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(→‎2024: Added presentation on UShER/hgPhyloPlace updates for H5N1 cattle outbreak, in Theiagen/CDPH weekly genomic epi meeting July 1)
 
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An archive of presentations by staff and researchers of the UCSC Genome Browser group and the Center for Biomolecular Science and Engineering (CBSE).  Please keep the list in order by date, newest ones at the top.
An archive of presentations by staff and researchers of the UCSC Genome Browser group and the Center for Biomolecular Science and Engineering (CBSE).  Please keep the list in order by date, newest ones at the top.
Please note there is a UCSC Genome Browser shared drive which has more files available at:
https://drive.google.com/drive/folders/0AD5CiKJJXgKhUk9PVA
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==2024==
* 1 July 2024 Angie Hinrichs - COVIDNet Dashboard Office Hours (CDPH) - UShER for H5N1 [https://docs.google.com/presentation/d/1PXRAa--4hPckqDGe97H2lYutgx4xd7kunYf5kK6r4G4/edit?usp=sharing Slides]
* 7 May 2024 Jairo Navarro - [https://meetings.cshl.edu/meetings.aspx?meet=GENOME&year=24 Biology of Genomes 2024] - Viewing Human Pangenome Research Consortium (HPRC) data on the UCSC Genome Browser [[Image:CSHL_BoG_2024.pptx]]
* 9 April 2024 Angie Hinrichs - [https://www.bv-brc.org/docs/news/2024/2024-04-08-bv-brc-workshop-subspecies.html BV-BRC Viral Sub-species Classification Workshop] - UShER and autolin: Identifying viral lineages [https://docs.google.com/presentation/d/1zLhh2txCBE3PVIv4J29w3fPf6TdvnXAo9r0IzEsd0Yo/edit?usp=sharing Slides]
* 18 January 2024 Hiram Clawson - BME 110 - Computational Biology Tools [[Image:BME-110.2024-01-18.pptx]]
* 13 January 2024 Jairo Navarro - PAG 31 - 31st annual Plant and Animal Genomes, San Diego - Visualizing your data on the UCSC Genome Browser [[Image:PAG31-2024.pptx]]
* 13 January 2024 Hiram Clawson - PAG 31 - 31st annual Plant and Animal Genomes, San Diego - GenArk assembly resources [[Image:Sat_Workshop2024.pptx]]
==2023==
* 06-09 December 2023 Hiram Clawson - Cold Spring Harbor Genome Informatics Meeting poster GenArk assembly resources [[Image:CSHL_GenomeInformatics_2023.pptx]]
* 08 November 2023 Hiram Clawson - BME-18 - Scientific Principals of Life - genome browser introduction [[Image:BME-18.2023-11-08.pptx]]
* 3 May 2023 Angie Hinrichs - ABPHM23 - Applied Bioinformatics and Public Health Microbiology, Hinxton, UK - UShER: pandemic-scale phylogenetics for SARS-CoV-2 and beyond [https://docs.google.com/presentation/d/1L2yJK3_MGyMYCGfciznBnKL_qV1lZ5zMeTrs11V4pkM/ Google Slides]
* 15 January 2023 Hiram Clawson - PAG-30 - 30th annual Plant and Animal Genomes, San Diego - Educational resources in the UCSC genome browser [[Image:PAG30_2023-01-15.pptx]]
* 14 January 2023 Hiram Clawson - PAG-30 - 30th annual Plant and Animal Genomes, San Diego - Introduction to the genome browser, GenArk hubs, creating an assembly hub and REST API interface [[Image:PAG30_2023-01-14.pptx]]
==2022==
* 04 November 2022 Hiram Clawson - BME-18 Scientific Principals of life ([[Image:BME-18.2022-11-04.pptx|pptx]])
* 25 May 2022 Angie Hinrichs, Pango lineages: a brief intro [[https://docs.google.com/presentation/d/1bIRCD5hslZokLeypZr1gfssefhpCh7CTeWWlU7fzWCk/edit?usp=sharing slides]] (in [[https://www.cdc.gov/coronavirus/2019-ncov/variants/spheres.html SPHERES]] meeting)
* 12 April 2022 Angie Hinrichs, pangolin v4.0 [[https://docs.google.com/presentation/d/1MiEWBbimkP8q9LFWhrIBnXjtH9LP60xl_I-QhiLKIS4/edit?usp=sharing slides]] (in Theiagen's "Office Hours" for public health bioinformaticians)
* 3 February 2022 Angie Hinrichs Pango lineages [[https://docs.google.com/presentation/d/1jdl-QWH-sRsX3jIN1DL2D808TibBSy95_TX35iR8aTk/edit?usp=sharing slides]] (in [[https://www.cdph.ca.gov/ CDPH]] Whole Genome Sequencing meeting)
==2021==
* 19 November 2021 Angie Hinrichs, pangolin --usher [[https://docs.google.com/presentation/d/1etFOE3cLOsPfWA7sOFDg3rxCTaPlBkpTEf5y9RYWRLg/edit?usp=sharing slides]]  [[https://staphb.org/assets/video_assets/2021-11-19-UShER-hinrichs-su-wang.pdf PDF including the next presentation, an eval on NYC data]]  [[https://www.youtube.com/watch?v=KNrQvvRtE7o&authuser=0 video]] (in [https://staphb.org/ StaPH-B (State Public Health Bioinformatics)] call
* 14 October 2021 Angie Hinrichs, UShER for Genomic Epi [[https://docs.google.com/presentation/d/1yT-rQTZklSQYVhi-EJOP02IrBMHH4JMIlKHKKQi8B-g/edit?usp=sharing slides]] (in [https://pha4ge.org/bioinformatics-pipelines-and-visualization/ PHA4GE Pipelines and Visualization working group] meeting)
* 1 June 2021 Angie Hinrichs, Pangolin v3.0: an UShER perspective [[https://docs.google.com/presentation/d/13GpVQpmvJectp1aNSZl_5OfYd4D998F0bsf41MRbw4c/edit?usp=sharing slides]] (in Theiagen's "Office Hours" for public health bioinformaticians)
* 21 May 2021 Hiram Clawson, VGP assembly resources in the UCSC Genome Browser [[:File:VGP_2021-05-21.pptx|PPTX]]
* 12 February 2021 Angie Hinrichs, Demo: NCBI Virus, UShER Web Interface, Nextstrain, UCSC SARS-CoV-2 Genome Browser (in Russ Corbett-Detig's class "Logic and Approaches to Scientific Discovery")
* 3 November 2021 Jairo Navarro, Cold Spring Harbor Laboratory: Genome Informatics (virtual), ''UCSC Genome Browser in a Cloud (GBiC)''. [[:File:CSHL_2021.pdf|PDF]]
==2020==
* 23 November 2020 Angie Hinrichs, Big trees of tiny genomes [https://docs.google.com/presentation/d/1REWyqHfdrgpaP5WGPQwcKSeN3FVUhlOCz1hilNSkz60/edit?usp=sharing Slides]
* 4 November 2020 Jorge Garcia,  THE GENOME BROWSER – UNDER THE HOOD  [[:File:browsermap2020.pdf|2020 PDF]]  [https://hgwdev.gi.ucsc.edu/~brianlee/misc/videos/SysArch_Jorge/zoom_0.mp4 mp4]   
* 15 January 2020 Brian Lee, talk for [http://www.intlpag.org/ PAG] (Plant and Animal Genomes) XXVIII in San Diego, CA: ''Comparative Genomics, Assembly Hubs and New API Data Access on the UCSC Genome Browser''. [[:File:2020_PAG_UCSC_part1.pdf|PDF_part1]]  [[:File:2020_PAG_UCSC_part2.pdf|PDF_part2]]  [[:File:2020_PAG_UCSC_part3.pdf|PDF_part3]]
