Tag Archives: bioinformatics

Job: Assistant Prof Bioinformatics at UC Riverside

University of California, Riverside
POSITION ANNOUNCEMENT:
ASSISTANT PROFESSOR OF BIOINFORMATICS

POSITION: The University of California, Riverside is searching for a new faculty member at the ASSISTANT PROFESSOR level in the area of Bioinformatics. Areas of preferred interest include developing and deploying methods for genomic data analysis such as variant identification, transcriptomics, genome assembly, comparative genomics. An emphasis on development and application of statistical methods and software to next generation sequencing data and large dataset analysis is desired. However, candidates developing approaches for analysis of metabolomic, proteomic, image analysis for biological systems are also in the scope of the position. Candidates employing experimental data collection as well as computational methods are welcomed. Study systems that address research in plant, animal, and microbial organisms are all encouraged to apply. Appointees in this series are expected to conduct mission oriented, translational research that has an ultimate goal of solving societal problems relevant to the mission of the Agricultural Experiment Station http://cnas.ucr.edu/about/anr/.

TITLE/RANK: Assistant Professor. Salary will be competitive and commensurate with accomplishments.

LOCATION: University of California, Riverside. The successful candidate will become a member of a major academic department within the College of Natural and Agricultural Sciences in his/her area of expertise with opportunities for a secondary appointment in a variety of departments and colleges.

BACKGROUND: The college is actively expanding its bioinformatics program which impacts many of its departments and interdepartmental graduate programs. Interdisciplinary bioinformatics research at UCR involves multiple departments, centers, and institutes including the Institute for Integrative Genome Biology. The Institute for Integrative Genome Biology (IIGB) connects theoretical and experimental researchers from different departments in Life, Physical and Mathematical Sciences, Medicine, Engineering and various campus based Centers. The IIGB is organized around a 10,000 sq.ft. suite of instrumentation facilities that serve as a centralized, shared-use resource for faculty, staff and students, offering advanced tools in bioinformatics, microscopy and imaging, proteomics and genomics. The IIGB Center for Bioinformatics is equipped with a modern high-performance compute (HPC) and high performance data storage infrastructure.

QUALIFICATIONS: Applicants must have a Ph.D. and postdoctoral experience.

RESPONSIBILITIES: Qualified candidates are expected to have excellent publication and research records in bioinformatics or related areas, such as computational biology, genome biology and genomics, statistics, or computer science. The successful candidate will be expected to establish and maintain a vigorous, innovative and well-funded, state-of-the-art research program, teach effectively at the undergraduate and graduate levels, and participate in departmental and interdepartmental graduate programs. Teaching responsibilities will include participating in the current bioinformatics curriculum and contributing to development of new offerings at graduate and undergraduate level.

TO APPLY: Review of applications will begin December 3, 2014 for full consideration and will continue until the position is filled. Interested individuals should apply at https://aprecruit.ucr.edu/apply/JPF00269 with required documents: (1) a curriculum vitae, (2) a statement of research interests, and (3) three letters of reference. For additional information, visit http://genomics.ucr.edu/jobs.html or http://cnas.ucr.edu

The University of California is an Equal Opportunity/Affirmative Action/Disability/Veterans Employer.

Job: Asst Prof of Computational Systems Biology at UC Riverside

Assistant Professor of Computational Systems Biology

The Department of Botany and Plant Sciences at the University of California, Riverside seeks outstanding candidates for an open Computational Systems Biologist position at the rank of Assistant Professor. We are interested in candidates involved in research in systems biology, using computational approaches or a combination of both experimental and computational approaches. A Ph.D. in a relevant discipline is required including several years of postdoctoral research. The successful candidate will hold an academic appointment in the Department of Botany and Plant Sciences with the option of a secondary cooperating faculty appointment in a quantitative department such as statistics, computer science, engineering or related. The candidate will also join the innovative and multidisciplinary Institute for Integrative Genome Biology (IIGB) which connects theoretical and experimental researchers from different departments in Life, Physical and Mathematical Sciences, Medicine, Engineering and various campus based Centers. The IIGB is organized around a 10,000 sq.ft. suite of Instrumentation Facilities that serve as a centralized, shared-use resource for faculty, staff and students, offering advanced tools in bioinformatics, microscopy, proteomics and genomics. Its bioinformatic component is equipped with a modern high-performance compute (HPC) infrastructure. This position will include an appointment in the Agricultural Experiment Station, which includes the responsibility to conduct research and outreach relevant to the mission of the California Agricultural Experiment Station (http://cnas.ucr.edu/about/anr/).

