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Education
- Post-Doc., 1998-2000, Molecular Virology/Bioinformatics, Purdue University
- Ph.D., 1998, Comparative Pathobiology, Purdue University
- M.S., 1992, Molecular Biology, Mississippi State University
- D.V.M., 1988, Veterinary Medicine, Ankara University, Turkey
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Positions and Employment
- 2008-Now Deputy Director, Center for Cancer Nanotechnology Excellence, School of Medicine, Stanford University
- 2006-2008 Assistant Research Professor-Nanomedicine, School of Biomedical Engineering, Purdue University
- 2005-2008 Manager, BioMEMS and BioNano Laboratories, Birck Nanotechnology Center, Purdue University
- 2002-2006 Senior Research Scientist, School of Electrical and Computer Engineering, Purdue University
- 2002-2006 Manager, BioMEMS Laboratory/LIBNA, Purdue University
- 2000-2001 Research Scientist-Genomics, Applied Intelligent Systems Lab, School of Nuclear Engineering, Purdue University
- 1998-2000 Research Associate, Indiana State ADDL, Purdue University
- 1995-1998 Fellow, Purdue Research Foundation, Purdue University
- 1993-1998 Research Assistant, Department of Comparative Pathobiology, Purdue University
Academic Affiliations
| Stanford University (2008-Present) |
Purdue University (1998-2008) |
- Center for Cancer Nanotechnology Excellence-TR (CCNE-TR, Deputy Director)
- Department of Radiology,
Stanford School of Medicine
- Molecular Imaging Program at Stanford
- Stanford Nanofabrication Lab (CCNE Affiliate)
- Stanford Nanocharacterization Lab (CCNE Affiliate)
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- Birck Nanotechnology Center (Manager, BioMEMS and Nanobio Labs)
- School of Biomedical Engineering (Asst. Res. Professor, Nanomedicine)
- LIBNA, School of Electrical Engineering (Manager, LIBNA and Senior Research Scientist, EE)
- Oncological Sciences Center (Member)
- Applied Intelligent Systems Lab, School of Nuclear Engineering (Research Scientist, AI/Genomics)
- Boron Neutron Capture Therapy for Breast Cancer (Member)
- Drug Design, Development and Delivery Group
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Professional Activities
- 2008-Present Member, NCI Alliance for Nanotechnology in Cancer, National Cancer Institute
- 2008-Present Member, NCI Designated CCNE-TR, Stanford Univ.
- 2008-Present Member, Molecular Imaging Program (MIPS), Stanford Univ.
- 2006-Present Member, nanoHUB, NSF Network for Computational Nanotechnology, Purdue Univ.
- 2006-2008, Member, Oncological Sciences Center, Purdue Univ.
- 2005-2008, Member, Bindley Biosciences Center, Purdue Univ.
- 2005-2008, Member, Birck Nanotechnology Center, Purdue Univ.
- 2006-2008 Member, NIH Designated Nanomedicine Development Center, Purdue Univ.
- 2005
Founding
Member, American Academy of Nanomedicine
- 2002-Present Member, Science Advisory Board
- 2002-2004 Member, The Inter. Soc. for BioMEMS and Biomed. Nanotechnology
- 2001-Present Member, Bioinformatics Organization
- 2001-2002 Member, International Society for Computational Biology (ISCB)
- 1993-2000 Member, Phi Zeta Research Society, Omicron Chapter
- 1989-1994 Member, Veterinary Medical Association, Ankara, Turkey
- Review Panelist, Department of Defense, CDMRP, Radiation Oncology Program
- Review Panelist, Department of Defense, Breast Cancer Research Program, Clinical and Experimental Therapeutics
- Review Panelist, Department of Defense, Breast Cancer Research Program, Concept Award.
- Grant Reviewer, U.S. Civilian Research & Development Foundation (CRDF).
- Grant Reviewer, Biomedical Research Council, A*STAR, Singapore.
- Grant Reviewer, Qatar National Research Foundation.
- Grant Reviewer, New Zealand Research Foundation.
