Editing BioMicroCenter:BIG meeting

{{BioMicroCenter}}

==2020-2021 academic year==

Meetings will start out as virtual (on your platform of choice, or ask [mailto:gbell@wi.mit.edu George Bell] to set up a Zoom or Meet meeting).  If we return to work interactions, they will be at MIT Biology (68-156), the Whitehead Institute (7th floor larger classroom), or anywhere else as selected by the speaker.  A session leader is welcome to present a project, a published work (like a journal club), share notes from a conference, or present anything else of interest to our group of applied bioinformatics scientists.  The format can be a presentation and/or a discussion, and the venue need not be MIT or Whitehead. Questions? Contact George.

'''UPDATE: The BIG meeting series will be taking a hiatus during the 2020-2021 academic year.  We'll start up again in the fall of 2021 -- see you then!'''

==2019-2020 academic year==
Meetings will be at MIT Biology (68-156), the Whitehead Institute (7th floor larger classroom), or anywhere else as selected by the speaker.  A session leader is welcome to present a project, a published work (like a journal club), share notes from a conference, or present anything else of interest to our group of applied bioinformatics scientists.  The format can be a presentation and/or a discussion, and the venue need not be MIT or Whitehead. Questions? Contact Barry Kesner or George Bell.
{| border=1 
 !width 150px align="center"|Date
 !width 150px align="center"|Time
 !width 150px align="center"|Presenter 
 !width 150px align="center"|Location 
 !width 150px align="center"|Room 
 !width 150px align="center"|Topic, notes, etc.
 |-align="center"
 |Dec 5
 |11 am
 |George Bell (WI) 
 |WI
 |Founders Room (2nd floor) 
 |Engineering and characterizing human microglia
 |-align="center"
 |Dec 19
 |11 am
 |Vincent Butty (MIT) 
 |MIT
 |68-156
 |Trajectory Inference in scRNA-Seq
 |-align="center"
 |Jan 9
 |11 am
 |Dikshant Pradhan (MIT)
 |MIT
 |68-156
 |FAIR data management using SEEK
 |-align="center"
 |Jan 23
 |11 am
 |Troy Whitfield (WI) 
 |WI
 |7th floor classroom
 |&nbsp; HIV-1 protease (fitness measurements and machine learning) &nbsp; 
 |-align="center"
 |Feb 27 
 |11 am
 |Prat Thiru (WI) 
 |WI
 |7th floor classroom
 |Challenges of scRNA-seq [http://barc.wi.mit.edu/education/BIG_Meeting/scRNASeq_Challenges.pdf (slides)]
 |-align="center"
 |Mar 19
 |11 am
 |Stuart Levine (MIT) 
 |MIT
 |videoconference
 |AGBT / ABRF Technology review
 |-align="center"
 |Apr 2
 |11 am
 |Charlie Whittaker (MIT)
 |MIT
 |videoconference
 |ABRF GBIRG 2020 - Ontology Analyses Study
 |-align="center"
 |Apr 16
 |11 am
 | &nbsp; John Hutchinson (HSPH) &nbsp;
 |MIT
 |videoconference
 |
 |-align="center"
 |Apr 23
 |11 am
 |Duanduan Ma (MIT) 
 |MIT
 |videoconference
 |Causal inference and its potential application in RNA-seq time series data
 |-align="center"
 |May 14
 |11 am
 |Inma Barrasa (WI)
 |WI
 |videoconference
 |Antigen receptor sequence reconstruction and clonality inference from scRNA-Seq data
 |-align="center"
 |June 4
 |11 am
 |Bingbing Yuan (WI)
 |WI
 |videoconference
 |Identifying differentially expressed genes in scRNA-seq experiments
 |-align="center"
|}

