- AgBioData-LIST - Main Bioinformatics Lab

AgBiodata Webinar September 2026 -- Emily Clough on Single-Cell Data Submissions to NCBI-GEO

by MARCELA KAREY TELLO-RUIZ

*From single cells to FAIR data! * Working with single-cell data? Make your next GEO submission FAIR from the start! Join us next *Wednesday, September 2nd*, to learn best practices for submitting single-cell data to NCBI’s Gene Expression Omnibus (GEO). As part of the monthly AgBioData Webinar Series <https://www.agbiodata.org/webinars>, *Emily Clough* of the National Center for Biotechnology Information (NCBI) will present the talk titled: “*Single-cell data submissions to NCBI’s Gene Expression Omnibus (GEO)*.” Full abstract and Zoom link below. We hope you can join us! Best, Marcela -- * Wednesday, September 2nd, 1PM ET* | 1P ET | 12P CT | 11A MT | 10A PT | Find your local time here <https://www.timeanddate.com/worldclock/fixedtime.html?msg=AgBioData+Sept+20…> . Join Zoom Meeting https://us06web.zoom.us/j/82038356125?pwd=YVFMRElMdEpHZmtObXFvZlA4QVFXQT09 Meeting ID: 820 3835 6125 Passcode: 160683 -- * Speaker: *Emily Clough (NCBI) *Title:* Single-cell data submissions to GEO *Abstract: *The Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) is an international public repository that archives gene expression and epigenomics data sets generated by next-generation sequencing and microarray technologies. The GEO repository is built and maintained by the National Center for Biotechnology Information (NCBI), a division of the National Library of Medicine (NLM). For 25 years GEO has been growing and adapting to emerging new technologies and now contains over 280,000 studies. The newest revolution in transcriptomics is single-cell technology which accounts for ~30% of all public RNA-seq studies in GEO. Single-cell data are large, structurally complex, and present unique challenges for archiving and data delivery. GEO has updated submission documentation with a section dedicated to single-cell data (https://www.ncbi.nlm.nih.gov/geo/info/seq.html#singlecell) describing required data formats, sample organization, and metadata. GEO’s metadata template provides examples for single-cell RNA-seq and multi-omics studies. This webinar will focus on best practices for single-cell submissions to GEO to meet FAIR (Findable, Accessible, Interoperable, and Reuseable) data principles. -- Marcela Karey Tello-Ruiz, PhD AgBioData Program Manager https://www.agbiodata.org/ Phoenix Bioinformatics

1 day, 11 hours

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THIS WEDNESDAY: McKenzie Mabry on Crop Wild Relatives, Herbaria, and Food Security

by MARCELA KAREY TELLO-RUIZ

Hello Everyone, Join us this *Wednesday, August 5, at 1:00 PM ET* for the next webinar in the AgBioData Webinar Series <https://www.agbiodata.org/webinars>. *McKenzie Mabry* (iDigBio), of the *Florida Museum of Natural History, University of Florida, and the New York Botanical Garden*, will present: *"Crop Wild Relatives and the Role of Herbaria in Future Food Crop Security"* This webinar will explore the important role that herbarium collections and crop wild relatives play in supporting future food security. The Zoom link and webinar abstract are included below. We hope you'll be able to join us! Best, Marcela *Wednesday, August 5th, 1PM ET* | 1P ET | 12P CT | 11A MT | 10A PT | Find your local time here <https://www.timeanddate.com/worldclock/fixedtime.html?msg=AgBioData+Aug+202…> . Join Zoom Meeting https://us06web.zoom.us/j/82038356125?pwd=YVFMRElMdEpHZmtObXFvZlA4QVFXQT09 Meeting ID: 820 3835 6125 Passcode: 160683 -- Speaker:* McKenzie Mabry* (Florida Museum of Natural History, University of Florida & New York Botanical Garden; iDigBio) Title: *Crop Wild Relatives And The Role Of Herbaria In Future Food Crop Security* Abstract: Although Nikolai Vavilov recognized the potential of crop wild relatives (CWR) in the early 1900s, the advent of genome editing technologies such as CRISPR now enables scientists to more fully leverage CWRs as a source of genetic diversity for cultivated crops. As global agriculture faces escalating pressures from climate change, plant biologists are increasingly focused on sustaining crop productivity under shifting environmental conditions while meeting the demands of a growing population. CWRs represent a critical reservoir of genetic variation that can be harnessed to address these challenges. While efforts to expand germplasm collections of CWRs are ongoing, herbaria remain an underutilized resource. At the same time, the growing availability of digitized herbarium data provides new opportunities to address large-scale research questions. In this study, occurrence records for CWRs of several important crop species are obtained from repositories such as iDigBio and Global Biodiversity Information Facility. Following data cleaning, ecological niche modeling is used to estimate global habitat suitability under both current and future climate scenarios. This work highlights the increasingly important role of herbaria and digitized biodiversity data in supporting crop improvement efforts, particularly in the context of ongoing climate change. -- Marcela Karey Tello-Ruiz, PhD AgBioData Program Manager https://www.agbiodata.org/ Phoenix Bioinformatics

