DPB – Plant Biology

Research Assistantships available at Carnegie Institution of Science’s Department of Plant Biology

Department: DPB – Plant Biology

Salary:

Location: Stanford, CA

Research Assistantships available at Carnegie Institution of Science’s Department of Plant Biology

We are looking for talented recent graduates to work as research assistants in the laboratory of Dr. Sue Rhee at the Carnegie Institution for Science, Department of Plant Biology, located in Stanford, California. Plants are essential to life on Earth and provide us with the air, food, fuel, clothing, and shelter. Plant metabolism is the engine that enables plants to provide these things. The Rhee lab strives to uncover how plant metabolism is organized, regulated and evolves. The successful candidates will be part of a team called the Plant Metabolic Network (PMN, www.plantcyc.org) where we develop computational algorithms and pipelines to predict and annotates enzymes, transporters, and metabolic networks of plants.

Bioinformatics Research Assistant: The successful candidate will participate in developing a machine-learning pipeline to better predict enzyme functions using features such as sequence homology, protein structure, phylogeny, protein domain, and enzyme active sites.

Must have a BS or BA degree in computational biology, bioinformatics, computer science, data science or related fields. Proficiency in at least one programming language is required. Familiarity/proficiency with python, java and R are pluses. Knowledge of biology and sequence analysis are highly desired. The person must have the ability for critical thinking and problem-solving, and has excellent communication and teamwork attitude and skills.

Curator Assistant: Specific duties of the position include, but not limit to,: 1) running computational pipelines for data processing, database creation and release; 2) conducting data quality checking, debugging, and data curation; 3) writing and revising protocols and documentations; 4) participating in web User Interface enhancement.

Must have a BS or BA degree in biology, biochemistry or related fields. Experience in using Unix and a scripting language is highly desired. Must be a self-starter who is motivated to deliver quality work, pays attention to details, has the ability for critical thinking and problem-solving, and has excellent communication and teamwork attitude and skills.

Bioinformatics postdoc position to develop semi-automatic pipelines to create genome-scale metabolic models of plants and other organisms

Department: DPB – Plant Biology

Salary:

Location:

A postdoctoral researcher position is available immediately in the laboratory of Dr. Sue Rhee at the Carnegie Institution for Science, Department of Plant Biology, to create and analyze metabolic models with a focus on plants covered at Plant Metabolic Network (PMN, www.plantcyc.org). Plants are the foundation of many industrial sectors and a better understanding of their metabolism by simulation will impact our way on how we use plants for our benefit. The successful candidates will lead the development of computational tools and methods for converting the present tools and databases at Plant Metabolic Network (PMN, www.plantcyc.org) for metabolic modeling with subsequent large-scale analysis of the created networks and models testing hypotheses regarding the evolution of plants and their metabolic pathways.

Qualified candidates must have a Ph.D. or equivalent in Bioinformatics, Computational Biology, Biology, Plant biology, Microbiology, Systems Biology, Biochemistry or a related field, and a strong background in reconstructing constraint based metabolic models, statistics and programming, as well as a strong interest in plant metabolism and its biochemistry and in development of new computational approaches to address interesting biological problems. Candidates with experience in programming in MATLAB and/or the use of the COBRA toolbox are especially encouraged to apply. Working experience (either wet lab or dry lab) with plants, phylogenomics, use of high performance computers (clusters), and proficiency in programming languages of Python and/or Perl are pluses. The successful candidates should also have demonstrated ability for independent and critical thinking, excellent communication and teamwork skills, and enthusiasm for learning new things.

The Carnegie Institution, a private, nonprofit organization engaged in basic research and advanced education in biology, astronomy, and the earth sciences, was founded and endowed by Andrew Carnegie in 1902 and incorporated by an act of Congress in 1904. Andrew Carnegie conceived the Institution’s purpose “to encourage, in the broadest and most liberal manner, investigation, research, and discovery, and the application of knowledge to the improvement of mankind.” The Department of Plant Biology engages in basic research on the mechanisms involved in the growth and development of plants and algae. The Department of Plant Biology is co-located with the Carnegie Department of Global Ecology on a seven-acre site on the campus of Stanford University.

