Presentations2

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iSEEM 2

2014

  • May 2014: Thomas Shaprton -- Metagenomic Investigations of the Human Microbiome. OSU Department of Nutrition Seminar. Corvallis, OR.
  • April 2014: Patrick Bradley -- Assessing the stability of protein family abundance in the gut microbiome. Exploiting and understanding chemical biotransformations in the human microbiome, Keystone Symposium, Big Sky, MT.
  • April 2014: Josh Ladau -- Mapping historic, current, and future soil biodiversity. iDIV Workshop: A framework to improve our understanding of the distribution of global soil biodiversity: establishing the first quantitative synthesis. Leipzig, Germany.
  • April 2014: Thomas Sharpton -- From Noise to Signal: Mining Human Exome Sequences Reveals the Hunter-Gatherer Oral Microbiome. Center for Genome Research and Biocomputing Spring Symposium. Corvallis, OR.
  • March 2014: Katie Pollard -- Statistics and bioinformatics challenges in shotgun metagenomics. Genome Sciences seminar, U Washington, Seattle, WA.
  • January 2014: Katie Pollard -- Quantifying the taxonomic and functional diversity of metagenomes. BCATS conference, Stanford University, Palo Alto, CA.
  • January 2014: Katie Pollard -- Promises and pitfalls of studying microbial communities with shotgun metagenomics data. Bioinformatics & Systems Biology Colloquium, UC San Diego, San Diego, CA.

2013

  • September 2013: Katie Pollard -- Bioinformatics and statistical challenges in metagenome analysis. Next-generation sequencing seminar, UC Berkeley, Berkeley, CA.
  • August 2013: Josh Ladau -- Universal scaling of beta-diversity across taxa and terrestrial and marine ecosystems. Ecological Society of America Annual Meeting. Minneapolis, MN.
  • December 2013: Thomas Sharpton -- Metagenomic Investigations of Microbiomes. University of Oregon META Center Seminar. Eugene, OR
  • May 2013: Josh Ladau - Predicting Microbial Distributions on a Global Scale using Niche Models. 113th General Meeting American Society for Microbiology. Denver, CO.
  • May 2013: Jonathan Eisen - Phylogeny-Driven Approaches to Genomics and Metagenomics. Fresno State. Slideshare
  • April 2013: Katie Pollard – Quantifying the taxonomic and functional diversity of metagenomes from shotgun sequencing data. Society for Molecular Biology & Evolution Eukaryotic ‘Omics Meeting. Davis, CA.
  • April 2013. Jonathan Eisen – The Need for a Phylogeny Driven Genomic Encyclopedia of Eukaryotes. Society for Molecular Biology & Evolution Eukaryotic ‘Omics Meeting. Davis, CA.
  • January 2013: Katie Pollard – Decoding our genomes: what can our DNA tell us about our close relatives and who is traveling with us? Castro Valley Educational Foundation. Castro Valley, CA.


2012

  • July 2012: Katie Pollard – Invited talk at the Joint Statistical Meetings, San Diego, CA.
  • July 2012: Jonathan Eisen. Phylogenomic approaches to functional prediction. At AFP “Automated functional prediction” submeeting during ISMB 2012. Slideshare Youtube
  • September 2012: Katie Pollard – Seminar at the VanBUGS cross-institutional bioinformatics group, Vancouver, BC.
  • September 2012: Jonathan Eisen. Phylogenomic approaches to the study of microbial diversity. Keynote Talk at Lake Arrowhead Microbial Genomes Meeting.
  • September 2012: Jonathan Eisen. Phylogenomic approaches to the study of microbial diversity. At Bay Area Illumina Users Meeting. Slideshare. Slideshow on Youtube.
  • October 2012: Tom Sharpton – Seminar at the Center for Genome Research and Biocomputing, Oregon State University.
  • October 2012: Jonathan Eisen. Sequencing and Microbes, the Now Generation. At UC Davis Food for Health Symposium. Slideshow on Youtube.
  • November 2012: Katie Pollard – Invited talk at Systems Biology Symposium, Johns Hopkins Medical School, Baltimore, MD.

