BioMicroCenter:BIG meeting: Difference between revisions
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==2016-2017 academic year== | |||
Meetings will be at MIT Biology (room TBA) or at Whitehead (for Whitehead presenters; 7th floor larger classroom). 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. 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"|Notes | |||
|-align="center" | |||
|Oct 6 | |||
|11 am | |||
|Prat Thiru (WI) | |||
|Whitehead | |||
|7th floor | |||
|[http://jura.wi.mit.edu/bio/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 | |||
| | |||
|-align="center" | |||
|Dec 1 | |||
|11 am | |||
|George Bell (WI) | |||
|Whitehead | |||
|7th floor | |||
| | |||
|-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 | |||
| | |||
|-align="center" | |||
|Feb 2 | |||
|11 am | |||
|Ruslan Sadreyev (MGH) | |||
| | |||
| | |||
| | |||
|-align="center" | |||
|Feb 16 | |||
|11 am | |||
|Matt Shirley (NIBR) | |||
|MIT | |||
|68-156 | |||
| | |||
|-align="center" | |||
|Mar 2 | |||
|11 am | |||
|Stuart Levine (MIT) | |||
|MIT | |||
|68-156 (confirmed) | |||
|Review of AGBT | |||
|-align="center" | |||
|Mar 16 | |||
|11 am | |||
|Bingbing Yuan (WI) | |||
|Whitehead | |||
|7th floor | |||
| | |||
|-align="center" | |||
|Apr 6 | |||
|11 am | |||
|Huiming Ding (MIT) | |||
|MIT | |||
|68-156 | |||
| | |||
|-align="center" | |||
|Apr 20 | |||
|11 am | |||
|Duanduan Ma (MIT) | |||
|MIT | |||
|68-156 | |||
| | |||
|-align="center" | |||
|May 4 | |||
|11 am | |||
|John Hutchinson (HSPH) | |||
|MIT | |||
|68-156 | |||
| | |||
|-align="center" | |||
|May 18 | |||
|11 am | |||
|Inma Barrasa (WI) | |||
|Whitehead | |||
|7th floor | |||
| | |||
|} | |||
==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== | ==2011== | ||
Line 74: | Line 711: | ||
| BioPython | | BioPython | ||
|- | |- | ||
| 6/ | | 6/28 | ||
| 12p | | 12p | ||
| Ruslan Sadreyev | | Ruslan Sadreyev | ||
| | | MIT | ||
| | | 76-659 | ||
| Teaching Statistics | | Teaching Statistics | ||
|- | |- | ||
Line 85: | Line 722: | ||
| Kip Bodi | | Kip Bodi | ||
| MIT | | MIT | ||
| 68-121 | |||
| Data analysis for DSRG / ABRF | |||
|- | |||
| 7/26 | |||
| 12p | |||
| Toshiro Ohsumi | |||
| MGH | |||
| TBA | | 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> | <BR> |
Revision as of 18:44, 16 January 2017
HOME -- | SEQUENCING -- | LIBRARY PREP -- | HIGH-THROUGHPUT -- | COMPUTING -- | OTHER TECHNOLOGY |
2016-2017 academic year
Meetings will be at MIT Biology (room TBA) or at Whitehead (for Whitehead presenters; 7th floor larger classroom). 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. Questions? Contact Barry Kesner or George Bell.
