- AgBioData-LIST - Main Bioinformatics Lab

AgBiodata June 2026 webinar -- Gaurav Moghe on where AI meets Biochemistry

by MARCELA KAREY TELLO-RUIZ

Hello Everyone, Join us next Wednesday, June 3rd at 1 pm ET for an exciting talk tackling one of plant genomics' most pressing challenges: predicting enzyme function at scale. Discover how large language models (LLMs), protein language models (PLMs), and phylogenetics are being combined into an end-to-end annotation workflow to make it possible. As part of the AgBioData webinar series, *Gaurav Moghe*, Associate Professor in the School of Integrative Plant Science at Cornell University, will present the talk titled: “*Advancing biochemical studies with LLMs and PLMs*”. The zoom link and abstract are below. We hope you can join us! Best, Marcela -- Wednesday, May 6th, 1PM ET 10A PT | 11A MT | 12P CT | 1P ET Find your local time *here* <https://www.timeanddate.com/worldclock/fixedtime.html?msg=AgBioData+June+20…> . Join Zoom Meeting https://us06web.zoom.us/j/82038356125?pwd=YVFMRElMdEpHZmtObXFvZlA4QVFXQT09 Meeting ID: 820 3835 6125 Passcode: 160683 -- Speaker: Gaurav Moghe, Associate Professor, Integrative Plant Science @ Cornell University Title: Advancing biochemical studies with LLMs and PLMs Abstract: As the number of sequenced plant genomes continues to accumulate rapidly, innovation in functional annotation of genes is increasingly becoming a critical endeavor. However, allelic divergence, duplication-divergence, promiscuity, and redundancy are major hurdles in function prediction. In this talk, I will describe a workflow we have developed for enzyme function prediction that includes LLM-assisted extraction from literature (FuncFetch), organizing in databases (FuncZymeDB), functional prediction using phylogeny (FuncPred-OG) and using protein language models (FuncPred-AI). Together, this workflow enables rapid prediction of substrate classes utilized by BAHD acyltransferases (our test enzyme family), has high data provenance, is expandable to other families, and will complement manual biocuration efforts. -- Marcela Karey Tello-Ruiz, PhD AgBioData Program Manager Phoenix Bioinformatics

1 week, 2 days

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AgBiodata May 2026 webinar -- Olivia Haley on Delivering AI-Ready Genomics with MaizeGDB

by MARCELA KAREY TELLO-RUIZ

Hello everyone, Join us next *Wednesday, May 6th at 1 pm ET* for a compelling look at how MaizeGDB is transforming maize research with AI-ready data infrastructure. Discover how cutting-edge DNA and protein language models, precomputed features, and interactive tools are unlocking faster gene discovery and smarter crop improvement. See how standardized, accessible genomics data is paving the way for the next generation of agricultural innovation. As part of the AgBioData webinar series, *Olivia Haley*, a USDA-ARS Postdoctoral Research Fellow at the Oak Ridge Institute for Science and Education, will present the talk titled: “*Delivering AI-Ready Genomics with MaizeGDB*”. The zoom link and abstract are below. We hope you can join us! Best, Marcela -- Wednesday, May 6th, 1PM ET | 1P ET | 12P CT | 11A MT | 10A PT | Find your local time *here* <https://www.timeanddate.com/worldclock/fixedtime.html?msg=AgBioData+May+202…> . Join Zoom Meeting https://us06web.zoom.us/j/82038356125?pwd=YVFMRElMdEpHZmtObXFvZlA4QVFXQT09 Meeting ID: 820 3835 6125 Passcode: 160683 -- Speaker: *Olivia Haley, *USDA-ARS Postdoctoral Research Fellow at the Oak Ridge Institute for Science and Education Title: Delivering AI-Ready Genomics with MaizeGDB Abstract: The integration of Artificial Intelligence (AI) into computational biology is changing biological research, particularly in agriculture, where large and complex datasets offer opportunities for discovery and crop improvement. Maize (Zea mays L.), a globally critical crop with extensive genomic, genetic, proteomic, and functional resources, stands to benefit from AI integration. The Maize Genetics and Genomics Database (MaizeGDB) is proactively building an AI-ready infrastructure by standardizing datasets, pre-computing complex features, developing novel interactive tools, and providing reproducible workflows. This paper details MaizeGDB's strategic initiatives to create a foundation of AI-ready data in standardized formats and generate precomputed embeddings from cutting-edge DNA and protein language models. We introduce new functionalities, including zero-shot variant effect scoring derived from biological language models (protein and DNA) and genome browser tracks for visualizing nucleotide conservation (conveying potential functional significance). Furthermore, we provide custom dataset assembly resources and reproducible workflows via GitHub. By providing access to and organization of maize data, MaizeGDB enables the maize research and breeding community to leverage AI for the accelerated discovery of gene function, variant interpretation, and the development of improved maize varieties. -- Marcela Karey Tello-Ruiz, PhD AgBioData Program Manager Phoenix Bioinformatics

