- Computer Engineering Dept., Middle East Technical University, Ankara, Turkey (2001-2008)
Ph.D. in Computer Engineering (Graduate Field of Bioinformatics)
Thesis Title: Similarity Search and Analysis of Protein Sequences and Structures
Prof.Dr. I. Hakki Toroslu, Middle East Technical University, Turkey
Assoc.Prof.Dr. Hakan Ferhatosmanoglu, The Ohio State University, USA
- University of Michigan, Ann Arbor, MI (1997-2001)
B.Sc. in Computer Science
B.Sc. in Cell & Molecular Biology
- Hacettepe University, Faculty of Medicine, Ankara, Turkey (1996-1997)
Associate Teaching Professor
(Sep '16 - present)
Assistant Professor (Sep '09 - Sep '16)
School of Biomedical Engineering, Science and Health Systems, Drexel University
Post Doctoral Researcher
(Oct '08 - Sep '09), Visiting Scholar
Dept. of Computer Sci. & Eng., The Ohio State University
General Research Strategy:
The advances in large scale identification of biological macromolecules have allowed compilation of large amounts of data in public databases through concerted efforts around the globe. While these databases harbor important biological information that can lead to new discoveries, we are still far from having definitive computational tools for efficient and scalable analysis of such data. Therefore, my primary research goal is to develop methods that can face the data size challenge and can push the limits of what can be extracted from biomolecular databases. The application areas where these methods will be utilized are in the rational design of anti-malarial drugs, and in the biomarker discovery for mental and neurological disorders.
Certain relational aspects are common across different biomolecular databases and we have been developing an object relational mapping based approach to integrate biological knowledge-bases. This integrative data oriented approach is especially important in the context of current national and international focus on data-driven science. We have been applying this data-modeling method in reconstruction of regulatory networks from microarray data and in micro-RNA modulation of gene expression data.
While this general modeling approach allows us to simultaneously utilize heterogenous data sources, each of these data sources additionally require specific data indexing and mining strategies. We have previously utilized a metric-indexing method to efficiently search sequence and structure databases. Our state of the art protein structure search method has stood the test of time and has been validated by several research groups. We are now applying this method to functional annotation of proteins and to identification of drug-protein interactions to minimize off-target affects during drug screening process. We are furthermore demonstrating that the same indexing strategy can improve utilization of gene expression data.
In addition to the general research focus on bioinformatics databases, we are also involved in biomedical imaging informatics, specifically in the automated image segmentation problem. Our CellTrack program has been found by us and others to have superior tracking accuracy for cellular image sequences; our efforts in automated segmentation will complement the tracking performance.
Below, I describe the details of the research projects that fit the research agenda described above and also a teaching-related project in online technologies for programming education.
Identification of Protein Functional Sites from Novel Surface Representations:
Protein Structure Initiatives are generating experimentally determined structures of proteins, and most of these target proteins have unknown functions. Annotation of these new protein structures requires careful comparison with the compendium of known functions. We are utilizing a novel representation of protein surfaces that map important biochemical features to 2D image representations that are computationally more practical to study. Comparison of these surface representations will aid in functional annotation and yield insights into functional evolution of protein families. The same surface representation will provide a means by which protein-protein interactions can be studied and predicted.
Integration of Biological Knowledgebases:
With the advent of high-throughput experimental methods in biology, and similar advances in information analysis methods has prompted many national and international efforts to catalogue the data generated from these high-throughput experiments. The heterogeneity of these data and differences in the data access methods have made an integrated utilization of the available data a major technical challenge. We are building novel data representation and communication methods to integrate the world of biological data. A graphical user interface utilizing this integrated data is being developed to enable its utilization for bioinformatics education and by non-programmers.
Gene Regulatory Network Reconstruction from Microarray Data:
Microarray experiments provide the expression levels of tens of thousands of genes and are nowadays routinely used to study cellular responses to stimuli. The ability to identify differentially expressed genes from microarray experiments has enabled discovery of genetic biomarkers for human diseases. In order to understand the biological mechanism of the identified genes, they are considered in the context of regulatory and metabolic networks. Our knowledge of these networks is limited to a small set of well-studied interactions. We are utilizing various genomic and expression data to reconstruct these networks. The integration of time-series microarray data, co-expression profiles obtained from different microarray datasets, sequence and evolutionary profiles of genes will improve the accuracy and coverage of the predicted interactions.
Micro-RNA Modulation of Gene Expression:
Micro-RNAs are a recently discovered class of small non-coding RNA molecules that degrade or inhibit translation of mRNAs. Aberrant Micro-RNA expression has been indicated in a variety of human diseases. Micro-RNA's regulate protein levels by destabilizing mRNA molecules and/or by their inhibiting translation. While several hundreds of conserved micro-RNAs have been identified, their effects on the gene expression levels are not well established. We are developing novel analysis methods for prediction of regulatory effects of micro-RNAs. Our case studies of microRNAs include their involvement in Chronic Regional Pain Syndrome and Spinal Chord Injury.
