Main Scientific Lectures

Total Lectures: 285

(Last updated Sat Jan 16 16:12:32 2021 (EST))

-- 2021 (1) --

5 min intro to the lab
5' introduction to the Gerstein lab with Doodly illustration
Subject: intro, overview, talkmovie Date Given: 1/15/2021
Lecture ID: 5-min-intro--20210115

-- 2020 (6) --

Topics in Precision Oncology: Addressing the role of the non-coding genome in cancer
15' virtual talk at Biological Data Science 2020, sponsored by CSHL
Subject: talkmovie, jpegslides, encodec, tfmem, papere Date Given: 11/5/2020
Lecture ID: Topics-in-Precision-Oncology--20201105-i0bds20

Using ENCODE Data for Cancer Genomics
For the ENCODE 2020 Users Meeting (with a 14' movie!)
Subject: radar, larva, moat, nimbus, encodec, talkmovie, tfmem Date Given: 10/1/2020
Lecture ID: Using-ENCODE-Data-for-Cancer-Genomics--20201001-i0encusr

Privacy & Functional Genomics Data
Keynote talk for Genopri20 (associated with GA4GH 8th Plenary). 40' talk + 5' Qs, over zoom. (Actually took 35'.)
Subject: privacy, privaseq3, privasig, jpegslides, privaseq Date Given: 10/28/2020
Lecture ID: Privacy-n-Func-Genomics-Data--20201028--i0genopri20

Evaluation of "Near coding" Elements: uORFs & RBP sites
Gencode call presentation
Subject: uorf, radar Date Given: 6/9/2020
Lecture ID: gencode-call

Thoughts on repurposing our current bioinformatics research to address COVID-19
15' talk with Michael Rutenberg Schoenberg at the COVID HASTE workshop, related to Yale Datascience
Subject: covid19, gslide, decoasthma, evotum, excerpt Date Given: 4/20/2020
Lecture ID: Yale-COVID-HASTE-042120

Measuring the Impact of Non-coding Mutations: Repurposing an Additive Effects Model & Developing New Annotations
15' talk at the GSP-TopMed workshop at Mt. Sinai in NYC
Subject: papere, pcawg, uorf, radar Date Given: 2/13/2020
Lecture ID: Measuring-the-Impact-of-Noncoding-Mutations--20200213-i0top19

-- 2019 (20) --

Topics in Cancer Genomics: Measuring Regulatory Network Change, Modeling Tumor Evolution & Evaluating the Impact of "Putative" Passenger Mutations
45' talk at UC Berkeley Center for Computational Biology. (Actual talk time was 51' with one Q.)
Subject: encodec, tfmem, papere, prcc, moat, larva, evotum, jpegslides Date Given: 12/12/2019
Lecture ID: Topics-in-Cancer-Genomics--201901212-i0ucb19

DAC Update
DAC Update at ENCODE meeting. Extracted selection of slides relevant to the Gerstein Lab.
Subject: encodec, tfmem, starrpeaker, hasshadow Date Given: 12/9/2019
Lecture ID: i0ucb19-EXTRACT-from--DAC-Presentation

Computational analysis of variants: coding versus non-coding
40' talk in Yale Genetics's Rare Disease Analysis Workshop.
Subject: radar, frustration, stress, jpegslides, hotcommics, gram, uorf, aloft Date Given: 12/3/2019
Lecture ID: Computational-analysis-variants-coding-v-non-coding--201901203-i0ycc-rare

Annotating Non-coding Variants, Measuring Regulatory Network Rewiring, Building Background Mutation Models, Analyzing Tumor Evolution & Evaluating the Overall Impact of Passenger Mutations
30' talk in Yale Cancer Center's Grand Rounds Presentation. New slides on Tumor Evolution, Network Rewiring & Passenger Mutations. (Took 29' after shortening.)
Subject: encodec, tfmem, papere, prcc, moat, larva, evotum, hasshadow Date Given: 12/3/2019
Lecture ID: Topics-in-Cancer-Genomics--201901203-i0ycc-noncoding

Enhancing open data sharing for functional genomics experiments: Measures to quantify genomic information leakage & identify file formats for privacy preservation
15' talk w/ Qs at GenoPri 2019 in Boston, which is part of the GA4GH 2019 Plenary
Subject: privacy, privasig, privaseq3, fancy, jpegslides Date Given: 10/22/2019
Lecture ID: Enhancing-open-data-sharing-for-functional-genomics--20191022-i0genopri19

15' Overview of the Lab
For prospective students. (Did a youtube of this in Sep. 2020.)
Subject: overview, talkmovie Date Given: 9/13/2019
Lecture ID: 13-slide-overview--20190913

PsychENCODE: Using population-scale functional genomics to understand neuro-psychiatric disease
30' talk with Qs at a Yale Dean's workshop
Subject: capstone4, psychencode, jpegslides Date Given: 7/12/2019
Lecture ID: PsychENCODE--20190712-i0psy19

Personal Genomics & Data Science: Using population-scale functional genomics to understand neuropsychiatric disease & interpreting the data exhaust from this activity
1 hr talk at the MRC LMB in Cambridge. Includes updated capstone4 slides, relating to the devcapstone and data exhaust
Subject: privasig, privaseq, capstone4, psychencode, jpegslides, genomicsandprivacy, devcapstone Date Given: 6/20/2019
Lecture ID: Personal-Genomics-Data-Sci--20190620-i0lon19+cam

Disease Genomics: Thoughts on Genome Annotation, Prioritizing Variants, Highlighting Dysregulation & the Application of all of these to Cancer
1 hr talk at the Department for BioMedical Research (DBMR) at the University of Bern. Includes new slides on encodec and a new cancer genomics intro.
Subject: encodec, funseq, uorf, radar, cancer, larva, moat, matchfilter, jpegslides Date Given: 6/14/2019
Lecture ID: Annotation-Variants-Dysregulation-Cancer--20190614-i0lon19+bern

Quantification of sensitive information leakage from functional genomics data: Obvious v subtle leakages & practical file formats for addressing this
30' talk (w/ Qs) at IEEE-EMBS BHI in Chicago. New slides on using blockchain to secure logs (iDASH challenge)
Subject: privacy, privasig, privaseq, idash, privaseq3, jpegslides Date Given: 5/21/2019
Lecture ID: Quantification-of-sens-info-leakage--20190521-i0bhi

Brain Genomics: Finding drug targets for neuropsychiatric disorders via deep-learning & Designing a predictor for the sensitivity of drugs to human population variation
30' talk with Qs for the SynGen Series in Boston. Similar to i0brd but has some new Genodock slides.
Subject: capstone4, psychencode, jpegslides, genodock, molmovdb Date Given: 5/15/2019
Lecture ID: Finding-drug-targets-n-predicting-sensitivity-of-drugs-to-variants--20190515-i0ox19

Interpretable deep learning model, embedding the gene regulatory network, for understanding functional genomics in neuropsychiatric disorders
20' (w/ Qs) highlights talk at RECOMB 2019 in DC
Subject: capstone4, psychencode Date Given: 5/5/2019
Lecture ID: Interpretable-deep-learning-model--20190505-i0recomb19

Comparing RNA & Protein Abundance
20' talk for NIDA advisory board workshop
Subject: empire, uorfs, pare, nida, jpegslides, gslide, hasshadow Date Given: 5/1/2019
Lecture ID: Protein-v-RNA--20190501-i0nida

Genomics & Data Science
1 hr talk for convening Yale at the Yale School of Mgt. (SOM). Took 32' sans data exhaust section (last sect.).
Subject: dsg, costseq2, costseq, cbb752, privacy, genomicsandprivacy, nethier, jpegslides, capstone4 Date Given: 4/23/2019
Lecture ID: Genomics-n-Data-Sci--20190423-i0cy18

Introduction to Biomedical Data Science
General overview of the field at Horace Mann's SciTech Symposium. ~1 hr talk.
Subject: dsg, costseq2, costseq, cbb752, privacy, genomicsandprivacy Date Given: 4/16/2019
Lecture ID: Biomed-DataSci-Intro--20190416-i0hm19

Thoughts on AI, Society & Ethics
3 slides for a panel discussion
Subject: privacy, dsg Date Given: 4/4/2019
Lecture ID: Thoughts-on-AI-n-Soc--20190405-i0aisoc

Population-scale functional genomics to suggest potential neuropsychiatric drug targets & building a hybrid classifier to ascertain differential drug sensitivity
1 hr talk at the Broad Institute in the Cell Circuits & Epigenomics series. Refinement of i0mcbios. Focusing on psychENCODE with new slides onthe DeepLearning model & drug-SNV interactions
Subject: capstone4, devcapstone, psychencode, brainspan, jpegslides, genodock, molmovdb Date Given: 4/1/2019
Lecture ID: Func-genomics-suggest-drug-targets-n-building-hybrid-classifier--20190401-i0brd19

Brain Genomics: Using population-scale functional genomics to suggest potential drug targets for neuropsychiatic disease & building a hybrid classifier to predict the differential sensitivity of individuals to drugs
1 hr talk (w/ 15' Qs) at MCBIOS '19 in Alabama (16th Annual Conference of the Midsouth Computational Biology & Bioinformatics Society). An even more expanded psychENCODE presentation plus new GenoDock slides
Subject: capstone4, devcapstone, psychencode, brainspan, jpegslides, genodock, molmovdb Date Given: 3/29/2019
Lecture ID: Func-genomics-drug-targets-n-hybrid-classifier-predict-diff-sens-to-drugs--20190329-i0mcbios

Results of the PsychENCODE consortium on using population-scale functional genomics to understand neuropsychiatric disease and privacy aspects of this type of study
60' talk at the Duke Human Genetics Retreat. New slides on psychencode developmental work + enhancers
Subject: capstone4, devcapstone, privacy, privasig, privaseq, psychencode, brainspan, jpegslides Date Given: 3/15/2019
Lecture ID: Results-of-PsychENCODE-n-privacy--20190315-i0duke19

Overview of the PsychENCODE resource
5' talk at PsychENCODE meeting giving an overview of the Phase I capstone resource & some thoughts for the future
Subject: capstone4, psychencode, brainspan, gslides Date Given: 2/26/2019
Lecture ID: Overview-of-PsychENCODE-resource--20190226-i0pec19

-- 2018 (12) --

Using population-scale functional genomics to understand mental disease & interpreting the data exhaust from this activity
1 hr talk at Sigma Xi meeting. Fit in the whole things in ~55'. Then Qs. Has new capstone4 slides.
Subject: privasig, privaseq, capstone4, psychencode Date Given: 10/26/2018
Lecture ID: Using-population-scale-functional-genomics-mental-disease-n-exploiting-data-exhaust-20181025-i0sigma

Thoughts on Genome Annotation, Prioritizing Variants & the Application of these Concepts in a Disease Context
1 hr informal seminar at UCSF; now adding in matchfilter slides. Fit in the whole thing in ~45' but went v. fast over middle (FunSeq to uORF sections). Has new matchfilter slides.
Subject: matchfilter, music, larva, moat, funseq, radar, capstone4, psychencode Date Given: 10/25/2018
Lecture ID: Thoughts-on-Annotation-Variants-Application-disease-context--20182310-i0sigma+ucsf

Transcriptome Mining: Population-scale genomic analysis to better understand mental disease & the subtle privacy risks of this activity
1 hr talk at Mt. Sinai Genetics. Updated "transcriptome mining" talk, now with a bit on PsychENCODE & some slides on PrivaSig. (Had to leave out "encodeauthors" to fit in time.)
Subject: capstone4, privacy, privaseq, privasig, privaseq3, encodeauthors Date Given: 9/21/2018
Lecture ID: Pop-scale-genomics-for-mental-disease-n-privacy-risks--20180921-i0mssm18

2 Sides of the Coin for RNA-seq: Ensuring Individual Privacy v. Allowing Easy Mining
30' talk at Yale MBB summer camp. Now includes new PrivaSIG.gersteinlab.org slides
Subject: privseq, privasig, jpegslides Date Given: 8/8/2018
Lecture ID: 2-sides-of-a-coin-privacy-v-mining--20180808-i0camp18

Leveraging Protein Structure & Dynamics for Variant Interpretation in Coding Regions
15' talk at American Crystallographic Assoc. Annual Meeting in Toronto
Subject: jpegslides, aloft, stress, frustration Date Given: 7/23/2018
Lecture ID: Leveraging-Protein-Structure-Variant-Interpretation--20180723-i0aca18

RADAR: Annotation & prioritization of variants in the post-transcriptional regulome for RBPs
20' talk (w/ 5' Qs) for ISMB '18
Subject: jpegslides, funseq, uorfs, radar Date Given: 7/8/2018
Lecture ID: RADAR-Annot-prioritization-var-20180708-i0ismb18

Updates on Pseudogene Analysis in Human and Mouse
Short talk, split w/ PM, at Gencode Annual Meeting
Subject: mspgenes, hasshadow, pgenes, gencode Date Given: 7/21/2018
Lecture ID: GENCODE-20180621-i0lond18

Prioritizing Variants in Personal Genomes: Using functional impact, with particular application to cancer
35' talk for Engineering the Genome Workshop at Brunel U. i0mcg18+ new slides on RADAR.gersteinlab.org. Took 49' w/ many Qs.
Subject: jpegslides, funseq, frustration, costseq2, prcc, uorfs, radar Date Given: 6/25/2018
Lecture ID: Prioritizing-Variants-Cancer-App--20180625-i0lond18+brunel

Transcriptome Mining: Tackling core issues related to gene regulation & also analyzing the "data exhaust" associated with this activity
Data Science talk at QuantumBlack (in London). i0ds2 slides + some privaseq3 . In the hour allocated, didn't get to the encodeauthors part.
Subject: driess, privaseq, privaseq3, orthoclust, encodeauthors, cmptxn, encode, loregic, jpegslides Date Given: 6/19/2018
Lecture ID: Transcriptome-Mining-Core-issues-related-to-regulation-n-mining-the-data-exhaust--20180619-i0lond18+qb

Prioritizing Variants in Personal Genomes: Using functional impact & recurrence, with particular application to cancer
60' talk at McGill. Similar to i0dana talk but now w/ uORFs & some update of the costseq2 stuff
Subject: jpegslides, aloft, vat, funseq, mrtadfinder, larva, moat, frustration, costseq2, prcc, uorfs Date Given: 4/18/2018
Lecture ID: Prioritizing-Variants-Cancer-App--20180418-i0mcg18