1 month

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Fwd: Seminar 18 May 2026 by G Saldi on analysis of scRNA-seq data

by MARCELA KAREY TELLO-RUIZ

Dear AgBioData Community: Please see below an event on single-cell RNA-seq analysis that may be of interest to some of you. Regards, Marcela *From: *Alex Clop <alex.clop(a)cragenomica.es> *Date: *Monday, April 27, 2026 at 9:30 AM *To: *faang-SingleCell(a)animalgenome.org <faang-singlecell(a)animalgenome.org>, Giuseppe-Antonio Saldi <gas361(a)nyu.edu> *Subject: *Seminar 18 May 2026 by G Saldi on analysis of scRNA-seq data Dear colleagues, Within the framework of the regular seminar series organized by the FAANG Single Cell Task Force, we are pleased to announce an upcoming online seminar by Dr Giuseppe A. Saldi (New York University Abu Dhabi, UAE). Dr Saldi is a bioinformatician with extensive expertise in the analysis of single cell RNA sequencing (scRNA-seq) data and in the development of computational methodologies and tools for single cell transcriptomics (*https://scholar.google.com/citations?user=o7hIBDwAAAAJ&hl=fr__;!!D9dNQwwGXtA!TtXNLgMw37gAnM6lXo0OjOEgUVNTMnd-6QSm357Ny8ggn1vgEGZzMLGGZulOSlfgMPrDyEofuxImdvzfEtviiA$ <https://scholar.google.com/citations?user=o7hIBDwAAAAJ&hl=fr__;!!D9dNQwwGXt…>* ). In this seminar, Dr Saldi will present an overview of the core analytical steps in scRNA-seq data analysis, with emphasis on the statistical and biological rationale underlying each step, from raw data pre-processing through differential gene expression (DGE) testing. The focus will be on conceptual frameworks, assumptions, and common pitfalls associated with standard scRNA-seq workflows (e.g. quality control metrics, dimensionality reduction, and DGE design). Given the limited duration, the seminar will not provide an exhaustive comparison of alternative methods or software packages (e.g. detailed benchmarking of normalization strategies) but will instead aim to clarify why specific analytical steps are required and how analytical choices propagate downstream. Date: Monday, May 18, 2026 Time: 17:00–19:40 (Central European Summer Time, CEST) (Time conversions for other time zones are provided at the end of this email) Format: Online The session is structured to encourage active discussion, with dedicated question and discussion periods following each module. Title: Analytical considerations in single cell RNA seq: from pre-processing to differential gene expression analysis Program (~2 h 40 min): • 17:00 – Welcome and introduction (~5 min) • 17:05 – Background and high-level workflow overview (~15 min) *Data structure, noise sources in scRNA-seq, and positioning of key analytical steps* • 17:20 – Quality control considerations (~25 min) *Cell and gene level QC metrics; mitochondrial transcript proportions; detection of doublets/multiplets; ambient RNA contamination and background correction* • 17:45 – Discussion (~15 min) • 18:00 – Break (15 min) • 18:15 – Feature selection and dimensionality reduction (~30 min) *Normalization and variance stabilization; log1p transformation; identification of highly variable genes (HVGs); principal component analysis (PCA)* • 18:45 – Discussion (~15 min) • 19:00 – Differential gene expression (DGE) analysis (~25 min) *DGE strategies in single cell contexts; pseudo replication; statistical power; appropriate experimental and model design* • 19:25 – Discussion (~15 min) • 19:40 – Closing remarks Access: The seminar will be held online via Teams: *Joseph FAANG SC | Meeting-Join | Microsoft Teams <https://teams.microsoft.com/meet/348312092317295?p=jgru5YQSAWnvSG00a2>* Time zone conversions: • CEST (Barcelona): 17:00–19:40 • New York (EDT): 11:00–13:40 • Los Angeles (PDT): 08:00–10:40 • Beijing (CST): 23:00–01:40 (+1 day) • Tokyo (JST): 00:00–02:40 (+1 day) • Sydney (AEST): 01:00–03:40 (+1 day) Note that you may have received, in parallel, an automatic email from Teams informing about this seminar, as a result of the schedule of this meeting in the Teams calendar. With kind regards, Alex Clop¹ and Christopher K. Tuggle² ¹ Centre for Research in Agricultural Genomics (CRAG) Campus UAB 08193 Cerdanyola del Vallès Catalonia, Spain *https://www.cragenomica.es <https://www.cragenomica.es/>* ² Iowa State University — Department of Animal Science C. F. Curtiss Distinguished Professor in Agriculture and Life Sciences 806 Stange Road, 2255 Kildee Hall Ames, IA 50011, USA Email: *cktuggle(a)iastate.edu <cktuggle(a)iastate.edu>* Phone: +1 515 294 4252 FAX 515-294-2401 *http://www.ans.iastate.edu/people/christopher-tuggle <http://www.ans.iastate.edu/people/christopher-tuggle>* -- Marcela Karey Tello-Ruiz, PhD AgBioData Program Manager Phoenix Bioinformatics

