Sheema Sameen
New York,NY
Summary
Computational biologist with extensive experience in multi-omics analysis to investigate complex diseases, including Alzheimer’s disease and colorectal, lung, and skin cancers. At Columbia University, leading glycoproteomic studies to uncover the role of glycosylation in neurodegeneration using LC-MS/MS data and advanced methods such as QTL mapping, TWAS, and colocalization. Skilled in machine learning and mathematical modeling for studying drug resistance and therapeutic response. Bringing expertise in statistical genetics, systems biology, and molecular network analysis to uncover mechanisms underlying complex diseases.
Overview
16
16
years of professional experience
Work History
Postdoctoral Researcher
Columbia University, Irving Medical Center
09.2023 - Current
- Analyzed glycoproteomic data to investigate the role of glycosylation in Alzheimer’s disease (AD) using LC-MS/MS data from the ROSMAP cohort.
- Characterized 9,100 glycopeptiforms derived from 1,282 proteins in the dorsolateral prefrontal cortex (DLPFC), including 7,500 glycosylated and 1,600 glycated peptiforms.
- Tackled the complexity of brain glycoproteomics caused by variable glycan compositions across single or multiple glycosylation sites within the same protein.
- Applied integrative computational methods such as glycoQTL mapping, TWAS, and colocalization analysis to identify disease-relevant glycopeptiforms and prioritize causal variants and glycosylation sites associated with AD.
Postdoctoral Researcher
IBM, T J Watson Research Center
10.2016 - 05.2019
Selected Projects:
- Genetics of Alzheimer’s Disease (in collaboration with NIH):
Worked on understanding the genomics of complex neurodegenerative disorders such as Alzheimer’s disease by applying statistical, machine learning, and network-based approaches to large-scale whole-genome data. Developed computational pipelines for variant prioritization and disease mechanism inference. - Copy Number Variation in Acral Melanoma (in collaboration with Yale):
Performed copy number variation (CNV) analysis on genomic data from Acral Melanoma patients to identify structural alterations associated with disease progression and therapeutic response. Integrated CNV data with clinical and molecular features to uncover potential biomarkers. - Mathematical Modeling of Immunotherapy (Melanoma Case Study):
Developed a mathematical model to simulate tumor-immune dynamics in melanoma, focusing on response to immune checkpoint inhibitors. Used the model to evaluate therapeutic strategies and predict patient-specific responses to immunotherapy.
Phd Researcher
University of Pisa
03.2013 - 08.2016
- Developed formal mathematical and computational models to study cancer drug resistance mechanisms in lung and colorectal cancer.
- Investigated the impact of KRAS and EGFR mutations on the efficacy of monoclonal antibody therapies and disease progression rates.
- Designed simulation-based case studies to predict treatment response and optimize therapeutic strategies for targeted cancer therapies.
Research Fellow
International Institute for Software Technology United Nations University
09.2012 - 02.2013
Worked on Formal modeling of gene regulatory networks
Researcher
Research Center for Modeling & Simulation (RCMS)
03.2012 - 08.2012
- Company Overview: NUST, Pakistan
- Participated in the Bioinformatics Project: Modification of Vector Space Model for Sequence Alignment
- NUST, Pakistan
Internship
National Tuberculosis Control Program (NTP)
03.2010 - 03.2011
- Company Overview: Islamabad, Pakistan
- Participated in the Project of Modelling TB Epidemiological Data of Pakistan
- Islamabad, Pakistan
Internship
Institute of Biomedical & Genetic Engineering
04.2009 - 06.2009
- Company Overview: KRL, Islamabad, Pakistan
- Participated in the Project for finding Genetic Predisposition of Heart Diseases in Pakistan
- KRL, Islamabad, Pakistan
Education
Doctor of Philosophy - Computer Science
University of Pisa
05.2016
Masters of Science - Bioinformatics
International Islamic University
02.2012
Bachelors of Science - Bioinformatics
International Islamic University
08.2009
Skills
- Genomic Data Analysis: QTL mapping, Transcriptome-Wide Association Studies (TWAS), colocalization analysis, fine-mapping