Learning to See: Segmentation and Tracking using Pre-annotated Images:
Many of the image processing and computer vision methods have been developed as general purpose methods whose application to domain-specific problems is non-trivial and labor intensive. We are building image segmentation and object tracking methods that can make use of a small set of pre-annotated images. A novel representation of existing information is utilized to train pattern classifiers that can segment new images or track new objects. The developed methods are being applied to wound images and live cell microscopy images.
Online Technologies for Programming Education:
Computer programming has become a required skill in engineering and is becoming so in many other data oriented fields. In response to this change, computer programming is being taught more widely in secondary and post-secondary education. Online technologies to assist in self-centered learning and evaluation have not been sufficient to provide for the expanded interest in programming. We are building ProgramminBank as an online technology to assist programming education in engineering and other fields. ProgrammingBank will host a repository of questions that are closely tied to learning objectives and will provide real-time assessment of student work.
Peer Reviewed Journal Articles:
Peer Reviewed Conference Proceedings:
- Therapeutic and prophylactic effects of macrophage-derived small extracellular vesicles in the attenuation of inflammatory pain
Brain Behavior and Immunity, 2021.
- Xist attenuates acute inflammatory response by female cells.
Botros B. Shenoda, Sujay Ramanathan, Richa Gupta, Yuzhen Tian, Renee Jean-Toussaint, Guillermo M. Alexander, Sankar Addya, Srinivas Somarowthu, Ahmet Sacan, Seena K.Ajit. Cellular and Molecular Life Sciences, 2020.
- Proteome characterization of small extracellular vesicles from spared nerve injury model of neuropathic pain.
Renee Jean-Toussaint, Yuzhen Tian, Amrita Datta Chaudhuri, Norman J.Haughey, Ahmet Sacan, Seena K.Ajit. Journal of Proteomics, Volume 211, 2020.
- Exosome microRNA signatures in patients with complex regional pain syndrome undergoing plasma exchange
Sujay Ramanathan, Sabrina R. Douglas, Guillermo M. Alexander, Botros B. Shenoda, James E. Barrett, Enrique Aradillas, Ahmet Sacan, Seena K. Ajit. Journal of Translational Medicine, 2019.
- Inflammation potentiates miR-939 expression and packaging into small extracellular vesicles.
Sujay Ramanathan, Botros B. Shenoda, Zhucheng Lin, Guillermo M., Alexander, Arthur Huppert, Ahmet Sacan, Seena K. Ajit. Journal of Extracellular Vesicles (ZJEV), 2019.
- Investigation of data-driven optical neuromonitoring approach during general anesthesia with sevoflurane.
Gabriela Hernandez-Meza, Meltem Izzetoglu, Ahmet Sacan, Michael Green and Kurtulus Izzetoglu. Neurophotonics, 2017.
- Regulation of proinflammatory genes by the circulating microRNA hsa-miR-939.
Marguerite K. McDonald, Sujay Ramanathan, Andrew Touati, Yiqian Zhou, Rushi U. Thanawala, Guillermo M. Alexander, Ahmet Sacan, and Seena K. Ajit. Sci Rep., 6:30976, 2016.
- UniAlign: Protein structure alignment meets evolution.
Chunyu Zhao and Ahmet Sacan. Bioinformatics, 31(19):3139-46, 2015.
- Circulating microRNA signatures in rodent models of pain.
Rehman Qureshi, et.al., Seena Ajit, and Ahmet Sacan. Molecular Neurobiology, (5):3416-3427, 2016.
- Analgesic response to intravenous ketamine is linked to a circulating microRNA signature in female complex regional pain syndrome patients.
Sabrina R. Douglas, Botros B. Shenoda, Rehman A. Qureshi, Ahmet Sacan, Guillermo M. Alexander, Marielle Perreault, James E. Barrett, Enrique Aradillas-Lopez, Robert J. Schwartzman and Seena K. Ajit. Journal of Pain, 16(9):814-24, 2015.
- Content-based Retrieval of Gene Expression Datasets Using Fingerprints.
Francis Bell and Ahmet Sacan. Network Modeling Analysis in Health Informatics and Bioinformatics, 4(1):1-10, 2015.
- Effect of the Histone Deacetylase Inhibitor JNJ-26481585 in Pain.
Kathryn Capasso, Melissa Manners, Rehman Qureshi, Yuzhen Tian, Ruby Gao, Huijuan Hu, James Barret, Ahmet Sacan, and Seena Ajit. Journal of Molecular Neuroscience. 2014.
- Functional significance of macrophage-derived exosomes in inflammation and pain.
Marguerite McDonald, Yuzhen Tian, Rehman Qureshi, Michael Gormley, Adam Ertel, Ruby Gao, Enrique Aradillas Lopez, Guillermo Alexander, Ahmet Sacan, Paolo Fortina, and Seena Ajit. PAIN. 155(8):1527-1539, 2014.
