[Ml-stat-talks] QCB Seminar 4/7/14: Jeff Leek (JHU)

Neo Christopher Chung nc at princeton.edu
Sat Apr 5 13:10:05 EDT 2014


It will be a great talk*!*



 *4:15pm Seminar*: *Dissecting variation in RNA-seq measurements*



*Abstract:*  RNA-sequencing is the most common tool for measuring gene
expression. The reasons for its popularity include dramatically reduced
costs over the last 10 yeas and increased flexibility over previous
technologies such as microarrays. The price for this flexibility is a much
larger quantity of raw data and greater computational cost associated with
quantification of expression. Dealing with this data poses for
statisticians, computer scientists, and consumers of sequencing data. In
this talk I will discuss computational experiments we have performed to
dissect variation in sequencing experiments due to biological,
technological, and developmental variation. I will also discuss variation
in RNA-seq due to often overlooked sources of variability such as
annotation, assembly, and bioinformatic variability. I will introduce tools
my group has been developing for modeling variation at single base
resolution (https://github.com/lcolladotor/derfinder) and the transcript
level (https://github.com/alyssafrazee/ballgown) in a range of experimental
conditions. This is joint work with Alyssa Frazee, Leonardo Collado Torres,
Geo Pertea, Andrew Jaffe, Ben Langmead, Rafael Irizarry, and Steven
Salzberg.



*Bio:  Jeff Leek *is an Associate Professor of Biostatistics and Oncology
and Biostatistics Department Career Development Chair at the Johns Hopkins
Bloomberg School of Public Health. His data analyses have focused on the
molecular profiles of brain development, breast cancer, stem cell
self-renewal, and the immune response to major blunt force trauma. He is
the co-editor of the Simply Statistics Blog (http://simplystatistics.org/)
and co-director of the Johns Hopkins Specialization in Data Science (
https://www.coursera.org/specialization/jhudatascience/1). His Data
Analysis course on Coursera has enrolled more than 180,000 students.
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