LiveStreaming 7/27-28 – Workshop: Computational Advances in Microbiome Research

**Please forward to interested colleagues. Flyer attached.**

The National Institute for Mathematical and Biological Synthesis (NIMBioS) invites you to join the live stream of our Investigative Workshop, "Computational Advances in Microbiome Research," to be held July 27-28, 2015, at NIMBioS.

Objectives: Recent years have seen a tremendous upswing in microbial community research, ranging from studies of the human microbiome to investigations of biogeochemical cycling in global soil and oceans and coral mucus ecosystems. This has been triggered in large part by the decreasing cost, increasing ubiquity, and democratization of analysis methods for high-throughput sequencing, which has made both amplification-based and shotgun metagenomic profiling of microbial communities accessible to diverse research fields. Microbial community studies have a long history derived from a variety of research areas, however, including ecology, soil and ocean biochemistry, human and environmental toxicology, air quality and environmental monitoring, agriculture, and biodefense. As the methods necessary for modern data analysis have become more complex, new computational approaches have developed independently in many of these subfields, but there have been few opportunities to integrate knowledge and bioinformatic techniques across microbial community research areas.

The overarching goal of this workshop is to bring together and integrate novel bioinformatic techniques from diverse areas of microbial community research. This will allow us more specifically to:

  • Share the state of the art in microbial community analysis from diverse fields.
  • Identify techniques from one field that are useful in others.
  • Identify gaps in computational and statistical techniques not currently addressed in any subfields.
  • Identify gaps in biological knowledge that could be addressed by new quantitative methods.

The workshop is designed as a small, focused workshop bringing together the top thought leaders in computational microbial community analysis techniques from a variety of biological application areas. We anticipate this will foster new ideas, accelerate the pace of biological discovery by disseminating current techniques across fields, provide a starting point for new collaborations, and identify gaps that might be targeted by future funding opportunities. Participation in the workshop is by invitation only.

Co-Organizers: Jill Banfield, Earth and Planetary Science and Environmental Science, Policy and Management, Univ. of California, Berkeley and Curtis Huttenhower, Biostatistics (Computational Biology and Bioinformatics), School of Public Health, Harvard Univ.

Live Stream. The Workshop will be streamed live. Note that NIMBioS Investigative Workshops involve open discussion and not necessarily a succession of talks. In addition, the schedule as posted may change during the Workshop. To view the live stream, visit http://www.nimbios.org/videos/livestream. Join the discussion on Twitter using #CAMRws.

For more information, visit http://www.nimbios.org/workshops/WS_microbiome

The National Institute for Mathematical and Biological Synthesis (NIMBioS) (http://www.nimbios.org) brings together researchers from around the world to collaborate across disciplinary boundaries to investigate solutions to basic and applied problems in the life sciences. NIMBioS is sponsored by the National Science Foundation, with additional support from The University of Tennessee, Knoxville.

microbiomeWS_flyer.pdf

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Postdoc positions in O’Dwyer lab on theoretical ecology

Postdoctoral fellowships in theoretical ecology are available to work with PI James O’Dwyer on projects centering around the theme of "Macroecology for Microbes". Our primary goal is to develop new ecological theory to understand what drives universal behavior in large-scale, spatial and temporal patterns of taxonomic and phylogenetic diversity. A second focus of these projects will be to identify which macroecological patterns are more indicative of taxon-specific differences and ecological mechanism.

The O’Dwyer lab (http://publish.illinois.edu/odwyerlab/) at the University of Illinois is highly interdisciplinary, drawing from mathematics, physics, and bioinformatics, while the collaborative environment here at UIUC provides an opportunity for postdoctoral fellows to bridge multiple fields, across different departments and institutes. We are closely affiliated with the UIUC Program in Ecology, Evolution and Conservation (http://sib.illinois.edu/peec/) and the Institute for Genomic Biology (http://www.igb.illinois.edu/research-areas/biocomplexity).

We are seeking enthusiastic and talented individuals to join the lab, and the specific project will be determined in collaboration with the PI. We welcome candidates with training in theoretical ecology, and also in other quantitative fields. Start date is flexible, and funding is available for multiple years, contingent on satisfactory progress. To apply, send a CV, a one page statement of research interests, a representative paper, and contact information for three references to James O’Dwyer at jodwyer. Applications will be considered as they arrive, and informal inquiries are welcome.

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#DavisCA Science Cafe – 6/10 – Bats and Walnuts

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Grad Scholar position at Bayer Biologics

The primary responsibilities of this role, as a Grad Scholar, are to:

• Participating in a multi-disciplinary team of scientists to offer bioinformatics, genomics, transcriptomics and metagenomics for controlling pests and diseases in plant and promoting plant health using microbes;

• Proactively identifying and incorporating new algorithms and technology to automate the analysis of microbial genomes and to extend the features of existing analysis pipelines;

• Understanding the dynamics of plant, microbe and pest/pathogen interaction using various omics technologies;

• Managing next-generation sequencing (NGS) data and analyses;

• Training scientific staff on the use of relevant bioinformatics software and tools;

• Working with other non-bioinformatics team member in the CLS group to understand their roles and to serve as backups as needed;

• Communicating effectively through listening, documentations and presentations, especially using compelling visualization tools to share analysis and interpretation of data.

