BioMicroCenter:BIG meeting: Difference between revisions

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{{BioMicroCenter}}
{{BioMicroCenter}}


Please fill out the [http://www.doodle.com/8aetbhdxx4p68byx survey] to help us schedule the next academic year.
Full Speaker Rotation is '''[[BioMicroCenter:BIG_Rotation||HERE]]'''.
==2013-2014 academic year==
{| border=1
! width 100 align="center"|DATE
! width 100 align="center"|TIME
! width 100 align="center"|Presenter
! width 100 align="center"|Location
! width 100 align="center"|Room
! width 100 align="center"|NOTES
|-
| Sept 12
| noon
| Matthew McCormack (MolBio)
| MGH
| Simches 7.240
| call 617-726-5944 to get upstairs
|-
| Sept 26
| noon
| Vincent Butty (MIT)
| MIT
| 68-156
| Reference-free sequence variation discovery
|-
| Oct 24
| noon
| Mark Borowski (Novartis)
| MIT
| 68-156
| Life in Pharmaa
|-
| Nov 14
| noon
| George Marnellos (HMS)
| MIT
| 68-156
| non-reference organism RNA-seq analysis (assembly and differential <BR> expression) using tools like Trinity and edgeR/DESeq
|-
| Dec 5
| noon
| Charlie Whittaker (MIT)
| MIT
| 68-156
|
|-
| Jan 9, 2014
| noon
| Jie Wu (MIT)
| MIT
| 68-156
| [http://nar.oxfordjournals.org/content/41/10/5149 OLego] and [http://bioinformatics.oxfordjournals.org/content/27/21/3010 SpliceTrap]
|-
| Jan 23
| noon
| George Bell (WI)
| Whitehead
| 4th floor Conference Room
| Resource Sharing (code, data, web tools, methods, etc.) <BR> within our group, across Whitehead, and to the public.
|-
| Feb 6
| noon
| Lax Iyer (Tufts)
| MIT
| 68-156
| RNASeq study on Astroglia Development
|-
| Feb 27
| noon
| Rory Kirchner
| MIT
| 68-156
| bcbio.rnaseq, an automated way to compare different RNA-seq differential expression callers
|-
| Mar 13
| noon
| Huiming Ding
| MIT
| 68-156
| Transposition and cancer
|-
| Mar 27
| noon
| Yanqun Wang
|
|
| Novartis
|-
| Apr 10
| noon
| Jingzhi Zhu
| MIT
| 68-156
|
|-
| May 1
| noon
| Penny Wang
|
|
| MGH
|-
| May 15
| noon
| Duan Ma
| MIT
| 68-156
|
|-
| May 29
| noon
| '''OPEN'''
|
|
|
|}
 
==2013==
{| border=1
! width 100 align="center"|DATE
! width 100 align="center"|TIME
! width 100 align="center"|Presenter
! width 100 align="center"|Location
! width 100 align="center"|Room
! width 100 align="center"|NOTES
|-
| 1/10 (Thursday)
| 12p
| Vincent Butty
| MIT
| 68-156
| Proteomics application of Next-Gen sequencing technologies
|-
| 2/14
| 12p
| Huiming Ding
| MIT
| 68-156
| Evaluation of Cuffdiff2 for RNA-seq Differential Analysis and CaBlast for Compressive Genomics
|-
| 3/14
| 12p
| Lakshmanan Iyer
| MIT
| 68-156
| Communicating ENCODE data and using it to analyze rare diseases
|-
| 3/28
| 12p
| Stuart Levine / George Bell / Mark Borowski
| MIT
| 68-156
| AGBT & ABRF Meeting Reviews
|-
|}
 
