Amarda Shehu

Amarda Shehu, Daniel Barbará, Kevin Molloy, 2013, 2013 IEEE 3rd International Conference on Computational Advances in Bio and medical Sciences (ICCABS).

Traffic Flow Forecasting with Maintenance Downtime via Multi-Channel Attention-Based Spatio-Temporal Graph Convolutional Networks pdf

Amarda Shehu, David Lattanzi, Parastoo Kamranfar, 2021, ArXiv.

From mutations to mechanisms and dysfunction via computation and mining of protein energy landscapes

E. Plaku, Amarda Shehu, Wanli Qiao, 2018, BMC Genomics.

Investigation of a dilated cardiomyopathy-associated variant in BAG3 using genome-edited iPSC-derived cardiomyocytes.

Amarda Shehu, I. Benjamin, K. Musunuru, 2019, JCI insight.

Interpretable Molecular Graph Generation via Monotonic Constraints

Amarda Shehu, Yuanqi Du, Liang Zhao, 2022, SDM.

A novel method to improve recognition of antimicrobial peptides through distal sequence-based features

Amarda Shehu, Uday Kamath, Daniel Veltri, 2014, 2014 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

Binary Response Models for Recognition of Antimicrobial Peptides

Amarda Shehu, Daniel Veltri, Elena G. Randou, 2013, BCB.

Systematic analysis of global features and model building for recognition of antimicrobial peptides

Amarda Shehu, Daniel Veltri, Elena G. Randou, 2013, 2013 IEEE 3rd International Conference on Computational Advances in Bio and medical Sciences (ICCABS).

Computing the Structural Dynamics of RVFV L Protein Domain in Aqueous Glycerol Solutions

Amarda Shehu, S. Silayi, Gideon K Gogovi, 2021, Biomolecules.

Attenuating dependence on structural data in computing protein energy landscapes

Erion Plaku, Amarda Shehu, Tatiana Maximova, 2019, BMC Bioinformatics.

From Optimization to Mapping: An Evolutionary Algorithm for Protein Energy Landscapes

Amarda Shehu, Emmanuel Sapin, Kenneth A. De Jong, 2018, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Sample-Based Models of Protein Energy Landscapes and Slow Structural Rearrangements

Erion Plaku, Amarda Shehu, Daniel Carr, 2018, J. Comput. Biol..

Reconstructing and mining protein energy landscape to understand disease

Erion Plaku, Amarda Shehu, Xiaowen Fang, 2017, 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

Out of one, many: Exploiting intrinsic motions to explore protein structure spaces

Erion Plaku, Amarda Shehu, Tatiana Maximova, 2017, ICCABS.

Statistical Analysis of Computed Energy Landscapes to Understand Dysfunction in Pathogenic Protein Variants

Erion Plaku, Amarda Shehu, Tatiana Maximova, 2017, BCB.

Sample-based Models of Protein Structural Transitions

Erion Plaku, Amarda Shehu, Daniel Carr, 2016, BCB.

Evolutionary search strategies for efficient sample-based representations of multiple-basin protein energy landscapes

Kenneth A. De Jong, Amarda Shehu, Emmanuel Sapin, 2015, 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

Computing transition paths in multiple-basin proteins with a probabilistic roadmap algorithm guided by structure data

Erion Plaku, Amarda Shehu, Tatiana Maximova, 2015, 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

Computational Structural Biology: Successes, Future Directions, and Challenges

Ruth Nussinov, Amarda Shehu, Hyunbum Jang, 2019, Molecules.

Exploring the Structure Space of Wildtype Ras Guided by Experimental Data

Amarda Shehu, Rudy Clausen, Amarda Shehu, 2013, BCB.

Protein-protein Docking Using Information from Native Interaction Interfaces

Amarda Shehu, Irina Hashmi, Amarda Shehu, 2013, BCB.

A PCA-guided Search Algorithm to Probe the Conformational Space of the Ras Protein

Amarda Shehu, Rudy Clausen, Amarda Shehu, 2013, BCB.

Populating Local Minima in the Protein Conformational Space

Amarda Shehu, Brian S. Olson, Amarda Shehu, 2011, 2011 IEEE International Conference on Bioinformatics and Biomedicine.

In Search of the protein Native State with a Probabilistic Sampling Approach

Amarda Shehu, Kevin Molloy, Brian S. Olson, 2011, J. Bioinform. Comput. Biol..

Mapping the Protein Conformational Landscape with Adaptive Probabilistic Search

Amarda Shehu, Brian S. Olson, Brian Olson, 2011 .

Guiding the Search for Native-like Protein Conformations with an Ab-initio Tree-based Exploration

Amarda Shehu, Brian S. Olson, Amarda Shehu, 2010, Int. J. Robotics Res..

An Ab-initio tree-based exploration to enhance sampling of low-energy protein conformations

Amarda Shehu, Amarda Shehu, 2009, Robotics: Science and Systems.

