Posts Tagged ‘cbb752’

Vertabelo – Design Your Database Online

January 23, 2019

https://www.vertabelo.com/

(4) MIT Computational Biology: Genomes, Networks, Evolution, Health – Fall 2018 – 6.047/6.878/HST.507 – YouTube

December 22, 2018

https://www.youtube.com/playlist?list=PLypiXJdtIca6GBQwDTo4bIEDV8F4RcAgt

Explaining Odds Ratios

November 16, 2018

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2938757/

Calendar adjustments and course demand

September 3, 2018

course stats
https://ivy.yale.edu/course-stats/
via
https://courses.yale.edu/

specifically, for 752:

https://ivy.yale.edu/course-stats/course/courseDetail?termCode=201801&courseNumbers=CB%26B+752%2FCPSC+752%2FMB%26B+452%2FMB%26B+752%2FMB%26B+753%2FMB%26B+754%2FMCDB+452%2FMCDB+752%2FS%26DS+352&subjectCode=CB%26B

Comparing Classifiers · Martin Thoma

June 6, 2018

Great talk today @Yale by @MooreJH. He describes flow of calculations in biomed. #DataScience, including feature construction, machine learning & downstream interpretation.

Great slide on ML derived from
https://martin-thoma.com/comparing-classifiers

Carl Zimmer To Speak At Bio-IT World, Tackle Heredity, Genes, And How Our Understanding Of The Two Is Changing – Bio-IT World

May 11, 2018

http://www.bio-itworld.com/2018/05/09/carl-zimmer-to-speak-at-bio-it-world-tackle-heredity-genes-and-how-our-understanding-of-the-two-is-changing.aspx

QT:{{”
“It was a huge amount of fun watching them take that raw data and put it through their own pipelines,” Zimmer told me, but he also felt uncomfortable pointing out discrepancies to the scientists he worked with. “I still remember, I was sitting down with Chris Mason at Weill Cornell. He and his students were so enthusiastically going through their findings with me… and they showed me, among other things, how many SNPs I had. Not too long beforehand I’d gone through the same experience with Mark Gerstein and his team at Yale, and their numbers for my SNPs were off by hundreds of thousands. … It was a little awkward with Chris, but I just said, ‘Hey, I got a very different number from Mark Gerstein,’ and Chris just shrugged and said, ‘Oh yeah, that happens.’”

It turns out, there’s a lot about our current understanding of our genes and how we pass them on that isn’t perfectly clear cut. “}}

Carl Zimmer’s tweets from the last class – for ref.

May 1, 2018

https://twitter.com/carlzimmer/status/989191766745272320

https://twitter.com/carlzimmer/status/989196672503812102

https://twitter.com/carlzimmer/status/989197056060284928

https://twitter.com/carlzimmer/status/989214467882934272

Reporting Grades < Yale University

April 22, 2018

http://catalog.yale.edu/handbook-instructors-undergraduates-yale-college/grades/reporting/

QT:{{"
Term grades for the spring term are due seven days after the end of final examination period; in 2017–2018, this date is May 16, 2018. In the spring term, grades are due for seniors within forty-eight hours of the end of final examination period; in 2017–2018, this date is May 11, 2018.
"}}

Points of significance: Machine learning: supervised methods

March 3, 2018

Points of significance – #MachineLearning: supervised methods https://www.Nature.com/articles/nmeth.4551 Nice discussion of the k in k-NN & the slack parm. C, penalizing misclassified points in SVM — both which act somewhat analogously as regularizers. Good for #teaching

Genic Intolerance to Functional Variation and the Interpretation of Personal Genomes

February 24, 2018

Genic Intolerance to Functional Variation & the Interpretation of Personal Genomes
http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1003709 Nice plot of the number of rare v common variants in each gene to find outliers particularly tolerant to impactful (eg #LOF) mutations

http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1003709

Petrovski et al ’13