* 14 January 2020 Brian Lee, Poster for [http://www.intlpag.org/ PAG] (Plant and Animal Genomes) XXVIII in San Diego, CA: 'UCSC Genome Browser API''. [[:File:PAG_Poster_API.pdf|PDF]]
* 11 January 2020 Brian Lee, talk for [http://www.intlpag.org/ PAG] (Plant and Animal Genomes) XXVIII in San Diego, CA: ''Hosting Data at CyVerse to Visualize and Analyze on the UCSC Genome Browser''. [[:File:PAG_Hubs_CyVerse.pdf|PDF]]
==2019==
* 4/11 December 2019 Clinical Diagnostics talk by Ana Benet Pages [https://hgwdev.gi.ucsc.edu/~brianlee/misc/videos/ClinicalDiagnostics/anaTalk1.mp4 mp4_1] [https://hgwdev.gi.ucsc.edu/~brianlee/misc/videos/ClinicalDiagnostics/anaTalk2.mp4 mp4_2]
* 18 October 2019 Bob Kuhn, ASHG (American Society of Human Genetics) in Houston, TX [https://hgwdev.gi.ucsc.edu/~brianlee/misc/videos/ASHG19/ASHGworkshop.mp4 mp4]
* 17 October 2019 Brian Lee, Poster for ASHG (American Society of Human Genetics) in Houston, TX: UCSC Genome Browser: New Interact Format and GeneHancer Data.[[:File:ASHG_2019_Interact.pdf| PDF]]
* 22 April 2019 Angie Hinrichs, Browser Team meeting, "dbSNP 2.0 & bigDbSnp" [https://docs.google.com/presentation/d/1KvWFBknvM13uaL13ivZtahrG9BIWFVJ82qozu7rxVDw/edit?usp=sharing Slides]
* 1 February  2019 Brian Lee,  Talk at [https://genomics.uoregon.edu/schedule/ Genomics In Action] in Eugene, OR:  ''New features and hidden treasures of the UCSC Genome Browser for visualizing genomics'' [[:File:UO_UCSC.pdf|PDF]]
* 31 January 2019 Brian Lee and Luis Nassar, [https://genomics.uoregon.edu/schedule/ Genomics In Action] in Eugene, OR: ''UCSC Genome Browser Workshop'' [[:File:UO_UCSC_CustomTracks.pdf| Custom Tracks PDF]] [[:File:UO_Hubs.pdf|Hubs PDF]]
* 16 January 2019 Brian Lee, talk for [http://www.intlpag.org/ PAG] (Plant and Animal Genomes) XXVII in San Diego, CA: ''UCSC Browser Assembly Hubs''. [[:File:PAG_Hubs.pdf|PDF]]
* 14 January 2019 Brian Lee, Poster for [http://www.intlpag.org/ PAG] (Plant and Animal Genomes) XXVII in San Diego, CA: ''Annotating Variants and Displaying Multiple Alignments on Your Assemblies Using the UCSC Genome Browser''. [[:File:UCSC_PAG_2019_AssemblyHub.pdf|PDF]]
==2018==
* 15 Nov 2018 Kate Rosenbloom, [https://www.umassmed.edu/zlab  Program in Bioinformatics and Integrative Biology, U Mass Medical Center] Worcester, MA: ''UCSC Genome Browser:  New Features and Hidden Features (Nov 2018)'' [[:File:GB_New_And_Hidden_Nov2018.pdf|PDF]] [[:File:GB_New_And_Hidden_Nov2018.pptx|PPT]]
* 14 Nov 2018, Jorge Garcia, The Genome Browser - Under The Hood 2018 review [http://genomewiki.ucsc.edu/images/2/27/Browsermap2018.pdf Browsermap2018.pdf] (See 2010 and 2017 entry for earlier machine maps).
* 05 Nov 2018 Kate Rosenbloom, Genome Browser team meeting: "Interact (and bigInteract) tracks in the UCSC browser".  [[:File:UCSC_BoG_2018_GtexPoster.pdf|PDF]] [[:File:UCSC_BoG_2018_GtexPoster.pptx|PPT]]
* 30 Oct. 2018 Angie Hinrichs, Genome Browser team meeting: [https://docs.google.com/presentation/d/1spahCblhX6nK1iMCQ8K253AZC3FnzT4T7ThOZbjt7lM/edit?usp=sharing "Patchwork"]: adding new alternate haplotype and fix patch sequences to an existing db
* 16-17 May 2018 Kate Rosenbloom, [https://www.tasmc.org.il/sites/en/Internalmed/Pages/Genetics.aspx Tel Aviv Medical Center, Genetics Institute] and [https://www.weizmann.ac.il/LS_CoreFacilities/ Weizmann Institute, Life Sciences Core] Tel Aviv and Rehovot, Israel: [https://docs.google.com/presentation/d/1ZPE-mwW8EKlUqKnaBwQROXkOHbJczKnkBhSGgp7cPho/edit?usp=sharing ''UCSC Genome Browser:  New Features and Hidden Features (May 2018)'']
* 09 May 2018 Kate Rosenbloom, [http://meetings.cshl.edu/Genome18/ Biology of Genomes 2018] Cold Spring Harbor, NY. Poster: ''GTEx resources and new ‘barChart’ and ‘interaction’ track displays inspired by GTEx''. [[:File:UCSC_BoG_2018_GtexPoster.pdf|PDF]] [[:File:UCSC_BoG_2018_GtexPoster.pptx|PPT]]
* 25 April 2018 Brian Lee,  Talk at [http://rna-seqsummit.com/about/agenda/ RNA Seq 2018] in San Francisco, CA:  ''Display of RNA-seq data in the UCSC Genome Browser''
* 01 March 2018 Jairo Navarro, [https://uspa.ucsc.edu/symposium/ 3rd Annual Postdoc Symposium] Santa Cruz, CA: ''Visualizing RNA-seq data in the UCSC Genome Browser'';  A Discussion of Tools for Visualizing RNA-seq Data. [[:File:UcscPostDoc 2018.pdf|PDF]] [[:File:UcscPostDoc 2018.pptx|PPT]]
* 17 January 2018 Brian Lee, Talk at [http://www.intlpag.org/ PAG] (Plant and Animal Genomes) XXVI in San Diego, CA: ''Assembly Hubs at UCSC;''  A Discussion of Assembly Track Hubs at UCSC. [[:File:2018_PAG_Wed_1_17.pdf|PDF]]
* 15 January 2018 Brian Lee, Talk at [http://www.intlpag.org/ PAG] (Plant and Animal Genomes) XXVI in San Diego, CA: ''Viewing Data Hosted at CyVerse on the UCSC Genome Browser'';  A Discussion of hosting Assembly Track Hubs at CyVerse). [[:File:CyVerseAssemblyHubsPAG2018.pdf|PDF]]
* 13 January 2018 Brian Lee, Talk at [http://www.intlpag.org/ PAG] (Plant and Animal Genomes) XXVI in San Diego, CA: ''Benefits of Track Hubs and Byte-Range Requests''; A Discussion of Assembly Track Hubs and the benefits of binary indexed data formats in that only portions of the file needed to display in a particular genomic region are transferred over the Internet and cached as a sparse file). [[:File:AssemblyHubsPAG2018.pdf|PDF]]
==2017==
* 6 December 2017, Jorge Garcia, The Genome Browser - Under The Hood  2017 review (recording available) [[Image:browsermap2017.pdf]] (See 2010 entry for earlier machine maps).
* 27 Nov 2017 Angie, [https://docs.google.com/presentation/d/1MeyBa-Zydegk4vYs_Vgvm4dGj5P_3C2RHuiUaznQYWo/edit?usp=sharing Slides: Genome Informatics 2017 - Angie's summary of conference, for staff meeting]
* 2 Nov 2017 Angie, [https://meetings.cshl.edu/abstracts.aspx?meet=INFO&year=17 Genome Informatics], CSHL: "HGVS variant nomenclature in the UCSC Genome Browser" poster [[Media:GenomeInformatics2017.pdf|PDF]] [[Media:GenomeInformatics2017.pages|Pages(Mac)]]
* 12 Sep 2017 Angie: Building upon Personalis’s “Ground Truth Set” [https://docs.google.com/presentation/d/1QEzzH_tkMAIdImKxCRFVI6yifyBWy1IxCe0esnjWo-w/edit?usp=sharing slides] presented in GA4GH Variant Annotation Task Team conference call
