Job at #UCDavis: Associate Dean for Graduate Programs, Graduate Studies


RE: Recruitment of Associate Dean for Graduate Programs, Graduate Studies

The Office of Graduate Studies is pleased to invite nominations and applications for the position of Associate Dean for Graduate Programs. The initial term of the appointment is 3 years beginning October 1, 2016 (preferably), with the possibility of renewal after a review. This is a 50% administrative appointment, reporting to the Dean of Graduate Studies. Candidates should be tenured members of the Academic Senate. Compensation will include: 1) release from course load proportional to the 50% effort, with replacement teaching funds provided to the home department and summer compensation provided at 50% effort; and 2) an administrative stipend.

The Associate Dean for Graduate Programs plays a leadership role in policy development and implementation and is a liaison with colleagues in graduate programs, Graduate Council, administrative offices, other UC campuses, the Office of the President, and other institutions of higher education. The Associate Dean for Graduate Programs is responsible for the curriculum offered by Office of Graduate Studies and for merits and promotions of academic staff in the Office.

The Associate Dean for Graduate Programs has the following primary responsibilities:

o Serves as an administrative liaison to the Graduate Council and as an ex officio member of subcommittees of the Graduate Council.

o Oversees Office of Graduate Studies’ role with regard to graduate program review, provides consultation with graduate programs on matters such as formulation of by-laws, nomination of graduate program chairs and graduate advisers, and new program proposals.

o Directs administrative follow-up of graduate program reviews.

o Participates in the development of concepts and policy, and in the planning and coordination of graduate academic programs and allocation of resources to graduate programs.

o Oversees orientation of new graduate program chairs and advisers.

o Oversees administration of and, in cooperation with the Graduate Council, development of policy pertaining to graduate programs

o Serves as a resource to faculty and administration regarding graduate program matters.

o Responsible for all academic appointees in the Office of Graduate Studies including merits and promotions.

o Responsible for all graduate group chair appointments including writing merit letters.

o Responsible for Designated Emphasis Recommendations.

o Responsible for Lecturer Without Salary appointments/reviews in designated Organized Research Units.

o Represents the Vice Provost and Dean on campus and university-wide task forces and planning committees.

Interested candidates should submit a cover letter stating their interest in and qualifications for this position, a current curriculum vitae, any additional supporting information the candidate chooses to provide, and the names of three individuals who can serve as references. Questions in advance of the deadline should be addressed to Vice Provost and Dean Prasant Mohapatra (crokeefe.


Prasant Mohapatra, PhD

Vice Provost – Graduate Education and Dean – Graduate Studies

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Today at #UCDavis John Roth: Uprooting the tree of life

MIC 291: Selected Topics in Microbiology

Work-in-Progress Seminars

Dr. John Roth

"Uprooting the tree of life"

Wednesday, May 4, 2016

4:10 pm

1022 Life Sciences

Roth 5-4-16.doc

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Alex Sczyrba talk on “Critical Assessment of Metagenome Interpretation” Tue 1 PM GBSF 4202

Special Seminar

Tuesday May 3, 2016

GBSF 4202


Critical Assessment of Metagenome Interpretation (CAMI) 

Alex Sczyrba

Head of Bielefeld University Bioinformatics Services

University of Bielefeld, Germany

The interpretation of metagenomes relies on sophisticated computational approaches such as short read assembly, binning and taxonomic classification. All subsequent analyses can only be as meaningful as the outcome of these initial data processing methods. Tremendous progress has been achieved during the last years. However, none of these approaches can completely recover the complex information encoded in metagenomes. Simplifying assumptions are needed and lead to strong limitations and potential inaccuracies in their practical use.

The accuracy of computational methods in metagenomics has so far been evaluated in publications presenting novel or improved methods. However, these snapshots are hardly comparable due to the lack of a general standard for the assessment of computational methods in metagenomics. Users are thus not well informed about general and specific limitations of computational methods. This may result in misinterpretations of computational predictions. Furthermore, method developers need to individually evaluate existing approaches in order to come up with ideas and concepts for improvements and new algorithms. This consumes substantial time and computational resources, and may introduce unintended biases.

We suggest tackling this problem by a new initiative, aiming at the “Critical Assessment of Metagenome Interpretation” (CAMI). It aims at evaluating methods in metagenomics independently, comprehensively and without bias. The initiative should supply users with exhaustive quantitative data about the performance of methods in all relevant scenarios. It will therefore guide users in the selection and application of methods and in their proper interpretation. Furthermore, it will provide valuable information to developers, allowing them to identify promising directions for their future work. In the talk I will present the current status of the evaluation of the results of the first CAMI challenge, which took place in 2015.


Hosts: Jonathan Eisen and Matthias Hess

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Today at #UCDavis – Britt Koskella on bacteria-phage interactions

“Bacteria-phage interactions within long lived hosts: how they happen and why it matters”

Speaker: Britt Koskella

Assistant Professor

University of California, Berkeley

Monday, May 2, 2016

4:00-5:00 PM

1022 Life Sciences

Host: Perot Saelao (psaelao)

(If you would like to meet with the speaker, please contact their host)

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Dr. Catherine Lozupone at #UCDavis Friday 4/29: Anti-inflammatory bacteria and HIV

“Identifying anti-inflammatory bacteria in the human gut and their prevalence in HIV patients”

Catherine Lozupone, Ph.D.

Assistant Professor, Division of Biomedical Informatics and Personalized Medicine, School of Medicine, University of Colorado Denver

Friday, April 28, 2016 12:10 – 1:00 PM

Genome and Biomedical Sciences Facility Auditorium – GBSF 1005

Please post and distribute to faculty, staff and students.