iSEEM 1

Green Lab

  1. Field Theory and Community Assembly. James O'Dwyer. Talk presented at the Moorcroft lab meeting, Department of Organismal and Evolutionary Biology, University of Harvard, September 2009. Also presented at the Plotkin lab meeting, University of Pennsylvania, September 2009.
  2. Community Assembly across the Tree of Life. James O'Dwyer. Talk presented at the Population Biology Seminar, University of Leeds, UK, January 2010.
  3. From Field Theory to Ecology. James O'Dwyer. Talk presented at the Biomathematics Seminar, University of Durham, UK, January 2010.
  4. Ecology without species: phylogenetic perspectives on microbial diversity. S.W. Kembel and J.L. Green. Invited speaker, Organized Oral Session on ‘Species interactions and community ecology in the context of relatedness’, Ecological Society of America Annual Meeting, August 2009.
  5. Measuring phylogenetic diversity. S.W. Kembel. Invited workshop instructor, ‘Ecological approaches to analyzing complex community datasets’ workshop for Fungal Environmental Sampling and Informatics Network members, Botanical/Mycological Societies of America Annual Meeting, July 2009.
  6. Ecology without species: phylogenetic perspectives on microbial diversity. S.W. Kembel. Invited speaker, Early Career Scientists Symposium on ‘Phylogenies and Ecology’, University of Michigan, March 2009.
  7. Metagenomics approaches to biodiversity and biogeography. Jessica Green. Talk presented at the University of Ioannina, March 2009.
  8. Theory and Metagenomics-based Biogeography. Jessica Green. ASM 109th General Meeting in Philadelphia, at the special interest session Genomics Enabled Biogeography of Planet Earth organized by Tiedje and Klugman. May 2009.
  9. The Rainforest Within: Biodiversity of the Human Body and its Relationship to Health and Disease. Jessica Green was the moderator of this symposium at the Ecological Society of America, which was covered by Nature News (http://www.nature.com/news/2009/090807/full/news.2009.808.html) and their blog (http://blogs.nature.com/news/blog/2009/08/esa_2009_sweater_by_grandma_gu.html).
  10. Exploring the Invisible. Jessica Green. TED2010, Long Beach, February 2010.
  11. Biodiversity Theory and Metagenomics-based Biogeography. Jessica Green. Stanford Symposium on Evolution and Genomics, April 2010.
  12. Ecology without species: phylogenetic diversity and microbial ecology. Steven Kembel. Invited speaker, 'Frontiers in Biodiversity: a phylogenetic perspective' Symposium, Barcelona, Spain, October 2010.
  13. Phylogenetic ecology and metagenomics. Steven Kembel. Invited speaker, 18th Annual Meeting on Microbial Genomics, Lake Arrowhead, September 2010.
  14. Field Theory, Biogeography and Metagenomics. James O'Dwyer. Talk presented at Arizona State University Biophysics colloquium, November 2010.
  15. Field Theory, Biogeography and Metagenomics. James O'Dwyer. Talk presented at Los Alamos Center for Nonlinear Sciences weekly seminar, May 2011.

Pollard Lab

  1. The iSEEM Project: Phylogenetic approaches to microbial metagenomics. Thomas J. Sharpton, Samantha J. Riesenfeld, Joshua Ladau, Steven W. Kembel, Jessica L. Green, Jonathan A. Eisen, Katherine S. Pollard. Talk presented by Katie Pollard at Cold Spring Harbor Biology of Genomes Meeting, May 2010.
  2. Building phylogenies with metagenomic sequence reads. Samantha J. Riesenfeld, Thomas J. Sharpton, Steven W. Kembel, Jessica L. Green, Katherine S. Pollard. Talk presented by Samantha Riesenfeld at Cold Spring Harbor Biology of Genomes Meeting, May 2010.
  3. PhylOTU: A high-throughput procedure that identifies Operational Taxonomic Units from metagenomic data. Thomas J. Sharpton, Samantha J. Riesenfeld, Steven W. Kembel, Joshua Ladau, James O'Dwyer, Jessica L. Green, Jonathan A. Eisen, Katherine S. Pollard. Talk presented by Thomas Sharpton at the International Society for Microbial Ecology Annual Meeting, August 2010.
  4. Resolving the Hidden Biosphere: A high-throughput procedure that identifies OTUs from metagenomic data. Thomas J. Sharpton, Samantha J. Riesenfeld, Steven W. Kembel, Joshua Ladau, James O'Dwyer, Jessica L. Green, Jonathan A. Eisen, Katherine S. Pollard. Talk presented by Thomas Sharpton at Evolution, June 2010.
  5. PhylOTU: Quantifying Microbial Diversity and Identifying Novel Taxa from Metagenomic Data. Thomas J. Sharpton, Rebecca Lamb, Samantha J. Riesenfeld, Joshua Ladau, Steven W. Kembel, James O'Dwyer, Jessica L. Green, Jonathan A. Eisen, Katherine S. Pollard. Talk presented by Thomas Sharpton at the International Human Microbiome Conference, March 2011.
  6. Inferring the shapes of species ranges from distance-decay relationships. Joshua Ladau, Jessica L. Green, Katherine S. Pollard. Talk presented by Joshua Ladau at the Ecological Society of America Meeting, August 2010.
  7. Inferring the shapes of species ranges from distance-decay relationships. Joshua Ladau, Jessica L. Green, Katherine S. Pollard. Talk presented by Joshua Ladau at the International Society for Microbial Ecology Annual Meeting, August 2010.
  8. Linking beta diversity to the shapes of species ranges and niches using geometric probability. Joshua Ladau, Jessica L. Green, Katherine S. Pollard. Talk presented by Joshua Ladau as an invited seminar at Stony Brook University, October 2010.
  9. Phylogenetic Approaches to Microbial Metagenomics - Who is out there and what are they doing? Seminar presented by Katherine S. Pollard at New York University, Department of Biology, November, 2010.

