Zeb Arendsee

B.S. in Molecular Biology from the University of Wyoming

Zeb visited Iowa State and the BCB Program in March 2012 and met with Drena Dobbs, Eve Wurtele, Steven Cannon, Pat Schnable, Julie Dickerson, Hui-Hsien Chou, and Carolyn Lawrence.

Past research experiences included a Summer 2010 Bioinformatics Internship at Iowa State under Dr. Anne Bronikowski where he:

• Researched the metabolism of garter snakes
• Responsible for writing Perl script to parse transcriptome sequence data and extract information from Genbank files, and creating pipelines to manage automated BLAST searches

From 2007 and 2009 he was a Research Assistant under Dr. Mark Gomelsky at the Univ. of WY where he:

• Researched the light dependency of Klebsiella pneumonia biofilms
• Responsible for all stages of molecular cloning: primer design, plasmid construction, restriction mapping, transformation via electroporation, and sequencing
• Responsible for experimental design, preparing media and cultures, and
running PCR and gel electrophoresis experiments

He has many interests. "In the biological arean, these include the use of biotechnology to solve human prpblems. De novo metabolic engineering holds the promise of clean chemical synthesis. the flexible metabolic pathways of fungi could revolutionize waste management and remediation of polluted land. Crops engineered to be perennial could greatly increase the efficiency of agriculture and help stave off climate change."

B.S. in Biotechnology and M.S. in Bioinformatics from the University of Pune

Bhagyashree's project work included:

B.Sc.: Worked on screening of medicinal plants and testing the effects of secondary metabolites as potential molecules to help in regeneration of neuronal axons.

M.Sc.: Currently working on the structure, function and interaction analysis of the apurinic endonuclease protein.

Research Interests: There is some interesting research going on at Iowa State in the area of neurobiology and stem ceslls involving mathematical modeling. It is very interesting to unravel the intricacies associated with neuronal function and pattern formation. Neurobiology was a part of my under graduate project. I am well versed with wet lab experiments and so if computational problems need experimental validation, I can come up with a solution for it.

B.S. in Animal Science from Iowa State University and M.S. from the University of Flority in Phamacy (Forensics)

Jessica has worked in the veterinary diagnostics field for 11 years with the National Veterinary Services Laboratory (NVSL). Through her education and experiences, she has learned a great deal about the field, the science behind it, and its far-reaching effects. She has seen first-hand some of the dilemmas faced when current tools do not provide the necessary answers. "The molecular technology needed to analyze many of the problems encountered at the NVSL is currently availalble, but it cannot be put to use wirthout the incorporation of bioinformatics." She believes the education gained from a degree in Bioinformatics and Computational Biology would allow her to use her skills in this real-world application.

She would like to study the process of data mining and interpretation, as well as the methods for incorporating the data into current diagnostic tools and developing new tests and methods. The need for bioinformatics has been identified in numerous areas such as processing the entire genome sequence data to better understand organisms of diagnostic importance for various purposes, development of more specific diagnostic techniques to help improve speed, precision, and accuracy of a diagnosis. "Knowledge in these areas would give me opportunities to use my education in several ways to contribute to the scientific community as well as serving the general public."

B.S. and M.S. in Biotechnology from Huazhong Agricultual University and a PhD in Genetics from the Chinese Academy of Sciences

Birthplace: Hubei , China

Education:

Sept. 2001-Jul. 2005 Ph.D. Genetics. Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China

Sept. 1998-Jun. 2001 M.S. Biochemistry and Molecular Biology. Huazhong Agricultural University, Wuhan, Hubei, China

Sept. 1995-Jun.1999 B.S. Biotechnology. Huazhong Agricultural University, Wuhan, Hubei, China

Work Experience:

May. 2009-Oct. 2011 Postdoc Associate. University of Massachusetts Medical School, Worcester, MA, USA

Nov. 2005-Apr. 2009 Research Associate. Howard Hughes Medical Institute, University of Colorado at Boulder, CO, USA

Hobbies: Reading Watching movies, Exercising

Haibo is interested in the genetic improvement of crop plants, such as maize, wheat, potato, etc. by combinatory using modern high-throughout genomic approaches and bioinformatics. He has mastered several important genetic techniques which can greatly contribute to the research of genetic improvement of crop plants. These techniques include: 1) solid and comprehensive basic molecular cloning techniques, including DNA recombination, transformation, cDNA library construction, yeast one/two hybridization, DNA/RNA/protein preparation, purification and detection and microscopy. These basic techniques are the premises to carry out genomic studies.