- Weighted Set Enrichment of Gene Expression Data.
Rehman Qureshi and Ahmet Sacan. BMC Systems Biology (impact factor: 3.15). 7(4):S10 2013.
- A novel method for the normalization of microRNA RT-PCR data.
Rehman Qureshi and Ahmet Sacan. BMC Medical Genomics (impact factor: 3.69). 6(1):S14, 2013.
- Protein Surface Representation and Analysis by Dimension Reduction.
Heng Yang, Rehman Qureshi, and Ahmet Sacan. Journal of Proteome Science (impact factor: 2.49). 10(1):S1, 2012.
- Data Simulation and Regulatory Network Reconstruction from Time-series Microarray Data Using Stepwise Multiple Linear Regression.
Yiqian Zhou, Rehman Qureshi, and Ahmet Sacan. Network Modeling Analysis in Health Informatics and Bioinformatics. 1(1): 3-17, 2012.
- MicroRNA modulation in complex regional pain syndrome.
Irina Orlova, Guillermo Alexander, Rehman Qureshi, Ahmet Sacan, Alessandro Graziano, James E. Barrett, Robert Schwartzman, and Seena Ajit. Journal of Translational Medicine (impact factor: 3.51). 9:195, 2011.
- Comparison of Feature-based and Image Registration-based Retrieval of Image Data Using Multidimensional Data Access Methods.
Serdar Arslan, Ahmet Sacan, I. Hakki Toroslu, Adnan Yazici. Data and Knowledge Engineering (impact factor: 1.4). 8:124-145, (2013).
- Smolign: A Spatial Motifs Based Multiple Protein Structures Alignment Method.
Hong Sun, Ahmet Sacan, Hakan Ferhatosmanoglu, and Yusu Wang. IEEE/ACM Transactions on Computational Biology and Bioinformatics (impact: 2.25), 9(1), 2012.
- Comparing the Yeast Retrograde Response and NF-kB Stress Responses.
Visish Srinivasan, Andres Kriete, Ahmet Sacan, and S. Michal Jazwinski. Aging Cell (impact factor: 7.15), 9(6): 933--941, 2010.
- Sequence alignment reveals possible MAPK docking motifs on HIV proteins.
Perry Evans, Ahmet Sacan, Lyle Ungar, Aydin Tozeren. PLoS ONE (impact factor: 4.41), 5(1):e8942, 2010.
- MicroarrayDesigner: an online search tool and repository for near-optimal microarray experimental designs.
Ahmet Sacan, Nilgun Ferhatosmanoglu, Hakan Ferhatosmanoglu. BMC Bioinformatics (impact factor: 3.03), 10:304-309, 2009.
- Integrated Search and Alignment of Protein Structures.
Ahmet Sacan, I. Hakki Toroslu, and Hakan Ferhatosmanoglu. Bioinformatics (impact factor: 4.88), 24(24):2872-2879, 2008.
- CellTrack: An Open-Source Software for Cell Tracking and Motility Analysis.
Ahmet Sacan, Hakan Ferhatosmanoglu, and Huseyin Coskun. Bioinformatics(impact factor: 4.88), 24(14):1647-1649, 2008.
- LFM-Pro: A Tool for Detecting Significant Local Structural Sites in Proteins.
Ahmet Sacan, Ozgur Ozturk, Hakan Ferhatosmanoglu, and Yusu Wang. Bioinformatics (impact factor: 4.88), 23(6):709-716, 2007.
- Analysis of Paired miRNA-mRNA Microarray Expression Data Using a Stepwise Multiple Linear Regression Model.
Yiqian Zhou, Rehman Qureshi, Ahmet Sacan. International Symposium on Bioinformatics Research and Applications (ISBRA), 2017
- Unfolding the Protein Surface for Pattern Matching
Heng Yang, Chunyu Zhao, Ahmet Sacan. International Symposium on Bioinformatics Research and Applications (ISBRA), 2017
- Prediction of HIV-1 and human protein interactions based on a novel evolution-aware structure alignment method.
Chunyu Zhao, Ahmet Sacan. International Conference on Bioinformatics & Computational Biology (BIOCOMP). 2013.
- Prediction of dihedral angles and 3D structure of proteins using neural network.
Chunyu Zhao, Bo Song, Heng Yang, Ahmet Sacan. International Symposium on Bioinformatics Research and Applications (ISBRA). 2013.
- Similarity Search in Protein Sequence Databases using Metric Access Methods.
Ahmet Cetintas, Ahmet Sacan, I. Hakki Toroslu. International Conference on Bioinformatics and Computational Biology (BICoB). 2013.
- A Weighted Hypergeometric Statistic for the Enrichment of Gene Sets.
Rehman Qureshi and Ahmet Sacan. IEEE International Conference on Bioinformatics & Biomedicine (BIBM). 2012.
