The past 15 years have been exciting ones in plant biology. Hundreds of plant genomes have been sequenced, RNA-seq has enabled transcriptome-wide expression profiling, and a proliferation of "-seq"-based methods has permitted protein-protein and protein-DNA interactions to be determined cheaply and in a high-throughput manner. These data sets in turn allow us to generate hypotheses at the click of a mouse. For instance, knowing where and when a gene is expressed can help us narrow down the phenotypic search space when we don't see a phenotype in a gene mutant under "normal" growth conditions. Coexpression analyses and association networks can provide high-quality candidate genes involved in a biological process of interest. Using Gene Ontology enrichment analysis and pathway visualization tools can help us make sense of our own 'omics experiments and answer the question "what processes/pathways are being perturbed in our mutant of interest?" Structure: each of the 6 week hands-on modules consists of a ~2 minute intro, a ~20 minute theory mini-lecture, a 1.5 hour hands-on lab, an optional ~20 minute lab discussion if experiencing difficulties with lab, and a ~2 minute summary. Tools covered [Material updated in June 2025]: Module 1: GENOMIC DBs / PRECOMPUTED GENE TREES / PROTEIN TOOLS. Araport, TAIR, Gramene, EnsemblPlants Compara, PLAZA, SUBA5 and Cell eFP Browser, 1001 Genomes Browser, PlantConnectome Module 2: EXPRESSION TOOLS. eFP Browser / eFP-Seq Browser, Araport, ARDB, TravaDB, NCBI Genome Data Viewer for exploring RNA-seq data for many plant species, MPSS database for small RNAs, SCEA and Ecker Lab Seed-to-Seed scAtlas Module 3: COEXPRESSION TOOLS. ATTED II, Expression Angler, AraNet, AtCAST2 Module 4: PROMOTER ANALYSIS. Cistome, MEME, ePlant Module 5: GO ENRICHMENT ANALYSIS AND PATHWAY VIZUALIZATION. AgriGO, AmiGO, Classification SuperViewer, TAIR, g:profiler, AraCyc, MapMan (optional: Plant Reactome) Module 6: NETWORK EXPLORATION. Arabidopsis Interactions Viewer 2, ePlant, TF2Network, Virtual Plant, GeneMANIA
HD
I am able to learn the different tools in transcritpom analysis. I become familair with the next generation sequencing technologies too.
AK
Overall the course is good. However, lecture should be more in detail.
SB
Very helpful to understand the different tools of bioinformatics
SS
That was so insightful and learning course about plants bioinformatic out of basic methods.Also help in working project to give meaningful answers with validation
RI
I really enjoyed the course. Got teary eyed after finishing the course. I really put my extra time in this course and I learned so much. Thank you
SH
excellent resource for various plant based tools to be used in functional genomics studies
SW
This course is desingned very well. I have learned a lot about bioinformatic analysis of plants. I recommend this course.
LS
I am new in this skills. I am excited because I completed this course. I have new experiences. Thank you. I recommend this course for learn plant bioinformatic.
DD
Very nice and informative course. I would love to interact with you personally and learn more.
KK
An informative course. I gathered practical knowledge about Plant bioinformatic tools and their applications.
RG
Lectures were short, but very informative and the lab exercise helped to explore multiple bioinformatics tools and database.
JF
Thank you very much Dr. Provart for a wonderful lectures and lab experiments!
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Very good course for mastering bioinformatics skills. Genetics and molecular biology students/professionals should take this course to augment their research skills.
Overall the course is good. However, lecture should be more in detail.
Professor Provart is very good and the labs taught us in simple and direct instructions how to perform a wide range of analysis regarding Plant Bioinformatics.
I really enjoyed the course. Got teary eyed after finishing the course. I really put my extra time in this course and I learned so much. Thank you
I found this course very interactive. From theory to practical, all aspects are explained very well. Questions in between the lab and their explanation at the end of the week help understand and retain the knowledge gained through the different platforms. Queries are answered in the discussion box. Suitable for anyone who may not have prior experience of bioinformatics tools.
A really enjoyable and interesting course, well taught. I really enjoyed working through the lab practicals, getting hands on experience with many of the tools used for plant bioinformatics was a good learning exercise. I liked the course presenter too, he was clear and engaging!
El curso es muy interesante y presenta un conjunto de herramientas que son realmente muy útiles a la hora de entender el contexto de las redes de regulación de casi cualquier gen vegetal. Lo recomiendo fuertementes para aquellos que hagan biología molecular vegetal!
An excellent class that introduced me to many relevant topics in Plant Bioinformatics. I can now use these skills to not only better understand current research but also apply them to data obtained in the lab where I volunteer.
Great course!! I really liked most of the labs and the way the course is organized. Thank you very much to the professor N. Provart and to the University of Toronto
In- depth learning of the various tools and softwares available to study plant bioinformatics. Guidance of the author through the labs is insightful and informative.
That was so insightful and learning course about plants bioinformatic out of basic methods.
Also help in working project to give meaningful answers with validation
I am new in this skills. I am excited because I completed this course. I have new experiences. Thank you. I recommend this course for learn plant bioinformatic.
The course had very useful content, and the explanations and labs were excellent to understand how to perform the bioinformatics analysis yourself.
I am able to learn the different tools in transcritpom analysis. I become familair with the next generation sequencing technologies too.
Offers very relevant, intuitive and necesary training for the usage of different bioinformatic tools for plant molecular biology.
Lectures were short, but very informative and the lab exercise helped to explore multiple bioinformatics tools and database.
VERY DETAILED INSTRUCTIONS THAT INDUCE INVOLVEMENT FROM THE READER. VERY HELPFUL METHODOLOGY OF STUDY. COURSE IS WORTH IT.
This course is desingned very well. I have learned a lot about bioinformatic analysis of plants. I recommend this course.
An informative course. I gathered practical knowledge about Plant bioinformatic tools and their applications.
Excellent Course for understanding advance bioinformatics across plant genome and proteome databses.