Date | Time | Presenter | Location | Room | Notes |
---|---|---|---|---|---|
Oct 6 | 11 am | Prat Thiru (WI) | Whitehead | 7th floor | Highlights of ECCB 2016 |
Oct 20 | 11 am | Vincent Butty (MIT) | MIT | 68-156 | High-throughput 3' digital gene expression analysis for low input RNA samples. |
Nov 3 | 11 am | Brad Chapman (HSPH) | MIT | 68-156 | bcbio and the Common Workflow Language slides recording |
Nov 17 | 11 am | Matthew McCormack (Harvard) | MIT | 68-156 | |
Dec 1 | 11 am | George Bell (WI) | Whitehead | 7th floor | |
Dec 15 | 11 am | Lorena Pantano (HSPH) | MIT | 68-156 | small RNA analysis slides video |
Jan 5 | 11 am | **NO MEETING** | |||
Jan 19 | 11 am | Charlie Whittaker (MIT) | MIT | 68-156 | |
Feb 2 | 11 am | Ruslan Sadreyev (MGH) | |||
Feb 16 | 11 am | Matt Shirley (NIBR) | MIT | 68-156 | |
Mar 2 | 11 am | Stuart Levine (MIT) | MIT | 68-156 (confirmed) | Review of AGBT |
Mar 16 | 11 am | Bingbing Yuan (WI) | Whitehead | 7th floor | |
Apr 6 | 11 am | Huiming Ding (MIT) | MIT | 68-156 | |
Apr 20 | 11 am | Duanduan Ma (MIT) | MIT | 68-156 | |
May 4 | 11 am | John Hutchinson (HSPH) | MIT | 68-156 | |
May 18 | 11 am | Inma Barrasa (WI) | Whitehead | 7th floor |
2015-2016 academic year
DATE | TIME | Presenter | Location | Room | NOTES |
---|---|---|---|---|---|
OCT22 | 11a | VINCENT BUTTY (MIT) | MIT | 68-156 | Dimensionality reduction for single cell data |
NOV5 | 11a | BRAD CHAPMAN (HSPH) | MIT | 68-156 | bcbio development work supporting human build 38, low frequency variant calling and support for Docker and the Common Workflow Language: validation slides, Docker/CWL slides |
NOV19 | 11a | Jie Wu (MIT) | MIT | 68-156 | Finding methods for reliable detection of megabase-scale CNV in single cell sequencing data. |
DEC3 | 11a | Lorena Pantano (HSPH) | |||
DEC17 | 11a | Inma Barrasa (WI) | WI | 7th floor classroom | |
JAN7 | 11a | Duanduan Ma (MIT) | MIT | 68-156 | An easy and convenient TCGA gold miner for biologists |
JAN21 | 11a | George Bell (WI) | WI | 7th floor classroom | Genome and gene representations: Options for expression analysis |
FEB4 | 11a | George Marnellos (Harvard) | |||
Feb 25 | 11a | STUART LEVINE (MIT) | MIT | 68-156 | AGBT/ABRF Meeting Review |
MAR10 | 11a | Prat Thiru (WI) | WI | 7th floor classroom | |
MAR24 | 11a | Matt McCormack (MGH) | |||
APR14 | 11a | Huiming Ding (MIT) | MIT | 68-156 | |
APR28 | 11a | Laurent Gautier (Novartis) | |||
MAY12 | 11a | BARRY KESNER (MGH) | |||
MAY26 | 11a | Yanmei Huang (WI) | WI | 7th floor classroom |
2014-2015 academic year
DATE | TIME | Presenter | Location | Room | NOTES |
---|---|---|---|---|---|
SEP17 | noon | JIE WU (MIT) | MIT | 68-156 | Copy Number Variation from single mammalian cells. |
OCT15 | noon | BRAD CHAPMAN (HSPH) | MIT | 68-156 | Validation with bcbio-nextgen on structural variation, joint calling and cancer tumor/normal. slides |
OCT29 | noon | VINCENT BUTTY (MIT) | MIT | 68-156 | Single-molecule barcoding: applications and analytic challenges |
NOV5 | noon | GEORGE BELL (WI) | WI | WI-332 | Happy yeast and fast fish |
NOV19 | noon | RUSLAN SADREYEV (MGH) | |||
DEC3 | noon | CHARLIE WHITTAKER (MIT) | MIT | 68-156 | |
DEC17 | noon | GEORGIOS MARNELLOS (HMS) | |||
JAN7 | noon | DM | MIT | 68-156 | |
JAN21 | noon | MATTHEW MCCORMACK (MGH) | |||
FEB11 | noon | PRAT THIRU (WI) | WI | WI-332 | |
MAR4 | noon | STUART LEVINE (MIT) | MIT | 68-156 | AGBT Meeting Review |
MAR18 | noon | YANQUN WANG (MGH) | |||
APR1 | noon | INMA BARRASA (WI) | WI | WI-332 | |
APR15 | noon | HUIMING DING | MIT | 68-156 | |
APR29 | noon | BINGBING YUAN (WI) | WI | WI-332 | |
MAY13 | noon | BARRY KESNER (MGH) |
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. |
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 |