- Automated Wound Identification System Based on Image Segmentation and Artificial Neural Networks.
Bo Song and Ahmet Sacan. IEEE International Conference on Bioinformatics & Biomedicine (BIBM). 2012.
- Meta-analysis of Protein Structural Alignment.
Jim Havrilla and Ahmet Sacan. IEEE International Conference on Bioinformatics & Biomedicine (BIBM). 2012.
- Content Based Searching Of Gene Expression Databases Using Binary Fingerprints Of Differential Expression Profiles.
Francis Bell and Ahmet Sacan. IEEE Transactions on International Symposium on Health Informatics and Bioinformatics (HIBIT). 2012.
- Reconstruction Of Gene Regulatory Networks By Stepwise Multiple Linear Regression From Time-Series Microarray Data.
Yiqian Zhou, Rehman Qureshi, and Ahmet Sacan. IEEE Transactions on International Symposium on Health Informatics and Bioinformatics (HIBIT). 2012.
- Protein structure visualization by dimension Reduction and texture mapping.
Heng Yang, Rehman Qureshi, and Ahmet Sacan. IEEE International Conference on Bioinformatics & Biomedicine (BIBM). 2011.
- Letting All Have a Say: A Novel Method for microRNA RT-PCR Normalization.
Rehman Qureshi and Ahmet Sacan. International Conference on Bioinformatics & Computational Biology (BIOCOMP), 2011.
- Comparison of Multidimensional Data Access Methods Using Feature-based Similarity Measures.
Serdar Arslan, Esra Acar, Ahmet Sacan, I. Hakki Toroslu and Adnan Yazici. Proceedings of the 20th International Conference on Pattern Recognition (ICPR), 2010.
- Online Education Experiences: Information Technologies Certificate Program at METU.
Erman Yukselturk, Adnan Yazici, Ozgur Kaya, and Ahmet Sacan. ACM Annual Conference on Innovation and Technology in Computer Science Education (ITiCSE), 2010.
- Secondary Bitmap Indexes with Vertical and Horizontal Partitioning.
Guadalupe Canahuate, Tan Apaydin, Ahmet Sacan, and Hakan Ferhatosmanoglu. 13th International Conference on Extending Database Technology (EDBT). Saint-Petersburg, Russia, March 2009.
- Distance-based Indexing of Residue Contacts for Protein Structure Retrieval and Alignment.
Ahmet Sacan, I. Hakki Toroslu, and Hakan Ferhatosmanoglu. IEEE Proc. of the 8th International Symposium on Bioinformatics & Bioengineering (BIBE), Athens, Greece, Oct 2008.
- Approximate Similarity Search in Genomic Sequence Databases using Landmark-Guided Embedding.
Ahmet Sacan and I. Hakki Toroslu. 1st International Workshop on Similarity Search and Applications (SISAP, an ICDE'08 workshop) Cancun, Mexico, April 2008.
- Automated Data Discovery in Similarity Score Queries.
Fatih Altiparmak, Ali Tosun, Hakan Ferhatosmanoglu, and Ahmet Sacan. In Database Systems for Advanced Applications (DASFAA), LNCS, 4947:440-451, Springer, 2008.
- Amino acid substitution matrices based on 4-body Delaunay contact profiles.
Ahmet Sacan and I. Hakki Toroslu. IEEE Proc. of the 7th International Symposium on Bioinformatics & Bioengineering (IEEE-BIBE), 796-801, 2007.
Conference Proceedings Edited:
- Reconstruction of Regulatory Networks from Microarray Data.
Yiqian Zhou, Rehman Qureshi, Francis Bell, and Ahmet Sacan. In Microarray Image Analysis: Theory and Practice. Luis Rueda (Ed.), CRC Press. 2014.
- Applications and limitations of in-silico models in Drug discovery.
Ahmet Sacan and Sandhya Kortagere. In Bioinformatics and Drug Discovery (Methods in Molecular Biology), 2nd Edition. Richard S. Larson (Ed.), 910:87-124, 2012.
Abstracts and Reports:
- Proceedings of the VLDB Endowment, Volume 5.
Gustavo Alonso, Ugur Cetintemel, Nilesh Dalvi, Julianne Freire, Hank Korth, Z. Meral Ozsoyoglu, Ahmet Sacan, Nesime Tatbul, Anthony Tung (Eds.), 2011-2012.
- Computer and Information Science: Proceedings of the 25th International Symposium on Computer and Information Sciences.
Erol Gelenbe, Ricardo Lent, Georgia Sakellari, Ahmet Sacan, Hakki Toroslu, and Adnan Yazici (Eds.). Lecture Notes in Electrical Engineering (Vol. 62). Heidelberg: Springer., 2010.
- Proceedings of the 24th International Symposium on Computer and Information Sciences.
Fatos Yarman Vural, Adnan Yazici, Hakki Toroslu, Tolga Can, Pinar Senkul, and Ahmet Sacan (Eds.). IEEE Computer Society, 2009.
