BioMicroCenter:BIG meeting: Difference between revisions
No edit summary |
|||
(222 intermediate revisions by 11 users not shown) | |||
Line 1: | Line 1: | ||
{{BioMicroCenter}} | {{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 | |||
| HIV-1 protease (fitness measurements and machine learning) | |||
|-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 | |||
| John Hutchinson (HSPH) | |||
|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" | |||
| Oct 25 | |||
| 11 am | |||
| George Bell (WI) | |||
| Whitehead | |||
| 7th floor | |||
| Experimental design: Make a good one, or make the most of what you get | |||
|-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 | |||
| 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 | |||
|-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) | |||
| Whitehead | |||
| 7th floor | |||
|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 | |||
| Radhika Khetani and Mary Piper (HSPH) | |||
|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 | {| border=1 | ||
!width 150px align="center"|DATE | !width 150px align="center"|DATE | ||
Line 10: | Line 466: | ||
!width 150px align="center"|Room | !width 150px align="center"|Room | ||
!width 150px align="center"|NOTES | !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 | |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 | |NOV5 | ||
|noon | |noon | ||
| | |GEORGE BELL (WI) | ||
| | |WI | ||
| | |WI-332 | ||
| | |Happy yeast and fast fish | ||
|- | |-align="center" | ||
|NOV19 | |NOV19 | ||
|noon | |noon | ||
|RUSLAN SADREYEV (MGH) | |||
| | | | ||
| | | | ||
| | | | ||
|-align="center" | |||
|- | |||
|DEC3 | |DEC3 | ||
|noon | |noon | ||
|CHARLIE WHITTAKER (MIT) | |CHARLIE WHITTAKER (MIT) | ||
|MIT | |MIT | ||
|68-156 | |||
| | | | ||
|-align="center" | |||
|- | |||
|DEC17 | |DEC17 | ||
|noon | |noon | ||
|GEORGIOS MARNELLOS (HMS) | |||
| | | | ||
| | | | ||
| | | | ||
|-align="center" | |||
|- | |||
|JAN7 | |JAN7 | ||
|noon | |noon | ||
| | |DM | ||
|MIT | |MIT | ||
|68-156 | |||
| | | | ||
|-align="center" | |||
|- | |||
|JAN21 | |JAN21 | ||
|noon | |noon | ||
Line 80: | Line 644: | ||
| | | | ||
| | | | ||
|- | |-align="center" | ||
|FEB11 | |FEB11 | ||
|noon | |noon | ||
|PRAT THIRU (WI) | |||
|WI | |||
|WI-332 | |||
| | | | ||
|-align="center" | |||
|- | |||
|MAR4 | |MAR4 | ||
|noon | |noon | ||
|STUART LEVINE (MIT) | |STUART LEVINE (MIT) | ||
|MIT | |MIT | ||
| | |68-156 | ||
|AGBT Meeting Review | |AGBT Meeting Review | ||
|- | |-align="center" | ||
|MAR18 | |MAR18 | ||
|noon | |noon | ||
|YANQUN WANG (MGH) | |||
| | | | ||
| | | | ||
| | | | ||
|-align="center" | |||
|- | |||
|APR1 | |APR1 | ||
|noon | |noon | ||
|INMA BARRASA (WI) | |||
|WI | |||
|WI-332 | |||
| | | | ||
|-align="center" | |||
|- | |||
|APR15 | |APR15 | ||
|noon | |noon | ||
| | |HUIMING DING | ||
|MIT | |MIT | ||
|68-156 | |||
| | | | ||
|-align="center" | |||
|- | |||
|APR29 | |APR29 | ||
|noon | |noon | ||
|BINGBING YUAN (WI) | |||
|WI | |||
|WI-332 | |||
| | | | ||
|-align="center" | |||
|- | |||
|MAY13 | |MAY13 | ||
|noon | |noon |
Latest revision as of 08:59, 4 December 2020
HOME -- | SEQUENCING -- | LIBRARY PREP -- | HIGH-THROUGHPUT -- | COMPUTING -- | OTHER TECHNOLOGY |
2020-2021 academic year
Meetings will start out as virtual (on your platform of choice, or ask 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.
