Tessera

Rhea knowledgebase

@rhea-db.bsky.social

Rhea is an expert curated knowledgebase of biochemical reactions based on the chemical ontology ChEBI, and the reference for annotation of enzyme chemistry in UniProt. website: https://www.rhea-db.org SPARQL endpoint: https://sparql.rhea-db.org/sparql

5 Posts66 Follower 137 Folgt

Ricardo D. Righetto @lifeonthewedge.bsky.social · 5mo ago

Meet Stoic from @daniil-litvinov.bsky.social and @ninjani.bsky.social: embeddings to predict stoichiometry of protein complexes from sequence fast and accurately 🧬🧩💻🤩 www.biorxiv.org/content/10.6...

Stoic: Fast and accurate protein stoichiometry prediction (preprint header with authors and affiliations)

Rhea knowledgebase @rhea-db.bsky.social · 6mo ago

The first release of 2026 of the Rhea database is out! Release 140 (2026-01-28) contains 18,343 unique reactions and 15,125 unique reaction participants, with 25M protein sequence entries annotated with Rhea reactions in UniProtKB.

Marc Robinson-Rechavi @marcrr.bsky.social · last yr.

Very nice preprint on the importance of #FAIR data resources in the life sciences, for AI and generally for science, by a great @sib.swiss team led by @dessimoz.bsky.social. With @bgee.org inside ;) zenodo.org/records/1572...

The missing link in FAIR data policy: data resources

zenodo.org

Alexey Amunts @amunts.bsky.social · last yr.

Speak up to prevent a major loss for the field. CASP, which helped shaping structural biology including AlphaFold is on the verge of shutting down. NIH funding has lapsed, UC Davis support ends and the core team is being let go. Painfully shortsighted.

Exclusive: Famed protein structure competition nears end as NIH grant money runs out

Agency silent on funding renewal for contest that inspired creation of AIs that predicted how proteins would fold

science.org

Dr. Rabbithole @drrabbithole.bsky.social · last yr.

A science fair of cancelled grants. The research that will be represented at this event (Tuesday) ranges from neuroscience, to astrophysics, to STEM education. The awarding agencies of the now-canceled grants include the EPA, DHS, NIH, NSF, USAID, and DOD. Open to the public.

Congressional Event: A Science Fair of Canceled Grants

The Things We’ll Never Know: A Science Fair of Canceled Grants.

nasawatch.com

Colbie Reed, PhD, MS @mindandmatter.bsky.social · last yr.

Latest paper from the de Crecy lab is out! A finding that answers a ~40 year old question: a eukaryotic high-specificity transporter for Q/q

The oncogene SLC35F2 is a high-specificity transporter for the micronutrients queuine and queuosine | PNAS

The nucleobase queuine (q) and its nucleoside queuosine (Q) are micronutrients derived from bacteria that are acquired from the gut microbiome and/...

doi.org

Chris Mungall @cmungall.bsky.social · last yr.

This is a must-read piece by @math-rachel.bsky.social about AI evaluation, and how the system of reward and apportioning credit in AI research is broken rachel.fast.ai/posts/2025-0.... TL;DR -- we need deep fact checkers!

Rachel Thomas, PhD - Deep learning gets the glory, deep fact checking gets ignored

an AI researcher going back to school for immunology

rachel.fast.ai

@vdecrecy.bsky.social · last yr.

www.linkedin.com/posts/chrism...

This is a great piece, summarizing amazing deep fact checking by Valerie… | Chris Mungall

This is a great piece, summarizing amazing deep fact checking by Valerie De Crecy, a must read for anyone in AI or genomics. Especially pertinent against the backdrop of the administration terminating...

linkedin.com

Jerven @jerven.akademienl.social.ap.brid.gy · last yr.

Got a #knowledgegraph want some use cases and example queries and how to share them: Read our paper in GigaScience https://academic.oup.com/gigascience/article/doi/10.1093/gigascience/giaf045/8133871?searchresult=1 Join us in #SPARQLing your #SPARQL to improve your #SPARQL ;)

A large collection of bioinformatics question–query pairs over federated knowledge graphs: methodology and applications

academic.oup.com

Christoph Steinbeck @csteinbeck.bsky.social · last yr.

