ADARSH JOSE
4130-A 4th Floor, 1140 Bio-renewables Research Laboratory Building, Ames, Iowa, ajose@iastate.edu, (515)-230-3429
http://ajose.public.iastate.edu/ https://www.linkedin.com/in/ajose1
EDUCATION
PhD, Bioinformatics and Computational Biology (BCB)
Fall 2015
Iowa State University, IA (ISU)
(Analysis of Next Generation Sequencing Data and Complex Biological Networks)
Master of Science, Biomedical Engineering
The University of Akron, OH
(Signal Processing in Computational Biology)
May 2009
Bachelor of Science, Electronics & Biomedical Engineering
The Cochin University of Science & Technology, India
May 2005
RESEARCH EXPERIENCE
Graduate Research Assistant with Dr. Basil J. Nikolau, BCB/BBMB, Ames, Iowa (July 2010 –Current):
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Designed, implemented and is maintaining an automated NGS RNA-Seq data analysis pipeline on an AMD
Opteron high performance cluster which is used to analyze data generated by Illumina GA and HiSeq systems.
Designed and developed a fast, parallel and scalable software package named Orthofuzz
(http://orthofuzz.github.io/) for analysis of denovo assembled transcriptomes which includes a set of
interdependent java programs which:
§ Assigns weighted functional annotations combining data from multiple sources of user-defined quality.
§ Summarizes expression levels of enzymes involved in metabolic pathways and identifies pathways that are
significantly differentially expressed in the studied conditions.
§ Predicts interactions and identifies protein interaction complexes that are co-expressed in the data.
§ Generates gene-set and gene-list enrichment statistics.
§ Predicts cross-species, cross-organism fuzzy orthologs from de novo assembled transcriptome sequences
using a modified maximal clique finding algorithm and edge weighted random walk with restart algorithm.
Combined knowledge from NGS sequence, gene expression, metabolic and pathway data and previous literature
to generate hypothesis about enzymes and pathways involved in biosynthesis of hydrocarbon in biosphere.
Worked in a highly interactive environment collaborating with an interdisciplinary team of Geneticists,
Biochemists, Chemical Engineers Microbiologists and Bioinformaticians managing multiple collaborative
projects.
Graduate Assistant with Bionformatics & Computational Biology Program, Ames, Iowa (August 2009 – June 2010):
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Alignment of within organism protein-protein interaction networks between Cyanobacteria and Arabidopsis
thaliana using to identify evidence of the endosymbiosis of the chloroplast into plants from cyanobacteria.
Graduate Research Student with Dr. Dale Mugler, Biomedical Engineering, Akron, Ohio (August 2007 – April 2009):
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Explored the combination of discrete wavelets and Gaussian Mixture Models as a statistical learning tools for
gene expression microarray data.
RELEVANT TECHNICAL SKILLS
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Experienced in design of RNA-Seq experiments and exposed to state of the art tools/algorithms for assembly,
alignment, and statistical analysis of NGS data.
Development and implementation of complex high performance algorithms for integrating sequence, expression
and functional data to generate testable hypothesis.
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Hands on experience in curation and functional annotation of microbial transcriptomes & genomes.
Design, analysis and implementation of high performance serial and parallel computer algorithms using Java
Concurrency and MPI for optimal use of a 672 processor, 17 node AMD Opteron cluster.
