Dr. Zeeshan AHMED : Research

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Zeeshan AhmedBioinformatics Software for Metabolic and Health Care Data Management: Software Analysis, Design and Development towards MFA, HCDM and MIDA. 01/2013; Scholars' Press., ISBN: 978-3639511529.

Computer Science approaches (software, database, management systems) are powerful tools to boost research. Here they are applied to metabolic modelling in infections as well as health care management. Starting from a comparative analysis this research shows own steps and examples towards improvement in metabolic flux analysis (MFA) software and health care data management (HCDM). This research presents newly proposed, designed, developed and validated software solutions i.e. LS-MIDA and Isotopo, towards mass isotopomer distribution analysis (MIDA) with user friendly graphical interface, efficient data classification module, statistical abundance predictions and spectrum visualizations. This book is printed from doctoral research on the topic. However, it serves also as a helpful primer for anybody interested in doing metabolic research including fundamentals, examples and a computer science perspective regarding further applications.


 Recent Articles 

-. Zeeshan Ahmed. Ucar D. A standalone software platform for the interactive management and pre-processing of ATAC-seq samples. PeerJ, 5:e2942v1, 2017.

-. Zeeshan Ahmed, Dandekar T. MSL: Facilitating Automatic and Physical Analysis of Published Scientific Literature in PDF FormatF1000Research, Faculty 1000 Publishers, 4(1543), 2017.
-. Zeeshan Ahmed, Bolisetty M, Saman Z, Anguiano E, Ucar D. MAV-seq: An interactive platform for the Management, Analysis, and Visualization of Sequence Data. Human Genomics,  BioMed Central, 10(Suppl 1):12, HGM-2016. 

-. Zeeshan Ahmed, Saman Z, and Dandekar T. Mining biomedical images towards valuable information retrieval in biomedical and life sciences. Database:  The Journal of Biological Databases and Curation, Oxford University Press, Oxford Journals, 2016.





Books
     
  1. Zeeshan Ahmed: Bioinformatics Software for Metabolic and Health Care Data Management: Software Analysis, Design and Development towards MFA, HCDM and MIDA. 01/2013; Scholars' Press., ISBN: 9783639511529

  2. Zeeshan Ahmed: I-HMI and LT-SOS in PDM Systems; Implementing AI Concepts for The Advancement of Multiple Role Based User Oriented PDM System. 04/2011; VDM Verlag Dr. Muller., ISBN: 9783639310702
  3. Zeeshan Ahmed: Integration of Variants Handling in M-System NT Empirically evaluated approach towards the identification of correlation between Traditional and Product Line measures. 01/2010; VDM Verlag Dr. Muller., ISBN: 9783639325539
  4. Zeeshan Ahmed, M Ali: Smart House; Towards Artificially Intelligent Home Automation System. 08/2011; VDM Verlag Dr. Muller., ISBN: 978-3-639-32410-5
  5. Zeeshan Ahmed: Contributions to advance Product Data Management Systems - PDMs: Towards Flexible Graphical User Interface and Semantic Oriented Search for Web based PDMs. 03/2010; Lambert Academic Publishing., ISBN:9783838324951
  6. Zeeshan Ahmed: Ele-Comp-Hus: Digitally Mobile and Computerized House. 03/2010; LAP Lambert Academic Publishing, ISBN: 9783838352091
  7. Zeeshan Ahmed: Variant Handling using ZAC Variability Analysis of Product Line Architectures developed in C/C++. 01/2010; LAP Lambert Academic Publishing., ISBN: 9783838341033
  8. Ina Tacheva, and Zeeshan Ahmed: Integration of NLP Search with ISOAS. 10/2010; LAP Lambert Academic Publishing., ISBN: 978-3-8433-5851-4. [Last Author]
Patent Article
  1. A. Neuberger, Zeeshan Ahmed, T. Dandekar. A system for non-contact monitoring of reaction vessels with electronic bearing support, preparation of suitable vessels and monitoring technology. (Ein System zur beruehrungsfreien Ueberwachung von Reaktionsgefaessen mit elektronischer), DE102014005549A1, Deutsche Patent- und Markenamt (DPMA), 2014. [Joint First Author]

Book-Chapter Articles
  1. Zeeshan Ahmed, Saman M.: Measurement, Analysis with Visualization for better Reliability. Chapter 4, Book: Artificial Intelligence and Hybrid Systems, Edition: 1, Editors: Claudio Rocha, Fernando Akune, Ahmed El-Shafie, ISBN: 978-1-922227-065 (Hardcover, Color), 978-1-477554-739 (Paperback, Color), Publisher: iConcept Press Ltd., 2014.
  2. Zeeshan Ahmed: Measurement Analysis and Fault Proneness Indication in Product Line Applications (PLA).  Chapter 7:  Intelligent Software Design and Maintenance, Series: Frontiers in Artificial Intelligence and Applications, Book: New Trends in Software Methodologies, Tools and Techniques, Vol. 161., Pages: 391-400, Editors: Hamido Fujita, Domenico Pisanelli, ISBN: 978-1-58603-794-9 (print) | 978-1-60750-281-4 (online), Publisher: IOS Press, 2007.
Journal Articles
  1. Zeeshan Ahmed, C. Y Ngan. Match & Scratch Barcodes: Tools for the Demultiplexing and Extraction of Target Sequences from PacBio Amplicon Data. Nature Methods, Nature Publishing Group, 2017.
  2. Zeeshan Ahmed, Ucar D. A standalone software platform for the interactive management and pre-processing of ATAC-seq samples. PeerJ, 5:e2942v1, 2017. [Pre-print, manuscript in revision]
  3. Zeeshan Ahmed, Ucar D. Tutoral I-ATAC. Supplementary material: A standalone software platform for the interactive management and pre-processing of ATAC-seq samples. PeerJ, 5:e2942v1, 2017. [Pre-print, manuscript in revision]