Manuscripts Under Preparation:
- The Application of MicroRNA Analysis of Blood Samples to Complex Regional Pain Syndrome (CRPS).
Rehman Qureshi, Irina A. Orlova, Bill Alexander, Seena Ajit, and Ahmet Sacan. Drexel Discovery Day, 2013.
- BioGUI: A Graphical User Interface for Bioinformatics Applications.
Francis Bell and Ahmet Sacan. International Conference on Intelligent Systems for Molecular Biology (ISMB), 2014.
- Protein Structure Alignment meets Evolution.
Chunyu Zhao and Ahmet Sacan. International Conference on Intelligent Systems for Molecular Biology (ISMB), 2014.
- Protein functional sites predicted by Surface dimension reduction.
Heng Yang, Chunyu Zhao and Ahmet Sacan. International Conference on Intelligent Systems for Molecular Biology (ISMB), 2014.
- Gene Regulatory Networks Reconstruction by Multiple Linear Regressions from Time-series Microarray Data.
Yiqian Zhou, Jacqueline Gerhart, and Ahmet Sacan. IEEE International Conference Bioinformatics & Biomedicine, 2011. [Best poster award.]
- BioDB: Integration of Biological Knowledgebases.
Jacqueline Gerhart and Ahmet Sacan. IEEE International Conference on Bioinformatics & Biomedicine (BIBM11), 2011.
- Planar shape representation based Protein function prediction.
Heng Yang, Rehman Qureshi, and Ahmet Sacan. International Conference on Intelligent Systems for Molecular Biology (ISMB), and European Conference on Computational Biology (ECCB), 2011. 1st IEEE Symposium on Biological Data Visualization, 2011
- Protein structure visualization by dimension Reduction and texture mapping.
Heng Yang, Rehman Qureshi, and Ahmet Sacan. 3DSIG Structural Bioinformatics and Computational Biophysics, 2011.
- Toward Optimal Seeding of Protein Pairwise Structural Alignments.
Rehman Qureshi, Shakil Khan Ahmed, Mihir Solanki, Ahmet Sacan, and Hakan Ferhatosmanoglu. 3DSIG Structural Bioinformatics and Computational Biophysics. 2010.
- Prediction of Cysteine Bridges using Sequence Alignments.
Ahmet Sacan. Technical Report, METU-CENG-TR-2008-05, Department of Computer Engineering, METU, 2008.
- Contacts-based indexing, retrieval, and alignment of protein structures. (poster & demo)
Ahmet Sacan, I. Hakki Toroslu, and Hakan Ferhatosmanoglu. Fifth Midwest Database Research Symposium, Chicago, IL, Oct 2008.
- Smolign: A Spatial Motifs Based Multiple Protein Structures Alignment Method. (poster & oral presentation)
Hong Sun, Ahmet Sacan, Hakan Ferhatosmanoglu, and Yusu Wang. Ohio Collaborative Conference on Bioinformatics (OCCBIO), Toledo, OH, 2008.
- LFM-Pro: a tool for mining family-specific sites in protein structure databases. (poster)
Ahmet Sacan, Ozgur Ozturk, Hakan Ferhatosmanoglu, and Yusu Wang. Third Midwest Database Research Symposium, Apr 2006.
- Mapping Protein Sequences and Structures to Feature Spaces for Efficient Indexing
Ahmet Sacan. Proc. of the International Symposium on Health Informatics and Bioinformatics (HIBIT), 2005.
Invited Talks and Guest Lectures
- Exosomal microRNA signatures in patients with complex regional pain syndrome undergoing plasma exchange.
Sujay Ramanathan, Sabrina Douglas, Guillermo Alexander, Botros Shenoda, Enrique Aradillas-Lopez, Ahmet Sacan, and Seena K. Ajit. (under review: Journal of Extracellular Vesicles)
- A role for XIST in the regulation of inflammatory response by female cells.
Botros Shenoda, Yuzhen Tian, Guillermo Alexander, Ahmet Sacan, Sujay Ramanathan1, Srinivas Somarowthu, Sankar Addya, Enrique Aradillas-Lopez, Robert J. Schwartzman, and Seena K. Ajit. (to be submitted)
- Prediction of miRNA and mRNA expression using regression models.
Yiqian Zhou, Rehman Qureshi, Francis Bell, and Ahmet Sacan. Bioinformatics. (to be submitted: July 2014).
- Evolution-based protein structure alignment.
Chunyu Zhao and Ahmet Sacan. Bioinformatics. (to be submitted: August 2014).
- Ahmet Cetintas, Ahmet Sacan, and I. Hakki Toroslu. Metric Indexing Protein Sequences. Bioinformatics (to be submitted: December 2014)
- Supervised Classification of Raman Spectra from Diabetic Foot Ulcers.
Xiang Mao, Michael Neidrauer, Michael S. Weingarten, and Ahmet Sacan. Wound Repair and Regeneration. 2012 (under submission).