Programming Languages: Java (Bio-Java) & C
Data Analysis Platforms: R (Bioconductor and ggplot2) and MATLAB
Scripting Languages: Perl (Bio-Perl), awk, grep and sed
Operating Systems: Linux (Centos, Ubuntu), Mac (OS X 10.9+), Windows (XP – 7)
RESEARCH PROJECTS, CONFERENCE PRESENTATIONS AND JOURNAL ARTICLES:
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Cross-organism clustering and functional annotation of transcriptomes assembled denovo using maximal
clique enumeration & fuzzy clustering using edge weighted random walk with restart. (Presented at HitSeq
Special Interest Group meeting and Student Council Symposium at ISMB-2014 (July, 2014), Genome-Informatics meeting at
Cold-Spring
Harbour
Laboratory,
November,
2013,
Conference on New Statistical Methods for NextGeneration Sequencing Data Analysis, ISU, May, 2012)
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A cross-organism, cross-species transcriptomics study using the freshwater microbe Botryrococcus braunii, the
marine microbe Emiliania huxleyi and two plants - Zea mays and Pisum sativum to generate hypothesis about
the mechanism by which organisms synthesize hydrocarbons: in collaboration with Dr. Wenmin Qin and Dr. Marna
Yandeau Nelson at ISU. (Selected for a seminar talk at Gordon Research Conference on Plant Lipids: Structure, Metabolism
& Function at Galveston, Texas (February,2015). The Zea Mays data was presented at the 54th Annual Maize Genetics
Conference, March 15-18,2012 – Portland, Oregon,USA).
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RNA-Seq analysis of Emiliania huxleyi across eight growth stages and nutrient levels: In collaboration with Dr.
Gordon Wolfe, University of California, Chico (http://www.csuchico.edu/~gwolfe2/).
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Transcriptomics of Botryococcus braunii: Exploring hydrocarbon accumulation under different growth
conditions in collaboration with Dr. Wenmin Qin in the Nikolau group and Mark Brown from the Shanks
(http://www.cbe.iastate.edu/jshanks/) Group at Iowa State University.
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Utilizing Publicly Available RNA-Seq Data for Constructing and Inferring, Co-expression Networks for B-73ZeaMays Genes. (Work presented at 8th International Purdue Symposium on Statistics "Diversity in the Statistical Sciences
for the 21st Century" Purdue University, June, 2012)
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Differentially expressed genes in hypericin-containing Hypericum perforatum leaf tissues as revealed by denovo assembly of RNA-Seq. Sotak, Miroslav; Czerankova, Odeta; Klein, Daniel; Nigutova, Katarina;
Altschmied, Lothar; Li, Ling; Jose, Adarsh; Wurtele, Eve; Cellarova, Eva, Submitted to Plant Journal.
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Integrating metabolomics and transcriptomics data to discover a novel biocatalyst needed for alkamide
biosynthesis in Echinacea by Ludmila Rizhsky, Basil Nikolau, Huanan Jin, Michael Shepard, Harry Scott, Alicen
Teitgen, Ann perera, Vandana Mhaske, Adarsh Jose, Xiaobin Zheng, Matt Crispin, Eve Wurtele, Dallas Jones,
Manhoi Hur, Elsa Góngora. Castillo, C. Robin Buell, and Robert Minto Submitted to Plant Cell
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A global approach to analysis and interpretation of metabolic data for plant natural product discovery Nat.
Prod. Rep., 2013,30, 565-583 in collaboration with the Wurtele Group (http://www.public.iastate.edu/~mash/) at
Iowa State University.
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A Gene Selection Method for Classifying Cancer Samples Using 1-D Discrete Wavelet Transform. International
Journal of Computational Biology and Drug Design, 2:398-411, 2009, Adarsh Jose, Dale Mugler, Zhong-Hui Duan,
(Presented at the 16th Annual International Conference Intelligent Systems for Molecular Biology held at Toronto, Canada)
RELEVANT COURSES
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Design and Analysis of Microarray and RNA-Seq experiments Advanced Genome Informatics, Systems Biology,
Introduction to Parallel Algorithms and Programming, Molecular Genetics and Biochemistry.
TEACHING AND LEADERSHIP EXPERIENCE
Teaching Assistant
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Structure and Reactions in Biochemical Processes. (Fall 2012) - (125 undergraduates) at Iowa State University.
Graduate Course: Medical signal and image processing. (Fall 2008) at University of Akron.
Graduate and Professional Student Senator
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Represented the Bionformatics & Computational Biology program of Iowa State University in the Graduate and
Professional Student Senate for the year 2012-13.