BioMicroCenter:BIG meeting
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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 |
