People

Current Students

  • Preston Lee
  • Karthika Sivaprakasam
  • Curtis King
  • Andrea Gillespie
  • Madhu Mukundan
  • Julia Varkey
  • Sunny Mahesh
  • Shobana Shekar (with Garrick Wallstrom)
  • Rachel Beard (with Matt Scotch)
  • Michelle Winerip (with Garrick Walstrom)
  • Samantha Tangen (with Dawn Coletta)

Alumni: Thank you!

Graduated PhD Students

  • Sen Peng (12/2015 – committee chair)
    Dissertation: “Integrative Analysis of Genomic Aberrations in Cancer and Xenograft Models”
    Post graduation: Bioinformatics Scientist, Translational Genomics Research Institute (TGen), Phoenix, AZ
  • Hu Duan (12/2015, committee member; with Stephen Johnston as chair)
    Dissertation: “Early Detection and Treatment of Breast Cancer By Random Peptide Array In neuN Transgenic Mouse Model”
    Post graduation: Research Associate, Biodesign Institute, ASU, Tempe, AZ
  • Venkata Yellapantula (12/2014 – committee chair)
    Dissertation: “Informatics approaches for integrative analysis of disparate high-throughput genomic datasets in cancer”
    Post graduation: Bioinformatics Postdoctoral Researcher, Washington University, St. Louis, MO
  • Sheetal Shetty (5/2014 – committee chair)
    Dissertation:  “Structural Variant Detection:  A Novel Approach”
    Post graduation: Bioinformatics Postdoctoral Researcher, Complex Adaptive Systems Initiative (CASI), ASU, Tempe, AZ
  • Gazi Islam (9/2013 – committee member, with Jianming Liang as chair)
    Dissertation:  “Informatics Approach to Improving Surgical Skills Training”
    Post graduation: Technology Development Engineer, Intel Corporation, Hillsboro, OR
  • Clinton Mielke (7/2013 – committee member, with Larry Mandarino as chair)
    Dissertation:  “Towards a Systems Biology Understanding of Metabolic Disorder”
    Post graduation: Founder and CEO, Infinome, Phoenix, AZ; Data Scientist Memory and Aging Center, UCSF, San Francisco, CA
  • Justin Brown (5/2012 – committee chair)
    Dissertation:  “Computational Approaches for Addressing Complexity in Biomedicine”
    Post graduation: Scientist, HTG Molecular, Tucson, AZ; CEO, JRB Analytics, Phoenix, AZ
  • Jeffrey Kriseman (5/2012 – committee chair)
    Dissertation:  “An Informatics Approach to Establishing a Sustainable Public Health Community”
    Post graduation: Informatics Scientist, Southern Nevada Health District; Branch Chief Division of Notifiable Diseases and Healthcare Information at Centers for Disease Control and Prevention (CDC), Atlanta, GA; Chief Data and Informatics Officer at Tennessee Department of Health, Nashville, TN
  • Muskan Kukreja (8/2012, Biological Design PhD Program; with Stephen Johnston as chair)
    Dissertation:  “Analysis of Immunosignaturing Case Studies”
    Post graduation: Bioinformatics Scientist at Prognosys Biosciences, San Diego, CA; Senior Data Scientist at Microsoft
  • Mithra Vankipuram (6/2012, with Bob Greenes and Vimla Patel as co-chairs)
    Dissertation:  “Understanding Adaptive Behaviors in Complex Clinical Environments”
    Post graduation: Postdoctoral Researcher, HP Labs, Palo Alto, CA