- Francis Bell and Ahmet Sacan. BioGUI: A Graphical User Interface for Bioinformatics.
- Rehman Qureshi and Ahmet Sacan. Model-based Enrichment of Gene Expression.
- "The Role of Micro-RNAs in Pain: A Cross-Model Investigation", Invited Talk at Drexel University Workshop on Advances in microRNA: Implications for Molecular Medicine.
- "Applications in Translational Informatics", Keynote speech at International Conference on Health Informatics and Bioinformatics (HIBIT), 2012.
- "Bioinformatics II" and "Bioinformatics Conference", Guest Lecture in Drexel DUCOM Biomedical Graduate Programs, Core Curriculum - Cells to Systems, 2012,2013.
- "Bioinformatics Research Topics", University-101, 2011,2012,2013.
- "Contact-based indexing and analysis of Protein Data Bank", Seminar at UPenn Structural Biology Group (Bill Degrado), 2010.
- "Making the Most of the Protein Structure Data Bank", Seminar at Drexel Biochemistry and Molecular Biology, 2010.
- "Structural Bioinformatics", BMES-375 Computational Bioengineering. Guest Lecture & Lab, 2010.
- "Structural Bioinformatics", BMES-483/583 Quantitative Systems Biology. Guest Lecture & Lab, 2010.
- "Recent Progress in Structural Bioinformatics", BMES-864 Seminar, 2010.
- Exosome-mediated signaling in neuropathic pain.
NIH R01. 2017-2022. $1,900,000
Abstract: Exosome uptake results in modulation of gene expression in recipient cells and represents a novel mechanism of cellular communication. There are no studies to date investigating alterations in exosome composition, function, and signaling mechanisms in a neuropathic pain state. Our preliminary data characterizing exosomes in serum from a mouse model of neuropathic pain four weeks after surgery showed a distinct exosomal miRNA and protein signature compared to sham control. We hypothesize that alterations in exosomal composition following nerve injury render them pronociceptive and contribute to the maintenance of chronic neuropathic pain. Using in vitro, ex vivo and in vivo approaches, we will investigate gene expression changes induced by uptake of exosomes from the serum of nerve injury model compared to sham control mice. Differences in exosomal uptake by recipient cells, preference for neurons, astrocytes or glia, alterations in proinflammatory mediators, thermal and mechanical hypersensitivity induced by exosomes and reversal of hypersensitivity by inhibition of exosome release will be investigated. These studies will provide insights on novel signaling mechanisms resulting from exosome release under chronic neuropathic pain and their role in the maintenance of pain.
- MicroRNAs as Biomarkers in Complex Regional Pain Syndrome.
Seena Ajit, Irina Orlova, Ahmet Sacan, Guillermo Alexander, Robert J. Schwartzman.
U.S. Provisional Patent Application No. 61/487,560, filed May 18, 2011. Drexel ref.: 10-1235D/P
- Methods of diagnosing neuropathic pain.
Seena Ajit, Ahmet Sacan, Guillermo Alexander, Robert J. Schwartzman.
U.S. Patent Application No. 14/117,735, filed November 14, 2013. Drexel ref.: 10-1235D/P
- BMES 547: Machine Learning in Biomedical Engineering
- BMES 484/544: Genome Information Engineering (Bioinformatics I)
- BMES 483/543: Quantitative Systems Biology (Bioinformatics II)
- BMES 201-202: Programming and Modeling for Biomedical Engineering I and II
- BMES 546: Biocomputational Languages
- BMES 550: Advanced Biocomputational Languages
- BMES 673 Biosimulation II
- BMES 375: Computational Bioengineering
- BMES 511: Principles of Systems Analysis II
- BMES 480/680: Scientific Computing & Visualization
- Phd, 2013.
- Thesis: Normalization and Enrichment of Gene Expression Microarray Experiments, with Application to Chronic Regional Pain Syndrome.
Heng (Daisy) Yang
- PhD, August 2013.
- Thesis: Reconstruction of Cell Cycle Pathway from Gene Expression Data.
- PhD, 2014
- Thesis: Protein Comparison and Annotation using 2D Surface Projections.
Chunyu (April) Zhao
- PhD, 2014.
- Thesis: Content-based Retrieval of Gene Expression Datasets and Biomarker Discovery in Neuro-degenerative Disorders
- PhD, 2015
- Thesis: Utilizing Evolutionary Information in Protein Structure Analysis.
- PhD, 2012
- Thesis: Evaluation of Chronic Wounds by Raman Spectroscopy and Image Processing
- MSc, 2012.
- Thesis: Automated Segmentation of Wound Images.
- MSc, 2012.
- Thesis: Meta-analysis of Protein Structural Alignment.
- MSc, 2014.
- Thesis: Identification of dTip60 binding partners through bioinformatic analysis of ChIP-Seq data.