==2012==
==2012==
{| border=1  
{| border=1  
Line 30: Line 184:
  | MIT
  | MIT
  | [http://whereis.mit.edu/?go=68 68-181]
  | [http://whereis.mit.edu/?go=68 68-181]
  |  
  | RNA-Seq quality control and quantitation of alternative RNA processing
  |-
  |-
  | 4/12 (Thursday)
  | 4/12 (Thursday)
Line 48: Line 202:
  | 5/24  
  | 5/24  
  | 12p  
  | 12p  
  | Laks Iyer
  | Joshua Ainsley (Tufts) - Hosted by Lakshmanan Iyer
  | TBA
  | Tufts
  | TBA
  | [http://campusmaps.tufts.edu/boston/?fid=B011 Sackler 851]
  | TBA
  | Characterizing dendritic translation with RNA-Seq
  |-
  |-
  | 6/7
  | 6/7
  | 12p  
  | 12p  
  | Toshi Ohsumi
  | Toshi Ohsumi
  | TBA
  | MGH
  | TBA
  | Sinches 5 - Darwin Room
  | TBA
  | MolBioLib: a C++11 Bioinformatics Framework
  |-
  |-
  | 6/7
  | 6/21
  | 12p  
  | 12p  
  | Juli Klemm (NIH/NCI)
  | Juli Klemm (NIH/NCI)
  | MIT
  | MIT
| [http://whereis.mit.edu/?go=68 68-156]
| [[BioMicroCenter:BIG_meeting:KlemmTalk|Informatics at NCI]]
|-
| 7/12
| 12p
| Ryan Abo
| MIT
| [http://whereis.mit.edu/?go=68 68-274]
| discovery of active enhancers using GRO-seq data. <BR>
Core, LJ, Waterfall, JJ, Lis, JT (2008). Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science, 322, 5909:1845-8. <BR>
Melgar, MF, Collins, FS, Sethupathy, P (2011). Discovery of active enhancers through bidirectional expression of short transcripts. Genome Biol., 12, 11:R113.
|-
| 7/26
| 12p
| Yanqun Wang
| MGH
  | TBA
  | TBA
  | TBA
  | TBA
  |-|}
  |-
| 9/13
| 12p
| Stuart Levine
| MIT
| [http://whereis.mit.edu/?go=68 68-156]
| Replicates in Informatics: http://genome.cshlp.org/content/22/9/1813.full.pdf+html
|-
| 9/27
| 12p
| Charlie Whittaker
| KI
| [http://whereis.mit.edu/?go=68 68-156]
| Teaching Bioinformatics
|-
| 10/18
| 12p
| Brad Chapman
| MIT
| [http://whereis.mit.edu/?go=68 68-156]
| Biological resources for Amazon: CloudBioLinux, CloudMan, BioCloudCentral [http://www.slideshare.net/chapmanb/big-cloud-2012 slides]
|-
| 11/8
| 12p
| Ruslan Sadreyev
| MGH
| Darwin Room
| Methods for analyzing allelic expression of RNA.
|-
| 11/29
| 12p
| George Bell
| WI
| 4th floor conference room
| TargetScan
|-
| 12/13
| 12p
| Rory Kirchner
| MIT
| 68-156
| iPython and iPython Notebook
|-
|}


==2011==
==2011==

Revision as of 18:34, 17 March 2014

HOME -- SEQUENCING -- LIBRARY PREP -- HIGH-THROUGHPUT -- COMPUTING -- OTHER TECHNOLOGY

Full Speaker Rotation is |HERE.

2013-2014 academic year

DATE TIME Presenter Location Room NOTES
Sept 12 noon Matthew McCormack (MolBio) MGH Simches 7.240 call 617-726-5944 to get upstairs
Sept 26 noon Vincent Butty (MIT) MIT 68-156 Reference-free sequence variation discovery
Oct 24 noon Mark Borowski (Novartis) MIT 68-156 Life in Pharmaa
Nov 14 noon George Marnellos (HMS) MIT 68-156 non-reference organism RNA-seq analysis (assembly and differential
expression) using tools like Trinity and edgeR/DESeq
Dec 5 noon Charlie Whittaker (MIT) MIT 68-156
Jan 9, 2014 noon Jie Wu (MIT) MIT 68-156 OLego and SpliceTrap
Jan 23 noon George Bell (WI) Whitehead 4th floor Conference Room Resource Sharing (code, data, web tools, methods, etc.)
within our group, across Whitehead, and to the public.
Feb 6 noon Lax Iyer (Tufts) MIT 68-156 RNASeq study on Astroglia Development
Feb 27 noon Rory Kirchner MIT 68-156 bcbio.rnaseq, an automated way to compare different RNA-seq differential expression callers
Mar 13 noon Huiming Ding MIT 68-156 Transposition and cancer
Mar 27 noon Yanqun Wang Novartis
Apr 10 noon Jingzhi Zhu MIT 68-156
May 1 noon Penny Wang MGH
May 15 noon Duan Ma MIT 68-156
May 29 noon OPEN