- Grant Reviewer, Cariplo Foundation, Italy.
- Selection Committee Member, Associate Dean of Research, School of Engineering, Purdue Univ.
- Nanobio
Laboratory Design and Estabilishment,and Administration of Biosafety
Training, Micro and Nanotechnology Lab (MNTL), University of Illinois
at Urbana-Champaign.
- Consultant: BioAbility Inc., SRA International, Inc.
- Advisory Board, International Genetically Engineered Machines (iGEM) Stanford Team
- Reviewer,
Biomacromolecules, Nano Letters, American Chemical Society,
ChemBioChem, ChemMedChem, Advanced Materials, Biosensors and Actuators,
European Chemical Society, Biomedical Microdevices.
Research Interests
Biological Engineering and Micro/Nanomedicine
- Chip-based
biomedical micro and nano-integrated systems for sensing, diagnosis,
and therapeutics; micro and nano-scale biosensors for cells, proteins,
DNA: Biomimetically Inspired Engineered Systems
- Integration of biology and engineering disciplines for biomedical sensing, imaging and improved medical devices: Biosensors, Intelligent Medical Devices utilizing machine learning, artificial intelligence and expert systems to improve functionality and performance
- PDMS-PMMA
Polymer-based microfludic and silicon micromachined chips for
infectious agent detection and molecular, biophysical study of DNA-DNA,
DNA-Protein and Protein;Protein interactions.
- Single molecule imaging
and image analysis to study cell:pathogen interactions, DNA:Protein
interactions. Fluorescent Microscopy (molecular beacons for
intracellular gene expression analysis), Atomic Force Microscopy
(transcription factor screening, DNA aptamers, viral capsid
biomechanics and assembly)
- Microbial and cellular engineering: Use of intracellular bacteria (L. monocyogenes)
and viruses for improved sensing of intracellular chemicals (free
radicals, NO), proteins and nucleic acids and targeted
drug-delivery. Study and engineering of bacterial molecular responses to environmental signals.
- Stimuli responsive polymers such as hydrogels for development of micro/nano-devices
for drug delivery and biomedical sensing applications.
Functionalization and patterning of biosensor surfaces and assembly of
biologically-inspired nanodevices by using DNA hybridization and synthetic peptides/proteins with known ligands/receptors.
Genomics/Systems Biology
- Reverse Engineering of
Signal Transduction Networks and Molecular Pathways by using DNA,
protein and antibody microarrays and bionformatics analysis (data
mining) of commercially and publicly available data sets: Fuzzy
logic/machine learning based computational modeling and simulation of signal transduction pathways and gene regulatory networks involved in normal cellular proliferation, differentiation and development of cancers: SilicoCyte, Virtual Cellular communities
- Applications of genomics and bioinformatics
in molecular profiling of cancer and apoptosis. Identification of
predictive tumor markers and anti-cancer small molecule drug
leads. Use of the array technologies to ii) monitor response to
anti-neoplastic interventions; iii) improve clinicians’ decision-making
process by better molecular classification of cancers iv) deduce
mechanism of action of pharmaceuticals at genomic level.
- Artificial intelligence-based collaborative software development for
prediction of regulatory sequences such as promoters, transcriptin
factor binding sites and enhancers on DNA and study of semantics of DNA
language (gene activation and inactivation): Fuzzy
logic, Neural Nets, Genetic Algorithms, Expert Systems, Pattern
Finding, Data Warehousing and Mining, Bayesian Nets, Hidden Markov
Modeling
Gene Therapy/Microbiology/Virology
- Microbial and cellular engineering:
Use of intracellular bacteria and viruses for improved sensing of
intracellular chemicals (free radicals, NO), proteins and nucleic acids
and targeted drug-delivery. Study and engineering of bacterial
molecular responses to environmental signals.