Challenge 4 - Moving beyond coding regions
My short talk at the recent NHGRI genome-sequencing meeting. Discussion provoking thoughts on WGS & noncoding analysis for the exome-oriented CMG group
Subject: cmg, cmg2 Date Given: 4/4/2018
Lecture ID: Challenges-for-CMG-Moving-beyond-coding-regions--20180404-i0gsp18

Biomedical Data Science: An Introduction
Short ~10' talk introducing Biomedical Data Science to a Med. School audience. (Took more like ~15'.)
Subject: datascience, cbds, jpegslides, hasshadow Date Given: 2/7/2018
Lecture ID: Intro-to-biomed-datasci--20180207-cbds7feb

-- 2017 (14) --

Prioritizing Variants in Personal Genomes: Using functional impact & recurrence, with particular application to cancer
My talk for Dana Farber's Seminars in Oncology. (60' talk conjoins MOAT, LARVA, ALoFT &c tools w/ kidney cancer case study.) Fit into time w/ Qs.
Subject: jpegslides, aloft, vat, funseq, mrtadfinder, larva, moat, frustration, costseq2, prcc, talkmovie, recorded Date Given: 12/12/2017
Lecture ID: Prioritizing-Variants-Cancer-App--20171212-i0dana

Transcriptome Mining: Tackling core issues related to gene regulation & also analyzing the "data exhaust" associated with this activity
1:15 talk for Applied Data Science Series at Yale. Now includes update DREISS slides, incl. on cancer cell line analysis
Subject: driess, privaseq, orthoclust, encodeauthors, cmptxn, encode, loregic, jpegslides Date Given: 11/27/2017
Lecture ID: Transcriptome-Mining-Core-issues-related-to-regulation-n-mining-the-data-exhaust--20171127-i0ds2

Genomics & Data Science: Approaches to identifying key variants through functional impact & recurrence
30' talk w/ 5' Qs for UConn Institute for Systems Genomics 5-year Anniversary Celebration
Subject: aloft, vat, funseq, mrtadfinder, larva, moat, frustration, gslide, costseq2, publishedgslide Date Given: 11/8/2017
Lecture ID: Genomics-n-DataSci--20171108-i0isg

Passenger mutations in >2500 cancer genomes: Overall functional impact
20' talk incl. Qs at Genome Informatics at CSHL. Same as i0hgvs+ashg below w/ pRCC tree analysis & slide updates
Subject: papere, pcawg, prcc, funseq Date Given: 11/4/2017
Lecture ID: Mutations-in-2500-cancer-genomes--20171104-i0gi2017

Passenger mutations in >2500 cancer genomes: Overall molecular functional impact
15' talk incl. Qs at ASHG in Orlando. Took 3' too long.
Subject: papere, pcawg, prcc, funseq Date Given: 10/18/2017
Lecture ID: Mutations-in-2500-cancer-genomes--20171018-i0hgvs+ashg

Prioritizing somatic variants: Approaches to identifying key variants through functional impact & recurrence. Trying to lay this out w/ gslide.
40' talk at HGVS in Orlando (ASHG17 Satellite)
Subject: prcc, aloft, vat, funseq, mrtadfinder, larva, moat, frustration, gslide Date Given: 10/17/2017
Lecture ID: Prioritizing-somatic-variants--20171017-i0hgvs+main

Genomic Privacy & the 2-sided Nature of RNA-seq: Quantifying the Leakage of Individual Information
20' talk at NIH DataScience (BD2K) block at iDASH Security & Privacy Workshop in Orlando (ASHG17 Satellite)
Subject: hasshadow, privaseq, privasig, privacy, mrf, rseqtools Date Given: 10/14/2017
Lecture ID: Genomic-Privacy-n-RNAseq-Quantifying-Leakage--20171014-i0hgvs+idash

Transcriptome Analysis: Tackling core issues related to gene regulation & also mining the "data exhaust" produced by this activity
Similar to i0labroots17 but without loregic sect.
Subject: driess, privaseq, orthoclust, encodeauthors, cmptxn, encode Date Given: 10/10/2017
Lecture ID: Core-issues-related-to-regulation-n-mining-the-data-exhaust--20171010-i0umass17

Harnessing AI to Make Sense of Large, Complex Datasets & Re-Invigorate R&D Innovation: Evolution of Element Annotation, from Calling ChIP Peaks to Determining Genome Folding
30' talk at AI-Pharma Summit in Boston, MA
Subject: hic-spector, mrtadfinder, music Date Given: 7/27/2017
Lecture ID: Evol-of-Annotation-from-Calling-Peaks-to-Genome-Folding--20170727-i0aibos

Analysis of Personal Genomes: Multi-scale Element Annotation & Variant Prioritization
30' talk for Clinical Genomics Track at BioIT World. Has some new bits on TAD finding & analysis.
Subject: mrtadfinder, music, funseq Date Given: 5/24/2017
Lecture ID: Multiscale-Elt-Annotation-n-Var-Prioritization--20170524-i0bioit17

Scaling Computation to Keep Pace with Data Generation
7' talk for GP Write workshop
Subject: costseq, costseq2, encodeauthors Date Given: 5/10/2017
Lecture ID: Scaling-Computation-to-Keep-Pace-w-Data-Gen--20170510-i0gpwrite

Transcriptome Analysis: Tackling core issues related to regulation & also mining the "data exhaust" of this activity
58' talk for online labroots series. Too many slides for allocated time and ended up going to fast & skipping last section on encodeauthors. Hasshadow (extra slide). Has YouTube w/ video of the talk.
Subject: driess, privaseq, loregic, orthoclust, hasshadow Date Given: 5/4/2017
Lecture ID: Core-issues-related-to-regulation-n-mining-the-data-exhaust--20170504-i0labroots17

Large-scale Transcriptome Mining: Clustering, Dynamic Modelling & Logic-gate Analysis while Protecting Individual Privacy
My 60' talk at the retreat of the Program in Structural and Computational Biology and Molecular Biophysics (SCBMB) at Baylor College of Medicine (BCM) [Took 56' w/o Qs.]
Subject: encode, privacy, encodeauthors, orthoclust, dreiss, loregic, privaseq Date Given: 3/17/2017
Lecture ID: Large-scale-Transcriptome-Mining--20170317-i0scbmb

7 Slide Overview of the Lab
Created for this year's prospective student visiting day
Subject: overview Date Given: 2/3/2017
Lecture ID: 7-slide-overview-of-the-GersteinLab-20170203

-- 2016 (23) --

Large-scale Transcriptome Mining: Building Integrative Regulatory Models, while Protecting Individual Privacy
Talk for NEC Machine Learning Dept. Seminar Series
Subject: privaseq, privacy, rseqtools, driess, orthoclust, rnaseq Date Given: 12/19/2016
Lecture ID: Large-scale-Transcriptome-Mining--20161219-i0nec16

Comparing Diverse Transcriptomes to Determine Deeply Conserved Aspects of Gene Expression
My talk at UNC Charlotte. Comparative transcriptome analysis, with updated dreiss slides
Subject: encode, encodeauthors, cmppgene, cmptxn, orthoclust, dreiss Date Given: 11/18/2016
Lecture ID: Comparing-Transcriptomes-of-Distant-Org--20161118-i0uncc16

Key Drivers for Making Personal Genomic Sequencing into a Useful Tool
My talk for the Technology and Innovation Council. New slides on the Game of Genomes & an overview of cancer genomes. 30' in total.
Subject: subjectz, zimmerome, nrgnccan, funseq, stress, costseq2 Date Given: 11/14/2016
Lecture ID: Drivers-for-Making-Personal-Genomics-into-Tool-20161114-i0siem

Genomic Privacy & Individualized RNA-seq: Incompatible or Feasible?
45' talk for iDASH Privacy & Security workshop in Chicago. Has updated PrivaSeq slides. (Finished on time, moving slide 44 after 37, as this describes outlier genotyping better.)
Subject: privacy, privaseq, rseqtools, alleledb, alleleseq, allele Date Given: 11/11/2016
Lecture ID: Genomic-Privacy-n-Individualized-RNAseq-Incompatible-or-Feasible--20161111-i0idash16

Education in Biological Data Science: What to teach students ?
15' Talk at Education Forum at CSHL Biological Data Science Meeting
Subject: cbb752, cbbplan0mg, cbb Date Given: 10/28/2016
Lecture ID: Education-in-Bio-DataScience--20161028-i0bds16

Personal Genomics: Identifying High-impact Variants in Coding & Non-coding Regions
Talk at Biomedical Informatics Seminar Series at Ohio State. Updated frustration slides.
Subject: frustration, larva, funseq, stress, costseq2, music, intensification Date Given: 10/14/2016
Lecture ID: Identifying-High-Impact-Variants-Coding-n-Noncoding--20161014-i0os16

Analysis of Personal Genomes: Evaluating the impact of variants in exomes using protein structure & allelic activity
30' talk (w/ Qs) for 2nd Annual Next Generation Sequencing USA Congress in Boston. Talk now includes motifvar (intensification) & combines that with Stress & Frustration.
Subject: stress, frustration, alleledb, motifvar Date Given: 10/4/2016
Lecture ID: Evaluating-exome-variants-using-structures-n-allelic-activity--20161004-i0ng16

Overall thoughts related to integration of genomic information with clinical phenotypes and issues related to data privacy
10' perspective talk for NHGRI Computational Genomics & Data Science Workshop. Focused on privacy issues (mentioning privaseq as an example) & advocating a hybrid soc-tech solution. Fits into time w/ many Qs afterwards.
Subject: privacy, privaseq Date Given: 9/29/2016
Lecture ID: Bullets-for-NHGRI-workshop-M-Gerstein--20160929-i0cgds

Personal Genomics: Managing Rapid Data Scaling through Prioritizing High-impact Variants
My updated talk on variant prioritization for the Penn Bioinformatics Forum. Now includes new frustration analysis.
Subject: frustration, larva, funseq, stress, costseq2, music Date Given: 9/7/2016
Lecture ID: Managing-Rapid-Scaling-via-Prioritizing-Variants--20160907-i0pbf

Personal Genomics: Managing Rapid Data Scaling through Prioritizing High-impact Variants
Talk given at BMS. 57' in total.
Subject: frustration, larva, funseq, stress, costseq2 Date Given: 8/9/2016
Lecture ID: Managing-Rapid-Scaling-via-Prioritizing-Variants--20160809-i0bms14

Genomic Privacy & Individualized RNA-seq: Incompatible or Feasible?
Talk at the Birkbeck Inst. for Data Analytics (~45')
Subject: privacy, privaseq, rseqtools, alleledb, alleleseq, allele Date Given: 7/14/2016
Lecture ID: Genomic-Privacy-n-Individualized-RNAseq-Incompatible-or-Feasible--20160714-i0genc16+bida

Personal Genomics: Managing Rapid Data Scaling through Prioritizing High-impact Variants
Talk at Royal Holloway. Incremental update of my rare variant talk (eg i0mssm16). Talk took 50' w/o Qs, going fast over funseq & netsnp and slow over the costseq2 intro.
Subject: music, costseq2, stress, funseq, funseq2, netsnp, larva Date Given: 7/13/2016
Lecture ID: Managing-Rapid-Scaling-via-Prioritizing-Variants--20160613-i0genc16+rh

The Blind Men & the Elephant: Relating Pseudogenes, LOF, Retrodup Variation & Personalized Annotation
20' talk w/ Qs at Gencode Annual meeting in Cambridge, UK
Subject: hasshadow, vat, aloft, refgeneset, svpgene, 1000gphase3, unitary, alleledb Date Given: 7/7/2016
Lecture ID: Blind-Man-n-Elephant--20160707-i0genc16+cam

Mining an ENCODE Data Exhaust
5' Lightening talk at the ENCODE meeting. Updated encodeauthors slides. Has axis flip on slide 4. Additional talks on EN-TEX
Subject: encode, encodeauthors, hasshadow Date Given: 6/16/2016
Lecture ID: Mining-an-ENCODE-Data-Exhaust--20160616-i0enc16

Personal Genomics: Managing Exponential Data Scaling through Prioritizing High-impact Variants
Long talk for 2 hr block at Genomics, Big Data & Medicine Series at Mt. Sinai. Has rare variant prioritization talk (from i0jhhsb, w/o stress) w/ updated scaling slides & encodeauthors as a postscript.
Subject: music, costseq2, alleledb, funseq, funseq2, netsnp, larva, encodeauthors Date Given: 6/6/2016
Lecture ID: Managing-Exponential-Scaling-via-Prioritizing-Variants--20160606-i0mssm16

Prevalence of noncoding transcription in the human genome, in relation to lncRNAs: From noisy TARs to regulatory pseudogenes
20' talk at NHLBI workshop of LncRNAs. Fits into time.
Subject: universalarray, cmppgene, cmptxn, dart, incrna, encodepgenes, gapdh-pgenes Date Given: 6/1/2016
Lecture ID: Noncoding-Transcription-Noisy-TARs-to-Regulatory-Pgenes--20160601-i0nhlbi

Personal Genomics: Handling Exponential Data Scaling through Prioritizing High-impact Variants
25' talk at GCT bio conf. Parts of earlier talk (i0pcccsm) on prioritizing rare variants, now with a much fuller discussion of the scaling of sequencing & computation costs. Talk took 27' for just costseq2 & stress sections, leaving out alleleDB & FunSeq.
Subject: costseq2, alleledb, stress, funseq2 Date Given: 5/27/2016
Lecture ID: Handling-Data-Scaling-via-Prioritizing-Variants--20160527-i0gctbio

Analyzing the Structure of Genomic Science: Mapping the Diffusion of Ideas & Data across Disciplines
15' talk at Modelling Science & Technology meeting at NAS in DC
Subject: infoflow, encodeauthors, costseq2, pubnet, rnai, celltextmining Date Given: 5/18/2016
Lecture ID: Mapping-Diffusion-Ideas-n-Data--20160518-i0scisipc

SV Call Sets & Personal Genomes: new retroduplication calls & building a personal genome with PacBio SVs
10' talk at SV project meeting at CSHL satellite meeting of BOG '16, summarizing recent work on SVs
Subject: svpgene, alleleseq, alleledb, 1000g, sv2anal Date Given: 5/15/2016
Lecture ID: SV-callsets-n-PersonalGenomes--20160514-i0bog16+sv2

Personal Genomics: Prioritizing High-impact Rare & Somatic Variants
60' talk (w/ Qs) at Yale Pulmonary Sect. focusing on rare variant prioritization. Similar to i0jhhsb but now w/ new slides on personal genome in relation to RNA-seq. Went slow in intro. & over personal genomes. Skipped most of FunSeq & Larva.
Subject: stress, costseq2, alleledb, funseq, funseq2, larva, alleleseq, personalgenome, 1000g Date Given: 5/5/2016
Lecture ID: Personal-Genomics-Prioritizing-High-impact-Variants--20160503-i0pccsm

