How to get some extra eyes on your publication – email everyone cited in it

Interesting way of getting people to look at a paper. I am sure other places do this but I have not seen it too often (though this was in SPAM and I only found it by searching SPAM for some key words which I occasionally do to find mislabelled messages.


——— Forwarded message ———-
From: Gabriel Valiente / De Gruyter Open <>
Date: Thu, Jun 9, 2016 at 6:45 AM
Subject: Metagenomics-Mathematical, Statistical and Computational Methods

Dear Colleague,

It is my pleasure to inform you that your paper has been cited in an article “Machine learning for metagenomics: methods and tools” published recently in Metagenomics – Mathematical, Statistical and Computational Methods (

Here is the link to the article:

Metagenomics – Mathematical, Statistical and Computational Methods is a fully peer-reviewed, open access, electronic journal covering the emerging field of metagenomics. The scope of the journal covers mathematical, statistical and computational methods for metagenomics and their use in biomedical and biotechnological applications.

The journal is now free both for readers and authors. We publish research papers as well as surveys on the subject and all accepted papers are quickly published online. All manuscripts should be submitted to the Editorial Office via

Using this opportunity, we would like to invite you to consider publishing your work in Metagenomics – Mathematical, Statistical and Computational Methods.

Best regards,

Gabriel Valiente
EiC, Metagenomics

Posted in Misc. | Leave a comment

Flow Cytometry Course for Aquatic Sciences @ Bigelow Laboratory Sept 12-16, 2016

Introduction to Flow Cytometry for Aquatic Sciences

September 12-16, 2016
Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, USA

Course information and Registration:

This course is organized by Dr. Nicole Poulton, Director of the J.J. MacIsaac Facility for Aquatic Cytometry ( and will include additional lecturers who are experts within their fields. Registration is limited to 10 participants.

The 5-day course will include both lecture and laboratory sessions, and provides aquatic and environmental scientists and/or commercial entities an introduction to flow cytometry, including the theory of operation as well as an introduction to different flow cytometric instrumentation (analyzers and cells sorters) including imaging cytometry tools (FlowCAM). Both breakfast, coffee breaks and lunch are provided on all days and will also include one group dinner with the lecturers (Maine Lobster Bake). Lodging is not included.

Throughout the week topics will include discussions on the wide number of applications within the aquatic sciences including, but not limited to:

1. Culture & Environmental sample enumeration (viruses, bacteria, phytoplankton and heterotrophic protists), including preservation techniques.

2. Cell Sorting for Biogeochemical analyses (C, N, & P)

3. Cell sorting for isolation and cultivation.

4. Imaging Cytometry for Aquatic applications (using FlowCAM).

5. Single cell sorting for whole genome amplification (WGA) and genome analysis.

Guest lecturers will include:

Dr. Michael Lomas, Director of the National Center for Marine Microalgae (
Dr. Ramunas Stepanauskas, Director of the Single Cell Genomics Center (

With additional assistance from the following Facility & Bigelow Laboratory staff members:
Dr. Steven Baer
Laura Lubelczyk
Brian Thompson

Corporate Participants include:

Fluid Imaging Technologies

Please forward this information on to anyone interested in learning aquatic flow cytometric techniques in a laboratory-intensive week-long course on the coast of Maine this fall. For questions or additional information, or specific aquatic application requests, please contact Nicole Poulton: npoulton

Thank you!