Your success will be driven by your demonstration of our LIFE values. More specifically related to this position, Bayer seeks an incumbent who possesses the following:

• PhD in Computational Biology, Ecology and Evolution, Plant Biology,Bioinformatics, Genomics or related field with 0-1 year of post-graduate experience or a Master’s with 4+ years, or BSc. with 6+ years of post-graduate experience and currently enrolled in a graduate program.

• Proven ability to handle large data sets efficiently using scripts, databases, and other tools;

• Familiar with state-of-the-art open source and commercial bioinformatics tools;

• In depth familiarity with various public genomic databases, statistical software tools and packages such as R and bioinformatics algorithms, particularly for the analysis of NGS data (Illumina and PacBio);

• Should be comfortable enough with some basic statistical concepts and able to converse with other scientists about how to interpret basic statistical analyses such as ANOVA, linear regression, and power analyses.

• Experiences in three or more of the following areas: Comparative genomics; Transcriptome sequencing analysis; Phylogenetic analysis; Pathway modeling and analysis; and/or Metagenomics analysis;

Preferred Skills/Qualifications:

• Familiarity with SQL and relational database, particularly PostgreSQL;

• Fluent in Python, Perl, or other scripting languages;

• Previous laboratory experience;

• Knowledge of fungal, bacterial, insect, or plant genetics;

• Working with high performance computing clusters and/or cloud services.

Interested applicants should please send a resume and a cover letter to

Dilara Ally : email: dilara.ally

GradScholar.docx

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Brooke Borel at #UCDavis 6/4 Discussing her New Bed Bug Book “Infested”

9780226041933

Brooke Borel

“Infested: How the Bed Bug Infiltrated Our Bedrooms and Took Over the World”

Thursday June 4, 2015

10:00 AM – 11:30 AM

UC Davis Memorial Union – MU II

Host: Jonathan Eisen


Brooke Borel is a science writer who is a Contributing Editor at Popular Science and has written for Slate, Aeon, PBS’s Nova Next, and many other publications and sites.  Her first book has just been published by the University of Chicago Press.  The book is   Infested: How The Bed Bug Infiltrated Our Bedrooms and Took Over the World and it is getting praise from all over the place (see some reviews below). She will be at UC Davis on June 4 to discuss the book and some of the fun, interesting, scary and wonderful things about bed bugs.


Some reviews of the book below:

New York Times Book Review (by Marlene Zuk)

“A book about bedbugs is, by necessity, a book about nearly everything: about travel and adventure, about our ­relationship to nature, about how scientists solve problems, about trust and whether we view strangers as friends or foes. It is a book about what people will do under extreme circumstances, and about environmental politics, and art and mental illness. It is even a book about kinky sex. Borel deftly takes us through this arthropod microcosm of the universe, as she traces the culture and biology of a resurgent scourge.”

Carl Zimmer, author of A Planet of Viruses

“Our encounters with bed bugs used to be limited to wishes for a good night’s sleep. But now they’re everywhere—in hotels, apartments, and even subways. In her fascinating book Infested,  Borel chronicles the renaissance of this frightful insect and leaves us marveling at their remarkable biology.”

Maryn McKenna, author of Superbug: The Fatal Menace of MRSA

“In an odyssey that begins with understandable loathing and ends with surprising sympathy, Borel takes us on a smart, subtle, witty journey through the biology and history of the bed bug—an insect that has been our companion for hundreds of millennia, yet one that we barely understand and have no clue how to control. Borel captures the persistence of the bug, the obsessiveness of its foes, and the eagerness of entrepreneurs to turn a quick profit with no thought for the long consequences. It is impossible to read Infested without experiencing fascination, respect—and just maybe, a phantom itch.”

Seth Mnookin, author of The Panic Virus: The True Story Behind the Vaccine-Autism Controversy

“Borel has done the seemingly impossible: written an absolute page-turner of a book about bed bugs. Infested is as engaging as it is erudite, as fun as it is informative. This is popular science writing at its best.”

Dan Vergano, National Geographic

“A fun, wild romp through the wily world of bed bugs and the folks hunting them down. Borel travels from Brooklyn bedposts to Bohemian benches on the trail of this burgeoning pest, itching for the reader as she goes. Infested unveils the secrets of these frankly weird bloodsuckers, right down to their unlikely sex lives, and introduces readers to the obsessives looking to stop their march into your own bed. A terrific science book.”