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2026 AgBioData Community Workshop -- last chance to register & join us!

by MARCELA KAREY TELLO-RUIZ

Dear AgBioData Community, Tomorrow, Monday April 19, will be the kickoff of our 2026 AgBioData Community Workshop! This workshop is a great opportunity to connect, share ideas, and collaborate on advancing agricultural data resources. If you have not yet registered and want to join virtually, please respond now: https://tinyurl.com/agbiodata2026 The workshop program is available on our website: https://www.agbiodata.org/2026-agbcomworks Our Working Agenda <https://docs.google.com/document/d/1nZNyadmxqOEQcDyxiotahVOnxFkmAUswavMs5PD…> (subject to change) includes logistics and Zoom links for all sessions. All sessions will use Zoom and Slack. Please join Slack in advance if you have not already. Workshop channels are prefixed with *ag-workshop26-*, organized by breakout session, and will include Zoom links as well as serve as hubs for discussion and resource sharing. Highlights include: - AgBioData Working Groups and Funding updates 🌱 🐄 🧬 🖥️ - Interactive breakout discussions on Artificial Intelligence for Data FAIRification & Data Biocuration, FAIR Scientific Literature, etc. 🤖 🧠 - Database Sustainability: One-pagers for scientific research stakeholders (Researchers, Industry Partners, Legislators, Publishers) 🔬 🚜 ⚖️ 📚 - Network Sustainability: Discussions on shared infrastructure, resources and funding for keeping AgBioData going strong! 👩‍🌾 💻 💪 - International priorities open discussion 🌍 🌎 🌏 These sessions are interactive, and your participation is highly encouraged. If you have any questions or need assistance ahead of the workshop, please don’t hesitate to reach out. We look forward to a productive and engaging event. Best regards, Marcela Karey Tello-Ruiz On behalf of the AgBioData Community Workshop Organizing Committee -- Marcela Karey Tello-Ruiz, PhD AgBioData Program Manager Phoenix Bioinformatics

1 month, 1 week

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nominate an colleague for an AgBioData Award by April 8

by MARCELA KAREY TELLO-RUIZ

Hello AgBioData Friends, Please take a minute to nominate a colleague <https://agbiodata.us18.list-manage.com/track/click?u=fa993e8c3bab82b2a98140…> or two for the following AgBioData Awards categories before next *Wednesday, April 8*: - Mission and Leadership - Best Working Group Member - FAIRification The awards ceremony will take place on the last day of the Community Workshop (April 22). Also note that the deadline for Ambassador Awards <https://agbiodata.us18.list-manage.com/track/click?u=fa993e8c3bab82b2a98140…> was extended to *April 13*. Enjoy the holidays if you celebrate! Marcela -- Marcela Karey Tello-Ruiz, PhD AgBioData Program Manager Phoenix Bioinformatics