Posted in Misc. | Leave a comment

Interesting: Letters from grad school

of possible interest – just got this in email


Call for submissions:
For every graduate student, graduate school is a different experience filled with ups, downs, failures, and successes. The goal of Letters from Graduate School is to build a collective of graduate school experiences from graduate students in the biomedical/biology PhD programs–your experience, in your own voice!
We are looking for graduate students who are interested in writing about their stories and experiences in graduate school–the good and the bad. We are creating a platform for sharing these stories to highlight the diversity of graduate school experiences. These stories will be shared through our web platform, and a selected set of entries will be compiled into a book.
We encourage your entry to be focused on a single topic that was formative in your graduate school experience. We have a few sample topics listed below, but don’t feel limited to our suggestions; we want to include as many unique perspectives as possible.
If you are interested in writing for us, please fill out the short form on our website – and we will get back to you. All essays will be edited in collaboration with the author before publication. We will respect authors who wish to share their story anonymously.
For any questions, email us at
Looking forward to hearing from you,
 Kayla Lee
 Chiara Ricci-Tam
 Yarden Katz
The example topics below are divided into four sections, corresponding to graduate school stages: “Early years”, “The grind”, “Final stretch” and “Post-PhD”. Submissions should be under 2,000 words.
Early years
  • Why go to graduate school?
  • How to choose a lab?
  • Making friends in graduate school
  • Managing graduate school with a family
  • Rotations: getting the most out of them
The grind (mid-graduate school)
  • Intra-lab conflicts
  • On paper writing and publishing
  • Scooping: the threats, reality and recovery
  • Finance and graduate school
  • Depression and anxiety in graduate school
  • Switching labs
  • Deciding to quit graduate school
  • Being a minority in science
  • Sexism, racism, and classism in science
Final stretch (writing thesis)
  • Writing the thesis
  • Leaving things behind
  • Keeping in touch
Post-PhD (transitioning out of graduate school, finding next step)
  • Asking (and writing) your letters of recommendation
  • Finding a postdoc
  • Finding alternative (non-academic) paths
  • Learning from the graduate school experience
Posted in Misc. | Leave a comment

Special Seminar hosted by Alliance for Diversity in Science and Engineering_ Friday, June 24

Dr. Denneal Jamison-McClung will give a talk hosted by Alliance for Diversity in Science and Engineering – UC Davis (ADSE-UCD) on Friday, June 24th at 2:00-3:30 (see attached flyer).  Anyone interested in the subject matter is welcome to attend.

Denneal Jamison-McClung Diversity in Pathways.pdf

Posted in Misc. | Leave a comment

Faculty Positions at #UCDavis in Disease Biology (1 in Entomology, 1 in PlantPath)


UC Davis is recruiting two faculty, one each in Entomology and Plant Pathology, to work on organisms related to disease biology. These hires are part of a number of recent and potential future hires in research and teaching in vector-borne diseases, virology, and other plant and animal health-related sciences and will complement a vibrant affiliated faculty community on the campus.


The Department of Plant Pathology in the College of Agricultural and Environmental Sciences at the University of California, Davis, is recruiting an Assistant Professor of Plant Pathology, with an emphasis in Virology. This is an academic year (9-month), tenure track, Assistant/Associate Professor position that includes translational research and outreach relevant to the mission of the California Agricultural Experiment Station (AES). The successful candidate is expected to develop an independent, productive and competitively funded research program in fundamental and/or applied Virology, particularly regarding viruses and/or subviral agents associated with plants. The appointee will be responsible for teaching at the undergraduate level in courses supporting Plant Pathology and the Global Disease Biology major, and at the graduate level in virology supporting the graduate program in Plant Pathology. Mentoring of graduate students, undergraduate student advising, curricular development, participation in and development of outreach programs, and performance of departmental and university service is expected. Applicants should submit curriculum vitae including publication list, a statement of research and a separate statement describing teaching interests and background, a summary or abstract of the Ph.D. dissertation, and the names, addresses including e-mail, and telephone numbers of three references online at A statement of contributions of diversity is required.

Inquiries should be directed to Dr. Bryce Falk, Search Committee Chair,; 530-752-0302. The position will remain open until filled but to ensure consideration, applications should be received by September 1, 2016. A more detailed job description can be obtained at


The University of California, Davis, is pleased to announce the recruitment for a tenure-track faculty position in the molecular and cellular basis of arthropod vector-human pathogen interactions. The successful candidate will join the Department of Entomology and Nematology in the College of Agricultural and Environmental Sciences at the rank of Assistant Professor. Criteria for appointment include: a Ph.D., M.D./Ph.D., or D.V.M./Ph.D. in Entomology or an appropriate field of Life or Biomedical Sciences, a record of excellence in scholarly research, and demonstrable potential to establish a competitively-funded research program. The appointee will be responsible for teaching undergraduate courses in Entomology and/or Animal Biology, be actively involved in undergraduate advising, curricular development and department and university service. The appointee is also expected to guide and mentor graduate students and participate in research and outreach/engagement programs consistent with the mission of the California Agricultural Experiment Station.

Applicants should submit materials via the following website: Additional inquiries can be directed to Dr. Shirley Luckhart, Search Committee Chair, Professor, Department of Medical Microbiology and Immunology (School of Medicine) and Department of Entomology and Nematology (College of Agricultural and Environmental Sciences), Email The position will remain open until filled but to ensure consideration, applications should be received by September 1, 2016.

