“Stochastic models for pandemic spread under policy changes”. CIS Department Seminar, University of Melbourne, March 2021. Felisa Vázquez-Abad

Simulating sars-cov-2 transmission in the New York subway Authors: Alex Washburn, Ye Paing, Pauline Lin, Felisa Vázquez-Abad Publication date: 2021/12/12 Conference: 2021 Winter Simulation Conference (WSC)

Pandemic model with data-driven phase detection, a study using COVID-19 data Authors: Yuansan Liu, Saransh Srivastava, Zuo Huang, Felisa J Vázquez-Abad Publication date: 2021/9/22 Journal: Journal of the Operational Research Society

Interests, Difficulties, Sentiments, and Tool Usages of Concurrency Developers: A Large-Scale Study on Stack Overflow Authors: Mehdi Bagherzadeh, Syed Ahmed, Srilakshmi Sripathi, Raffi Khatchadourian Publication date: 2021/9/7 Journal: arXiv preprint arXiv:2109.03138

What Do Concurrency Developers Ask About? A Large-Scale Study on Stack Overflow Authors: Mehdi Bagherzadeha, Syed Ahmeda, Srilakshmi Sripathia, Raffi Khatchadourianb Publication date: 2021/9 Journal: arXiv preprint arXiv:2109.03138

An empirical study of refactorings and technical debt in Machine Learning systems Authors: Yiming Tang, Raffi Khatchadourian, Mehdi Bagherzadeh, Rhia Singh, Ajani Stewart, Anita Raja Publication date: 2021/5/22 Conference: 2021 IEEE/ACM 43rd International Conference on Software Engineering (ICSE)

CSCI 40500/77100: Software Engineering Authors: Raffi T Khatchadourian Publication date: 2021

An empirical study of refactorings and technical debt in Machine Learning systems Authors: Yiming Tang, Raffi Khatchadourian, Mehdi Bagherzadeh, Rhia Singh, Ajani Stewart, Anita Raja Publication date: 2021/5/22 Conference: 2021 IEEE/ACM 43rd International Conference on Software Engineering (ICSE)

An empirical study of refactorings and technical debt in Machine Learning systems Authors: Yiming Tang, Raffi Khatchadourian, Mehdi Bagherzadeh, Rhia Singh, Ajani Stewart, Anita Raja Publication date: 2021/5/22 Conference: 2021 IEEE/ACM 43rd International Conference on Software Engineering (ICSE)

VECTrust: trusted resource allocation in volunteer edge-cloud computing workflows Authors: Ashish Pandey, Prasad Calyam, Saptarshi Debroy, Songjie Wang, Mauro Lemus Alarcon Publication date: 2021/12/6

EFFECT: Energy-efficient fog computing framework for real-time video processing Authors: Xiaojie Zhang, Amitangshu Pal, Saptarshi Debroy Publication date: 2021/5/10 Conference: 2021 IEEE/ACM 21st International Symposium on Cluster, Cloud and Internet Computing (CCGrid)

Trust Model for Efficient Honest Broker based Healthcare Data Access and Processing Authors: Mauro Lemus Alarcon, Minh Nguyen, Saptarshi Debroy, Naga Ramya Bhamidipati, Prasad Calyam, Abu Mosa Publication date: 2021/3/22 Conference: 2021 IEEE International Conference on Pervasive Computing and Communications Workshops and other Affiliated Events (PerCom Workshops)

Correction to “Structural Insights into Characterizing Binding Sites in Epidermal Growth Factor Receptor Kinase Mutants” Z Zhao, L Xie, PE Bourne Journal of Chemical Information and Modeling 62 (1), 223-224

AD-linked R47H-TREM2 mutation induces disease-enhancing microglial states via AKT hyperactivation FA Sayed, L Kodama, L Fan, GK Carling, JC Udeochu, D Le, Q Li, L Zhou, ... Science translational medicine 13 (622), eabe3947

Brain connectivity alteration detection via matrix‐variate differential network model J Ji, Y He, L Liu, L Xie Biometrics 77 (4), 1409-1421

