PSB 2021: Bioinformatics of Corals Workshop

We invite you to a special workshop as part of PSB 2021

About the workshop

Corals are important natural resources that are key to the oceans’ vast biodiversity and provide economic, cultural, and scientific benefits. As a result of anthropogenic activities, locally and globally, coral reefs are declining rapidly. The environmental sensitivity and symbiotic biological complexity of corals makes understanding the genomic variability that influences vulnerability and resilience of local coral reef systems very challenging. Corals are made up of thousands of different organisms, including the animal host and single celled dinoflagellate algae, bacteria, viruses, and fungi that coexist as a holobiont, or metaorganism. Thus, corals are more like cities than individual animals, as they provide factories, housing, restaurants, nurseries, and more for an entire ecosystem, both at the micro and macro levels.

A large amount of genomic, transcriptomic and other omics data from different species of reefbuilding corals, the uni-cellular dinoflagellates, plus coral microbiome data (where corals have possibly the most complex microbiome yet discovered, consisting of over 20,000 different species), is becoming increasingly available for corals. This is a terrific opportunity for bioinformatics researchers and computational biologists to contribute to a timely, compelling and urgent investigation of critical factors that influence reef health and resilience.

We have recruited  some of the premier experts who are working on bioinformatics of coral reefs to participate in our workshop already. We will introduce this exciting topic to the PSB  community, with the goal of energizing collaborations and approaches to address the compelling problems in this captivating and complex system. It is particularly relevant for this session to occur in Hawai'i given the abundance of and reliance on coral reefs in the region. Coral genomes from this location show some of the highest complexity to date, exemplifying the bioinformatic challenges faced by the field in the study of the coral metaorganism. This convergence of complex multi-organism data and critical need to address this globally declining ecosystem provides a timely and impactful topic for a Workshop at PSB 2021. 

Invited Speakers

Christian Voolstra research area is environmental genomics with a focus on acclimation and adaptation of marine invertebrates. In particular, Dr. Voolstra studies coral metaorganism function combining ecological, environmental, microbial, and molecular approaches. Corals are metaorganisms composed of the coral host, intracellular photosynthetic dinoflagellate symbionts, and associated microbiota. Together these so-called coral holobionts form the keystone species of reef ecosystems. Dr. Voolstra’s most recent research has particularly advanced knowledge of how the bacterial microbiome contributes to coral animal host acclimation and adaptation. Dr. Voolstra has published over 200 peer-reviewed research papers, various book chapters, and holds patents related to bioactive lead structures from marine organisms. Dr. Voolstra is a Scientific Coordinator of the Tara Pacific consortium and a steering committee member of the Global Invertebrate Genomics Alliance (GIGA). Dr. Voolstra received his PhD at the Institute for Genetics in Cologne, Germany in 2006 and was a Postdoctoral scholar at the University of California, Merced from 2007-2009. He was appointed Assistant Professor of Marine Science at KAUST’s Red Sea Research Center in 2009, and in 2015 was promoted to Associate Professor. From 2016 to 2019, Dr. Voolstra served as the Associate Director of the Red Sea Research Center at KAUST. In 2019, Dr. Voolstra became Professor of Genetics of Adaptation in Aquatic Systems at the University of Konstanz, Germany.

Cheong Xin (CX) Chan is a Research Fellow at the School of Chemistry and Molecular Bioscience, and a Team Leader at the Australian Centre for Ecogenomics of the University of Queensland, Australia. Chan's core research interest is the genome evolution of microbes and their symbiotic interactions with other species. His team routinely adopts cutting-edge genomic technologies and transformative computational approaches in comparative de novo genomics and scalable phylogenomics. A core research theme in his group is the evolutionary transition of dinoflagellate algae from free-living to symbiotic, and how these algae diversified to become one of the most successful symbionts in corals and coral reefs.

Zachary Fuller has an undergraduate degree in Biology from Creighton University and received his PhD in Biology at Penn State (2017) where he worked with Steve Schaeffer. His dissertation focused on investigating the mechanisms establishing chromosomal inversions in populations of Drosophila, as well as analyzing adaptive evolution in African honey bees. For his postdoc, advised by Molly Przeworski at Columbia University, Zach is investigating the dynamics of deleterious alleles in humans, funded by an NRSA fellowship, as well as the population genetics of corals. Along with his collaborators, he has developed resources for assembling chromosome-scale coral genomes and imputing genotypes in low-coverage sequencing of large sample sizes to investigate the genetic basis of bleaching response.

Ross Cunning is a research scientist at the John G. Shedd Aquarium in Chicago, IL, where he studies the biology and conservation of reef corals under climate change. Cunning completed his Ph.D. at the University of Miami and an NSF Postdoctoral Research Fellowship in Biology at the Hawaii Institute of Marine Biology, and works on reefs in the Pacific and Caribbean. His research aims to identify genetic and ecological factors that promote heat tolerance in corals, and apply this knowledge in coral conservation and restoration.

Call for participation

We invite the community to submit abstracts on relevant research which is in progress or has been published after January 1, 2019  for consideration as short talks and posters. Presenters of accepted abstracts are required to make the presentation themselves, and must register and pay to attend the PSB 2021 conference by September 30, 2020.  If you submit an abstract by the August 15, 2020 deadline, you will be notified whether or not your abstract has been accepted by September 1, 2020. 

  • Authors are required to submit a brief abstract (maximum 200 words) by the abstract deadline (August 15, 2020. Timezone of your choice).
  • The abstract should be a brief and concise summary of the background/motivation for the study, method, and result(s), as well as conclusion/statement of significance. If the abstract represents published work, the full reference should be included and does not count towards the 200 word limit.
  • Selected abstract talks will be presented during the workshops, PSB style. The length of a talk will be 15 minutes (10 minute talk, plus 5 minutes for questions).
  • All submissions must be submitted directly by email to Lenore Cowen:

Key Dates

  •  Abstract Submissions due: August 15, 2020 at midnight (timezone of your choice)
  •   Notification of acceptance: September 1, 2020
  •   Meeting: January 3-7, 2021

Session Organizers

 Lenore Cowen

Tufts University

Department of Computer Science

Judith Klein-Seetharaman

Colorado School of Mines

Department of Chemistry

 Hollie Putnam

University of Rhode Island

Department of Biological Sciences