==2018-2019 academic year==
{| border=1 
 !width 150px align="center"|Date
 !width 150px align="center"|Time
 !width 150px align="center"|Presenter 
 !width 150px align="center"|Location 
 !width 150px align="center"|Room 
 !width 150px align="center"|Notes
 |-align="center"
 |Oct 11 
 |11 am
 |**NO MEETING** 
 |MIT
 |68-156
 |
 |-align="center"
 | &nbsp; Oct 25 &nbsp; 
 | &nbsp; 11 am &nbsp; 
 | &nbsp; George Bell (WI) &nbsp;
 | &nbsp; Whitehead &nbsp; 
 | &nbsp; 7th floor &nbsp; 
 | &nbsp; Experimental design: Make a good one, or make the most of what you get &nbsp;
 |-align="center"
 |Nov 15
 |11 am
 |Kris Richardson (WI)
 |Whitehead
 |7th floor
 |ATAC-Seq analysis
 |-align="center"
 |Dec 6
 |11 am
 |Lorena Pantano (HSPH)
 |MIT
 |68-156
 |miRNA Wars: the isomiR menace 
 |-align="center"
 |Dec 20
 |11 am
 |Charlie Whittaker (KI, MIT)
 |MIT
 |68-156
 |Intragenic Tandem Repeats
 |-align="center"
 |Jan 10
 |11 am
 |Prat Thiru (WI)
 |Whitehead
 |7th floor
 |&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; Visualization: principles & software ([http://barc.wi.mit.edu/education/BIG_Meeting/BIG_MeetingJan2019_Viz.pdf slides]); D3 demo  ([http://barc.wi.mit.edu/education/BIG_Meeting/demo_viz.zip code]), tested on Firefox &nbsp;&nbsp; &nbsp; &nbsp; &nbsp;  
 |-align="center"
 |Jan 24
 |11 am
 |Vincent Butty (MIT)
 |MIT
 |68-156
 |RNA processing analysis in single-cell RNA-Seq
 |-align="center"
 |Feb 7
 |11 am
 |Ruslan Sadreyev (MGH/HMS)
 |MIT
 |68-156
 |Causal interactions between DNA replication and chromatin remodeling
 |-align="center"
 |Feb 28 
 |11 am
 |**NO MEETING** 
 |MIT
 |68-156
 |
 |-align="center"
 |Mar 28
 |11 am
 |Brad Chapman (Harvard Chan)
 |MIT
 |[http://whereis.mit.edu/?go=68 68-156]
 |Data organization, normalization and modeling; ([https://github.com/chapmanb/bcbb/blob/master/talks/ginkgo_dataorg/ginkgo_dataorg.pdf slides])
 |-align="center"
 |Apr 11
 |11 am
 |Inma Barrasa (WI)
 |Whitehead
 |7th floor
 |Discussion of [https://www.ncbi.nlm.nih.gov/pubmed/30827895 Li et al., 2019], highlighting the computational analysis
 |-align="center"
 |May 2
 |11 am
 |Huiming Ding (MIT)
 |MIT
 |68-156 
 |Recent trends in FAIR data management and machine learning algorithms
 |-align="center"
 |May 16
 |11 am
 |Duanduan Ma (MIT)
 |MIT
 |68-156 
 |Machine learning and its applications in genomics
 |-align="center"
 |May 30
 |11 am
 |Bingbing Yuan (WI)
 |Whitehead
 |7th floor
 |Creating client-side interactive plots in R ([http://barc.wi.mit.edu/education/BIG_Meeting/BigMeeting_May2019.pdf slides]) ([http://barc.wi.mit.edu/education/BIG_Meeting/BigMeeting_May2019_RmarkdownFiles.zip R markdown and sample input/output])
 |-align="center"
|}

