BioMicroCenter:BIG meeting

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2017-2018 academic year

Meetings will be at MIT Biology (68-156) 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 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
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)
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
JAN7 noon DM MIT 68-156
FEB11 noon PRAT THIRU (WI) WI WI-332
MAR4 noon STUART LEVINE (MIT) MIT 68-156 AGBT Meeting Review
APR15 noon HUIMING DING MIT 68-156

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


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


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:
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


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
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