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6/10 at #UCDavis: Workshop on “The Social Life of Medical Data”

The Social Life of Medical Data

A one-day workshop on sharing, pooling and appropriating medical information

http://icis.ucdavis.edu/?tribe_events=workshop-the-social-life-of-medical-data

Wednesday, June 10, 10 am to 5 pm
UC Davis campus (location TBA)

Once digitized, medical information – such as data, images, standards, and codes – travels across different spaces and communities. Smartphones produce and transmit data coming from our bodies, which is shared and discussed in social media platforms and then gathered and analyzed in data centers. Medical information intended for professional use can be appropriated, circulated and used to create communities of caring or participate in biomedical research. At the same time new power asymmetries can emerge, as public institutions and private corporations claim control over increasingly valuable health data.

In this one-day workshop we will analyze the trajectories of digitized medical data. We will discuss how patient communities, care providers, social activists, governments and corporations are designing, fostering and managing alternative approaches to healing and increasingly look towards open source, distributed, and participatory research to do this. Data created from bodies has the potential to expand our understanding of health-related research and scholarly communication practices.

In addition, we will explore different ways of including patient communities in participatory design of tools that assist in the management and analysis of health data. We aim to foster a discussion amongst anthropologists, media scholars and biomedical researcher about the emergent forms of sociality and the politics of health and illness in our digital era.

Speakers include:

Nick Anderson, UC Davis
Carlos Andres Barragan, UC Davis
Dav Clark, UC Berkeley
Alessandro Delfanti, UC Davis
Joe Dumit, UC Davis
Allison Fish, UC Davis
Marina Levina, University of Memphis
Hélène Mialet, UC Berkeley
Kim Surkan, MIT
Orkan Telhan, University of Pennsylvania

Detailed program TBA

Lunch will be served. Please RSVP at this link if you plan to attend http://bit.ly/1PxzbQ6

UC Davis Innovating Communication in Scholarship
icis.ucdavis.edu

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Post-doctoral position in Human Microbiome Research and Women’s Health

POSTDOCTORAL POSITION BIOINFORMATICS & HUMAN MICROBIOME RESEARCH

The Institute for Genome Sciences at the University of Maryland School of Medicine encompasses an inter-disciplinary, multi-departmental team of collaborative investigators with a broad research program related to the genomics of infectious diseases, human microbial metagenomics, functional genomics, and bioinformatics.

TWO POSTDOCTORAL FELLOW positions are currently opened at the Institute for Genome Sciences for collaborative projects between Drs. Jacques Ravel and Rebecca Brotman. Qualified candidates will be enthusiastic, highly motivated and interested in studying the role of the human microbiome in relation to women’s health. The research in this position will focus on how the vaginal microbiome provides protection from sexually transmitted infections (STIs) and in the development of bacterial vaginosis (BV). Projects will apply computational, statistical and bioinformatics approaches on multi-omics’ datasets such as genome sequences, metabolomics, metagenomics, and metatranscriptomics.

The ideal applicant will possess a demonstrable understanding of bioinformatics and computational biology with a background in molecular biology, microbial ecology, statistics and/or molecular epidemiology. The candidate will have a doctoral degree in Genetics, Biology, Microbiology, Computer Science or a related field. Programming and statistical skills in languages such as Perl, Python, C/C++ and R, though not essential, are a plus.

Postdoctoral fellows at IGS benefit from a community of interactive research labs, bioinformatics experts and a variety of state of the art sequencing, and computational resources in a world-class institute dedicated to genomic, basic, and translational research.

To apply, please send a CV, a statement of research interests (2 pages maximum), and contact information for three references to IGS-jobs.

Additional inquiries about the position can be sent to Drs. Jacques Ravel and Rebecca Brotman

jravel@som.umaryland.edu
rbrotman@som.umaryland.edu

Ravel Brotman bioinformatics postdoc description.pdf

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CPB Seminar at #UCDavis today: Environmental gradients and interactions with soil biota shape adaptation in teosinte

CPB Spring Quarter Seminar Reminder – Tuesday, May 19, 2015 – 4:10pm – 1022 Life Sciences

May 19: Anna O’Brien
Graduate Student, Population Biology Graduate Group, UC Davis
Title: “Environmental gradients and interactions with soil biota shape adaptation in teosinte”

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At #UCDavis today Sam Diaz-Munoz, 11:15 am

Department of Microbiology & Molecular Genetics Recruitment Seminar

Samuel Diaz-Munoz, Ph.D.
(NYU)

"The Evolution of Viral Social Interactions"

Monday, May 18, 2015

11:15 am*


197 Briggs*

*note time and location

Diaz-Munoz Seminar 5-18-15.doc

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Talk at #UCDavis today: Michael Fischbach on Small molecules from the human microbiota – GBSF noon

Seminar today

“Insights from a global view of secondary metabolism: Small molecules from the human microbiota”

Michael Fischbach, Ph.D.

Assistant Professor, Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco

Friday, May 15, 2015 12:10 – 1:00 PM

Genome and Biomedical Sciences Facility Auditorium (GBSF 1005)

Fischbach.pdf

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