Exploration of Dark Chemical Genomics Space via Portal Learning: Applied to Targeting the Undruggable Genome and COVID-19 Anti-Infective Polypharmacology T Cai, L Xie, M Chen, Y Liu, D He, S Zhang, C Mura, PE Bourne, L Xie arXiv preprint arXiv:2111.14283

COVID-19 multi-targeted drug repurposing using few-shot learning Y Liu, Y Wu, X Shen, L Xie Frontiers in Bioinformatics 1

Crowdsourced mapping of unexplored target space of kinase inhibitors A Cichońska, B Ravikumar, RJ Allaway, F Wan, S Park, O Isayev, S Li, ... Nature communications 12 (1), 1-18

MSA-regularized protein sequence transformer toward predicting genome-wide chemical-protein interactions: application to GPCRome deorphanization T Cai, H Lim, KA Abbu, Y Qiu, R Nussinov, L Xie Journal of chemical information and modeling 61 (4), 1570-1582

A deep learning framework for high-throughput mechanism-driven phenotype compound screening and its application to COVID-19 drug repurposing TH Pham, Y Qiu, J Zeng, L Xie, P Zhang Nature machine intelligence 3 (3), 247-257

TranSynergy: Mechanism-driven interpretable deep neural network for the synergistic prediction and pathway deconvolution of drug combinations Q Liu, L Xie PLoS computational biology 17 (2), e1008653

DeepREAL: A Deep Learning Powered Multi-scale Modeling Framework Towards Predicting Out-of-distribution Receptor Activity of Ligand Binding T Cai, KA Abbu, Y Liu, L Xie bioRxiv

Predictive Modeling of Multiplex Chemical Phenomics for Novel Cells and Patients: Applied to Personalized Alzheimer's Disease Drug Repurposing Q Liu, Y Qiu, L Xie bioRxiv

Robust prediction of patient-specific clinical response to unseen drugs from in vitro screens using context-aware deconfounding autoencoder D He, Q Liu, L Xie bioRxiv

Differentiation via logarithmic expansions Authors: Michael C Fu, Bernd Heidergott, Haralambie Leahu, Felisa J Vázquez-Abad Publication date: 2020/2/17 Journal: Asia-Pacific Journal of Operational Research

Deep learning for mental illness detection using brain SPECT imaging Authors: Felisa J Vázquez-Abad, Silvano Bernabel, Daniel Dufresne, Rishi Sood, Thomas Ward, Daniel Amen Publication date: 2020/1/20 Conference: International Conference on Medical Imaging and Computer-Aided Diagnosis

Actor concurrency bugs: a comprehensive study on symptoms, root causes, API usages, and differences Authors: Mehdi Bagherzadeh, Nicholas Fireman, Anas Shawesh, Raffi Khatchadourian Publication date: 2020/11/13 Journal: Proceedings of the ACM on Programming Languages

Collections in Scala Authors: Raffi Khatchadourian Publication date: 2020/10/20

Deep reinforcement learning based energy-efficient task offloading for secondary mobile edge systems Authors: Xiaojie Zhang, Amitangshu Pal, Saptarshi Debroy Publication date: 2020/11/16 Conference: 2020 IEEE 45th LCN Symposium on Emerging Topics in Networking (LCN Symposium)

Energy efficient task offloading for compute-intensive mobile edge applications Authors: Xiaojie Zhang, Saptarshi Debroy Publication date: 2020/6/7 Conference: ICC 2020-2020 IEEE International Conference on Communications (ICC)

Formal modeling and analysis of multi-rogue backoff manipulation attacks in unlicensed networks Authors: Jordi Navarrette, Subash Shankar, Xiaojie Zhang, Saptarshi Debroy Publication date: 2020/3/25 Conference: 2020 16th International Conference on the Design of Reliable Communication Networks DRCN 2020

Frequency-minimal utility-maximal moving target defense against DDoS in SDN-based systems Authors: Saptarshi Debroy, Prasad Calyam, Minh Nguyen, Roshan Lal Neupane, Bidyut Mukherjee, Ajay Kumar Eeralla, Khaled Salah Publication date: 2020/3/4 Journal: IEEE Transactions on Network and Service Management

