Holly M Bik

SMBE Satellite Meeting on Eukaryotic -Omics: April 29 – May 2, 2013, UC Davis Conference Center

admin — Sun, 17 Feb 2013 03:52:01 +0000

Myself and my former PI (Kelley Thomas at the University of New Hampshire) recently received funding from The Society for Molecular Biology and Evolution to hold an SMBE Satellite Meeting focused on Eukaryotic -Omics at UC Davis this spring. All interested researchers are encouraged to attend!

Meeting description: The SMBE Satellite Meeting on Eukaryotic -Omics will bring together an interdisciplinary pool of researchers to discuss current efforts, challenges, and future directions for high-throughput sequencing approaches focused on microbial eukaryotes (environmental studies of non-model organisms). The meeting program will encompass investigations of eukaryote biodiversity, ecology, and evolution, using approaches such as rRNA marker genes, shotgun metagenomics, metatranscriptomics, and computational biology tools and software pipelines. In addition, we are hosting a 2.5 day QIIME workshop directly following the main meeting, running Thursday afternoon May 2nd until Saturday May 4th.

Abstract submission is now open (Deadline February 22, 2013), and travel grants are available. Registration details available here on on the SMBE meeting website.

PLoS ONE paper – oil spill impacts in the Gulf of Mexico

admin — Fri, 13 Jul 2012 05:42:06 +0000

The first results are out from our ongoing work investigating the impacts of the 2010 Deepwater Horizon oil spill on sediment microbial eukaryote communities. This work was made possible by an NSF RAPID grant awarded to our collaborative group at the University of New Hampshire, Auburn University, and the University of Texas San Antonio. You can read our new PLoS ONE paper here:

Bik H.M., Halanych K.M., Sharma J., Thomas W.K. (2012) Dramatic Shifts in Benthic Microbial Eukaryote Communities following the Deepwater Horizon Oil Spill. PLoS ONE, 7(6):e38550. http://dx.plos.org/10.1371/journal.pone.0038550

TREE Review and Spring Travel Schedule

admin — Thu, 23 Feb 2012 06:19:09 +0000

Pleased to announce the publication of our new review paper in Trends in Ecology and Evolution – this paper is an overview of high-throughput marker gene sequencing approaches (18S rRNA), aimed at a general audience of biologists and ecologists. If you’ve been searching for a non-technical overview of the current computational pipelines (e.g. you have some imminent data analysis to do), then I highly recommend you give it a read:

Bik, H.M., Porazinska, D.L, Creer, S., Caporaso, J.G., Knight, R. & Thomas, W.K.T. (advance access) Sequencing our way towards understanding global eukaryotic biodiversity. Trends in Ecology and Evolution http://dx.doi.org/10.1016/j.tree.2011.11.010

This spring I’ll be doing quite a bit of travel. I’m currently attending the Ocean Sciences Meeting in Salt Lake City until Friday February 24th, and my upcoming trips are as follows:

March 5-7 – Participant at the 13th Workshop of the Genomic Standards Consortium, Shenzhen, China (hosted at BGI)
March 12-13 – Invited participant at the NIGMs workshop for Postdocs transitioning to independent positions, Bethesda, Maryland (NIH campus)
March 18-19 – Panel discussion and invited speaker at the Association of Biomolecular Resource Facilities annual meeting (ARBF 2012), Orlando, Florida (Disney’s Contemporary Resort)
April 3-6 – Invited session chair at the Evolution of Caenorhabditis and Other Nematodes meeting, Cold Spring Harbor, New York (CSH Laboratory)
April 9-11 – Invited participant at the Advancing Towards Professorship in Biology, Ecology and Earth Systems Sciences workshop (ATPinBEESS), Corvallis, Oregon (Oregon State University)

New year, New job, New website

admin — Mon, 30 Jan 2012 18:03:01 +0000

2012 is turning out to be a year of fresh starts. After almost 2 years working at the University of New Hampshire, I’ve now officially relocated myself 3000 miles to the West. I’m very excited to join Jonathan Eisen’s lab in the Genome Center at the University of California, Davis. I’ll be continuing to work with high-throughput environmental sequence datasets (454, Illumina) generated from microbial eukaryotes (nematodes, protists, fungi – anything that is tiny and lives in marine sediment!), but in the Eisen Lab I’ll be moving beyond rRNA genes to tackle eukaryotic metagenomic/transcriptomic data. We’ll be working to improve computational pipelines and hopefully figure out a way to informatively link these disparate data types. The goal, after all, is to obtain a complete view of ecosystem function.

I’ve committed to update this website frequently – keep watching this space for more exciting news on the horizon!