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BF821

Bioinformatics Graduate Seminar

course type
Seminar
instructor Yu (Brandon) Xia
time Wednesday 1:00pm - 3:00pm
recurrence Weekly from 2013-01-16 until 2013-05-01
first session
2013-01-16 1:00pm - 3:00pm
location new location: PSY B39

* Please select two papers from two different weeks and email your choices to Brandon (yuxia@bu.edu) as soon as possible.  The paper assignments will be made on a first come, first serve basis.

* Each presentation will be roughly 30-40 minutes, followed by discussions.

* Please log in to view course materials. Email Brandon if you forgot the login name or password.

Course Schedule

date
paper
presenter
Jan 16
Introduction and overview
Brandon Xia
Jan 16
Rate of de novo mutations and the importance of father's age to disease risk
Nature 488: 471-475 (2012)
Charles Dumont
Jan 16
De novo discovery of mutated driver pathways in cancer
Genome Res 22: 375-385 (2012)
John Hogan
Jan 23
An integrated map of genetic variation from 1,092 human genomes
Nature 491: 56–65 (2012)
Adam Labadorf
Jan 23
Comprehensive genomic characterization of squamous cell lung cancers
Nature 489: 519–525 (2012)
Charles Dumont
Jan 23
Genomic landscape of non-small cell lung cancer in smokers and never-smokers
Cell 150: 1121-1134 (2012)
Joe Perez-Rogers
Jan 30
Comprehensive molecular portraits of human breast tumours
Nature 490: 61–70 (2012)
Ana Pavel
Jan 30
Whole-genome sequencing in autism identifies hot spots for de novo germline mutation
Cell 151: 1431-1442 (2012)
Allyson Byrd
Jan 30
Diagnostic exome sequencing in persons with severe intellectual disability
N Engl J Med 367: 1921-1929 (2012)
Sara Howell
Feb 6
Genomic variation landscape of the human gut microbiome
Nature 493: 45–50 (2012)
Michael Platt
Feb 6
Ecological populations of bacteria act as socially cohesive units of antibiotic production and resistance
Science 337: 1228-1231 (2012)
Brenna LaBarre
Feb 6
An anatomically comprehensive atlas of the adult human brain transcriptome
Nature 489: 391–399 (2012)
Allyson Byrd
Feb 13
Revisiting global gene expression analysis
Cell 151: 476-482 (2012)
Michael Platt
Feb 13
Systematic localization of common disease-associated variation in regulatory DNA
Science 337: 1190-1195 (2012)
Jaeyoon Chung
Feb 13
Landscape of transcription in human cells
Nature 489: 101–108 (2012)
Gracia Bonilla
Feb 20
MONDAY SCHEDULE. NO CLASS.

Feb 27
The long-range interaction landscape of gene promoters
Nature 489: 109–113 (2012)
Yu Fu
Feb 27
Genome-wide protein-DNA binding dynamics suggest a molecular clutch for transcription factor function
Nature 484: 251-255 (2012)
Gracia Bonilla
Mar 6
The evolutionary landscape of alternative splicing in vertebrate species
Science 338: 1587-1593  (2012)
Deep Shah
Mar 6
Decoding human cytomegalovirus
Science 338: 1088-1093 (2012)
Joe Perez-Rogers
Mar 6
Functional screening identifies miRNAs inducing cardiac regeneration
Nature 492: 376–381 (2012)
Sara Howell
Mar 6
Evolutionary dynamics of gene and isoform regulation in mammalian tissues
Science 338: 1593-1599 (2012)
Ana Pavel
Mar 13
SPRING RECESS. NO CLASS.

Mar 20
An integrated encyclopedia of DNA elements in the human genome
Nature 489: 57-74 (2012)
Yu Fu
Mar 20
An expansive human regulatory lexicon encoded in transcription factor footprints
Nature 489: 83–90 (2012)
John Hogan
Mar 27
Architecture of the human regulatory network derived from ENCODE data
Nature 489: 91–100 (2012)
Jaeyoon Chung
Mar 27
Principles for designing ideal protein structures
Nature 491: 222-227 (2012)
Shun Yip
Mar 27
Computational design of self-assembling protein nanomaterials with atomic level accuracy
Science 336: 1171-1174 (2012)
Jessica Keenan
Mar 27
The spatial architecture of protein function and adaptation
Nature 491: 138-142 (2012)
Raymond Yan
Apr 3
Automated design of ligands to polypharmacological profiles
Nature 492: 215–220 (2012)
Shun Yip
Apr 3
Chemical genetic discovery of targets and anti-targets for cancer polypharmacology
Nature 486: 80-84 (2012)
Heather Selby
Apr 3
Identification of small RNA pathway genes using patterns of phylogenetic conservation and divergence
Nature doi:10.1038/nature11779 (2012)
Lingqi Luo
Apr 10
Structure-based prediction of protein-protein interactions on a genome-wide scale
Nature 490: 556-560 (2012)
Lingqi Luo
Apr 10
Circuitry and dynamics of human transcription factor regulatory networks
Cell 150: 1274-1286 (2012)
Raymond Yan
Apr 10
Epistasis as the primary factor in molecular evolution
Nature 490: 535–538 (2012)
Kristina Holton
Apr 10
Seventy-five genetic loci influencing the human red blood cell
Nature 492: 369–375 (2012)
Kylee Bergin
Apr 17
The mystery of missing heritability: Genetic interactions create phantom heritability
PNAS 109: 1193-1198 (2012)
Deep Shah
Apr 17
Interaction landscape of membrane-protein complexes in Saccharomyces cerevisiae
Nature 489: 585–589 (2012)
Arjan van der Velde
Apr 17
Aggravating genetic interactions allow a solution to redundancy in a bacterial pathogen
Science 338: 1440-1444 (2012)
Kylee Bergin
Apr 24
Kinetic responses of β-Catenin specify the sites of Wnt control
Science 338: 1337-1340 (2012)
Heather Selby
Apr 24
Bacterial quorum sensing and metabolic incentives to cooperate
Science 338: 264-266 (2012)
Brenna LaBarre
Apr 24
Genetic programs constructed from layered logic gates in single cells
Nature 491: 249–253 (2012)
Jessica Keenan
May 1
Spontaneous network formation among cooperative RNA replicators
Nature 491: 72–77 (2012)
Arjan van der Velde
May 1
A whole-cell computational model predicts phenotype from genotype
Cell 150: 389-401 (2012)
Adam Labadorf
May 1
Multiplex targeted sequencing identifies recurrently mutated genes in autism spectrum disorders
Science 338: 1619-1622 (2012)
Kristina Holton

Course Description

BF821 is a graduate seminar covering current topics in bioinformatics.  This is achieved through the critical reading, presentation, and discussion of recent literature.  Additionally, the course is intended to give students the opportunity to practice and improve their scientific presentation abilities.  As such, peer feedback on presentations is an integral aspect of the course.  Students will present two times during the semester so that they may improve upon their presentation skills based on peer comments.

Final Report (due May 1 by email: yuxia@bu.edu)

You are asked to write a report on a paper that other people presented.  The report should consist of approximately 700-1000 words.  You can choose between one of the two following formats:

  • Referee report: Write a referee report of the paper for consideration of publication in a highly selective journal.  You have the choice of rejecting or accepting the paper with or without revisions.  To learn more, check out the online journal Biology Direct which publishes the referee report along with the papers.
  • News & Views article: Write a commentary aimed at a broad audience of biologists.  To learn more, check out the News & Views articles in the journal Nature.

Grading

The course is graded on a pass-fail basis, where attendance, participation, and the final report are required for a passing grade.

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