Security-aware Resource Brokering for Bioinformatics Workflows across Federated Multi-cloud Infrastructures Authors: Minh Nguyen, Saptarshi Debroy, Prasad Calyam, Zhen Lyu, Trupti Joshi Publication date: 2020/1/4 Book: Proceedings of the 21st International Conference on Distributed Computing and Networking

Molecular mechanics-driven graph neural network with multiplex graph for molecular structures S Zhang, Y Liu, L Xie arXiv preprint arXiv:2011.07457

A cross-level information transmission network for predicting phenotype from new genotype: Application to cancer precision medicine D He, L Xie arXiv preprint arXiv:2010.04824

Improving attention mechanism in graph neural networks via cardinality preservation S Zhang, L Xie IJCAI: Proceedings of the Conference 2020, 1395

A Bayesian approach to accurate and robust signature detection on LINCS L1000 data Y Qiu, T Lu, H Lim, L Xie Bioinformatics 36 (9), 2787-2795

The cancer microbiome: distinguishing direct and indirect effects requires a systemic view JB Xavier, VB Young, J Skufca, F Ginty, T Testerman, AT Pearson, ... Trends in cancer 6 (3), 192-204

Heterogeneous multi-layered network model for omics data integration and analysis B Lee, S Zhang, A Poleksic, L Xie Frontiers in genetics 10, 1381

A new weighted imputed neighborhood-regularized tri-factorization one-class collaborative filtering algorithm: application to target gene prediction of transcription factors H Lim, L Xie IEEE/ACM transactions on computational biology and bioinformatics 18 (1 …

Molgnn: Self-supervised motif learning graph neural network for drug discovery X Shen, Y Liu, Y Wu, L Xie Machine Learning for Molecules Workshop at NeurIPS 2020, 4

The cancer microbiome: distinguishing direct and indirect effects requires a systemic view. Trends Cancer 6: 192–204 JB Xavier, VB Young, J Skufca, F Ginty, T Testerman, AT Pearson, ...

AD-linked R47H-TREM2 mutation induces disease-enhancing proinflammatory microglial states in mice and humans FA Sayed, L Kodama, JC Udeochu, L Fan, GK Carling, D Le, Q Li, L Zhou, ... bioRxiv

A deep learning framework for elucidating whole-genome chemical interaction space T Cai, H Lim, KA Abbu, Y Qiu, R Nussinov, L Xie bioRxiv

Exploration of Chemical Space with Partial Labeled Noisy Student Self-Training for Improving Deep Learning Performance: Application to Drug Metabolism Y Liu, H Lim, L Xie bioRxiv

Machine learning strategies for identifying repurposed drugs for cancer therapy H Lim, L Xie Drug Repurposing in Cancer Therapy, 55-79

Small Molecule Modulation of Microbiome Ecosystem: A Systems Pharmacology Perspective Q Liu, B Lee, L Xie bioRxiv

“Weak convergence for stochastic approximations using constant learning rates”, Faculty of Economics and Business, Vrije Universiteit, Amsterdam, November 2019. Felisa Vázquez-Abad

“A dynamic mollifier approach to increase accuracy for neural network models”, CIS Department Seminar, University of Melbourne, April 2019. Felisa Vázquez-Abad

“Deep learning transfer model for brain scans”, CIS Department Seminar, , University of Melbourne, May 2019. Felisa Vázquez-Abad

A simultaneous perturbation weak derivative estimator for stochastic neural networks Authors: Thomas Flynn, Felisa Vázquez-Abad Publication date: 2019/10 Journal: Computational Management Science

Going big: a large-scale study on what big data developers ask Authors: Mehdi Bagherzadeh, Raffi Khatchadourian Publication date: 2019/8/12

Safe automated refactoring for intelligent parallelization of Java 8 streams Authors: Raffi Khatchadourian, Yiming Tang, Mehdi Bagherzadeh Publication date: 2019 Conference: 2019 IEEE/ACM 41st International Conference on Software Engineering (ICSE)

Gibbs/MCMC Sampling for Multiple RNA Interaction with Sub-Optimal Solutions Authors: Syed Ali Ahmed, Saad Mneimneh Publication date: 2019/1/10 Journal: IEEE/ACM Transactions on Computational Biology and Bioinformatics