Transcriptome Analysis: Large-scale data, high-throughput pipelines & privacy considerations
30' Talk (w/ 5' Qs) at exRNA conference in Boston, incl. new bits on exceRpt & the exRNA consortium
Subject: exrna, excerpt, privaseq, rseqtools Date Given: 4/5/2016
Lecture ID: Transcriptome-Largescale-data-HTP-pipelines-n-privacy--20160405-i0xrnabos

Analyzing Personal Genomes: Prioritizing High-impact Rare & Somatic Variants
Talk for Hopkins Systems Biology. Targeted at 60'. Now has almost uniform formatting. (Note slides not conforming.) New bits on allelic & allosteric analyses + revamped intro.
Subject: stress, music, costseq2, alleledb, funseq, funseq2, netsnp, larva Date Given: 3/29/2016
Lecture ID: Personal-Genomes-Prioritizing-High-impact-Variants--20160329-i0jhhsb

Thoughts on Publication Rollout Structure for the ENCODE Project
One of 3 talks at psychENCODE meeting, describing an analysis of ENCODE publication structure
Subject: encodeauthors, psychencode, hasshadow Date Given: 2/9/2016
Lecture ID: Thoughts-on-ENCODE-rollout-structure--20160209-i0pec16

-- 2015 (18) --

Large-scale Transcriptome Mining: Building Integrative Regulatory Models, while Protecting Individual Privacy
Keynote at Genome Informatics 2015. Total time is ~50'.
Subject: privaseq, privacy, rseqtools, driess, loregic Date Given: 10/30/2015
Lecture ID: Transcriptome-Mining-Building-Models-while-Protecting-Privacy--20151030-i0gi2015

(Human Genome Analysis) Large-scale Transcriptome Mining: Building Interpretative Models while Protecting Individual Privacy
Talk from Next-Gen Sequencing Congress in Boston. Talk included new analysis of privacy in RNA-seq (PrivaSeq). It was 31' w/o DRIESS part at end, just focusing on privacy.
Subject: privacy, privaseq, rseqtools, dreiss Date Given: 10/27/2015
Lecture ID: Transcriptome-Mining-Building-Models-while-Protecting-Privacy--20151027-i0ngs15

LARVA: An integrative framework for Large-scale Analysis of Recurrent Variants in noncoding Annotations
Talk for 'Opening Up Big Data' session at ASHG '15. Should be 10' w/ 5' for Qs. (Clocked in at less than 10'.)
Subject: larva, funseq, funseq2 Date Given: 10/10/2015
Lecture ID: LARVA--20151010-i0ashg15

Genomic Privacy: Intertwined Social & Technical Aspects
Talk for Personalized & Precision Medicine (Satellite meeting for ASHG15 in Baltimore). 30' including Qs.
Subject: hasshadow, privacy, privaseq, rseqtools, genomicsandprivacy, ajobcloud, wincompatible Date Given: 10/6/2015
Lecture ID: Genomic-Privacy-Soc-n-Tech--20151006-i0pgx

Personal genome construction with SVs
Talk at SV meeting, which was a satellite to ASHG'15 in Baltimore, MD
Subject: svs, alleledb Date Given: 10/5/2015
Lecture ID: Personal-genome-construction-w-SVs--20151005-i0pgx+svmtg

Transcriptome Analysis: Expression Clustering across Distant Organisms
20' talk for RNA Center Retreat. Expression Clustering Across Worm & Fly, now w/ DREISS state-space modeling.
Subject: dreiss, cmptxn, orthoclust Date Given: 9/18/2015
Lecture ID: Expression-Clustering-across-Distant-Organisms--20150918-i0rnacent

Explorations in Summer Camp in CT: Prioritizing non-coding mutations as potential cancer drivers
Talk on prioritizing cancer variants, now w/ new slides larva recurrence module, for Yale faculty summer camp. 30' slot that talk approx. fills.
Subject: larva, funseq, music Date Given: 7/12/2015
Lecture ID: Prioritizing-noncoding-mutations-in-cancer--20150812-i0camp15

ENCODE: Evolution of Approaches to Annotate the Human Genome & Interpret its Variants
15 min. talk at CSHL Conferences on the History of Molecular Biology and Biotechnology - THE EVOLUTION OF SEQUENCING TECHNOLOGY: A HALF-CENTURY OF PROGRESS. Talk fits into time (1' over), w/ joke on cog slide and lots of Qs. New slides for ENCODE over time, what is annotation, and encode & constraint
Subject: encode, modencode, history, funseq Date Given: 7/19/2015
Lecture ID: Evolution-of-Approaches-to-Annotate-Genome--20150719-ibiohist15

An Overview of the Data & Some of the Key Analyses of the ENCODE & modENCODE Consortia: Interpreting the Transcriptome in terms of the Regulome
30' talk at RNA-seq Boston 2015. Has updated hierarchy & loregic slides w/ std. HM-TF model ending. Left off TF model sect. in presentation. Everything in win-compatible.
Subject: encode, hinet, loregic, worm_hm, cmptxn, wincompatible Date Given: 6/25/2015
Lecture ID: Interpreting-Transcriptome-in-terms-of-Regulome--20150625-i0rnaseq15

SVs & Pseudogenes, Tricky but Crucial Genomic Features, Targeted by Long-read Sequencing: Current Short-read Results & Future Prospects
30' talk (w/ 5' Qs) at the Festival for Genomics in Boston. Updated slides on breakpoints & pseudogenes, focusing on need for long reads. Fits but running out of time at RDVs. Not win-compatible (slide 28).
Subject: encode, cmppgene, phase1bkpt, winincompatible Date Given: 6/23/2015
Lecture ID: SVs_n_Pseudogenes_Tricky_but_Crucial_Genomic_Features--20150623-i0flg

Comparative Genome Analysis: Comparing Transcriptomes of Distant Organisms
Comparative ENCODE slides with updated orthoclust figures for talk at Tel Aviv U. 45' slot. Talk was a bit too long with only 5' for models part after a slow start.
Subject: cmptxn, orthoclust, encode, hasshadow Date Given: 6/10/2015
Lecture ID: Comparing-Transcriptomes-of-Distant-Org--20150610-i0isgc-tau

Analysis of Protein Networks: Using 3D-structure into interpret networks & deep sequencing data
35' talk for Deep Sequencing Meets Structural Biology. ISCG 2015. 30' tot. not going fast. Then Qs to fit 35' slot.
Subject: motions, vat, dynasin, netsnp, funseq Date Given: 6/8/2015
Lecture ID: 3D-struct-to-interpret-networks-deep-sequencing--i0isgc-20150608

Activities in SVs, focusing on breakpoint characterization
10' talk at SV project meeting at JAX summarizing recent work on SVs, focusing on breakpoints.
Subject: svs, 1000g, hasshadow Date Given: 5/4/2015
Lecture ID: Activities-in-SVs-focusing-on-breakpoint--20150504-i01kgsv15

Human Genome Analysis: Progressive summarization of large-scale data, to interpret mutations & dis-regulation in cancer
Talk at BioIT World 2015 in Boston. Budget for 25' incl. Qs. Actually: 27' w/ no Qs
Subject: funseq, funseq2, loregic, music, netsnp Date Given: 4/22/2015
Lecture ID: Progressive-summarization-large-scale-data-interpret-cancer--20150423-i0bioIT15

Genomic Privacy: Proposed Social & Technological Solutions to Issues of Data Privacy in Personal Genomics (Licensure, Secondary Datasets, Enclaves)
Short talk at the 8th Intl. Conf. in Ethics in Biology, Engineering & Medicine (ICEBEM 2015). 15' talk. Skipped end (MRF).
Subject: privacy, rseqtools Date Given: 4/23/2015
Lecture ID: Soc-n-Tech-Soln-to-Privacy-in-Personal-Genomics--20150424-i0icebem15

Biological Network Analysis: Hierarchies, Mutational Constrains & Logical Circuits in Regulation
Talk at Case Western Reserve U., Dept. of Epidemiology & Biostat., 60 min. estimated. (Actually takes 51' w/o Qs.) Now w/ new slides on Loregic & Hinet.
Subject: encode, loregic, hinet, encodenets, netheir, networks Date Given: 3/30/2015
Lecture ID: BioNets-Hierarchies-Mut-Constraints-Logical-Circuits--20150330--i0cwru

Thoughts on ENCODE Annotations
Talk on Additional thoughts on a Simplified Annotation in Encyclopedia session at ENCODE meeting at CSHL, est. 7'
Subject: encode, hasshadow Date Given: 3/15/2015
Lecture ID: thoughts-on-ENCODE-annotations--final-i0enc15

Recommendations related to genome function from NHGRI Planning Workshop on the Future Opportunities for Genome Sequencing & Beyond
Talk at NHGRI workshop From Genome Function to Biomedical Insight: ENCODE and Beyond (available via http://www.genome.gov/27560819). Total talk was ~20 min & was split with R Myers.
Subject: encode, nhgri Date Given: 3/10/2015
Lecture ID: FutureEncodeWorkshop-Gerstein-and-Myers-Mar10-15-final--i0beyondenc

-- 2014 (31) --

Applications of Machine Learning for Comparing Transcriptomes of Distant Organisms
Talk at NIPS 2014 Workshop on Machine Learning in Computational Biology. 50' talk w/ Qs.
Subject: cmptxn, cmppgene Date Given: 12/13/2014
Lecture ID: App-MachineLearning-Comparing-Transcriptomes--20141213-i0nips

Thoughts on Computational Biology at Yale Related to Research, Education & Infrastructure
Excerpts from a presentation to a Yale Basic Science Planning Committee. [~60' w Qs for 1st half.] Has shadow with more detail on program and proposal. (Search on i0yufut2.)
Subject: cbb752, hasshadow Date Given: 12/4/2014
Lecture ID: Thoughts-on-Compbio-at-Yale-Research-Education-Infrastructure--20141204-i0yufut2.EDIT

Comparative Genomics: What we Learn about the Activity of the Human Genome by Comparing it with Distant Organisms
Stanley lecture at CSHL
Subject: modencode, cmptxn, encode, cmppgene Date Given: 12/3/2014
Lecture ID: What-we-Learn-about-Activity-of-Genome-by-Comparing-it--20141203-i0cshl13

A computational framework to prioritize regulatory variants from whole-genome sequencing in cancer: Progressive summarization of large-scale data
Talk given at CSHL Biological Data Sciences Meeting. 15' w. 5' Qs. Updated FunSeq2 slides, focusing on data context & enhancers.
Subject: funseq, funseq2, music Date Given: 11/8/2014
Lecture ID: Framework-to-prioritize-Regulatory-variants-Progressive-summarization-of-large-scale-data--20141108-i0biods14

Overview of non-coding annotation
Part of PCAWG drivers group (2,5,9,14) presented at Boston meeting (at Broad Inst.). Longer presentation in a gpresentation (contains acknowledgements)
Subject: ncannotation, pcawg, cancer, hasshadow, nrgnccan Date Given: 11/4/2014
Lecture ID: nc-annotation-sect-from--PAWG-2-5-9-14_prep_for_Boston_mtg

Overview of Genome Annotation & ENCODE Elements
12' talk for ENCODE workshop at ASHG. It gives an overview of the project's simplified annotation. 7 slide extraction used for ENCODE AWG call on 14-Nov.
Subject: encode Date Given: 10/19/2014
Lecture ID: Overview_ENCODE_Elements--20141018-i0ashg14

Analysis of SVs in human populations: SVs & Pseudogenes
25' Invited talk at ASHG '14, San Diego, CA. (In addition, there's other fill-in talks at this meeting, filled under i0ashg14)
Subject: svs, pgenes, svpgene, hasshadow, cmppgene Date Given: 10/18/2014
Lecture ID: SVs_n_Pgenes--20141019-i0ashg14+SV

Human Genome Analysis:Large-scale Non-coding Annotation & Application to Cancer Genomics
Talk at Beyond the Genome 2014: Cancer Genomics. Took 24' total w/o Qs.
Subject: funseq, funseq2, music Date Given: 10/8/2014
Lecture ID: Noncoding_Annotation_App_Cancer_Genomics--20141008-i0beyond

Computational Biology at Yale
Overview of the CBB Program & Biocompute Infrastructure for "Important Future Directions in Biology: Half-Day Symposium" at Yale. Has shadow with more detail on program and proposal. (Search on i0yufut.)
Subject: cbb752, hasshadow Date Given: 10/7/2014
Lecture ID: CBB-program-n-Biocompute-Prop--20141007-i0yufut.EDIT

Biological Data Science:Making a Map of the Genome & Turning it into Tool Against Cancer
20' talk for Yale Day of Data. (Took more like 25'.)
Subject: bigdata, encode, funseq, funseq2 Date Given: 9/26/2014
Lecture ID: Biological_Data_Science_Making_a_Map_of_Genome_n_Turning_it_into_Tool_Against_Cancer--20140926-i0dataday

Overview of time in Levitt Lab ('93-'96) & subsequent work with the extended "Levitt Legacy," in 3 themes
Short 5-slide talk given at Symposium celebrating Levitt 2013 Nobel (Levitt Lab Group & Alumni), celebrating '13 Chemistry award, in Woodside, CA.
Subject: levittnobel, cmptxn, modencode, structint, molmovdb Date Given: 9/11/2014
Lecture ID: Talk-at-Levitt-alumni-gathering--20140911-i0levalum-final

Human Genome Analysis: Building the Regulatory Network, Using it to Interpret Cancer Mutations & Practical Software Tool
Standard FunSeq talk for ~1hr.
Subject: funseq Date Given: 9/12/2014
Lecture ID: Building_RegNet_Using_to_Interpret_Cancer_n_Practical_Tool-20140912-i0levalum+bin

Overview of some of the data & models involved in ENCODE Genome Annotation
Tutorial style talk at SAMSI comp. bio. workshop. Targeted for 1 hr 15 min. Took about this long with a number of Qs. Left out last model section & found pgene family slide didn't display well on the PC.
Subject: encode, cmptxn, cmpreg, cmppgene, modencode Date Given: 9/8/2014
Lecture ID: Overview_of_data_n_models_in_ENCODE_Annotation--20140908-i0samsi

