Postdoctoral Researcher

Three new papers published in 2014

As we roll into spring 2014, I’m happy to announce the publication of three new manuscripts related to different projects I’ve been involved with:

Our manuscript for the PhyloSift pipeline was selected for the PeerJ Picks 2014 Collection. I’ve been working as a member of the software development team for this pipeline during my current postdoc position at UC Davis:

Darling A., Bik H.M., Jospin G., Lowe E., Eisen, J.A. (2014) PhyloSift: A pipeline for phylogenetic taxonomy assignments from environmental metagenome data, PeerJ, 2: e243.

A second manuscript has resulted from a project focused on using high-throughput sequencing as an environmental monitoring tool in marine sediments (carried out in collaboration with CSIRO Australia and US EPA):

Chariton A., Ho K., Proestou D., Bik H., Simpson S., Portis L., Cantwell M., Baguley J., Burgess R., Pelletier M., Perron M., & Gunsch C. (2014) A molecular-based approach for examining responses of microcosm-contained eukaryotes to contaminant-spiked estuarine sedimentsEnvironmental Toxicology and Chemistry, 33(2): 359-369.

Last but not least is a community response and commentary discussing the existence of species in meiofaunal taxa <1mm in size:

Morgan, M.J., Bass, D., Birky, C.W., Bik H., Blaxter, M., Crisp, M.D., Derycke, S., Fitch, D., Fontaneto, D., Hardy, C.M., King, A.J., Kiontke, K.C., Moens, T., Pawlowski, J.W., Porazinska, D., Tang, C.Q., Thomas, W.K., Yeates, D.K., Creer, S. (2014) A critique of Rossberg et al.: noise obscures the genetic signal of meiobiotal ecospecies in ecogenomic datasets. Proceedings of the Royal Society B, 281: 20133076.

New affiliation with the Center for Population Biology at UC Davis

I’ve recently been awarded Postdoctoral Associate status with the Center for Population Biology (CPB) at UC Davis, following an internal application process. This is an exciting honor, and I’m looking forward to participating in this prestigious scientific community in 2014! A full list of CPB Postdoctoral Associates can be found here.Continue Reading

Funding awarded for NSF Research Coordination Network

The National Science Foundation recently recommended our Research Coordination Network proposal focused on Eukaryotic Biodiversity Research for funding. Now the paperwork is complete and the award is official!  This project is entitled “RCN EukHiTS: Eukaryotic Biodivesity Research using High-throughput Sequencing”, and represents a collaborative effort between the University of California Davis (myself as PI) andContinue Reading

New Paper: Intragenomic Variation in Nematode rRNA

Hot off the presses! Our new paper is out this week in PLoS One: Bik HM, Fournier D, Sung W, Bergeron RD, Thomas WK (2013) Intra-Genomic Variation in the Ribosomal Repeats of Nematodes. PLoS ONE, 8(10): e78230. doi:10.1371/journal.pone.0078230 The above link takes you to the PLoS article page – and here’s the abstract: Ribosomal loci represent aContinue Reading

Professors for the Future 2013-14 Fellowship

I’m excited to announce my participation in the “Professors for the Future” program at UC Davis for the 2013-14 academic year. I was selected as a fellow following faculty nomination, a written application and interview process. Here’s a bit more about the program: Professors for the Future (PFTF) is a year-long competitive fellowship program designedContinue Reading

Graduate Student Opportunity in Marine Biology and High-Throughput Sequencing

I have a recently-funded project in need of a graduate student, to be admitted spring 2014. This project will be applying high-throughput DNA sequencing techniques in the study of meiofaunal communities in the Arctic. The student will be based at the University of Alaska, Fairbanks (PIs Sarah Hardy and Arny Blanchard), but will work closely with myselfContinue Reading

Sloan Foundation Award for Data Visualization tools

I’m ecstatic to announce that I’ve just been awarded my first research grant as PI – a $250k, 1-year grant from the Alfred P. Sloan foundation to develop a software prototype: “A Research-Driven Data Visualization Framework for High-Throughput Environmental Sequence Data” This project will be carried out in collaboration with Pitch Interactive, a data visualizationContinue Reading

An Introduction to Social Media for Scientists

Miriam Goldstein and I have been humbled by the overwhelmingly positive reception of our recent paper in PLOS Biology, entitled An Introduction to Social Media for Scientists. Since being published in April 2013, the article has had >40,000 page views and >3,000 PDF downloads – and added to that, active social media sharing and discussions.Continue Reading

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

UPDATE: I’ve written a wrap-up blog post here that amalgamates presentation links and notes from the SMBE Satellite meeting. Thanks everyone for coming to UC Davis, the event was a great success! Myself and my former PI (Kelley Thomas at the University of New Hampshire) recently received funding from The Society for Molecular Biology andContinue Reading

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

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. YouContinue Reading