- Experimental Therapeutics and Diagnostics: Endogenously (Self)-Regulated Gene Therapy; Cellular Re-programming via intracellular modulation of signal transduction pathways. Therapeutic Transgenics, Correction of genetic defects by Ribozymes via gene replacement. genomic and molecular aspects of drug targets and discovery
- Molecular basis of disease resistance , susceptibility and coordinated gene regulation. Enhancement of disease resistance via manipulation of host immune components, DNA vaccines and therapeutic modulation of signal transduction pathways by small molecule drugs
- Prediction and computational modeling of genome evolution of RNA viruses (Coronaviridae).
Forced evolution of viruses by selective artificial pressure by
antibodies, non-permissive host adaptation, anti-viral drug
treatments. Evaluation of the artificially evolved viruses (field
un-emerged viral strains) by comparative sequence analysis and
predictive modeling. These experiments should yield information
on identification of hot-spots on the viral genome for recombination,
emergence of new strains or quasi-species formation, potential
acquisition of cellular genes by particularly RNA viruses.
Teaching Interests and Experinece
- Fundamentals of Bionanotechnology and Nanomedicine
- Molecular Virology and Applied Virology
- General Microbiology, Medical Microbiology, Pathogenic Microbiology
- Cell Culture Techniques, Immuno-Molecular Laboratory Diagnostic Methods
- Genetic Engineering/Applied Recombinant DNA Technology
- Applied Microbiological Techniques for Engineers / Quantitative biology
- BioMEMS and Biosensors for Life Sciences
- Advanced Microscopy, Atomic Force Microscopy, BioMedical Imaging and Image Analysis
- Genomics, Bioinformatics, Computational Biology (team taught)
- EE-21N,
Nanotechnology (guest lectures, primary instructor is Dr. P.H. Wong),
Dept. of Electrical Engineering, Stanford University, Winter Quarters
of 2008 and 2009.
- Nuclear Medicine Grand Rounds Lecture (Host: Dr. S.S. Gambhir), School of Medicine, Stanford University, 2008.
- Nanobio Lecture, Center for Cancer Nanotechnology Excellence, (Host: Dr. S.S. Gambhir), Stanford University, 2008.
- Biochips
and Nanomedicine, in preparation to be offered through Departments of
Bioengineering and Electrical Engineering, Stanford University in
Spring 2010 Quarter. Instructors: Drs. S.X. Wang and D. Akin.
- BioE222B,
Chemistry of Molecular Probes for Imaging in Living Subjects (Dr. C.
Contag is the primary instructor), Stanford University in Spring 2010
Quarter.
- Nuclear Medicine Grand Rounds Lecture, School of Medicine, Stanford Univ., planned for 2010.
- Biosafety
Level 2/3 Lecture and Training, Micro/Nano Technology Laboratory
(MNTL), University of Illinois at Urbana-Champaign, 2008.
- BME
595R-EE595B Fundamentals of MEMS and Micro-Integrated Systems (primary
instructor: Dr. R. Bashir, D. Akin BioMEMS modules), School of
Electrical Engineering, Purdue University, Spring Semesters 2003, 2004.
- Designed
and instructed modular training sessions on cell culture, aseptic
technique, biosafety, general microbiology laboratory methods to
engineering graduate students and postdocs in the Department of
Electrical and Computer Engineering and at Birck Nanotechnology Center
at Purdue University.
Funded Research Projects and Collaborative Participations
- Oncological Sciences Center, Purdue, IL12 and INF-Gamma-Based Immunotherapy for non-Hodgkin's lymphoma via Nanoparticle-Mediated Delivery System. 2008-2009, $75.000. Role: Purdue-PI
Goal: Novel delivery of DNA-loaded smart nanoparticles and preliminary
assessment of cytokine therapy for non-Hodgkin’s lymphoma.
- National Institutes of Health, R21.
Micromechanical sensors for virus detection. R. Bashir, D. Akin,
M. Ladisch and S. Broyles. 2002-2004, $450.000. Role: co-PI.
Goal: To develop a micromachined hand held device for ultra sensitive
and rapid detection of human coronavirus, influenza virus and vaccinia
virus. Novel dielectrophoretic separation and purification
technologies will be used to trap airborne viral pathogens on surface
deriviatized microcantilever beam sensors. The immobilization of
antibodies and artificial anti-receptor compounds will also be studied.
