Author Archives: Jeremy Yoder

About Jeremy Yoder

Jeremy B. Yoder is an Associate Professor of Biology at California State University Northridge, studying the evolution and coevolution of interacting species, especially mutualists. He is a collaborator with the Joshua Tree Genome Project and the Queer in STEM study of LGBTQ experiences in scientific careers. He has written for the website of Scientific American, the LA Review of Books, the Chronicle of Higher Education, The Awl, and Slate.

STITCH, in time, could save a lot of array design

Posted on 12 Jul, 2016 by Jeremy Yoder

A new algorithm for processing DNA sequence data, STITCH, could lower costs for studies of genetic variation within species by reconstructing, or “imputing”, the sequences of individual samples within a larger dataset. The ongoing proliferation of high-throughput (or, ugh, “next … Continue reading →

Posted in association genetics, bioinformatics, genomics, methods, next generation sequencing, software | Tagged | Leave a comment

Making Maps in R, volume 2: ggplots

Posted on 1 Jul, 2016 by Jeremy Yoder

The open-source statisical programming environment R is truly a Swiss Army knife for molecular ecology. With the right code, R can processes genetic data and trait measurements, analyze how genetic variants relate to traits, reconstruct phylogenetic trees, and illustrate the … Continue reading →

Posted in howto, R, software | Tagged , | 7 Comments

The Fourth Reviewer: Pre-print reviews, parental monikers, and points for student participation

Posted on 14 Jun, 2016 by Jeremy Yoder

Tim Vines is an evolutionary ecologist who found his calling in the process of peer review. He was Managing Editor of Molecular Ecology from 2008 to 2015, launched The Molecular Ecologist in 2010, and he’s now the founder and Managing Editor of Axios Review. Here, Tim … Continue reading →

Posted in community, peer review, science publishing, The Fourth Reviewer | Tagged , , | Leave a comment

#Evol2016: See you in Austin!

Posted on 13 Jun, 2016 by Jeremy Yoder

We’re a few days out from Evolution 2016, the biggest conference of a North American evolutionary biologist’s year. It’s the joint annual meeting of the American Society of Naturalists, the Society of Systematic Biologists, and the Society for the Study … Continue reading →

Posted in community, conferences | Tagged | 4 Comments

The Fourth Reviewer: What problem is open peer review trying to solve?

Posted on 16 May, 2016 by Jeremy Yoder

Tim Vines is an evolutionary ecologist who found his calling in the process of peer review. He was Managing Editor of Molecular Ecology from 2008 to 2015, launched The Molecular Ecologist in 2010, and is the founder and Managing Editor of Axios Review. Here, Tim is … Continue reading →

Posted in community, peer review, science publishing, The Fourth Reviewer | Tagged | 5 Comments

Docker: making our bioinformatics easier and more reproducible

Posted on 13 May, 2016 by Jeremy Yoder

This is a guest post by Alicia Mastretta-Yanes, a CONACYT Research Fellow assigned to CONABIO, Mexico. Her research uses molecular ecology and genomic tools to examine the effect of changes on species distributions due to historical climate fluctuations as well … Continue reading →

Posted in bioinformatics, software | Tagged , | 1 Comment

The Fourth Reviewer: More suggestions about suggesting reviewers

Posted on 19 Apr, 2016 by Jeremy Yoder

Tim Vines is an evolutionary ecologist who found his calling in the process of peer review. He was Managing Editor of Molecular Ecology from 2008 to 2015, launched The Molecular Ecologist in 2010, and is the founder and Managing Editor … Continue reading →

Posted in community, peer review, science publishing, The Fourth Reviewer | Leave a comment

A note about e-mail subscriptions

Posted on 4 Apr, 2016 by Jeremy Yoder

If you recieve The Molecular Ecologist by e-mail, you’re far from alone — we have almost 650 subscribers recieving e-mailed posts via the Feedburner service. (How do you know if you’re one of them? You are if you’re reading this … Continue reading →

Posted in housekeeping, technical | Tagged | Leave a comment

Thanks!

Posted on 31 Mar, 2016 by Jeremy Yoder

Our crowdfunding campaign wrapped up last night at midnight, with a total of $1240 pledged by 24 supporters — enough to support the basic costs of the blog, and to tackle some of our more ambitious plans for the future, … Continue reading →

Posted in community, funding, housekeeping | 1 Comment

The Fourth Reviewer: Help! A reviewer just contacted me directly.

Posted on 29 Mar, 2016 by Jeremy Yoder

Tim Vines is an evolutionary ecologist who found his calling in the process of peer review. He was Managing Editor of Molecular Ecology from 2008 to 2015, he launched The Molecular Ecologist in 2010, and he’s the founder and Managing … Continue reading →

Posted in community, peer review, science publishing, The Fourth Reviewer | 2 Comments