Graduated MS Students as Committee Chair

  • Marcus Naymick (5/2016, BMI)
    Thesis: An Integrative Analysis of Borderline Type II Diabetes in Obese Humans
    Post graduation: Bioinformatics Scientist at the Translational Genomics Research Institute (TGen), Phoenix, AZ
  • Mark Teng (12/2015, BMI)
    Thesis: Next Generation RNA-Sequencing Analysis on the Desmoplastic Small Round Cell Tumor
  • Eric Holden (5/2015, BMI)
    Thesis: Statistical and Pathway Analysis of Epigenetic Markers Differentiating Lean and Obese Individuals
  • Alexis Christoforides (5/2014, BMI)
    Thesis: VariantDB: A prototype scheme for structured storage and analysis of large-scale genomic variant results
    Post graduation: Software Developer, Xamarin, Boston, MA
  • Sen Peng (5/2013, BMI)
    Thesis: Identification and characterization of aberrant variants associated with non small cell lung carcinoma
    Post graduation: PhD candidate, BMI, ASU
  • Stuart Stein (12/2012, BMI)
    Thesis: “Identification of Novel One-Carbon Pathway Gene Variants as Stroke Risk Markers: Combined Data Mining, Logistic Regression, Pathway Analysis, and Functional and RNA Splicing Analysis”
    Post graduation: CEO of NeuroSonicks LLC (medical device company), Orange County, CA
  • Immanuel Purushothaman (8/2012, BMI)
    Thesis: A Bioinformatics Approach for Discovering Distinctions Between High and Low Risk HPV Sequences as Potential Sites Significant to Oncogenicity; Global HPV Databank: A comprehensive, centralized, source for retrieval of Human Papillomavirus nucleotide and protein data
    Post graduation: Bioinformatics Scientist at the Biodesign Institute, Tempe, AZ; Bioinformatician, Icahn School of Medicine at Mount Sinai, New York, NY
  • Karthik Velmurugan (8/2012, BMI)
    Thesis: Bioinformatics analysis of copy number variation events in tamoxifen resistant and sensitive MCF-7 sub clones
    Post graduation: Bioinformatics Scientist at the Biodesign Institute, Tempe, AZ; PhD Candidate, Bioinformatics, Virginia Tech
  • John Penn (12/2010, Computational Biosciences CBS)
    Thesis: Utilizing Proteomic Knowledge of Drusen to Identify Regions of Interest for GWA Study of Single Nucleotide Polymorphisms
    Post graduation: Bioinformatics Scientist at Transgenomic Inc, Seattle, WA; Manager, NGS Data Analysis at Regeneron Genetics Center, New York area
  • Natalia Briones (5/2010, Computational Biosciences CBS)
    Thesis: Data mining of high density genomic variant data for prediction of Alzheimer’s disease risk
    Post graduation: Bioinformatics Scientist at the Biodesign Institute, Tempe, AZ
  • Siddarth Selvaraj (12/2009, Computational Biosciences CBS)
    Thesis: Rule based mining of High Throughput Sequence data to discover MicroIndels
    Post graduation: Bioinformatics Analyst at the National Institutes of Health (NIH), Bethesda, MD; Founder and CEO, Arima Genomics, San Diego, CA
  • Tyler Izatt (12/2009, Computational Biosciences CBS)
    Thesis: SolPicker: Designing a software suite for picking oligo probes
    Post graduation: Bioinformatics Scientist at the Translational Genomics Research Institute TGen, Phoenix, AZ
  • Charles Li (5/2009, BMI)
    Thesis: Informatics for managing genomic mutations in application to cancer vaccine and synthetic biology
    Post graduation: Bioinformatics Scientist at the Biodesign Institute, Tempe, AZ