Human Genome Analysis -- Between humans & distant species, great similarities, also great differences: Promoters & Pseudogenes
Talk at Epigenomics-Boston-2014. It expands the cmppgene slides. 51' in total without Qs. In detail, 11'20" (intro), 17'40" (pgenes w/o hum. var), 12' (HM models), 8'30" (TF models), 2'15" (summary).
Subject: cmptxn, cmppgene, modencode, encode Date Given: 8/26/2014
Lecture ID: Betw_humans_distant_species_great_similarities_great_diffs_Promoters_n_Pseudogenes--20140825-i0epi14

Understanding & Annotating Promoters Using Statistical Models
30' talk with many Qs
Subject: statmodels, models, cmptxn, encode Date Given: 8/20/2014
Lecture ID: Understanding_Promoters_using_Stat_Models--20140820-summer-camp

Understanding & Annotating Promoters Using Statistical Models
30' online talk given for BioConferenceLive's Genetics and Genomics 2014. (Removal of slides with blue in upper left hand corner gives a shortened version for "MBB summer camp (above).") Actual time is ~35'. Extra link contains ~100Mb MP4 with online video of talk.
Subject: statmodels, models, cmptxn, encode Date Given: 8/20/2014
Lecture ID: Understanding_Promoters_using_Stat_Models--20140820-i0bioconfweb0mg

Human Genome Annotation & Predicting Disease Drivers
40' talk at Gordon Conf. on Human SNPs & Disease (Easton, MA). Updated FunSeq slide pack to include a little of FunSeq2
Subject: funseq, funseq2 Date Given: 8/7/2014
Lecture ID: Genome_Annotation_n_Predicting_Drivers--20140807-i0grc14

Integrating functional genomics with DNA sequence variants
Brief talk on functional annotation of variants at NHGRI planning meeting (split with Rick Myers) ["Future Opportunities for Genome Sequencing and Beyond: A Planning Workshop for the National Human Genome Research Institute"]. Total allocated time was 15' of which I went for 7'.
Subject: nhgri, i0gspplan Date Given: 7/29/2014
Lecture ID: NHGRI-Breakout-Session-func-n-variants-summary-MG-1030p

Human Genome Analysis: Prioritizing Noncoding Mutations in Cancer
Talk at special session (#SS04) for the Levitt Nobel at ISMB 2014 in Boston. Adding in a few slides at the beginning, presented by S Brenner, introducing Michael Levitt & his alumni. The whole talk was 26' including the intro. section (with the SV sect. of the talk just briefly summarized).
Subject: fig, funseq, 1000g, svs, levitt, levittnobel Date Given: 7/13/2014
Lecture ID: Human_Genome_Analysis_Prioritizing_Noncoding_Mutations_in_Cancer--20140713-i0ismb14

Function Prediction on a Genome scale: Statistical Models Predicting Cell-type-specific Expression Levels from Upstream Promotor Activity
Talk for the AFP SIG at ISMB 2014 in Boston. 25' talk w. 5' for Qs (left out the hierarchy slides at end). Adding in function prediction intro (including gene names discussion).
Subject: encode, cmptxn, statmodels, funnygene Date Given: 7/11/2014
Lecture ID: Func_Pred_on_Genome_scale_Stat_Models_Predicting_Celltype_Specific_Expression_from_Promotor_Activity--20140711-i0afpsig

Pseudogenes
Gencode meeting presentation. First attempt at presentation of cmppgene
Subject: i0se14, gencode, cmppgene, hasshadow Date Given: 6/22/2014
Lecture ID: GENCODE-Cambridge-MeetingJune2014-v4

Genome Analysis: Using Inter-phyla Comparisons to Understand Highly Conserved Aspects of the Human Genome
Initial talk on the comparative transcriptome paper at the Dept. of Cell & Molecular Biology, Uppsala; talk was 52' w/ Qs in middle; forgot last 3 slides
Subject: cmptxn, modencode Date Given: 6/18/2014
Lecture ID: Inter-phyla-Comparisons-to-Understand-Conserved-Aspects-of-Human-Genome--20140618-i0se14

Human Genome Analysis: Building the Regulatory Network & Using it to Interpret Cancer Mutations
25' talk for Epigenetic Mechanisms in Cancer 2014 in Toronto. On time for 30' total but decided that constraint associated with connectivity section is a little out of order.
Subject: encode, 1000g, fig, funseq, encodenets Date Given: 6/4/2014
Lecture ID: Genome_Analysis_Building_Reg_Net_n_Using_to_Interpret_Cancer_Mut--20140604-i0tor14

Proposed Social and Technological Solutions to Issues of Data Privacy in Personal Genomics (Licensure, Secondary Datasets, Enclaves)
Talk at 2014 IEEE International Symposium on Ethics in Engineering, Science, and Technology: IEEE Ethics 2014. Chicago, IL. Finished 15' talk with a little rushing at end. Elaborate new lecture on privacy, summarizing many papers on privacy & security.
Subject: privacy Date Given: 5/23/2014
Lecture ID: Soc-n-Tech-Soln-to-Privacy-in-Personal-Genomics--20140523-i0ieeeE

FIG Ideas for Phase 3
15' talk summarizing past FIG work with extensions for phase 3. Talk at 1000 Genomes Project Meeting.
Subject: 1000g, edit, hasshadow Date Given: 5/6/2014
Lecture ID: FIG-Ideas-for-Phase3--20140506-i0bog14+1000write-v3-edit

Human Genome Analysis using Molecular Networks
Talk on molecular networks for Yale Inst. for Network Sciences (YINS). Meant to be accessible. Around 35'.
Subject: networks, callgraph Date Given: 4/2/2014
Lecture ID: Human-Genome-Analysis-using-Molecular-Networks--20140402-i0yins

Big Data in Genome Annotation: Using Networks to Help in the Interpretation
Talk for Keystone Big Data in Biology Conf. (SF, CA). 25' talk w. 10' Qs. Built from i0ccam talk w/ updated slides for SeqUniverse, call graph analysis, big data intro & cost-of-sequencing. No rewiring slides. Actual talk last 29' leaving out RNAi & FunSeq.
Subject: networks, encode, encodenets, funseq, bigdata, callgraph, rnai, nethier Date Given: 3/25/2014
Lecture ID: Big-Data-in-Genome-Annotation-Using-Networks--20140325-i0keybdata

Human Genome Analysis: Building the Regulatory Network and Using it to Interpret Cancer Mutations
Talk for Lecture Series in Clinical Genomics at the NY Genome Center. 45' talk with 15' Qs. Elaborated version of i0gatech talk, now with SeqUniverse slide & more on allelic effects.
Subject: networks, encodenets, funseq, alleleseq, netsnp Date Given: 3/20/2014
Lecture ID: Genome_Analysis_Building_Reg_Net_n_Using_to_Interpret_Cancer_Mut--20140320-i0clingen

Comparative network analysis of ENCODE and modENCODE data: Inter-phyla Comparison of Regulation & Transcription
Short 15' talk for the CSH Sys. Biol. meeting. First time presenting the comparative transcriptome work.
Subject: cmptxn, cmpreg, modencode Date Given: 3/18/2014
Lecture ID: Comp-network-analysis-ENCODE-data--20140318-i0cshsb

5 Slide Overview of the Lab
For prospective students visiting
Subject: intro Date Given: 2/7/2014
Lecture ID: 5-slide-overview-of-the-lab

Human Genome Analysis: from Constructing Informative Regulatory Networks, to Relating them to Variation, to Practical Cancer Tools
Talk at Center for Cell Analysis and Modeling (CCAM), University of Connecticut Health Center (UCHC), Farmington, CT; 1h 5' w/o Qs. Talk presents ENCODE regulatory networks in a broader networks & big data context. Now including new slides for FunSeq & ENCODE enhancer work.
Subject: networks, encodenets, funseq, rewiring, nethier, metatracks, callgraph Date Given: 1/30/2014
Lecture ID: Constructing-Reg-Net-to-relating-to-Variation-to-prac-Tools--20140130-i0ccam

-- 2013 (20) --

Comparison of Human, Worm & Fly Transcriptomes
Short 8' summary of comparative transcriptome work at ENCODE consortium meeting. Also, 2nd "shadow" talk giving an overview of the DAC at this meeting.
Subject: cmptxn, modencode, hasshadow Date Given: 5/30/2013
Lecture ID: 8min_cmptxn_at_ENCODE_mtg--20130530-i0enc13

FunSeq analysis of non-coding mutations in Prostate Cancer... in 10'
Overview of FunSeq for TCGA Prostate Workshop in DC
Subject: funseq, cancer Date Given: 11/20/2013
Lecture ID: FunSeq-analysis-non-coding-mutations-in-Prostate-Cancer-in-10min--20131120-i0tcga13

Human Genome Analysis: Building the Regulatory Network and Using it to Interpret Cancer Mutations
Talk for 9th Georgia Tech and Emory University International Conference "Genome Biology and Bioinformatics". 40' talk with Qs. Shortened version of i0hartford talk, with more SVs and updated intro.
Subject: encode, funseq, 1000g Date Given: 11/8/2013
Lecture ID: Genome_Analysis_Building_Reg_Net_n_Using_to_Interpret_Cancer_Mut--20131108-i0gatech

Integrative Annotation of Variants from 1092 Humans: Application to Cancer Genomics
Talk for CSHL Genome Informatics, mostly following FIG/FunSeq paper but with more SV slides (15' w/ 5' Qs)
Subject: funseq, sv, netsnp, 1000g Date Given: 11/2/2013
Lecture ID: Integ_Annot_Var_from_1092_App_to_Cancer--20131102-i0gi2013

Human Genome Analysis: from biological Big Data to informative Regulatory Networks and practical Cancer Tools
Talk for Duke Physics. FunSeq w/ more emphasize on SVs. 1 hr, 7' in total. just up to FunSeq part, going extra slow for lots of Qs. (Video available via "extra" link.)
Subject: funseq, encode, 1000g, video Date Given: 10/30/2013
Lecture ID: Genome_Analysis_from_BigData_to_Reg_Networks_n_Cancer_Tools--20131030-i0duke

Non-coding variant annotation, with the FunSeq Workflow
15' presentation at NHGRI Sequencing Network Meeting in Bethesda, MD. Focuses on FunSeq and puts it in perpsective of ENCODE & 1000G efforts.
Subject: funseq, encode, 1000g Date Given: 10/10/2013
Lecture ID: Noncoding_variant_annotation--20131010-i0seqnet

Human Genome Analysis: Applying basic annotation efforts to practical problems in cancer
New cancer genomics application as ending on ENCODE networks talk. A 45' talk in Clinical Genomics in the 21st Century, a JAX/UConn symposium in Hartford.
Subject: funseq, encodenets, netsnp Date Given: 10/5/2013
Lecture ID: Hum_Genome_Analysis_Applying_Basic_Annotation_Efforts_to_Cancer--20131005-i0hartford

Biological Networks: Next Generation Annotation for the Human Genome
Overview of the Lab for 1st Year CBB Students
Subject: encodenets Date Given: 8/27/2013
Lecture ID: ENCODE_Nets_as_Nextgen_Annotation--20120827-cbb-1st-day

FIG Plans for Additional Analyses Beyond the Phase I Paper
2012 1000G meeting at CSHL (i0bog13)
Subject: fig, 1000g Date Given: 5/12/2013
Lecture ID: 1000G-FIG-Plans-Beyond-Phase-I

Human Genome Analysis: Non-coding, Regulatory Annotation & its Use in Prioritizing Cancer Mutations
Talk at Vanderbilt, almost 46'.
Subject: funseq, encode, encodenets Date Given: 10/1/2013
Lecture ID: Hum_Genome_Analysis_Noncoding_Reg_Annotation_n_Use_in_Cancer--20131001-i0vand

Statistical Methods in Functional Genomics -- or How Biology Grapples with Big Data (Illustrations of Models, Networks and Practical Tools)
New big data intro. then normal encode stat. models & networks, followed by an overview of chipseq and RNAseq tools (including privacy & allelic aspects). 2hr talk at CSHL course on Statistical Methods in Functional Genomics. (Video available on youtube, via "extra" link.)
Subject: encode, tools, peakseq, privacy, encodenets, rnaseq, alleleseq, stat-models, bigdata, video, youtube Date Given: 6/27/2013
Lecture ID: Stat_Meth_in_Func_Genomics-How_Bio_Grapples_w_Big_Data-Models_Nets_Tools--20130627-i0cshcourse

Developing novel tools for transcriptome analysis to optimally utilize RNA-Seq data (Issues in Dealing with High-level v Low-level Data: Privacy Considerations and Allelic Analysis)
Talk at conference RNA-seq 2013 in Boston. 30' talk with 5' for Qs. Some AlleleSeq slides, particularly for personal genome and allelic read mapping, are corrupted in pdf and ppt. Good in future to include URLs. Contains for 1st time update to alleleseq summarizing results from Djebali et al '12.
Subject: rnaseq, tools, privacy, alleleseq Date Given: 6/19/2013
Lecture ID: Developing_Tools_for_Transcriptome_Analysis_Issues_Privacy_n_Alleleic_Effects--20130619-i0rnaseq13

Networks and Human Genomics (Stories Contrasting Traditional Annotation with Newer Network Approaches: Pseudogenes v. Regulatory Networks)
Talk at Dana-Farber Cancer Center, Harvard. Std. 1 hr slot.
Subject: encode, networks, encodenets, pgenes Date Given: 5/17/2013
Lecture ID: Nets_and_Hum_Genomics_Cont_Trad_w_Nets_Pgenes_n_Regnets--20130520-i0farb

Human Genome Analysis (Stories Contrasting Traditional Annotation with Newer Network Approaches: Pseudogenes v. Regulatory Networks)
Talk at conference "Automated Personal Genome Analysis for Clinical Advisors: Challenges and Solutions" . 45' slot has a shortened version of my ENCODE networks & pseudogenes talk now with neat movies from Z Gumus (see extra link for multigifs) . Talk now includes some positive selection on the reg. network, pseudgene population variation, and more on netsnp.
Subject: encodenets, networks, netsnp, svpgenes, pgenes, encodeprodpgenes, fig Date Given: 5/3/2013
Lecture ID: Hum_Genome_Analysis_Cont_Trad_w_Nets_Pgenes_n_Regnets--20130503-i0cmu13

Human Genome Annotation (Stories Contrasting Traditional Annotation with Newer Network Approaches: Regulatory Networks v Track Models)
Talk at MSKCC. 1 hr (w. Qs). Usual ENCODEnets + Stat models talk, slightly updated.
Subject: encodenets, netsnp, stat-models, callgraph, tfhm-mouse Date Given: 3/28/2013
Lecture ID: Hum_Genome_Annotation_Cont_Trad_w_Nets_Statmodels_v_Regnets--20130328-i0mskcc