Bioinformatics postdoc position to study plant host-pathogen relationships

Department: DPB – Plant Biology

Salary:

Location:

A postdoctoral researcher position is available immediately in the laboratory of Dr. Sue Rhee at the Carnegie Institution for Science, Department of Plant Biology, to analyze metabolic networks and models of plants and fungal plant-pathogens and their interaction with each other. Pathogens impact growth and productivity of plants and thus are a supreme target in a future of scarce food resources due to changes in climate with subsequent changes in pathogen prevalence. The successful candidate will lead the curation of metabolic reactions of pathogen metabolism and development of computational tools and methods for predicting the interaction between plants and fungal pathogens. The successful candidate will have opportunities to investigate novel questions regarding evolution, co-evolution, and emergence of pathogenicity and biotrophy by leveraging the tools and data generated at the Plant Metabolic Network (PMN, www.plantcyc.org) and the Rhee lab, in collaboration with research groups at Berkley and Lawrence Berkley National labs.

Qualified candidates must have a Ph.D. or equivalent in Bioinformatics, Computational Biology, Biology, Plant biology, Microbiology, Systems Biology, Biochemistry or a related field, and a strong background in applying constraint based metabolic models, statistics and programming, as well as a strong interest in metabolism and its biochemistry and in development of new computational approaches to address interesting biological problems. Candidates with experience in programming in MATLAB and/or the use of the COBRA toolbox are especially encouraged to apply. Working experience (either wet lab or dry lab) with fungal pathogens or plants, and proficiency in programming languages of Python and/or Perl are pluses. The successful candidate should also have demonstrated ability for independent and critical thinking, excellent communication and teamwork skills, and enthusiasm for learning new things.

The Carnegie Institution, a private, nonprofit organization engaged in basic research and advanced education in biology, astronomy, and the earth sciences, was founded and endowed by Andrew Carnegie in 1902 and incorporated by an act of Congress in 1904. Andrew Carnegie conceived the Institution’s purpose “to encourage, in the broadest and most liberal manner, investigation, research, and discovery, and the application of knowledge to the improvement of mankind.” The Department of Plant Biology engages in basic research on the mechanisms involved in the growth and development of plants and algae. The Department of Plant Biology is co-located with the Carnegie Department of Global Ecology on a seven-acre site on the campus of Stanford University.

Computational biology postdoc position to study transcriptional regulation of metabolism in plants

Department: DPB – Plant Biology

Salary:

Location:

A postdoctoral researcher position is available immediately in laboratory of Dr. Sue Rhee at Carnegie Institution for Science, Department of Plant Biology. The project aims to systematically examine the transcriptional regulation of plant metabolism using multiomics approaches. The successful candidate will lead the collaborative project and develop novel computational methods and algorithms for multi-omics datasets integration (e.g. RNA-seq, ChIP-seq, HiC, and ATAC-seq).

Qualified candidates must have a Ph.D. or equivalent in Bioinformatics, Computational Biology, Computer Science, Plant Biology, or a related field, and a strong background in programming, statistics as well as a strong interest in development of new computational algorithms to address interesting biological problems. Candidates with experience in machine learning are especially encouraged to apply. The successful candidates should also have demonstrated ability for independent and critical thinking, excellent communication and teamwork skills, and enthusiasm for learning new knowledge.

The Carnegie Institution, a private, nonprofit organization engaged in basic research and advanced education in biology, astronomy, and the earth sciences, was founded and endowed by Andrew Carnegie in 1902 and incorporated by an act of Congress in 1904. Andrew Carnegie conceived the Institution’s purpose “to encourage, in the broadest and most liberal manner, investigation, research, and discovery, and the application of knowledge to the improvement of mankind.” The Department of Plant Biology engages in basic research on the mechanisms involved in the growth and development of plants and algae. The Department of Plant Biology is co-located with the Carnegie Department of Global Ecology on a seven-acre site on the campus of Stanford University.

Postdoc position to functionally characterize transcriptional regulation of metabolism in plants

Department: DPB – Plant Biology

Salary:

Location:

A postdoctoral researcher position is available immediately in laboratory of Dr. Sue Rhee at Carnegie Institution for Science, Department of Plant Biology. The project aims to elucidate regulatory mechanisms as well as functionally examine regulators (epigenomic modifiers and transcription factors) that control the expression of metabolic genes and pathways in plants.

Qualified candidates must have a Ph.D. or equivalent in Plant Biology, Cell Biology, Biochemistry or a related field, and a strong background in molecular genetics, chromatin biology, and statistics. Candidates with experiences in ChIP-sequencing, large-scale yeast-one-hybrid assays are especially encouraged to apply. Work experience in plant biochemistry, imaging or R programming are pluses. The successful candidates should also have demonstrated ability for independent and critical thinking, excellent communication and teamwork skills, and enthusiasm for learning new knowledge.