  4. Zeeshan Ahmed, Dandekar T. MSL: Facilitating Automatic and Physical Analysis of Published Scientific Literature in PDF Format. F1000Research, Faculty 1000 Publishers, 4(1543), 2017. [Pre-print, manuscript in revision]

  5. Zeeshan Ahmed. MAV-seq: Management, Analysis and Visualization of Sequence Data. Nature Methods, Nature Publishing Group, 2016

  6. Zeeshan Ahmed, Saman Z, Dandekar T. Mining biomedical images towards valuable information retrieval in biomedical and life sciences. Database: The Journal of Biological Databases and Curation, Oxford University Press, Oxford Journals, 2016.
  7. Zeeshan Ahmed, Bolisetty M, Saman Z, Anguiano E, Ucar D. MAV-seq: An interactive platform for the Management, Analysis, and Visualization of Sequence Data. Human Genomics, BioMed Central, 10(Suppl 1):12, HGM-2016.
  8. Zeeshan Ahmed, Saman Z, Dandekar T. MSL: Mining published scientific literature for the extraction and classification of text and images to support IR capabilities. Frontiers in Neuroinformatics, Frontiers Publishers & INCF, 2016.

  9. Zeeshan AhmedInteractive Quality and Pre-Processing Pipeline for ATAC-seq Data. Frontiers in Neuroinformatics, Frontiers Publishers & INCF, 2016.
  10. Zeeshan Ahmed. MAV-seq: Platfomr for the NGS Data Workflow Management and Automation. Frontiers in Neuroinformatics, Frontiers Publishers & INCF, 2016

  11. Zeeshan Ahmed, Michel M, Saman Z, Dandekar T, Mueller M, and Fekete A. Lipid-Pro: A computational lipid identification solution for untargeted lipidomics on data-independent acquisition tandem mass spectrometry platforms. Bioinformatics, Oxford University Press, Oxford Journals, 31(7), 2015.

  12. Zeeshan AhmedSaman Z, Fleischmann P, Roessler W, Dandekar T. Ant-App-DB: A Smart Ecological Solution for Monitoring the Arthropods' Activities, Experimental Data Management and Solar Calculations without GPS in Behavioural Field Studies. F1000Research, Faculty 1000 Publishers, 3(311), 2015.
  13. Zeeshan Ahmed, Saman Z, Peschel N, Dandekar T. GenomeVX: Bioinformatics Solution towards Understanding the Genome-Wide Comparative Analyses of Different Human Populations. Frontiers in Neuroscience, Frontiers Publishers; INCF, 2015.
  14. Zeeshan Ahmed. Essential design modeling for scientific software development.  PeerJ, PrePrints,  PeerJ, Inc., 3(e1776), 2015.

  15. Zeeshan Ahmed, Michel M, Saman Z, Dandekar T, Mueller M, Fekete A. Lipid-Pro: Work Flow, UML Designs, Configuration and Calculation Steps. Bioinformatics, Oxford University Press, Oxford Journals; 31 (7), Supplementary. PMID: 25433698, 2015.
  16. Zeeshan Ahmed, Fleischmann P, Saman Z, Roessler W, Dandekar T. Ant-App-DB: Work Flow, UML Designs, Configuration and Calculation Steps. F1000Research, Faculty 1000 Publishers, 3(7), Supplementary. PMID: 25977753, 2015
  17. Zeeshan Ahmed, Saman Z., Dandekar T. Butterfly: A Paradigm towards  Stable Bio & Neuro Informatics Tools Development. Frontiers in Neuroscience, Frontiers Publishers; INCF, 2015.
  18. Zeeshan Ahmed, Saman Z., Dandekar T, Mueller M. J., Fekete A. Lipid-Pro: A Bioinformatics Tool for Rapid Identification of Lipids in Pre-processed DIA Data. Frontiers in Neuroscience, Frontiers Publishers; INCF, 2015.

  19. Zeeshan Ahmed. Intelligent Semantic Oriented Agent based Search (I-SOAS). PeerJ, PrePrints,  3:e1898, 2015.

  20. Zeeshan Ahmed. Bioinformatics tools toward GC-MS and LC-MS data analysis, management and visualization. Journal of Proteomics & Bioinformatics, Vol. 8, 2015.
  21. Dandekar T, Fieselmann A, Saman M, and Zeeshan AhmedSoftware Applications Toward Quantitative Metabolic Flux Analysis and Modeling. Briefings in Bioinformatics, Oxford University Press, Oxford Journals; 15 (1), 2014. 
  22. Zeeshan Ahmed, Saman Z, Huber C, Hensel M, Schomburg D, Muench R, Eylert E, Eisenreich W, and Dandekar T. 'Isotopo' a Database Application for Facile Analysis and Management of Mass Isotopomer Data. Database: The Journal of Biological Databases and Curation, Oxford University Press, Oxford Journals, 2014.

  23. Zeeshan Ahmed, Saman Z, Huber C, Hensel M, Schomburg D, Muench R, Eylert E, Eisenreich W, Dandekar T. Information on Isotopo Work Flow, UML Designs, Entity Relationships, Configurations and Calculation Steps. Database, Oxford University Press, Oxford Journals; Supplementary. PMID: 25204646, 2014.
  24. Zeeshan Ahmed, Saman Z, Dandekar T. Developing sustainable software solutions for bioinformatics by the "Butterfly" paradigm. F1000Research, Faculty 1000 Publishers, 3(71), 2014.
  25. Zeeshan Ahmed. Ant-App-Database towards Neural, Behavioral Research on Deserts Ants and Approximate Solar Estimations. Frontiers in Neuroinformatics, Frontiers Publishers; 8, 2014.
  26. Zeeshan Ahmed, Saman Z. Cultivating Software Solutions Development in the Scientific Academia. Recent Patents on Computer Science, 7(1), 2014. 
  27. Zeeshan Ahmed, Saman Z. Applying WEKA towards Machine Learning with Genetic Algorithm and Back Propagation Neural NetworksJournal of Data Mining in Genomics & Proteomics, 5(2), 2014.