Computational Methods to Prioritize Variants in Exome Sequencing: Filtering out Artifacts Due to Pseudogenes, Finding True LoF Mutations, Using High Network Connectivity
20' Analysis Talk at Centers for Mendelian Genomics in Washington, DC (Rockville); 13' then Qs
Subject: netsnp, vat, lof, pgenes, i0cmg Date Given: 3/19/2013
Lecture ID: Comp_Meth_Prioritizing_Var_Exome_Seq_Pgenes_trueLoF_nethubs--20130319-i0cmg

Human Genome Annotation (Stories Contrasting Traditional Annotation with Newer Network Approaches: Regulatory Networks v Track Models)
Talk at Genomic Medicine at U Chicago; 1 hr slot, only had time for 1st half with Qs in the middle
Subject: i0chi12 Date Given: 3/14/2013
Lecture ID: Hum_Genome_Annotation_Cont_Trad_w_Nets_Statmodels_v_Regnets--20130314-i0chi13

Human Genome Annotation (Large-scale Comparative & Functional Description in terms of Variable Block Deletions & Regulatory Networks)
Talk a NY Bioinformatics Users Group (NYBUG) at Simons Foundation; 1 hr slot, talk took 45' w/o Qs, skipping network motifs, cooperation betw. levels, allelic effects. Including for the first time somatic mosaicism (IPS) and results of 1000G phase I (1000gphase1).
Subject: encodenets, bigdata, callgraph, svs, cnvnator, sric, ips, 1000gphase1, i0simons Date Given: 3/22/2013
Lecture ID: Genome_Annotation_Compare_n_Func_Description_SVs_n_Nets--20130322-i0simons

Human Genome Annotation (Stories Contrasting Traditional Annotation with Newer Network Approaches: Pseudogenes v. Regulatory Networks)
Talk at Rockefeller U. 1 hr talk; further update integrating NetSNP slides in ENCODEnets talk but now without callgraph
Subject: encodenets, netsnp, pgenes, networks Date Given: 2/21/2013
Lecture ID: Hum_Genome_Annotation_Cont_Trad_w_Nets_Pgenes_n_Regnets--20130221-i0nygc

Grappling with a Big Data Blizzard in Genomics: Reproducible & Open Annotation, Networks, Models & Tools
Talk in stat/reproducibility course at Columbia U. Allocated 2 hrs so prepared very expanded ENCODE talk, including many associated tools . For the first time had some slides on NetSNP and the reproducibility of ENCODE data.
Subject: encode, bigdata, statmodels, networks Date Given: 2/13/2013
Lecture ID: Bigdata_Blizzard_in_Genomics_Open_Annotation_Nets_Models_Tools--20130213-i0curepro.ppt

-- 2012 (25) --

Human Genome Annotation: Finding new elements (pseudogenes) & Building models relating existing elements
Talk at HIT symposium at Johns Hopkins; 38' talk with 4' Qs; More depth on pgenes (*encodeprodpgenes) than previously with an abbreviated models discussion
Subject: encode, pgenes, encodeprodpgenes, stat-models Date Given: 11/15/2012
Lecture ID: GenomeAnnotation_Finding_new_elts_pgenes_and_Building_models_relating_elements--20121115-i0jhgen2

Big Data Approaches in Human Genome Analysis: Inter-relating groups of elements with statistical models & organizing elements into networks
Talk at Computation Inst. (CI) at U Chicago. Presentation of ENCODE nets & stat models with a big data spin (i.e. containing *infoflow, *costseq, & *callgraph); Total talks was 50' with 20' at the beginning for models.
Subject: encode, networks, encodenets, bigdata, stat-models Date Given: 11/9/2012
Lecture ID: Bigdata_in_Human_Genomics_Stat_Models_and_Networks--20121101-i0chi12

Introduction to the Big Data Science Symposium at Yale
Overview of Big Data and Martin Schultz's career in it; 15' talk + 5' ending by Martin. (Contains Infoflow & costseq .)
Subject: bigdata Date Given: 10/26/2012
Lecture ID: Intro_to_BigData_Symp--20121026-bdatasymp0mg

Human Genome Annotation (Mining for new genomic elements & Organizing existing ones with networks -- 2 vignettes on grappling with big data )
Talk at Pfizer in Groton. ENCODE talk on Networks & pgenes with a big data intro. Pgenes bit was somewhat extended, and networks section contained more detail on motifs as well brief bit about callgraph; Well over an hour in total.
Subject: bigdata, encode, pgenes, networks Date Given: 10/24/2012
Lecture ID: Mining_new_genomic_elements_n_Organizing_existing_w_nets_2_bigdata_vignettes--20121024-i0pfizer

Human Genome Annotation(Two vignettes on grappling with big data in genomics : Mining for new elements & Building statistical models relating elements)
Talk at Harvard School of Public Health Biostat, 1 hr 10 min tot. incl. 10 min. of Qs. Added a big data intro. on ENCODE talk. Models sect. still not sequenced that well
Subject: encode, bigdata, pgenes, stat-models Date Given: 10/16/2012
Lecture ID: Big_data_in_genomics_Mining_elements_and_Building_stat_models--20121016-i0hsph

Human Genome Annotation (Stories Contrasting Traditional Annotation with Newer Network Approaches: Pseudogenes & Regulatory Networks)
Talk at Sixth Annual Young Investigators Symposium on Genomics and Bioinformatics at Johns Hopkins; 60' talk slot, but timing was not that precise. Nice if this included some more background on dupl. & processed pgenes & the rel. of UTR divergence to pgenes.
Subject: encode, networks, pgenes Date Given: 10/4/2012
Lecture ID: Hum_Genome_Annotation_Cont_Trad_w_Nets_Pgenes_n_Regnets--20121004-i0jhgen

Biological Networks: a Next Generation Annotation for the Human Genome (Inter-relating Annotations for Transcription, Chomatin & TFs and Analyzing the Regulatory Network)
talk at Cornell Computational Biology, Ithaca, NY; it took 1 hr exactly to present all the slides w/o Qs; Extra link contains a video.
Subject: encode, networks, stat-models Date Given: 9/15/2012
Lecture ID: ENCODE_Nets_as_Nextgen_Annotation_v_HM_TF_Models_For_GeneExpr--20120917-i0corn

Analysis of Biological Networks: Integrating a Structural Interaction Network with Motion Dynamics
talk at US-HUPO12, 10' talk on Dynasin
Subject: networks, motions Date Given: 9/12/2012
Lecture ID: Analysis_of_Nets_Integ_SIN_w_Motion--Dynasin--20121912-i0hupo12

Biological Networks: Next Generation Genome Annotation
Talk at CBB annual retreat at Lawn Club, New Haven; 30' omitting allele slides; has new ENCODE cover
Subject: encode, networks Date Given: 9/7/2012
Lecture ID: ENCODE_Nets_as_Nextgen_Annotation--20120907-cbb-retreat

Bioinformatics Approaches for RNA-seq Analysis in the Brainspan Project
Talk at Brainspan Annual Meeting in New Haven, 10' intro. before RK's talk
Subject: rna-seq, brainspan Date Given: 9/5/2012
Lecture ID: Bioinfo_for_Brainspan_RNAseq-20120905

Tools for processing nextgeneration sequencing data: Statistical models connecting Chip-seq Inputs to RNA-seq Outputs
Talk at CHI conference in Providence, RI
Subject: encode, stat-models Date Given: 8/15/2012
Lecture ID: Tools_for_Nextgen_Data_as_Stat_Models_Connecting_RNAseq_and_Chipseq--20120815-i0ngx

Next-Generation Annotation for Personal Genomics: Gene Fossils & Integrative Models
Talk in Boston; Only time for pgene part
Subject: encode, pgenes Date Given: 8/2/2012
Lecture ID: Nextgen_Annotation_Fossils_and_Models--i0ngenddev-20120802

Insights from integrative analysis of the C. elegans genome: What approaches we learned that were applicable to annotating the human genome
Talk at NIH at ModENCODE Symposium; This was filmed and put on GenomeTV as a video
Subject: modenocde, networks, stat-models, video, youtube Date Given: 6/21/2012
Lecture ID: Insights_from_Worm_modENCODE_Human_Applicable--i0modsymp-20120620

Biological Networks: Next Generation Annotation for the Human Genome (Statistically Modeling Transcription from Chomatin & TFs and Analysis of the Human Regulatory Network)
Talk at UCLA
Subject: encode, networks, stat-models Date Given: 6/4/2012
Lecture ID: ENCODE_Nets_as_Nextgen_Annotation_v_HM_TF_Models_For_GeneExpr--20120604-i0ucla

Biological Networks: Next-Generation Annotation for Personal Genomes
Talk at Harvard Sys. Biol.
Subject: encode, networks, pgenes Date Given: 5/30/2012
Lecture ID: ENCODE_Nets_as_Nextgen_Annotation_v_Partially_Active_Pgenes--20120530-i0hsb

Biological Networks: Next Generation Annotation for the Human Genome
Talk at U Del
Subject: encode, networks, pgenes Date Given: 5/24/2012
Lecture ID: ENCODE_Nets_as_Nextgen_Annotation_v_Partially_Active_Pgenes--20120524-i0udcbcbrs

Biological Networks: Next Generation Annotation for the Human Genome 2 of 1.5
Talk at U of Toronto OICR
Subject: encode, networks, pgenes Date Given: 5/18/2012
Lecture ID: ENCODE_Nets_as_Nextgen_Annotation_v_Partially_Active_Pgenes--20120518-i0tor12-oicr

Architecture of the human regulatory network derived from ENCODE data
Talk at Biology of Genomes 2012
Subject: encode, networks Date Given: 5/10/2012
Lecture ID: Architecture_Hum_Reg_Net_from_ENCODE--20120510-i0bog12

Biological Networks: Next Generation Annotation for the Human Genome 1 of 1.5
Talk at U of Toronto CCBR
Subject: encode, networks, stat-models Date Given: 5/17/2012
Lecture ID: ENCODE_Nets_as_Nextgen_Annotation_v_HM_TF_Models_For_GeneExpr--20120517-i0tor12-ccbr

Biological Networks: Next Generation Annotation for the Human Genome
Talk at CMU CS
Subject: encode, networks, pgenes Date Given: 4/30/2012
Lecture ID: ENCODE_Nets_as_Nextgen_Annotation_v_Pgenes--20120430-i0cmu12

Biological Networks: Next Generation Annotation for the Human Genome
Talk at CBCB at U Maryland
Subject: encode, networks, pgenes Date Given: 4/20/2012
Lecture ID: ENCODE_Nets_as_Nextgen_Annotation_v_Pgenes--20120420-i0cbcb

Tools and Approaches for Integrating Multiple Genetic and Cellular Networks: Evolutionary Dynamics & Changes Across Different Environments
Talk at DOE GTL conference in Bethesda, MD. Fits into 24' (with 5' for Qs), omitting slides 4, 11, 12, 17, 21, 38, 41.
Subject: metagenomics, networks, rewiring Date Given: 2/27/2012
Lecture ID: Nets_Evo_Dynamics_and_Chg_across_Env--20120227-i0gtl2012

Annotating Non-coding Regions of the Genome: Approaches and Issues for Processing RNA-seq and ChIP-seq data
Talk at Berkeley Statistics & Genomics. Fits into 60' w. some Qs spilling over past the hour. Similar to i0george talk earlier but now with full description of RNA-seq tools and their relationship to privacy.
Subject: tools, rnaseq, privacy Date Given: 2/16/2012
Lecture ID: Annotating_Non_coding_Regions_Approaches_Issues_for_RNA_seq_and_ChIP_seq--20120216-i0sf12-ucb

Biological Networks: Next Generation Annotation for the Human Genome
Talk at Stanford, fits into 60' w. Qs. Pseudogenes as 1st gen. annotation and networks as 2nd gen. First mention of LOF. Brief mention of encodeprodpgenes & encodenets.
Subject: pseudogenes, networks Date Given: 2/13/2012
Lecture ID: BioNets_as_Nextgen_Genome_Annotation--20110213-i0sf12-su

Functional Genomics Data Integration : Should we store & share high or low level data ?
Talk at FGED '12 at Broad Inst. in Cambridge, MA. 20' talk fits apx. into allocated time.
Subject: privacy, rnaseq, alleleseq Date Given: 1/26/2012
Lecture ID: Should_we_store_hi_low_lev_data--20120126-i0fged

-- 2011 (21) --

Annotating Noncoding Regions of the Genome
Talk at Georgetown Bioinformatics & PIR, 45' 'till var. sect, then 70' tot. to finish
Subject: non-coding annotation, variation Date Given: 11/29/2011
Lecture ID: Noncoding_Annotation_w_Rel_to_Var--20111129-i0george

Analysis of Molecular Networks
Talk at Imperial College Systems Biology Symposium, Talk is 55' w. only a little of CRIT
Subject: networks Date Given: 11/16/2011
Lecture ID: Analysis-of-Networks--20111116-i0crg-i0icsysb

Annotating Non-coding Regions of the Genome
Talk at X CRG Annual Symposium "Computational Biology of Molecular Sequences," went through alleleseq sect. quickly
Subject: non-coding annotation, variation Date Given: 11/11/2011
Lecture ID: Noncoding-Annotation-and-Rel-to-Var-20111111-i0crg

Analysis of the full spectrum of genomic variations in relation to TFBSes and ncRNAs
Talk at Genome Informatics, CSHL, Fall 2011, 15' w. 5' of Qs
Subject: 1000g Date Given: 11/4/2011
Lecture ID: Spectrum-of-genomic-var-in-rel-to-TFBSes-n-ncRNAs--20111104-i0geninf

Integrated Technologies for Genome Characterization
Talk at annual CEGS meeting, which was in Boston in '11. Talk was 25' followed by Qs. POP stuff in Integ_Tech_for_Genome_Characterization--20111021-i0cegsbos-w-POP.ppt .
Subject: non-coding annotation, variation, pop Date Given: 10/21/2011
Lecture ID: Integ_Tech_for_Genome_Characterization--20111021-i0cegsbos

Tools for Genome Annotation
Talk at U of Florida at Gainsville, pre-talks for i0cegsbos, 1st mention of SRiC; 52' tot. (13' to end RD, 11' to end SRiC, 10' to end AlleleSeq, 8.5' to end pers. genomics, 9.5' to end ncVAR, left off RSeqTools). POP stuff in Tools_for_Genome_Annotation--20111018-i0uflg-w-POP.ppt .
Subject: non-coding annotation, variation Date Given: 10/18/2011
Lecture ID: Tools_for_Genome_Annotation--20111018-i0uflg