UC Davis is an affirmative action/equal employment opportunity employer and is dedicated to recruiting a diverse faculty community. We welcome all qualified applicants to apply, including women, minorities, veterans, and individuals with disabilities.

Posted in Misc. | 1 Comment

PostDoc at UC Davis on Prunus replant disease (PRD) (including microbiome related studies)

Postdoctoral Scholar

Position Available

Plant Pathology Department

University of California, Davis Campus

Job Details:

The successful candidate will conduct basic and applied research contributing to sustainable management of Prunus replant disease (PRD; a soilborne disease complex), especially as it affects almond orchards. Areas of focus will include (i) metagenomic and transcriptomic examinations of PRD and (ii) optimization of soil-amendment-based strategies, including anaerobic soil disinfestation, to manage the disease. The research will be conducted in lab, greenhouse, and field settings. The lab is committed to development of sustainable, practical management strategies for soilborne diseases of fruit and nut trees. Lab team projects include determining etiology of emerging diseases, development of soil-amendment-based control strategies for soilborne diseases, and development of rootstocks that resist key soilborne pathogens. The desired start date for this postdoctoral position is no later than July 1, 2016.


The position requires a recent Ph.D. degree in plant pathology, soil microbiology, or a closely related field. Knowledge and experience with modern molecular methods used in environmental examinations (e.g., extraction and purification of nucleic acids from complex samples, PCR, metagenomics, transcriptomics, proteomics), experience with plants, and high motivation to solve complex agricultural problems will be essential. Knowledge and experience in bioinformatics are desirable.

Application Materials:

To apply, please provide (1) a cover letter that captures your related interests, experiences, and career goals, (2) a current CV, (3) contact information for three references that may be consulted, and (4) a listing of pertinent coursework (unofficial transcripts may be used). Please email all application materials, combining where possible into a single pdf file, to Dr. Greg Browne: gtbrowne

Work location: USDA-ARS lab, Plant Pathology Department, UC Davis, One Shields Ave, Davis, CA 95616, USA. Position will involve travel to various field sites in California. UC Davis is a Land Grant University. For more information, see

For additional information, contact Dr. Greg Browne, (530)754-9351 or gtbrowne

Salary commensurate with experience, per the UCD postdoc pay scale (see


Desired start date is July 1, 2016. Preference will be given to applications received by June 10, 2016.

UC is an AA/EO employer

UC Davis is a smoke and tobacco free campus effective January 1, 2014. Smoking, the use of smokeless tobacco products, and the use of unregulated nicotine products (e-cigarettes) will be strictly prohibited on any UC Davis owned or leased property, indoors and outdoors, including parking lots and residential space.

BrownePostdocPositionAvailableAd fin(004).docx

Posted in Misc. | Leave a comment

Lee Kump 6/1 at #UCDavis – How did the atmosphere become oxygen-rich?


Seminar Announcement

The Dept. of Earth and Planetary Sciences is hosting the Eldridge Moores Distinguished Visiting Scholar, Professor Lee Kump of Penn State University who will be delivering the Distinguished Lecture “How did the atmosphere become oxygen-rich?” at 4:10 pm June 1st in 55 Roessler Hall.

Please see the attached flyer for details -an abstract follows as well.

How did the atmosphere become oxygen-rich?

Two things are certain about the history of atmospheric oxygen: when Earth first formed, there was none, and today we have 21%. To piece together the rest one uses geological, isotopic and biological proxies and tolerances. Most scientists now agree that the Archean (prior to 2.5 billion years ago) the atmospheric was essentially anoxic except, perhaps, for geologically brief intervals of oxygenation. Then, with the transition from the Archean to the Proterozoic Eon, the atmosphere passed through a low threshold set by the appearance of mass-independent sulfur isotope fractionation of some 1/100,000th of the modern level. How high it rose is unclear, but the proxies suggest a Proterozoic atmosphere of 0.1 to 1% of modern oxygen levels and a second rise into the Phanerozoic to near modern levels.

This talk will focus neither on the timing of these stepwise increases nor on an assessment of the constraints on oxygen level. Rather it will explore the long-term drivers and feedbacks that together may explain why atmospheric oxygen levels followed this trajectory. The first topic is the initial rise (the Great Oxidation Event) at 2.4 Ga, an enigma because of indications that oxygenic photosynthesis was invented and exploited globally long before then. We propose that a shift in the dominant style of volcanism from submarine in the Archean and subaerial in the post-Archean, tied to the stabilization of the continental cratons, can account for this first rise in atmospheric oxygen.