* 16 Aug 2017 Angie: HGVS for QA [https://docs.google.com/presentation/d/1hh4RPlg_ShkKloGXoegBPBfnaCfYsA6dedm4sAWhkqU/edit?usp=sharing slides] presented to QA group
* 15 May 2017 Chris E, Kate R and Chris L: Bar charts in the browser [https://docs.google.com/presentation/d/14R7Nw5FYuHcqkVXwGB-uwvnNvQFDP007-Z0oSyeQ5X8/edit?ts=5919f0aa#slide=id.g1defec0434_0_30 Slides by Chris E presented in GB mtg]
* 26 January 2017 Hiram Clawson, BME230 browser introduction, assembly hub demonstration, table browser intersection [[:File:BME230_Winter_2017.ppt|PPT]]
* 18 January 2017 Brian Lee, [http://www.intlpag.org/ PAG] (Plant and Animal Genomes) XXV in San Diego, CA: ''UCSC Genome Browser -- Assembly Hubs: Display Any Organism''  A Discussion of Custom Annotations, Building an Assembly Hub, GenBank Assembly Hubs, Assembly Hub BLAT, and Hosting Assembly Hubs on GBiB and CyVerse (Here is an associated [http://hgwdev.cse.ucsc.edu/~brianlee/examples/PAG_hub.html  page with quick links] from the talk). [[:File:assemblyHubsUCSC.pdf|PDF]]
==2016==
* 15 Nov 2016, Kate Rosenbloom, GTEx in the UCSC Genome Browser: December 2016 Update (presentation for the GTEx Steering Committee at Dec meeting in DC) [[:File:GtexAtUcsc_Dec2016.pptx | PPTX]]
* 20 Aug 2016, Max Haeussler, Evaluation of scoring algorithms for Crispor and the UCSC Genome Browser, CSHL Crispr Meeting 2016, Poster [[File:CrisporCshl2016.pdf | PDF]]
* 12 July 2016, Kate Rosenbloom, GTEx in the UCSC Genome Browser: July 2016 Update (presentation to the GTEx Steering Committee, Stanford) [[Media:GtexAtUcscTalkJuly2016.pptx | PPTX]]
* 11 July 2016, Christopher Lee poster presented at the 2016 GTEx Community Meeting at Stanford [[:File:GTEX_2016_Poster.pdf | PDF]]
* 09 June 2016, Hiram Clawson presentation to Bejerano Lab, Stanford, assembly nomenclature, assembly hubs, lastz/chain/net procedures [[:File:BejeranoLab_2016-06-09.pptx | PPTX]]
* 24 May 2016, Chris Eisenhart phone conference presentation, explaining the new data transfer to the CIRM CRP and CIP labs [https://docs.google.com/presentation/d/16tsxBkYvrTVLlyYrTKIcTJnkKYTWIO0mUbViU0d7tlQ/edit?usp=sharing  google doc]
* 10 May 2016, Galt Barber, Multi-Region (Exon Mostly) at Biology of Genomes [[Media:Multi-region-BoG2016.pdf | PDF‎]]
* 29 April 2016, Chris Eisenhart presentation at the 2nd Annual CIRM retreat, CDW, Stem cell hub, current lab status [https://docs.google.com/presentation/d/1xmxfROdgSkqlxXhQwBiQ2cPnfV1N8BPp6ChkXFG-IJk/edit?usp=sharing  google doc]
* 29 April 2016, Clay Fischer poster presented at the 2nd Annual CIRM retreat [[:File:CIRMposter2016.pdf | PDF]]
* 04 April 2016, Robert Kuhn.  poster presented at International Congress of Human Genetics (ICHG) in Kyoto.  Reformatted from Luvina's ACMG poster.  Thanks, Luvina [[:File:PosterIchg2016.pdf | PDF]]
* 11 March 2016, Luvina Guruvado presented poster about about accessing variation data in the GBiB and Data Integrator at the American College of Medical Genetics (ACMG) annual meeting in Tampa [[:File:ACMGposter2016.pdf | PDF]]
* 17 February 2016, Kate Rosenbloom, GTEx in the UCSC Genome Browser (presentation at Genecats) [[Media:GTExAtUcscFeb2016.pptx | PPTX]] [[Media:GTExAtUcscFeb2016.pdf | PDF]]
* 12 January 2016 Hiram Clawson, BME230 browser introduction, assembly hub demonstration, table browser intersection [[:File:BME230_Winter_2016.ppt|PPT]]
==2015==
* 4 December 2015, Kate Rosenbloom, GTEx in the UCSC Genome Browser (presentation at the December 2015 GTEx Steering Committee meeting) [[Media:GTExAtUcsc_Dec2015.pptx | PPTX]] [[Media:GTExAtUcsc_Dec2015.pdf | PDF]]
* 28-30 September 2015, Kate Rosenbloom, Visualizing proteomics data in genomic context using the UCSC Genome Browser (poster presented by collaborator Eric Deutsch (PeptideAtlas Project, Institute for Systems Biology) at the HUPO2015 (Human Proteomics Organization)  Congress in Vancouver) [[Media:UCSC_Proteomics_HUPO2015_Poster.pptx | PPTX]]
* 29 June - 1 July 2015, Pauline Fujita, [https://www.encodeproject.org/tutorials/encode-users-meeting-2015/ ENCODE Users Meeting] Visualizing ENCODE Data in the UCSC Genome Browser. [[Media:ENCODEusersMtg.ppt | PPTX]]
* 23 June 2015, Kate Rosenbloom, GTEx Data in the UCSC Genome Browser (poster presented at the June 2015 GTEx Community Meeting in Chicago) [[Media:GTEX2015Poster.pptx | PPTX]]  [[Media:GTEX2015Poster.pdf | PDF]]
* 22-24 June 2015, Matthew Speir, Use The UCSC Genome Browser To Visualize And Analyze Your Genomic Data (poster presented at [https://bioeng-symposium-2015.soe.ucsc.edu/ UC-wide Bioengineering Symposium 2015] at UCSC)  [[BioengSymp2015Poster | wiki]] [[Media:bioengSymp2015Poster.pptx | PPTX]]  [[Media:bioengSymp2015Poster.pdf | PDF]]
* 9 May 2015, Angie Hinrichs, The Data Integrator: a new way to combine datasources underlying the UCSC Genome Browser (poster presented at [http://meetings.cshl.edu/meetings/2015/genome15.shtml Biology of Genomes 2015] at CSHL)  [[BoG2015DataIntegratorPoster | wiki]] [[Media:BoG2015DataIntegrator.pptx | PPTX]]  [[Media:BoG2015DataIntegrator.pdf | PDF]]
* 11 March 2015, Angie Hinrichs, Annotation Integrator [[Media:HgAi_genecats_15_03_11.pdf‎|PDF]] [[Media:HgAi_genecats_15_03_11.pptx|PPTX]]
* 5 March 2015, Brian Raney, Genome 10K, Poster on assembly hubs and GBiB.  [[:File:G10K2015.pdf|PDF]]
* 26 Feb 2015, Robert Kuhn, ACMG meeting, Salt Lake.  UCSC Genome Browser and Variant Annotation Integrator [[Media:acmg2015poster.pdf‎|PDF]]
==2014==
* 13 October 2014, Brian Raney, The American Society of Human Genetics, Poster on assembly hubs and GBiB.  [[:File:Ashg2014.pdf|PDF]]
* 20 September 2014, Galt Barber, Genome Informatics 2014 Poster on hubs, security, and GBiB. [[:File:GenomeInformatics2014Poster.pdf|PDF]]
*  19 Sept 2014 Jim Kent, Ebola Scramble [[Media:ebolaUcsfSept192014.pptx|PPTX]]
* 22 Aug 2014 Jim Kent, hg38, mapping sponge, and ENCODE [[Media:spongeAwg.pptx|PPTX]]
* 19 May 2014, Karen Miga, GRCh38 Centromere Reference Models [[:File:KarenMigaCentromere.pdf‎|PDF]]
* 11 February 2014, Hiram Clawson, BME230 browser introduction, assembly hub demonstration, table browser intersection [[:File:BME230_Winter_2014.ppt|PPT]]