Simple Variations on The Tower of Hanoi: A Study of Recurrences and Proofs by Induction Author: Saad Mneimneh Publication date: 2019 Journal: Teaching Mathematics and Computer Science

Adaptive task offloading over wireless in mobile edge computing Authors: Xiaojie Zhang, Saptarshi Debroy Publication date: 2019/11/7 Book: Proceedings of the 4th ACM/IEEE Symposium on Edge Computing

Migration-driven resilient disaster response edge-cloud deployments Authors: Xiaojie Zhang, Saptarshi Debroy Publication date: 2019/9/26 Conference: 2019 IEEE 18th International Symposium on Network Computing and Applications (NCA)

SpEED-IoT: Spectrum aware energy efficient routing for device-to-device IoT communication Authors: Saptarshi Debroy, Priyanka Samanta, Amina Bashir, Mainak Chatterjee Publication date: 2019/4/1 Journal: Future Generation Computer Systems

Database of adverse events associated with drugs and drug combinations A Poleksic, L Xie Scientific reports 9 (1), 1-9

Biological representation of chemicals using latent target interaction profile M Ayed, H Lim, L Xie BMC bioinformatics 20 (24), 1-10

Prediction of off-target specificity and cell-specific fitness of CRISPR-Cas System using attention boosted deep learning and network-based gene feature Q Liu, D He, L Xie PLoS computational biology 15 (10), e1007480

Pathway-centric structure-based multi-target compound screening for anti-virulence drug repurposing L Xie, L Xie International journal of molecular sciences 20 (14), 3504

Rational discovery of dual-indication multi-target PDE/Kinase inhibitor for precision anti-cancer therapy using structural systems pharmacology H Lim, D He, Y Qiu, P Krawczuk, X Sun, L Xie PLoS computational biology 15 (6), e1006619

Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen MP Menden, D Wang, MJ Mason, et al. Nature Communications 10, 2674

Omics Data Integration and Analysis for Systems Pharmacology H Lim, L Xie Methods Mol Biol. 1939, 199-214

Structure-Unbinding Kinetics Relationship of p38α MAPK Inhibitors X Ge, H Tan, L Xie bioRxiv, 510255

Unbinding Kinetics and Multiple Pathways of p38 MAPK Inhibitors X Ge, H Tan, L Xie bioRxiv, 510255

CR-Honeynet: A cognitive radio learning and decoy-based sustenance mechanism to avoid intelligent jammer Authors: Suman Bhunia, Edward Miles, Shamik Sengupta, Felisa Vázquez-Abad Publication date: 2018/5/8 Journal: IEEE Transactions on Cognitive Communications and Networking

F.J. Vazquez-Abad, D. Dufresne, S. Bernabel, D. Amen, T. Ward, “Deep learning for medical diagnosis using simulation analytics,” Workshop on Simulation Analytics: Smart Simulation in Big Data Era, College of engineering, Pekin University, June 2018.

D. Dufresne, F.J. Vazquez-Abad, T. Flynn, “Mollifiers for Classification Using Neural Networks,” Workshop on Simulation Analytics: Smart Simulation in Big Data Era, College of engineering, Pekin University, June 2018.

F.J. Vazquez-Abad and D. Dufresne, “Deep Learning for detection of Mental Illness,” INFORMS International, Taipei, June 2018.

A Tool for Optimizing Java 8 Stream Software via Automated Refactoring Authors: Raffi Khatchadourian, Yiming Tang, Mehdi Bagherzadeh, Syed Ahmed Publication date: 2018/9/23 Conference: 2018 IEEE 18th International Working Conference on Source Code Analysis and Manipulation (SCAM)

Towards safe refactoring for intelligent parallelization of java 8 streams Authors: Yiming Tang, Raffi Khatchadourian, Mehdi Bagherzadeh, Syed Ahmed Publication date: 2018/5/27 Book: Proceedings of the 40th International Conference on Software Engineering: Companion Proceeedings

Making multiple RNA interaction practical Authors: Syed Ali Ahmed, Saman Farhat, Saad Mneimneh Publication date: 2018/12/15 Conference: International Conference on Combinatorial Optimization and Applications

Simple Variations on the Tower of Hanoi to Guide the Study of Recurrences and Proofs by Induction