Qualified candidates are expected to have excellent publication and research records in computational systems biology or related areas, such as bioinformatics or computational genome biology. The research program should be heavily focused on involving modern high-throughput data, especially from next generation sequencing technologies. An additional requirement is a strong commitment to teaching in computational systems biology.

Review of applications will begin November 7, 2014 and continue until the position is filled. Interested individuals should: (1) submit a curriculum vitae, (2) provide a statement of research, and (3) three letters of reference. A teaching statement is strongly recommended. Please submit your applications through the AP Recruit job link: https://aprecruit.ucr.edu/apply/JPF00230

The University of California is an Equal Opportunity/Affirmative Action/Disability/Veterans Employer.

LEARN MORE

More information about this recruitment: http://plantbiology.ucr.edu/

Postdoc: Institute for Environmental Genomics, University of Oklahoma

Postdoctoral Positions Available at the University of Oklahoma

Multiple postdoctoral positions are available at the Institute for Environmental Genomics (IEG) and Department of Microbiology and Plant Biology, the University of Oklahoma (OU) located in Norman, Oklahoma. The city of Norman is a university town with approximately 100,000 people and easy access to Oklahoma City, OK and Dallas, TX, and the University is working closely with the City on community and economic development. Norman was ranked #6 among the best places to live in 2008 by the CNN/Money Magazine on America’s best small cities.

The Institute for Environmental Genomics, led by Dr. Jizhong Zhou, has state-of-the-art facilities for the study of microbial functional genomics, microbial ecology, metagenomics, and biotechnology development to address fundamental scientific questions.

Three research themes are pursued at IEG:

  1. functional and comparative genomics for understanding gene function, regulation, networks and evolution,
  2. microbial ecology and community genomics for understanding the diversity, composition, structure, function and dynamics of microbial communities related to global change, bioremediation, land use, bioenergy, and agricultural practices as well as their linkages with ecosystem functioning using metagenomics approaches, such as functional gene arrays, high-throughput sequencing, and single cell genomics, and
  3. development of metagenomic and bioinformatic tools for high throughput data analysis and predictive modeling of molecular ecological networks.

IEG researchers have pioneered the development and application of functional gene arrays (e.g., GeoChips), and metagenomic sequencing (e.g., MiSeq sequencing of phylogenetic and functional gene amplicons) approaches for microbial community analysis. IEG is also establishing Raman-based single cell genomics facility.

The selected candidates will apply these technologies to understand the diversity, composition, structure, function, dynamics and interaction of microbial communities, and address fundamental questions related to global change, bioremediation, land use, and agricultural operations.

Candidates with strong background, interests, and experience in microbiology, microbial ecology, soil science, theoretical ecology, and/or metagenomics are encouraged to apply. Additional experience is desirable but not required in bioinformatics, mathematics, computer science, and/or statistics. All individuals will work cooperatively with scientists at different institutions, such as Lawrence Berkeley National Laboratory, Oak Ridge National Laboratory, Stanford University, University of California at Berkeley, Michigan State University, University of Florida, University of New Mexico, University of Arizona, and Georgia Institute of Technology as well as foreign countries like China, Korea and Singapore. Interested individuals should send their curriculum vita, a description of research interests and accomplishments (e.g., publications), and the names and telephone numbers of at least three references to Dr. Jizhong Zhou (jzhou@ou.edu). Salary will be competitive, depending on experience, expertise and skills. Further information can be found on the IEG web site. The University of Oklahoma is an Affirmative Action/Equal Opportunity employer and encourages diversity in the workplace.

A printable flier is available PostdocPositions-OU-13Jun2014.