==2017-2018 academic year==
{| border=1 
 !width 150px align="center"|Date
 !width 150px align="center"|Time
 !width 150px align="center"|Presenter 
 !width 150px align="center"|Location 
 !width 150px align="center"|Room 
 !width 150px align="center"|Notes
 |-align="center"
 |Oct 5 
 |11 am
 |**NO MEETING**
 |MIT
 |68-156
 |
 |-align="center"
 |Oct 19
 |11 am
 |Vincent Butty (MIT)
 |MIT
 |68-156
 |RNA-Seq-based alternative isoform quantification, and benchmarking with spike-ins.
 |-align="center"
 |Nov 2  
 |11 am
 |Brad Chapman (HSPH)
 |MIT
 |[http://whereis.mit.edu/?go=68 68-156]
 |[https://gist.github.com/chapmanb/8ee026fd85d07518570ac5a0cd7239f5 bcbio and Common Workflow Language interoperability progress]; [https://github.com/chapmanb/bcbb/blob/master/talks/big2017_bcbio_cwl/big2017_bcbio_cwl.pdf slides]; [https://youtu.be/nJEDS9Qol8M video]
 |-align="center"
 |Nov 16
 |11 am
 |**NO MEETING**
 |MIT
 |68-156
 | 
 |-align="center"
 |Dec 7
 |11 am
 |Lorena Pantano (HSPH)
 |MIT
 |68-156
 |Analyzing hundreds of small RNA samples with bcbio-nextgen; miRTop
 |-align="center"
 |Dec 21
 |11 am
 |Charlie Whittaker
 |MIT
 |68-156
 |Vignettes: Gene expression, search for diagnostic markers; logFC shrinkage methods
 |-align="center"
 |Jan 4
 |11 am
 |**NO MEETING**
 |MIT
 |7th floor
 |
 |-align="center"
 |Jan 18
 |11 am
 |Prat Thiru (WI)
 |Whitehead
 |7th floor
 |Reproducible research for bioinformatics: best practices [http://barc.wi.mit.edu/education/BIG_Meeting/BIG_MeetingJan2018.pdf (slides)]
 |
 |-align="center"
 |Feb 1
 |11 am
 |Kris Richardson (WI)
 | &nbsp; Whitehead &nbsp; 
 | &nbsp; 7th floor &nbsp; 
 |Highlights from Genome Informatics (Nov. 2017)
 |-align="center"
 |Feb 15 
 |11 am
 |George Bell (WI)
 |Whitehead
 |7th floor
 |Fungal genome assembly and annotation 
 |-align="center"
 |Mar 1
 |11 am
 |Stuart Levine (MIT)
 |MIT
 |68-156
 |Review of AGBT meeting: What is that light coming down the tunnel?
 |-align="center"
 |Mar 15
 |11 am
 | &nbsp;  &nbsp; Radhika Khetani and Mary Piper (HSPH) &nbsp;  &nbsp; 
 |MIT
 |68-156
 |Adventures in Bioinformatics Training
 |-align="center"
 |Apr 5
 |11 am
 |Bingbing Yuan (WI)
 |Whitehead
 |7th floor
 |Interactive Figures with R [http://barc.wi.mit.edu/education/BIG_Meeting/interactivePlots_Apr2018.pdf (slides)]
 |-align="center"
 |Apr 19
 |11 am
 |Huiming Ding (MIT)
 |MIT
 |68-156 
 |Application of Machine Learning In Analyzing Cancer Mutations
 |-align="center"
 |May 3
 |2pm
 |Priyanka Shivdasani, Renato Umeton, and Matthew Dukar
 |DFCI
 |Rm D1620, Dana building, 450 Brookline Ave, Boston
 |Building tools to fight cancer: three vignettes from the DFCI Data Science and Bioinformatics group
 |
 |-align="center"
 |May 17
 |11 am
 |Inma Barrasa (WI)
 |Whitehead
 |7th floor
 |
 |-align="center"
 |May 30 (Wed.)
 |11 am
 |Duanduan Ma (MIT)
 |MIT
 |68-156  
 |Reflection of 2018 May Institute: Computation and Statistics for mass spectrometry and proteomics
|}

