Birmingham Fellow, University of Birmingham UK

Manuscript preprint now online – Phinch data visualization framework

Our preprint for the Phinch software paper is now online! Please enjoy the PDF on bioRxiv while we patiently wait for the manuscript to go through the peer review process:

Bik, H.M. and Pitch Interactive (2014) Phinch: An interactive, exploratory data visualization framework for –Omic datasets, bioRxiv, doi: http://dx.doi.org/10.1101/009944

If you’re not familiar with this project – Phinch (http://phinch.org) is an open-source framework for visualizing biological data, funded by a grant from the Alfred P. Sloan foundation. This project has been an interdisciplinary collaboration between researchers (driven by myself at UC Davis) and Pitch Interactive, a data visualization studio in Oakland, CA. If you’re interested in loading up some data in this visualization tool, check out our GitHub wiki for full instructions on preparing files and metadata (if you’re already using the QIIME pipeline, you should be ready to go in ~10 minutes…we tried to make it that easy!)

Faculty Position at the University of Birmingham, UK

It’s official, I’ve landed myself back overseas! As of August 29, 2014, I’ve begun a faculty position at the University of Birmingham, UK – I’ve joined the School of Biosciences with a stated research focus in “Environmental Genomics”. My appointment is part of the Birmingham Research Fellowships scheme, aimed at recruiting interdisciplinary early-career researchers to develop campus expertise within specific focusContinue Reading

microBEnet: Lessons Learned from Building an Interdisciplinary Scientific Community in the Online Sphere

The Microbiology of the Built Environment Network (http://microBE.net – a project I’ve been involved with in the Eisen lab at UC Davis) has made it into the community page at PLoS Biology! Our article has been in the works for some time, and we’re now pleased to announce its official publication: Bik HM, Coil DA, Eisen JAContinue Reading

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 currentContinue Reading

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.

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