blue carbon ecosystems and marine microbes will receive $3.4 million to demonstrate the use of genetic rescue as a tool for climate adaptation and mitigation. https://lnkd.in/gfUVp2sGRevive & Restore Announces Inaugural Climate Resilience Fund CohortRevive & Restore Announces Inaugural Climate Resilience Fund Cohort
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Josh L Espinoza reacted on thisJosh L Espinoza reacted on this**RIP J. Craig Venter (1946–2026)** Craig Venter died yesterday at 79, and #biology lost one of the few people in its history who genuinely accelerated the pace at which the field was willing to ask questions about itself. The genome race gets the headlines, and it deserves them. Standing at the White House in June 2000 alongside Clinton and Collins, having built Celera from scratch and raced the entire federal consortium to a draft sequence — that was an act of institutional will as much as scientific achievement. He proved that competitive pressure could compress timelines that the scientific community had accepted as fixed. But the moment that matters more to anyone working in the biology of information is 2010: the first self-replicating cell booted from a chemically synthesized genome. That experiment established, formally, that the genetic program of a living system could be written, compiled, and executed. The implications of that proof are still propagating forward. At Eigen Bio, we work in a layer of the regulatory genome that Venter's generation helped expose but didn't yet have the tools to fully interpret. The transcriptome — the RNA layer where gene expression becomes biological decision-making — is downstream of everything genomics opened up. We stand in a tradition that Craig Venter helped make possible, even when the questions we're asking now would have seemed premature in 2000. He once said: "If you want immortality, do something meaningful with your life." He did. The field he helped build is the foundation on which the next generation of biological intelligence is being constructed. Rest well, Dr. Venter.
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Josh L Espinoza liked thisAwesome opportunity to join the Chief Scientific Officer team at Thermo Fisher Scientific!Josh L Espinoza liked thishttps://lnkd.in/gJQswyP4 An exciting opportunity to lead the integration of advanced artificial intelligence and machine learning capabilities into Thermo Fisher Scientific's life science research and product development pipelinesDirector of R&D, Artificial Intelligence in Waltham, Massachusetts, United States of America | Research & Development at Thermo Fisher ScientificDirector of R&D, Artificial Intelligence in Waltham, Massachusetts, United States of America | Research & Development at Thermo Fisher Scientific
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Josh L Espinoza reacted on thisJosh L Espinoza reacted on thisFriends, It is with a mix of sentimentality and excitement for the future that I write to share a decision to move on from my full-time position at Homeworld. The seeds of Homeworld began to grow as early as 2019, when Daniel Goodwin, Sarah Sclarsic and a few other wonderful friends and I set out to find impactful problems to work on in climate biotech. A community began to snowball as we met others on a similar journey. Dan and I started Homeworld to expand that same mission: helping people find and work on impactful problems at the intersection of biology and planetary health. Three and a half years later, Homeworld has touched thousands. I was initially just searching for a path in climate biotech, and I have found that and so much more. I couldn’t be more grateful to our amazing community and the Homeworld team for making it all possible. There are too many people to thank by name. Given everything Homeworld has brought to me and the opportunities for impact it has provided, the decision to move on was very challenging. It comes not long after I chose to transition into the ED role when Dan moved on – the ~8 months or so I have spent in the role have led me to accept that, even though I believe deeply in Homeworld’s mission and love the organization, leading Homeworld is not a fit for me at this point in my life. I will remain as a board director alongside Dan, who is still committed and engaged as our board president, and I will stay involved in select near-term projects. With Dan and I both having transitioned to the board, the remaining team that has been building Homeworld day-to-day is carrying the work forward. Homeworld has solid momentum and a track record of success, and there is genuine energy to keep building across the work of field-building and research community support that has been central to Homeworld's identity. Paul Himmelstein will be Homeworld's interim ED. Paul H is an excellent operator who has been at the core of Homeworld since the beginning, most recently as our COO. Jayme Feyhl-Buska continues to lead the Critical Minerals program and is deeply embedded in our community, and Kaila Sims-Austin continues to anchor operations. They are all fantastic. I’m proud of the technological and community progress we have catalyzed together, and am grateful that they are continuing to build. The experience of working with so many brilliant people who are motivated to address the environmental polycrisis, and learning about so many possible solutions, has been deeply encouraging. Much work still remains to organize the community, and to identify and solve problems, but I believe we are capable of building the technology required to make a healthy world possible. I will continue working toward that goal. Thank you to everyone who shows up for the community and the cause. I’ll still be around. Please reach out if you think I can be helpful, as always!
Experience
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Education
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Durban University of Technology // J. Craig Venter Institute (Joint Program)
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Dissertation:
https://github.com/jolespin/publications/blob/master/PDFs/Espinoza_2022__PhD-Dissertation-DUT.pdf -
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Licenses & Certifications
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Research with data or laboratory specimens (Human Research)
CITI Program
Issued ExpiresCredential ID 8654089
Publications
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Publications
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See publicationGoogle Scholar:
https://scholar.google.com/citations?hl=en&user=r9y1tTQAAAAJ&view_op=list_works
NCB My Bibliography:
https://www.ncbi.nlm.nih.gov/myncbi/josh.espinoza.1/bibliography/public/
PDFs for my publications on GitHub:
https://github.com/jolespin/publications
Projects
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Science Writer & Artist for Teros Magazine
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See projectTeros Magazine is an outlet for creative minds
Honors & Awards
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Dean's Award for Research Symposium Presentation
San Diego State University
Through the internship I was eligible to participate in SDSU’s Student Research Symposium by presenting my own research for a panel of judges in a graduate-defense type setting. I was presented with the Dean’s Award allocated to only 2 students from a collection of a several hundred graduate and undergraduate researcher presentations from all fields.
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Dean's List [Spring | Fall 2011, Fall 2012, Spring 2013]
SDSU
GPA > 3.5
Languages
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Python
Full professional proficiency
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R
Professional working proficiency
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Bash
Full professional proficiency
Organizations
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American Association for the Advancement of Science [AAAS]
Member
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Scholars Without Borders
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Sigma Alpha Lambda
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- Present
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Duke Center for HIV Structural Biology
Check out two pre-publications available in bioRxiv, by lead-author Jacob Croft, from Kelly Lee's lab, at the University of Washington in collaboration with our Center’s Computational Biology Core scientists, Hung Do and S. Gnanakaran from Gnana's lab at Los Alamos National Laboratory. Croft et al. used cryo-electron tomography and sub-tomogram averaging of HIV-1 virus-like particles (VLPs), Hydrogen/Deuterium-Exchange Mass Spectrometry and Molecular Dynamics to capture the structural dynamics of HIV-1 Env proteins in the context of the cell membrane. They identified critical interactions and Env structural rearrangements providing insight to essential roles the membrane plays in presenting the Envs in its native conformation on the virion surface and dig deeper in a follow-up paper, revealing critical interactions inside the cell, between the Env cytoplasmic tail and matrix domain of Gag polyprotein, required for Env assembly, presentation, clustering, receptor binding and membrane fusion, all essential for viral propagation. These exciting results reveal the power of these synergistic approaches and the importance of studying Env structures in the context of a membrane. Inside the cell, Gag polyproteins ,recruited to the inner leaflet, help package and present the Env on the outside cell surface. The cell now poised to infect new cells while, simultaneously, exposing the Env to an unrelenting barrage of antibodies seeking to neutralize further infection. Paper #1 https://lnkd.in/eizZwbJF Follow-up Paper https://lnkd.in/exxQxax9
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