BioMicroCenter:BIG meeting: Difference between revisions

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Please fill out the [http://www.doodle.com/8aetbhdxx4p68byx survey] to help us schedule the next academic year.
==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
!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==
==2012==
{| border=1  
{| border=1  
Line 30: Line 877:
  | 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 895:
  | 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==

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.
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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