This page lists my publications. For a more more updated list and/or the links for the papers, please visit my Google Scholar page.
- Analysis of deterministic cyclic gene regulatory network models with delays, Ahsen ME, Hitay Ozbay, S-I Niculescu, Birkhauser (2015).
- A Secant Condition for Cyclic Systems with Time Delays, Ahsen ME, Hitay Ozbay, S-I Niculescu, Time Delay Systems, Springer Verlag (2017).
- Analysis of gene regulatory networks under positive feedback, Ahsen ME, Hitay Ozbay, S-I Niculescu, Delay Systems, Springer Verlag (2014).
Publications In Peer-Reviewed Journals
- R/PY-SUMMA: An R/Python Package for Unsupervised Ensemble Learning for Binary Classification Problems in Bioinformatics. Ahsen, M. E., Vogel, R., & Stolovitzky, G. A. (2020). Journal of Computational Biology.
- Intratumoral heterogeneity and clonal evolution in liver cancer. Losic, B., Craig, A. J., Villacorta-Martin, C., Martins-Filho, S. N., Akers, N., Chen, X.,Ahsen ME,…,Villanueva Augusto. (2020). Nature communications, 11(1), 1-15.
- Evaluation of Combined Artificial Intelligence and Radiologist Assessment to Interpret Screening Mammograms. Schaffter, T.,(6 Authors), Ahsen ME, (15 Authors), Stolovitzky G. (2020). JAMA network open, 3(3), e200265-e200265.
- The transcriptomic response of cells to a drug combination is more than the sum of the responses to the monotherapies. Diaz, J. E., Ahsen, M. E., Schaffter, T., Chen, X., Realubit, R. B., Karan, C., … & Stolovitzky, G. (2020). Elife, 9, e52707.
- Gene selection for optimal prediction of cell position in tissues from single-cell transcriptomics data. Tanevski, J., Nguyen, T., Truong, B., Karaiskos, N., Ahsen, ME, Zhang, X., … & Pham, H. V. (2020). Life science alliance, 3(11).
- COSIFER: a python package for the consensus inference of molecular interaction networks. Manica, M., Bunne, C., Mathis, R., Cadow, J., Ahsen, ME., Stolovitzky, G. A., & Martínez, M. R. (2020). Bioinformatics.
- Unsupervised Evaluation and Weighted Aggregation of Ranked Classification Predictions. Ahsen, M. E., Vogel, R. M., & Stolovitzky, G. A. (2019). Journal of Machine Learning Research, 20(166), 1-40.
- NeTFactor, a framework for identifying transcriptional regulators of gene expression-based biomarkers. Ahsen, ME, Chun, Y., Grishin, A., Grishina, G., Stolovitzky, G., Pandey, G., & Bunyavanich, S. (2019).Nature Scientific Reports, 9(1), 12970-12970.
- Inferring Genome-Wide Interaction Networks Using the Phi-Mixing Coefficient, and Applications to Lung and Breast Cancer, Singh N, Ahsen ME, et. al., IEEE Transactions on Molecular, Biological, and Mulstiscale Communications (2019).
- Leveraging Crowdsourcing to accelerate global health solutions, Sage Davis, (3 Authors), Ahsen ME, et al., Nature Biotechnology (2019).
- Robust and interpretable assessment of network module identification methods, Choobdar S, Ahsen ME, (21 Authors), Nature Methods (2019).
- Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen, Menden MP, (13 Authors), Ahsen ME, (11 Authors), Nature Communications (2019).
- Radiogenomics Consortium Genome-Wide Association Study Meta-analysis of Late Toxicity after Prostate Cancer Radiotherapy, Kerns SL, (9 Authors), Ahsen ME, (27 Authors), Journal of Natl Cancer Institute (2019).
- ExRNA Atlas analysis reveals distinct extracellular RNA cargo types present across human biofluids, Murillo OD, Thistlethwaite W, (19 Authors), Ahsen ME, (35 Authors), Milosavljevic A, Cell (2019).
- An Approach to One-Bit Compressed Sensing Based on Probably Approximately Correct Learning Theory, Ahsen ME, Vidyasagar M, Journal of Machine Learning (2019).
- Integrated nanoscale deterministic lateral displacement arrays for seperation of extracellular vesicles from clinically-relevant volumes of biological samples, Smith J, Wunsch B and Dogra N and Ahsen ME et. al. , Lab on a Chip (2018).
- When Algorithmic Predictions Use Human-Generated Data: A Bias-Aware Classification Algorithm for Breast Cancer Diagnosis, Ahsen ME, Ayvaci MUS, Raghunathan S , Information Systems Research (In Press).
- A crowdsourced analysis to identify ab initio molecular signatures predictive of susceptibility to viral infection, Slim Fourati,(7 Authors), Ahsen ME et al. , Nature Communications (In Press).
- Preference-Sensitive Management of Post-Mammography Decisions in Breast Cancer Diagnosis, Ayvaci MUS, Alagoz O, Ahsen ME, Burnside ES, Production and Operations Management (2018).