The Carnegie Institution, a private, nonprofit organization engaged in basic research and advanced education in biology, astronomy, and the earth sciences, was founded and endowed by Andrew Carnegie in 1902 and incorporated by an act of Congress in 1904. Andrew Carnegie conceived the Institution’s purpose “to encourage, in the broadest and most liberal manner, investigation, research, and discovery, and the application of knowledge to the improvement of mankind.” The Department of Plant Biology engages in basic research on the mechanisms involved in the growth and development of plants and algae. The Department of Plant Biology is co-located with the Carnegie Department of Global Ecology on a seven-acre site on the campus of Stanford University.

Postdoctoral Research Associate

Department: DPB – Plant Biology

Salary: DOE

Location: Stanford, CA

Postdoctoral Research Associate

A postdoctoral position is available immediately to work on a project with the long term objective to re-engineeralgal and (crop) plant plastids for N2fixation. A combination of bioinformatics, molecular and synthetic biology tools will be used to design and re-engineer the N2 fixation gene cluster into a non-N2 fixing cyanobacterium along with other significant modifications.

A highly motivated and creative person, with strong training in molecular biology/bioinformatics and preferably experience working with cyanobacteria/microbes or synthetic biology will be ideal. Postdoctoral fellows will have the unique opportunity to work closely with other members of the multi-disciplinary international team.

The Carnegie Institution for Science is on the Stanford campus, in the San Francisco Bay area, with opportunities for extensive social and scientific interactions. The project is funded by NSF and the contract will be for one year at time and renewable based on performance.

The Carnegie Institution of Science is an equal opportunity employer.

A bioinformatics postdoc position to study the origin and diversification of metabolic gene clusters in plants

Department: DPB – Plant Biology

Salary:

Location: Palo Alto, CA

A postdoctoral researcher position is available immediately in the laboratory of Dr. Sue Rhee (https://dpb.carnegiescience.edu/labs/rhee-lab) in the Department of Plant Biology at the Carnegie Institution for Science in Stanford, CA.

The main goal of the project is to develop computational methods to predict and analyze metabolic gene clusters involved in producing novel secondary metabolites in plants. The project has opportunities to use genomics and functional genomics data in plants to develop algorithms that can accelerate the discovery of secondary metabolic pathways in plants.

The Rhee Lab has pioneered the development of new computational algorithms to predict metabolic gene clusters:

  • Schlapfer et al. Genome-Wide Prediction of Metabolic Enzymes, Pathways, and Gene Clusters in Plants. Plant Physiology. 2017.
  • Chavali and Rhee. Bioinformatics tools for the identification of gene clusters that biosynthesize specialized metabolites. Briefings in Bioinformatics. 2017.

 

The successful candidate may build upon existing methods in the Rhee Lab to develop algorithms with improved performance. In addition to predicting metabolic gene clusters, the candidate will be motivated to study the origin and diversification of metabolic gene clusters by using evolutionary and comparative genomics approaches. The postdoc will be part of a consortium that includes several pioneering labs in synthetic biology and metabolic engineering to experimentally test the functions of these gene clusters in yeast and in planta.

Qualified candidates must have: 1) a Ph.D. or equivalent in Computer Science, Bioinformatics, Mathematics, Evolutionary or Population Biology, Biochemistry, Plant Biology, Engineering or related field; 2) expertise or fluency in large-scale data analysis, statistics, genomics, machine learning, and/or related field; and 3) proficiency in programming (R, Perl, Python, MATLAB, etc.). The successful candidate should also be able to demonstrate independent and critical thinking, ability and initiative to learn new things, excellent communication and teamwork skills, and a passion for biological research.

The Carnegie Institution, a private, nonprofit organization engaged in basic research and advanced education in biology, astronomy, and the earth sciences, was founded and endowed by Andrew Carnegie in 1902 and incorporated by an act of Congress in 1904. Andrew Carnegie conceived the Institution’s purpose “to encourage, in the broadest and most liberal manner, investigation, research, and discovery, and the application of knowledge to the improvement of mankind.” The Department of Plant Biology engages in basic research on the mechanisms involved in the growth and development of plants and algae. The Department of Plant Biology is co-located with the Carnegie Department of Global Ecology on a seven-acre site on the campus of Stanford University.

Please submit your application by clicking on the ‘Apply’ button below.