1 month

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AgBiodata August 2026 webinar -- McKenzie Mabry (iDigBio) on Crop Wild Relatives and the Role of Herbaria in Future Food Crop Security

by MARCELA KAREY TELLO-RUIZ

*Genome editing has revived interest in crop wild relatives as a source of genetic diversity — but are we fully tapping herbaria to find them? Join us next Wednesday 5th of August to learn how digitized biodiversity records and niche modeling are mapping where climate-resilient crop relatives may be found, now and in the future.* Hello Everyone, As part of the monthly AgBioData Webinar Series <https://www.agbiodata.org/webinars>, McKenzie Mabry (iDigBio) of the Florida Museum of Natural History, University of Florida & New York Botanical Garden, will present the talk titled: “*Crop Wild Relatives And The Role Of Herbaria In Future Food Crop Security*”. Full abstract and zoom link below. We hope you can join us! Best, Marcela -- * Wednesday, August 5th, 1PM ET* | 1P ET | 12P CT | 11A MT | 10A PT | Find your local time here <https://www.timeanddate.com/worldclock/fixedtime.html?msg=AgBioData+Aug+202…> . Join Zoom Meeting https://us06web.zoom.us/j/82038356125?pwd=YVFMRElMdEpHZmtObXFvZlA4QVFXQT09 Meeting ID: 820 3835 6125 Passcode: 160683 -- Speaker:* McKenzie Mabry* (Florida Museum of Natural History, University of Florida & New York Botanical Garden; iDigBio) Title: *Crop Wild Relatives And The Role Of Herbaria In Future Food Crop Security* Abstract: Although Nikolai Vavilov recognized the potential of crop wild relatives (CWR) in the early 1900s, the advent of genome editing technologies such as CRISPR now enables scientists to more fully leverage CWRs as a source of genetic diversity for cultivated crops. As global agriculture faces escalating pressures from climate change, plant biologists are increasingly focused on sustaining crop productivity under shifting environmental conditions while meeting the demands of a growing population. CWRs represent a critical reservoir of genetic variation that can be harnessed to address these challenges. While efforts to expand germplasm collections of CWRs are ongoing, herbaria remain an underutilized resource. At the same time, the growing availability of digitized herbarium data provides new opportunities to address large-scale research questions. In this study, occurrence records for CWRs of several important crop species are obtained from repositories such as iDigBio and Global Biodiversity Information Facility. Following data cleaning, ecological niche modeling is used to estimate global habitat suitability under both current and future climate scenarios. This work highlights the increasingly important role of herbaria and digitized biodiversity data in supporting crop improvement efforts, particularly in the context of ongoing climate change. -- Marcela Karey Tello-Ruiz, PhD AgBioData Program Manager https://www.agbiodata.org/ Phoenix Bioinformatics

1 month

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Join the New AgBioData Education & Training Working Group!

by MARCELA KAREY TELLO-RUIZ

Dear AgBioData Community, *Passionate about teaching, training, or improving agricultural research data practices? **This one is for you!* The AgBioData Consortium is launching a new Education & Training Working Group <https://www.agbiodata.org/working_groups/edu-training>. Building on the success of the original Education Working Group—which developed the AgBioData Curriculum for teaching FAIR data practices <https://zenodo.org/records/14278084>—we are expanding our efforts to create more accessible, practical, and community-driven training resources for researchers, educators, students, and database professionals. This next phase will focus on: - Identifying AgBioData community training needs and priorities. - Updating the AgBioData curriculum for diverse audiences. - Developing a structured AgBioData certification program. - Creating online training modules on bioinformatics data management, reporting, publication, and data submission best practices. Participation requires approximately 2 hours per month for meetings, plus flexible offline contributions based on your interests and availability. By joining this working group, you will: - Help shape the future of AgBioData education and training. - Earn authorship on publications, training modules, and other community outputs. - Contribute your expertise in ways that fit your interests and schedule. - Connect with a multidisciplinary network of researchers, educators, curators, and database professionals. Interested in joining? Sign up here: https://forms.gle/CLKYAuyrDxqQtiRG7 If you have any questions, please contact Jodi at jhumann(a)wsu.edu. We hope you’ll join us in building the next generation of FAIR data education resources for the agricultural genomics community. Kind regards, Marcela On behalf of the AgBioData Steering Committee -- Marcela Karey Tello-Ruiz, PhD AgBioData Program Manager Phoenix Bioinformatics

1 month, 4 weeks

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TOMORROW: AgBiodata June 2026 webinar -- Gaurav Moghe on where AI meets Biochemistr

by MARCELA KAREY TELLO-RUIZ

Hello Everyone, Join us tomorrow 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, June 3rd, 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

2 months, 4 weeks

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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

3 months, 1 week

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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

4 months

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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

4 months

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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

4 months, 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

5 months

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