  28. Zeeshan Ahmed. Scientific Software Solution Modelling using Butterfly Model. Journal of Proteomics & Bioinformatics, Vol. 7, 2014.
  29. Zeeshan AhmedBioinformatics Tool towards GC-MS Data Analysis, with Extraction, Classification, Standardization, Visualization and Management Features. Metabolomics, 4(2), 177,  2014.
  30. Zeeshan AhmedDesign & Implementation of an Automation System based on the Desktop and Mobile  Technologies. Int. Journal of Sensors, Wireless Communications and Control, 4(1), 2014.
  31. Zeeshan Ahmed, Saman Zeeshan, Claudia Huber, Michael Hensel, Dietmar Schomburg, Richard Meunch, Wolfgang Eisenreich, Thomas Dandekar. Software LS-MIDA for efficient mass isotopomer distribution analysis in metabolic modelling. BMC Bioinformatics, BioMed Central Publishers; 14(1):218, 2013.
  32. Zeeshan Ahmed, Saman Z, Huber C, Hensel M, Schomburg D, Muench R, Eisenreich W, Dandekar T. Tutorial , installation, evaluation, further data, glossary of LS-MIDA. BMC Bioinformatics, Supplementary. PMID: 23837681, 2013. 

  33. Zeeshan Ahmed, Helfrich-Foerster C: DroLIGHT Real Time Embedded System towards Endogenous Clock Synchronization of Drosophila, Frontiers in Neuroinformatics, Frontiers Publishers; 7,  2013. 
  34. Zeeshan Ahmed, Helfrich-Foerster C: DroLIGHT-2: Real Time Embedded and Data Management System  for Synchronizing Circadian Clock to the Light-Dark Cycles. Recent Patents on Computer Science, 6(3), 2013.
  35. Zeeshan Ahmed, Helfrich-Foerster C, Dandekar T: Integrating formal UML designs and HCI patterns with spiral SDLC in DroLIGHT implementation. Recent Patents on Computer Science, 6(2):85-98, 2013.  [Editor Choice Award]
  36. Zeeshan Ahmed, Saman M, Dandekar T:Computational feature performance and domain specific architecture evaluation of software applications towards metabolic flux analysis.  Recent Patents on Computer Science, 5(3):165-176, 2012.
  37. Zeeshan Ahmed, Saman M, Dandekar T: Formal UML Modelling of Isotopo, Bioinformatical Software  for Mass Isotopomers Distribution Analysis, Software Engineering; 2(4):147-159, 2012.
  38. Zeeshan AhmedDistributed Real Time PCM System, UML Design and Development with Embedded Programming. Software Engineering; 2(4):129-137, 2012.
  39. Zeeshan AhmedReview Research: Learning using Web Application I-SOAS. International Journal of Web Applications; 4(3):151-167, 2012.
  40. Zeeshan Ahmed, Dandekar T, Saman M: Semantic web; Ontology Specific Languages for Web Application Development. International Journal of Web Applications; 4(1):33-41, 2012.
  41. Zeeshan Ahmed, Dandekar T, Saman M: Role of Ontology in NLP Grammar Construction for Semantic based  Search Implementation in Product Data Management Systems. International Journals of Management, IT & Engineering; 2(2):32, 2012.
  42. Zeeshan Ahmed, Saman M, Dandekar T: ADAM; Potential of PDM into Clinical Patient Data Management. International Journal of Emerging Sciences; 2(2):280-299, 2012.
  43. Zeeshan Ahmed, Saman M, Dandekar T:Unified Modeling and HCI Mockup Designing towards MIDA. International Journal of Emerging Sciences; 2(3):361-382, 2012.
  44. Zeeshan AhmedDesigning Flexible GUI to Increase the Acceptance Rate of Product Data Management Systems in Industry. International Journal of Computer Science & Emerging Technologies; 2(1):100-109, 2011.
  45. Zeeshan AhmedArtificial intelligence based approach for Product Data Management. International Journal of Web Applications; 3(1):12-16, 2011.
  46. Zeeshan Ahmed, Saman M: Middleware Technologies; Chain Web Grid Services International Journal of Web Applications; 3(4):197-205, 2011.
  47. Zeeshan Ahmed, Saman M: NLP Syntax Structure using ANTLR in I-SOAS. International Journal of Information Technology and Web Engineering; 2(2):51-57, 2011.
  48. Zeeshan AhmedDesigning Knowledge Base towards PDMS. International Journal of Information Technology and Web Engineering; 2:9-12, 2011.
  49. Zeeshan Ahmed, Mujataba A, Saman M: Implementing Computerized and Digitally Mobile Home Automation System towards Electric Appliance Control and Security System.  International Journal of Emerging Sciences; 1(3):15, 2011.
  50. Zeeshan Ahmed, Saman M: Machine Learning and Data Optimization using BPNN and GA in DOC. International Journal of Emerging Sciences; 1(2):108-119, 2011.
  51. Zeeshan Ahmed:Towards Performance Measurement and Metrics based Analysis of PLA Applications. International Journal of Software Engineering & Applications; 1(3):66-80, 2010.
  52. Zeeshan AhmedProposing LT based Search in PDM Systems for Better Information Retrieval. International Journal of Computer Science & Emerging Technologies; 1(4):86-100, 2010.
  53. Zeeshan Ahmed, Saman M: Towards Increase in Quality by Preprocessed Source Code and Measurement Analysis of Software Applications. IST Transactions on Information Technology- Theory and Applications; 1(1):8-13, 2010.
  54. Zeeshan Ahmed, Saman M, Dandekar T: Towards Design and Implementation of a Language Technology based  Information Processor for PDM Systems. IST Transactions on Information Tech.- Theory and Applications; 1(1): 1-7, 2010.