Whack-a-Mole: Software-defined Networking driven Multi-level DDoS defense for Cloud environments Authors: Minh Nguyen, Amitangshu Pal, Saptarshi Debroy Publication date: 2018/10/1 Conference: 2018 IEEE 43rd Conference on Local Computer Networks (LCN)

Analyzing moving target defense for resilient campus private cloud Authors: Minh Nguyen, Priyanka Samanta, Saptarshi Debroy Publication date: 2018/7/2 Conference: 2018 IEEE 11th International Conference on Cloud Computing (CLOUD)

Multi-cloud performance and security driven federated workflow management Authors: Matthew Dickinson, Saptarshi Debroy, Prasad Calyam, Samaikya Valluripally, Yuanxun Zhang, Ronny Bazan Antequera, Trupti Joshi, Tommi White, Dong Xu Publication date: 2018/6/22 Journal: IEEE Transactions on Cloud Computing

Collaborative adversarial modeling for spectrum aware IoT communications Authors: Priyanka Samanta, Elizabeth Kelly, Amina Bashir, Saptarshi Debroy Publication date: 2018/3/5 Conference: 2018 International Conference on Computing, Networking and Communications (ICNC)

Structural insights into characterizing binding sites in epidermal growth factor receptor kinase mutants Z Zhao, L Xie, PE Bourne Journal of chemical information and modeling 59 (1), 453-462

A new insight into underlying disease mechanism through semi-parametric latent differential network model Y He, J Ji, L Xie, X Zhang, F Xue BMC bioinformatics 19 (17), 5-19

A crowdsourced analysis to identify ab initio molecular signatures predictive of susceptibility to viral infection S Fourati, A Talla, M Mahmoudian, JG Burkhart, R Klén, R Henao, T Yu, ... Nature communications 9 (1), 1-11

Target gene prediction of transcription factor using a new neighborhood-regularized tri-factorization one-class collaborative filtering algorithm H Lim, L Xie Proceedings of the 2018 ACM International Conference on Bioinformatics …

Predicting serious rare adverse reactions of novel chemicals A Poleksic, L Xie Bioinformatics 34 (16), 2835-2842

ANTENNA, a multi-rank, multi-layered recommender system for inferring reliable drug-gene-disease associations: Repurposing diazoxide as a targeted anti-cancer therapy A Wang, H Lim, SY Cheng, L Xie IEEE/ACM transactions on computational biology and bioinformatics 15 (6 …

Dynamic Brain Connectivity Alternation Detection via Matrix-variate Differential Network Model J Ji, Y He, L Xie bioRxiv, 446237

Exploring landscape of drug-target-pathway-side effect associations H Lim, A Poleksic, L Xie AMIA Summits on Translational Science Proceedings 2018, 132

Data-driven adaptive threshold control for bike share systems Authors: Felisa J Vázquez-Abad, Silvano Bernabel, Michael C Fu Publication date: 2017/12/3 Conference: 2017 Winter Simulation Conference (WSC)

Data driven stochastic approximation for change detection Authors: Thomas Flynn, Olympia Hadjiliadis, Ioannis Stamos, Felisa J Vázquez-Abad Publication date: 2017/12/3 Conference: 2017 Winter Simulation Conference (WSC)

A game-theoretic and stochastic survivability mechanism against induced attacks in cognitive radio networks Authors: Saad Mneimneh, Suman Bhunia, Felisa Vázquez-Abad, Shamik Sengupta Publication date: 2017/9/1 Journal: Pervasive and Mobile Computing

Defaultification refactoring: A tool for automatically converting java methods to default Author: Raffi Khatchadourian, Hidehiko Masuhara Publication date: 2017/10/1 Conference: 2017 32nd IEEE/ACM International Conference on Automated Software Engineering (ASE)

Automated refactoring of legacy java software to default methods Authors: Raffi Khatchadourian, Hidehiko Masuhara Publication date: 2017/5/20 Conference: 2017 IEEE/ACM 39th International Conference on Software Engineering (ICSE)

A game-theoretic and stochastic survivability mechanism against induced attacks in cognitive radio networks Authors: Saad Mneimneh, Suman Bhunia, Felisa Vázquez-Abad, Shamik Sengupta Publication date: 2017/9/1 Journal: Pervasive and Mobile Computing

