Benjamin Gyori
@benjamingyori
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Sysbio & AI researcher at Northeastern University. Previously Harvard Medical School. Leading https://t.co/apJa2IJPs0.
Boston, MA
Joined May 2016
NEW: We’re working to make data easier to use! 📢Announcing the performer teams to develop a Biomedical Data Fabric (BDF) Toolbox. (1/2)
arpa-h.gov
The Advanced Research Projects Agency for Health (ARPA-H) supports transformative research to drive biomedical and health breakthroughs ranging from molecular to societal to provide transformative...
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In their Comment, @olgavitek and @benjamingyori describe how AI approaches will help researchers exploit knowledge from fragmented mass spectrometry-based proteomics data sources to gain insights into biological function. https://t.co/K0yHRBRXPO
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@benjamingyori and I comment on a new frontier of AI-assisted interpretation of proteomic investigations
nature.com
Nature Methods - Mass spectrometry-based proteomics provides broad and quantitative detection of the proteome, but its results are mostly presented as protein lists. Artificial intelligence...
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How every pain condition is different, and immune cells might hold the key to these differences - @Aakanksha__Jain
@NatImmunol @sarainthelab @willrenthal @benjamingyori
https://t.co/CZ1MiTFeHo
#Cancer #CancerResearch #ChronicPain #Immunology #OncoDaily #Oncology
oncodaily.com
Aakanksha Jain: How every pain condition is different, and immune cells might hold the key to these differences / Aakanksha Jain, Boston Children’s Hospital,
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Excited that our work is now out in @NatImmunol - the result of a very rewarding collaboration and the application of our INDRA system in a new area of biology. Congratulations @Aakanksha__Jain and team!
Check out our recent work @NatImmunol highlighting how every pain condition is different, and immune cells might hold the key to these differences. As a cherry on top, our DRG image was chosen as the cover art 😃 P.C. @sarainthelab
https://t.co/Vx2YsbsvjX
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Biomedicine has discovered innumerable proteins, molecules, and pathogens, but has no unified database for researchers to parse them. Now, Northeastern's Ben Gyori and Charlie Hoyt are removing the roadblock to discovery. Read more: https://t.co/G8NPEIuLmD
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Together, @eLife and Biofactoid are creating new ways for authors to communicate their research! eLife recommends authors use Biofactoid as the repository (@FAIRsharing_org) to share pathways and interactions from their paper. Get started at https://t.co/wUHo7Tu8Mz
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As the new academic year begins, Khoury College is excited to welcome its largest-ever cohort of new faculty. Check out our roundup to learn about them, their research and teaching interests, and what makes them tick. Read more here: https://t.co/JJKlqzWQpc
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Congratulations @cthoyt, very well deserved!
🎉Congratulations to @cthoyt for winning the International Society for Biocuration (@biocurator) Excellence in Biocuration Early Career Award! 🔗 https://t.co/jO4PiIrIh3
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Mappings between identifiers plays a crucial role in knowledge/data integration across fragmented resources. This is one of the key challenges in the knowledge assembly process @IndraSysBio implements. Biomappings is convenient and scalable to predict/curate missing mappings.
We're delighted to announce that our paper on Biomappings has been published Oxford Bioinformatics. 🧵 https://t.co/LPmftJ7Rwg
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It's been a pleasure to work with @dexterpratt and the @NDExProject team on iQuery. Interpreting gene sets w/ respect to causal, mechanistic networks can reveal more than simple terms. Automated assembly of mechanisms with @indrasysbio enables scaling up network creation.
🔬Do you have a list of genes from your latest experiment? 🌐You can paste them into iQuery on @NDExProject to calculate enrichment against biological networks from @news4go, @signor_database, @WikiPathways, and @theNCI-PID iQuery is available at:
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The NDEx IQuery paper is published in Bioinformatics! Thanks to @xanderpico, @benjamingyori and the whole @NDExProject team for their hard work! Read it now: https://t.co/LwsVsv6GDD
@WikiPathways @IndraSysBio @sigpathproject @signor_database @cbioportal @cytoscape #nciitcr
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🚀Check out BioCypher ( https://t.co/sXfYRzOLVN), a new framework for streamlining KG construction and making KGs more interoperable. Excited to see @bioregistry as the basis for identifying biomedical concepts. Looking forward to making a connection with INDRA-assembled data!
Building a knowledge graph for biomedical tasks usually takes months or years. 😰 What if you could do it in weeks or days? 🏃 We created BioCypher ( https://t.co/9eGe9RDkNj) to make it easier than ever, but still flexible and transparent. 🧵⬇️
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We're kicking off this project in San Francisco today! I'm very excited to be the PI for the Harvard team incl @cthoyt. We'll work on knowledge assembly and causal modeling for vaccine/pathogen mechanisms, collaborating closely with @djinnome at @PNNLab.
A machine-learning tool predicting the most suitable technologies for a given #pathogen could streamline the #vaccine development process — increasing the rate of success and reducing the number of initial vaccine candidates required. https://t.co/j3NNu1UHQw
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Using machine-assembled networks for keeping human-curated resources up to date is a promising direction for many structured resources. These networks can also be the basis of causal/mechanistic analysis of high-throughput data.
Excited to officially release the INDRA-assembled networks of GO-term gene sets and automated INDRA-driven extensions to @NCIsysbio's NCI-PID pathways via @NDExProject. Looking forward to continuing this awesome collaboration with @NDExProject!
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The HiTS website got a facelift! Come learn about what we're doing to advance the fundamental science underlying human diseases and drug discovery. ➡️ https://t.co/zJElyblKno
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Thrilled to share that our team led by @benjamingyori will be a key performer in the ASKEM program! @cthoyt @IndraSysBio
We’ve selected teams to help improve how scientists build/sustain their models and simulations. ASKEM performers will create #AI tools to produce timelier and more reliable expert guidance in areas like space weather, climate modeling, etc. https://t.co/dCcfwXPnXu
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Excited to be leading the Harvard Medical School project on this DARPA program to accelerate scientific modeling!
We’ve selected teams to help improve how scientists build/sustain their models and simulations. ASKEM performers will create #AI tools to produce timelier and more reliable expert guidance in areas like space weather, climate modeling, etc. https://t.co/dCcfwXPnXu
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This alone is a big deal for text mining and knowledge aggregation: if repositories have useful APIs and provide full, machine readable text (i.e. not PDF), it can unlock substantial value.
6/ The peer-reviewed publications must be deposited in "agency-designated" OA repositories and in "formats that allow for machine-readability and enabling broad accessibility through assistive devices."
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I am honored to have received the @DARPA Director's Fellowship Award for 2022-23 to continue our research on large-scale biomedical knowledge assembly and human-machine collaboration with the @IndraSysBio team @HiTSatHarvard. https://t.co/HYhzlZ6ZzB
labsyspharm.org
Benjamin Gyori received the Director’s Fellowship Award from the Defense Advanced Research Projects Agency (DARPA)
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