2 months

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AgBiodata April 2026 webinar -- Omar Harb on VEuPathDB, a pathogen database with a unique sustainability funding model

by MARCELA KAREY TELLO-RUIZ

Hello Everybody, Let's together explore how *VEuPathDB* integrates multi-omics data, advanced analytics, and AI-driven tools to accelerate infectious disease research, and learn about the innovative community-supported funding model designed to sustain this critical open resource! On Wednesday, April 1st, 1PM ET, *Omar Harb* <https://www.omarharb.org/>, Senior Project Manager & Director Scientific Outreach & Education(VEuPathDB.org) at the University of Pennsylvania, will present the talk titled: “VEuPathDB: A Comprehensive Informatics Resource for Eukaryotic Pathogen, Vector, and Host Biology”. Zoom link and abstract below. We hope you will join us! Marcela -- Wednesday, April 1st, 1PM ET | 1P ET | 12P CT | 11A MT | 10A PT | Find your local time *here* <https://www.timeanddate.com/worldclock/fixedtime.html?msg=AgBioData+April+2…> . Join Zoom Meeting https://us06web.zoom.us/j/82038356125?pwd=YVFMRElMdEpHZmtObXFvZlA4QVFXQT09 Meeting ID: 820 3835 6125 Passcode: 160683 -- Speaker: *Omar Harb* <https://www.omarharb.org/> (Director of Scientific Outreach & Education; Project Manager, VEuPathDB) Title: VEuPathDB: A Comprehensive Informatics Resource for Eukaryotic Pathogen, Vector, and Host Biology Abstract: VEuPathDB (the Eukaryotic Pathogen, Vector, and Host Informatics Resource) is an integrated bioinformatics platform that empowers researchers with comprehensive data, advanced analytical tools, and emerging artificial intelligence capabilities to accelerate discovery in infectious disease biology. The resource consolidates high-quality genomic, transcriptomic, proteomic, and functional data for eukaryotic pathogens, vectors, and relevant host systems, coupled with curated metadata and standardized ontologies. VEuPathDB’s suite of tools enables complex in-silico analyses, including comparative genomics, gene expression profiling, metabolic pathway exploration, and customizable data mining workflows. Recent enhancements leverage AI-driven methods for summarizing transcriptomic data, facilitating hypothesis generation and the interpretation of large-scale experimental results. Through an intuitive web-based interface and APIs, VEuPathDB supports reproducible science and community-driven annotation efforts. To remain open access and sustain its development, maintenance, and ongoing expansion of data and computational capabilities, VEuPathDB employs a voluntary subscription-based funding model. Under this approach, participating labs, institutions, and companies contribute annual subscription fees that support core infrastructure, curation activities, and user support services. The model balances broad access for the scientific community with stable funding streams, enabling strategic investments in AI integration and responsive tool enhancement. Subscription revenues complement competitive grant funding and are essential for long-term platform growth, ensuring that VEuPathDB continues to meet evolving research needs in pathogen, vector, and host informatics. -- Marcela Karey Tello-Ruiz, PhD AgBioData Program Manager Phoenix Bioinformatics

2 months, 2 weeks

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2026 AgBioData Community Workshop -- Schedule and Registration

by MARCELA KAREY TELLO-RUIZ

Hi Everybody, We are pleased to share the schedule and *registration link* for the *AgBioData Community Workshop*, to be held April 20–22, 2026, in Olathe, Kansas, and *online*. *REGISTER:* https://tinyurl.com/agbiodata2026 If you plan to attend in person (and have not already registered), it is *very important* that you REGISTER no later than *Friday, March 6*, using the link above. Early next week, U.S.-based in-person participants will be contacted by a K-State travel agent to arrange flights to MCI and lodging (two nights). Ground transportation in Kansas City and meals will also be provided. International colleagues are welcome to participate in person with their own funding or join remotely. Details for virtual participation will be shared soon. We hope you will be able to join us. Kind regards, Marcela On behalf of AgBioData's Community Workshop Committee -- Marcela Karey Tello-Ruiz, PhD AgBioData Program Manager Phoenix Bioinformatics