- Machine Learning: Random Forest, Support Vector Machine (SVM)
- Feature Selection: Minimum Redundancy Maximum Relevance (mRMR)
- Computational Formalisms: Hybrid Automata, Hybrid Petri Nets, P Systems
- Network Analysis: Cytoscape
- Statistical Analysis: Gene set enrichment, association testing
- Clustering & Visualization: Heatmaps, hierarchical clustering
- Mathematical Modeling: Ordinary Differential Equations (ODEs)
Honors And Awards
- Recipient of fully funded research fellowship from Department of computer science, University of Pisa, Italy, 03/01/16 - 09/30/16
- Recipient of fully funded PhD scholarship from United Nations University, International Institute for Software Technology UNU-IIST, Macau (SAR China), 03/01/13 - 05/31/16
- Recipient of fully funded fellowship from United Nations University, International Institute for Software Technology UNU-IIST, Macau (SAR China), 09/01/12 - 02/28/13
Presentations
The contributions to glycoproteomic research at Columbia have been presented at:
- AD/PD™ 2025, International Conference on Alzheimer’s and Parkinson’s Diseases and related neurological disorders (April 1 - 5 April 2025, Vienna, Austria)
- 14th Annual Taub Institute Retreat, Taub Institute for Alzheimer’s Disease Research, Columbia University (September 30, 2024, New York)
- Neuroimmunology Divisional Retreat 2024, Department of Neurology, Columbia University (May 30–31, 2024, New York)
- 3rd Annual functional genomics consortium program meeting, FunGen-AD xqtl workshop (April 29, 2024, New York)
Selected Publications
- Sheema Sameen, Anqi A, Cao X, Feng R, Hila Levy H, Dey KK, Morgenstern D, Levin Y, Bennett DA, Wang G, Beeri MS, Buchman AS, Klein HU, Genetic architecture of the human brain glycoproteome implicates tmem106b and ace glycosylation in alzheimer's disease pathogenesis, Manuscript under preparation
- Sameen, S., Barbuti, R., Milazzo, P., Cerone, A., Del Re, M., & Danesi, R., Mathematical modeling of drug resistance due to KRAS mutation in colorectal cancer, Journal of theoretical biology, 389, 263-273, 2.405, 2016
- Sameen, S., Barbuti, R., Milazzo, P., & Cerone, A., A Mathematical Model for Assessing KRAS Mutation Effect on Monoclonal Antibody Treatment of Colorectal Cancer, In Software Engineering and Formal Methods, 243-258, 2.64, 2014
- Del Re, M., F. Pietrantonio, M. Palombi, Sameen, S., F. Loupakis, C. Barbara, T. Latiano et al., Pattern of Dihydropyrimidine Dehydrogenase Genetic Variants in Patients with Various Degrees of Tolerability of Fluoropyrimidine Treatment, Annals of Oncology, 25, iv77, 51.769, 2014
- Rauf, U., Sameen, S., Cerone, A., Formal Analysis of Oscillatory Behaviors in Biological Regulatory Networks: An Alternative Approach, Elec. Notes in Theoretical Computer Science (ENTCS), 299, 85-100, 0.964, 2013
- Sameen, S., Khalid, Z., & Malik, S. I., Role of pyruvate dehydrogenase kinases (PDK's) and their respective microRNA's in human ovarian cancer, J Med Genet Genomics, 3, 115-121, 2011
- Malik, S.I., Khalid, Z., Sameen S., In Silico Gene Expression Based Analysis on Claudin Family Members Association with Human Thyroid Cancer, J Proteomics Bioinform, 4, 278-283, 10.40, 2011
- Rauf, U., Shehab, M., Qamar, N., Sameen, S., Formal Approach to Thwart Against Insider Attacks: A Bio-Inspired Auto-Resilient Policy Regulation Framework, Accepted in Future Generation Computer Systems, 7.187, 2021
Timeline
Postdoctoral Researcher
Columbia University, Irving Medical Center
09.2023 - Current
Postdoctoral Researcher
IBM, T J Watson Research Center
10.2016 - 05.2019
Phd Researcher
University of Pisa
03.2013 - 08.2016
Research Fellow
International Institute for Software Technology United Nations University
09.2012 - 02.2013
Researcher
Research Center for Modeling & Simulation (RCMS)
03.2012 - 08.2012
Internship
National Tuberculosis Control Program (NTP)
03.2010 - 03.2011
Internship
Institute of Biomedical & Genetic Engineering
04.2009 - 06.2009
Masters of Science - Bioinformatics
International Islamic University
Bachelors of Science - Bioinformatics
International Islamic University
Doctor of Philosophy - Computer Science
University of Pisa
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