To improve the quality and transition of healthcare, robust data management platforms are necessary to analyze heterogeneous genomics 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.
-. 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 Format. F1000Research, Faculty 1000 Publishers, 4(1543), 2018.
-. 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.
-. 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.
*Among Top Ranked Journals World Wide, by Nature Publishing Group*
-. Zeeshan Ahmed. MAV-seq: Management, Analysis and Visualization of Sequence Data. Nature Methods, Nature Publishing Group, 2016.
-. 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, 2015. *Among Top Ranked Journals World Wide, by Nature Publishing Group*
*Among Top Ranked Bioinformatics Journals, by the Oxford University Press*
-. 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 Isotopmer Data. Database, Oxford University Press, Oxford Journals, 2014.
* Among Top Ranked Database Journals, by the Oxford University Press*
*Top Ranked Bioinformatics Journal published by the Oxford University Press*