FIG subgroup
Brief talk at 1000 Genomes Fall 2011 meeting at ICHG in Montreal, Canada. Purpose of the talk was to introduce Functional Interpretation Group.
Subject: 1000g Date Given: 10/10/2011
Lecture ID: Montreal-FIG-premeeting--i01kgmont-20111010

Annotating Non-coding Regions of the Genome
CHI's Next-Generation Sequencing Data Management in Providence, RI. Fits into 30'.
Subject: non-coding annotation Date Given: 9/28/2011
Lecture ID: Noncoding-Annotation-i0ngdmri-20110928

Thoughts on Ripe Opportunities for Integrating Proteomics with Other Omics
Talk at NIH Workshop on the Human Proteome, Bethesda, MD. Fits into 20' slot with 5' of questions. (i0cfwhumprot)
Subject: proteomics Date Given: 9/26/2011
Lecture ID: Proteomics-Opportunities-20110926-i0cfwhumprot

Using Networks for Mining Biological Data
Talk at RPI-NSF Workshop on Multiscale Modeling of Complex Data, September 12-14, 2011. Data Science Research Center (DSRC) at RPI. Center for Biotechnology and Interdisciplinary Studies Auditorium. Networks talk now including dynasin + CRIT. Fits into allocated 50' slot. [[* i0rpi *]]
Subject: networks Date Given: 9/12/2011
Lecture ID: 20110912-i0RPI-Networks

Biological Network Analysis
Talk on podcast FIB83. Similar to KITP talk below.
Subject: networks Date Given: 7/8/2011
Lecture ID: FIB83-20110708-Nets

Tools for Relating Functional Annotation to 1000G Variants
Brief talk at 1000 Genomes Spring 2011 meeting at CSHL (Analysis group pre- and post-meeting get together) (i01kg11)
Subject: 1000g Date Given: 5/11/2011
Lecture ID: 1000g-may2011-prelim-MG-edit3

Next-Generation Sequence Data for Functional Genomics (RNA-seq & ChIP-seq)
Talk at NIH Workshop, "The Collection, Storage, Management, and Distribution of Next-Generation Sequence Data," May 4-5, 2011, Gaithersburg Marriott, MD.
Subject: data management Date Given: 5/4/2011
Lecture ID: Nextgen-Seq-DataMgt-Workshop-Func-Genomics-i0ngdwkp-20110504

ANNOTATING NON-CODING REGIONS OF THE GENOME
Talk at McGill Biology Dept., Montreal, Canada. Similar to USC talk earlier.
Subject: non-coding annotation Date Given: 6/14/2011
Lecture ID: Noncoding-Annotation-SVs-i0mcg-20110614

Interactome Networks Discussion
Discussion of Interactome Networks presented with M Vidal at mod/ENCODE annual meeting in Washington, DC.
Subject: networks, encode Date Given: 5/25/2011
Lecture ID: encode-mtg-interactome-discussion-i0menc11

Encode meeting report back
Report back with L Stein at mod/ENCODE annual meeting in Washington, DC. Breakout Session #2: Future of Functional Genomics; Group 2: Comparative Analysis & Data Integration.
Subject: encode Date Given: 5/25/2011
Lecture ID: encode-mtg-breakout2-group2-reportback

Relating the Full-spectrum of 1000 Genomes Variations to Diverse Genome Annotation
Informal Talk at Harvard (15'). First overview of ncVar.
Subject: non-coding variation Date Given: 3/31/2011
Lecture ID: ncvar-pgenes-i0bossvanal-20110331

Annotating Non-coding Regions of the Genome
Talk at Genome at 10 Conference, La Jolla, CA; 25' + Qs
Subject: non-coding annotation Date Given: 2/22/2011
Lecture ID: Noncoding-Annotation-i0jcvigenomeat10-20110222

Approaches to non-coding annotation
Talk at USC Computational Biology, LA, CA. Contains mod/ENCODE overview talk with a refined section on SVs (compared to 2.21 talk). 1 hr in total but not enough time for local reassembly sect.
Subject: non-coding annotation + svs Date Given: 2/25/2011
Lecture ID: Noncoding-Annotation-SVs-i0jcvigenomeat10-usc-20110225

Biological Network Analysis
Talk at Kavli Inst. Theoretical Physics (KITP), UCSB; 60' Networks talk, incl. net comparison across species for 1st time, but leaving out metagenomics sect. for lack of time.
Subject: networks Date Given: 2/24/2011
Lecture ID: Networks-201102240-i0at10+kitp

Approaches to non-coding annotation
Talk at Pfizer in La Jolla. Contains mod/ENCODE overview talk with a rough section on SVs. 1 hr in total but not enough time for Kim et al. SV/SD analysis.
Subject: non-coding annotation + svs Date Given: 2/21/2011
Lecture ID: Noncoding-Annotation-SVs-i0jcvigenomeat10-pfizer-20110221

-- 2010 (19) --

Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project
Overview of the final modENCODE worm integrative paper for ENCODE AWG call (25' apx.)
Subject: encode Date Given: 11/18/2010
Lecture ID: encodeawg-20101118-wormawg

Modencode Worm Integrative Analysi
Overview of worm modENCODE integrative paper at encode/modencode meeting in the spring of 2010 (to be contrast with final product, 20' apx.)
Subject: encode Date Given: 3/10/2010
Lecture ID: Worm-AWG-10Mar10-MG-talk

Tools for Genome Annotation
Chem. Engr., U Conn, Storrs, CT, 2010.10.05, 11:00-12:00; [i0uconnengr] (Long GenomeTechAnnote talk, focusing on tools. Now with RSEQTools & FusionSeq . Took ~55' with questions.)
Subject: genomeannotation Date Given: 10/5/2010
Lecture ID: i0uconnengr-20101005-GenomeTechAnnotate

Biological Network Analysis
Quantitative Biology: From Complex Networks to Simple Models in Montauk, NY, 2010.09.07 9:00-10:00 [i0montauk10] (med. length networks talk)
Subject: networks Date Given: 8/7/2010
Lecture ID: i0montauk10-20100907-Nets

Biological Network Analysis
International Conference On Bioinformatics and Computational Biology (ACM-BCB) in Niagara Falls, NY, 2010.08.03, 9:00-10:00; [I:ACMBIOINFO] (Medium-length networks talk, to take ~50 min.)
Subject: networks Date Given: 8/3/2010
Lecture ID: ACMBIOINFO-20100803-Nets

Biological Network Analysis
Computer Sci. Dept, Royal Holloway, University of London, London, 2010.07.02, 14:00-15:00; [I:ROYALH] (Medium-length networks talk, takes ~50 min.)
Subject: networks Date Given: 7/2/2010
Lecture ID: ROYALH-20100702-Nets

Scientific Publishing in the Future
PLOS Workshop at ISMB 2010: Where & How to Get Publishhere & How to Get Published, 2010.07.13, 10:45-12:45; [I:ISMB10] (5' total)
Subject: textmining Date Given: 7/13/2010
Lecture ID: ismb10-20100713-textmining

Relating Variation data to GENCODE
Short 10' talk about the impact of 1000G Variation Data on Gencode gene and pseudogene annotation. Given at Gencode annual meeting.
Subject: encode Date Given: 6/30/2010
Lecture ID: Gencode10-20100630-variation

Analysis of Pseudogenes and Segmental Duplications
Given at Gencode annual meeting.
Subject: pseudogenes Date Given: 6/30/2010
Lecture ID: gencode10-20100630-sdpgenes

Biological Network Analysis
Structural Bioinformatics session tomorrow at OCCBIO, Columbus, Ohio, 2010.06.16, 15:10-16:00; [i0OCCBIO] (Medium-length networks talk.) Talk fits within 45'.
Subject: networks Date Given: 6/16/2010
Lecture ID: i0occbio-20100616-Nets

Biological Network Analysis
New York Academy of Sciences, A Look at the Tools and Comparative Approaches of Systems Biology, 2010.06.10, 17:00-17:40; [I:NYSYSBIO] (Medium-length networks talk, derived from [I:BROWNMATH] with metagenomics updated.)
Subject: networks Date Given: 6/10/2010
Lecture ID: i0nysysbio-20100610-Nets

Human Genome Annotation
6th Intl. Symp. on Bioinformatics Research & Applications (ISBRA), U Conn, Storrs, CT, 2010.05.24, 9:00-10:00; [i0ISBRA] (Long GenomeTechAnnote talk, building on [I:IBM] . Should take 60' with questions. Talk takes 50'.)
Subject: genomeannotation Date Given: 5/24/2010
Lecture ID: i0ISBRA-20100524-GenomeTechAnnotate

Human Genome Annotation
Institute for Genomics & Systems Biology, U Chicago, Chicago, IL, 2010.05.18, 16:00-17:00; [I:CHICAGOIGSB] (Long GenomeTechAnnote talk, building on [I:IBM] and including for the first time breakseq* . Talk takes 65' without questions.)
Subject: genometechannote Date Given: 5/18/2010
Lecture ID: ChicagoIGSB-20100518-GenomeTechAnnotate

Biological Network Analysis
Institut de recherches cliniques de Montreal (IRCM), Montreal, Quebec; 2010.05.03, 11:30-12:30; [I:IRCM] (Long networks talk, derived from [I:BROWNMATH], including metamembrane* for 1st time. Takes 55' without callgraph sect.)
Subject: networks Date Given: 5/3/2010
Lecture ID: IRCM-20100503-Nets

Biological Network Analysis
Brown Applied Math, Providence, RI; 2010.04.09, 16:00-17:00; [I:BROWNMATH] (Long networks talk, derived from [I:MBINETS], including callgraph*, coregscaling*, reghier*, & motips* for 1st time. Whole talk took 2 hrs. with questions.)
Subject: networks Date Given: 4/9/2010
Lecture ID: BrownMath-20100409-Nets

Gencode Mar '10 Meeting: Pseudogene Project Update
2010.03.09, apx 19:00-17:10, Gencode meeting at ENCODE meeting [I:ENCODE10]. Takes 10' + and includes an adaption of unitary pseudogenes leading into polymorphic ones.
Subject: pseudogenes Date Given: 3/9/2010
Lecture ID: Gencode-20100309-Pseudogenes

Human Genome Annotation
Computational Biology Center, IBM T J Watson Research Center, Yorktown Heights, NY, 2010.02.11, 13:00-14:00; [I:IBM] (Long GenomeTechAnnote talk, building on [I:LMB] and including for the first time unitarypgenes* . Takes 60' without questions.)
Subject: genometechannote Date Given: 2/11/2010
Lecture ID: IBM-20100211-GenomeTechAnnotate

The BreakSeq Project
Computational Biology Center, IBM T J Watson Research Center, Yorktown Heights, NY, 2010.02.11, 11:00-12:00; [I:IBM] (Takes 25' with many questions questions.)
Subject: assembly Date Given: 2/11/2010
Lecture ID: IBM-20100211-Breakseq

Biological Network Analysis
CSHL, Cold Spring Harbor, NY; 2010.01.06, 12:00-13:00; [I:CSHL2] (Long networks talk, derived from [I:MBINETS], including rlm* & new intro. for 1st time)
Subject: networks Date Given: 1/6/2010
Lecture ID: CSHL2-20100106-Nets

-- 2009 (22) --

Human Genome Annotation
Structural Studies, LMB, Cambridge, UK, 2009.12.01, 10:15-11:15; [I:LMB] (Long GenomeTechAnnote talk, building on [I:UCSC] .)
Subject: genometechannote Date Given: 12/1/2009
Lecture ID: LMB-20091201-GenomeTechAnnotate

Understanding Protein Function on aGenome-scale through the Analysis of Molecular Networks
Functional Genomics & Systems Biology Workshop, Welcome Trust workshop, Cambridge, UK; 2009.11.30, 17:20-17:50; [I:WTSYSBIO] (Medium networks talk, shortened from [I:MBINETS].)
Subject: networks Date Given: 11/30/2009
Lecture ID: WTSYSBIO-20091130-Nets

Structured Digital Literature, a perspective on sharing code and data
Data and Code Sharing in Computational Science Meeting, Yale Law 2009.11.21, 9:30-9:40; [I:ISPSHARING](Fits into apx. 13 min. with ~10 min of discussion.)
Subject: textmining Date Given: 11/21/2009
Lecture ID: ispsharing-20091121-textmining

Detection and analysis of structural variants in personal genomes
Banbury meeting on Structural Variation in the Human Genome, Lloyd Harbor, NY 2009.11.17, 9:00-9:20; [I:BANBURYCNV] (Adaption of GenomeAssembly talk, building on [I:BIBM].)
Subject: genomeassembly Date Given: 11/17/2009
Lecture ID: BANBURYCNV-20091117-GenomeAssembly

Human Genome Annotation
IEEE International Conference on Bioinformatics & Biomedicine (BIBM-2009), 2009.11.02, 15:45-16:15; [I:BIBM] (Short adaption of GenomeTechAnnote talk, building on [I:UCSC] focusing just on SV reconstruction and analysis, includes updates msb* . Takes 29' with 2 questions, or ~24' of talk time with sdcnvcorr* sect.)
Subject: genomeassembly Date Given: 11/2/2009
Lecture ID: BIBM-20091102-GenomeAssembly

Understanding Protein Function on a Genome-scale through the Analysis of Molecular Networks
Network Biology: Understanding metabolic and protein interactions, VIB workshop on the future of proteome research, Ghent, Belgium; 2009.10.08, 9:30-10:10; [I:VIB] (Medium networks talk, shortened from [I:MBINETS].)
Subject: networks Date Given: 10/8/2009
Lecture ID: VIB-20091008-Nets

Human Genome Annotation
The ninth international conference for the Critical Assessment of Massive Data Analysis (CAMDA 2009), 2009.10.05, 10:00-10:50; [I:CAMDA] (Long GenomeTechAnnote talk, building on [I:UCSC] with some subtractions and a first time addition gapdh-pgenes* .)
Subject: genometechannote Date Given: 10/5/2009
Lecture ID: CAMDA-20091005-GenomeTechAnnotate

Large-scale Analysis of Molecular Networks
Laufer Center Inaugural Symposium, Stony Brook University, NY; 2009.09.25, 09:00-09:30; [I:STONEYBROOK] (Short networks talk. Fits into 25' with questions. Modifications of rescore* compared to previous networks talk.)
Subject: networks Date Given: 9/25/2009
Lecture ID: STONEYBROOK-20090925-Nets