  55. Zeeshan Ahmed:Web to Semantic Web and Role of Ontology in its Development. The journal Semantic Web - Interoperability, Usability, Applicability, 2010.
  56. Zeeshan AhmedProposing Semantic Oriented Agent and Knowledge base Product Data Management. Information Management and Computer Security; Vol. 17 (5), 2009. [IF: 1.09] [The Donn B. Parker International Award for Excellence ]
Conference Proceeding Articles
  1. Zeeshan Ahmed, Bolisetty M, Saman Z, Anguiano E, Ucar D. MAV-Seq: MAV-seq: An interactive platform for the Management, Analysis, and Visualization of Sequence Data.  Human Genome Meeting (HGM) by Human Genome Organisation (HUGO), Session: Big Data, Paper ID: O45, 2016. [Invited Talk-29 Feb 2016, 14:00]

  2. Zeeshan Ahmed. MAV-seq: Platfomr for the NGS Data Workflow Management and Automation. Neuroinformatics 2016, INCF congress,  Reading, UK on September 3-4 2016.

  3. Zeeshan AhmedInteractive Quality and Pre-Processing Pipeline for ATAC-seq Data. Neuroinformatics 2016, INCF congress,  Reading, UK on September 3-4 2016.

  4. Zeeshan Ahmed, Saman Z, Dandekar T. MSL: Mining published scientific literature for the extraction and classification of text and images to support IR capabilities. Neuroinformatics 2016, INCF congress,  Reading, UK on September 3-4 2016
  5. Zeeshan Ahmed, Saman Z, Mayr M, Dandekar T, Mueller M, and Fekete A. Lipid-Pro: A Bioinformatics Tool towards Lipid Identification. 11th Annual International Conference of the Metabolomics Society, the University of California, Davis, San Francisco Bay, USA, 29 June-2nd July 2015. [Excellent Research, NIH Award]
  6. Zeeshan Ahmed, Saman Z, Peschel N, Dandekar T. GenomeVX: Bioinformatics Solution towards Understanding the Genome-Wide Comparative Analyses of Different Human Populations. 8th INCF Congress Neuroinformatics, Cairns, Australia, August 20 - 22, 2015.
  7. Zeeshan Ahmed, Saman Z., Dandekar T. Butterfly: A Paradigm towards  Stable Bio & Neuro Informatics Tools Development. 8th INCF Congress Neuroinformatics, Cairns, Australia, August 20 - 22, 2015. 
  8. Zeeshan Ahmed, Saman Z., Dandekar T, Mueller M. J., Fekete A. Lipid-Pro: A Bioinformatics Tool for Rapid Identification of Lipids in Pre-processed DIA Data. 8th INCF Congress Neuroinformatics, Cairns, Australia, August 20 - 22, 2015.

  9. Zeeshan AhmedAnt-App-Database towards Neural, Behavioral Research on Deserts Ants and Approximate Solar  Estimations, International Neuroinformatics Coordinating Facility (INCF) Neuroinformatics Congress, Leiden University, Leiden, the Netherlands, 25-27 August 2014.
  10. Zeeshan AhmedScientific Software Solution Modelling using Butterfly Model, 4th International Conference on Proteomics & Bioinformatics (Proteomics-2014), Chicago, USA, 04-06 August 2014. 
  11. Zeeshan Ahmed. Bioinformatics Tool towards GC-MS Data Analysis, with Extraction, Classification, Standardization, Visualization and Management Features. 3rd International Conference and Exhibition on Metabolomics & Systems Biology, USA, 24-26 March 2014.

  12. Zeeshan Ahmed, Charlotte Helfrich-Foerster: DroLIGHT: Real Time Embedded System towards Endogenous Clock Synchronization of Drosophila. International Neuroinformatics Coordinating Facility Neuroinformatics Congress, Karolinska Institutet, Sweden, 27-29 August 2013.
  13. Zeeshan Ahmed, Saman M, Eisenreich W, Dandekar T: Isotopo towards Quantitative Mass Isotopomers Distribution Analysis using Spectral Data. 9th Symposium on the Practical Applications of Mass Spectrometry in the Biotechnology Industry (Mass Spec 2012), San Diego, CA USA, 09/2012
  14. Zeeshan Ahmed, Ina Tacheva:Integration of Agile Ontology Mapping towards NLP Search in I-SOAS. 6th Virtual Conference, Innovative Production Machines and Systems, Cardiff University, UK; 11/2010. Innovative Production Machines and Systems, ISBN: 978-1471050268, 02/2012. [Potential Paper Award]
  15. Zeeshan Ahmed, Vasil Popov: Integration of Flexible RIA Based GUI in I-SOAS. 6th Virtual Conference, Innovative Production Machines and Systems, Cardiff University, UK 11/2010. Innovative Production Machines and Systems, ISBN: 978-1471050268, 02/2012.

  16. Zeeshan Ahmed, G. Detlef: Design implementation of I-SOAS IPM for advanced product data management. Computer, Control and Communication, 2009. IC4 2009. 2nd International Conference on; 2009. [Best Conference Paper Award]
  17. Zeeshan AhmedIntelligent semantic oriented agent based search (I-SOAS). 7th International Conference on Frontiers of Information Technology, FIT '09, ACM-SIGMOD 2009.
  18. Zeeshan AhmedIntelligent human machine interface design for advanced product life cycle management systems.  7th International Conference on Frontiers of Information Technology, FIT '09, ACM-SIGMOD 2009.

