Publications

Nasrin Akhter, Kazi Lutful Kabir, Gopinath Chennupati, Raviteja Vangara, Boian Alexandrov, Hristo N Djidjev, Amarda Shehu (2021). Improved protein decoy selection via non-negative matrix factorization. IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB).

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Xiao Chen, Nasrin Akhter, Zhiye Guo, Tianqi Wu, Jie Hou, Amarda Shehu, Jianlin Cheng (2020). Deep Ranking in Template-free Protein Structure Prediction. ACM Conference of Bioinformatics and Computational Biology (BCB).

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Jing Lei, Nasrin Akhter, Wanli Qiao, Amarda Shehu (2020). Reconstruction and Decomposition of High-Dimensional Landscapes via Unsupervised Learning. The 26th ACM SIGKDD Conference on Knowledge Discovery and Data Mining.

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Nasrin Akhter, Gopinath Chennupati, Hristo Djidjev, Amarda Shehu (2020). Decoy selection for protein structure prediction via extreme gradient boosting and ranking. BMC Bioinformatics.

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Sivani Tadepalli, Nasrin Akhter, Daniel Barbará, Amarda Shehu (2020). Anomaly Detection-based Recognition of Near-Native Protein Structures. IEEE Transactions on NanoBioscience.

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Kazi Lutful Kabir, Liban Hassan, Zahra Rajabi, Nasrin Akhter, Amarda Shehu (2019). From Molecular Energy Landscapes to Equilibrium Dynamics via Landscape Analysis and Markov State Models. Journal of Bioinformatics and Computational Biology (JBCB).

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Sivani Tadepalli, Nasrin Akhter, Daniel Barbará, Amarda Shehu (2019). Identifying Near-Native Protein Structures via Anomaly Detection. IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

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Nasrin Akhter, Raviteja Vangara, Gopinath Chennupati, Boian S Alexandrov, Hristo Djidjev, Amarda Shehu (2019). Non-negative matrix factorization for selection of near-native protein tertiary structures. IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

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Nasrin Akhter, Gopinath Chennupati, Kazi Lutful Kabir, Hristo Djidjev, Amarda Shehu (2019). Unsupervised and supervised learning over the energy landscape for protein decoy selection. Biomolecules.

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Kazi Lutful Kabir, Liban Hassan, Zahra Rajabi, Nasrin Akhter, Amarda Shehu (2019). Graph-Based Community Detection for Decoy Selection in Template-Free Protein Structure Prediction. Molecules, 24(3), 741.

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Kazi Lutful Kabir, Nasrin Akhter, Amarda Shehu (2019). Connecting Molecular Energy Landscape Analysis with Markov Model-based Analysis of Equilibrium Structural Dynamics. Intl. Conf. on Bioinformatics and Computational Biology (BICOB) (Best paper award).

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Kazi Lutful Kabir, Nasrin Akhter, Amarda Shehu (2019). Unsupervised Learning of Conformational States Present in Molecular Dynamics Simulation Data for Summarization of Equilibrium Conformational Dynamics. Biophysical Journal, Volume 116, Issue 3, Supplement 1, Pages 291a-292a.

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Nasrin Akhter, Amarda Shehu (2019). Unsupervised Learning for Decoy Selection in Protein Structure Prediction. Biophysical Journal, Volume 116, ISSUE 3, SUPPLEMENT 1, 192a.

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Nasrin Akhter, Gopinath Chennupati, Hristo Djidjev, Amarda Shehu (2018). Improved Decoy Selection via Machine Learning and Ranking. IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS).

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Wanli Qiao, Nasrin Akhter, Xiaowen Fang, Tatiana Maximova, Erion Plaku, Amarda Shehu (2018). From Mutations to Mechanisms and Dysfunction via Computation and Mining of Protein Energy Landscapes. BMC Genomics 19 (Suppl7):671.

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Liban Hassan, Zahra Rajabi, Nasrin Akhter, Amarda Shehu (2018). Community Detection for Decoy Selection in Template-free Protein Structure Prediction. ACM BCB Workshops.

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Nasrin Akhter, Wanli Qiao, Amarda Shehu (2018). An Energy Landscape Treatment of Decoy Selection in Template-free Protein Structure Prediction. Computation 6(2), 39.

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Nasrin Akhter, Liang Zhao, Desmond Arias, Huzefa Rangwala, Naren Ramakrishnan (2018). Forecasting Gang Homicides with Multi-level Multi-task Learning. SBP-BRiMS 2018.

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Nasrin Akhter, Amarda Shehu (2018). Analysis of Energy Landscapes for Improved Decoy Selection in Template-free Protein Structure Prediction. BICoB. (Finalist for best paper award).

Nasrin Akhter, Liban Hassan, Zahra Rajabi, Daniel Barbará, Amarda Shehu (2018). Learning Organizations of Protein Energy Landscape: An Application on Decoy Selection in Template-Free Protein Structure Prediction. Protein Supersecondary Structures, pp. 147-171.

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Nasrin Akhter, Jing Lei, Wanli Qiao, Amarda Shehu (2018). Reconstructing and Decomposing Protein Energy Landscapes to Organize Structure Spaces and Reveal Biologically-active States. IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

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Nasrin Akhter, Amarda Shehu (2018). From Extraction of Local Structures of Protein Energy Landscapes to Improved Decoy Selection in Template-free Protein Structure Prediction. Molecules, 2018, 23(1), 216.

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