Understanding Protein Function on a Genome-scale through the Analysis of Molecular Networks
Network Biology: Understanding metabolic and protein interactions, Mathematical Biosciences Institute, Columbus, OH; 2009.09.14, 13:30-14:30; [I:MBINETS] (Long networks talk, adding in for the first time: rescore*, mirnatargevolrate* & netdynamicsrev*. Fits easily into 55' w. 5' questions. PPT works on mac & PC and has many photos.)
Subject: networks Date Given: 9/14/2009
Lecture ID: MBINETS-20090914-Nets

Understanding Protein Function on a Genome-scale through the Analysis of Molecular Networks
Joint Statistical Meetings 2009, Washington, DC, 2009.08.02, 14:00-14:20; [I:JSM] (Very short networks talk, just with tse*, multilevel*, and metagenomics*. Justs fits into 19' w. 1 questions (with some skipping of slides). PPT works on mac & PC and has many photos.)
Subject: networks Date Given: 8/2/2009
Lecture ID: JSM-20090802-Nets

Understanding Protein Function on a Genome-scale through the Analysis of Molecular Networks
Summit on Systems Biology 2009, The Microbial World and Beyond, Richmond, VA, 2009.05.19, 13:00-14:00; [I:3RDSUMMIT] (Long networks talk, adding in for the first time: evolrate*. Fits easily into 50' w. 10' questions. PPT works on mac & PC and has many photos.)
Subject: networks Date Given: 6/19/2009
Lecture ID: 3RDSUMMIT-20090619-Nets

Exploratory analysis of the ENCODE TF binding data using biplot
15' talk on ENCODE AWG call describing bioplots.
Subject: encode Date Given: 6/4/2009
Lecture ID: AWG-20090604-ENCODE

Human Genome Annotation
UCSC, 2009.05.22, 12:00-13:00; [I:UCSC] (Long GenomeTechAnnote talk, incl. topics such as 'junk DNA', anonymity*, peakseq*, reseqsim*... Similar to [I:CSHL] but with a reworked reseqsim* and disc. of genome variation. Too long, fits into 60'. PPT works on mac & PC and has many photos w. EXIF tags Some detailed timings: 6' to get through intro.,13' to end of TF sect, 24' to end of cnv/sd, 28' to beg. of pgene sect., 41' to beg. of what is gene discussion, 43' to summary, 48' to end, & 50' done.
Subject: genometechannote Date Given: 5/22/2009
Lecture ID: UCSC-20090522-GenomeTechAnnotate

Understanding Protein Function on a Genome-scale through the Analysis of Molecular Networks
Talk at Stanford Research Institute (SRI) 2009.05.21, 15:30-16:30; [I:SRI] (Full networks talk, I:RECOMB09 with nethierarchy* and more metagenomics*. Fits with a rush into 60' w. 10' questions. (PPT works on mac & PC.)
Subject: networks Date Given: 5/21/2009
Lecture ID: SRI-20090521-Nets

Human Genome Annotation
Talk at Stanford Frontiers Symposium
Subject: genometechannote Date Given: 5/19/2009
Lecture ID: stanford-20090519-GenomeTechAnnotate

Understanding Protein Function on a Genome-scale through the Analysis of Molecular Networks
Ulam Lecture at Recomb 2009, 2009.05.18, 08:45-09:45; [I:RECOMB09] (Long networks talk, incl. the following topics: why networks w. amsci*, funnygene*, net. prediction intro, tse*, sandy*, metagenomics*, netpossel*, tyna* + topnet*, & pubnet* . Fits easily into 60' w. 10' questions. In particular, 5' to after GO DAG and then 11.5' to centraility discussion. PPT works on mac & PC and has many photos.)
Subject: networks Date Given: 5/18/2009
Lecture ID: RECOMB09-20090518-Nets

Human Genome Annotation
CSHL, 2009.04.29, 12:00-13:00; [I:CSHL] (Long GenomeTechAnnote talk, incl. the following topics: junk DNA, anonymity*, chip-seq-simu*, peakseq*, breakptr*, msb*, pemer*, reseqsim*,tredist*, sdcnvcorr* , cosbcnv*, pseudofam*, pseudopipe*, encodepgenes*, rp-pgenes*, sirnapgene*, encode-pilot*, pgene-classify*. Too long, fits into 70'. PPT works on mac & PC and has many photos w. EXIF tags .)
Subject: genometech, genomeannotation, pseudogenes, annotation Date Given: 4/29/2009
Lecture ID: CSHL-20090429-GenomeTechAnnotate

Understanding Protein Function on a Genome-scale through the Analysis of Molecular Networks
National Academy of Engineering, Meeting at Columbia U, 2009.04.14, 14:00-14:30; [I:NAECU] (Short networks talk, incl. the following topics: why networks w. amsci*, funnygene*, bottleneck*, nethierarchy*, metagenomics*, tyna* + topnet*, & pubnet* . Fits into 30' w. 5' questions. PPT works on mac & PC and has many photos w. EXIF tag kwtimewemet .)
Subject: networks Date Given: 4/14/2009
Lecture ID: NAECU-20090414-Nets

Human Genome Annotation
Sarkar Lecture at Sick Kids Hosp., U Toronto , 2009.03.16, 13:15-14:15; [I:SARKAR] (Long GenomeTechAnnote talk, incl. the following topics: 'junk DNA', anonymity*, pgenes-rev*, whatisgene*, chip-seq-simu*, peakseq*, msb*, pemer*, tredist*, sdcnvcorr* , cosbcnv*, pseudofam*, pseudopipe*, encodepgenes*, rp-pgenes*, sirnapgene*, encode-pilot*, pgene-classify*, & pubnet* . Too long, fits into 60' w. skipping most of pgene sect. PPT works on mac & PC and has many photos w. EXIF tags .)
Subject: genometechannote, genomics, intergenic, pseudogenes Date Given: 3/16/2009
Lecture ID: Sarkar-20090316-GenomeTechAnnotate

What is a gene? Insights gleaned from annotating the human genome
Rhode Island College, Young Lecture at Biology Dept. , 2009.02.25, 19:00-20:00; [I:RIC] (Long talk based on GenomeTechAnnotate Flow, incl. the following topics: 'junk DNA' w. whatisgene*, amsci*, peakseq*, tredist*, rnaseq*, hoxa*, dart*, encodepgenes*, rp-pgenes*, encode-pilot*, pseudofam*, pseudopipe*, sirnapgene*, pgene-classify*, & pubnet* ... Lots of additional background material. Too long, fits into 60' w. skipping most of pgene sect. PPT works on mac & PC and has many photos w. EXIF tags .)
Subject: whatisgene Date Given: 2/25/2009
Lecture ID: RIC-20090225-GenomeTechAnnotate-Whatisgene

Understanding Protein Function on a Genome-scale through the Analysis of Molecular Networks
Cornell Medical School, Physiology, Biophysics and Systems Biology (PBSB) graduate program, 2009.01.26, 16:00-17:00; [I:CORNELL-PBSB] (Long networks talk, incl. the following topics: why networks w. amsci*, funnygene*, net. prediction intro, memint*, tse*, essen*, sandy*, metagenomics*, netpossel*, tyna*+ topnet*, & pubnet* . Fits easily into 60' w. 10' questions. PPT works on mac & PC and has many photos w. EXIF tag kwcornellpbsb .)
Subject: networks Date Given: 1/26/2009
Lecture ID: Cornell-PBSB-20090126-Nets

Yale Pseudogene Analysis as part of GENCODE Project
Sanger Center 2009.01.20, 11:20-11:40
Subject: pseudogenes Date Given: 1/21/2009
Lecture ID: Gencode-winter08-20090121-pseudogenes

-- 2008 (18) --

Understanding Protein Function on a Genome-scale through the Analysis of Molecular Networks
University of Chicago, Inst. of Biophysical Dynamics, 2008.12.02, 12:00-13:00; [I:CHICAGOBIOPHYS](Long networks talk, incl. the following topics: why networks w. amsci*, funnygene*, net. prediction intro, memint*, tse*, essen*, sandy*, metagenomics*, netpossel*, tyna*+ topnet*, & pubnet* . Fits easily into 60' w. 10' questions. PPT works on mac & pc. and has many photos w. EXIF tag kwchicagobiophys .)
Subject: networks Date Given: 12/2/2008
Lecture ID: ChicagoBiophys-20081202-Nets

Annotating Non-coding Regions of the Human Genome
Robert Cedergren Bioinformatics Colloquium Montreal, Canada 2008.11.03, 16:30-17:30; Genome tech and Genome annotation talk, including: mismatch, uniarray, DART, pgenes-general, pseudofam, encode-pgenes, sdcnvcorr, gen-encode, sirna-pgene, what-is-gene [I:CEDERGREN]. Fits into ~50' .
Subject:   Date Given: 11/3/2008
Lecture ID: Cedergren-20081103-GenomeTechAnnotate

Annotating Non-coding Regions of the Human Genome
RECOMB Satellite Meeting on Regulatory Genomics Cambridge, MA ; 2008.10.31, 18:45-19:15M Genome tech and Genome annotation talk, including: Seq. Sim + PeakSeq ; MSB; DART TAR classification ; TRE clustering + biplot, BoCaTFBS, sdcnvcorr [I:RECOMBSAT] . Fits into time
Subject:   Date Given: 10/31/2008
Lecture ID: RECOMBSAT-20081031-GenomeTechAnnotate

Using Networks to Integrate Omic and Semantic Data: Towards Understanding Protein Function on a Genome Scale
Biomarker Data Analysis 2008.10.01, 9:25-9:50 (Very Short Nets talk: predess + SANDY [I:IBIOMARKER])
Subject: networks Date Given: 10/1/2008
Lecture ID: BioMarker-20081001-Nets

CEGS informatics presentation for SAB
Presentation for CEGS SAB, focusing on informatics for arrays and for calling and analyzing genome structural variation (15' + 20')
Subject: Date Given: 9/18/2008
Lecture ID: cegs-SAB-20080918

Annotating Non-coding Regions of the Human Genome
Genome tech and Genome annotation talk, including: Non-specific, Cross-hyb. Corrections + Seq. Sim, MM.; DART TAR classification ; bkptr, pemmer, sdcnvcorr, pseudogene annotation and integration with SDs, transcription and siRNA; and part of "what is a gene" summary. [I:BMS]
Subject: genometech, genomeannotation, svs, pseudogenes Date Given: 9/15/2008
Lecture ID: BMS-20080915-GenomeTechAnnotate

Text Mining to Study the Structure of Science
Special Session on the Future of Scientific Publishing; ISMB'08, Toronto; 2008.07.23 10:45-11:15; Textmining talk, fits into ~25' but without discussing last two impediments. Not "full" version is missing graphic from A Rzhetsky. Some images have Picassa tag "kwismb08ppt".
Subject: textmining Date Given: 7/23/2008
Lecture ID: ismb08pub-20080723-textmining

Annotation Non-coding Regions of the Human Genome in the ENCODE Pilot
Genome-scale Pattern Analysis in the Post-ENCODE Era Special Interest Group (SIG) at ISMB 2008, Toronto 2008.07.21, 14:20-14:45 [I:ISMB08-SIG]
Subject: genometechannotate Date Given: 7/21/2008
Lecture ID: ISMB08-SIG-20080721-GenomeTechAnnotate

Understanding Protein Function on a Genome-scale using Networks and Relating this to Disease
Special Session 3, Interaction Networks and disease, ISMB, Toronto (Short Nets talk, 2008.07.21, 10:45-11:05: Netpossel,CD4, SIN,disorder, tools. Fits into ~20' w. rushing through SIN. I:ISMB08-SS)
Subject: networks Date Given: 7/21/2008
Lecture ID: ISMB08-SS-20080721-Nets

Studying Protein Motions in a Database Framework
ISMB ISCB Student Council Symposium ISMB, Toronto, Canada 2008.07.18, 13:30-14:15 (motions talk with ex motions, HingeAtlas, NMA, HingeMaster, filled 45' with last minute additions)
Subject: motions Date Given: 7/18/2008
Lecture ID: ISCB-SC-20080718-motions

Thoughts on Integrative Genome Analysis -- as Stimulus for a Discussion towards Consortium Publication(s)
modENCODE Consortium meeting, Rockville, MD ; 2008.06.17, 9:15-10:30 (10' near beginning of session) (Quick overview of the ENCODE pilot results, focusing on G&T results, pgenes + DART. [I:ENCODE], fit into time )
Subject: encode Date Given: 6/17/2008
Lecture ID: modENCODE-awg-talk-20080617

Quo Vadis Structural Biology: Networks, Variation, Flexibility (Motions Part)
Quo Vadis, Boston, MA , 2008.05.05, 19:00-20:00 (Compact vers. of Networks Talk then Compact Motions Talk: Nets-Intro (w.o. names) + SIN + Disorder + Netpossel + CD4 + Net-Tools (tyna+coev) + Brief MolMovDB + HingeAtlas + FlexOracle + HingeMaster ; To get movies to work put contents of zipfile below into same directory as this ppt: http://lectures.gersteinlab.org/ppt/pfizer-motions-20061201/movies-put-in-same-dir-as-ppt.pfizer-motions-20061201.zip ; Everything fits within 50 min)
Subject: networks, motions Date Given: 5/5/2008
Lecture ID: Harvard-CMCD-20080505-motions

Quo Vadis Structural Biology: Networks, Variation, Flexibility (Networks Part)
Quo Vadis, Boston, MA , 2008.05.05, 19:00-20:00 (Compact vers. of Networks Talk then Compact Motions Talk: Nets-Intro (w.o. names) + SIN + Disorder + Netpossel + CD4 + Net-Tools (tyna+coev) + Brief MolMovDB + HingeAtlas + FlexOracle + HingeMaster ; To get movies to work put contents of zipfile below into same directory as this ppt: http://lectures.gersteinlab.org/ppt/pfizer-motions-20061201/movies-put-in-same-dir-as-ppt.pfizer-motions-20061201.zip ; Everything fits within 50 min)
Subject: motions, nets Date Given: 5/5/2008
Lecture ID: Harvard-CMCD-20080505-Nets

Annotation of "Most" of the Human Genome: Focusing on the 99% in Non-coding Regions
Center for Computational Biology & Bioinformatics, Indiana University School of Medicine, Indianapolis, IN ; 2008.04.28, 12:00-13:00 ;Genome tech and Genome annotation talk, including: HMM segmentation; Non-specific, Cross-hyb. Corrections, Seq. Sim.; DART TAR and TRE classification (w. deserts + biplot); pseudogene annotation (w. NRs) and integration with SDs, transcription and binding sites; and part of "what is a gene" summary. Fits into 60 min. w. fast presentation of pseudogenes, skipping part of what is a gene and pseudogene relationships to SDs. [TRIP:IUPUI]
Subject: genometech, genomeannotation, pseudogenes Date Given: 4/28/2008
Lecture ID: IUPUI-20080428-GenomeTechAnnotate