User Behavior Modelling for Fake Information Mitigation on Social Web

Amarda Shehu, Hemant Purohit, Zahra Rajabi, 2019, SBP-BRiMS.

Physicochemical Determinants of Antimicrobial Activity

Amarda Shehu, Daniel Veltri, 2012 .

A Multi-channel BiLSTM-CNN Model for Multilabel Emotion Classification of Informal Text

Özlem Uzuner, Amarda Shehu, Zahra Rajabi, 2020, 2020 IEEE 14th International Conference on Semantic Computing (ICSC).

Informatics-driven Protein-protein Docking

Amarda Shehu, Irina Hashmi, Amarda Shehu, 2013, BCB.

A General, Adaptive, Roadmap-Based Algorithm for Protein Motion Computation

Amarda Shehu, Kevin Molloy, Amarda Shehu, 2016, IEEE Transactions on NanoBioscience.

Guiding Probabilistic Search of the protein conformational Space with Structural Profiles

Amarda Shehu, Kevin Molloy, Brian S. Olson, 2012, J. Bioinform. Comput. Biol..

Property-Controllable Generation of Quaternary Ammonium Compounds

Amarda Shehu, Shiva Ghaemi, Yuanqi Du, 2022, 2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

Attenuating dependence on structural data in computing protein energy landscapes

E. Plaku, Amarda Shehu, T. Maximova, 2019, BMC Bioinformatics.

Deep Latent-Variable Models for Controllable Molecule Generation

Amarda Shehu, Yuanqi Du, Liang Zhao, 2021, 2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

Sampling Conformation Space to Model Equilibrium Fluctuations in Proteins

Lydia E. Kavraki, Cecilia Clementi, Amarda Shehu, 2007, Algorithmica.

Interpretable Deep Graph Generation with Node-edge Co-disentanglement

Yanfang Ye, Xiaojie Guo, Amarda Shehu, 2020, KDD.

Deep Ranking in Template-free Protein Structure Prediction

Nasrin Akhter, Amarda Shehu, Jianlin Cheng, 2020, BCB.

PsychBERT: A Mental Health Language Model for Social Media Mental Health Behavioral Analysis

Uday Kamath, Amarda Shehu, Vedant Vajre, 2021, 2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

A stochastic roadmap method to model protein structural transitions

Amarda Shehu, Kevin Molloy, Rudy Clausen, 2015, Robotica.

Antigen Binding Reshapes Antibody Energy Landscape and Conformation Dynamics

Ruth Nussinov, Amarda Shehu, Kazi Lutful Kabir, 2021, 2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

Balancing multiple objectives in conformation sampling to control decoy diversity in template-free protein structure prediction

Ahmed Bin Zaman, Amarda Shehu, 2019, BMC Bioinformatics.

Probabilistic Search and Energy Guidance for Biased Decoy Sampling in Ab Initio Protein Structure Prediction

Amarda Shehu, Kevin Molloy, Sameh Saleh, 2013, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Biased decoy sampling to aid the selection of near-native protein conformations

Amarda Shehu, Kevin Molloy, Amarda Shehu, 2012, BCB.

Physicochemical Determinants of Antimicrobial Activity Supplemental Materials

Amarda Shehu, Daniel Veltri, 2013 .

An evolutionary-based approach for feature generation: Eukaryotic promoter recognition

Kenneth A. De Jong, Amarda Shehu, Uday Kamath, 2011, 2011 IEEE Congress of Evolutionary Computation (CEC).

Off-lattice protein structure prediction with homologous crossover

Kenneth A. De Jong, Amarda Shehu, Brian S. Olson, 2013, GECCO '13.

An Evolutionary Search Algorithm to Guide Stochastic Search for Near-Native Protein Conformations with Multiobjective Analysis

Amarda Shehu, Brian S. Olson, Brian Olson, 2013, AAAI 2013.

Generative deep learning for macromolecular structure and dynamics.

Amarda Shehu, Liang Zhao, Pourya Hoseini, 2020, Current opinion in structural biology.

idDock+: Integrating Machine Learning in Probabilistic Search for Protein-Protein Docking

Amarda Shehu, Irina Hashmi, Amarda Shehu, 2015, J. Comput. Biol..

Generating Tertiary Protein Structures via an Interpretative Variational Autoencoder

Xiaojie Guo, Amarda Shehu, Liang Zhao, 2020, ArXiv.

An Energy Landscape Treatment of Decoy Selection in Template-Free Protein Structure Prediction

Nasrin Akhter, Amarda Shehu, Wanli Qiao, 2018, Comput..

Decoy Selection in Protein Structure Determination via Symmetric Non-negative Matrix Factorization

Gopinath Chennupati, Hristo Djidjev, Amarda Shehu, 2020, 2020 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

Examining DNA Breathing with pyDNA-EPBD

Amarda Shehu, B. Alexandrov, Anowarul Kabir, 2023, bioRxiv.