  19. Zeeshan Ahmed, Sudhir Kumar Ganti: Removal of Communication Gap. 5th Virtual Conference, Innovative Production Machines and Systems, Cardiff University, UK; 07/2009. Innovative Production Machines and Systems, ISBN: 978-184995-006-0, 01/2010.

  20. Zeeshan AhmedI-SOAS Data Repository for Advanced Product Data Management. IADIS European Conference on Data Mining; 06/2009.
  21. Zeeshan Ahmed. Aero Fighter -2D Gaming. 9th National Research Conference on Management and Computer Sciences, SZABIST Institute of Science and Technology, Pakistan; 06/2009.
  22. Zeeshan AhmedHome Automation. 9th National Research Conference on Management and Computer Sciences, SZABIST Institute of Science and Technology, Pakistan; 06/2009.
  23. Zeeshan Ahmed. AI 3D Cybug Gaming. 9th National Research Conference on Management and Computer Sciences, SZABIST Institute of Science and Technology, Pakistan; 06/2009.
  24. Zeeshan AhmedPDM based I-SOAS Data Warehouse Design. 5th International Conference on Statistical Sciences, COMSATS Lahore, Pakistan; 01/2009.
  25. Zeeshan Ahmed, Detlef Gerhard: Design Implementation of Semantic Oriented Agent and Knowledge based approach for Intelligent Human Machine Data Manipulation. 4th Virtual International Conference on Innovative Production Machines and Systems (IPROMS 2008); 11/2009. Intelligent Human Machine Data Manipulation. Innovative Production Machines and Systems, ISBN: 9781904445814, 01/2009.
  26. Zeeshan AhmedSoftware product line based approach towards the software product quality improvement. The 7th International Conference on Software Methodologies, Tools and Techniques, SoMeT_08,  Sharjah; United Arab Emirates, 10/2008.

  27. Zeeshan AhmedSemantic Oriented Intelligent Electronic Learning. IEEE International conference on Information & Communication Technologies; 08/2008.
  28. Zeeshan Ahmed, Detlef Gerhard: I-SOAS towards Product Data Management (PDM) based Application's Problems. IEEE Doctoral Symposium on Research in Computer Science; 08/2008.
  29. Zeeshan Ahmed, Detlef Gerhard: Semantic Oriented Agent based Approach towards Engineering Data Management, Web Information Retrieval and User System Communication Problems. 3rd International Conference for Internet Technology and Secured Transactions; 06/2008.
  30. Zeeshan Ahmed, Sudhir Kumar Ganti, Hans Kyhlback: Design Artifact's, Design Principles, Problems, Goals and Importance. 4th International Conference of Statistical Sciences, Gujrat Pakistan; 05/2008.
  31. Zeeshan AhmedStatistical Semantic Modeling of Preprocessed Source Code to Identify, Measure and Visualize the Complexities in Software Product Line Applications. 4th International Conference of Statistical Sciences, Gujrat Pakistan; 05/2008.
  32. Zeeshan AhmedStatistical Trading Using Target Oriented Trading Agent. 4th International Conference of Statistical Sciences, Gujrat Pakistan; 05/2008.
  33. Zeeshan Ahmed, Detlef Gerhard: Intelligent Graphical User Interface, Information Processing and Data Management based Solution towards Intelligent Data Manipulation and Representation. I*PROMS 2008 conference presentations - 4th Virtual International Conference on Innovative Production Machines and Systems (IPROMS 2008); 07/2008.
  34. Zeeshan Ahmed, Detlef Gerhard: Information Engineering and Knowledge Management based approach towards Intelligent E-Learning Systems Development. 4th Virtual International Conference on Innovative Production Machines and Systems (IPROMS 2008); 07/2008.
  35. Zeeshan Ahmed, Detlef Gerhard: An Agent based Approach towards Metadata Extraction, Modelling and Information Retrieval over the Web. The 6th International Semantic Web Conference and the 2nd Asian Semantic Web Conference, Cultural Heritage on the Semantic Web Workshop, Busan, Korea; 11/2007.
  36. Zeeshan Ahmed, Detlef Gerhard: Contributions of PDM Systems in Organizational Technical Data Management. International Conference on Computer, Control and Communication, IEEE, Pakistan Marine Engineering College - PNEC Auditorium, Karachi Pakistan; 11/2007.
  37. Zeeshan Ahmed, Detlef Gerhard: Role of Ontology in Semantic Web Development. The 6th International Semantic Web Conference and the 2nd Asian Semantic Web Conference, Cultural Heritage on the Semantic Web Workshop, Busan, Korea; 11/2007.
  38. Zeeshan AhmedHow Does Ontology Contribute in Semantic Web Development?. 6th CIIT Workshop on Research in Computing (CWRC 07), Pakistan; 10/2007.
  39. Zeeshan Ahmed, Detlef Gerhard: Designing a Dynamic Components and Agent based Approach for Semantic Information Retrieval. 6th CIIT Workshop on Research in Computing, (CWRC 07), Pakistan; 10/2007.
  40. Zeeshan Ahmed, Detlef Gerhard: Personal Assistant towards Semantic Information Retrieval. Fifth International Workshop on Ontologies and Semantic Web for E-Learning (SWEL'07), 13th International Conference on Artificial Intelligence in Education (AIED 2007); 07/2007.
  41. Zeeshan Ahmed, Detlef Gerhard: Web to Semantic Web & Role of Ontology. National Conference on Information and Communication Technologies; 05/2007.
  42. Zeeshan AhmedMeasurement Analysis and Fault Proneness Indication in Product Line Applications (PLA). New Trends in Software Methodologies, Tools and Techniques - Proceedings of the Sixth SoMeT 2007, November 7-9, 2007, Rome, Italy; 01/2007.
  43. Zeeshan AhmedA Middleware road towards Web (Grid) Services. Blekinge Institute of Technology Student Workshop on Architectures and Research in Middleware (BITSWARM); 01/2006
Poster and Abstract Articles
  1. Zeeshan Ahmed, Saman Z, Mayr M, Dandekar T, Mueller M, and Fekete A: Lipid-Pro: A Bioinformatics Tool towards Lipid Identification. 11th Annual International Conference of the Metabolomics Society, the University of California, Davis, San Francisco Bay, USA, ID: 166, 29 June-2nd July 2015. F1000Research 4:968, 2015. [Excellent Research, NIH Award]
  2. Zeeshan AhmedBioinformatics Tool towards GC-MS and LC-MS Data Analysis, Management and Visualization. 5th International Conference on Proteomics and Bioinformatics, Spain, 01-03 September, Spain, 2015.
  3. Zeeshan Ahmed. Scientific software solutions: lipid-pro, droLIGHT, ant-app-database modelled using butterfly paradigmDFG SFB-CRC-1047 Project Annual Meeting, Tagungshaus Schoenenberg Germany, F1000Research, 6:63, 2015.
  4. Zeeshan Ahmed, Helfrich-Foerster C: DroLIGHT: Real Time Embedded System towards Endogenous Clock Synchronization of Drosophila. In the Neuroinformatics Congress, International Neuroinformatics Coordinating Facility (INCF), F1000Research 4:948, Stockholm Sweden, August 27-29, 2013.