- Co-Advisor: Felice Elefant (Biology)
UNDERGRADUATE RESEARCH PROJECTS:
- Freshman STAR Project: Modeling microRNA-target interactions. 2012.
- Senior Design Project: WoundTracer: A robust, user-friendly tool for evaluating wound surface area in busy wound care clinics. 2010-2011.
- Freshman STAR Project: BioDB: Integrating Biological Databases, 2011.
- Freshman Design Project: Micro RNA Expression Analysis Software, 2010-2011.
- Freshman Design Project: BioGUI: Protein Circleplot Visualization, 2010-2011.
I am the sole developer of the software listed below, unless otherwise noted. Some of the software listed here have associated research publications.
- http://sacan.biomed.drexel.edu/progbank/, ProgrammingBank is an online repository and automated grading tool for computer programming problems. The system supports Matlab, and support for C/C++ and Java are under development. ProgrammingBank is currently being used to support BMES201 Programming and Modeling for Biomedical Engineering.
- BioDB: An Object Oriented Approach to Bioinformatics Databases. (Alpha Release available upon request).
- BioGUI: A Graphical User Interface for Bioinformatics. [Ph.D. advisee Francis Bell is the lead developer].
- Smolign: Spatial Motifs Based Multiple Protein Structure Alignment (Java, php). [Developed together with Hong Sun.]
- CellTrack: An Open-Source Software for Cell Tracking and Motility Analysis (C++, wxWidgets, OpenCV) [see the Photonics-Spectra magazine story].
- MaD - Microarray Designer: An Online Search Tool and Repository for Near-Optimal Microarray Experimental Designs (Matlab, php, GraphViz).
- YASARA - Yet Another Scientific Artificial Reality Application: a molecular molecular graphics, modeling, and simulation program (C, OpenGL). The main author is Elmar Krieger; I was a contributing developer.
- RCIndex: Distance-based Indexing of Residue Contacts for Protein Structure Retrieval and Alignment (Matlab, php)
- Vorometric: Integrated search and alignment of protein structures using Voronoi contacts. (Matlab, php, C++)
- LFM-Pro: A Tool for Detecting Significant Local Structural Sites in Proteins (C++, Matlab, Python, CGAL)
- CysAlign: Prediction of Cysteine Bridges using Sequence Alignment (Perl, Python, SOAP, BLAST, C4.5)
- Turing's Reaction-Diffusion: A Simulator for Pattern Formation by Reaction Diffusion (C++, Borland CBuilder)
- MediaPlayer Controller: A Windows Media Player Plugin to control playback and manage library. (VC++, MFC, MediaPlayer SDK)
- mySet -- Visual Perception Card Game (C#, .NET)
- Mancala Game (VC++, MFC)
- Vocabuilder: Improve Your Foreign Language Vocabulary (VC++, MFC)
- EPI - Educational Programming Interface: A simple Windows interface to TurboC compiler. Currently used by introductory programming courses in several universities. (C++, Borland C++ Builder, TurboC)
- http://cow.ceng.metu.edu.tr, COW, An Online Course and Department Automation System. I authored almost all of the framework and automation modules. Currently used by Computer Engineering, and Biology Departments of Middle East Technical University. (php, mysql, C++).
- ICDE 2007, ISCIS 2003, and ISCIS 2009. Authoring and administration of conference websites and electronic submission systems. (php, perl, mysql, Mambo)
- http://www.ceng.metu.edu.tr Installation, customization, and module development for Dept. of Computer Engineering website (php, Mambo)
- http://idea.metu.edu Installation, customization, and module development for IDE_A, an online education system (php, Moodle)
- http://www.columbusrowing.org Upgrade and add-on development for Greater Columbus Rowing Association's Drupal-based website (php, Drupal)
- http://db.cse.ohio-state Website design and development for the Database Research Group in Computer Sci. & Eng. at The Ohio State University (php, css)
- http://bio.cse.ohio-state Website design and development for the Bioinformatics Group in Computer Sci. & Eng. at The Ohio State University (php, css)
- Pickle: A simple and Easy PHP Online Picture Gallery. (php, ImageMagick)
- Moodle Chat Module Revamped A Live Chat Module for Moodle, with HTML and drawing capabilities.
- Dokuwiki Plugins: Extended gCalendar, AutoSearch, Distribute, MyLatex
(Sep '09 - present)
Center for Integrated Bioinformatics
School of Biomedical Engineering, Science and Health Systems
Post Doctoral Researcher
- Courses Taught: Scientific Computing & Visualization, Biocomputational Languages, Quantitative Systems Biology and Bioinformatics, Genome Information Engineering
(Oct '08 - Sep '09), Visiting Scholar
Dept. of Computer Sci. & Eng., The Ohio State University
- Member of the Bioinformatics and Database Research Groups
- Working with Assoc.Prof. Hakan Ferhatosmanoglu and Asst.Prof. Yusu Wang on Indexing and Mining Protein Sequence and Structure Databases, and Microarray Design and Analysis.