On the Stochastic Roadmap to Model Functionally-related Structural Transitions in Wildtype and Variant Proteins

Amarda Shehu, Kevin Molloy, Rudy Clausen, 2010 .

Exploring Deep Neural Network Architectures: A Case Study on Improving Antimicrobial Peptide Recognition

Amarda Shehu, Daniel Barbará, Manpriya Dua, 2020 .

Guiding Exploration of Antimicrobial Peptide Space with a Deep Neural Network

Amarda Shehu, Daniel Veltri, Manpriya Dua, 2018, 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

Multiscale characterization of protein conformational ensembles

L. Kavraki, Amarda Shehu, C. Clementi, 2009, Proteins.

Generating tertiary protein structures via interpretable graph variational autoencoders

Amarda Shehu, Yuanqi Du, Liang Zhao, 2021, Bioinformatics advances.

Protein Decoy Generation via Adaptive Stochastic Optimization for Protein Structure Determination

Amarda Shehu, Toki Tahmid Inan, Ahmed Bin Zaman, 2020, 2020 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

Decoy selection for protein structure prediction via extreme gradient boosting and ranking

Gopinath Chennupati, Hristo Djidjev, Nasrin Akhter, 2020, BMC Bioinformatics.

From Interatomic Distances to Protein Tertiary Structures with a Deep Convolutional Neural Network

Yuanqi Du, Amarda Shehu, Liang Zhao, 2020 .

Variational Autoencoders for Protein Structure Prediction

Amarda Shehu, Fardina Fathmiul Alam, Amarda Shehu, 2020, BCB.

Reconstruction and Decomposition of High-Dimensional Landscapes via Unsupervised Learning

Jing Lei, Nasrin Akhter, Amarda Shehu, 2020, KDD.

Reducing Ensembles of Protein Tertiary Structures Generated De Novo via Clustering

Amarda Shehu, Carlotta Domeniconi, Parastoo Kamranfar, 2020, Molecules.

Anomaly Detection-Based Recognition of Near-Native Protein Structures

Nasrin Akhter, Amarda Shehu, Sivani Tadepalli, 2020, IEEE Transactions on NanoBioscience.

Evaluating Autoencoder-Based Featurization and Supervised Learning for Protein Decoy Selection

Amarda Shehu, Fardina Fathmiul Alam, Taseef Rahman, 2020, Molecules.

Building maps of protein structure spaces in template-free protein structure prediction

Amarda Shehu, Ahmed Bin Zaman, Amarda Shehu, 2019, J. Bioinform. Comput. Biol..

Balancing multiple objectives in conformation sampling to control decoy diversity in template-free protein structure prediction

Amarda Shehu, Ahmed Bin Zaman, Amarda Shehu, 2019, BMC Bioinformatics.

Graph-Based Community Detection for Decoy Selection in Template-Free Protein Structure Prediction

Nasrin Akhter, Amarda Shehu, Kazi Lutful Kabir, 2019, Molecules.

Reconstructing and Decomposing Protein Energy Landscapes to Organize Structure Spaces and Reveal Biologically-active States

Jing Lei, Nasrin Akhter, Amarda Shehu, 2018, 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

Community Detection for Decoy Selection in Template-free Protein Structure Prediction

Nasrin Akhter, Amarda Shehu, Zahra Rajabi, 2018, BCB.

From Extraction of Local Structures of Protein Energy Landscapes to Improved Decoy Selection in Template-Free Protein Structure Prediction

Nasrin Akhter, Amarda Shehu, Amarda Shehu, 2018, Molecules.

Evolving Conformation Paths to Model Protein Structural Transitions

Kenneth A. De Jong, Amarda Shehu, Emmanuel Sapin, 2017, BCB.

Modeling protein structural transitions as a multiobjective optimization problem

Kenneth A. De Jong, Amarda Shehu, Emmanuel Sapin, 2017, 2017 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB).

An evolutionary algorithm to model structural excursions of a protein

Kenneth A. De Jong, Amarda Shehu, Emmanuel Sapin, 2017, GECCO.

Multi-Objective Stochastic Search for Sampling Local Minima in the Protein Energy Surface

Amarda Shehu, Brian S. Olson, Amarda Shehu, 2013, BCB.

Probabilistic Search and Energy Guidance for Biased Decoy Sampling in Ab Initio Protein Structure Prediction

Amarda Shehu, Kevin Molloy, Sameh Saleh, 2013, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Learning Organizations of Protein Energy Landscapes: An Application on Decoy Selection in Template-Free Protein Structure Prediction.

Amarda Shehu, N. Akhter, Zahra Rajabi, 2019, Methods in molecular biology.

A Principled Comparative Analysis of Dimensionality Reduction Techniques on Protein Structure Decoy Data

Amarda Shehu, Rohan Pandit, Amarda Shehu, 2016 .

Using Sequence-Predicted Contacts to Guide Template-free Protein Structure Prediction

Amarda Shehu, Ahmed Bin Zaman, Prasanna Venkatesh Parthasarathy, 2019, BCB.