==2013==
==2013==
* 10 May 2013, Brooke Rhead, New variation resources at the UCSC Genome Browser. Poster presented at [http://meetings.cshl.edu/meetings/2013/genome13.shtml | Biology of Genomes] at CSHL. [[BoG2013VariationPoster | wiki]], [[Media:BoG2013variation.pptx | PPTX]], [[Media:BoG2013variation.pdf | PDF]].
* 19 June 2013, Tracy Ballinger, Track Hubs and Assembly Hubs presentation for Epigenome Roadmap working group meeting. [[:File:TrackHub_presentation.ppt|PPT]] [[:File:TrackHub_presentation.pdf|PDF]]
* 20 Mar 2013, Brian Raney, UCSC Genes Genecats talk [[:File:ucscGenes.ppt|PPT]] [[:File:ucscGenes.pdf|PDF]]
* 10 May 2013, Brooke Rhead, New variation resources at the UCSC Genome Browser. Poster presented at [http://meetings.cshl.edu/meetings/2013/genome13.shtml Biology of Genomes 2013] at CSHL. [[BoG2013VariationPoster | wiki]], [[Media:BoG2013variation.pptx | PPTX]], [[Media:BoG2013variation.pdf | PDF]].
* 08 May 2013, Hiram Clawson, Assembly Hubs poster presentation at [http://meetings.cshl.edu/meetings/2013/genome13.shtml Biology of Genomes 2013] at CSHL. [[Assembly_Hubs | wiki]], [[Media:AssemblyHubs_BoG_2013.pdf | PDF]], [[Media:AssemblyHubs_BoG_2013.pptx| PPTX]]
* 20 Mar 2013, Brian Raney, UCSC Genes Genecats talk [[:File:ucscGenes.ppt|PPT]] [[:File:ucscGenes.pdf|PDF]]