Postdoc: Univ of Minnesota Fungal Genomics

Postdoctoral Position – Fungal Genomics and Metabolomics
University of Minnesota, St. Paul, MN

Position description:

A postdoctoral position focused on comparative genomics, metabolomics, and regulatory mechanisms of secondary metabolites in fungi is available in the Bushley lab. This project will focus on population genomics of fungi (Fusarium, Tolypocladium spp.) to investigate regulation and evolution of secondary metabolite genes, clusters, and metabolites. The project will
adopt an interdisciplinary approach that integrates next-generation genome sequencing and assembly, comparative genomics, and RNA-Seq experiments with analyses of chemical products. Genome resequencing will examine the roles of structural variation, transposition, selection, genome methylation, and other evolutionary processes in driving the diversification of secondary metabolite genes and clusters. Strain specific differences in metabolite expression will be investigated under a variety of different media conditions and data will be integrated to develop and analyze metabolic and regulatory networks involved in controlling secondary metabolism.

Minimum requirements:
A Ph.D. in molecular biology and genetics, mycology, genomics, chemistry, biochemistry, or related fields. The ideal candidate will have existing skills in two or more of the following: experience in sequencing and analysis of next-generation sequence data, bioinformatics and comparative genomics, molecular biology, mass spectrometry, NMR, and a willingness to learn new techniques. The initial appointments is for 1 year, with an opportunity for renewal for a second year. The position is available beginning in June 2014. Start date is flexible. Salary range $38,000 – $43,000 depending on experience, plus health benefits.

To apply:
Any questions regarding the position should be directed to kbushley@umn.edu. Informal inquiries are welcome. Applicants must apply through the University of Minnesota Office of Human Resources website (http://employment.umn.edu/applicants/Central?quickFind=119828) and include a CV, a cover letter detailing research interests and experience, and contact information for three references. Screening of applicants will begin May 15 until a suitable candidate is found.

Kathryn Bushley
Assistant Professor
University of Minnesota
Department of Plant Biology
822 BioSci Bldg
1445 Gortner Avenue
St. Paul, MN 55108

Postdoc: Colletotrichum genomics

via Jo Anne Crouch

Post-Doctoral Research Position, Colletotrichum genomics

We are seeking applications for a Post-Doctoral Researcher to study transcriptome and genome evolution of five closely related species of Colletotrichum fungi impacting the health and productivity of grasses used for bioenergy, food, and turfgrass.  The incumbent will: (1) Develop and test hypotheses related to infection and cellulolytic degradation of host tissue by diverse Colletotrichum strains, (2) Take the lead on performing inoculations of grasses with these pathogens for RNA-Seq analysis from the host/pathogen interaction, and (3) Contribute to a larger collaborative Colletotrichum genome sequencing initiative.

Using genomic and transcriptomic (RNA-Seq) resources provided through a grant from the DOE/Joint Genome Institute (JGI), we seek to understand the molecular basis of host specialization, pathogenicity, cellulosic biomass degradation and other traits that characterize this diverse, yet closely related group of grass pathogens.  Fully assembled genomic datasets will soon be available for 20 Colletotrichum isolates and mapped transcriptomes for 14 of these isolates.  Data analysis will be facilitated through inclusion in the JGI MycoCosm Fungal Genome pipeline.

The incumbent will work under the joint direction of Dr. Bruce Clarke, Rutgers University, Dept. of Plant Biology & Pathology, and Dr. Jo Anne Crouch, USDA-ARS.  The position will be physically located at the Rutgers University’s Cook Campus in New Brunswick, NJ.

Qualifications

A Ph.D. in plant pathology, microbiology, mycology or a closely related field is required.  Candidates should be proficient in working with large datasets, and must have strong analytical, statistical and writing skills.  Candidates with experience working with fungi and/or plant pathogenic microorganisms, or any of the following areas are especially encouraged to apply: next-generation sequencing datasets; comparative genomics using Galaxy tools; experience analyzing RNA-Seq data; population and evolutionary genetics; phylogenetics.  Skills in bioinformatics (python, perl, R, etc) are desirable.

Terms of Appointment

Starting salary is $37,000 – $45,000 depending on experience, plus Rutgers University benefits.  Funds are guaranteed for one year, and renewable for a second year pending satisfactory research progress and availability of funds.

Review of applications will begin January 23, 2013, and continue until a suitable candidate is found.

Applications should be sent to:

Bruce Clarke (clarke@aesop.rutgers.edu) and Jo Anne Crouch (joanne.crouch@ars.usda.gov) and must include: (1) a cover letter containing a brief description of research interests and career goals, (2) curriculum vitae, (3) PDFs of two publications, and (4) contact information for three references.

Rutgers University is an equal opportunity, affirmative action educator and employer. Applications from women and minorities are encouraged.