  5. Zeeshan Ahmed, Eisenreich E., Dandekar T: Intelligent Metabolic Isotopomer Data Extraction, Classification, Standardization and Management. In the 6th NEDB Summit, Computer Science and Artificial Intelligence Laboratory (CSAIL), the Massachusetts Institute of Technology (MIT), USA, 2013.

  6. Zeeshan Ahmed, Saman M, Eisenreich W., Dandekar T: Isotopo towards Quantitative Mass Isotopomers Distribution Analysis using Spectral Data. In the 9th Symposium on the Practical Applications of Mass Spectrometry in the Biotechnology Industry, USA, 11-14 September 2012.

  7. Zeeshan Ahmed., Saman M., Eisenreich W., Dandekar T: Isotopo: Software towards Quantitative Mass Isotopomers Distribution Analysis, Visualization and Data Management. In the Fifth Annual New England Database Summit (NEDB Summit), by EMC, Microsoft, and Paradigm4, Computer Science and Artificial Intelligence Laboratory (CSAIL), the Massachusetts Institute of Technology (MIT), USA , 2nd February 2012.

  8. Zeeshan AhmedEfficient Data Management, Intelligent Information Retrieval and Flexible User Interface in PDM Systems. In the Fifth Annual New England Database Summit (NEDB Summit), by EMC, Microsoft, and Paradigm4, Computer Science and Artificial Intelligence Laboratory (CSAIL), the Massachusetts Institute of Technology (MIT), F1000Research 4:952, USA, 2nd February 2012.

  9. Zeeshan Ahmed, Saman M., Dandekar T. et al.: Intelligent Information Management for efficient Computational Biology. In the Information and Networking Day: Intelligent Information Management, by Information and Communication Technology Research (ICT), European Commission, at Jean Monnet Conference Centre, F1000Research 4:951, Luxembourg, 26 September 2011.

  10. Zeeshan AhmedIntelligent Information Retrieval and Flexible GUI in PDM Systems. In the Information and Networking Day: Intelligent Information Management, by Information and Communication Technology Research (ICT), EU Commission, Luxembourg, 26 Sep. 2011.

  11. Zeeshan Ahmed, Dandekar T.et al.: Data integration and refined metabolic modeling. In the Review Meeting of Priority Program! Host Adapted Metabolism of Bacterial Pathogens, (SPP 1316), by DFG, German Research Foundation, Bonn - Bad Godesberg Germany, 06 April 2011.

  12. Zeeshan AhmedIntegration of DB in I-SOAS towards PDMs. In the NEDB Database Summit 2011 at Computer Science and Artificial Intelligence Laboratory (CSAIL), The Massachusetts Institute of Technology (MIT), USA, January 2011.

  13. Zeeshan AhmedNLP TU I-SOAS. In the Startup Weekend Vienna, Microsoft Innovation Center, Vienna Austria, 05 June 2009.

  14. Zeeshan AhmedIntelligent Semantic Oriented Agent Based Search (I-SOAS). In the Innovation Goes Business, by European Commission and INiTS, Austria Center, Vienna Austria, 7 May 2009.

  15. Zeeshan AhmedJava Preprocessed Source Code Analyzer (ZAJ). In Innovation Goes Business, by European Commission and INiTS, Austria Center, Vienna Austria, 7 May 2009.
  16. Zeeshan Ahmed. I-SOAS Graphical Interface towards Product Data Management, In Fall 2008 Northeast Database & Information Retrieval Day (Northeast DB/IR Day), 2008.
  17. Zeeshan AhmedI-SOAS Information Processing towards Product Data Management, In Fall 2008 Northeast Database & Information Retrieval Day (Northeast DB/IR Day) , 2008.
  18. Zeeshan AhmedIGUI, IP and IDM towards Intelligent Information Processing and Presentation, In Fall 2008 Northeast Database & Information Retrieval Day (Northeast DB/IR Day) , 2008.
  19. Zeeshan AhmedIntelligent Human Machine Interaction and Information Engineering based E-Learning, In Fall 2008 Northeast Database & Information Retrieval Day (Northeast DB/IR Day) , 2008.
  20. Zeeshan AhmedIntelligent Measurement Analysis based Solution towards Preprocessed Object Oriented Source Code Analysis, In Fall 2008 Northeast Database & Information Retrieval Day (Northeast DB/IR Day) , 2008.
  21. Zeeshan AhmedI-SOAS Knowledge Management towards Product Data Management, In Fall 2008 Northeast Database & Information Retrieval Day (Northeast DB/IR Day) , 2008.