==2012==
==2012==
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* 27 April 2011, Jim Kent, Accelerating Biomedical Research for 10 Years and Counting. [[Image:AcceleratingBiomedicine2011.pptx]]
* 27 April 2011, Jim Kent, Accelerating Biomedical Research for 10 Years and Counting. [[Image:AcceleratingBiomedicine2011.pptx]]
* 06 April 2011, Angie Hinrichs, Recent work on human variation tracks.  [[Media:VariationGenecats20110406.pptx|.pptx]] [[Media:VariationGenecats20110406.pdf|PDF]] (PDF has squashed animations)
* 06 April 2011, Angie Hinrichs, Recent work on human variation tracks.  [[Media:VariationGenecats20110406.pptx|.pptx]] [[Media:VariationGenecats20110406.pdf|PDF]] (PDF has squashed animations)
* 24 March 2011, Robert Kuhn. poster presented at Genomic Disorders meeting, Hinxton.  [[Image:genomicDisorders2011.pdf]]
* 09 March 2011, Josh Stuart, Ph.D., Integrated Pathway Modeling.  [[Image:jstuart.pptx]]
* 09 March 2011, Josh Stuart, Ph.D., Integrated Pathway Modeling.  [[Image:jstuart.pptx]]
* 03 March 2011, Andreas Sundquist, Ph.D., DNAnexus -- Data Management for the First 1,000,000 Human Genomes.  [[Image:DNAnexus.pptx]]
* 03 March 2011, Andreas Sundquist, Ph.D., DNAnexus -- Data Management for the First 1,000,000 Human Genomes.  [[Image:DNAnexus.pptx]]
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* 05 May 2010, Hiram Clawson, [[Unix environment]]
* 05 May 2010, Hiram Clawson, [[Unix environment]]
* 21 April 2010, Mitchell Skinner, JBrowse - An AJAX Genome Browser [[Image:UCSC-4-21-10.pdf]]
* 21 April 2010, Mitchell Skinner, JBrowse - An AJAX Genome Browser [[Image:UCSC-4-21-10.pdf]]
* 10 February 2010, Jorge Garcia, The Genome Browser - Under The Hood [[Image:Browsermap.pdf]]
* 10 February 2010, Jorge Garcia, The Genome Browser - Under The Hood [[Image:Browsermap.pdf]] and 2013 review [[Image:Dependency-Review-20130826.pdf]] and 2016 review [[Image:Browsermap2016.pdf]] and 2017 review  [[Image:browsermap2017.pdf]] and 2018 review  [http://genomewiki.ucsc.edu/images/2/27/Browsermap2018.pdf Browsermap2018.pdf]  
* 03 February 2010, Melissa Cline, Coordinated Alternative Splicing [[Image:CoordinatedSplicing.ppt]]
* 03 February 2010, Melissa Cline, Coordinated Alternative Splicing [[Image:CoordinatedSplicing.ppt]]
* 05,07 January 2010 BME 230 class, Hiram Clawson, introduction to the UCSC genome browser and programming with the kent source tree.  [[Image:BME230_Winter_2010.ppt]]  Browser [[http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Hiram&hgS_otherUserSessionName=BME230%20Winter%202010 Session]] for example intersection.
* 05,07 January 2010 BME 230 class, Hiram Clawson, introduction to the UCSC genome browser and programming with the kent source tree.  [[Image:BME230_Winter_2010.ppt]]  Browser [[http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Hiram&hgS_otherUserSessionName=BME230%20Winter%202010 Session]] for example intersection.

