Tag: Misc.

#UCDavis Department of Evolution & Ecology Faculty Search for an "Ecologist"

ECOLOGIST, UNIVERSITY OF CALIFORNIA, DAVIS — The College of Biological Sciences, University of California, Davis invites applications and nominations for a tenure-track position in the Department of Evolution and Ecology at the ASSISTANT PROFESSOR level. Candidates must have a Ph.D. (or equivalent) in the biological sciences or related fields. We seek a terrestrial or freshwater ecologist with research interests that will complement and build upon existing faculty strengths to address important ecological questions. We welcome applicants who address important ecological questions at any spatial or temporal scale.   We seek a colleague who is committed to participating in the departmental community through collaborative teaching, research, service and graduate mentoring. Letters of recommendation should specifically address this aspect of the application. The successful candidate will be expected to teach in undergraduate and graduate programs, and should be committed to mentoring and fostering diversity. Applicants should submit materials online at
https://recruit.ucdavis.edu/apply/JPF00130
which contains additional information about the position. These should include: cover letter, curriculum vitae, description of current and projected research, summary of teaching interests and experience, and three publications. Applicants should also provide the information requested for three referees (fourth referee optional). Once entered, applicants will electronically request letters from referees who will then be prompted by email with upload instructions for their letters. Closing Date: Open until filled, but all application materials, including letters of recommendation, must be received by October 15th, 2013 to assure full consideration. Administrative contact: Carla Munoz (camunoz@ucdavis.edu). Faculty contacts: Jay Stachowicz (jjstachowicz@ucdavis.edu), Sharon Strauss (systrauss@ucdavis.edu). The University of California is an Equal Opportunity/Affirmative Action Employer with a strong institutional commitment to the development of a climate that supports equality of opportunity and respect for differences.
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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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YAMMGM – yet another mostly male genomics meeting (series): Plant Genomic Congresses by Global Engage

Just got invited to the “Plant Genomics Congress Asia” meeting. As usual, the first thing I look at now is gender ratio.  From their web site I got a list of their speakers (so far) and their advisory board.  I highlighted in Yellow ones I am inferring are male and in green ones I am inferring are female.  For the meeting the ratio so far is 17:4 male to female.  Not the worst I have seen but still pretty bad.  Though if you look at their advisory board at least the ratio for the speakers is better — it is 17:0 for the Advisory Board.

  1. John Manners, Chief, CSIRO Plant Industry, Australia 
  2. Dave Edwards, Principal Research Fellow, School of Agriculture and Food Sciences, University of Queensland, Australia 
  3. Nagendra Singh National Professor-BP Pal Chair, National Research Centre on Plant Biotechnology, Indian Council of Agricultural Research, India 
  4. Han Zhao, Professor of Biology and Biotechnology, Institute of Biotechnology Jiangsu, Academy of Agricultural Sciences, China 
  5. Huaan Yang, Department of Agriculture and Food (DAFWA), Australia 
  6. Rajeev K. Varshney, Principal Scientist (Applied Genomics) & Director, Centre of Excellence in Genomics, ICRISAT, India 
  7. Apichart Vanavichit, Professor, The Rice Gene Discovery Unit, Kasetsart University, Thailand 
  8. Norman Warthmann, Senior Post Doc, Borevitz Laboratory, ANU College of Medicine, Biology and Environment, Australian National University, Australia 
  9. Chungui Lu Lecturer in Post-Genomics, Faculty of Science, Nottingham University, UK 
  10. Beng Kah (Bk) Song, Lecturer, Monash University, Sunway Campus, Australia/ Malaysia 
  11. Kenneth Olsen, Associate Professor Department of Biology, Washington St Louis University, USA 
  12. Yue-Ie Hsing, Distinguished Research Fellow, Institute of Plant and Microbial Biology, Academica Sinica, Taiwan 
  13. Meilina Ong Abdullah, Breeding and Tissue Culture Unit, The Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board (MPOB) Malaysia 
  14. Yijun Ruan, Professor and Director, Systems Biology Center, HuaZhong Agricultural University, Wuhan, China 
  15. Sachiko Isobe, Head Applied Plant Genomics, Kaduza DNA Research Institute (KDRI), Japan 
  16. Yuan-Ming Zhang, Professor of Statistical Genomics, State Key Lab. of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, China 
  17. Parveen Chhuneja, Geneticist, Bioinformatics Centre School of Agricultural Biotechnology, Punjab Agricultural University, India 
  18. Shengyi Liu, Professor and Head, The Key Lab of Oil Crops Biology, the Ministry of Agriculture, PRC Department of Genomics, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, China 
  19. Wen-Hsiung Li, Director and Distinguished Research Fellow, Biodiversity Research Center, Institute of Plant and Microbial Biology, Academica Sinica, Taiwan 
  20. Graham King, Director, Southern Cross Plant Science Professor of Plant Genomics and Epigenetics, Southern Cross University, Australia 
  21. Ryan Lister, Professor/ARC Future Fellow, Plant Energy Biology ARC CoE, School of Chemistry and Biochemistry, The University of Western Australia 
  22. Amitabh Mohanty, Lead Trait Discovery, E.I. DuPont India Pvt Ltd. 