This year's International Workshop on Open Molecular Informatics (IWOMI) (12.-16.05.25) will focus on the curation of open molecular data using multimodal large language models (LLM). If you are interested, please register at www.iwomi.net

International Workshop on Open Molecular Informatics (IWOMI) – Getting things done for open science

iwomi.net

SIB Swiss Institute of Bioinformatics @sib.swiss · last yr.

[BC]² Basel Computational Biology Conference 2025 will take place on 8-10 September. The conference brings together over 500 international scientists from academia, industry, and healthcare to explore advancements at the intersection of #bioinformatics and artificial intelligence. See bc2.ch

WikiPathways @wikipathways.fosstodon.org.ap.brid.gy · last yr.

Februari 2025 WikiPathways update: 313 edits by 10 contributors and 4 new pathways in the last month. Accessible via #webservices, #rstats, Pathvisio, and Cytoscape. Supported by AWSOpen https://www.wikipathways.org/download.html #biology #bioinformatics #openscience

New pathway "Mitochondrial carrier deficiency associated with shuttle disturbances (WP5507)" https://www.wikipathways.org/pathways/WP5507

"Reflecting the pathway as shown in Figure 43.2 of Blau et al. "Physician’s guide to the diagnosis, treatment, and follow-up of inherited metabolic diseases"

New pathway "GIP and GLP-1 function by tissue (WP5509)" https://www.wikipathways.org/pathways/WP5509

"Functions of GIP and GLP-1, two agonists of which are found in the weight-loss drug tirzepatide (a.k.a. Mounjaro). "Pancreatic and exopancreatic function of glucose‐dependent insulinotropic polypepide (GIP) and glucagon‐like peptide (GLP)‐1. GIP acts directly on the endocrine pancreas, bone, fat, gastrointestinal (GI) tract and brain. GLP‐1 acts directly on the endocrine pancreas, gastrointestinal tract, heart and brain." From Figure 2 in https://pmc.ncbi.nlm.nih.gov/articles/PMC4020673/."

New pathway: "Vedolizumab therapy for irritable bowel syndrome (WP5512)" https://www.wikipathways.org/pathways/WP5512

"Vedolizumab is a humanized monoclonal antibody with a predominantly gastrointestinal effect. It specifically inhibits leucocyte integrin α4β7, thus preventing its interaction with mucosal vascular addressin cell adhesion molecule 1 (MAdCAM-1), which is involved in the migration of lymphocytes from the blood stream to the intestinal tissue. Vedolizumab is indicated in the treatment of moderate to severe active Crohn's disease and ulcerative colitis in adult patients with poor response, loss of response, or intolerance to conventional treatment or to tumour necrosis factor alpha (TNF-α) antagonists." Inspired by Figure 1 in https://pubmed.ncbi.nlm.nih.gov/31470005/. Vedolizumab is also known by its trade name, Entyvio.

New pathway: "NSAIDs mechanism of action (WP5513)" https://www.wikipathways.org/pathways/WP5513

"Nonsteroidal anti-inflammatory drugs (NSAIDs) inhibit the cyclooxygenase isoenzymes COX1 and COX2 with varying degrees of specificity for the COX2 isoform. As a result, the conversion of arachidonic acid to prostaglandins (PGs) is inhibited. The main effects of PGs throughout the body are listed." Inspired by Figure 1 in PMID:32322101.

Anne Kupczok @annecmg.bsky.social · last yr.

Next BioSB @biosb.bsky.social HotTopics meeting: BioSB HotTopics meeting on Data representation of small molecules and their application March 25 in Amsterdam www.dtls.nl/data-represe... with Daniel Probst @skepteis.bsky.social, Gerard van Westen @gjpvwesten.bsky.social, and Gabriel Vogel

'Data representation of small molecules and their application' - Dutch Techcentre for Life Sciences

BioSB HotTopics 2025 Spring meeting 25 March, 12:30, VU auditorium O2, Amsterdam Programme of the day: Registration is free! Please register until 7 March 2025 via this google form

dtls.nl

Rhea knowledgebase @rhea-db.bsky.social · last yr.

Out now, release 137 of Rhea featuring 17,422 reactions and 14,335 unique compounds from 18,284 publications. Rhea is used to annotate over 28 million proteins in UniProt (see www.uniprot.org/uniprotkb?qu...).

UniProt

uniprot.org