Bioinformatics postdoc position to develop computational pipelines to identify and annotate enzymes in plant genomes

Department: DPB – Plant Biology

Salary:

Location: Stanford, CA

A postdoctoral researcher position is available immediately in the laboratory of Dr. Sue Rhee at the Carnegie Institution for Science, Department of Plant Biology, to create and analyze metabolic networks of plants. Plant metabolism is the biological engine that feeds the world, not only humans but also microbes and animals. The successful candidate will lead the development of computational tools and methods for predicting plant metabolic enzymes as a part of a team called the Plant Metabolic Network (PMN, www.plantcyc.org). The successful candidate will have opportunities to investigate novel questions regarding evolution, function, or regulation of enzymes and transporters as well as metabolic networks in plants by leveraging the tools and data generated at the PMN and the Rhee lab.

Qualified candidates must have a Ph.D. or equivalent in Bioinformatics, Computational Biology, Biology, Biochemistry or a related field, with a strong background in machine learning or phylogenomics. Working experience in large-scale amino acid sequence analysis and proficiency in programming languages such as Python and/or Perl are highly desired. The successful candidate should also have a demonstrated ability for independent and critical thinking, excellent communication and teamwork skills, and enthusiasm for learning new things.

The Carnegie Institution, a private, nonprofit organization engaged in basic research and advanced education in biology, astronomy, and the earth sciences, was founded and endowed by Andrew Carnegie in 1902 and incorporated by an act of Congress in 1904. Andrew Carnegie conceived the Institution’s purpose “to encourage, in the broadest and most liberal manner, investigation, research, and discovery, and the application of knowledge to the improvement of mankind.” The Department of Plant Biology engages in basic research on the mechanisms involved in the growth and development of plants and algae. The Department of Plant Biology is co-located with the Carnegie Department of Global Ecology on a seven-acre site on the campus of Stanford University.

Biological Laboratory Technician

Department: DPB – Plant Biology

Salary: TBD Competitive

Location: Stanford, CA

Immediate openings are available for full-time or part-time laboratory technicians in laboratory of Dr. Jose Dinneny in the Department of Plant Biology located on the Stanford University campus at Carnegie Institution for Science. This is an opportunity to work in an outstanding academic environment and to gain experience in biological sciences.

Responsibilities:

  • Prepare chemical solutions, such as bacterial and plant growth media
  • Maintain lab inventory, restocking and ordering as required
  • Autoclave and discharge waste reagents
  • Grow plants (Arabidopsis, tobacco) and harvest seeds
  • Other duties as assigned

 

Qualifications:

  • Strong academic record in Molecular Biology, Plant Biology, or equivalent
  • Experience growing and harvesting plants
  • Familiarity with sterile technique and preparing chemical solutions
    Excellent communication and organizational skills
  • Specific opportunities to develop independent research projects. Lab duties will involve keeping track of lab orders, lab organization, maintaining cultures and other stocks. Assisting and interacting with lab members on specific projects.
  • Good judgment and common sense as well as critical thinking and attention to detail are required. Must possess excellent analytical, presentation, and written/verbal communication skills.

CV should include GPA if applicant is a recent graduate.  Cover Letter should indicate earliest joining date possible.

Carnegie Institution for Science (http://carnegiescience.edu/) is a private, nonprofit organization for scientific discovery founded by Andrew Carnegie in 1902. He intended the institution to be home to exceptional individuals with imagination, intelligence and enjoyment capable of creating and expanding the cutting edge of their fields. Today, Carnegie scientists work in six scientific departments on the West and East Coasts. The Department of Plant Biology engages in basic research on the mechanisms involved in the growth and development of plants and algae. The Department of Plant Biology is located on the campus of Stanford University. Carnegie is an equal opportunity employer.

Part-Time Laboratory Technician

Department: DPB – Plant Biology

Salary: DOE

Location: Stanford, CA

Part-Time Laboratory Technician

 

Immediate opening for a 1-year half-time technician in the laboratory of Dr. Devaki Bhaya at the Carnegie Institution for Science, Department of Plant Biology at Stanford.

 

Qualifications:

– Strong academic record and Bachelor’s degree in molecular biology/ or equivalent.

– 1-2 years of lab experience (outside of coursework) and familiarity with common molecular biology techniques such as PCR and cloning. Familiarity with computers/programming/ bioinformaticsstrongly preferred.

– Specific opportunities to develop independent research projects. Lab duties will involve keeping track of lab orders, lab organization, maintaining cultures and other stocks. Assisting and interacting with lab members on specific projects.

