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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. labsyspharm.org/gyori-receives…

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.

Excited to be leading the Harvard Medical School project on this DARPA program to accelerate scientific modeling!

Thrilled to share that our team led by Benjamin Gyori will be a key performer in the ASKEM program! @cthoyt @IndraSysBio

The HiTS website got a facelift! Come learn about what we're doing to advance the fundamental science underlying human diseases and drug discovery. ➡️hits.harvard.edu

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.

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 Pacific Northwest National Laboratory.

🚀Check out BioCypher (biocypher.org), 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!

The NDEx IQuery paper is published in Bioinformatics! Thanks to Alexander Pico, Benjamin Gyori and the whole The NDEx Project team for their hard work! Read it now: bit.ly/3L63S0M WikiPathways @IndraSysBio Signaling Pathways Project @signor_database cBioPortal Cytoscape #nciitcr

It's been a pleasure to work with Dexter Pratt and the The NDEx Project 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.

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.

Congratulations @cthoyt, very well deserved!

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: bit.ly/3EKltXL

Together, eLife - the journal and Biofactoid are creating new ways for authors to communicate their research! eLife recommends authors use Biofactoid as the repository (@fairsharing.bsky.social) to share pathways and interactions from their paper. Get started at  biofactoid.org

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: bit.ly/3ILJHm7

How every pain condition is different, and immune cells might hold the key to these differences - Aakanksha Jain Nature Immunology Sara Hakim Will Renthal Benjamin Gyori oncodaily.com/blog/100900.ht… #Cancer #CancerResearch #ChronicPain #Immunology #OncoDaily #Oncology

Excited that our work is now out in Nature Immunology - 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!

Benjamin Gyori and I comment on a new frontier of AI-assisted interpretation of proteomic investigations nature.com/articles/s4159…

In their Comment, Olga Vitek and Benjamin Gyori describe how AI approaches will help researchers exploit knowledge from fragmented mass spectrometry-based proteomics data sources to gain insights into biological function. nature.com/articles/s4159…

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/news-and-event…