- Research challenges include maintenance and scalable querying of high-dimensional biomedical data, and utilizing distributed grid-computing resources to improve data analysis.
- Web Programming. IDE_A, SEM, METU, Ankara, Turkey. (Spring '04,'05,'06)
- Introduction to C Programming. Computer Eng., METU, Ankara, Turkey. (Summer '02,'03)
(Feb '02 - Aug '07)
Computer Eng. Dept., METU, Ankara, Turkey
- Undergraduate Courses: Introduction to Bioinformatics, Data Communications and Computer Networking, Introduction to Database Management Systems, Introduction to Natural Language Processing, Algorithms, Introduction to C Programming, Introduction to Fortran Programming, Rapid Application Development using Delphi
- Graduate Courses: Data Structures and Algorithms, Database Management Systems, Design and Analysis of Algorithms, Computer Networks and Communications
- Head Teaching Assistant (Aug '01 - Oct '03) : Led a team of 50 teaching/research assistants in accomplishing both administrative and academic tasks.
(May '03 - Mar '07)
IDEA - Online Asynchronous Education Program , SEM, METU, Ankara, Turkey
System Administrator and Web Developer
- Courses: Computer Systems, Data Structure and Algorithms, Software Development, Database Management Systems, and Web Programming.
(Sep '03 - Aug '07)
Computer Eng. Dept., METU, Ankara, Turkey
System Administrator and Web Developer
- Provided maintenance, development and support for IT services provided to department's students and staff (about 500 active users each semester).
- Administered services including email, web, database (MySql, PostgreSql, Oracle), cvs, DNS, DHCP, NNTP news, Samba, printing, remote login, and online course management system.
- Maintained Linux, MS Windows, and Sun OS systems on 120 PCs and 10 server machines.
- Developed COW:Ceng On the Web (http://cow.ceng.metu.edu.tr), a comprehensive online management system to automate department's educational and administrative tasks, including course management, document sharing, NNTP-based communication, hardware inventory, seminar system, and other staff and student services.
- Configured and developed add-ons for department's Mambo-based online content management system (http://www.ceng.metu.edu.tr)
(Jun '04 - Apr '07)
IDEA, SEM, METU, Ankara, Turkey
Academic Computer Consultant
- Provided services for IDEA - Asynchronous Online Education Program, offered to off-campus students of varying backgrounds, career and age-groups.
- Led a team of 10 teaching assistants in providing course content and help to students.
- Configured and developed add-ons for Moodle-based online course management system. (System uptime: 1500+ days)
(Jan '00 - May '01)
Information Technology Division
, Univ. of Michigan
- Assisted faculty, staff and students with their usage of Campus Computing Sites facilities and services. Resolved equipment and software problems.
(Jun '98 - Jan '99)
Radiology Dept., Univ. of Michigan Hospital
- Assisted in retrieving and organization of diagnostic data to be used in digital evaluations through Signal Processing.
- Designed and managed patient database for a Breast Cancer Research.
OTHER PROFESSIONAL ACTIVITIES:
(2003 - 2009)
Public Project Auditing
('02 - '07, Turkey)
Expert Court Witness
- Worked in the Audit and Acceptance Team for Turktrace , a multi-hundred million $ project on tracking and trace of tobacco and alcoholic products.
('02 - '07, Turkey)
- Acted as expert in criminal and civil courts, on cases related to computer and information systems.
- Programming Languages: C, C++, C#, Java, Php, Perl, Matlab, ASP, Delphi, Prolog, Haskel, Python, R, Fortran
- Tools: Mysql, PostgreSql, Oracle, SQL Server, OpenGL, GTK toolkit, .NET, standard bioinformatics sequence and structure tools.
- Domains: Bioinformatics, Image Processing, Computer Vision, Graphics, Network Communication, Artificial Intelligence, Web services
- Best Poster Award, IEEE International Conference on Bioinformatics and Biomedicine (BIBM) (2011)
- Best Thesis Award, Middle East Technical University (2008)
- The Scientific and Technological Research Council of Turkey (TUBITAK), Scientific Publication Promotion Award (Turkey, 2007 and 2008)
- Middle East Technical University, Scientific Publication Award (Turkey, 2007 and 2008)
- Graduate academic performance award (4.0 GPA in all graduate courses) (Turkey, 2006)
- Ranked 11th among 79,827 university graduates taking LES (Graduate Record Examination) (Turkey, 2001)
- Univ. of Michigan Class Honors (1998, 1999, 2000), and James B. Angell Scholar (1999)
- Full scholarship from Turkish Government to study abroad. (1997-2001)
- Haci Omer Sabanci Foundation scholarship (1996-1997)
- Ranked 47th among 888,615 high school graduates taking OSYS (University Entrance Examination). (Turkey, 1996)
- Ranked 80th and 90th in two nationwide high school placement examinations. (Turkey, 1993)