Advisory Board:

  1. Robin G Allaby, Associate Professor, School of Life Sciences, University of Warwick, UK
  2. Todd Blevins, Senior Postdoctoral Associate, Pikaard Lab, Indiana University
  3. Roger Bossé, Global Product Line Leader, PerkinElmer
  4. James Coomer, Senior Technical Advisor for Europe. Data Direct Networks
  5. Tamas Dalmay, Professor of RNA Biology, School of Biological Sciences, University of East Anglia, Norwich 
  6. Massimo Delledonne, Professor, Department of Biotechnology & Director, Functional Genomics Center,  University of Verona, Italy
  7. Joe Duran, Director – HPC Systems, Technology Solutions Division, Fujitsu
  8. Alberto Ferrarini , Biotechnology Professional, University of Verona 
  9. Keywan Hassani-Pak, Group Leader Applied Bioinformatics, Computational and Systems Biology, Rothamsted Research
  10. Julin Maloof, Professor, Department of Plant Biology, University of California, Davis
  11. Piotr Mieczkowski, Director of NGS Facility, Research Assistant Professor, University of North Carolina
  12. Stephen P. Moose, Associate Professor, Maize Genomics, Department of Crop Sciences,, Program Leader, Feedstock Genomics, Energy Biosciences Institute, University of Illinois at Urbana Champaign
  13. Lukas Mueller, Professor, Plant Breeding and Genetics, Boyce Thompson Institute, Cornell University
  14. Odd-Arne Olsen, Professor at Department of Plant and Environmental Sciences (IPM), Norwegian University of Life Sciences (UMB) , Faculty of Education & Natural Sciences, Hamar University College (HUC), Norway
  15. Chris Pires, Associate Professor Division of Biological Sciences, University of Missouri-Columbia
  16. Uwe Scholz, Group Leader, Research Group Bioinformatics and Information Technology, IPK
  17. Alan Schulman, MTT Agrifood Research and Institute of Biotechnology, University of Helsinki 
So after checking out this meeting I decided – at their suggestion to check out the meetings in Europe and the USA they are organizing.  The speakers for the US meeting are a whopping 33:4 male to female according to my count and the ratio for the European meeting is about the same (mind you I like some of the speakers – am not blaming them — but this meeting should be avoided in my opinion).  Definitely not impressed with the organizers here or the Global Engage organization behind these meetings.  Uggh. What is wrong with people?  It is really not actually that hard to do better than this.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Institutional repository success story: Master’s on "War Eagles" contributes to amazing ring recovery story

Image from NPR.

So I just heard this amazing story on NPR. “Journey Of The Ring: Lost In WWII, Now Back With POW’s Son.”  In summary – a US Military member David Cox was taken as a POW in World War II in Germany.  While a captive he ended up trading a treasured ring for some chocolate. He returned home and made a replica of the ring but always felt bad about having had to trade the ring for food.  He passed away a few years ago.  Three or so weeks ago, two Americans – Mark and Mindy Turner – were invited to a dinner at the house of Martin and Regina Kiss and it turns out the Kiss’s had the ring.  But they did not know who the original owner was.  So the Turners did some searching based on the inscription on the ring and the figured out who the original owner was and it has now been returned to David Cox’s son.

