AgBioData-LIST April 2026

agbiodata-list@bioinfo.wsu.edu

1 participants
4 discussions

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, 1 week

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

1 month, 1 week

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, 2 weeks

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

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AgBioData-LIST April 2026