==2016-2017 academic year==
{| border=1 
 !width 150px align="center"|Date
 !width 150px align="center"|Time
 !width 150px align="center"|Presenter 
 !width 150px align="center"|Location 
 !width 150px align="center"|Room 
 !width 150px align="center"|Notes
 |-align="center"
 |Oct 6 
 |11 am
 |Prat Thiru (WI)
 |Whitehead
 |7th floor
 |[http://barc.wi.mit.edu/education/BIG_Meeting/BIG_Meeting2016_Oct.pdf Highlights of ECCB 2016]
 |-align="center" 
 |Oct 20
 |11 am
 |Vincent Butty (MIT)
 |MIT
 |68-156
 |High-throughput 3' digital gene expression analysis for low input RNA samples.
 |-align="center"
 |Nov 3  
 |11 am
 |Brad Chapman (HSPH) 
 |MIT
 |[http://whereis.mit.edu/?go=68 68-156]
 |[https://gist.github.com/chapmanb/f1ccdd2e2e23b0383b6e6857b59a431b bcbio and the Common Workflow Language] [https://github.com/chapmanb/bcbb/blob/master/talks/big2016_bcbio_cwl/big2016_bcbiocwl.pdf slides] [https://youtu.be/375QSYmaidk recording]
 |-align="center"
 |Nov 17
 |11 am
 |Matthew McCormack (Harvard)
 |MIT
 |68-156
 |The human splicing code and disease ( [https://www.ncbi.nlm.nih.gov/pubmed/25525159 Xiong et al., Science])
 |-align="center"
 |Dec 1
 |11 am
 |George Bell (WI)
 |Whitehead
 |7th floor
 |Under-replication analysis; 3D printing of biomolecules  
 |-align="center"
 |Dec 15
 |11 am
 |Lorena Pantano (HSPH)
 |MIT
 |68-156
 | [https://gist.github.com/chapmanb/87ce4db49792ed7e98081c97c011372c small RNA analysis] [https://github.com/lpantano/mypubs/blob/master/talks/BIG_Dec_15_2016.pdf slides] [https://youtu.be/l5nI8GICCPg video]
 |-align="center"
 |Jan 5
 |11 am
 |**NO MEETING**
 |
 |
 |
 |-align="center"
 |Jan 19
 |11 am
 |Charlie Whittaker (MIT)
 |MIT
 |68-156
 |Using SOMs for RNA-seq analysis  
 |-align="center"
 |Feb 2
 |11 am
 |Ruslan Sadreyev (MGH)
 |MIT
 |68-156
 | 5C HiC analysis [https://www.youtube.com/watch?v=8F1UZjUyK04 video]
 |-align="center"
 |Feb 16 
 |11 am
 |Matt Shirley (NIBR)
 |MIT
 |68-156
 | PISCES: alignment free RNA-seq quantiation and QC pipeline; [http://www.openwetware.org/images/6/6b/2017-02-16_BIG-meeting.pdf slides]; [https://www.youtube.com/watch?v=6uS5JENyDg0 video]
 |-align="center"
 |Mar 2
 |11 am
 |Stuart Levine (MIT)
 |MIT
 |68-156 (confirmed)
 |Review of AGBT  
 |-align="center"
 |Mar 16
 |11 am
 |**NO MEETING**
 |
 |
 |  
 |-align="center"
 |Apr 6
 |11 am
 |Huiming Ding (MIT)
 |MIT
 |68-156
 |Running a scRNA-Seq pipeline in the Amazon cloud
 |-align="center"
 |Apr 20
 |11 am
 |Duanduan Ma (MIT)
 |MIT
 |68-156 
 |Weighted Correlation Network Analysis (WGCNA) and its application in cancer genomics study  
 |-align="center"
 |May 4
 |11 am
 |Michael Steinbaugh (HSPH)
 |MIT
 |68-156  
 |R-based methods for scRNA-seq analysis 
 |-align="center"
 |May 18
 |11 am
 |Inma Barrasa (WI)
 |Whitehead
 |7th floor
 |Identifying antibody repertoires using high-throughput sequencing
|}