Date | Time | Presenter | Location | Room | Topic, notes, etc. |
---|---|---|---|---|---|
Dec 5 | 11 am | George Bell (WI) | WI | Founders Room (2nd floor) | Engineering and characterizing human microglia |
Dec 19 | 11 am | Vincent Butty (MIT) | MIT | 68-156 | Trajectory Inference in scRNA-Seq |
Jan 9 | 11 am | Dikshant Pradhan (MIT) | MIT | 68-156 | FAIR data management using SEEK |
Jan 23 | 11 am | Troy Whitfield (WI) | WI | 7th floor classroom | HIV-1 protease (fitness measurements and machine learning) |
Feb 27 | 11 am | Prat Thiru (WI) | WI | 7th floor classroom | Challenges of scRNA-seq (slides) |
Mar 19 | 11 am | Stuart Levine (MIT) | MIT | videoconference | AGBT / ABRF Technology review |
Apr 2 | 11 am | Charlie Whittaker (MIT) | MIT | videoconference | ABRF GBIRG 2020 - Ontology Analyses Study |
Apr 16 | 11 am | John Hutchinson (HSPH) | MIT | videoconference | |
Apr 23 | 11 am | Duanduan Ma (MIT) | MIT | videoconference | Causal inference and its potential application in RNA-seq time series data |
May 14 | 11 am | Inma Barrasa (WI) | WI | videoconference | Antigen receptor sequence reconstruction and clonality inference from scRNA-Seq data |
June 4 | 11 am | Bingbing Yuan (WI) | WI | videoconference | Identifying differentially expressed genes in scRNA-seq experiments |
2018-2019 academic year
Date | Time | Presenter | Location | Room | Notes |
---|---|---|---|---|---|
Oct 11 | 11 am | **NO MEETING** | MIT | 68-156 | |
Oct 25 | 11 am | George Bell (WI) | Whitehead | 7th floor | Experimental design: Make a good one, or make the most of what you get |
Nov 15 | 11 am | Kris Richardson (WI) | Whitehead | 7th floor | ATAC-Seq analysis |
Dec 6 | 11 am | Lorena Pantano (HSPH) | MIT | 68-156 | miRNA Wars: the isomiR menace |
Dec 20 | 11 am | Charlie Whittaker (KI, MIT) | MIT | 68-156 | Intragenic Tandem Repeats |
Jan 10 | 11 am | Prat Thiru (WI) | Whitehead | 7th floor | Visualization: principles & software (slides); D3 demo (code), tested on Firefox |
Jan 24 | 11 am | Vincent Butty (MIT) | MIT | 68-156 | RNA processing analysis in single-cell RNA-Seq |
Feb 7 | 11 am | Ruslan Sadreyev (MGH/HMS) | MIT | 68-156 | Causal interactions between DNA replication and chromatin remodeling |
Feb 28 | 11 am | **NO MEETING** | MIT | 68-156 | |
Mar 28 | 11 am | Brad Chapman (Harvard Chan) | MIT | 68-156 | Data organization, normalization and modeling; (slides) |
Apr 11 | 11 am | Inma Barrasa (WI) | Whitehead | 7th floor | Discussion of Li et al., 2019, highlighting the computational analysis |
May 2 | 11 am | Huiming Ding (MIT) | MIT | 68-156 | Recent trends in FAIR data management and machine learning algorithms |
May 16 | 11 am | Duanduan Ma (MIT) | MIT | 68-156 | Machine learning and its applications in genomics |
May 30 | 11 am | Bingbing Yuan (WI) | Whitehead | 7th floor | Creating client-side interactive plots in R (slides) (R markdown and sample input/output) |
2017-2018 academic year
Date | Time | Presenter | Location | Room | Notes | |
---|---|---|---|---|---|---|
Oct 5 | 11 am | **NO MEETING** | MIT | 68-156 | ||
Oct 19 | 11 am | Vincent Butty (MIT) | MIT | 68-156 | RNA-Seq-based alternative isoform quantification, and benchmarking with spike-ins. | |
Nov 2 | 11 am | Brad Chapman (HSPH) | MIT | 68-156 | bcbio and Common Workflow Language interoperability progress; slides; video | |
Nov 16 | 11 am | **NO MEETING** | MIT | 68-156 | ||
Dec 7 | 11 am | Lorena Pantano (HSPH) | MIT | 68-156 | Analyzing hundreds of small RNA samples with bcbio-nextgen; miRTop | |
Dec 21 | 11 am | Charlie Whittaker | MIT | 68-156 | Vignettes: Gene expression, search for diagnostic markers; logFC shrinkage methods | |
Jan 4 | 11 am | **NO MEETING** | MIT | 7th floor | ||
Jan 18 | 11 am | Prat Thiru (WI) | Whitehead | 7th floor | Reproducible research for bioinformatics: best practices (slides) | |
Feb 1 | 11 am | Kris Richardson (WI) | Whitehead | 7th floor | Highlights from Genome Informatics (Nov. 2017) | |
Feb 15 | 11 am | George Bell (WI) | Whitehead | 7th floor | Fungal genome assembly and annotation | |
Mar 1 | 11 am | Stuart Levine (MIT) | MIT | 68-156 | Review of AGBT meeting: What is that light coming down the tunnel? | |
Mar 15 | 11 am | Radhika Khetani and Mary Piper (HSPH) | MIT | 68-156 | Adventures in Bioinformatics Training | |
Apr 5 | 11 am | Bingbing Yuan (WI) | Whitehead | 7th floor | Interactive Figures with R (slides) | |
Apr 19 | 11 am | Huiming Ding (MIT) | MIT | 68-156 | Application of Machine Learning In Analyzing Cancer Mutations | |
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 | |
May 17 | 11 am | Inma Barrasa (WI) | Whitehead | 7th floor | ||
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
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 | The human splicing code and disease ( Xiong et al., Science) |
Dec 1 | 11 am | George Bell (WI) | Whitehead | 7th floor | Under-replication analysis; 3D printing of biomolecules |
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 | Using SOMs for RNA-seq analysis |
Feb 2 | 11 am | Ruslan Sadreyev (MGH) | MIT | 68-156 | 5C HiC analysis video |
Feb 16 | 11 am | Matt Shirley (NIBR) | MIT | 68-156 | PISCES: alignment free RNA-seq quantiation and QC pipeline; slides; video |
Mar 2 | 11 am | Stuart Levine (MIT) | MIT | 68-156 (confirmed) | Review of AGBT |
Mar 16 | 11 am | **NO MEETING** | |||
Apr 6 | 11 am | Huiming Ding (MIT) | MIT | 68-156 | Running a scRNA-Seq pipeline in the Amazon cloud |
Apr 20 | 11 am | Duanduan Ma (MIT) | MIT | 68-156 | Weighted Correlation Network Analysis (WGCNA) and its application in cancer genomics study |
May 4 | 11 am | Michael Steinbaugh (HSPH) | MIT | 68-156 | R-based methods for scRNA-seq analysis |
May 18 | 11 am | Inma Barrasa (WI) | Whitehead | 7th floor | Identifying antibody repertoires using high-throughput sequencing |
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 |