So – how on earth is this a story connected to institutional archives.  Well, it turns out that the Turners figured out who the original owner of the ring was because their Google searches based on the ring’s inscriptions took them within a few minutes to this Master’s Thesis posted in 2006 at the NC State Digital Repository: War Eagles: A Bird’s Eye View of 305th Bomb Group and the Eighth Air Force from the experiences of David C. Cox and Joseph B. Boyle – NCSU Digital Repository.  The thesis was written by Norwood McDowell, who happens to be the younger Cox’s son in law.  And his thesis was about the elder Cox and had a brief discussion of the ring.

Kudos to all involved, including NC State and Norwood McDowell for making his Masters thesis available.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Strange emails about microbes: probiotic water

I get some strange emails about microbes.  Here is one I got today:

Dear Prof. Jonathan,

I am nothing, but I write my wish because of duty for the great future of Probiotics, which shall be big fortune of earth people.

I, by G-d’s grace, made Probiotics Multiplication “Water” at my kitchen to help my sister’s intestine problem.

And I soon found out how many many applications of the Probiotics Multiplication Water shall be opened for most peoples in the earth.

Please invite me at your cost and let me introduce the Probiotics Water and the vary applications in front of your team, then, I will show 100ml spray and mist of Probiotics Water to them.  It would be great great opportunity of your meeting if you will do.

You said in Video of TED website that we have to surround ourselves by good bacteria.
How?  I convince the Probiotics Water Mist and Spray is the answer. Easy and economic valuable answer!

– Probiotics Water’s color is plain, light pale yellow and near transparency white.
Smell is some sour, and disappeared immediately after spray. –

If you have questions, please send me your reply asap.

My smart phone number : XX-XX-XXXX-XXXX /Phone: XX-XX-XXXX-XXXX

Please send me your message before calling. Thanks very much,

XXXXXX, XX
Pohang City, South Korea 

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Closed access irony of the day: Who Will Pay for Access to Research Data? You Will …

Though I would share this with people who read this blog but don’t follow me on Twitter.  

//platform.twitter.com/widgets.js

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Great use of metagenomic data: community wide adaptation signatures

OK I have been dreaming about doing something like this for many years.  One of the potentially most useful aspects of shotgun metagenomic data is that you get a sample of many/all members of a microbial community at once.  And then in theory one could look across different species and taxa and ask – do they all have similar adaptations in response to some sort of environmental pressure.  There have been a few papers on this over the last few years (e.g. check out this one from Muegge et al on Diet Driving Convergence in Gut Microbes).  But this new paper is really the type of thing I have been hoping to see: Environmental shaping of codon usage and functional adaptation across microbial communities.  Basically they looked at codon usage in organisms in different metagenomic samples and found major metagenome specific signatures, suggesting that different taxa were in essence converging on common codon usage.

The paper is definitely worth a look.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Perhaps this meeting should be renamed "Of Microbiomes and Men" ….

Well, just got an email inviting me to participate in a meeting on microbiomes. The full invite is at the bottom of this posting.  Alas, at first glances it seems this meeting, has, well, some gender issues.

Confirmed Keynote Speakers: both male.

  • Mark Adams, Ph.D., Scientific Director, J. Craig Venter Institute, San Diego
  • Sarkis K. Mazmanian, Professor of Biology, California Institute of Technology

Confirmed other speakers: all seven male

  • Pierre Belichard, Co-founder and CEO, Enterome
  • Adam Godzik, Ph.D., Bioinformatics and Systems Biology, Professor & Program Director, Sanford-Burnham Research Institute
  • JunHua Li, Team Leader of Reference Metagenomics, BGI Research
  • Victor Nizet, MD, Professor & Division Chief, Department of Pediatrics, UCSD School of Medicine, San Diego
  • Steve Orndorff, NuMe Health
  • Andrei Osterman, Ph.D., Professor, Bioinformatics & Systems Biology, Infectious and Inflammatory Disease Center, Sanford-Burnham Medical Research Institute
  • Bernd Schnabl, MD, Assistant Professor, Division of Gastroenterology, UCSD School of Medicine, TSRI California Campus

I suppose one could say “Well, they are still working on their agenda … maybe they will have some female speakers.”  So I decided to dig around a little bit more. They provide a link to the outline agenda here. Alas that is even worse.  There we find out who some invited speakers are who have not yet accepted

  • David Odelson, R&D Program Director, Life Technologies
  • Peter B. DiLaura, President & CEO, Second Genome
  • Chris Christofferson, Morganthaler Ventures 
  • Lou Tartaglia, Third Rock Ventures
  • Mike Grey, Pappas Ventures
  • Justin L. Sonnenburg, Assistant Professor, Microbiology & Immunology, Stanford School of Medicine, Palo Alto, CA

So that is 9 confirmed speakers and six invited speakers – all of whom are male.  Great.  Here is a suggestion.  DO NOT GO TO THIS MEETING.