B.Tech. in Bioinformatics from Bharath University

Sambit is interested in studying structural biology of proteins and nucleic acids. He is interested in Drena Dobbs research aiming to understand the mechanisms behind the 3 dimensional structures of proteins and the interactions between proteins, nucleic acids and other molecules in a cell, the work of Michael Cho involving the prediction of antigen structures and antigen design for HIV-1 through Computational Biology and Dr. Oliver Eulenstein, in his work on developing algorithms for protein folding. He is interested in Vasant Honavar's research concerning protein-RNA and protein-DNA interactions automated protein structure and function annotation, and modeling and inference of signal transduction and metabolic pathways. Dr. Robert Jernigan involving the study of the structures of proteins, nucleic acids and their interations and the research carried out by Dr. Taner Sen on protein stucture prediction and structral and functional interpretation of protein-protein interaction networks.

After graduation in April 2008, Sambit has worked for Helixinfosystems as a Research Analyst and most recently at Athenahealth India as a software developer where he took part in extensive coding in Perl to develop new projects, provide enhancements to existing projects and refactoring legacy modules. He uses ORACLE SQL to write complex queries to manipulate and fetch information from the database. His skills include HTML, CSS and JavaScript as well as Linux Operating system and shell scripting.

B.S. in Biotechnology from University of Mumbai and an M.S. in Biotechnology from Northwestern University

Viraj currently resides in Mumbai, India. He has a B.Sc. in Biotechnology from Mumbai University and an M.S. in Biotechnology from Northwestern University, Illinois. There, he worked uder Dr. Nicholas Cianciotto and studied biofilm characteristics of Legionella Pneumophila, the causative agent of the Legionnaire's Disease. the principle aim was to establish amulti-microorganism persistence model to study Type II secrtion mutants of Legionella pneumophila. Through the research, he learned to work with bioreactors.

He also worked at Rutgers University, New Jersey after completing his M.S. Here he worked in a genomics lab under Dr. Bhattacharya. He studied the molecular biology involved in library preparation for Single Cell Genomics, using an Illunina Sequencer. Here he saw the importance of computational biology in genomics and biotechnology.

His hobbies include reading, writing poems and trekking. He also has a passion for working in NGO's and social organisations. 

B.Tech. in Biotechnology, Chemistry and Genetics from Anna University and an M.S. in Biological Sciences/Genomics from National University of Singapore

Vishnu is from the city of Madurai in South India. In addition to his primary interest in Genomics, he is also interested in Neuroscience and Cell Biology. For his graduate research work in Dr. Thomas Lufkin's lab at the Genomic Institute of Singapore, he did 3 major projects:

Dissecting gene regulatory networks in cell-type specification: The project aims to study gene regulatory networks (GRNs) involved in the chondrogenic specification pathway in developing mouse embryos. He used a combination of transgenic methods, FACS and Gene expression microarrays to study the GRNs.

Identification of cis-regulatory elements for dlx5a/dlx6a in zebrafish: The aim of this project is to identify enhancers for the dlx5a/dlx6ag genes and standardize a method to identify long and short-range enhancers for developmental control genes. The method used a combination of comparative genomics and in vivo transgenic reporter assay in developing zebrafish embryos.

In a third project, he generated mouse ES cell lines over-expressing epitope tagged Oct4 for TAP-MS analysis for pluripotency network.

He also spent 3 months in Dr. Guillame Bourque's lab at the Genome Institute of Singapore learning computational tools to analyse data from whole genome studies.

He has experience as a Research Technician at Kuwait University where he is working as a microarray specialist and bioinformatics assistant and conducts microarray experiments and data analysis. He is also called upon to assist in on going molecular biology experiments as needed.

His hobbies include reading, writing and photography.

B.S. in Biotechnology from Bangalore University and an M.S. in Bioinformatics from Birla Institute of Technology and Science, Mesra, Ranchi, India

Sweta's research interests include comparative genomics/proteomics, evolutionary biology, structural biology, drug design, gene therapy and the use of her skills in helping researchers in these fields.

She did a six-month project on "Expression of Mycobacteriophage D29 gene 66, encoding a putative phosphatase in E.coli and purification of the expressed project" under the guidance of Dr. Sujoy Dasgupta from Bose Institute, Kolkata.

A one-year project was done as a Project Assistant on Green Chemistry entitled: " Indigenous generation of natural biodegradable and renewable plastic for industrial purpose" in Calcutta University under Dr. Sumana Chatterjee.

Lindsay Rutter