Magazine Articles

  1. Zeeshan AhmedIndividual Efforts for the Mutual and National IT Benefits. Technology Times, Vol. 4, Issue 24, June 2013.

  2. Zeeshan AhmedNatural Language Processing; a brief Introduction to ANTLR. In NAYS e-Magazine, October 2012. 

  3. Zeeshan AhmedHuman Computer Interaction; Mockup. In NAYS e-Newsletter, Vol. Jan-Feb 2012. 

  4. Zeeshan AhmedWeb to Semantic Web; Online Data Search. In NAYS e-Newsletter, Vol. Nov-Dec 2011. 

  5. Zeeshan AhmedChain SPL; Individual Efforts with Mutual Benefits by Reducing Gaps between Academia & Industry. NAYS e-newsletter, Vol. Sep-Oct 2011. 

  6. Zeeshan AhmedHypothesis; Computer Science, A Revolutionary Field. In NAYS e-newsletter, Vol. July-Aug 2011.

  7. Zeeshan AhmedIntroduction to the field of Product Data Management (PDM). In NAYS e-Newsletter, Vol. May-June 2011. 
Thesis Reports
  1. Zeeshan AhmedBioinformatics Software for Metabolic and Health Care Data Management. Department of Bioinformatics, Biocenter, Faculty of Biology, University of Wuerzburg Germany in collaboration with  Department of Chemistry, Technical University of Munich Germany. Supervisors: Prof. Dr. Thomas Dandekar, Prof. Dr. Wolfgang Eisenreich. [Doctoral Thesis: Graded 'A' with 'Great Honor'].
  2. Zeeshan AhmedTowards Intelligent HMI and Semantic Oriented Search in PDM Applications. Mechanical Engineering Informatics and Virtual Product Development, Institute for Engineering Design and Logistics Engineering, Vienna University of Technology Austria. Supervisor: Prof. Dr. Detlef Gerhard. [Doctoral Thesis: Graded 'A' with great honor by External Reviewer]
  3. Zeeshan AhmedIntegration of variants handling in M-system NT. Department of Computer Science, Blekinge Institute of Technology, University of Blekinge Sweden In Co-operation with Fraunhofer Institute of Experimentells Software Engineering  Germany. Supervisor: Prof. Dr.  Rune Gustavsson, Dr. Adam Trendowicz, Axel Wickenkamp. [Master Thesis: Graded 'A']
  4. Zeeshan AhmedObject Oriented Framework Design Patterns, a Role Modeling Approach. Department of Computer Science, Punjab Institute of Computer Science (PICS), Faculty of Informatics, University of Central Punjab, Pakistan. MS, Supervisor: Taqdees Siddiqi.  [Master Thesis: Graded 'A']
  5. Zeeshan Ahmed Smart House. Punjab Institute of Computer Science (PICS), Department of Computer Science, Punjab Institute of Computer Science (PICS), Faculty of Informatics, University of Central Punjab, Pakistan.  [Bachelor Project & Thesis: Graded 'A']
Scientific Software
  1. Zeeshan Ahmed. I-ATAC. Zenodo. DOI: 10.5281/zenodo.46078, 2016.
  2. Zeeshan Ahmed, Saman Z, Mayr M, Dandekar T, Mueller M, and Fekete A. Lipid-Pro. Zenodo. DOI: 10.5281/zenodo.30942, 2015.
  3. Zeeshan Ahmed. Mining Scientific Literature (MSL). Zenodo. DOI: 10.5281/zenodo.30941, 2015.
  4. Zeeshan Ahmed. GenomeVX. Zenodo. DOI: 10.5281/zenodo.13815, 2015.
  5. Zeeshan Ahmed, Saman Z, Huber C, Hensel M, Schomburg D, Muench R, Eylert E, Eisenreich W, and Dandekar T. Isotopo. Zenodo. DOI: 10.5281/zenodo.30944, 2014.
  6. Zeeshan Ahmed. App-Ant-Database. Zenodo. DOI: 10.5281/zenodo.13223, 2014.
  7. Zeeshan Ahmed. Dataplus. Zenodo. DOI: 10.5281/zenodo.13226, 2014.
  8. Zeeshan Ahmed, Saman Zeeshan, Claudia Huber, Michael Hensel, Dietmar Schomburg, Richard Meunch, Wolfgang Eisenreich, Thomas Dandekar. LS-MIDA. Zenodo. DOI: 10.5281/zenodo.30943, 2013.
Invited Talks and Speaker
  1. Zeeshan Ahmed. MAV-seq: An interactive platform for the Management, Analysis, and Visualization of Sequence Data. Human Genome Meeting, Translational Genomics, by Human Genome Organisation (HUGO), Houston, TX, USA, 29 February 2016.
  2. Zeeshan Ahmed. Developing sustainable software solutions for bioinformatics by the "Butterfly" paradigm. The Jackson Laboratory for Genomic Medicine,  Farmington, CT, USA, 18 May 2015.
  3. Zeeshan Ahmed. Scientific software solutions development using "Butterfly" paradigm. Program in Bioinformatics and Integrative Biology, University of Massachusets Medical School, Greater Boston, MA, USA, 18 April 2015.
  4. Zeeshan Ahmed. New Scientific software solutions: DroLIGHT, Ant-App-DB and Lipid-Pro. German Research Foundation (DFG) SFB-CRC-1047 Project Annual Meeting, Tagungshaus Schoenenberg, Tauberbischofsheim, Germany, 02 October 2014.
  5. Zeeshan Ahmed. Intellieppi, A system for non-contact monitoring of reaction vessels:  Software Design & Implementation. Eppendorf, Hamburg, Germany, 31 August 2013.
  6. Zeeshan Ahmed. Bioinformatics Software for Metabolic and Health Care Data Management. Department of Bioinformatics, Biocenter, Faculty of Biology, University of Wuerzburg, Wuerzburg, Germany, 20 December 2012.
  7. Zeeshan Ahmed. Demonstration: Software for Metabolic Modeling. German Research Foundation (DFG) SPP 1316, Status Seminar, Host Adapted Metabolism of Bacterial Pathogens, Obergurgl University Center, Obergurgl, Austria, 07-10 October 2012.
  8. Zeeshan Ahmed. Project Z1:  Bioinformatic tools and OMICS databases. German Research Foundation (DFG) SFB/Transregio 34 Official Meeting at The Institute for Molecular Infection Biology (IMIB), University of Wuerzburg Germany, 21 July 2011.
  9. Zeeshan Ahmed. Metabolism of Bacterial Infections- LS-MIDA and Isotopo. German Research Foundation (DFG) SFB-1316 Meeting, Host Adapted Metabolism of Bacteris Pathogen, Technical University of Munich, Munich, Germany, 9 December 2011.
  10. Zeeshan Ahmed. LS-MIDA and Isotopo. German Research Foundation (DFG) SPP 1316, Review Meeting, European Institute for Conferences and Professional Training, Gustav-Stresemann-Institut (GSI), Bonn-Bad Godesberg Germany, 06 April 2011.
  11. Zeeshan Ahmed. Demonstration of Software for Biological Experimental Data Analysis (SBEDA). German Research Foundation (DFG) SFB-1316 Meeting, Institue of Biology & Chemistry, University Osnabrueck, Osnabrueck, Germany, 29-30 October 2010.
  12. Zeeshan Ahmed. SW, NLP and IUI using Intelligent Semantic Oriented Agent based Search (I-SOAS). Doctoral Symposium, Semantics Week, University of Amsterdam, Amsterdam, Netherlands, 25-26 June 2009.
  13. Zeeshan Ahmed. Integration of variants handling in M-system NT. Blekinge Institute of Technology, Ronneby/Karslkrona, Sweden, 31 August 2006.
Scientific Software Project Reports
  1. Zeeshan Ahmed: MAV-seq. The Jackson Laboratory for Genomic Medicine, USA, 2016.
  2. Zeeshan Ahmed: I-ATAC. The Jackson Laboratory for Genomic Medicine, USA, 2016.
  3. Zeeshan Ahmed: MSL. University of Wuerzburg Germany & The Jackson Laboratory for Genomic Medicine, USA, 2016.
  4. Zeeshan AhmedLipid-Pro. Department of Neurobiology and Genetics, Biocenter, University of Wuerzburg, Germany, 2015.
  5. Zeeshan Ahmed: GenomeVX. Department of Neurobiology and Genetics, Biocenter, University of Wuerzburg, Germany, 2014.
  6. Zeeshan AhmedAnt-App-Database. Department of Neurobiology and Genetics, Biocenter, University of Wuerzburg, Germany, 2014.
  7. Zeeshan AhmedDataplus. Department of Neurobiology and Genetics, Biocenter, University of Wuerzburg, Germany, 2014.
  8. Zeeshan AhmedDroLIGHT. Department of Neurobiology and Genetics, Biocenter, University of Wuerzburg, Germany, 2013.