3 months

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AgBioData March 2026 webinar -- John McNamara on Integrating Phenomics and Phenotypes into Agricultural Databases

by MARCELA KAREY TELLO-RUIZ

Hi Everybody, On Wednesday, March 4th,12 PM CT, *John McNamara* <https://serc.carleton.edu/person/53858.html>, Professor Emeritus of Animal Sciences at Washington State University, will present the talk titled: “*Integrating phenomics and phenotypes into agricultural databases.*” Zoom link and abstract below. We hope you will join us. Kind regards, Marcela -- Wednesday, March 4th, 12PM CT | 1P ET | 12P CT | 11A MT | 10A PT | Find your local time *here* <https://www.timeanddate.com/worldclock/fixedtime.html?msg=AgBioData+March+2…> . Join Zoom Meeting https://us06web.zoom.us/j/82038356125?pwd=YVFMRElMdEpHZmtObXFvZlA4QVFXQT09 Meeting ID: 820 3835 6125 Passcode: 160683 -- Speaker: *John McNamara* <https://serc.carleton.edu/person/53858.html>, Professor Emeritus of Animal Sciences at Washington State University Title: Integrating phenomics and phenotypes into agricultural databases Abstract: The United States agriculture and food systems research and education system remains the envy of the world, and the US Department of Agriculture and the Land-Grant University system lead the public and private partnerships that have improved agricultural productivity and human health phenomenally for over 160 years. The continuation of these improvements relies on equitable access to trustworthy data, particularly in genetics and phenomics, and the ability to leverage such data to address future scientific challenges. In the new article set forth by the Phenotypic Data Standardization and Management working group, we discuss the growing need in agriculture for phenomic databases that follow findable, accessible, interoperable, and reproducible (FAIR) data guidelines, as well as the need for public policy supporting a sustainable funding model for these databases. -- Marcela Karey Tello-Ruiz, PhD AgBioData Program Manager Phoenix Bioinformatics

3 months

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Spots available for in-person participation at the AgBioData Annual Workshop (April 20–22, 2026)

by MARCELA KAREY TELLO-RUIZ

Dear Colleagues, We have some spots available to attend the AgBioData Annual Workshop IN PERSON. This hybrid event will be held on April 20–22, 2026, in Olathe, Kansas. To be eligible for support, you will need to be affiliated at a US-based institution. We will pay for airfare or equivalent, two nights lodging, meals and ground transportation in Kansas. Please let me know ASAP if you would be willing and able to participate in person. There is no cost for national and international participants to join remotely. We hope you will be able to join us! Marcela On behalf of AgBioData Community Workshop Organizing Committee -- Marcela Karey Tello-Ruiz, PhD AgBioData Program Manager Phoenix Bioinformatics

3 months, 2 weeks

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THIS Wednesday -- AgBiodata February 2026 webinar: Pascale Gaudet, Gene Ontology and Network Modeling

by MARCELA KAREY TELLO-RUIZ

Hi Everybody, This Wednesday, February 4th, 12PM CT, Pascale Gaudet, Gene Ontology Project Manager at the Swiss Institute Bioinformatics, will present the talk titled: “*Extending the Gene Ontology for Biological Network Modeling*”. Zoom link and abstract below. We hope you will join us! Kind regards, Marcela -- Wednesday, February 4th, 12PM CT | 1P ET | 12P CT | 11A MT | 10A PT | Find your local time here https://www.timeanddate.com/worldclock/fixedtime.html?msg=AgBioData+Februar… . Join Zoom Meeting https://us06web.zoom.us/j/82038356125?pwd=YVFMRElMdEpHZmtObXFvZlA4QVFXQT09 Meeting ID: 820 3835 6125 Passcode: 160683 -- Speaker: Pascale Gaudet, Swiss Institute of Bioinformatics Title: Extending the Gene Ontology for Biological Network Modeling Abstract: The Gene Ontology (GO) is an essential resource in the bioinformatics landscape, supporting a wide range of applications. It serves both as a comprehensive encyclopedia of biological knowledge and as a key tool for interpreting high-throughput biological data. More recently, GO has expanded to support biological network modeling through the development of GO Causal Activity Models (GO-CAMs), which enable network analysis within the highly structured GO data framework. This presentation will introduce the GO-CAM data model, describe its relationship to standard GO annotations, and highlight ontology developments driven by GO-CAM requirements. It will also discuss how GO is leveraging artificial intelligence to enhance multiple aspects of the GO workflow, including ontology development, annotation, and quality control. -- Marcela Karey Tello-Ruiz, PhD AgBioData Program Manager Phoenix Bioinformatics

3 months, 4 weeks

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