~25' Overview of the GersteinLab in 2008
CS Visiting Students Day, 2008.03.26 15:00-15:30
Subject: overview Date Given: 3/26/2008
Lecture ID: Overview-25min-of-GersteinLab-20080326

Annotation of "Most" of the Human Genome: Focusing on the 99% in Non-coding Regions
Joint CMU-Pitt Ph.D. Program in Computational Biology, Pittsburgh, PA ; Genome tech and Genome annotation talk, including: HMM segmentation; Cross-hyb. Corrections; DART TAR and TRE classification (w. deserts + biplot); pseudogene annotation (w. NRs) and integration with SDs, transcription and binding sites; and "what is a gene" summary. Fits into 60 min. w. fast presentation of pseudogenes and no NRs.
Subject: genometechannotate Date Given: 3/21/2008
Lecture ID: CMU-20080321-GenomeTechAnnotate

A Vision for Using All the Data and Publications from Science on Web: Mining this to Study the Structure of Science
NSF Workshop on Knowledge Management and Visualization Tools ; 2008.03.11, 09:30-10:00 (Textmining talk, fits into ~30' w. interrupting questions)
Subject: textmining Date Given: 3/11/2008
Lecture ID: NSF-cdiwkshp1-20080311-textmine

Understanding Protein Function on a Genome-scale using Networks
Penn Center for Bioinformatics; 2008.02.22, 6:00-17:00 (Normal vers. of Networks Talk: Funnygene+EdgeOnto+SIN+Bottlnecks+RegHierarchy+NetPosSel, fits within 50 min)
Subject: networks Date Given: 2/22/2008
Lecture ID: UPenn-20080222-Nets

-- 2007 (19) --

Relating Protein Abundance & mRNA Expression
Yale (Comp. Bio. & Bioinformatics) NIDA site visit at Yale
Subject: protvsmrna Date Given: 12/19/2007
Lecture ID: NIDA-svisit-20071219-PARE

Annotation of the Human Genome: Focusing on Intergenic Regions and Non-coding RNAs
AACR conference on The Role of Non-Coding RNAs in Cancer, Boston, MA 2007.11.02, 11:15-11:45 (Genome annotation talk with core pseudogene analysis + NR close-up. Then inter-relating pseudogenes with tiling-derived transcription. Everything fits into ~25 min, with a bit of a rush through TAR sect.)
Subject: genomeannotation, pseudogenes Date Given: 11/2/2007
Lecture ID: AACR-20071102-GenomeAnnotation

Computational Proteomics: Studying Protein Motions from a Database Perspective
65th Pittsburgh Diffraction Conference, Buffalo, NY 2007.10.26, 11:00 - 11:45 (Std. Motions Talk with FlexOracle, HingeAtlas, Helix, NMA; Fits into allocated time. To get movies to work put contents of zipfile below into same directory as this ppt: http://lectures.gersteinlab.org/ppt/pfizer-motions-20061201/movies-put-in-same-dir-as-ppt.pfizer-motions-20061201.zip)
Subject: motions Date Given: 10/26/2007
Lecture ID: PittDiffSoc-20071026-motions

Yale CEGS: Integrated Technologies for Analyzing the Human Genome
NHGRI CEGS meeting 2007.10.10, 11:30-11:55 (Summary of Yale CEGS center at NHGRI CEGS mtg. Focuses on Breakpt, uniarray, & PEM. Everything fits into ~25 min.)
Subject: Date Given: 10/10/2007
Lecture ID: Yale-cegs-overview-20071010

Understanding Protein Function on a Genome-scale using Networks
MSCBB - Chicago 2007.10.06, 15:50-16:35 (Compact vers. of Networks Talk: EdgeOnto+SIN+Bottlnecks+RegHierarchy, fits with rush into allocated time)
Subject: networks Date Given: 10/6/2007
Lecture ID: MSCBB-20071006-Nets

Annotation of Intergenic Regions of the Human Genome
UPenn, Biochem. & Biophys. 2007.09.27, 12:00-13:00 (Genome annotation talk with core pseudogene analysis and then inter-relating pseudogenes with tiling-derived transcription and CNVs. In detail presentation of tiling technology with BreakPtr & Universal Array. Everything fits into ~50 min.)
Subject: genomeannotation Date Given: 9/27/2007
Lecture ID: UPenn-20070927-GenomeAnnotation-w-Bkptr-UniArray

Ten Minute Overview of the Lab
Ten minute overview of the lab presented at the annual CBB retreat
Subject: overview Date Given: 9/7/2007
Lecture ID: TenMinute-LabOverview-20070907

Proteomics: Networks and Motions
D E Shaw Research 2007.08.10, 11:30-12:30. Two ppt in total with movies, make sure movies are put into same directory as ppts. See files in "extra" directory. Networks Part: Compact vers. of Networks Talk -- SIN+Bottlnecks+RegHierarchy, fit with rush into allocated time. Motions Part: Compact vers. of Motions Talk -- volumes+helix but no NMA, only a little HAG.
Subject: networks, motions Date Given: 8/10/2007
Lecture ID: DESRES-20070810-Nets-Motions

Understanding Protein Function on a Genome-scale using Networks
Engineering Cell Biology - The Cell in Context, MIT 2007.08.06, 5:05-15:40 (Compact vers. of Networks Talk: EdgeOnto+SIN+Bottlnecks+RegHierarchy, fit with rush into allocated time)
Subject: networks Date Given: 8/6/2007
Lecture ID: ECB2007-MIT-20070806-Nets

Annotation of Intergenic Regions of the Human Genome, Focusing on Protein Fossils
Protein Society, Boston, MA 2007.07.24, 8:05-8:45 (Genome Annotation Talk with core pseudogenes, DART, binding sites, and pgene-transcription, No Tilescope. Everything except DART and binding sites fit into 37 minutes.)
Subject: pseudogenes, genomeannotation Date Given: 7/24/2007
Lecture ID: ProtSoc-20070724-GenomeAnnotation

Understanding Protein Function on a Genome-scale using Networks
EBI, Cambridge, UK, 2007.07.09, 13:30-14:30(Extended vers. of Networks Talk: EdgeOnto+SIN+Bottlnecks+RegHierarchy+NetPosSel+Motifs+tYNA+RNAi)
Subject: networks Date Given: 7/9/2007
Lecture ID: EBI-20070709-Nets

Annotation of Intergenic Regions of the Human Genome, Focusing on Protein Fossils
Proteins, Genomes, and Evolution, Cambridge, UK 2007.07.07, 11:00-11:30 (Genome Annotation Talk with core pseudogenes, DART, binding sites, and pgene-transcription, No Tilescope. All completed comfortably within time.)
Subject: genomeannotation Date Given: 7/7/2007
Lecture ID: MRC-CAM-20070707-GenomeAnnotation

Annotation of Intergenic Regions of the Human Genome, Focusing on Protein Fossils
CPI 2007, Ottawa, Canada; 2007.06.18, 11:15-12:00 (Genome Annotation Talk with core pseudogenes, DART, binding sites, and pgene-transcription, No Tilescope. All completed comfortably within time at 44' exact.)
Subject: pseudogenes, genomeannotation Date Given: 6/18/2007
Lecture ID: cpi07-20070618-GenomeAnnotation

Annotation of Intergenic Regions of the Human Genome
Cistrome 2007, Boston, MA ; 2007.04.30, 15:20-15:55 (Genome Annotation Talk without much pgenes, including Tilescope, HMMs, DART, binding sites, and pgene-transcription, All completed comfortably within time.)
Subject: genomeannotation Date Given: 5/31/2007
Lecture ID: Cistrome07-20070531-GenomeAnnotation

Understanding Protein Function on a Genome-scale using Networks
NetSci 2007, NYC; 2007.05.25, 09:25-10:00 (Compact vers. of Networks Talk: SIN+Bottlnecks+RegHierarchy+RNAi)
Subject: networks Date Given: 5/24/2007
Lecture ID: NetSci2007-20070524-Nets

Gerstein Lab Aims in ModENCODE
Snippet for presentation at CSHL modENCODE meeting describing GersteinLab aims in Transcript Grant
Subject: other Date Given: 5/8/2007
Lecture ID: modencode-gt-snippet-for-cshl-mtg

Understanding Protein Function on a Genome-scale using Networks
Brown Comp. Bio; 2007.05.02, 16:00-17:00 (Very full version of Nets talk, incl. bottlenecks and funcsim. Overall, ~60' leaving out motifs (Yu et al., GenomeBiology) + most dynamics (Luscombe et al.))
Subject: networks Date Given: 5/2/2007
Lecture ID: Brown-CompBio-20070502-Nets

Annotation of Intergenic Regions of the Human Genome
McGill University, Comp. Bio. 2007.04.30, 12:00-13:30 (Full but raw version of genome annotation talk, incl. updates pgenes with ENCODE & tilescope. Uploaded version incl. ink annotation.)
Subject: pseudogenes, genomeannotation Date Given: 4/30/2007
Lecture ID: McGill-CompBio-20070430-Genome-Annotation

Understanding Protein Function on a Genome-scale using Networks
Networks talk now including Bottlenecks and Functional Similarity Metric
Subject: networks Date Given: 2/15/2007
Lecture ID: mskcc-20070215

-- 2006 (13) --

Understanding Protein Function on a Genome-scale using Networks
Recomb 2006 Satellite Conferences on: Systems Biology & Computational Proteomics 2006.12.02, 09:15-10:00
Subject:   Date Given: 12/2/2006
Lecture ID: recomb06-20061202

Computational Proteomics: Studying Protein Motions from a Database Perspective
Pfizer Research, La Jolla; 2006.12.01, 14:30 - 15:30
Subject: motions Date Given: 12/1/2006
Lecture ID: pfizer-motions-20061201

Understanding Protein Function on a Genome-scale using Networks
3-D Structural Analysis of Protein Interaction Networks Gives New Insight Into Protein Function, Network Topology and Evolution + Genomic analysis of the hierarchical structure of regulatory networks
Subject: networks Date Given: 11/16/2006
Lecture ID: orfeome06-20061116

Computational Proteomics: Networks and Structures
 
Subject: motions Date Given: 10/23/2006
Lecture ID: Ottawa-motions-20061023

Computational Proteomics: Networks and Structures
Just networks part of talk
Subject: networks Date Given: 9/18/2006
Lecture ID: nyu-networks-20060918

Understanding Biological Function through Evaluation of Genome-scale Networks
 
Subject: networks Date Given: 9/8/2006
Lecture ID: DREAM-conf-Wavehill-20060908

Structured Abstracts of Yeast Literature: A Proposal to Stimulate Discussion
Mark B Gerstein Michael Seringhaus Dov Greenbaum Yale Yeast Meeting 2006 2006.07.29, 8' in 16:30-18:30
Subject: other, epublishing Date Given: 7/29/2006
Lecture ID: Yeast-Meet-20060729

Pseudogenes in the ENCODE Regions: Consensus Annotation, Analysis of Transcription and Evolution
Deyou Zheng, Adam Frankish, Robert Baertsch, Philipp Kapranov, Alexandre Reymond, Siew Woh Choo, Yontao Lu, France Denoeud, Stylianos Antonarakis, Michael Snyder, Yijun Ruan, Chia-Lin Wei, Thomas Gingeras, Roderic Guigo, Jennifer Harrow, Mark Gerstein Yale, Sanger, UCSC, GIS, AFFX, U Geneva, IMIM a GT effort with great thanks to MSA, VAR , TR Talk at ENCODE 2006,07.05 12' in 20:30-21:30
Subject: pseudogenes Date Given: 7/5/2006
Lecture ID: encode-pgenes-20060705-old

Pseudogenes in the ENCODE Regions: Consensus Annotation, Analysis of Transcription and Evolution
Deyou Zheng, Adam Frankish, Robert Baertsch, Philipp Kapranov, Alexandre Reymond, Siew Woh Choo, Yontao Lu, France Denoeud, Stylianos Antonarakis, Michael Snyder, Yijun Ruan, Chia-Lin Wei, Thomas Gingeras, Roderic Guigo, Jennifer Harrow, Mark Gerstein Yale, Sanger, UCSC, GIS, AFFX, U Geneva, IMIM a GT effort with great thanks to MSA, VAR , TR Talk at ENCODE 2006,07.05 12' in 20:30-21:30
Subject: pseudogenes Date Given: 7/5/2006
Lecture ID: encode-pgenes-20060705

Using Molecular Networks to Understand Protein Function on a Genome Scale
Mark B Gerstein Yale (Comp. Bio. & Bioinformatics) DIMACS Workshop on Sequence, Structure and Systems Approaches to Predict Protein Function
Subject:   Date Given: 5/5/2006
Lecture ID: dimacs-prot-func-20060505

Access to Scientific Knowledge (A2sciK) - Practical Issues Relating to it for Scientists
Mark B Gerstein Yale (CBB, MBB, CS) A2K at Yale Law 2006.04.22, 15' in 11:15-13:00
Subject: other Date Given: 4/22/2006
Lecture ID: A2K-at-Yale-20060422

Can we find reasonable metrics to evaluate the reconstructed networks of in-silico generated data of known topology?
Mark B Gerstein Yale U Talk at DREAM workshop 2006,03.10 -- 16:15-16:40
Subject: networks Date Given: 3/10/2006
Lecture ID: Dream-wkshp-20060310

Annotation of Intergenic Regions of the Human Genome, focusing on Pseudogenes
Mark B Gerstein Yale U Talk at NYAS 2006,01.26 18:20 - 19:00
Subject: pseudogenes Date Given: 1/26/2006
Lecture ID: nyas-20060126

-- 2005 (2) --

Annotation of Intergenic Regions of the Human Genome, focusing on Pseudogenes
Mark B Gerstein Yale U Talk at Princeton CS
Subject: pseudogenes Date Given: 9/28/2005
Lecture ID: princeton-cs-20050928

Putting It All Together: Integrating the Data (using molecular networks)
Mark B Gerstein Yale U Talk at AAAS 2005.02.18
Subject:   Date Given: 2/19/2005
Lecture ID: aaas-20050219

-- 2004 (1) --

Towards Protein Function: Relating mRNA Expression, Protein Abundance, and Protein-protein Interactions
Talk at Experimental Biology 2004
Subject: pare Date Given: 4/17/2004
Lecture ID: dc-expbio-20040417