– Good judgment and common sense as well as critical thinking and attention to detail are required. Must possess excellent analytical, presentation, and written/verbal communication skills.

CV should include GPA if applicant is a recent graduate and 2-3 references will be required.  Cover Letter should indicate earliest joining date possible. 

The Carnegie Institution of Science is an equal opportunity employer.

 

Computational biology postdoc position to study plant metabolism

Department: DPB – Plant Biology

Salary:

Location: Palo Alto, CA

A postdoctoral position is available immediately in the laboratory of Dr. Sue Rhee at the Carnegie Institution for Science, Department of Plant Biology, to create and analyze metabolic networks of plants. Plant metabolism is the biological engine that feeds the world, not only humans but also microbes and animals. The successful candidate will lead the development of computational tools and methods for predicting plant metabolic enzymes, transporters, and regulators as a part of a team called the Plant Metabolic Network (PMN, www.plantcyc.org). The successful candidate will have opportunities to develop novel questions regarding evolution, function, or regulation of metabolic networks in plants by leveraging the tools and data generated at the PMN and the Rhee lab, including standard molecular genetic tools and resources.

Qualified candidates must have a Ph.D. or equivalent in Computer Science, Statistics, Engineering, Mathematics, Biology, Biochemistry, Bioinformatics, Computational Biology, or a related field, and a strong background in algorithm development, statistics and programming, as well as a strong interest in applying machine learning and other computational approaches to address interesting biological problems. Candidates with experience in developing machine learning algorithms are especially encouraged to apply. Working experience in large-scale sequence analysis, and proficiency in programming languages of Python and/or Perl are pluses. The successful candidate should also have a demonstrated ability for independent and critical thinking, excellent communication and teamwork skills, and enthusiasm for learning new things.

The Carnegie Institution, a private, nonprofit organization engaged in basic research and advanced education in biology, astronomy, and the earth sciences, was founded and endowed by Andrew Carnegie in 1902 and incorporated by an act of Congress in 1904. Andrew Carnegie conceived the Institution’s purpose “to encourage, in the broadest and most liberal manner, investigation, research, and discovery, and the application of knowledge to the improvement of mankind.” The Department of Plant Biology engages in basic research on the mechanisms involved in the growth and development of plants and algae. The Department of Plant Biology is co-located with the Carnegie Department of Global Ecology on a seven-acre site on the campus of Stanford University.

Post Doctoral Fellow – Department of Plant Biology (Wang Lab)

Department: DPB – Plant Biology

Salary:

Location: Stanford, CA

The Carnegie Institution for Science is a non-profit, world-class research institution. Carnegie’s Plant Biology is located on Stanford University campus, California. Website: www.dpb.carnegiescience.edu.

A postdoctoral fellow position is available in the laboratory of Dr. Zhi-Yong Wang at the Carnegie Institution for Science, Department of Plant Biology, to study plant growth regulation mechanisms. The Wang lab uses a wide range of approaches, including genetics, proteomics and genomics, to elucidate the signaling networks through which plants respond to hormonal, environmental, and nutritional signals. The lab focuses on the model organism Arabidopsis, but is also interested in other model systems such as Chlamydomonas, maize, and sorghum. The specific research projects for the new postdoctoral fellow will be determined based on the interest and expertise of the candidate as well as the ongoing research of the lab. To learn more about our research, please visit our website at: https://dpb.carnegiescience.edu/labs/wang-lab

Qualified candidates must have a Ph.D. degree in a field broadly related to life science. To apply, please send email to zywang24@stanford.edu your CV and a brief statement of your experience, research interest, and how you may contribute to our science and how such training experience may advance your career goal.

The Carnegie Institution, a private, nonprofit organization engaged in basic research and advanced education in biology, astronomy, and the earth sciences, was founded and endowed by Andrew Carnegie in 1902. Andrew Carnegie conceived the Institution’s purpose “to encourage, in the broadest and most liberal manner, investigation, research, and discovery, and the application of knowledge to the improvement of mankind.” The Department of Plant Biology engages in basic research on the mechanisms involved in the growth and development of photosynthetic organisms. The Department of Plant Biology is co-located with the Carnegie Department of Global Ecology on a seven-acre site on the campus of Stanford University.

Carnegie is an Equal Opportunity Employer.  The Carnegie Institution for Science has a strong institutional commitment to the principle of diversity. In that spirit, we particularly encourage applications from women, members of ethnic minorities, veterans and individuals with disabilities.