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Bioinformatics

People

Bioinformatics Center Director

Dr. Susan J Brown

Dr. Susan J. Brown

University Distinguished Professor
Director K-INBRE Bioinformatics Core
Division of Biology
Kansas State University
Phone: (785) 532-6670
Email: sjbrown at ksu dot edu

 

Bioinformatics Center Associate Directors

DoinaDr. Doina Caragea

Associate Professor
216 Nichols Hall
Department of Computing and Information Sciences
Kansas State University
Phone: (785) 532-7908
Email: dcaragea at ksu dot edu

 
Bradley JSC OlsonBradley JSC Olson

Assistant  Professor
Division of Biology
Kansas State University
Office: 239E Chalmers
Lab: 241 Chalmers
Manhattan, KS 66506
Office Phone: (785) 532-6149
Lab Phone: (785) 532-6153
bjsco@k-state.edu
http://www.k-state.edu/olsonlab/

 

Bioinformatics Specialists

 
Nanayan LuNanyan Lu

Bioinformatics Specialist
Division of Biology
Kansas State University
Manhattan, Kansas 66506
Phone: (785)532-6347
Email: nanyan at ksu dot edu

Nanyan worked on microarray analysis and NGS analysis with GeneSpring.

Nic

Nic Herndon
Bioinformatics Specialist
Division of Biology
Kansas State University
Manhattan, Kansas 66506
Phone: (785)532-6347
Email: nherndon at k-state.edu

Nic currently uses NGS sequence data to "finish" the Tribolium castaneum Genome.

 

 

Former Bioinformatics Specialists / Outreach Coordinators

JenniferJennifer Shelton
Bioinformatics Analyst
New York Genome Center
New York, NY

Jennifer creates tools and workflows to analyze sequence data. https://impactstory.org/JenniferShelton http://orcid.org/0000-0002-3756-5270

 

 

wildcatSanjay S Chellapilla

 

 

 

Tony_graceTony Grace
 
Hee Shin KimHee Shin Kim

Hee Shin worked for two years in the K-State Bioinformatics group to annotate The T. Castaneum genome and develop a database using GMOD. At Baylor College of Medicine, he went on to contribute to the NIH Epigenomics Roadmap Initiative. Hee Shin is currently working at the Duke Center for Human Genome Variation. There he maintains next generation sequencing data analysis pipelines and develops innovative computational strategies for analyzing large datasets.

 
Youping DengLiangjiang Wang

Liangjiang is now an Assistant Professor of Molecular Biology at the University of Georgia. There he researches machine learning models for gene regulation and protein function prediction. His predictive models are made freely available to biologists on BindN, BindN+, and MuStab.

 
YoupingYouping Deng

Youping Deng has moved to the University of Southern Mississippi. There he works on metabolic profiling of cancer cells and the signal transduction pathway of the adaptor protein PSM/SH2-B and its family members.

 

Graduate Student Alumni

PaulPaul Cain

Paul is developing a RNA-seq analysis pipeline and planning to use Tophat, Cufflinks, Cuffcompare, and Cuffdiff (when a reference genome is available) and Trinity, Tophat, Cufflinks, Cuffcompare, and Cuffdiff otherwise. Once this analysis is finished, the data is saved to a database so that Biologists can easily filter and query the RNA-seq results to find important information.

 
Surya Teja KallumadiSurya Teja Kallumadi

M.S. student, Computer Science

 
Jing XiaJing Xia

M.S. student, Computer Science

Jing's research at K-State focused on prediction of alternative splicing events. He has gone on to use computational biology to investigate microRNAs (miRNAs) and small interfering RNA (siRNAs) at Washington University in St. Louis. His research addresses the role of these RNAs in complex diseases including Alheimer's and psoriasis as well as stress response in rice.

 
Swarnim KulkarniSwarnim Kulkarni

M.S. student, Computer Science

At K-State he developed a novel Link Analysis based Concept Extractor (LACE) as an alternative to the common keyword based search approach. Swarnim currently works as a software engineer for the Cerner Corporation, a health care information technology systems supplier.

 
VishwasVishwas Vaswani

Vishwas Vaswani is now a Business Technology Analyst at Deloitte Consulting in Kansas City.

 
SwapnilSwapnil Nagar

Swapnil used Textpresso (ontology based information retrieval and text-mining system) to mine for scientific literature for the organism 'Tribloium Castaneum'. He also developed the ontology for Tribolium Castaneum.

 
SuzhiSuzhi Wang

Her work primarily focuses on database construction and management, web tool development and maintenance, data quality control, and data analysis. She participated in the development of a web portal for the International Tribolium Genome project. Currently, she works at the bioinformaticist in the Division of Biostatistics at Washington University.

 
MartinMartin S.R. Paradesi

Martin worked on protein-protein interaction prediction in Saccharomyces cerevisiae. He is now a programmer at the science and technology consulting service Tessella Inc.

 
SurbhiSurbhi Mungre

At K-State she developed and implemented an algorithm for ontology engineering by extracting data from the web and developed a dimensionality reduction approach for the problem of DNA sequence classification. She currently works as a software engineer for the Cerner Corporation, a health care information technology systems supplier.

 
KarthikKarthik Tangirala

Karthik worked on Semi-supervised and Transductive Machine Learning Algorithms, Constraint Based Information Retrieval Techniques, Large Scale Data Processing and Monitoring. He also worked on the statistical analysis of the genomic sequences using PERL and R.

 

Collaborators

Dr. Alina AkhunovaDirector of Gene Expression Facility
Research Assistant Professor
Department of Plant Pathology
Kansas State University
Dr. Jianfa BaiAssistant Professor
Department of Diagnostic Medicine/Pathobiology
College of Veterinary Medicine
Kansas State University
Dr. Gerald ReeckProfessor of Biochemistry
Kansas State University
Dr. Mike KanostUniversity Distinguished Professor
Department of Biochemistry
Kansas State University
Dr. Bill WilsonResearch Microbiologist
Arthropod-Borne Animal Disease
Research
USDA Center for Grain and Animal
Health Research
Dr. Bradley OlsonAssistant Professor
Division of Biology
Kansas State University
Dr. William H. HsuAssociate Professor
Department of Computing and
Information Sciences
Kansas State University
Dr. Marce LorenzenAssistant Professor
Department of Entomology
North Carolina State University
Dr. Kristin MichelAssistant Professor
Division of Biology
Kansas State University
Dr. Sanjeev NarayananAssistant Professor
College of Veterinary Medicine
Kansas State University
Dr. Yoonseong ParkAssociate Professor
Department of Entomology
Kansas State University
Dr. Michael C. SmithProfessor
Department of Entomology
Kansas State University
Dr. Haiyan WangAssistant Professor
Department of Statistics
Kansas State University
Dr. Weiqun (George) WangAssociate Professor
Department of Human Nutrition
Kansas State University
Dr. Shie-Shien YangProfessor
Department of Statistics
Kansas State University
Dr.Youping DengProfessor
University of Southern Mississippi
Dr. Liangjiang WangAssistant Professor
Department of Genetics and Biochemistry
Clemson University

Former Collaborators

Dr. Richard BeemanResearch Entomologist
US Grain Marketing Research Lab
and Department of Entomology
Kansas State University
Dr. Robin DenellUniversity Distinguished Professor
Division of Biology
Kansas State University
Dr. James C. NelsonAssociate Professor
Department of Plant Pathology
Kansas State University

Interested in Bioinformatics research?

Students interested in pursuing bioinformatics research projects should contact the Bioinformatics groups about applying to K-State's Division of Biology or Department of Computing and Information Sciences.