Fuzzy zeros in percentile normalization method to correct for batch effects

We recently published a method to normalize data that corrects for batch effects and allows for pooling of raw data across studies. In this post, I want to discuss more about the important (but potentially confusing) aspect of our method, where we add noise to the zeros before performing the normalization. I’ve gotten a few …

Microbiome Bioinformatics Postdoctoral Scientist, Colorado State University

The Metcalf lab at Colorado State University is seeking a microbiome bioinformatics postdoctoral scientist. The scientist will analyze multi-omics data sets, including but not limited to: amplicon sequencing data, shotgun metagenomics data, and metabolomics data. Min. reqs. include: Ph.D. in bioinformatics, ecology, microbiology or similar field. Proficient in coding languages (Python preferred). Demonstrated knowledge of …

4th Annual MetaSUB Conference (Aug. 14-15) and Call for Abstracts

We are excited to announce the MetaSUB International Consortium’s 4th Annual Conference on urban metagenomics to be held at the Tivoli Ecoresort Praia do Forte Bahia in Brazil, from August 14-15, 2018. The conference is co-hosted by Weill Cornell Medicine and the AC Camargo Cancer Center. You can register for the meeting here: http://metasub.org/metasub-2018-conference-registration-form/ If you’d …

US Interagency Strategic Plan for Microbiome Research

Some important reading for those interested in microbiomes. NSF’s mission is to advance the progress of science, a mission accomplished by funding proposals for research and education made by scientists, engineers, and educators from across the country. From NSF: A group of 23 U.S. government agencies, including the National Science Foundation (NSF), have joined to …

Cool exhibit at Harvard: “Microbial Life: A Universe at the Edge of Sight.”

Neat article in the Harvard Gazette about an awesome-sounding exhibit, “Microbial Life: A Universe at the Edge of Sight.”.  Put together by Roberto Kolter and Scott Chimileski, the exhibit highlights microbial life… particularly the discoveries of microbial ecology over the last couple of decades.  Looks like a cool blend of science and art.

Podcast-Radio Joe Live From The 5th Annual SLOAN Microbiology of the Built Environment Conference – University of Colorado Boulder

This week Radio Joe was live from beautiful Boulder Colorado and Colorado University at the 5th SLOAN Microbiology of the Built Environment Conference. The conference is a gathering of the leading researchers in the world that study the microbiome of the built environment. A diverse group of scientists from around the world have been meeting …

Watercolours “created” by bacteria (sort of, but still really cool)

OK this is cool :This watercolour painting was created by artistic bacteria | WIRED UK Though not quite what the headline says. From the article With Park’s guidance, Roberts placed Serratia marcescens – a red pigmented bacteria – on to agar plates previously painted with watercolours. When coming into contact with the paint, the bacteria …

One last call for help with Sloan-funded MoBE paper collection

Back in September we posted a call for help with our “comprehensive” database of publications resulting from the Alfred P. Sloan Foundation program in the Microbiology of the Built Environment.   We’ve tried database scanning, begging people for help, public posting, manually digging through Google Scholar, grant reports, etc.  Our hope is to use this collection …