Biodiversity and Environment Network

Past Activities

Collaborative Fund in Biodiversity and Environment Population/Genomics Data Analysis Workshop (PDF)

  • April 6, 2015
    USC UPC, RRI 421
    Sergey Nuzhdin (USC): Opening remarks
    Angela DePace (Harvard): How enhancers create transcriptional circuits
    Paul Marjoram (USC): GRNs: why I care about them, and why they keep me awake at night
    Maria Samsonova (SPbSPU): Sequence-based model of gap gene regulatory network
    Remo Rohs (USC): Deconvolving the recognition of DNA shape from sequenc
    David Wild (Warwick): Causal structure identification 

Biodiversity Seminar

  • March 20, 2015: 12pm
    UPC; RRI 101
     (followed with BBQ at Captain Jack, San Pedro, contact Sergey Nuzhdin,
    Malaysian Palm Oil Board:
    Dr. Rajanaidu,
     Brief introduction to oil palm germplasm;
    Dr. Rajinder Singh, Oil palm genome sequence and mining of genes associated with agronomic traits for application in breeding. 

Biodiversity and Environment Science and Social Hour

  • August 21, 2014: 12pm
    UPC; RRI 301
    Stephen Jackson
     (Warwick Institute for Systems Biology the United Kingdom), FT–the lesser known sides to its character

Spring 2014 Expertise Exchange Sessions – Torrey Webb room, 4pm, Tuesday bi-weekly
Biodiversity and Environment Science and Social Hour, sessions followed with wine and cheese
Each session will feature two local speakers (20 min each) and discussion sessions on biodiversity topics of interest. 

  • February 25, 2014
    Eric Stein (S. Ca. Coastal Water Res. Project), Using aquatic community composition as a tool for evaluating stream condition and influencing management actions.
    Regina Wetzer (NHM, LA County), Is it Real? Museums as the Hub for Specimen-based Research.
  • March 11, 2014
    Eric von Wettberg (Florida International U), Conservation genetics of endangered plants of the Florida Keys: sea level rise and restoration planning
    Dan Gluesenkamp (Cali Native Plant Society), CNPS at 50: progress in preservation, prospects for the future.
  • March 25, 2014
    Travis Longcore (USC Spatial Sciences Institute),
    Use of Natural History Records in Reconstruction of Pre-urban Southern California Landscapes
    Sandy Eckel (USC Keck, Division of Biostatistics),
    Quantifying respiratory health effects of air pollution in the Southern California Children’s Health Study
  • April 22, 2014
    Ariel Levi Simons, The TIGER project: Geotagged environmental data and education.
    Caleb Finch, Air pollution neurotoxicology from cells to populations: new findings and remaining puzzles.

Spring 2014 Biodiversity Workshops

  • January 17-18, 2014: Joint Biodiversity Workshop at the Boone Center on Catalina Island
    Shellfish: Science and Production
    Invited Speakers:
    Darren Johnson, Brian Livingston, Douglas Pace (California State University, Long Beach)
    Peter Edmunds (California State University, Northridge)
    Daniel Campo, Nathan Churches, Megan Hall, Dennis Hedgecock, Dale Kiefer, Diane Kim, Hamdi Kitapci, Jacqueline Lin, Roberta Marinelli, Sergey Nuzhdin, Phil Taylor (University of Southern California)
    Paul Olin (CA Sea Grant, Aquaculture)
    Kelly Stromberg (Catalina See Ranch)
  • January 31, 2014: Collaborative Fund in Biodiversity and Environment Workshop at USC
    10:00am-4:30pm: RRI 101, Followed by BBQ at 5:00pm in RRI 421
    Population / Genomics Data Analysis
    Sergey Nuzhdin (USC) 10:00am, Opening Remarks
    Paul Marjoram (Keck, USC) 10:15am, Sequence-based follow-up to GWAS: a case study.
    Kim Siegmund (Keck, USC) 10:45am, Genealogically-based analysis of tumor growth using exome data.
    Kirk Lohmueller (UCLA) 11:15am, Cross-species analysis of the distribution of fitness effects of amino-acid mutations.
    Josh Akey (U Washington) 12:00pm, Adventures in recent human evolution told by massively large catalogs of human genetic variation.
    Lauren McIntyre (U Florida) 2:15pm, Reads are random: a Bayesian model of allele specific expression.
    Peter Ralph (College, USC) 3:00pm, Local adaptation: When does it happen and when can we tell?
    Christoph Lippert (Microsoft) 3:30pm, LIMIX: A flexible and efficient framework for the genetic analysis of multiple traits.
    Nicolo Fusi (Microsoft) 4:00pm, Detecting regulatory gene–environment interactions with unmeasured environmental factors.
  • February 13-14, 2014: Biodiversity and Environment Visionaries Workshop
    The evolution of regulatory networks
    Invited Speaker: Mike Lynch, (Indiana University), Host: Peter Ralph
    Thursday February 13, 11:00am-12:30pm, RRI 101 (talk and discussion), The evolution of transcriptionfactor binding sites
    Thursday February 14, 11:00am-12:00pm, RRI 101 (talk), Mutation, Drift, and the Origin of Subcellular Features
    Also please join us for informal discussions (just show up, or email for info):
    Thursday, Feb. 13th, 3-4pm, RRI 101
    Friday, Feb. 14th, 2-4pm, RRI 101
  • March 13, 2014: Biodiversity and Environment Mini-workshop
    10:00am-12:00pm: RRI 421, lunch provided
    Invited Speaker: Alexander Mikheev
    (Okinawa Institute of Science and Technology), Working with degraded DNA: laboratory and bioinformatic approaches
  • April 8, 2014: Biodiversity and Environment Mini-workshop
    4:00pm to 5:30pm: Torrey Webb Room, UPC
    Invited Speaker: Roberta Marinelli (USC Wrigley Institute), Alta Sea—past, present and future
  • May 2-4, 2014
    Invited Speaker: Sean Carroll
     (University of Wisconsin-Madison), Evolution, development, and novelty.
  • May 5, 2014: 2:00pm–5:00pm
    UPC; RRI 101

    Vasiliki Anest, Jennifer Dyer, Rick Friedman (USC Stevens Technology Transfer Services), From Industry Collaboration to Technology Commercialization.
    For more information and RSVP please email: or 213-821-0938.