Microbiome Masthead
The Microbiome / Microbiota R&D and Business Collaboration Forum
Special August Registration Discount SAVE 15%

use discount code NN/AUG15/AL
Keynote speakers:
Mark Adams, Ph.D., Scientific Director, J. Craig Venter Institute, San Diego
Sarkis K. Mazmanian, Professor of Biology, California Institute of Technology
Dear Jonathan

The announcement in June that Johnson & Johnson is collaborating with Second Genome, one of the first biotech companies focused entirely on the human microbiome, is, according to Forbes magazine, a turning point at which “big Pharma” money begins to back this new field of research.

The 1-2 kilograms of bacteria living inside, and on the surface of, all human beings – the Human Microbiome – constitutes both another “human” organ and a third protective “immune system” after the innate and adaptive immune systems. This mix of good and bad bacteria, long a subject of academic interest, has been linked to everything from infectious diseases like clostridium difficile to obesity and even mental health. Now that the commercial potential of this field of research is being recognized it is attracting venture capital and other funding.

The developments in research and the commercial possibilities are the subject of The Microbiome/Microbiota R&D and Business Collaboration Forum, which will take place in San Diego onOctober 7th & 8th 2013.

Register today to secure the August 15% booking discount:
www.globalengage.co.uk/microbiome.html

Any questions? email nnoakes@globalengage.co.uk or telephone +44 (0)1865 849841
Confirmed Keynote Speakers


Mark Adams
Mark Adams, Ph.D., Scientific Director, J. Craig Venter Institute, San Diego

Sarkis Mazmanian
Sarkis K. Mazmanian, Professor of Biology, California Institute of Technology
Confirmed Speakers


Pierre Belichard, Co-founder and CEO, Enterome
Adam Godzik, Ph.D., Bioinformatics and Systems Biology, Professor & Program Director, Sanford-Burnham Research Institute
JunHua Li, Team Leader of Reference Metagenomics, BGI Research
Victor Nizet, MD, Professor & Division Chief, Department of Pediatrics, UCSD School of Medicine, San Diego
Steve Orndorff, NuMe Health
Andrei Osterman, Ph.D., Professor, Bioinformatics & Systems Biology, Infectious and Inflammatory Disease Center, Sanford-Burnham Medical Research Institute
Bernd Schnabl, MD, Assistant Professor, Division of Gastroenterology, UCSD School of Medicine, TSRI California Campus
This first-in-class, microbiome-focused hybrid R&D and business conference attracting 150 attendees from all over the world, plus an exceptional speaker faculty, will provide an interactive networking forum to both further research and commercialization opportunities.  It also aims to answer your queries through a vibrant exhibition room full of technology providers showcasing their R&D platforms & services; as well as via scientific poster sessions; expert-led case-study presentations; and interactive Q&A panel discussions.
The Outline Agenda


Sequencing/Bioinformatics of the Microbiome

  • An overview of the human microbiome project
  • Contributions to Metagenomics and Data Analysis
  • Advances in sequencing technologies
  • The role of chip technologies (the Phylo chip) as a rapid readout vs. sequencing
  • The $1000 genome may cost $100Ms to interpret!

Venture Capital + Technology Transfer

  • Commercializing Microbiome Technologies from Government & Academic Entities
  • International Small Company Showcase

The microbiome of the GI tract

  • The role of commensal bacteria in regulating the immune system
  • Metabolic exchange in gut microbial communities: who needs vitamins?
  • Contemplating novel antibiotic therapies that do not destroy the healthy microbiome
  • Metagenomic profiling in IBD

Clinical Applications

  • The contribution of the gut microbiome to liver disease
  • Treatment of C. Difficile infections with fecal transplants

Connections to the Food World

  • The role of diet in regulating the microbiome mix
  • Prebiotics vs. probiotics vs. pharmaceuticals
  • Opportunities to treat diabetes and obesity via the microbiome
  • Panel Discussion – Pharma/Biotech/Food Industry Partnering
  • Small Company Showcases
www.globalengage.co.uk/microbiome.html
Not interested in the Microbiome/Microbiota?
Unsubscribe here

Nick Noakes: nnoakes@globalengage.co.uk Tel +44 (0) 1865 849841
Global Engage, The Kidlington Centre, Kidlington, Oxfordshire, OX5 2DL, UK.