Latest revision as of 00:14, 2 July 2024

An archive of presentations by staff and researchers of the UCSC Genome Browser group and the Center for Biomolecular Science and Engineering (CBSE). Please keep the list in order by date, newest ones at the top.

Please note there is a UCSC Genome Browser shared drive which has more files available at: https://drive.google.com/drive/folders/0AD5CiKJJXgKhUk9PVA

2024

2023

  • 06-09 December 2023 Hiram Clawson - Cold Spring Harbor Genome Informatics Meeting poster GenArk assembly resources File:CSHL GenomeInformatics 2023.pptx
  • 08 November 2023 Hiram Clawson - BME-18 - Scientific Principals of Life - genome browser introduction File:BME-18.2023-11-08.pptx
  • 3 May 2023 Angie Hinrichs - ABPHM23 - Applied Bioinformatics and Public Health Microbiology, Hinxton, UK - UShER: pandemic-scale phylogenetics for SARS-CoV-2 and beyond Google Slides
  • 15 January 2023 Hiram Clawson - PAG-30 - 30th annual Plant and Animal Genomes, San Diego - Educational resources in the UCSC genome browser File:PAG30 2023-01-15.pptx
  • 14 January 2023 Hiram Clawson - PAG-30 - 30th annual Plant and Animal Genomes, San Diego - Introduction to the genome browser, GenArk hubs, creating an assembly hub and REST API interface File:PAG30 2023-01-14.pptx

2022

  • 04 November 2022 Hiram Clawson - BME-18 Scientific Principals of life (File:BME-18.2022-11-04.pptx)
  • 25 May 2022 Angie Hinrichs, Pango lineages: a brief intro [slides] (in [SPHERES] meeting)
  • 12 April 2022 Angie Hinrichs, pangolin v4.0 [slides] (in Theiagen's "Office Hours" for public health bioinformaticians)
  • 3 February 2022 Angie Hinrichs Pango lineages [slides] (in [CDPH] Whole Genome Sequencing meeting)

2021

2020

  • 23 November 2020 Angie Hinrichs, Big trees of tiny genomes Slides
  • 4 November 2020 Jorge Garcia, THE GENOME BROWSER – UNDER THE HOOD 2020 PDF mp4
  • 15 January 2020 Brian Lee, talk for PAG (Plant and Animal Genomes) XXVIII in San Diego, CA: Comparative Genomics, Assembly Hubs and New API Data Access on the UCSC Genome Browser. PDF_part1 PDF_part2 PDF_part3
  • 14 January 2020 Brian Lee, Poster for PAG (Plant and Animal Genomes) XXVIII in San Diego, CA: 'UCSC Genome Browser API. PDF
  • 11 January 2020 Brian Lee, talk for PAG (Plant and Animal Genomes) XXVIII in San Diego, CA: Hosting Data at CyVerse to Visualize and Analyze on the UCSC Genome Browser. PDF

2019

  • 4/11 December 2019 Clinical Diagnostics talk by Ana Benet Pages mp4_1 mp4_2
  • 18 October 2019 Bob Kuhn, ASHG (American Society of Human Genetics) in Houston, TX mp4
  • 17 October 2019 Brian Lee, Poster for ASHG (American Society of Human Genetics) in Houston, TX: UCSC Genome Browser: New Interact Format and GeneHancer Data. PDF
  • 22 April 2019 Angie Hinrichs, Browser Team meeting, "dbSNP 2.0 & bigDbSnp" Slides
  • 1 February 2019 Brian Lee, Talk at Genomics In Action in Eugene, OR: New features and hidden treasures of the UCSC Genome Browser for visualizing genomics PDF
  • 31 January 2019 Brian Lee and Luis Nassar, Genomics In Action in Eugene, OR: UCSC Genome Browser Workshop Custom Tracks PDF Hubs PDF
  • 16 January 2019 Brian Lee, talk for PAG (Plant and Animal Genomes) XXVII in San Diego, CA: UCSC Browser Assembly Hubs. PDF
  • 14 January 2019 Brian Lee, Poster for PAG (Plant and Animal Genomes) XXVII in San Diego, CA: Annotating Variants and Displaying Multiple Alignments on Your Assemblies Using the UCSC Genome Browser. PDF

2018

  • 15 Nov 2018 Kate Rosenbloom, Program in Bioinformatics and Integrative Biology, U Mass Medical Center Worcester, MA: UCSC Genome Browser: New Features and Hidden Features (Nov 2018) PDF PPT
  • 14 Nov 2018, Jorge Garcia, The Genome Browser - Under The Hood 2018 review Browsermap2018.pdf (See 2010 and 2017 entry for earlier machine maps).
  • 05 Nov 2018 Kate Rosenbloom, Genome Browser team meeting: "Interact (and bigInteract) tracks in the UCSC browser". PDF PPT
  • 30 Oct. 2018 Angie Hinrichs, Genome Browser team meeting: "Patchwork": adding new alternate haplotype and fix patch sequences to an existing db
  • 16-17 May 2018 Kate Rosenbloom, Tel Aviv Medical Center, Genetics Institute and Weizmann Institute, Life Sciences Core Tel Aviv and Rehovot, Israel: UCSC Genome Browser: New Features and Hidden Features (May 2018)
  • 09 May 2018 Kate Rosenbloom, Biology of Genomes 2018 Cold Spring Harbor, NY. Poster: GTEx resources and new ‘barChart’ and ‘interaction’ track displays inspired by GTEx. PDF PPT
  • 25 April 2018 Brian Lee, Talk at RNA Seq 2018 in San Francisco, CA: Display of RNA-seq data in the UCSC Genome Browser
  • 01 March 2018 Jairo Navarro, 3rd Annual Postdoc Symposium Santa Cruz, CA: Visualizing RNA-seq data in the UCSC Genome Browser; A Discussion of Tools for Visualizing RNA-seq Data. PDF PPT
  • 17 January 2018 Brian Lee, Talk at PAG (Plant and Animal Genomes) XXVI in San Diego, CA: Assembly Hubs at UCSC; A Discussion of Assembly Track Hubs at UCSC. PDF
  • 15 January 2018 Brian Lee, Talk at PAG (Plant and Animal Genomes) XXVI in San Diego, CA: Viewing Data Hosted at CyVerse on the UCSC Genome Browser; A Discussion of hosting Assembly Track Hubs at CyVerse). PDF
  • 13 January 2018 Brian Lee, Talk at PAG (Plant and Animal Genomes) XXVI in San Diego, CA: Benefits of Track Hubs and Byte-Range Requests; A Discussion of Assembly Track Hubs and the benefits of binary indexed data formats in that only portions of the file needed to display in a particular genomic region are transferred over the Internet and cached as a sparse file). PDF