==2015-2016 academic year==
{| border=1 
 !width 150px align="center"|DATE
 !width 150px align="center"|TIME 
 !width 150px align="center"|Presenter 
 !width 150px align="center"|Location 
 !width 150px align="center"|Room 
 !width 150px align="center"|NOTES
 |-align="center"
 |OCT22 
 |11a
 |VINCENT BUTTY (MIT)
 |MIT
 |68-156   
 |Dimensionality reduction for single cell data
 |-align="center"
 |NOV5  
 |11a
 |BRAD CHAPMAN (HSPH) 
 |MIT
 |[http://whereis.mit.edu/?go=68 68-156]
 |[https://github.com/chapmanb/bcbio-nextgen bcbio development work] supporting [http://bcb.io/2015/09/17/hg38-validation/ human build 38], [https://github.com/bcbio/bcbio.github.io/blob/master/_posts/2015-10-05-vardict-filtering.md low frequency variant calling] and support for Docker and the Common Workflow Language: [https://github.com/chapmanb/bcbb/blob/master/talks/big2015_bcbio/big2015_bcbio.pdf validation slides], [https://github.com/chapmanb/bcbb/blob/master/talks/bioindocker2015_bcbio/chapman_bioindocker.pdf Docker/CWL slides]
 |-align="center"
 |NOV19  
 |11a 
 |Jie Wu (MIT)  
 |MIT  
 |68-156  
 |Finding methods for reliable detection of megabase-scale CNV in single cell sequencing data.  
 |-align="center"
 |DEC3  
 |11a 
 |Lorena Pantano (HSPH)
 |  
 |   
 |  
 |-align="center"
 |DEC17  
 |11a 
 |Inma Barrasa (WI)
 |WI  
 |7th floor classroom
 |  
 |-align="center"
 |JAN7  
 |11a 
 |Duanduan Ma (MIT)
 |MIT  
 |68-156   
 |An easy and convenient TCGA gold miner for biologists  
 |-align="center"
 |JAN21  
 |11a  
 |George Bell (WI)
 |WI  
 |7th floor classroom
 |Genome and gene representations: Options for expression analysis  
 |-align="center"
 |FEB4 
 |11a 
 |George Marnellos (Harvard)
 |  
 |
 |  
 |-align="center"
 |Feb 25 
 |11a
 |STUART LEVINE (MIT)
 |MIT  
 |68-156   
 |AGBT/ABRF Meeting Review  
 |-align="center"
 |MAR10  
 |11a
 |Prat Thiru (WI)
 |WI  
 |7th floor classroom
 |  
 |-align="center"
 |MAR24 
 |11a
 |Matt McCormack (MGH)
 |
 |
 |  
 |-align="center"
 |APR14  
 |11a 
 |Huiming Ding (MIT)
 |MIT  
 |68-156   
 |  
 |-align="center"
 |APR28 
 |11a
 |Laurent Gautier (Novartis)
 |
 | 
 |  
 |-align="center"
 |MAY12  
 |11a  
 |BARRY KESNER (MGH)
 |  
 |  
 |  
 |-align="center"
 |MAY26  
 |11a  
 |Yanmei Huang (WI)
 |WI  
 |7th floor classroom
 | 
|}

==2014-2015 academic year==
{| border=1 
 !width 150px align="center"|DATE
 !width 150px align="center"|TIME 
 !width 150px align="center"|Presenter 
 !width 150px align="center"|Location 
 !width 150px align="center"|Room 
 !width 150px align="center"|NOTES
 |-align="center"
 |SEP17  
 |noon  
 |JIE WU (MIT) 
 |MIT  
 |68-156  
 |Copy Number Variation from single mammalian cells.  
 |-align="center"
 |OCT15  
 |noon  
 |BRAD CHAPMAN (HSPH) 
 |MIT  
 |[http://whereis.mit.edu/?go=68 68-156]
 |Validation with [https://github.com/chapmanb/bcbio-nextgen bcbio-nextgen] on [http://bcbio.wordpress.com/2014/08/12/validated-whole-genome-structural-variation-detection-using-multiple-callers/ structural variation], [http://bcbio.wordpress.com/2014/10/07/joint-calling/ joint calling] and cancer tumor/normal. [https://github.com/chapmanb/bcbb/raw/master/talks/big2014_bcbio_val/chapman_bcbio.pdf slides]
 |-align="center"
 |OCT29  
 |noon 
 |VINCENT BUTTY (MIT)  
 |MIT  
 |68-156   
 |Single-molecule barcoding: applications and analytic challenges  
 |-align="center"
 |NOV5  
 |noon  
 |GEORGE BELL (WI)  
 |WI  
 |WI-332  
 |Happy yeast and fast fish  
 |-align="center"
 |NOV19  
 |noon  
 |RUSLAN SADREYEV (MGH)  
 |  
 |  
 |  
 |-align="center"
 |DEC3  
 |noon  
 |CHARLIE WHITTAKER (MIT)  
 |MIT  
 |68-156   
 |  
 |-align="center"
 |DEC17  
 |noon  
 |GEORGIOS MARNELLOS (HMS)  
 |  
 |  
 |  
 |-align="center"
 |JAN7  
 |noon  
 |DM 
 |MIT  
 |68-156   
 |  
 |-align="center"
 |JAN21  
 |noon  
 |MATTHEW MCCORMACK (MGH)  
 |  
 |  
 |  
 |-align="center"
 |FEB11  
 |noon  
 |PRAT THIRU (WI)
 |WI  
 |WI-332  
 |  
 |-align="center"
 |MAR4  
 |noon  
 |STUART LEVINE (MIT)
 |MIT  
 |68-156   
 |AGBT Meeting Review  
 |-align="center"
 |MAR18  
 |noon  
 |YANQUN WANG (MGH)  
 |  
 |  
 |  
 |-align="center"
 |APR1 
 |noon  
 |INMA BARRASA (WI)  
 |WI  
 |WI-332   
 |  
 |-align="center"
 |APR15  
 |noon  
 |HUIMING DING
 |MIT  
 |68-156   
 |  
 |-align="center"
 |APR29  
 |noon  
 |BINGBING YUAN (WI)  
 |WI  
 |WI-332    
 |  
 |-align="center"
 |MAY13  
 |noon  
 |BARRY KESNER (MGH)  
 |  
 |  
 |  
|}