- National Institutes of Health, R33.
Micromechanical sensors for virus detection. R. Bashir, D.
Akin, M. Ladisch and S. Broyles. 2005-2008, $1.6 million.
Role: co-PI.
Goal: To design and develop a silicon-micromachined
hand-held biosensor device for ultra sensitive and rapid detection of
airborne pathogenic viruses such as human respiratory coronavirus,
influenza virus and vaccinia virus. Commercialization of the
developed sensor device.
- National Science Foundation.
Nano-Scale Probe Array for Extraction of Genetic Material from
Viruses. R. Bashir, A. Bhunia, D. Akin. 2004-2005,
$100.000. Role: co-PI.
Goal: The objective of this project is
to design and develop a nano-scale probe array, within a microfluidic
device capable of extracting DNA and mRNA from viruses for molecular or
genetic analysis. Fully integrated microdevice will be able to
handle sample preparation functions, bacteria, spore and virus lysis,
nucleic acid isolation, concentration, and purification, with minimal
human intervention.
- Indiana State, 21st Century Research Fund.
Sorbent-based hemodialysis system. S. Ash, R. Decarlo, L.H.
Tsoukalas, D. Akin and R. Gao. $2.3 million for 18 months. Role:
Co-PI
The project was recommended for funding by the Indiana
State Board; however, prior to the awarding, the state funds were
diverted to cover Indiana State budget deficit in December 2001.
Task: To
design and develop, in collaboration with HemoCleanse Inc., and Renal
Solutions Inc., improved hemodialysis system with artificial
intelligence based novel sensor dynamic integration and fusion and
patient adaptability. The system will acquire and store
patient specific clinical and biochemical findings and make
predetermined decisions to adjust dialysis conditions to the current
health status of the patient.
Industrial/Academic/Outreach Activities
- Organizer, 1st Annual CCNE-TR Symposium, Stanford, California, hosted by Prof. S.S. Gambhir, MD, PhD, Stanford University
- Organizer, Stanford NanoForum 2008-Shared Nano Facilities, Stanford University
- School
of Medicine Nanomedicine representative, “Nano Storytelling” committee
of the Dean of Research, Stanford University, January 7, 2009.
- Bio-Nano-MEMS
Technology Lecture at theThin Film User Group of American Vacuum
Society, SEMI Headquarters, San Jose, CA, June 17 2009.
- Member, Departmental Biosafety Committee, Weldon School of Biomedical Engineering
- Member
and Collaborator, Breast Cancer and Boron Neutron Capture Therapy
Research Team, Purdue University, Horizon Oncology Institute, Indiana
University, 2003.
- Committee Member, North American Manufacturing Research Conference May 22-23, 2002, West Lafayette, IN.
- Member, Search Committee for Associate Dean of Research, College of Engineering, Purdue University, 2007.
- High
level collaborative interaction meetings with IBM Almedan, Sigma
Aldrich Inc., Nanomix Inc., Agilent, Stanford Research Institute (SRI
International) and other entities.
- Nanocleanroom
Biosafety Compliance Organizer and Biosafety Level 2 Trainer, Birck
Nanotechnology Center, Purdue University.
- Ad Hoc Equipment Selection Committee Member, Birck Nanotechnology Center, Purdue U.
- Member, software selection committee for Purdue University Libraries, 1999.
- High School Student Outreach Training for Purdue Regional Science Fair; trainee received the gold medal.
- Hands
on demonstrations to 25 K-12 middle school children from St. Joseph and
East Richland Middle Schools through "Future Problem Solving Teams" of
Purdue NASA Institute for Nanotechnology and Computing (INAC), 2003.
- Supervision of several undergraduate summer student projects, 2002-2003.
- Bioinformatics software reviewer, Elsevier, 2001-2002.
- Collaborator, Artificial Kidney, HemoCleanse Inc., West Lafayette, IN, 2001-2002.
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