Thank You!


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Tomorrow at #UCDavis: Eric Delwart “Koch’s Postulates in the Age of Viral Metagenomics”

Koch’s postulates in the age of viral metagenomics

28 April 2016, noon

A Virginia Perry Wilson endowed seminar featuring the great and mighty virus hunter:

Dr. Eric Delwart, PhD Blood Systems Research Institute, UCSF

1010 Valley Hall

Seminar (and lunch) coordinated by The Veterinary Pathology Club

A_Poster for Delwart.pdf

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May 2: New Research Methods for Critically Engaging the Equity Question in Higher Education

The Provost’s Forums
on the Public University and the Social Good

Monday, May 2, 2016

New Research Methods for Critically Engaging the Equity Question in Higher Education

Estela Mara Bensimon

Professor of Higher Education and Director of the Center for Urban Education at the University of

Southern California

Estela Mara Bensimon is particularly interested in place-based, practitioner- driven inquiry as a means of organizational change in higher education. Her current research is on issues of racial equity in higher education from the perspective of organizational learning and socio-cultural practice theories.

Dr. Bensimon has received grants from the National Science Foundation to study Latina and Latino students in higher education, the Bill and Melinda Gates and Ford Foundations to complete system-level work on college completion in Colorado, and the Teagle Foundation to examine the expanding role of private institutions in transfer pathways. Her publications about equity, organizational learning, practitioner inquiry, and change include: Confronting Equity Issues on Campus: Implementing the Equity Scorecard in Theory and Practice; The Underestimated Signi cance of Practitioner Knowledge in the Scholarship on Student Success; Doing Research that Makes a Difference; Equality in Fact, Equality in Results: A matter of institutional accountability; Measuring the State of Equity in Public Higher Education; and Closing the Achievement Gap in Higher Education: An Organizational Learning Perspective.

Previously, Dr. Bensimon has held the highest leadership positions in the Association for the Study of Higher Education and in the American Education Research Association Division on Postsecondary Education. She has served on the boards of the American Association for Higher Education and the Association of American Colleges and Universities.

In her lecture, Dr. Bensimon will discuss how the elimination of af rmative action has generated a strong and comprehensive line of research that documents empirically the educational bene ts of diversity. This movement provides legal and value-free justi cation for use of race in admissions to public universities. Despite its legal persuasiveness, this body of work has not eradicated inequity in higher education outcomes for subordinated groups. Professor Bensimon will analyze the intractable nature of racial inequity in higher education as an organizational learning problem. She will then discuss research methods pioneered by the Center for Urban Education, which seeks to assist scholars and practitioners to address racial inequity and remediate institu- tional practices and campus cultures, structures, and policies.


3 to 4:30 p.m. Multipurpose Room Student Community Center


4:30 to 5:30 p.m. Upstairs Patio
Student Community Center


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“Making Social Science Transparent” conference at #UCDavis 4/22/16: register today!

The Institute for Social Sciences at UC Davis cordially invites you to attend:

“Making Social Science Transparent: A Conference on the Issues of Transparency, Data and Code Accessibility, Replication, and Reproducibility”

Friday, April 22, 2016
8:30 a.m.-6:00 p.m.

Location: AGR Room, Walter A. Buehler Alumni Center, UC Davis

This conference is free and open to the public, but registration is required. Register now

For more information and a complete list of speakers, please visit the ISS website or see the attached poster. We hope you will join us!

MSST 4_22_16.pdf

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Reproducibility workshop at #UCDavis May 4

Workshop for increasing openness and reproducibility in

quantitative research

There are many actions researchers can take to increase the openness and reproducibility of their work. Please join us for a workshop, hosted by theCenterforOpenScience, to learn easy, practical steps researchers can take to increase the reproducibility of their work. The workshop will be hands-on. Using example studies, attendees will actively participate in creating a reproducible project from start to finish.

Topics covered:

* Project documentation

* Version control

* Pre-Analysis plans

* Open source tools like the Center for Open Science’sOpenScienceFramework to easily implement these concepts in a scientific workflow. You can think of OSF as an electronic notebook.

This workshop is aimed at faculty, staff, and students across disciplines, who are engaged in quantitative research. The workshop does not require any specialized knowledge of programming. Participants will gain a foundation for incorporating reproducible, transparent practices into their current workflows.

Attendees will need to bring their own laptop in order to fully participate.

Date: Wednesday, May 4th, 2016

Time: Two Sessions (9am-12pm; or 1pm-4pm)

Location: Shields Library, DSI Classroom, room 360

Pizza lunch will be provided at noon for attendees from both sessions.

Please RVSP by April 8th as space is limited.


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As more publishers require scholars to get ORCID id’s, the ORCID team to present on 4/20 at the Library

The Data Management Program at the UC Davis Library is hosting two seminars on the benefits of ORCID, an identifier for researchers, authors and creators. ORCID is now required by publishers like Science, PNAS, PLoS, EMBO, eLife, so this is an opportunity for faculty, staff and students in Ecology who publish in their journals to have their questions answered by Laurel Haak and Douglas Wright, Directors of the ORCID team. The seminars will be held on April 20th in the 2nd Floor Instruction Room in the Shields Library.

3:00 PM The Benefits of ORCID to Individual Researchers, Authors and Creators

4:00 PM The Benefits of ORCID to Research Institutions

Please, R.S.V.P. to vensberg.

Thank you,


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