Photo of Zeeshan  Ahmed, Ph.D.

Zeeshan Ahmed, Ph.D.

Assistant Professor, Genetics and Genome Sciences
Assistant Director, Bioinformatics: Medical Dean’s Precision Medicine Program
Faculty Member, Genetics and Developmental Biology Program
Faculty Member, Biomedical Science
Academic Office Location:
Genetics and Genome Sciences
UConn Health
263 Farmington Avenue
Farmington, CT 06030
Phone: 860-679-2643
Email: zahmed@uchc.edu
Website(s):

Ahmed lab.

Department of Genetics and Genome Sciences

Biomedical Science Faculty

Genetics and Developmental Biology Program

Institute for Systems Genomics

Education
DegreeInstitutionMajor
B.S.University of Central PunjabComputer Science
M.S.University of Central PunjabSofware Engineering
M.S.Blekinge Institute of TechnologyIntelligent Software Systems
OtherVienna University of TechnologyIntelligent Software Systems
Ph.D.University of WuerzburgBioinformatics

Post-Graduate Training
TrainingInstitutionSpecialty
FellowshipFraunhofer Institute for Experimental Software EngineeringIntelligent Software Systems
FellowshipVienna University of TechnologyIntelligent Software Systems
PostdoctoralUniversity of Massachusetts Medical SchoolBiomedical informatics
PostdoctoralUniversity of WuerzburgBioinformatics
Professional TrainingSchool of Medicine, Oregon Health & Science UniversityHealthcare Data Analytics