2017

  • 6 December 2017, Jorge Garcia, The Genome Browser - Under The Hood 2017 review (recording available) File:Browsermap2017.pdf (See 2010 entry for earlier machine maps).
  • 27 Nov 2017 Angie, Slides: Genome Informatics 2017 - Angie's summary of conference, for staff meeting
  • 2 Nov 2017 Angie, Genome Informatics, CSHL: "HGVS variant nomenclature in the UCSC Genome Browser" poster PDF Pages(Mac)
  • 12 Sep 2017 Angie: Building upon Personalis’s “Ground Truth Set” slides presented in GA4GH Variant Annotation Task Team conference call
  • 16 Aug 2017 Angie: HGVS for QA slides presented to QA group
  • 15 May 2017 Chris E, Kate R and Chris L: Bar charts in the browser Slides by Chris E presented in GB mtg
  • 26 January 2017 Hiram Clawson, BME230 browser introduction, assembly hub demonstration, table browser intersection PPT
  • 18 January 2017 Brian Lee, PAG (Plant and Animal Genomes) XXV in San Diego, CA: UCSC Genome Browser -- Assembly Hubs: Display Any Organism A Discussion of Custom Annotations, Building an Assembly Hub, GenBank Assembly Hubs, Assembly Hub BLAT, and Hosting Assembly Hubs on GBiB and CyVerse (Here is an associated page with quick links from the talk). PDF

2016

  • 15 Nov 2016, Kate Rosenbloom, GTEx in the UCSC Genome Browser: December 2016 Update (presentation for the GTEx Steering Committee at Dec meeting in DC) PPTX
  • 20 Aug 2016, Max Haeussler, Evaluation of scoring algorithms for Crispor and the UCSC Genome Browser, CSHL Crispr Meeting 2016, Poster File:CrisporCshl2016.pdf
  • 12 July 2016, Kate Rosenbloom, GTEx in the UCSC Genome Browser: July 2016 Update (presentation to the GTEx Steering Committee, Stanford) PPTX
  • 11 July 2016, Christopher Lee poster presented at the 2016 GTEx Community Meeting at Stanford PDF
  • 09 June 2016, Hiram Clawson presentation to Bejerano Lab, Stanford, assembly nomenclature, assembly hubs, lastz/chain/net procedures PPTX
  • 24 May 2016, Chris Eisenhart phone conference presentation, explaining the new data transfer to the CIRM CRP and CIP labs google doc
  • 10 May 2016, Galt Barber, Multi-Region (Exon Mostly) at Biology of Genomes PDF‎
  • 29 April 2016, Chris Eisenhart presentation at the 2nd Annual CIRM retreat, CDW, Stem cell hub, current lab status google doc
  • 29 April 2016, Clay Fischer poster presented at the 2nd Annual CIRM retreat PDF
  • 04 April 2016, Robert Kuhn. poster presented at International Congress of Human Genetics (ICHG) in Kyoto. Reformatted from Luvina's ACMG poster. Thanks, Luvina PDF
  • 11 March 2016, Luvina Guruvado presented poster about about accessing variation data in the GBiB and Data Integrator at the American College of Medical Genetics (ACMG) annual meeting in Tampa PDF
  • 17 February 2016, Kate Rosenbloom, GTEx in the UCSC Genome Browser (presentation at Genecats) PPTX PDF
  • 12 January 2016 Hiram Clawson, BME230 browser introduction, assembly hub demonstration, table browser intersection PPT

2015

  • 4 December 2015, Kate Rosenbloom, GTEx in the UCSC Genome Browser (presentation at the December 2015 GTEx Steering Committee meeting) PPTX PDF
  • 28-30 September 2015, Kate Rosenbloom, Visualizing proteomics data in genomic context using the UCSC Genome Browser (poster presented by collaborator Eric Deutsch (PeptideAtlas Project, Institute for Systems Biology) at the HUPO2015 (Human Proteomics Organization) Congress in Vancouver) PPTX
  • 29 June - 1 July 2015, Pauline Fujita, ENCODE Users Meeting Visualizing ENCODE Data in the UCSC Genome Browser. PPTX
  • 23 June 2015, Kate Rosenbloom, GTEx Data in the UCSC Genome Browser (poster presented at the June 2015 GTEx Community Meeting in Chicago) PPTX PDF
  • 22-24 June 2015, Matthew Speir, Use The UCSC Genome Browser To Visualize And Analyze Your Genomic Data (poster presented at UC-wide Bioengineering Symposium 2015 at UCSC) wiki PPTX PDF
  • 9 May 2015, Angie Hinrichs, The Data Integrator: a new way to combine datasources underlying the UCSC Genome Browser (poster presented at Biology of Genomes 2015 at CSHL) wiki PPTX PDF
  • 11 March 2015, Angie Hinrichs, Annotation Integrator PDF PPTX
  • 5 March 2015, Brian Raney, Genome 10K, Poster on assembly hubs and GBiB. PDF
  • 26 Feb 2015, Robert Kuhn, ACMG meeting, Salt Lake. UCSC Genome Browser and Variant Annotation Integrator PDF

2014

  • 13 October 2014, Brian Raney, The American Society of Human Genetics, Poster on assembly hubs and GBiB. PDF
  • 20 September 2014, Galt Barber, Genome Informatics 2014 Poster on hubs, security, and GBiB. PDF
  • 19 Sept 2014 Jim Kent, Ebola Scramble PPTX
  • 22 Aug 2014 Jim Kent, hg38, mapping sponge, and ENCODE PPTX
  • 19 May 2014, Karen Miga, GRCh38 Centromere Reference Models PDF
  • 11 February 2014, Hiram Clawson, BME230 browser introduction, assembly hub demonstration, table browser intersection PPT