Counting with code Authors: Saad Mneimneh, Alexey Nikolaev Publication date: 2017/6/1 Journal: Journal of Computing Sciences in Colleges

Controlled growth of simplicial complex networks Authors: Alexey Nikolaev, Saad Mneimneh, Amotz Bar-Noy, Ram Ramanathan Publication date: 2017/5/1 Conference: 2017 IEEE Conference on Computer Communications Workshops (INFOCOM WKSHPS)

Quantifying trust for robust fusion while spectrum sharing in distributed dsa networks Authors: Shameek Bhattacharjee, Saptarshi Debroy, Mainak Chatterjee Publication date: 2017/5/8 Journal: IEEE Transactions on Cognitive Communications and Networking

Radio Environment Maps and Its Utility in Resource Management for Dynamic Spectrum Access Networks Authors: Saptarshi Debroy, Mainak Chatterjee Publication date: 2017 Book: Resource Allocation in Next-Generation Broadband Wireless Access Networks

VariFunNet, an integrated multiscale modeling framework to study the effects of rare non-coding variants in genome-wide association studies: Applied to Alzheimer's disease Q Liu, C Chen, A Gao, HH Tong, L Xie 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM …

Mining FDA resources to compute population-specific frequencies of adverse drug reactions A Poleksic, C Turner, R Dalal, P Gray, L Xie 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM …

JDINAC: joint density-based non-parametric differential interaction network analysis and classification using high-dimensional sparse omics data J Ji, D He, Y Feng, Y He, F Xue, L Xie Bioinformatics 33 (19), 3080-3087

Confused or not confused? Disentangling brain activity from EEG data using bidirectional LSTM recurrent neural networks Z Ni, AC Yuksel, X Ni, MI Mandel, L Xie Proceedings of the 8th acm international conference on bioinformatics …

Cross-dependency inference in multi-layered networks: A collaborative filtering perspective C Chen, H Tong, L Xie, L Ying, Q He ACM Transactions on Knowledge Discovery from Data (TKDD) 11 (4), 1-26

Insights into the binding mode of MEK type-III inhibitors. A step towards discovering and designing allosteric kinase inhibitors across the human kinome Z Zhao, L Xie, PE Bourne PLoS One 12 (6), e0179936

Determining cysteines available for covalent inhibition across the human kinome Z Zhao, Q Liu, S Bliven, L Xie, PE Bourne Journal of medicinal chemistry 60 (7), 2879-2889

Harnessing big data for systems pharmacology L Xie, EJ Draizen, PE Bourne Annual review of pharmacology and toxicology 57, 245

Mixed optimization for constrained resource allocation, an application to a local bus service Authors: Felisa J Vázquez-Abad, Larry Fenn Publication date: 2016/12/11 Conference: 2016 Winter Simulation Conference (WSC)

Stochastic path optimization for robotic bees using cloud computing Authors: Felisa Vázquez-Abad, Silvano Bernabel Publication date: 2016/5/30 Conference: 2016 13th International Workshop on Discrete Event Systems (WODES)

Towards improving interface modularity in legacy java software through automated refactoring Authors: Raffi Khatchadourian, Olivia Moore, Hidehiko Masuhara Publication date: 2016/3/14 Book: Companion Proceedings of the 15th International Conference on Modularity

Controlling use of shared content items based on client device Inventors: Gianpaolo Fasoli, Augustin Farrugia, Apoorva Govind, Raffi Khatchadourian Publication date: 2016/1/21

Gibbs/MCMC sampling for multiple RNA interaction with sub-optimal solutions Authors: Saad Mneimneh, Syed Ali Ahmed Publication date: 2016/6/21 Conference: International Conference on Algorithms for Computational Biology

Testing Higher-Order Network Structures in an Online Experiment Authors: Jason Radford, Amotz Barnoy, Alexey Nikolaev, Saad Mneimneh, David Lazer, Ram Ramanathan Publication date: 2016/2/27

A Sampling Approach for Multiple RNA Interaction Authors: Saad Mneimneh, Syed Ali Ahmed Publication date: 2016/2/21