Awards
Name of Award/HonorAwarding Organization
Director Subsidy Award, HGM-HUGOThe Jackson Laboratory, USA
DAAD International AlumniUniversity of Wuerzburg, Germany
Early Career Award for Excellent ResearchInternational Conference of the Metabolomics Society, UC Davis, NIH, USA
Postdoc Research FellowshipUniversity of Massachusetts Medical School, NIH, USA
Postdoc Research FellowshipUniversity of Wuerzburg, DFG, Germany
Travel Grant AwardUniversity of Wuerzburg, DFG-SFB-1047, Germany
Travel Grant AwardThe 25th International Workshop on Description Logics, Italy
Travel Grant AwardThe 14th International Workshop on Non-Monotonic Reasoning, Italy
Nominated for Biocenter Science AwardUniversity of Wuerzburg, Germany
PhD with Magna Cum LaudeUniversity of Wuerzburg, Germany
Potential Conference Paper6th I*PROMS, Cardiff University, UK
The Donn B. Parker AwardInformation Management & Computer Security, Emerald Group Publishing, UK
Best Conference PaperIEEE International Conference on Computer, Control & Communication
Travel Grant AwardIEEE International Conference on Computer, Control & Communication
Doctoral Research FellowshipUniversity of Wuerzburg, Germany
Young Researcher Travel Grant AwardMicrosoft, Yahoo, Nokia, ACM Conference on Web Search & Data Mining, Spain
IEEE Young Researcher AwardIEEE International Conference on Computer, Control & Communication
Doctoral Research FellowshipVienna University of Technology, Austria
Pre-Doc FellowshipFraunhofer Institute for Experimental Software Engineering, Germany
Scholarship for MS programBlekinge Institute of Technology, Sweden
Scholarship for MS programUniversity of Central Punjab, Pakistan
Annual Advance Programming Competition Winner 2002University of Central Punjab, Pakistan
Annual On Spot Programming Competition Winner 2003University of Central Punjab, Pakistan
Name & DescriptionCategoryRoleTypeScopeStart YearEnd Year
American Association of University Professors (AAUP)Professional/Scientific OrganizationMemberUConn HealthUniversity2018
Liaison Committee on Medical Education (LCME)Professional/Scientific OrganizationMemberUConn HealthUniversity2018
Genetics and Developmental Biology Area of Concentration (GDB AoC)Professional/Scientific OrganizationMember & Advisor BioMed Doctoral StudentsUConn HealthUniversity2018
International Society for Computational Biology (ISCB)Professional/Scientific OrganizationMemberExternalInternational2018
Institute for Systems Genomics (ISG)Professional/Scientific OrganizationMemberUConn HealthUniversity2018
Partnership in Innovation and Education (PIE)Professional/Scientific OrganizationMentor Research StudentsUConn HealthUniversity2018
PLOS ONEProfessional/Scientific JournalEditorial Board MemberExternalInternational2018
Human Genome OrganisationProfessional/Scientific JournalMemberExternalInternational20162017
Bioinformatics, Oxford University Press, Oxford JournalsProfessional/Scientific JournalReviewerExternalInternational2016
LANGMUIR, Analytical Chemistry, American Chemical Society (ACS) PublicationsProfessional/Scientific JournalReviewerExternalInternational2016
Analytical Chemistry, American Chemical Society (ACS) PublicationsProfessional/Scientific JournalReviewerExternalInternational2016
Bioinformatics and Computational BiologyProfessional/Scientific JournalReview EditorExternalInternational2016
Frontiers in GeneticsProfessional/Scientific JournalReview EditorExternalInternational2016
Frontiers in Bioengineering and BiotechnologyProfessional/Scientific JournalReview EditorExternalInternational2016
Frontiers in Plant ScienceProfessional/Scientific JournalReview EditorExternalInternational2016
F1000Research, Faculty of 1000 PublishersProfessional/Scientific JournalReviewerExternalInternational2016
Frontiers in NeuroinformaticsProfessional/Scientific JournalReviewerExternalInternational2016
Metabolomics SocietyProfessional/Scientific JournalMemberExternalInternational20152016
Alumni University of Wuerzburg, GermanyProfessional/Scientific OrganizationMember & US Chapter RepresentativeExternalUniversity2015
Briefings in Bioinformatics, Oxford University Press, Oxford JournalsProfessional/Scientific JournalReviewerExternalInternational2015
PLOS OneProfessional/Scientific JournalReviewerExternalInternational2015
BioMed Central (BMC) PublishersProfessional/Scientific JournalReviewerExternalInternational2015
American Medical Informatics Association (AMIA)Workshop/ConferenceReviewerExternalInternational2015
Neural Computing and Applications, Springer PublishersProfessional/Scientific JournalReviewerExternalInternational2014
Social Network Analysis and Mining, Springer PublishersProfessional/Scientific JournalReviewerExternalInternational2014
Advances in Intelligent Systems and ComputingProfessional/Scientific JournalReferee Book ChaptersExternalInternational2014
Journal of Cases on Information Technology, IGI Global PublishersProfessional/Scientific JournalReviewerExternalInternational2013
Journal of Information Technology Research, IGI Global PublishersProfessional/Scientific JournalReviewerExternalInternational2013
Journal of Electronic Commerce in Organizations (JECO), IGI Global PublishersProfessional/Scientific JournalReviewerExternalInternational2013
Behavior & Information Technology Journal, Taylor & FrancisProfessional/Scientific JournalReviewerExternalInternational2013
Recent Patents on Computer ScienceProfessional/Scientific JournalReviewerExternalInternational2012
Symbiosis Center for Information Technology (SCIT) JournalEditorial BoardEditorial Board MemberExternalInternational2012
LNCS Transactions on Computational Collective Intelligence (TCCI)Professional/Scientific JournalReviewerExternalInternational2011
Alumni Vienna University of Technology, AustriaProfessional/Scientific OrganizationMemberExternalUniversity2010
Multimedia Tools and Applications, Springer PublishersProfessional/Scientific JournalReviewerExternalInternational2010
The International Association of Engineers (IAENG)Professional/Scientific JournalMemberExternalInternational2010
Association for Computing MachineryProfessional/Scientific JournalMemberExternalInternational20062010
Alumni Blekinge Institute of Technology, SwedenProfessional/Scientific OrganizationMemberExternalUniversity2006
Alumni Fraunhofer Society, GermanyProfessional/Scientific OrganizationMemberExternalInternational2006
IEEE Access, IEEE PublishersProfessional/Scientific JournalReviewerExternalInternational20062012

To improve the quality and transition of healthcare, robust data management platforms are necessary to analyze heterogeneous genomics, metabolomics and clinical data of high volume, velocity, variety and veracity. Healthcare data includes information about patient life style, medical history, visits to the practice, lab and imaging test, diagnoses, medications, surgical procedures, consulted providers, claims and genomics profile. Adequate and analytic access to the healthcare and genomics data has potential to revolutionize the field of medicine by developing better understanding of biological mechanisms and modelling complex biological interactions by integrating and analyzing knowledge in a holistic manner. To effectively meet the goals of implementing system for precision medicine, significant efforts are required from the experts in various disciplines (e.g. clinics, bench/wet labs, core/genome technologies, bioinformatics etc.), located within one or multiple organizational units. One of the major challenges is to establish an efficient and secure workflow that can connect all units to streamline transparent data flow, interoperability, cleansing, structuring, standardization, controlled accessibility, processing, quality inspection, processing, analysis, visualization, reporting and sharing. My lab focuses on dealing practical issues associated to the scientific software solutions and infrastructure development for the complex, diverse and large scaled healthcare, genomics, transcriptomics and epigenomics data management, processing, analysis, visualization and integration for the precision medicine. Aims include the development of one of the world's largest precision medicine platforms to help patients, providers, practices and scientists.


