Postdoctoral Associate at University of Florida, Bioinformatics
Gainesville, Florida Area
- Current
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- Postdoctoral Associate at University of Florida
- Past
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- Research Assistant at SUNY Binghamton
- Teaching Assistant at Binghamton University
- Research Assistant for the Medical School at University of Hawaii at Manoa
- Teaching Assistant at University of Hawaii at Manoa
- Web Developer at the Center for Instructional Research and Technology at Kean University
- Research Assistant for the Center for Applied Genomics at CAG/ ICPH
- Education
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- State University of New York at Binghamton
- Massachusetts Institute of Technology
- University of Hawaii at Manoa
- Kean University
- Connections
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56
connections
- Industry
- Biotechnology
- Websites
Heike Sichtig’s Summary
I would like to gain an extensive understanding of complex adaptive systems; specifically neurological systems, from their cell to molecular level and use this knowledge to develop novel computational tools for biomedical and bioinformatics research. I developed a simulation tool based on spiking neurons during my PhD studies at Binghamton University. The simulator can be used to model any system of interest to study information processing based on neurological coding and artificial evolutionary processes. My current position as a postdoctoral associate in Dr. Alberto Riva’s lab at the University of Florida allows me to carry out interdisciplinary research to apply computation with spiking neurons to bioinformatics problems. We are interested in using the simulator to automate reasoning for the prediction of transcription factor binding sites in DNA sequences. We are hoping that the tool will generate less false positives than previous methods.
In my future research, I would like to contribute to advancing the field of neurodegenerative disease research using information processing techniques. I plan to select a biological model system to be able to simulate neurological processes for neurodegenerative diseases based on realistic data. For example, the brain of drosophila melanogaster or mouse could be used to study its underlying cell and molecular processes. It is my ambition to use this knowledge to design and prototype neural cognitive prosthetic devices. My background in biomedical engineering and bioinformatics will help me foster collaborations across departments and universities that are needed to carry out such interdisciplinary research endeavor.
Heike Sichtig’s Specialties:
Languages:
C/C++, Lisp, Mathematica, Matlab, Bash Shell Scripting, Perl, Python, Oracle
Operating Systems:
Unix/Linux, OS X, Windows XP, Virtualization (VMWare)
Packages: Eclipse, Emacs, Microsoft Office Family, Adobe Photoshop, LaTex, TexShop, Blackboard, Solid Edge, Arena, LabVIEW, Macromedia MX, SAS, SPSS
Heike Sichtig’s Experience
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Postdoctoral Associate
University of Florida
(Educational Institution; Research industry)
May 2009 — Present (7 months)
I joined Dr. Alberto Riva’s lab for postdoctoral training to gain more experience in computational methods in bioinformatics. We are developing tools using computational biology and genetic programming to explore their application to computational identification of transcription factor binding sites (TFBS) in DNA sequences.
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Research Assistant
SUNY Binghamton
(Educational Institution; Higher Education industry)
May 2006 — May 2009 (3 years 1 month)
Ph.D. Related Research in Biomedical Engineering & Complexity,
The focus of my dissertation was to explore and model neurological systems from an information-processing perspective using complex systems techniques. My primary interest was to build smart learning machines based on nature. I developed a computational tool to prototype a neural prosthetic device using a combination of spiking neurons and a genetic algorithm. In addition to aiding the scientist in modeling the system, I was able to generate simulations of their model, not possible for a clinician or scientist to run in vivo to explore the model system exhaustively. Future work will use the tool to develop sensory neural prosthetics, possibly with applications to audio, visual, gustatory and brain impairment.
Software Developed
• C-based Simulator for spiking neurons with short and long term synaptic plasticity (SSNNS)
• Mathematica-based Model for short term synaptic plasticity based on Markram dynamics
Committee
• Dr. J. David Schaffer, Dr. Craig B. Laramee, Dr. Walker Land, Dr. Rene Doursat -
Teaching Assistant
Binghamton University
(Educational Institution; Higher Education industry)
May 2004 — May 2009 (5 years 1 month)
Engineering Design Department:
• Assist in instruction of exploring Engineering for college freshmen (Dr. Roy McGrann)
Systems Science and Bioengineering Department:
• Complex Biological Systems (Dr. Hiroki Sayama)
• Autonomous Agents (Dr. Jacques Beaumont)
• Probabilistic Systems (Dr. Mohammed Khasawneh)
• Biological Networks, Intelligent Systems (Dr. Craig Laramee)
o Helped to develop course curriculum and core teaching materials
o Used complexity research methods to program an interactive game for PDAs using collective intelligence to aid in teaching complex systems techniques
o Software Developed: Collective Intelligence Game (webMathemathica) -
Research Assistant for the Medical School
University of Hawaii at Manoa
(Educational Institution; Higher Education industry)
December 2003 — May 2004 (6 months)
Post Master’s Related Research in Computer Science,
I worked as a research assistant for the John A. Burns School of Medicine at the University of Hawaii. My research was part of the UH Tele-health Research Institute; project Touch, developing intelligent virtual reality medical simulations to train medical students in collaboration with the University of New Mexico’s School of Medicine. This interdisciplinary research experience sparked my interest to study intelligent systems, including neurological modeling, from a complex systems perspective. -
Teaching Assistant
University of Hawaii at Manoa
(Educational Institution; Higher Education industry)
May 2003 — December 2003 (8 months)
Computer Science Department:
• Programming Language Theory (Dr. David Chin) -
Web Developer at the Center for Instructional Research and Technology
Kean University
(Educational Institution; Information Technology and Services industry)
March 1999 — August 2002 (3 years 6 months)
Developed web sites and learning space applications for online courses.