==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==
{| 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
 |-
 | 1/26 (Thursday)
 | 12p 
 | Brian Haas (Broad Institute)
 | MIT
 | [http://whereis.mit.edu/?go=76 76-558]
 | [http://www.ncbi.nlm.nih.gov/pubmed/21572440 Trinity]
 |-
 | 2/23 (Thursday)
 | 12p 
 | Brad Chapman 
 | MIT
 | [http://whereis.mit.edu/?go=68 68-180]
 | Extending the GATK for variant comparisons; [http://chapmanb.github.com/bcbio.variation/presentations/gatk_clojure.pdf slides] [https://github.com/chapmanb/bcbio.variation code]
 |-
 | 3/22 (Thursday)
 | 12p 
 | Vincent Butty
 | MIT
 | [http://whereis.mit.edu/?go=68 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
 | [http://whereis.mit.edu/?go=68 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
 | [http://campusmaps.tufts.edu/boston/?fid=B011 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
 | [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
 |-
 | 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==
Schedule for 2011. 
{| 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
 |-
 | 1/18 
 | 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 <BR> ''Center for Biological Sequence Analysis, Denmark ''
 | MIT 
 | 76-259 
 | R-Python Interface <BR> http://www.cbs.dtu.dk/index.shtml
 |-
 | 4/26 
 | 12p 
 | Michael Reich <BR> ''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
 | [http://bcbio.wordpress.com/2011/08/19/distributed-exome-analysis-pipeline-with-cloudbiolinux-and-cloudman/ distributed exome analysis pipeline] [http://www.slideshare.net/chapmanb/developing-distributed-analysis-pipelines-with-shared-community-resources-using-cloudbiolinux-and-cloudman slides]
 |-
 | 10/6 (Thursday)
 | 12p 
 | Stuart Levine 
 | MIT 
 | 68-274
 | Comparison of ChIP-seq algorithms
 |-
 | 10/27 (Thursday)
 | 12p 
 | [http://about.me/pablopareja Pablo Pareja]
 | MIT 
 | [http://whereis.mit.edu/?go=76 76-258]
 | [http://www.bio4j.com/ Bio4j Graph based analysis and visualization] [http://www.slideshare.net/pablo_pareja/bio4j slides]
 |-
 | 11/?? (Thursday)
 | 12p 
 | Paola Favaretto 
 | MIT 
 | 
 | RNAseq - part I
 |-
 | 12/15
 | 12p 
 | Charlie Whittaker 
 | MIT 
 | 
 | RNAseq - part II
 |-
|}
<BR>