You might think that at some point some of the people organizing meetings

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Graduate Student Opportunity in Marine Biology /Environmental Sequencing of micro eukaryotes

Posting a grad student opportunity for a new project I’m involved in – The project will be using high-throughput sequencing techniques to study microbial eukaryotes in Arctic sediments.

Graduate Student Opportunity in Marine Biology / Biological Oceanography
UAF School of Fisheries and Ocean Sciences, Fairbanks, Alaska USA

We are seeking a graduate student research assistant for a project applying high-throughput DNA sequencing techniques in the study of meiofaunal communities in the Arctic. The student will take a lead role in sample processing and data analysis, including both standard microscopic analysis and morphological taxonomy and high-throughput sequencing approaches. Data will be used to assess meiofaunal community structure and diversity in the US Arctic, and identify possible environmental drivers of community structure. Skills developed will include DNA extraction, purification, and next-generation sequencing methods, and analysis of sequence data. Prior experience in molecular methods is desirable, but not essential. The student may also have the opportunity to participate in research cruises in the Arctic.

Prospective students are encouraged to apply at either the MS or PhD level (PhD candidates would be expected to develop additional research objectives that complement the project, and to work with the advisor in pursuing additional funding sources). The position will be based at the University of Alaska, Fairbanks, but the student will be expected to travel for extended periods to University of California, Davis to receive training in sequencing methods and data analysis. Funding is available for 2.5 years, including tuition, stipend (starting at ~$21,000 / year for MS students), and basic health insurance. The successful candidate will be expected to enroll in the graduate program in Spring 2014, but may be hired as a staff research technician as early as Oct. 1, 2013 if available.

To apply:
Application materials and general information about the graduate program are available at http://www.sfos.uaf.edu/prospective/graduate/. Application deadline for spring enrollment is October 15, 2013. Required materials include three letters of recommendation, general GRE scores, and transcripts from all institutions attended. If interested, or for additional information about the project or the position, contact Sarah Hardy (smhardy@alaska.edu) or Holly Bik (hbik@ucdavis.edu).

Another genomics meeting featuring men men men and men: International Forum on "Genomics, Innovation and economic growth"

Well this is just peachy.  Saw this tweet

And my first thought was – please – please – please let this meeting have a decent gender ratio. I am so so sick of genome meetings that have gender ratio issues. Alas, then I went to their site: International Forum “Genomics, Innovation and economic growth”

11 plenary speakers. All of them men.  See here.
Forum president: 1 man
Advisory Board: 5 men

Crap crap crap. What is WRONG WITH PEOPLE?

Nothing else to say really.  But I will not be going I guess I can say that.

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Postdoc position in innovating scholarly communication at #UCDavis w/ me, Mario Biagioli & Mackenzie Smith

7/26/13

Postdoc Position in Innovating Scholarly Communication

A new UC Davis initiative on “Innovating the Communication of Scholarship” is hiring a 3-year postdoctoral fellow, starting September 1, 2013. This is a cross-disciplinary project to study the future of academic publishing, involving faculty from the Center for Science and Innovation Studies, the Library, the Genome Center, and the School of Law (with additional collaborators in Computer Science, English, Philosophy, and the Graduate School of Management). Research topics include open access models, peer review, new forms of quality metrics, data publication, use of social media, and new forms of misconduct.
The successful candidate will conduct research, collaborate on or lead organization of conferences, workshops, pedagogical activities, and grant writing. A Ph.D. is required in a relevant field such as Science and Technology Studies, Library and Information Sciences, Communication, Law, Science, or English. Other disciplines will be considered depending on the specific focus of the candidate?s research and other experience. Qualified applicants will have experience working successfully in teams and managing multi-year projects. He or she will possess excellent written and oral communication and administrative skills.
Salary is based on experience and qualifications according to UC Davis guidelines.
To apply: E-mail a PDF file containing your CV, short description of your research experience relevant to this position, and contact details for three references to Mario Biagioli, MacKenzie Smith, Jonathan Eisen.
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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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