Coordinated and participated in the creation of digital classroom movie making. -
Research Assistant for the Center for Applied Genomics
CAG/ ICPH
(Biotechnology industry)
June 2001 — October 2001 (5 months)
Collaborated in the development of a Laboratory Inventory Management System using J Class and Oracle for the Bioinformatics group.
Heike Sichtig’s Education
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State University of New York at Binghamton
PhD , Complex Systems, Spiking Neural Networks, Evolutionary Computation , 2004 — 2009
- Activities and Societies:
- IEEE CIS,EMBS
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Massachusetts Institute of Technology
Certificate , Complex Physical, Biological & Social Systems , 2006 — 2006
One-Week Intensive Course at M.I.T., NECSI, Boston, MA, January 9-13 2006
I attended a course on “Complex Physical, Biological & Social Systems” at the New England Complex Systems Institute. Prof. Yaneer Bar-Yam of NECSI gave an introduction to the essential concepts of complex systems and related mathematical methods and simulation strategies with application to physical, biological and social systems. In our project, we used complexity research methods to track and visually demonstrate the degrees of divergence and convergence of participant’s perceptions of group formation processes. Our study explored the complexity profiles of group pattern formation across diverse research project groups. I have official credentials for this course.- Activities and Societies:
- Concepts and Methods Discussed
Emergence, complexity, networks, self-organization, pattern formation, evolution, adaptation, fractals, chaos, cooperation, competition, attractors, interdependence, scaling, dynamic response, information and function, Statistical methods, cellular automata, agent-based modeling, pattern recognition, system representation and informatics
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University of Hawaii at Manoa
Post Graduate Work , Computer Science , 2003 — 2004
I took graduate level computer science courses including Programming Languages, Autonomous Intelligent Agents, Mobile Computing, Data Security and Human Computer Interaction.
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Kean University
B.S., M.S. , Computer Science; Computing, Statistics and Math , 1998 — 2003
My graduate level courses included Bioinformatics, Artificial Intelligence, Multivariate Statistics and Partial Differential Equations. My project was “A Web-Based File Transfer Queuing System” and I used Linux, Tomcat 4.1, Servlets/JSP and Java under supervision of my adviser Dr. George Chang.
I graduated with summa cum laude in Computer Science and Technology with a minor in Statistics.
Additional Information
Heike Sichtig’s Websites:
Heike Sichtig’s Interests:
Neurological Modeling and Neural Prosthetic Device Design: My interest is in modeling and simulation of complex adaptive systems and their application to the design of neural cognitive prosthetic devices. I hope to contribute to advancing the field of neurodegenerative disease research using information processing techniques.
Heike Sichtig’s Groups:
• IEEE Computational Intelligence Society (GOLD Vice Chair)
• IEEE Biomedical Engineering Society
• BCIG NIH Biomedical Computing Interest Group
• ACM (Association for Computing Machinery)
• ASEE (American Society for Engineering Education) (External Reviewer)
• Upsilon Pi Epsilon (CS International Honor Society)
• Phi Kappa Phi (Academic Honor Society for all Disciplines)
• Epsilon Pi Tau (International Honor Society for Professions in Technology)
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University of Hawaii -
Binghamton University Alumni (and Faculty) -
Computational Biology -
Bioinformatics geeks -
Kean University Alumni of New Jersey -
Grey Thumb -
New England Complex Systems Institute (NECSI) -
Systems Biology for Medical Research -
ISCB - International Society for Computational Biology -
Binghamton University
Heike Sichtig’s Honors:
Student Workshop Travel Grants (2004, 2005, 2007, 2008)
• Computer Research Association, CRA-W Grad Cohort Workshop, Seattle, WA
• IEEE Symposium Series on Computational Intelligence, Honolulu, HI
International Student Scholarship for Academic Excellence (1999 - 2002)
• Dean’s List, Kean University, Union, NJ
Honolulu, HI
International Student Scholarship for Academic Excellence (1999 - 2002)
- Dean’s List, Kean University, Union, NJ
Heike Sichtig’s Contact Settings
Interested In:
- career opportunities
- consulting offers
- new ventures
- job inquiries
- expertise requests
- business deals
- reference requests
- getting back in touch
