[Arabidopsis] Application for the Plant Systems Biology position

Pankaj Jaiswal via arab-gen%40net.bio.net (by pj37 from cornell.edu)
Mon Oct 22 12:50:15 EST 2007

October 22, 2007

Ref: tenure track faculty position in the Department of Biology at the 
Michigan State University

Dear Members of the Plant Systems Biology Search Committee:

I am writing to apply for the tenure track faculty position in the 
Department of Biology at the Michigan State University in response to 
the advertisement on the Arabidopsis Mailing list, dated 7/23/07.  I am 
looking for the academic positions where my research interests on 
systems biology of plants including those on development of biochemical, 
genetic and signaling networks and pathways, genome annotation, building 
genotype-phenotype associations to the pathways,  investigating the role 
of small non-coding RNA molecules in seed and embryo development as well 
as on development of structured controlled vocabularies for plants, 
which will complement the strength of the current faculty in the 
Department of Biology at the Michigan State University and provide 
unique opportunities for postdoctoral, graduate and undergraduates training.

I am a Senior Research Associate at Cornell University and Co-Principal 
Investigator on two projects funded by the National Science Foundation 
(NSF-USA). (1) Gramene Database project (www.gramene.org); which 
primarily uses rice as a model plant and provides curated information 
related to markers, DNA/protein sequences, genomic diversity, gene 
function, association of gene/protein to metabolic or signaling 
pathways, and mutant phenotypes.  Since, genomes of cereal crop plants 
share many common features; the Gramene Database has used this bias and 
proven itself to be an effective way to organize, display, query and 
generate evidence based hypothetical models to carry out comparative 
studies in major cereal plants. Understanding crop genomes is the 
essential underpinning activity to improve the quality and yield of 
plant derived food and non-food products. Gramene database is the 
systems biology resource for grain crops (rice, maize, wheat, sorghum, 
barley and others) as evident from large number of database usage as 
well as publications citing the usefulness of Gramene. (2) Plant 
Ontology Consortium (POC) project (www.plantontology.org) is an attempt 
to establish the bridge between the various biological processes, 
molecular functions, gene interactions and the phenotypes.  Development 
of controlled vocabularies for describing plant anatomy, growth, 
developmental stages, and its response to various environmental factors 
is essential to integrate multi-faceted information in order to gain of 
the insights into the plant’s development and its response to various 
biotic/abiotic and biological processes. My group in collaboration with 
POC group members developed the first working model of the plant anatomy 
and a generic growth staging system for the model flowering plants in 
the ontology format. These ontologies are constantly evolving to 
integrate the new vocabularies to represent new species.

I have been working with Gramene database from the beginning, and I lead 
the group on functional annotation of the rice genome, development of a 
catalog of metabolic pathways database (RiceCyc) and development of 
various ontologies required make the necessary associations between the 
gene’s function and its phenotype. Compared to the KEGG’s metabolic 
pathway database, which is a reference metabolic pathway database, 
RiceCyc is the first such database exclusively developed for integrating 
metabolic pathways and in near future the signaling and genetic pathways 
will be added as well.

Prior to joining the Gramene project in 2001, I worked on my Ph.D. 
thesis (1992-1998) entitled ‘Nuclear-mitochondrial interactions involved 
in the cytoplasmic male sterility (CMS) in sorghum’. The graduate work 
was followed by two postdoctoral assignment (1) in the Eurofan-II 
project at University of Vienna, Austria (1998-1999), where I 
characterized the novel ORFs encoded by Yeast’s nuclear genome that are 
targeted to the mitochondria; (2) in David Stern’s Laboratory at Boyce 
Thompson Institute, Ithaca, NY (1999-2001), I continued a project on 
molecular characterization of maize organelle (plastid and 
mitochondrial) sigma factors and RNA polymerases.