Eisen Lab

Jonathan Eisen - sampling of talks with links to slides and in some cases audio

  1. July 2011 Talk for MBL Microbial Diversity Course
  2. June 2011 Talk for Indoor Air Meeting
  3. March 2011 Talk on "phylogenetic analysis of metagenomic data" for Keystone Symposium on Microbial Communities
  4. March 2011 Talk on 'Microbial Phylogenomics' for Bodega Bay Workshop on Applied Phylogenetics
  5. February 2011 Talk at UCSF
  6. February 2011 Talk at UC Berkeley
  7. January 2011 Talk on "Microbial phylogenomics" at JCVI
  8. September 2010 Talk at Lake Arrowhead Microbial Genomes Meeting
  9. April 2010 Talk about GEBA at ASBMB
  10. April 2009 Video of talk at DOE JGI User meeting

Aaron Darling

  1. March 2011. Next generation metagenomics, for Environmental Microbiology sound bites series at UNSW, Sydney, Australia
  2. January 2011. Comparative genomics and recombination in archaeal populations, for Sydney Joint Academic Microbiology Seminars, Sydney, Australia
  3. October 2010. de novo Metagenome phylogeny and linkage estimation, JGI, Walnut Creek, CA
  4. Poster presentation: September 2010. Estimating linkage among short metagenomic read fragments with Bayesian phylogenetics. Lake Arrowhead microbial genomes meeting.

Morgan Langille

  1. Langille MGI and Eisen JA (2010) “Characterizing Protein Families of Unknown Function” 18th Annual International Meeting on Microbial Genomics, September 12-16, 2010, Lake Arrowhead, California, USA.
  2. Langille MGI and Eisen JA (2010) “BioTorrents: a file sharing service for scientific data” 110th General Meeting of the American Society for Microbiology, May 23-27, 2010, San Diego, California, USA.
  3. Langille MGI and Eisen JA (2009) “BioTorrents: a file sharing service for scientific data” Biology and Mathematics in the Bay Area Meeting, Nov. 14, 2009, Santa Cruz, California, USA.
  4. July 2010. BioTorrents: A File Sharing Service For Scientific Data. Open Science Summit, Berkeley, California, USA.
  5. June 2010. BioTorrents: A File Sharing Service For Scientific Data” Bioinformatics Technology Forum, UC Davis, Davis, California, USA.

Guillaume Jospin

  1. Poster presentation: March 2011. Building de novo protein families. Keystone Symposia Microbial Communities Meeting in Breckenridge, CO


Dongying Wu

  1. Poster presentation: March 2011. Identify gene markers for different taxonomic groups in Archaea and Bacteria Genomes. Keystone Symposia Microbial Communities Meeting in Breckenridge, CO
  2. Poster presentation: March 2010. Identify Novel Phylogenetic Markers for the Archaea and Bacteria Genomes. Genomics of Energy & Environment 5th Annual DOE Joint Genome Institute User Meeting, Walnut Creek, California
  3. Poster presentation: March 2009. Phylogenetic Diversity Contributions of the Genomic Encyclopedia for Bacteria and Archaea Pilot Project. Genomics of Energy & Environment 4th Annual DOE Joint Genome Institute User Meeting, Walnut Creek, California
  4. Poster presentation: March 2007. Tree-Based Small Subunit rRNA Taxonomy Assigning Pipeline (STAP). Genomics of Energy & Environment 2th Annual DOE Joint Genome Institute User Meeting, Walnut Creek, California

Wu Lab

Martin Wu

  1. September 2010, Microbial Genomics and Evolution. Department of Biochemistry and Molecular Genetics, School of Medicine, UVA.
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