2013

DATE TIME Presenter Location Room NOTES
1/10 (Thursday) 12p Vincent Butty MIT 68-156 Proteomics application of Next-Gen sequencing technologies
2/14 12p Huiming Ding MIT 68-156 Evaluation of Cuffdiff2 for RNA-seq Differential Analysis and CaBlast for Compressive Genomics
3/14 12p Lakshmanan Iyer MIT 68-156 Communicating ENCODE data and using it to analyze rare diseases
3/28 12p Stuart Levine / George Bell / Mark Borowski MIT 68-156 AGBT & ABRF Meeting Reviews

2012

DATE TIME Presenter Location Room NOTES
1/26 (Thursday) 12p Brian Haas (Broad Institute) MIT 76-558 Trinity
2/23 (Thursday) 12p Brad Chapman MIT 68-180 Extending the GATK for variant comparisons; slides code
3/22 (Thursday) 12p Vincent Butty MIT 68-181 RNA-Seq quality control and quantitation of alternative RNA processing
4/12 (Thursday) 12p Kip Bodi Tufts Medical Journal Club
5/3 12p Huiming Ding MIT 68-180 "High-throughput generation, optimization and analysis of genome-scale metabolic models." by Henry, C. S. et al.
5/24 12p Joshua Ainsley (Tufts) - Hosted by Lakshmanan Iyer Tufts Sackler 851 Characterizing dendritic translation with RNA-Seq
6/7 12p Toshi Ohsumi MGH Sinches 5 - Darwin Room MolBioLib: a C++11 Bioinformatics Framework
6/21 12p Juli Klemm (NIH/NCI) MIT 68-156 Informatics at NCI
7/12 12p Ryan Abo MIT 68-274 discovery of active enhancers using GRO-seq data.

Core, LJ, Waterfall, JJ, Lis, JT (2008). Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science, 322, 5909:1845-8.
Melgar, MF, Collins, FS, Sethupathy, P (2011). Discovery of active enhancers through bidirectional expression of short transcripts. Genome Biol., 12, 11:R113.

7/26 12p Yanqun Wang MGH TBA TBA
9/13 12p Stuart Levine MIT 68-156 Replicates in Informatics: http://genome.cshlp.org/content/22/9/1813.full.pdf+html
9/27 12p Charlie Whittaker KI 68-156 Teaching Bioinformatics
10/18 12p Brad Chapman MIT 68-156 Biological resources for Amazon: CloudBioLinux, CloudMan, BioCloudCentral slides
11/8 12p Ruslan Sadreyev MGH Darwin Room Methods for analyzing allelic expression of RNA.
11/29 12p George Bell WI 4th floor conference room TargetScan
12/13 12p Rory Kirchner MIT 68-156 iPython and iPython Notebook

2011

Schedule for 2011.

DATE TIME Presenter Location Room NOTES
1/18 12p Toshiro Ohsumi MGH Simches 5290
2/1 12p Stuart Levine MIT 68-329 Illumina Quality Control Modules
2/15 12p Paola Favaretto MIT 76-358 Matlab
3/8 12p Fugen Li MIT 68-329 Enhancer Analysis
3/22 12p Charlie Whittaker MIT 76-247 Commercial versus public GO tools
4/12 12p Laurent Gautier
Center for Biological Sequence Analysis, Denmark 		MIT 76-259 R-Python Interface
http://www.cbs.dtu.dk/index.shtml
4/26 12p Michael Reich
Broad Institute 		MIT 68-151 GenePattern Enhancements
5/17 12p Mark Borowsky MGH Simches 5 / Darwin Schneeberger et al., 2009 NatureMethods
6/7 12p Brad Chapman MIT 68-151 BioPython
6/28 12p Ruslan Sadreyev MIT 76-659 Teaching Statistics
7/12 12p Kip Bodi MIT 68-121 Data analysis for DSRG / ABRF
7/26 12p Toshiro Ohsumi MGH TBA
8/23 12p Lakshmanan Iyer Tufts Medical RNAseq Analysis
9/15 (Thursday) 12p Brad Chapman MIT 76-558 distributed exome analysis pipeline slides
10/6 (Thursday) 12p Stuart Levine MIT 68-274 Comparison of ChIP-seq algorithms
10/27 (Thursday) 12p Pablo Pareja MIT 76-258 Bio4j Graph based analysis and visualization slides
11/?? (Thursday) 12p Paola Favaretto MIT RNAseq - part I
12/15 12p Charlie Whittaker MIT RNAseq - part II


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