- A Novel Nasal Brush-based Classifier of Asthma Identified by Machine Learning Analysis of Nasal RNA Sequence Data, Gaurav Pandey, Om Pandey, Angela Rogers, Ahsen ME et al., Scientific Reports, (2018).
- Two New Approaches to Compressed Sensing Exhibiting Both Robust Sparse Recovery and the Grouping Effect, Ahsen ME, Niharika Challapalli,Mathukumalli Vidyasagar, Journal of Machine Learning Research (2017).
- Error bounds for compressed sensing algorithms with group sparsity: A unified approach, Ahsen ME, Mathukumalli Vidyasagar, Applied and Computational Harmonic Analysis (2017).
- Sparse Feature Selection for Classification and Prediction of Metastasis in Endometrial, Ahsen ME et al., BMC Genomics, (2017).
- Timing the Use of Breast Cancer Risk Information in Biopsy Decision Making, Ayvaci MUS, Ahsen ME, Raghunathan S, Gharibi Z, Production and Operations Management, 26 (7), p. 1333-1358 (2017).
- Estimating Waiting Time for Deceased Donor Renal Transplantion in the Era of New Kidney Allocation System, Furkan Torlak, Mehmet U.S. Ayvaci, Ahsen ME et al., Transplantation Proceedings, 2016.
- Analysis of a Gene Regulatory Network Model with Time Delay Using the Secant Condition, Ahsen ME, Hitay Ozbay, S-I Niculescu, IEEE Life Sciences Letters (2016).
- Optimized Prediction of Extreme Treatment Outcomes in Ovarian Cancer, Burook Misganaw, Ahsen MEet al., Cancer Informatics (2015).
- Mixing Coefficients between discrete and real random variables: Computation and Properties, Ahsen ME, Mathukumalli Vidyasagar, IEEE Transactions on Automatic Control (2014).
- On the analysis of a dynamical model representing gene regulatory networks under negative feedback, Ahsen ME, Hitay Ozbay S-I Niculescu, International Journal of Robust and Nonlinear Control (2014).
Publications in Peer-Reviewed Conference Proceedings
- Modelling drug response and resistance in cancer: Oppurtunities and challenges, Niharika Challapalli,Ahsen ME, Mathukumalli Vidyasagar, Proceedings of the IEEE 55rd Annual Conference on Decision and Control (CDC) (2016).
- A Secant Condition for Cyclic Systems with Time Delays and its Application to Gene Regulatory Networks, Ahsen ME, Hitay Ozbay, S-I Niculescu, Proceedings of the 12th IFAC Workshop on Time Delay Systems (2015).
- A PAC learning approach to One-Bit Compressed Sensing, Ahsen ME, Mathukumalli Vidyasagar, Proceedings of the 2015 American Control Conference (ACC) (2015).
- An Approach to one-bit compressed sensing based on probably approximately correct learning theory, Ahsen ME, Mathukumalli Vidyasagar , Proceedings of the IEEE 54rd Annual Conference on Decision and Control (CDC) (2015).
- Optimized prediction of extreme treatment outcomes in ovarian cancer, Burook Misganaw, Ahsen ME et. al. , Proceedings of the IEEE 54rd Annual Conference on Decision and Control (CDC) (2015).
- Near-ideal behavior of some compressed sensing algorithms, Ahsen ME, M Vidyasagar, In proceedings of the 2014 European Control Conference (ECC) (2014).
- Opportunistic wireless charging for mobile social and sensor networks, Eyuphan Bulut, Ahsen ME, Boleslaw K Szymanski, Proceedings of the 2014 Globecom Workshop (2014).
- On the computation of mixing coefficients between discrete-valued random variables, Ahsen ME, M Vidyasagar, Proceedings of the 2013 Asian Control Conference (ASCC) (2013).
- A novel application of mixing coefficients for reverse-engineering gene interaction networks, Nitin Singh, Ahsen ME, Shiva Mankala, M Vidyasagar, Michael A White, In Proceedings of the 50th Annual Allerton Conference on Communication, Control, and Computing (2013).
- Stability analysis of a dynamical model representing gene regulatory networks, Ahsen ME, Hitay Ozbay, Silviu-Iulian Niculescu, In Proceedings of the 10th IFAC workshop on Time Delay Systems (2012).
- Inferring weighted and directed gene interaction networks from gene expression data using the phi-mixing coefficient, Nitin Singh, Ahsen ME, Shiva Mankala, M Vidyasagar, Michael White, In Proceedings of the 2012 IEEE International Workshop on, Genomic Signal Processing and Statistics,(GENSIPS) (2012).
- A new feature selection algorithm for two-class classification problems and application to endometrial cancer, Ahsen ME, Nitin Kumar Singh, Todd Boren, M Vidyasagar, Michael A White, In proceedings of the IEEE 51st Annual Conference on Decision and Control (CDC) (2012).