2013

  • 19 June 2013, Tracy Ballinger, Track Hubs and Assembly Hubs presentation for Epigenome Roadmap working group meeting. PPT PDF
  • 10 May 2013, Brooke Rhead, New variation resources at the UCSC Genome Browser. Poster presented at Biology of Genomes 2013 at CSHL. wiki, PPTX, PDF.
  • 08 May 2013, Hiram Clawson, Assembly Hubs poster presentation at Biology of Genomes 2013 at CSHL. wiki, PDF, PPTX
  • 20 Mar 2013, Brian Raney, UCSC Genes Genecats talk PPT PDF

2012

  • 06 Sep 2012, Brian Raney, Remote Data Track Storage for Viewing on the UCSC Genome Browser wiki,
  • 09 May 2012, Angie Hinrichs, Using the UCSC Genome Browser to evaluate putative genetic variants wiki, PPTX, PDF
  • 11 April 2012, Ted Pak, JavaScript/Ruby version of the UCSC Yeast Genome Browser PDF
  • 21 March 2012, Larry Meyer, Genome Browser API. (Genecats) PPT
  • 15 February 2012, Greg Roe & Venkat Malladi, Selenium Testing PPTX
  • 26 January 2012, Hiram Clawson, BME230 browser introduction, table browser intersection PPT
  • 18 January 2012, Jim Kent, Software Engineering and Testing. (Genecats) PPTX
  • 11 January 2012, Brooke Rhead, The QA Release Process: what gets pushed and when. (Genecats) PPTX or PDF

2011

  • 18-19 October 2011, XLDB presentations including from UCSC, the 5th lightning talk on the 18th of October. Note additional interesting genomics presentations, for example the NCBI sequence read archive architecture on the morning of the 19th.
  • 09 September 2011, Angie Hinrichs, Visually integrating genomic data in the UCSC Genome Browser. Poster presented at HGV2011. .pptx PDF
  • 24 August 2011, Sol Katzman, Ongoing GC-biased evolution is widespread in the human genome and enriched near recombination hotspots File:Sol GCBias GeneCats 2011-08-24.pdf
  • 27 July 2011, Larry Meyer, Browser Performance and Architecture
  • May 2011, Ann Zweig, UCSC Genome Browser Track Data Hubs. Poster given at Biology of Genomes conference at CSHL. File:BoG2011.pdf
  • May 2011, Gabor Marth, Toward a unified view of human genetic variation. Talk given at Biology of Genomes conference at CSHL. File:Marth-1000G-CSHL2011.pptx
  • 27 April 2011, Jim Kent, Accelerating Biomedical Research for 10 Years and Counting. File:AcceleratingBiomedicine2011.pptx
  • 06 April 2011, Angie Hinrichs, Recent work on human variation tracks. .pptx PDF (PDF has squashed animations)
  • 24 March 2011, Robert Kuhn. poster presented at Genomic Disorders meeting, Hinxton. File:GenomicDisorders2011.pdf
  • 09 March 2011, Josh Stuart, Ph.D., Integrated Pathway Modeling. File:Jstuart.pptx
  • 03 March 2011, Andreas Sundquist, Ph.D., DNAnexus -- Data Management for the First 1,000,000 Human Genomes. File:DNAnexus.pptx
  • 02 March 2011, MDB and CV in the shadow of the shadow of greatness. File:MdbAndCvPresentation.pdf or File:MdbAndCvPresentation.ppt Brian Raney and Tim Dreszer.
  • 02 February 2011, Benedict Paten, JobTree. File:JobtreeSlides.pdf
  • 06 January 2011, BME 230 class, Hiram Clawson, introduction to the UCSC genome browser and programming with the kent source tree. File:BME230 Winter 2011.ppt

2010

2009

2008

  • 18 December 2008 File:FrankJacobs181208.ppt - Frank Jacobs, Developmental Neurobiology, Rudolf Magnus Institute of Neuroscience, University of Utrecht, The Netherlands, "Pitx3 outSMRTs Nurr1 in dopamine neuron terminal differentiation"
  • Genecats - 17 December 2008 - Composite sketch: Nifty tricks for composite tracks (multi-view, dimensions, sorting, drag and drop, etc.). Tim Dreszer.
  • Genecats - 10 December 2008 - Ed Green from Max Planck Institute for Evolutionary Anthropology discusses the [Neandertal mtDNA] project
  • Sep. 2008 - Angie's "UCSC Genome Browser Tool Suite" poster presented at Genomics of Common Disease PPT PDF
  • 27 August 2008 - Jim Kent at the Computational Systems Bioinformatics Conference, Stanford CA, File:Kent decodingEncode.ppt a wide-ranging discussion of Encode research, using the Gene Sorter, using the Table browser, source code design issues
  • ISMB Toronto - July 2008 - Intelligent Systems for Molecular Biology File:ISMB2008 UCSC.ppt presentation by Hiram Clawson. A brief tutorial on browser usage with special emphasis on how to perform intersections with the table browser. Task demonstrated: finding highly conserved non-coding regions of the genome.
  • Genecats - 05 July 2008 - Jim Kent describing the all.joiner file used by the UCSC genome browser to specify database table relationships - the database "schema" behind the browser File:Kent allJoiner.ppt
  • Bejerano Lab (Stanford) - March 31, 2008 - File:Bejerano Lab 2008 03 31.ppt Angie's crash course on using the kent/src tools and libraries. Did a brief live demo (TB intersection -> custom track) first. Group was already very familiar with browser and had their own mirror.
  • BME 230 Winter 2008, 10 January 2008, Robert Baertsch File:Baertsch-code-talk.ppt genome browser introduction and kent src code preview

2007

2006

2005

2003

  • CSHL June 2003 "Evolution and the Santa Cruz Genome Browser" File:CSHL 2003 Jim Kent.ppt presentation by Jim Kent. Recent new functions in the genome browser, using the chain and net process to highlight evolutionary processes, a new rat genome assembly with 3-way human-mouse-rat multiple alignment.

2002

2000

  • October 2000 - "Details of the Genome Browser" File:CompBioOct2000 Jim Kent.ppt - Description of the genome browser software architecture, the early days. Jim Kent
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