Univ of Oregon Faculty position in Genomics, Bioinformatics, Statistical Genetics

UNIVERSITY OF OREGON

Faculty Positions in Genomics, Bioinformatics, Statistical Genetics

The Departments of Biology (http://biology.uoregon.edu) and Mathematics (http://math.uoregon.edu ) at the University of Oregon announce a cluster hire of up to three tenure-related faculty positions in Fall 2013. One of these positions may be at the level of Associate or Full Professor with indefinite tenure. These hires are part of an integrated effort to strengthen research and scholarship at the nexus of statistics/mathematics and biology at the University of Oregon, and will serve as a catalyst for future growth in this area. We are broadly interested in recruiting candidates working in areas developing statistical methodology related to the life sciences. Examples of these areas include, but are not limited to, statistical analysis of large data sets, algorithms for analyzing sequence data, and stochastic models for neuroscience, population genomics and molecular evolution. Successful candidates will bolster our emerging strengths in biomathematics, maintain an outstandi
ng research program that focuses on solving core problems in this area, and have a commitment to excellence in teaching. Ph.D. required. Position responsibilities include undergraduate teaching.

Interested persons should apply online to the MATHBIO SEARCH, University of Oregon at https://www.mathjobs.org/jobs/jobs/4035. Applicants should submit a cover letter, a curriculum vitae including a publication list, a statement of research accomplishments and future research plans, a description of teaching experience and philosophy, and three letters of recommendation. Ideally the research description and at least one of the letters of recommendation would include descriptions of the statistical/mathematical tools or models used in the applicant’s research. To ensure consideration, application materials should be uploaded by November 15th, 2012, but the search will remain open until the positions are filled.

Women and minorities are encouraged to apply. The University of Oregon is an Equal Opportunity/Affirmative Action Institution committed to cultural
diversity and compliance with the Americans with Disabilities Act, and supportive of the needs of dual career couples. We invite applications
from qualified candidates who share our commitment to diversity.

Summer courses for informatics and genomics

Cornwall School House Nº 4 (1892)Here’s a few courses to consider for the summer that cover informatics, genomics, and metagenomics analysis focusing on next generation sequencing. The deadlines are fast approaching so apply soon. (There are undoubtably more, and I’m happy to post here if you have suggestions)
Continue reading Summer courses for informatics and genomics

Lichen genome projects and the power shift prompted by next-gen sequencing

Genome Technology highlights the very cool thing about next-gen sequencing – it puts the power in the hands of the researchers to explore genome sequence and doesn’t limit them to projects only funded through sequencing centers. The Genome Technology piece highlights work at Duke to sequence the genome Cladonia grayi, a lichenized fungus, with 454 technology at Duke’s Institute for Genome Sciences and Policy through their next-gen sequencing program. This is the way of the future where sequencing core facilities will be able to generate sequence only having to wait in the queue at the own university rather than through community sequencing project or sequencing center proposal queues.

This isn’t the only lichen being sequenced. Xanthoria parietina is also in the queue at JGI, but has taken a while to get going because of some logistical problems getting the DNA (and any problems are amplified because it takes a long time to get new material since lichens grow very slow).

The transfer of the power for researchers to be able to quick exploratory whole-genome sequencing with next-gen and eventually, high quality genome sequences from next-gen sequencing is predicted to transform how this kind of science gets done. It means we’ll probably just sequence a mutant strain instead of trying to map the mutation – this is happening already in anecdotal stories in worms and in our work in mushrooms. N.B. this is done after a mutagenized strain has been cleaned up a bit to insure we’re looking for one or only a few mutations based on some crosses – but that is part of standard genetic approaches anyways.

This fast,cheap,whole-genome-sequencing is also the stuff of personal genomics, but for basic research it will also mean that a first pass exploring gene repertoire of an organism will be a multi-week instead of multi-year project. I just hope we’re training enough people who can efficiently extract the information from all this data with solid bioinformatics, computational, data-oriented programming, and statistical skills to support all the labs that will want to take this approach. You’ll need a life-vest to swim in the big data pool for a while until more tools are developed that can be deployed by non-experts.

A word about databases

Logo for fungal GenomesReport concludes that a fungal genome database is of “the highest priority”.

This is the title as listed in PubMed for this article from Future Medicine about the AAM report on charting future needs and avenues of research on the fungal kingdom.

