Tag: Misc.

Harold Varmus stepping down from the National Cncer Institute

Begin forwarded message:

From: "Exec Sec1 (NIH/OD)" <EXECSEC1>
To: List NIH-ALL-STAFF <NIH-ALL-STAFF>
Subject: Important Announcement from the Director, NIH – Dr. Varmus to Step Down as NCI Director
Date: March 4, 2015 at 4:41:23 PM EST

Dear Staff,

After nearly five years as director of the National Cancer Institute (NCI), Harold Varmus, M.D., has announced plans to step down from his post at the end of this month. I am deeply indebted to Harold for returning to the National Institutes of Health (NIH) to run the NCI, after having previously served as both the NIH director and president of Memorial Sloan-Kettering Cancer Center.

For the last five years, we at the NIH have had the distinct good fortune of having one of the world’s best minds focused on how to use science to fight cancer. Who better than Harold Varmus, who won the Nobel prize for discovering oncogenes, to lead the charge as we leap forward in our knowledge about the disease? And it’s not just about cancer. Few people in history have had as much influence and impact as Harold in shaping the course of modern biomedical science. Harold, indisputably, is a true giant, and we have been lucky to have him here not once, but twice, to help lead this great agency.

Douglas Lowy, M.D., the current Deputy Director, will serve as acting director for NCI, beginning on April 1.

I ask you to join me in congratulating Harold on a job extraordinarily well done, and wishing him the best for the next chapter of his distinguished scientific career. For more about his plans, please go to http://www.cancer.gov/aboutnci/director/messages/harold-varmus-resignation.

Sincerely yours,

Francis S. Collins, M.D., Ph.D.
Director

Talk at #UCDavis: Big Names: Attribution, Tribute and Technology in Brazilian Funk

Big Names: Attribution, Tribute and Technology in Brazilian Funk

When: Wednesday, March 11 from 12:00 – 1:30 PM
Where: Room SS&H 1246 (STS /CSIS Room)

Lunch provided. Please RSVP if you plan to attend.

Funk carioca, funk from Rio de Janeiro,becomes possible through extensive networks of people, sounds, payola, gifts, tribute, and technologies. I explore various economies of reciprocity in the music genreand how they relate to attribution of authorship and ownership. Names—of DJs, MCs, sound systems, and websites—become important as they are associated with, dubbed over, or erased from songs or sound samples to either expand or control their circulation. Furthermore, historically Brazilian patterns of patronage and personalismo shape how musicians utilize new technologies to extend their personal networks, build their names, and appeal to DJs to be played. The logics of intellectual property and authorship are inverted—musicians often pay to play and the song’s destination (the DJ) rather than its origin (the composer) is named and credited in the lyrics.

Alexandra Lippman is a Postdoctoral Fellow with the Innovating Communication in Scholarship project at the University of California, Davis and is affiliated with Science and Technology Studies. She holds a Ph.D. in Anthropology from the University of California, Irvine. Her primary research explores how globalizing alternative intellectual property practices impact digital media, access to knowledge, and music in Brazil. She has published in Norient and Anthropology Today and is the founder of the Sound Ethnography Project.

Note this is our Food for Thought format where everyone is asked to read a paper ahead of time. After you RSVP, you will be emailed with the paper to be discussed.

—

CPB Seminar today “Comparing taxonomic and genetic diversity in metagenomic samples”

Tuesday, March 3, 2015 – 4:10pm – 1022 Life Sciences *****

Sarah Hird

Postdoctoral Scholar, Department of Evolution and Ecology, UC Davis

Title: “Comparing taxonomic and genetic diversity in metagenomic samples”

Seminar at #UCDavis: Predicting Carriers of Ongoing Selective Sweeps without knowledge of the favored allele

Colloquium Speaker: Dr. Vineet Bafna

Title: Predicting Carriers of Ongoing Selective Sweeps without knowledge of the favored allele

Host: Dr. Ilias Tagkopoulos


When: Thursday, February 26th at 3:10pm

Where: 1127 Kemper Hall

Dr. Bafna is a Professor at the Department of Computer Science and Engineering at UC San Diego. For more information on Dr. Bafna, visit his website at: http://proteomics.ucsd.edu/vbafna

Abstract:

Methods for detecting the genomic signatures of natural selection are heavily studied, and have been successful in identifying many selective sweeps. For the vast majority of these sweeps, the adaptive allele remains unknown, making it difficult to distinguish carriers of the sweep from non-carriers. Because carriers of ongoing selective sweeps are likely to contain a future most recent common ancestor, identifying them may prove useful in predicting the evolutionary trajectory — for example, in contexts involving drug-resistant pathogen strains or cancer sub-clones. The main contribution of this paper is the development and analysis of a new statistic, the Haplotype Allele Frequency (HAF) score, assigned to individual haplotypes in a sample. The HAF score naturally captures many of the properties shared by haplotypes carrying an adaptive allele. We provide a theoretical model for the behavior of the HAF score under different evolutionary scenarios, including neutral Wright-Fischer evolution, exponential growth, and the trajectory of HAF-scores during a selective sweep.

We validate the theoretical analysis using extensive simulations, and demonstrate how the HAF-scores change dynamically with the progression of selective sweep, and are different for carriers and non-carriers of a favorable allele. We use this observation to design an algorithm, PreCIOSS (Predicting Carriers of Ongoing Selective Sweeps) to identify carriers of the adaptive allele in selective sweeps, and we demonstrate its power on simulations of both hard and soft selective sweeps, as well as on data from well-known sweeps in human populations.

#UCDavis student diagnosed with meningococcal disease

Aggie Alert: UC Davis student diagnosed with meningococcal disease

Feb. 23, 2015

A student who attends the University of California, Davis, has been diagnosed with meningococcal disease, a bacterial infection that can cause bloodstream infections and meningitis, the university and public health officials said today (Feb. 23).

The student is receiving medical care and treatment at a local hospital.

UC Davis and Yolo County Public Health teams are investigating the case, providing preventive antibiotics to contacts where indicated, and educating the university community about meningococcal disease. Close contacts of meningococcal cases who are recommended to receive preventive antibiotics include people who were exposed to the ill person’s respiratory and throat secretions through living in close quarters, or kissing or other prolonged close contact.

University and county health officials are identifying people who had close contact with the student and recommending antibiotics to protect them from becoming ill. Officials are not recommending antibiotic prophylaxis for community members or UC Davis students in general. Prophylaxis is recommended for people specifically identified as close contacts of the ill student.

Meningococcal disease signs and symptoms, which are sometimes mistaken for those of flu early in the course of illness, can include:

•       High fever
•       Severe headache
•       Rash
•       Body aches/joint pain
•       Nausea/vomiting
•       Increased sensitivity to light
•       Confusion

Anyone with the signs or symptoms of meningococcal disease should seek medical care immediately. Early treatment of meningococcal disease is critical as the infection can quickly become life threatening.

Students with questions or any of the above symptoms, contact: UC Davis Student Health and Counseling Services’ Advice Nurse Line, (530) 752-2349.

Parents, family members and the general public with questions or concerns, contact: Student Health and Counseling Services’ Directors Office, (530) 752-2333.

Covering coughs, keeping hands clean and being up to date with recommended vaccines, especially flu vaccine this time of year, are actions everyone can take to stay healthy, protect themselves from illness and prevent the spread of infections to others.

More information:
* CDC information on meningitis http://www.cdc.gov/meningococcal/index.html
* UC Davis Student Health and Counseling Services https://shcs.ucdavis.edu/

Media contacts:
* Beth Gabor, Yolo County PIO, (530) 666-8042, beth.gabor@yolocounty.org
* Andy Fell, UC Davis News & Media Relations, (530) 752-4533, ahfell@ucdavis.edu

At #UCDavis today: Katherine Amato “Variation and its consequences: Exploring host-gut microbe dynamics in nonhuman primates”

DEPARTMENT OF NEUROBIOLOGY, PHYSIOLOGY & BEHAVIOR

ORGANISM-ENVIRONMENT INTERACTION RECRUITMENT SEMINAR

Katherine Amato, Ph.D.

Postdoctoral Research Associate

University of Colorado Boulder

“Variation and its consequences: Exploring host-gut microbe dynamics in nonhuman primates"

Thursday, February 19, 2015

1:30pm

1022 Life Sciences Building

Amato Seminar February 19.pdf

Hungry researchers have hard time replicating “Subway” microbiome study

YORK, UNITED KINGDOM — After hearing about a new scientific study that found bubonic plague DNA in the subway microbiome, a group of intrigued researchers led by Dr. Patty Mayonnaise and Dr. Herbert Hoagie at the University of York rushed out to do a metagenomics study of their own.

Admittedly they had not read the methods of the paper in detail, but they figured that the Subway restaurant that just opened on Hamsandwichshire Road would be a good starting point. Thus began the “new York Subway” study.

In order to get help with sample collection, the study leads emailed an advertisement for free food to the graduate student listserv. This proved to be highly successful for recruiting volunteers and saved a lot of money on labor as graduate students seemed to be totally satisfied being paid in sandwiches.

Figure showing the diversity of subway samples tested

 

“I was aware that others had found bubonic plague, anthrax, and microscopic particles of pizza in connection to Subway,” one graduate student said, “but sometimes one must take risks in the name of scientific progress. Plus, I couldn’t say no to the sweet, sweaty smell of the Sweet Onion Chicken Teriyaki sandwich.”

Graduate student wearing proper PPE warily examines one of the Subway samples

Before devouring the samples, each student took a representative cross-section of each Subway and stuffed it into a tube to send off for DNA extraction and sequencing.

Sequencing results indicated that the food contained lots and lots of DNA. Most of the resulting sequences could be traced to the wheat genome, with others mapping to chicken, pig, cow,  lettuce, and tomato. “One of the biggest surprises for me personally,” said Dr. Hoagie, “was the presence of Arabidopsis DNA in my sandwich when I specifically asked for no mustard”.

Many bacterial sequences were also found in the Subways. Unfortunately none of them shared similarity to Yersinia pestis, the bacteria responsible for the bubonic plague. Scientists plan to repeat the study the next week around lunchtime to see if they can’t find something else historical or cool sounding for the media to pick up on when describing their study.

Critics worry that by following a DNA trail in their pursuit of the plague, York researchers may be headed down the wrong road to knowledge. Even if DNA that matched the plague was to be found in the new York Subway, it could come from a totally harmless related bacteria that we’ve never sequenced before. So rest assured that you can continue to eat sandwiches and ride the subway in peace without having to wear one of those freaky crow masks.

 

Two Eisen lab papers selected for the PeerJ 2015 Collection

Cool.  Two paper from my lab were selected as highlights of 2014 papers in the Peer J: PeerJ Collection: PeerJ Picks 2015 Collection

The papers were

The microbes we eat: abundance and taxonomy of microbes consumed in a day’s worth of meals for three diet types

Jenna M. Lang,  Jonathan A. Eisen,  Angela M. Zivkovic

and 
PhyloSift: phylogenetic analysis of genomes and metagenomes

Aaron E. Darling,  Guillaume Jospin,  Eric Lowe,  Frederick A. Matsen,  Holly M. Bik,  Jonathan A. Eisen

Thanks PeerJ and all the co-authors for their great work.  I love open science and I particularly think we need continuing experiments on the best ways to do open science.  Thus I like the experiment that is PeerJ in regard to how to publish and how to pay for open access fees.

Full disclosure: I am an Academic Editor at PeerJ.


——–
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.

——–

Winston Hide, is moving to Sheffield and is looking for a few good computational biologists …

Postdoctoral, Programming and Graduate Student opportunities in Computational Biology@Sheffield

The Hide Lab https://hidelab.wordpress.com is recruiting programmers, postdoctoral fellows and graduate students to a set of new and ongoing projects that are part of our new Centre for Genome Translation. Please go the positions available at the website to learn more.
The lab has relocated from Harvard School of Public Health to the Centre for Genome Translation at the Sheffield Institute for Translational Neuroscience (SITraN); a purpose built research facility which was opened in November 2010 by Her Majesty the Queen. The Institute houses computational, clinical and basic scientists with a focus on neurodegenerative disorders such as Motor Neurone Disease (MND) and Parkinson’s disease.

Successful candidates will be joining a global team working on best practice computational approaches and discovery in genome translation – literally working with the best clinicians, machine learning experts, wet lab scientists and a global bioinformatics team to deliver new interventions against lethal neurodegenerative diseases.

Requirements for postdocs: A PhD in an appropriate field. A strong publication record in peer-reviewed journals. Strong programming skills; strong oral and written communication skills in English; Strong knowledge of biology. Track record of excellence in publications.

Graduate students: You have a high calibre Masters degree (or equivalent qualification) in computational biology, biomedical research, genomics, computer science, mathematics, biostatistics, systems biology or combination of these. You have a strong biological background, and are skilled in scripting with demonstrated understanding of working together with biomedical researchers and quantitative biologists. You are confident in aspects of data integration and are enthusiastic about construction and analysis of biological networks and/or data integration. Highly motivated, you wish to work in a stimulating, international, scientific environment. You have excellent interpersonal, written and oral communication skills and seek exposure to a diversity of scientific projects.

Programmers: You have a combination of skills, with a strong emphasis upon programming, but with an understanding of biology, some statistics, and potentially machine learning. We welcome candidates with a desire and demonstrated ability to learn new areas and a desire to develop code in a global environment. Please include links to some of your previous code in GitHub or another repository hosting service, as well as a cover letter describing why this position interests you and how it fits your experience and interests.

Sheffield is an awesome place to live – the people are kind, professional and team oriented. The Peak district is within ten minutes and is a wonderful place to relax.

Programming applicants and Post doctoral candidates should send a C.V. and statement of interest as one PDF document to winhide [at] sheffield.ac.uk. Screening of applications begins immediately and will continue until the positions are filled. The positions are expected to start on or after April 2015.
Enquiries:
Interested candidates should in the first instance contact Prof. Winston Hide on +44 114 222 22233 or by email winhide – at – sheffield.ac.uk
Graduate student applicants:
Please complete a University Postgraduate Research Application form available from www.shef.ac.uk/postgraduate/research/apply 

Please clearly state the prospective main supervisor in the respective box and select (neuroscience) as the department.

Bioinformatics Tenure-track position at Howard University

Dear Colleagues,

I wanted to alert you that the Biology Department at Howard University currently has a search on for 3 tenure-track faculty, including one in Bioinformatics, that will close on Feb. 17th. Our Department has added several new faculty recently that have phylogenetics-focused research programs, so I wanted to make sure any potential candidates in your labs were aware of the position. Don’t hesitate to contact me, or search chair Dr. Fatimah Jackson (fatimah.jackson@howard.edu) if you have any questions. Thank you for your time, and all the best,
Three Tenure Track Biology Positions – HigherEdJobs.pdf