Graduated MS Students as Committee Member

  • Karen O’Connor (12/2015, BMI)
    Thesis: Pharmacovigilance on Twitter? Mining Tweets for Adverse Drug Reactions
  • Rachel Ginn (5/2015, BMI)
    Thesis: Mining Twitter for Adverse Drug Reaction Mentions: A Corpus and Classification Benchmark
    Post graduation: Clinical Performance Analyst, Banner Health, Phoenix, AZ
  • Saman Jirjies (5/2015, BMI)
    Thesis: Open Source Implementation of Jacquez’s Q Statistics for Space-Time Clustering in Case-Control Studies
    Post graduation: Programmer Analyst at Healthways, Scottsdale, AZ
  • Robert Rivera (12/2014, BMI)
    Thesis: Automatic identification and quantification of the “ring effect” on NAPPA images
    Post graduation: Medical student, Medical College of Wisconsin
  • Shobana Sekar (5/2014, BMI)
    Thesis: Study of Batch-to-Batch Reproducibility in Nucleic Acid Programmable Protein Array (NAPPA)
    Post graduation: PhD Candidate, BMI, ASU
  • Rob Lauder (11/2013, BMI)
    Thesis: Evaluation of Unstructured Reports from HealthMap as a Leading Indicator for West Nile Virus Cases Reported by the CDC
    Post graduation: Data Analyst, Mercer, Tempe, AZ
  • Abhinav Bhargava (8/2013, BMI)
    Thesis: Seizures localization using 3-D object detection algorithm
    Post graduation: Oracle Database Consultant, Robert Half, San Francisco, CA
  • Kiran Mankar (10/2012, BMI)
    Thesis: Experiences and Challenges of implementing electronic interfaces with EHR: results from a 2012 IIS Program Manager’s survey
    Post graduation: Clinical Informatics Analyst, Versant Holdings, Charlotte, NC
  • Ashutosh Singraur (5/2012, BMI)
    Thesis: A Novel Data Mining Approach to Predict Geographical Metadata Using Sequence Data
    Post graduation: Analyst, Contineo Health, Austin, TX
  • Pierina Ortiz (5/2012, BMI)
    Thesis: Use of the Bayesian Skyline Plot to Inform a Prediction Model of Zoonotic Infection in Animal Host
    Post graduation: Informatics Analyst at Health Services Advisory Group, Mesa, AZ; Health Informatics Analyst, Blue Cross Blue Shield of Arizona
  • Jing Lu (5/2012, BMI)
    Thesis: A 3-Layered Census Information Retrieving System
    Post graduation: Performance Architecture – Programmer Intern, Samsung Austin R&D Center, Austin, TX; Senior Software Engineer, Walmart Labs
  • Sheela Kanwar (10/2010, Computer Science CS)
    Thesis: BioEve : User Interface Framework bridging information extraction and information retrieval
    Post graduation: Software Engineer, Intel
  • Aaron Ashby (7/2009, BMI)
    Thesis: The effects of pre-operative warm-up on skills in operating room
    Post graduation: PhD candidate, BMI, ASU; System Engineer, Ventana Medical Systems, Tucson, AZ
  • Radhika Nair (7/2009, Computer Science CS)
    Thesis: Semantic classification and dependency parsing enabled automated bio-molecular event extraction from text
    Post graduation: Quality Engineer, Progressive Insurance; Lead Member of Technical Staff, Quality Engineering, salesforce.com

Past Undergraduate Advisees

  • Micah Rappazzo (Biochemistry, ASU Barrett Honors College, Senior Thesis 11/2013, with Dawn Coletta as chair)
    Thesis: Next-Generation Sequencing for DNA Methylation Profiling in Blood and Skeletal Muscle
  • Eileen Leaser (Biochemistry Junior, University of Arizona Honors College)
  • Chris Busick (School of Life Sciences/Bioinformatics, ASU)
  • Dan Neri (Computer Science Senior, ASU, Capstone Project)
  • Thomas Kieffer (Computer Science Senior, ASU, Capstone Project)
  • Ameer Ayoub (Computer Science Senior, ASU, Capstone Project)
  • Jonathan Phipps (Computer Science Senior, ASU, Capstone Project)
  • John Bailey (Computer Science Senior, ASU, Capstone Project)

Past Medical Student Advisees (University of Arizona College of Medicine, Phoenix)

David Hsieh (Advisor for Scholarly Project Thesis, 3/2013)
“The organization and role of international collaboration in research production”
This project was awarded one of four Scholarly Project Awards for the graduating class of 2013.

Past Research Advisees and Collaborators