My current research interests include the key components of the systems 
biology of the plants mainly in cereals on (1) Interactome for rice and 
model grass plants such as maize, sorghum, Brachypodium and Switch 
Grass, thus covering not only the protein-protein interactions but 
inclusive of genetic, signaling and regulatory interactions. (2) 
Identifying the small non-coding RNAs such as siRNA and miRNAs and their 
interactions to the genes and proteins regulating the grain quality 
traits in rice, maize, sorghum and Brachypodium. (3) Functional 
annotation of genes, proteins and alleles of rice and newly sequenced 
genomes of Sorghum and Brachypodium (4) Development of pathways catalog 
that includes known and predicted metabolic, genetic and signaling 
pathways in rice and other major cereal crops (5) Development of plant 
anatomy, developmental stage and phenotype trait ontologies.

My background and training in wet labs on Biochemistry, Plant Molecular 
Biology and the experience gained lately in Bioinformatics, while 
working with the two immensely popular plant databases; making viable 
and long terms collaborations, working in the national, international 
and multi-institutional projects, guiding the software and database 
development, making presentations, initiating new projects and dialog 
with in the research communities, teaching in the class rooms and 
workshop settings, are my important assets to bring with me if an 
opportunity to establish an independent program on plant systematics 
covering cellular, molecular and physiological levels of organization in 
plants is provided via this faculty position.

My application includes the cover letter, CV, research interests, 
teaching statement and the reprints in PDF format. The support letters 
from my referees will be received by you separately. I will gladly 
provide any other supporting materials upon request. Also I am truly 
sorry for sending my application past the review deadline of September 
7, 2007.


Pankaj Jaiswal

Jill Richey wrote:
> Please post the following job ad to your listserv.  Thank you!
> ______________________
> Jill M. Richey
> 138 Plant Biology
> Michigan State University
> East Lansing, MI  48824-1312
> ph: 517.353.9650
> fax: 517.353.1926
> E-mail:  jrichey from msu.edu
> www.plantbiology.msu.edu
> Faculty Position in Plant Systems Biology
>  Michigan State University
> As part of an initiative in Systems Biology, the Department of Plant
> Biology at Michigan State University seeks to fill a faculty position in
> genome-enabled plant systems biology. We are seeking an individual who
> will address fundamental biological questions in plants and/or in
> related model systems. Applications from individuals who generate and
> integrate complex or heterogeneous data from metabolomic, proteomic, and
> genomic studies or build models of metabolic or regulatory networks are
> especially encouraged. The successful candidate will be expected to
> develop a vigorous independent research program supported by extramural
> funding. We are particularly interested in recruiting a colleague who
> will participate in collaborative interdisciplinary research. The
> successful candidate may have a joint appointment with another suitable
> department and will contribute to undergraduate and graduate teaching in
> their area of expertise. 
> This faculty position is a tenure track, academic year appointment at
> the Assistant Professor level. An appointment at the Associate Professor
> level will be considered for exceptional candidates. Applicants must
> have a PhD and postdoctoral research experience is highly desirable.
> Applications should include a curriculum vitae, a summary of research
> accomplishments and future research objectives, a brief description of
> teaching philosophy/ goals and three letters of reference. Application
> materials should be sent electronically to PLBSYS from msu.edu. Information
> about the Department of Plant Biology can be found at
> http://www.plantbiology.msu.edu. The review of applications will begin
> September 7, 2007 and will continue until suitable candidates are
> identified. Questions regarding this position may be sent toYair
> Shachar-Hill (yairhill from msu.edu).
> MSU is an affirmative action, equal opportunity employer
> MSU is committed to achieving excellence through cultural diversity.
> The university actively encourages applications and/or nominations of
> women, persons of color, veterans and persons with disabilities.
> _______________________________________________
> Arab-gen mailing list
> Arab-gen from net.bio.net
> http://www.bio.net/biomail/listinfo/arab-gen

Pankaj Jaiswal
G-15, Bradfield Hall
Dept. of Plant Breeding and Genetics
Cornell University
Ithaca, NY-14853, USA

Ph. +1-607-255-3103 / 4199
fax: +1-607-255-6683

More information about the Arab-gen mailing list