60' talk at a Symposium on “Smart Solutions: AI Methods in Pharmacology” at Northwestern University. (Took 53' with rest of time for Qs.). (MPEG at 'extra link,' zoom video link, slide pics link.)
50' talk (+10' Qs) for Virtual Symposium on Personalized Medicine and Omics at Tel Aviv University. (Talk video and slide images available in 'extra' directory.)
30' talk in Yale Cancer Center's Grand Rounds Presentation. New slides on Tumor Evolution, Network Rewiring & Passenger Mutations. (Took 29' after shortening.)
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
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
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.
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.)
My short talk at the recent NHGRI genome-sequencing meeting. Discussion provoking thoughts on WGS & noncoding analysis for the exome-oriented CMG group
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.
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.]
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.)
30' talk (w/ Qs) for 2nd Annual Next Generation Sequencing USA Congress
in Boston. Talk now includes motifvar (intensification) & combines that with Stress & Frustration.
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.
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.
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.
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.
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.
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.
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.
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
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.
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).
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.
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.
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.
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.)
Part of PCAWG drivers group (2,5,9,14) presented at Boston meeting (at Broad Inst.). Longer presentation in a gpresentation (contains acknowledgements)
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.
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.)
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.
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).
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.
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'.
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
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).
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
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.
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.
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.
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.
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.
Short 8' summary of comparative transcriptome work at ENCODE consortium meeting. Also, 2nd "shadow" talk giving an overview of the DAC at this meeting.
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
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
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.
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.)
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.
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.
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).
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
Talk at HIT symposium at Johns Hopkins; 38' talk with 4' Qs; More depth on pgenes (*encodeprodpgenes) than previously with an abbreviated models discussion
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
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
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
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
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.
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
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
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 .
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 *]]
Talk at NIH Workshop, "The Collection, Storage, Management, and Distribution
of Next-Generation Sequence Data," May 4-5, 2011, Gaithersburg Marriott, MD.
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.
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
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.
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
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.)
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.)
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.)
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'.)
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.)
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.)
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.)
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.
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.)
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.)
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)
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.)
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].)
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.)
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].)
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* .)
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.)
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.)
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.)
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.
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.)
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.)
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
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 .)
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 .)
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 .)
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 .)
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 .)
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]
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".
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)
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)
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 )
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)
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)
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]
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.
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)
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.)
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)
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.)
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.)
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.
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)
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
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.)
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
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.)
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.))
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
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
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
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