Security Middleground for Resource Protection in Measurement Infrastructure-as-a-Service Authors: Ravi Akella, Saptarshi Debroy, Prasad Calyam, Alex Berryman, Kunpeng Zhu, Mukundan Sridharan Publication date: 2016/10/18 Journal: IEEE Transactions on Services Computing

End-to-End Security Formalization and Alignment for Federated Workflow Management Authors: Matthew Dickinson, Saptarshi Debroy, Prasad Calyam, Samaikya Valluripally, Yuanxun Zhang, Trupti Joshi, Dong Xu Publication date: 2016/6/27 Conference: 2016 IEEE 9th International Conference on Cloud Computing (CLOUD)

Network measurement recommendations for performance bottleneck correlation analysis Authors: Yuanxun Zhang, Saptarshi Debroy, Prasad Calyam Publication date: 2016/6/13 Conference: 2016 IEEE International Symposium on Local and Metropolitan Area Networks (LANMAN)

Network-wide anomaly event detection and diagnosis with perfsonar Authors: Yuanxun Zhang, Saptarshi Debroy, Prasad Calyam Publication date: 2016/3/25 Journal: IEEE Transactions on Network and Service Management

Improved genome-scale multi-target virtual screening via a novel collaborative filtering approach to cold-start problem H Lim, P Gray, L Xie, A Poleksic Scientific reports 6 (1), 1-11

Drug repurposing to target Ebola virus replication and virulence using structural systems pharmacology Z Zhao, C Martin, R Fan, PE Bourne, L Xie BMC bioinformatics 17 (1), 1-12

Molecular mechanisms involved in the side effects of fatty acid amide hydrolase inhibitors: a structural phenomics approach to proteome-wide cellular off-target deconvolution … S Dider, J Ji, Z Zhao, L Xie NPJ systems biology and applications 2 (1), 1-8

Large-scale off-target identification using fast and accurate dual regularized one-class collaborative filtering and its application to drug repurposing H Lim, A Poleksic, Y Yao, H Tong, D He, L Zhuang, P Meng, L Xie PLoS computational biology 12 (10), e1005135

FASCINATE: fast cross-layer dependency inference on multi-layered networks C Chen, H Tong, L Xie, L Ying, Q He Proceedings of the 22nd ACM SIGKDD international conference on knowledge …

Environmental governance and public participation in rural China L Xie China Information 30 (2), 188-208

Toward high-throughput predictive modeling of protein binding/unbinding kinetics SH Chiu, L Xie Journal of chemical information and modeling 56 (6), 1164-1174

Crowdsourced estimation of cognitive decline and resilience in Alzheimer's disease GI Allen, N Amoroso, C Anghel, V Balagurusamy, CJ Bare, D Beaton, ... Alzheimer's & Dementia 12 (6), 645-653

Long term stability of magnetorheological fluids using high viscosity linear polysiloxane carrier fluids L Xie, YT Choi, CR Liao, NM Wereley Smart Materials and Structures 25 (7), 075006

Delineation of polypharmacology across the human structural kinome using a functional site interaction fingerprint approach Z Zhao, L Xie, L Xie, PE Bourne Journal of medicinal chemistry 59 (9), 4326-4341

Protein‐fold recognition using an improved single‐source K diverse shortest paths algorithm J Lhota, L Xie Proteins: Structure, Function, and Bioinformatics 84 (4), 467-472

Providing data science support for systems pharmacology and its implications to drug discovery T Hart, L Xie Expert opinion on drug discovery 11 (3), 241-256

Testing and analysis of magnetorheological fluid sedimentation in a column using a vertical axis inductance monitoring system YT Choi, L Xie, NM Wereley Smart Materials and Structures 25 (4), 04LT01

PDID: database of molecular-level putative protein–drug interactions in the structural human proteome C Wang, G Hu, K Wang, M Brylinski, L Xie, L Kurgan Bioinformatics 32 (4), 579-586

Toward repurposing metformin as a precision anti-cancer therapy using structural systems pharmacology T Hart, S Dider, W Han, H Xu, Z Zhao, L Xie Scientific reports 6 (1), 1-13

The Plasmodium falciparum drugome and its polypharmacological implications Y Zhang, L Xie, L Xie, PE Bourne bioRxiv, 042481