Southern California Evolutionary Genetics and Genomics at USC
Saturday, March 1, 2014, 10:00am-2:30pm
More information and free registration at:

SCalE is a regional meeting for the many local labs working at the intersection of genetics, genomics, and evolution. Come on out to present your work, hear new ideas, find advice or collaborators, jobs or employees. Registration is free; please register at so we can make sure to have enough lunch for you (also free). 

June 6-7, 2013: Mini-Symposium II: Biodiversity and Environment Network: Year in Review

This 2-day symposium gathered affiliated USC researchers to focus on an academic year-end review of tasks and accomplishments by the program; joint planning and curriculum development; and discussions of potential collaborative proposals by network members. 

Spring 2013: Joint Seminar Series in Biodiversity and Environment (USC and the Natural History Museum)

  • January 17 (NHMLAC) Scott Edwards, Harvard (host Matt Dean)
    Genomic, geographic and temporal tracking of a rapidly evolving host-pathogen interaction: House Finches and Mycoplasma
  • February 14 (NHMLAC) Keith Crandall, George Washington University (host Regina Wetzer)
    Computational Biology: Bridging natural history and genomics
  • February 28 (USC) Greg Gibson, Georgia Tech (host Ian Ehrenreich)
    Genetic variation in human from evolutionary perspective
  • March 14 (USC) Doug Cook, UC Davis
  • March 28 (NHMLAC) Nancy Knowlton, Smithsonian Institution (host Regina Wetzer)
    Innovation in the Nation's Attic: Understanding and conserving a biodiverse planet
  • April 18 (USC) Mick Follows, MIT
    Resource competition and the biogeography of nitrogen fixing phytoplankton

Fall 2013 Expertise Exchange Sessions – USC Torrey Webb room, 4pm
Each session will feature two local speakers (20 min each) and discussion sessions on biodiversity topics of interest.

  • September 12, 2013:
    Dennis Hedgecock99% of oyster larvae die because of viability selection
    Fabrizio Ghizelli, Evolutionary and functional genomics in species with a doubly uniparental inheritance of mitochondria
  • September 24, 2013:
    Peter RalphMaking maps from genomes: how genetic identity reflects geography
    John Wilson, Mapping and Classifying Biophysical Landscape Attributes
  • October 8, 2013:
    Brad FoleyA novel Bayesian approach to social structure uncovers cryptic regulation of group dynamics
    Nicholas Weller, Cheap, easy, and connected: the conditions for coordination on a network
  • October 22, 2013: Evolution and Design in Flying Animals and Aircraft
    Michael HabibAnimals
    Geoff SpeddingAircraft
  • November 5, 2013:
    Matt DeanThe evolutionary genetics of penis shape variation
    Xiaoming WangDog evolution, a paleontologic perspective
  • November 19, 2013:
    Khalil IskarousHierarchy and Information, in English
    David LaurieSearching for Function: Signals of Strong Purifying Selection in Synonymous Sites
  • December 3, 2013: TBA
  • December 17, 2013: TBA

Distinguished Speaker (TBD) – November, 2013

Fall 2012: Joint Seminar Series in Biodiversity and Environment (USC and the Natural History Museum)

  • September 20, 2012 (USC):
    Sharon Strauss
    , UC Davis (host Sergey Nuzhdin), The inseparable, interacting effects of community complexity and evolution
  • October 4, 2012 (NHMLAC):
    Steve Kay
    , USC (host John Long), Architecture and comparative genomics of circadian networks
  • October 18, 2012 (USC):
    Brad Cardinale
    , University of Michigan (host Roberta Marinelli), Biodiversity loss and its impact on humanity
  • November 1, 2012 (NHMLAC):
    Mary Schweitzer
    , NCSU (host Luis Chiappe), Dinosaurs and diversity: How can fossils contribute?
  • November 15, 2012 (USC):
    Tony de Tomasso
    , UCSB (host Andrew Gracey), Natural transplantation and chimerism in the colonial tunicate, Botryllus schlosseri
  • November 29, 2012 (NHMLAC):
    Rob Guralnick
    , UC Boulder (host Dean Pentcheff), The New Vast Machine: Challenges and solutions to mapping global biodiversity and its change
  • December 13, 2012 (USC):
    Dave Stahl
    , University of Washington (host Jim Moffett) , The environmental significance of ammonia oxidizing Archaea

Sept 13-14, 2012: Mini-Symposium I: “Collaborations in Biodiversity: Interweaving Disciplines”

Designed to introduce biodiversity-associated researchers at USC’s Main Campus and Keck Medical Campus and the Natural History Museum of Los Angeles County to one another, and have a broad discussion about research interests, and potential future projects.  Guest speakers: Dr. Mark Rausher from Duke University, and Dr. Bret Payseur from University of Wisconsin-Madison.