SMLG (Statistical Machine Learning Group) Discussion Forum

Probabilistic Graphical Models, Fall 2017 class project information will be post here. Every Friday, please post what you have been working toward your class project.

Syllabus for Probabilistic Graphical Models, Fall 2017. I will ask students to post here whether Thursdays 2pm will work. Please note when we meet we will meet at AHC 475.

This week, I am spending time understanding GEO datasets that are out there, and the types of data they contain, so that I can decide on my research question for my class project. Thursdays 2pm would work for me.

Kaumudi wrote:This week, I am spending time understanding GEO datasets that are out there, and the types of data they contain, so that I can decide on my research question for my class project. Thursdays 2pm would work for me.

Great. I was told that now the Blackboard class site is up. I will ask you and other students to post your availability response there. Of course, keep on posting every Friday, what you have been working toward your class project here. Cheers,

cwyoo wrote:Syllabus for Probabilistic Graphical Models, Fall 2017. I will ask students to post here whether Thursdays 2pm will work. Please note when we meet we will meet at AHC 475.

The course Blackboard class site is up. I will ask all students to check the class web site every day. Of course, keep on posting every Friday, what you have been working toward your class project here.

Those who are not registered for the class, please email me at cyoo@fiu.edu so I can see what I can do to make you access the class web site.

Dear Professor Yoo

I am listening on-line coursera about introduction of bioformatics and basic python. It will take more time to complete the listening of on-line coursera.
And, I can use the Blackboard in FIU from the 1st week in September.
From Sungbae Park

Hi Professor: I am interested in the research you are doing on key genes that cause brain cancer, so we may talk in our next meeting about what can be done as a course research project in this topic. Thank you

cwyoo wrote:Syllabus for Probabilistic Graphical Models, Fall 2017. I will ask students to post here whether Thursdays 2pm will work. Please note when we meet we will meet at AHC 475.

Good afternoon Professor Yoo,

Thursday at 2pm will work for me.

Respectfully,

Efrain Gonzalez

I now have RNASeq median gene expression data for 154 patients from TCGA study. Need to learn how to access and use BANJO for analysis.

I tried to look for one place where one could get a simple list of the commonly acknowledged transcription factors (Tfs) in humans, but it is surprisingly non-trivial to find this! Any suggestions are welcome...

I have come across the following website
http://www.grnpedia.org/trrust/
TRRUST (version 2) is
a manually curated database of human and mouse transcriptional regulatory networks.

They have a list of 800 known human TFs, and 2095 genes regulated by these TFs - total of 8,444 regulatory links - all curated and compiled through sentence-based text mining.

I have taken their list, removed duplicates, and I am using this list of close to 3000 proteins to narrow down our focus on the data from the RNASeqV2RSEM. It will take me some time to fully accomplish this and double-check the data..and this is what I am currently working on.