The second rise, in the Neoproterozoic, is even more challenging to explain. We explore the hypothesis that it was tiedl to the “greening” of the land surface, i.e., the establishment of biotic soils with fungi that not only accelerated weathering whose metabolic wastes, together with their microbial collaborators, led to oxygen depletion in soils. To restore the balance between O2 production during organic carbon burial and O2 consumption during weathering, the O2 level had to rise.

Neither of these hypotheses has exceptionally strong support, so the take-home message is that the stepwise oxygenation of the atmosphere had to be the result of fundamental and permanent changes in the exogenic cycle; it can’t be the result of events (such as organic carbon burial events).


Posted in Misc. | Leave a comment

Today at #UCDavis: Kabir Peay on ‘Microbes, mutualism and the nature of soil biodiversity’

Kabir Peay

Stanford University

"Microbes, mutualism and the nature of soil biodiversity"


Social Sciences 1100.

Abstract: Microbes are a critical component of the diversity and function of ecosystems. Among microbes, fungi are key regulators of decomposition rates, facilitate plant nutrient uptake and have a profound impact on agriculture and industry. Technical breakthroughs in DNA sequencing have revealed incredible fungal diversity, and shown that fungal symbioses are ubiquitous in plants. Despite this, there is still a limited understanding of the ecological and evolutionary forces that structure high diversity fungal communities, and how fungal symbioses influence plant community structure and function. My lab uses a combination of ecological theory, molecular biology techniques, and field and laboratory experiments to study fungal communities in terrestrial soils. In particular, I focus on fungi involved in mycorrhizal symbiosis, the most common form of plant-microbe mutualism. My research is focused on three linked topics: (i) how fungal communities assemble at both local and continental scales, (ii) how the structure of fungal communities influences decomposition and nutrient availability, and (iii) how nutrient uptake through mycorrhizal symbiosis to influences plant growth. By integrating these three topics I hope to build a ‘roots-to-biomes’ understanding of ecological communities and ecosystem function.

Posted in Misc. | Leave a comment

#UCDavis summer program on “Girls Saving the World through Engineering”

The UC Davis Department of Civil and Environmental Engineering will be offering a free five day camp will engage girls in sustainable engineering design: "Girls Saving the World through Engineering." Through hands-on activities, design challenges, and discussions, girls will 1) understand how civil engineers help the public through environmentally-friendly, cost-effective solutions; 2) discover emerging areas in civil engineering, including bio-inspired design, and 3) envision different pathways to engineering and for engineers. The camp is funded by the National Science Foundation and organized through the Center for Bio-mediated, Bio-inspired Geotechnics. The Center focuses on ecologically friendly, cost-effective solutions, inspired by nature, for development and rehabilitation of resilient and sustainable civil infrastructure systems. It serves as a nexus for two transformative trends in engineering: biologically-based design and sustainability.

Please see our registration website for more information:

Dates: July 25th to July 29nd (9am – 4pm)

Location: 1065 Kemper Hall, UC Davis

Ages: Girls entering 3rd, 4th and 5th grades

Logistics: Breakfast, lunch and snacks will be provided for students. The camp will run from 9am to 4pm each day. To allow for transportation flexibility, students can be dropped off between 8am and 9am and picked up between 4pm and 5pm each day.

Register Online at

Contact: Colleen Bronner, Ph.D. (cebronner

Posted in Misc. | Leave a comment

Program Fellow position at the Gordon and Betty Moore Foundation in Symbiosis

Well, this could be a nice job …

The Gordon and Betty Moore Foundation’s science program supports exceptional scientists, invests in new technologies, and brings together new scientific partnerships. We believe in the inherent value of science and the sense of awe that discovery inspires. We believe that unleashing the potential of inquiry and exploration not only leads to scientific progress, but can also deliver important societal benefits. We take risks and look for opportunities to transform or create entire fields.

To complement activities in the Marine Microbiology Initiative (MMI) and other current science program grantmaking, we seek a program fellow to explore opportunities for further foundation impact in the realm of symbiosis. Here, we refer to symbiosis as the interactions between microbes (bacteria, archaea, and protists) and animals, plants, fungi, and other microbes. We also consider the role of viruses in these relationships. We consider symbiosis broadly in terms of habitat (terrestrial and marine), degree of interdependence (transient, obligatory, endosymbiotic, and that which results in organelle evolution), and time (ancient to modern).

Program Fellow Science Symbiosis.pdf

Posted in Misc. | Leave a comment