  9. Zeeshan AhmedISOTOPO. Department of Bioinformatics, Biocenter, University of Wuerzburg, Germany, 2012.
  10. Zeeshan AhmedMFA. Department of Bioinformatics, Biocenter, University of Wuerzburg, Germany, 2011.
  11. Zeeshan AhmedLS-MIDA. Department of Bioinformatics, Biocenter, University of Wuerzburg, Germany, 2011.

  12. Zeeshan Ahmed: I-SOAS. Vienna University of Technology, Austria, 2010.
  13. Zeeshan Ahmed: ZAJ. Vienna University of Technology, Austria, 2007.
  14. Zeeshan Ahmed: ZAC. Vienna University of Technology, Austria, 2007.
  15. Zeeshan Ahmed: M-System-NT. Fraunhofer IESE, Germany, 2006.
  16. Zeeshan AhmedWiz-Air, A Television - Media  Broad Casting Solution. Wiz-Links Pvt. Ltd Pakistan, 2005.

  17. Zeeshan AhmedSmart House. Faculty of Information Technology University of Central Punjab, Pakistan 2003.
  18. Zeeshan AhmedHome Automation System. Faculty of Information Technology University of Central Punjab, Pakistan 2003.
Supervised Thesis' Reports
  1. Vasil Popov: Advanced User Interface Technology for Intelligent Semantic Oriented Agent Based Search (I‐SOAS). Published and Archived in Institute for Engineering Design and Logistic Engineering Vienna University of Technology Austria and Technical University Sofia, ISBN‐13: 978‐3‐8433‐6892‐6, Sofia Bulgaria, 2009. ['A' Graded, Master Thesis]
  2. Ina Tacheva: Natural Language Processing Approaches for Intelligent Semantic Oriented Agent Based Search (I‐SOAS). Published and Archived in Institute for Engineering Design and Logistic Engineering, Vienna University of Technology Austria and Technical University Sofia, ISBN: 978-3-8433-5851-4,  Sofia Bulgaria, 2009. ['A' Graded, Bachelor Thesis]
  3. M.T. Hashmi: High IT Failure Rate: A Management Prospect. Published and Archived at Institute for Engineering Design and Logistic Engineering, Vienna University of Technology Austria and Department of Business Administration, School of Management, Blekinge Institute of Technology, ISBN-13: 978-3838393940, Ronneby Sweden, 2009. [Master Thesis]
  4. Omer Faraz: Ontological, Warehoused and Knowledge Management Based Product Data Management. Institute for Engineering Design and Logistic Engineering Vienna University of Technology, and Department of Computer and System, Stockholm University, 2009. [Master Thesis]