My lab is working at different Genomics, Healthcare, Bioinformatics, Precision Medicine and Informatics related research projects at UConn Health, as well as, in different collaborations with scientists and groups located at The Jackson Laboratory USA, University of Massachusetts Medical School USA, University of Cambridge UK, Columbia University USA, and the University of Wuerzburg Germany.


My lab is open for internal and external collaborations.

Accepting students for Lab Rotations: Summer '18, Fall '18, Spring '19.


Mainly interested in, but not limited to the followings:



  • Integration and analysis of Clinical and Genomics data towards Precision Medcine.

  • Bioinformatics tools and pipelines development for Genomics, Transcriptomics and Epigenomics data analysis.

  • Large scalled framework development for the Healthcare, Metabolomics and Genomics Big Data management, analysis and visualizaion.


Message for students: I try my best to guide but encourage students to explore their novel ideas and define hypothesis. The sucess of my students is very important to me. My expectations only include dicpline and honest willingness to do good work.

Journal Articles

Books

Book Chapters

Abstracts

Conference Papers

Other

Title or AbstractTypeSponsor/EventDate/YearLocation
PROMIS-Med: Precise and Reproducible OMICS-Data Management and Integrative System for Precision MedicineTalk26th Conference on Intelligent Systems for Molecular Biology (ISMB)2018Chicago, USA
Contributions of Computational Sciences in Life Sciences: A Venturous JourneyTalkUniversity of South Carolina2018Beaufort, SC
Dealing practical issues associated to the clinical and genomic data integration for precision medicineTalkDepartment of Genetics and Genome Sciences, UConn Health2017Farmington, CT
MAV-Clic: Management, Analysis, and Visualization of Clinical Data.TalkUMass Medical School, Center for Health Policy and Research2017Shrewsbury, MA
Dealing practical issues associated to the clinical and high throughput genomic data integration for precision medicine.TalkUniversity of Texas Health Science Center2017Houston, TX
MAV-seq: An interactive platform for the Management, Analysis, and Visualization of Sequence DataTalkHuman Genome Meeting, Translational Genomics, Human Genome Organisation2016Houston, TX
Developing sustainable software solutions for bioinformatics by the “Butterfly” paradigmTalkThe Jackson Laboratory for Genomic Medicine2015Farmington, CT
Scientific software solutions development using “Butterfly” paradigmTalkProgram in Bioinformatics and Integrative Biology, UMass Medical School2015Greater Boston, MA
New Scientific software solutions: DroLIGHT, Ant-App-DB and Lipid-Pro.TalkGerman Research Foundation (DFG) SFB-CRC-1047 Project Annual Meeting2014Tagungshaus Schoenenberg,Tauberbischofsheim, Germany
Intellieppi, A system for non-contact monitoring of reaction vessels: Software Design & Implementation.TalkEppendorf2013Hamburg, Germany
Bioinformatics Software for Metabolic and Health Care Data ManagementTalkDepartment of Bioinformatics, Biocenter, Faculty of Biology2012University of Wuerzburg, Wuerzburg, Germany
Software for Metabolic Modeling.TalkDFG-SPP1316 Meeting, Obergurgl University Center2012Obergurgl, Austria
Bioinformatic tools and OMICS databases. German Research Foundation (DFG) SFB/Transregio 34 Official Meeting at The Institute for Molecular Infection BiologyTalkDFG SFB/Transregio 34 Meeting, IMIB, University of Wuerzburg2011Germany
Metabolism of Bacterial Infections- LS-MIDA and Isotopo.TalkTechnical University of Munich2011Munich, Germany
LS-MIDA and Isotopo.TalkDFG-SPP1316 Meeting, Gustav-Stresemann-Institut (GSI)2011Bonn-Bad Godesberg, Germany
Demonstration of Software for Biological Experimental Data Analysis (SBEDA).TalkDFG Meeting, Institue of Biology & Chemistry, University Osnabrueck2010Osnabrueck, Germany
SW, NLP and IUI using Intelligent Semantic Oriented Agent based Search (I-SOAS)TalkDoctoral Symposium, Semantics Week, University of Amsterdam2009Amsterdam, Netherlands
Integration of variants handling in M-system NTTalkBlekinge Institute of Technology2006University of Blekinge, Sweden