Genomics for students

Currently maintained by other students. Ask around to find who are the current organizers of this group!

Below you can find the calendar and presentation slides (if they are sharable) for Genomics for students or papers to be discussed. Please properly contact and cite the author of a presentation if you are interested in re-using parts of it.

This series of presentations is organized by Jean-Philippe Fortin and L. Collado-Torres. The goals include learning about interesting research in genomics, hosting a time where students can feel free to ask about any detail they don't know, and integrating the genomics student community at Welch. It is a great complement to the "Joint Genomics Meetings" organized by Steven Salzberg and Jeff Leek.

Calendar

Fall 2014

For this semester we decided on the following guidelines for the group:

Only discuss papers: this is something both junior and senior students can participate in.
Don't present our work: use other venues for that.
Short presentations followed by rich discussion: if you skimmed through the paper you should be able to contribute.
Invite all the students working in the new Welch space.
Maximum 1 paper per session.
Students only

Here is the list of presentations for the term.

L. Myint presenting Normalization of RNA-seq data using factor analysis of control genes or samples
B. He presenting Statistical significance for genomewide studies
P. Parsana presenting Sigma: Strain-level Inference of Genomes from Metagenomic Analysis for Biosurveillance
Cancelled
K. Fletez-Brant presenting De novo detection of differentially bound regions for ChIP-seq data using peaks and windows: controlling error rates correctly
A. Frazee presenting Detecting and correcting systematic variation in large-scale RNA sequencing data
A. Saha presenting Using next-generation RNA sequencing to identify imprinted genes
J-P. Fortin presenting A high-resolution map of the three-dimensional chromatin interactome in human cells
L. Collado-Torres presenting A multivariate approach to the integration of multi-omics datasets
R. Longchamps presenting Friendship and natural selection

Organized by Jean-Philippe Fortin and L. Collado-Torres.

Spring 2014

This time around we invited students to share their ongoing research work with the group. Why? (1) to learn from each other + (2) many heads > one head + (3) build a strong community.

Metagenomics and the Human Microbiome Project by S. Cristiano.
About Hi-C and other high-dimensional beverages by Jean-Philippe Fortin.
The Role of Data Normalization in Gene Signature Development by Prasad Patil.

Organized by Jean-Philippe Fortin, Kasper Daniel Hansen and L. Collado-Torres.

Fall 2013

Introduction to Genomics by K-D. Hansen. Broke attendance record with 24 students; pictures available here.
Exploring high-throughput sequencing files by K-D. Hansen and L. Collado-Torres. Notes available here ().
Introduction to IRanges and GenomicRanges by K-D. Hansen and introduction to ggbio by L. Collado-Torres. ggbio presentation ().
ballgown presented by A. Frazee.
Bayesian mixture models for complex copy number polymorphisms by S. Cristiano ().
"Normalizing RNA-Sequencing Data by Modeling Hidden Covariates with Prior Knowledge" by Mostafavi, Battle et al paper discussion lead by L. Myint.
Cancelled
Practice defense talk by Y. Wei.