6.047/6.878 Computational Biology: Genomes, Networks, Evolution
Fall 2014
Professor: Manolis Kellis
TA: Abhishek Kulshreshtha Sarkar
Lecture:
TR1-2.30
(32-141)
Recitation: F3
(56-154)
Information:
Covers the algorithmic and machine learning foundations of computational biology combining theory with practice. We cover both foundational topics in computational biology, and current research frontiers. We study fundamental techniques, recent advances in the field, and work directly with current large-scale biological datasets.
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Genomes:
Biological sequence analysis, hidden Markov models, gene finding, comparative genomics, RNA structure, sequence alignment, hashing
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Networks:
Gene expression, clustering/classification, EM/Gibbs sampling, motifs, Bayesian networks, microRNAs, regulatory genomics, epigenomics
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Evolution:
Gene/species trees, phylogenomics, coalescent, personal genomics, population genomics, human ancestry, recent selection, disease mapping
In addition to the technical material in the course, the term project provides practical experience: (1) writing an NIH-style research proposal, (2) reviewing peer proposals, (3) planning and carrying out independent research, (4) presenting research results orally in a conference setting, and (5) writing results in a journal-style scientific paper. You will work on a project of your choice with regular feedback and advice from a mentor, your peers, and the teaching staff.
Schedule for the term:
https://stellar.mit.edu/S/course/6/fa14/6.047/courseMaterial/topics/topic1/syllabus/6047F14_Schedule/6047F14_Schedule4.pdf
Materials from last year https://stellar.mit.edu/S/course/6/fa13/6.047/materials.html and this year https://stellar.mit.edu/S/course/6/fa14/6.047/materials.html
Announcements
Final presentations slides/audio + Course Evaluations
You can also find all lecture slides compiled into one document for posterity here: https://stellar.mit.edu/S/course/6/fa14/6.047/courseMaterial/topics/topic2/lectureNotes/6047_Fall14_allSlides/6047_Fall14_allSlides.pdf
and you can still provide feedback for individual lectures here: https://docs.google.com/forms/d/1cATS_VGzkc2soT8ULjxtRNR_y7UsfD8tFeYYgN5V21c/viewform
Lastly, please take a moment to fill out the survey for the class, as they are very important for students considering to take the class in future years. You can find a link to the survey here: http://web.mit.edu/
Thank you all for a great term! We'll post grades as soon as possible. Please submit any remaining items asap! Manolis and Abhishek
Announced on 09 December 2014 5:39 p.m. by Manolis Kellis
Final presentation order - please check
I'm pasting the information here for convenience, but refer to the google doc for the latest order and presentation times. Let us know asap if you can't make the current times and we'll adjust asap. Thanks! Manolis and Abhishek
6.878/6.047 Fall 2014 Final Presentations
Closed session
Tuesday, December 9 at 1-2:30 PM, 32-141
|
Start |
End |
# |
Student 1 |
Student 2 |
Project Title |
|
1:00 PM |
1:08 PM |
1 |
Gabriel Filsinger |
Silvia Canas Duarte |
Predicting Expression Level Changes Caused by Synonymous Mutations |
|
1:09 PM |
1:17 PM |
2 |
Jerry Ding |
Dan Sosa |
Network Analysis of Type 2 Diabetes Rare Variants |
|
1:18 PM |
1:26 PM |
3 |
Matthew Fox |
Joseph Kim |
Age Prediction using DNA Methylation and Telomere Length |
|
1:27 PM |
1:35 PM |
4 |
Eric Mazumdar |
Nicolai Ludvigsen |
Genomic structure prediction using multiple annotations |
|
1:36 PM |
1:44 PM |
5 |
Kristjan Kaseniit |
Cathie Yun |
Investigating breast cancer subtypes using latent Dirichlet allocation |
|
1:45 PM |
1:53 PM |
6 |
Hilary Mulholland |
Sarah Walker |
Clustering Disease Networks |
|
1:54 PM |
2:02 PM |
7 |
Yuhao Wang |
|
Genome-wide Enhancer Acetylation Analysis for Alzheimer's Disease |
|
2:03 PM |
2:11 PM |
8 |
Yi-Shiuan Tung |
|
Positive Selection on the human opsin genes |
Open session
Tuesday December 9 at 2:30-5:30 PM, 32-D463 (Star conference room)
|
Start |
End |
# |
Student 1 |
Student 2 |
Project Title |
|
2:30 PM |
2:38 PM |
9 |
Divya Pillai |
Kris Shin |
Dynamic Network Analysis in Host Response to Infectious Disease |
|
2:39 PM |
2:47 PM |
10 |
David Lazar |
|
Privacy-preserving GWAS |
|
2:48 PM |
2:56 PM |
11 |
Yunpeng Liu |
Sahar Alkhairy |
Construction and Analysis of Integrated, Subtype-specific Glioblastoma Regulatory Networks |
|
2:57 PM |
3:05 PM |
12 |
Abdulaziz Alghunaim |
Muneeza Patel |
Identification of drugs targeting liver cancer. |
|
3:06 PM |
3:14 PM |
13 |
Ben Bauchwitz |
Pasha Muravyev |
An analysis of lincRNA sequence properties |
|
3:15 PM |
3:23 PM |
14 |
Aradhana Sinha |
Margaret Walker |
Simulation of Antiviral RNAi in Influenza |
|
3:50 PM |
4:00 PM |
|
Stretch Break / Catch up on time |
||
|
3:35 PM |
3:43 PM |
15 |
Clement Pit-Claudel |
William Leiserson |
Cascading Filter-based Classification |
|
3:44 PM |
3:52 PM |
16 |
Jenny Lin |
Michael Coulombe |
STAR-MP is NP-Complete |
|
3:53 PM |
4:01 PM |
17 |
Kevin Chen |
|
Compressive Algorithms for Protein HMM-HMM Alignment |
|
4:02 PM |
4:10 PM |
18 |
Tristan Bepler |
Grace Yeo |
Predicting involvement of RNA-binding proteins in differential transcript abundance |
|
4:11 PM |
4:19 PM |
19 |
Kathy Lin |
Adam Sealfon |
Exploring the human gut microbiome |
|
4:18 PM |
4:26 PM |
|
|
|
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Announced on 09 December 2014 10:27 a.m. by Manolis Kellis
Final presentation/report tips
Announced on 04 December 2014 10:44 a.m. by Abhishek Kulshreshtha Sarkar
6.047 project presentation sign up
Make sure to include your project title when you sign up.
Announced on 03 December 2014 6:24 p.m. by Abhishek Kulshreshtha Sarkar
Final project report + slides extension policy
1. Final project report: Due by Sunday 12/7 at 8pm
2. Final presentation slides: Due by Monday 12/8 at 8pm
The usual 'a few hours give or take' policy applies, but no later than 11:59pm each evening. Thanks!
Announced on 02 December 2014 2:34 p.m. by Manolis Kellis