The need for a comprehensive database for information about fungi, starting at least with systematic collections of genomic and transcript data, is highlighted as a major need.  Really and sort of new database effort should strive to be more comprehensive and include genetic and population data (alleles, strains) and information like protein-protein, protein-nucleic acid interactions (as Pedro mentioned). But on top of that it, it needs to be comparative so that information from systems that serve as great models can be transferred to other fungal systems that are being studied for their role as pathogens or interacting in the environmental.

Affordable next-gen sequencing will allow us to obtain genome and transcript sequence for basically all species or strains of interest.  Researchers with no bioinformatics support in their lab will likely be able to outsource this to a company or campus core facility.  But how can they easily map in the collective information about genes, proteins, and pathways onto this new data?  And have it be a dynamic system that can update as new information is published and curated in other systems.

I think this has to be the future beyond setting up a SGD, CGD, etc for every system.  The individual databases are useful for a large enough community where there are curators (and funding), but we will have to move to a more modular system in the future (aspects of which are in GMOD) that can have both an individual focus on a specific species/clade and a more comprehensive view of the that is comparable across the kingdom.  There are 100+ fungal genomes, but the community size for some of them are in the dozens of labs or less. How can they take advantage of the new resources without an existing infrastructure of curators?  Their systems serve an important need in a research aim, but how can discoveries there make its way back into the datastream of othe systems?

I see it as there are several ways one would interact with a system that provided single-genome tools as well as a framework for comparative information.  At a gene level, one might be looking for all information about a specific gene, based on sequence similarity searches, or starting with a cloned gene in one species. Something akin to Phylofacts or precomputed Orthogroups for defining a Gene but with more linking information about function by linking in information from all sources.  So a comparative resource, but also tapping into curated andliterature mined data.

At a genome level, one might want to do whole genome comparisons of gene content from evolutionarily defined families genes (gene family size change) or at a functional level.  To start out with, each gene/protein would already need a systematic functional mapping.  This could be as simple as running InterProScan on every protein, expanded to find Orthogroups (or OrthoMCL orthologs) and transfer function from model systems, and finally even more advanced, do further classified better with tools like SIFTER.

Interlinked with these orthologous and paralogous gene sets would be anchors for analyses of chromosomal synteny and even comparative assembly including tools like Mercator.  Certainly things like all of this exist but making it more pluggable for different sets of species would be an important additional component.

At a utility level, the gene annotation and functional mapping of all this information should be possible. I would imagine a researcher could upload the sequence assembly they received from the core facility and the system can generate multiple gene predictions, annotate the genes, and link these genes within the known orthogroups of the system (preserving their privacy for these genes if desired).  Presumably this sort of thing would be easier as a standalone in-house for the researcher, but web services could also be the place for this.

For fungal-sized genomes this amount of data is not too extereme.  Things like Genome Browser, BLAST, etc should all be rolled out of the box based on the basic builds.

On the DIY and community annotation front, there would also need to be a layer of community derived annotation that could be layered on all these systems.  I would imagine this both to be for gene structure annotation (genome annotation) and functional annotation (protein X does Y based on experiment Z, here is the journal reference).  I think aspects of this would be visible, auditable (tracked), but maybe not blessed as official until a curator could oversee these inputs. In my mind, whether or not this is in a Wiki per se or just new system that allows community input is less important to me than having it be a) structured (not a bunch of free text) b) tracked and versionable c) easy for researchers to input so that the knowledge is captured, even if it has to be reorganized later on.

Seems like a lot of work to be done, but really many of these things already exist through what  the GMOD project has built.  Many loose ends and software that doesn’t fully meet up to these needs, but I think the important concept is these are all general solutions that will be of benefit to most communities, not just the fungal ones.  One lingering question I always have when approaching genomic datas

that will be dynamic, what if any of this makes its way into GenBank?  How is this sort of thing banked so that it can be captured, and does the improved functional or gene structure annotation ever make its way into the repository databases to correct and improve what has already been submitted there?

Chlamy genome investigations

Chlamy coverThis month’s Genetics has a series of articles exploring the genome (published last year & freely available at Science) of the green algae Chlamydomonas reinhardtii. These manuscripts are primarily genome analyses making for a very bioinformatics focused issue of Genetics. Some of the highlights include: