The Current State of the Grid. - Jonathan Chin; Peter V. Coveney; Shantenu Jha (Comput. Sci. Eng., 2004)

SPICE: Simulated Pore Interactive Computing Environment. - Shantenu Jha; Peter V. Coveney; Matt J. Harvey (SC, 2005)

Scientific grid computing: the first generation. - Jonathan Chin; Matthew J. Harvey; Shantenu Jha; Peter V. Coveney (Comput. Sci. Eng., 2005)

Force field validation for nucleic acid simulations: Comparing energies and dynamics of a DNA dodecamer. - Shantenu Jha; Peter V. Coveney; Charles A. Laughton (J. Comput. Chem., 2005)

Using Lambda Networks to Enhance Performance of Interactive Large Simulations. - Matt J. Harvey; Shantenu Jha; Mary-Ann Thyveetil; Peter V. Coveney (e-Science, 2006)

Design and Implementation of Network Performance Aware Applications Using SAGA and Cactus. - Shantenu Jha; Hartmut Kaiser; Yaakoub El Khamra; Ole Weidner (eScience, 2007)

Grid Interoperability at the Application Level Using SAGA. - Shantenu Jha; Hartmut Kaiser; André Merzky; Ole Weidner (eScience, 2007)

NEKTAR, SPICE and Vortonics: using federated grids for large scale scientific applications. - Bruce M. Boghosian; Peter V. Coveney; Suchuan Dong; Lucas Finn; Shantenu Jha; George E. Karniadakis; Nicholas T. Karonis (Clust. Comput., 2007)

Distributed Replica-Exchange Simulations on Production Environments Using SAGA and Migol. - André Luckow; Shantenu Jha; Joohyun Kim 001; André Merzky; Bettina Schnor (eScience, 2008)

Abstractions for Distributed Systems (DPA 2008). - Shantenu Jha; Daniel S. Katz; Manish Parashar; Omer F. Rana; Murray Cole (Euro-Par Workshops, 2008)

Design and performance analysis of a distributed HPC molecular dynamics code on distributed resources. - Promita Chakraborty; Shantenu Jha (Mardi Gras Conference, 2008)

Programming Abstractions for Data Intensive Computing on Clouds and Grids. - Chris Miceli; Michael Miceli; Shantenu Jha; Hartmut Kaiser; André Merzky (CCGRID, 2009)

An innovative application execution toolkit for multicluster grids. - Zhifeng Yun; Zhou Lei; Gabrielle Allen; Daniel S. Katz; Tevfik Kosar; Shantenu Jha; Jagannathan Ramanujam (CLUSTER, 2009)

An Autonomic Approach to Integrated HPC Grid and Cloud Usage. - Hyunjoo Kim; Yaakoub El Khamra; Shantenu Jha; Manish Parashar (eScience, 2009)

A Fresh Perspective on Developing and Executing DAG-Based Distributed Applications: A Case-Study of SAGA-Based Montage. - André Merzky; Katerina Stamou; Shantenu Jha; Daniel S. Katz (eScience, 2009)

Introduction. - Domenico Talia; Jason Maassen; Fabrice Huet; Shantenu Jha (Euro-Par, 2009)

Application Level Interoperability between Clouds and Grids. - André Merzky; Katerina Stamou; Shantenu Jha (GPC Workshops, 2009)

Critical perspectives on large-scale distributed applications and production Grids. - Shantenu Jha; Daniel S. Katz; Manish Parashar; Omer F. Rana; Jon B. Weissman (GRID, 2009)

Developing Scientific Applications with Loosely-Coupled Sub-tasks. - Shantenu Jha; Yaakoub El Khamra; Joohyun Kim 001 (ICCS (1), 2009)

Self-adaptive Architectures for Autonomic Computational Science. - Shantenu Jha; Manish Parashar; Omer F. Rana (SOAR, 2009)

Using clouds to provide grids with higher levels of abstraction and explicit support for usage modes. - Shantenu Jha; André Merzky; Geoffrey C. Fox (Concurr. Comput. Pract. Exp., 2009)

Efficient Runtime Environment for Coupled Multi-physics Simulations: Dynamic Resource Allocation and Load-Balancing. - Soon-Heum Ko; Nayong Kim; Joohyun Kim 001; Abhinav Thota; Shantenu Jha (CCGRID, 2010)

SAGA BigJob: An Extensible and Interoperable Pilot-Job Abstraction for Distributed Applications and Systems. - André Luckow; Lukasz Lacinski; Shantenu Jha (CCGRID, 2010)

Exploring the Performance Fluctuations of HPC Workloads on Clouds. - Yaakoub El Khamra; Hyunjoo Kim; Shantenu Jha; Manish Parashar (CloudCom, 2010)

Abstractions for Loosely-Coupled and Ensemble-Based Simulations on Azure. - André Luckow; Shantenu Jha (CloudCom, 2010)

Exploring the RNA folding energy landscape using scalable distributed cyberinfrastructure. - Joohyun Kim 001; Wei Huang; Sharath Maddineni; Fareed Aboul-Ela; Shantenu Jha (HPDC, 2010)

Exploring application and infrastructure adaptation on hybrid grid-cloud infrastructure. - Hyunjoo Kim; Yaakoub El Khamra; Shantenu Jha; Manish Parashar (HPDC, 2010)

GRENDL: grid enabled distribution and control for Laptop Orchestras. - Stephen David Beck; Shantenu Jha; Brygg Ullmer; Chris Branton; Sharath Maddineni (SIGGRAPH Posters, 2010)

Modelling data-driven CO2 sequestration using distributed HPC cyberinfrastructure. - Yaakoub El Khamra; Shantenu Jha; Christopher D. White (TG, 2010)

Global-scale distributed I/O with ParaMEDIC. - Pavan Balaji; Wu-chun Feng; Heshan Lin; Jeremy S. Archuleta; Satoshi Matsuoka; Andrew S. Warren; João Carlos Setubal; Ewing L. Lusk; Rajeev Thakur; Ian T. Foster; Daniel S. Katz; Shantenu Jha; et al. (Concurr. Comput. Pract. Exp., 2010)

Large scale computational science on federated international grids: The role of switched optical networks. - Peter V. Coveney; Giovanni Giupponi; Shantenu Jha; Steven Manos; Jon MacLaren; Stephen Pickles; R. S. Saksena; Thomas Soddemann; James L. Suter; Mary-Ann Thyveetil; Stefan J. Zasada (Future Gener. Comput. Syst., 2010)

Using the TeraGrid to teach scientific computing. - Frank Löffler 001; Gabrielle Allen; Werner Benger; Andrei Hutanu; Shantenu Jha; Erik Schnetter (TG, 2011)

Towards high-throughput, high-performance computational estimation of binding affinities for patient specific HIV-1 protease sequences. - Owain Kenway; David W. Wright 001; Helmut Heller; André Merzky; Gavin J. Pringle; Jules Wolfrat; Peter V. Coveney; Shantenu Jha (TG, 2011)

Building gateways for life-science applications using the dynamic application runtime environment (DARE) framework. - Joohyun Kim 001; Sharath Maddineni; Shantenu Jha (TG, 2011)

Energy landscape analysis for regulatory RNA finding using scalable distributed cyberinfrastructure. - Joohyun Kim 001; Wei Huang; Sharath Maddineni; Fareed Aboul-Ela; Shantenu Jha (Concurr. Comput. Pract. Exp., 2011)

Understanding application-level interoperability: Scaling-out MapReduce over high-performance grids and clouds. - Saurabh Sehgal; Miklós Erdélyi; André Merzky; Shantenu Jha (Future Gener. Comput. Syst., 2011)

A practical and comprehensive graduate course preparing students for research involving scientific computing. - Gabrielle Allen; Werner Benger; Andrei Hutanu; Shantenu Jha; Frank Löffler 001; Erik Schnetter (ICCS, 2011)

Autonomic management of application workflows on hybrid computing infrastructure. - Hyunjoo Kim; Yaakoub El Khamra; Ivan Rodero; Shantenu Jha; Manish Parashar (Sci. Program., 2011)

P∗: A model of pilot-abstractions. - André Luckow; Mark Santcroos; André Merzky; Ole Weidner; Pradeep Kumar Mantha; Shantenu Jha (eScience, 2012)

Pilot abstractions for compute, data, and network. - Mark Santcroos; Sílvia Delgado Olabarriaga; Daniel S. Katz; Shantenu Jha (eScience, 2012)

Towards a common model for pilot-jobs. - André Luckow; Mark Santcroos; Ole Weidner; André Merzky; Sharath Maddineni; Shantenu Jha (HPDC, 2012)

FutureGrid education: using case studies to develop a curriculum for communicating parallel and distributed computing concepts. - Jerome E. Mitchell; Judy Qiu; Massimo Canonio; Shantenu Jha; Linda B. Hayden; Barbara Ann O'Leary; Renato Figueiredo; Geoffrey C. Fox (XSEDE, 2012)

Running many molecular dynamics simulations on many supercomputers. - Rajib Mukherjee; Abhinav Thota; Hideki Fujioka; Thomas C. Bishop; Shantenu Jha (XSEDE, 2012)

The anatomy of successful ECSS projects: lessons of supporting high-throughput high-performance ensembles on XSEDE. - Melissa Romanus; Pradeep Kumar Mantha; Matt McKenzie; Thomas C. Bishop; Emilio Gallicchio; André Merzky; Yaakoub El Khamra; Shantenu Jha (XSEDE, 2012)

Survey and Analysis of Production Distributed Computing Infrastructures - Daniel S. Katz; Shantenu Jha; Manish Parashar; Omer F. Rana; Jon B. Weissman (CoRR, 2012)

Distributed Application Runtime Environment (DARE): A Standards-based Middleware Framework for Science-Gateways. - Sharath Maddineni; Joohyun Kim 001; Yaakoub El Khamra; Shantenu Jha (J. Grid Comput., 2012)

Exploring Dynamic Enactment of Scientific Workflows Using Pilot-Abstractions. - Mark Santcroos; Barbera D. C. van Schaik; Shayan Shahand; Sílvia Delgado Olabarriaga; André Luckow; Shantenu Jha (CCGRID, 2013)

A framework for flexible and scalable replica-exchange on production distributed CI. - Brian K. Radak; Tai-Sung Lee; Peng He; Melissa Romanus; Ole Weidner; Wei Dai; Emilio Gallicchio; Nan-Jie Deng; Darrin M. York; Ronald M. Levy; Shantenu Jha (XSEDE, 2013)

Scalable online comparative genomics of mononucleosomes: a BigJob. - Jack A. Smith; Yaakoub El Khamra; Melissa Romanus; Thomas C. Bishop; Pradeep Kumar Mantha; Shantenu Jha (XSEDE, 2013)

Distributed computing practice for large-scale science and engineering applications. - Shantenu Jha; Murray Cole; Daniel S. Katz; Manish Parashar; Omer F. Rana; Jon B. Weissman (Concurr. Comput. Pract. Exp., 2013)

Pilot-Data: An Abstraction for Distributed Data - André Luckow; Mark Santcroos; Ole Weidner; Ashley Zebrowski; Shantenu Jha (CoRR, 2013)

The Impact of a Ligand Binding on Strand Migration in the SAM-I Riboswitch. - Wei Huang; Joohyun Kim 001; Shantenu Jha; Fareed Aboul-Ela (PLoS Comput. Biol., 2013)

A Tale of Two Data-Intensive Paradigms: Applications, Abstractions, and Architectures. - Shantenu Jha; Judy Qiu; André Luckow; Pradeep Kumar Mantha; Geoffrey C. Fox (BigData Congress, 2014)

Towards a Comprehensive Set of Big Data Benchmarks. - Geoffrey C. Fox; Shantenu Jha; Judy Qiu; Saliya Ekanayake; André Luckow (High Performance Computing Workshop, 2014)

Gateways to high-perfomance and distributed computing resources for global health challenges. - Sandra Gesing; Jarek Nabrzyski; Shantenu Jha (IHTC, 2014)

Advancing next-generation sequencing data analytics with scalable distributed infrastructure. - Joohyun Kim 001; Sharath Maddineni; Shantenu Jha (Concurr. Comput. Pract. Exp., 2014)

Comparative analysis of nucleotide translocation through protein nanopores using steered molecular dynamics and an adaptive biasing force. - Hugh S. C. Martin; Shantenu Jha; Peter V. Coveney (J. Comput. Chem., 2014)

HPC-ABDS High Performance Computing Enhanced Apache Big Data Stack. - Geoffrey C. Fox; Judy Qiu; Supun Kamburugamuve; Shantenu Jha; André Luckow (CCGRID, 2015)

Big Data, Simulations and HPC Convergence. - Geoffrey C. Fox; Judy Qiu; Shantenu Jha; Saliya Ekanayake; Supun Kamburugamuve (WBDB, 2015)

Pilot-Abstraction: A Valid Abstraction for Data-Intensive Applications on HPC, Hadoop and Cloud Infrastructures? - André Luckow; Pradeep Kumar Mantha; Shantenu Jha (CoRR, 2015)

Synapse: Bridging the Gap Towards Predictable Workload Placement. - André Merzky; Shantenu Jha (CoRR, 2015)

RADICAL-Pilot: Scalable Execution of Heterogeneous and Dynamic Workloads on Supercomputers. - André Merzky; Mark Santcroos; Matteo Turilli; Shantenu Jha (CoRR, 2015)

A Comprehensive Perspective on the Pilot-Job Abstraction. - Matteo Turilli; Mark Santcroos; Shantenu Jha (CoRR, 2015)

Pilot-Data: An abstraction for distributed data. - André Luckow; Mark Santcroos; Ashley Zebrowski; Shantenu Jha (J. Parallel Distributed Comput., 2015)

ExTASY: Scalable and flexible coupling of MD simulations and advanced sampling techniques. - Vivekanandan Balasubramanian; Iain Bethune; Ardita Shkurti; Elena Breitmoser; Eugen Hruska; Cecilia Clementi; Charles A. Laughton; Shantenu Jha (eScience, 2016)

Ensemble Toolkit: Scalable and Flexible Execution of Ensembles of Tasks. - Vivekanandan Balasubramanian; Antons Treikalis; Ole Weidner; Shantenu Jha (ICPP, 2016)

RepEx: A Flexible Framework for Scalable Replica Exchange Molecular Dynamics Simulations. - Antons Treikalis; André Merzky; Haoyuan Chen; Tai-Sung Lee; Darrin M. York; Shantenu Jha (ICPP, 2016)

Hadoop on HPC: Integrating Hadoop and Pilot-Based Dynamic Resource Management. - André Luckow; Ioannis Paraskevakos; George Chantzialexiou; Shantenu Jha (IPDPS Workshops, 2016)

Synapse: Synthetic Application Profiler and Emulator. - André Merzky; Shantenu Jha (IPDPS Workshops, 2016)

A Scalable Pipeline for Transcriptome Profiling Tasks with On-Demand Computing Clouds. - Shayan Shams; Nayong Kim; Xiandong Meng; Ming Tai Ha; Shantenu Jha; Zhong Wang 003; Joohyun Kim 001 (IPDPS Workshops, 2016)

Integrating Abstractions to Enhance the Execution of Distributed Applications. - Matteo Turilli; Feng Liu; Zhao Zhang 007; André Merzky; Michael Wilde; Jon B. Weissman; Daniel S. Katz; Shantenu Jha (IPDPS, 2016)

EnsembleMD Toolkit: Scalable and Flexible Execution of Ensembles of Molecular Simulations. - Vivekanandan Balasubramanian; Antons Treikalis; Ole Weidner; Shantenu Jha (CoRR, 2016)

A Building Blocks Approach towards Domain Specific Workflow Systems? - Shantenu Jha; Matteo Turilli (CoRR, 2016)

Analysis of Distributed Execution of Workloads. - Matteo Turilli; Yadu Nand Babuji; André Merzky; Ming Tai Ha; Michael Wilde; Daniel S. Katz; Shantenu Jha (CoRR, 2016)

Application skeletons: Construction and use in eScience. - Daniel S. Katz; André Merzky; Zhao Zhang 007; Shantenu Jha (Future Gener. Comput. Syst., 2016)

Application Skeleton: Generating Synthetic Applications for Infrastructure Research. - Zhao Zhang 007; Daniel S. Katz; André Merzky; Matteo Turilli; Shantenu Jha; Yadu Nand Babuji (J. Open Source Softw., 2016)

Conceptualizing a Computing Platform for Science Beyond 2020: To Cloudify HPC, or HPCify Clouds? - Geoffrey C. Fox; Shantenu Jha (CLOUD, 2017)

High-Throughput Computing on High-Performance Platforms: A Case Study. - Danila Oleynik; Sergey Panitkin; Matteo Turilli; Alessio Angius; Sarp H. Oral; Kaushik De; Alexei Klimentov; Jack C. Wells; Shantenu Jha (eScience, 2017)

Evaluating Distributed Execution of Workloads. - Matteo Turilli; Yadu Nand Babuji; André Merzky; Ming Tai Ha; Michael Wilde; Daniel S. Katz; Shantenu Jha (eScience, 2017)

Hacking at the Divide Between Polar Science and HPC: Using Hackathons as Training Tools. - Jane Wyngaard; Heather J. Lynch; Jaroslaw Nabrzyski; Allen Pope; Shantenu Jha (IPDPS Workshops, 2017)

Parallel Analysis in MDAnalysis using the Dask Parallel Computing Library. - Mahzad Khoshlessan; Ioannis Paraskevakos; Shantenu Jha; Oliver Beckstein (SciPy, 2017)

Introducing distributed dynamic data-intensive (D3) science: Understanding applications and infrastructure. - Shantenu Jha; Daniel S. Katz; André Luckow; Neil P. Chue Hong; Omer F. Rana; Yogesh Simmhan (Concurr. Comput. Pract. Exp., 2017)

On the complexities of utilizing large-scale lightpath-connected distributed cyberinfrastructure. - Jason Maassen; Ben van Werkhoven; Maarten A. J. van Meersbergen; Henri E. Bal; Michael Kliphuis; Sandra E. Brunnabend; Henk A. Dijkstra; Gerben van Malenstein; Migiel de Vos; Sylvia Kuijpers; Sander Boele; Jules Wolfrat; et al. (Concurr. Comput. Pract. Exp., 2017)

Converging High-Throughput and High-Performance Computing: A Case Study. - Alessio Angius; Danila Oleynik; Sergey Panitkin; Matteo Turilli; Kaushik De; Alexei Klimentov; Sarp H. Oral; Jack C. Wells; Shantenu Jha (CoRR, 2017)

Toward Common Components for Open Workflow Systems. - Jay Jay Billings; Shantenu Jha (CoRR, 2017)

Harnessing the Power of Many: Extensible Toolkit for Scalable Ensemble Applications. - Vivek Balasubramanian; Matteo Turilli; Weiming Hu; Matthieu Lefebvre; Wenjie Lei; Guido Cervone; Jeroen Tromp; Shantenu Jha (CoRR, 2017)

Learning Neural Markers of Schizophrenia Disorder Using Recurrent Neural Networks. - Jumana Dakka; Pouya Bashivan; Mina Gheiratmand; Irina Rish; Shantenu Jha; Russell Greiner (CoRR, 2017)

Enabling Trade-offs Between Accuracy and Computational Cost: Adaptive Algorithms to Reduce Time to Clinical Insight. - Jumana Dakka; Kristof Farkas-Pall; Vivek Balasubramanian; Matteo Turilli; Shunzhou Wan; David W. Wright 001; Stefan J. Zasada; Peter V. Coveney; Shantenu Jha (CCGrid, 2018)

Building Blocks for Workflow System Middleware. - Matteo Turilli; André Merzky; Vivek Balasubramanian; Shantenu Jha (CCGrid, 2018)

Towards Exascale Computing for High Energy Physics: The ATLAS Experience at ORNL. - V. Ananthraj; Kaushik De; Shantenu Jha; Alexei Klimentov; Danila Oleynik; Sarp H. Oral; André Merzky; Ruslan Mashinistov; Sergey Panitkin; P. Svirin; Matteo Turilli; Jack C. Wells; et al. (eScience, 2018)

Pilot-Streaming: A Stream Processing Framework for High-Performance Computing. - Georgios Chantzialexiou; André Luckow; Shantenu Jha (eScience, 2018)

Concurrent and Adaptive Extreme Scale Binding Free Energy Calculations. - Jumana Dakka; Kristof Farkas-Pall; Matteo Turilli; David W. Wright 001; Peter V. Coveney; Shantenu Jha (eScience, 2018)

Modeling Impact of Execution Strategies on Resource Utilization. - Alexey A. Poyda; Mikhail Titov; Alexei Klimentov; Jack C. Wells; Sarp H. Oral; Kaushik De; Danila Oleynik; Shantenu Jha (eScience, 2018)

Task-parallel Analysis of Molecular Dynamics Trajectories. - Ioannis Paraskevakos; André Luckow; Mahzad Khoshlessan; George Chantzialexiou; Thomas E. Cheatham; Oliver Beckstein; Geoffrey C. Fox; Shantenu Jha (ICPP, 2018)

Harnessing the Power of Many: Extensible Toolkit for Scalable Ensemble Applications. - Vivek Balasubramanian; Matteo Turilli; Weiming Hu; Matthieu Lefebvre; Wenjie Lei; Ryan T. Modrak; Guido Cervone; Jeroen Tromp; Shantenu Jha (IPDPS, 2018)

Using Pilot Systems to Execute Many Task Workloads on Supercomputers. - André Merzky; Matteo Turilli; Manuel Maldonado; Mark Santcroos; Shantenu Jha (JSSPP, 2018)

High-throughput binding affinity calculations at extreme scales. - Jumana Dakka; Matteo Turilli; David W. Wright 001; Stefan J. Zasada; Vivek Balasubramanian; Shunzhou Wan; Peter V. Coveney; Shantenu Jha (BMC Bioinform., 2018)

A parallel unidirectional coupled DEM-PBM model for the efficient simulation of computationally intensive particulate process systems. - Chaitanya Sampat; Franklin E. Bettencourt; Yukteshwar Baranwal; Ioannis Paraskevakos; Anik Chaturbedi; Subhodh Karkala; Shantenu Jha; Rohit Ramachandran; Marianthi Ierapetritou (Comput. Chem. Eng., 2018)

Rapid, concurrent and adaptive extreme scale binding free energy calculation. - Jumana Dakka; Kristof Farkas-Pall; Vivek Balasubramanian; Matteo Turilli; David W. Wright 001; Shunzhou Wan; Stefan J. Zasada; Peter V. Coveney; Shantenu Jha (CoRR, 2018)

Design and Performance Characterization of RADICAL-Pilot on Titan. - André Merzky; Matteo Turilli; Manuel Maldonado; Shantenu Jha (CoRR, 2018)

Towards General Distributed Resource Selection. - Ming Tai Ha; Matteo Turilli; André Merzky; Shantenu Jha (CoRR, 2018)

Task-parallel Analysis of Molecular Dynamics Trajectories. - Ioannis Paraskevakos; André Luckow; George Chantzialexiou; Mahzad Khoshlessan; Oliver Beckstein; Geoffrey C. Fox; Shantenu Jha (CoRR, 2018)

Implementing Adaptive Ensemble Biomolecular Applications at Scale. - Vivek Balasubramanian; Travis Jensen; Matteo Turilli; Peter M. Kasson; Michael R. Shirts; Shantenu Jha (CoRR, 2018)

Use Cases of Computational Reproducibility for Scientific Workflows at Exascale. - Line Pouchard; Sterling Baldwin; Todd Elsethagen; Carlos Gamboa; Shantenu Jha; Bibi Raju; Eric G. Stephan; Li Tang 007; Kerstin Kleese van Dam (CoRR, 2018)

A Comprehensive Perspective on Pilot-Job Systems. - Matteo Turilli; Mark Santcroos; Shantenu Jha (ACM Comput. Surv., 2018)

Synapse: Synthetic application profiler and emulator. - André Merzky; Ming Tai Ha; Matteo Turilli; Shantenu Jha (J. Comput. Sci., 2018)

Performance Characterization and Modeling of Serverless and HPC Streaming Applications. - André Luckow; Shantenu Jha (IEEE BigData, 2019)

Learning Everywhere: A Taxonomy for the Integration of Machine Learning and Simulations. - Geoffrey C. Fox; Shantenu Jha (eScience, 2019)

Understanding ML Driven HPC: Applications and Infrastructure. - Shantenu Jha; Geoffrey C. Fox (eScience, 2019)

Workflow Design Analysis for High Resolution Satellite Image Analysis. - Ioannis Paraskevakos; Matteo Turilli; Bento Collares Gonçalves; Heather J. Lynch; Shantenu Jha (eScience, 2019)

Learning Everywhere: Pervasive Machine Learning for Effective High-Performance Computation. - Geoffrey C. Fox; James A. Glazier; J. C. S. Kadupitiya; Vikram Jadhao; Minje Kim; Judy Qiu; James P. Sluka; Endre T. Somogyi; Madhav V. Marathe; Abhijin Adiga; Jiangzhuo Chen; Oliver Beckstein; et al. (IPDPS Workshops, 2019)

Deep Generative Model Driven Protein Folding Simulations. - Heng Ma; Debsindhu Bhowmik; Hyungro Lee; Matteo Turilli; Michael T. Young; Shantenu Jha; Arvind Ramanathan (PARCO, 2019)

DeepDriveMD: Deep-Learning Driven Adaptive Molecular Simulations for Protein Folding. - Hyungro Lee; Matteo Turilli; Shantenu Jha; Debsindhu Bhowmik; Heng Ma; Arvind Ramanathan (DLS@SC, 2019)

Characterizing the Performance of Executing Many-tasks on Summit. - Matteo Turilli; André Merzky; Thomas J. Naughton; Wael R. Elwasif; Shantenu Jha (IPDRM@SC, 2019)

RADICAL-Cybertools: Middleware Building Blocks for Scalable Science. - Vivek Balasubramanian; Shantenu Jha; André Merzky; Matteo Turilli (CoRR, 2019)

MolSSI and BioExcel Workflow Workshop 2018 Report. - Levi N. Naden; Sam Ellis; Shantenu Jha (CoRR, 2019)

Incorporating Scientific Workflows in Computing Research Processes. - Shantenu Jha; Scott Lathrop 001; Jarek Nabrzyski; Lavanya Ramakrishnan (Comput. Sci. Eng., 2019)

Middleware Building Blocks for Workflow Systems. - Matteo Turilli; Vivek Balasubramanian; André Merzky; Ioannis Paraskevakos; Shantenu Jha (Comput. Sci. Eng., 2019)

Computational reproducibility of scientific workflows at extreme scales. - Line Pouchard; Sterling Baldwin; Todd Elsethagen; Shantenu Jha; Bibi Raju; Eric G. Stephan; Li Tang 007; Kerstin Kleese van Dam (Int. J. High Perform. Comput. Appl., 2019)

Supporting High-Performance and High-Throughput Computing for Experimental Science. - Eliu A. Huerta; Roland Haas; Shantenu Jha; Mark S. Neubauer; Daniel S. Katz (Comput. Softw. Big Sci., 2019)

Methods and Experiences for Developing Abstractions for Data-intensive, Scientific Applications. - André Luckow; Shantenu Jha (IPDPS Workshops, 2020)

ICEBERG: Imagery Cyber-infrastructure and Extensible Building blocks to Enhance Research in the Geosciences. (A Research Programmer's Perspective). - Bradley D. Spitzbart; Heather J. Lynch; Matteo Turilli; Shantenu Jha (PEARC, 2020)

Parallel performance of molecular dynamics trajectory analysis. - Mahzad Khoshlessan; Ioannis Paraskevakos; Geoffrey C. Fox; Shantenu Jha; Oliver Beckstein (Concurr. Comput. Pract. Exp., 2020)

Targeting SARS-CoV-2 with AI- and HPC-enabled Lead Generation: A First Data Release. - Yadu N. Babuji; Ben Blaiszik; Tom Brettin; Kyle Chard; Ryan Chard; Austin Clyde; Ian T. Foster; Zhi Hong; Shantenu Jha; Zhuozhao Li; Xuefeng Liu; Arvind Ramanathan; et al. (CoRR, 2020)

Scalable HPC and AI Infrastructure for COVID-19 Therapeutics. - Hyungro Lee; André Merzky; Li Tan; Mikhail Titov; Matteo Turilli; Dario Alfè; Agastya Bhati; Alex Brace; Austin Clyde; Peter V. Coveney; Heng Ma; Arvind Ramanathan; et al. (CoRR, 2020)

Adaptive Ensemble Biomolecular Applications at Scale. - Vivek Balasubramanian; Travis Jensen; Matteo Turilli; Peter M. Kasson; Michael R. Shirts; Shantenu Jha (SN Comput. Sci., 2020)

Dynamic and Adaptive Monitoring and Analysis for Many-task Ensemble Computing. - Shantenu Jha; Allen D. Malony (CLUSTER, 2021)

Exploring Task Placement for Edge-to-Cloud Applications using Emulation. - André Luckow; Kartik Rattan; Shantenu Jha (ICFEC, 2021)

IMPECCABLE: Integrated Modeling PipelinE for COVID Cure by Assessing Better LEads. - Aymen Al Saadi; Dario Alfè; Yadu N. Babuji; Agastya Bhati; Ben Blaiszik; Alexander Brace; Thomas S. Brettin; Kyle Chard; Ryan Chard; Austin Clyde; Peter V. Coveney; Ian T. Foster; et al. (ICPP, 2021)

Pilot-Edge: Distributed Resource Management Along the Edge-to-Cloud Continuum. - André Luckow; Kartik Rattan; Shantenu Jha (IPDPS Workshops, 2021)

Scalable HPC & AI infrastructure for COVID-19 therapeutics. - Hyungro Lee; André Merzky; Li Tan; Mikhail Titov; Matteo Turilli; Dario Alfè; Agastya Bhati; Alex Brace; Austin Clyde; Peter V. Coveney; Heng Ma; Arvind Ramanathan; et al. (PASC, 2021)

ExaWorks: Workflows for Exascale. - Aymen Al-Saadi; Dong H. Ahn; Yadu N. Babuji; Kyle Chard; James Corbett; Mihael Hategan; Stephen Herbein; Shantenu Jha; Daniel E. Laney; André Merzky; Todd S. Munson; Michael Salim; et al. (WORKS, 2021)

A Community Roadmap for Scientific Workflows Research and Development. - Rafael Ferreira da Silva; Henri Casanova; Kyle Chard; Ilkay Altintas; Rosa M. Badia; Bartosz Balis; Tainã Coleman; Frederik Coppens; Frank Di Natale; Bjoern Enders; Thomas Fahringer; Rosa Filgueira; et al. (WORKS, 2021)

Pandemic Drugs at Pandemic Speed: Accelerating COVID-19 Drug Discovery with Hybrid Machine Learning- and Physics-based Simulations on High Performance Computers. - Agastya P. Bhati; Shunzhou Wan; Dario Alfè; Austin R. Clyde; Mathis Bode; Li Tan; Mikhail Titov; André Merzky; Matteo Turilli; Shantenu Jha; Roger R. Highfield; Walter Rocchia; et al. (CoRR, 2021)

Workflows Community Summit: Bringing the Scientific Workflows Community Together. - Rafael Ferreira da Silva; Henri Casanova; Kyle Chard; Dan Laney; Dong H. Ahn; Shantenu Jha; Carole A. Goble; Lavanya Ramakrishnan; J. Luc Peterson; Bjoern Enders; Douglas Thain; Ilkay Altintas; et al. (CoRR, 2021)

Achieving 100X faster simulations of complex biological phenomena by coupling ML to HPC ensembles. - Alexander Brace; Hyungro Lee; Heng Ma; Anda Trifan; Matteo Turilli; Igor Yakushin; Todd S. Munson; Ian T. Foster; Shantenu Jha; Arvind Ramanathan (CoRR, 2021)

RADICAL-Pilot and Parsl: Executing Heterogeneous Workflows on HPC Platforms. - Aymen Alsaadi; André Merzky; Kyle Chard; Shantenu Jha; Matteo Turilli (CoRR, 2021)

Workflows Community Summit: Advancing the State-of-the-art of Scientific Workflows Management Systems Research and Development. - Rafael Ferreira da Silva; Henri Casanova; Kyle Chard; Tainã Coleman; Dan Laney; Dong H. Ahn; Shantenu Jha; Dorran Howell; Stian Soiland-Reyes; Ilkay Altintas; Douglas Thain; Rosa Filgueira; et al. (CoRR, 2021)

Protein-Ligand Docking Surrogate Models: A SARS-CoV-2 Benchmark for Deep Learning Accelerated Virtual Screening. - Austin Clyde; Thomas S. Brettin; Alexander Partin; Hyun Seung Yoo; Yadu N. Babuji; Ben Blaiszik; André Merzky; Matteo Turilli; Shantenu Jha; Arvind Ramanathan; Rick Stevens (CoRR, 2021)

ExaWorks: Workflows for Exascale. - Aymen Al-Saadi; Dong H. Ahn; Yadu N. Babuji; Kyle Chard; James Corbett; Mihael Hategan; Stephen Herbein; Shantenu Jha; Daniel E. Laney; André Merzky; Todd S. Munson; Michael Salim; et al. (CoRR, 2021)

Comparing workflow application designs for high resolution satellite image analysis. - Aymen Al-Saadi; Ioannis Paraskevakos; Bento Collares Gonçalves; Heather J. Lynch; Shantenu Jha; Matteo Turilli (Future Gener. Comput. Syst., 2021)

Co-design Center for Exascale Machine Learning Technologies (ExaLearn). - Francis J. Alexander; James A. Ang; Jenna A. Bilbrey; Jan Balewski; Tiernan Casey; Ryan Chard; Jong Choi 001; Sutanay Choudhury; Bert J. Debusschere; Anthony M. DeGennaro; Nikoli Dryden; J. Austin Ellis; et al. (Int. J. High Perform. Comput. Appl., 2021)

AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamics. - Lorenzo Casalino; Abigail C. Dommer; Zied Gaieb; Emília P. Barros; Terra Sztain; Surl-Hee Ahn; Anda Trifan; Alexander Brace; Anthony T. Bogetti; Austin Clyde; Heng Ma; Hyungro Lee; et al. (Int. J. High Perform. Comput. Appl., 2021)

RAPTOR: Ravenous Throughput Computing. - André Merzky; Matteo Turilli; Shantenu Jha (CCGRID, 2022)

The Ghost of Performance Reproducibility Past. - Srinivasan Ramesh; Mikhail Titov; Matteo Turilli; Shantenu Jha; Allen D. Malony (e-Science, 2022)

Coupling streaming AI and HPC ensembles to achieve 100-1000× faster biomolecular simulations. - Alexander Brace; Igor Yakushin; Heng Ma; Anda Trifan; Todd S. Munson; Ian T. Foster; Arvind Ramanathan; Hyungro Lee; Matteo Turilli; Shantenu Jha (IPDPS, 2022)

RADICAL-Pilot and PMIx/PRRTE: Executing Heterogeneous Workloads at Large Scale on Partitioned HPC Resources. - Mikhail Titov; Matteo Turilli; André Merzky; Thomas J. Naughton; Wael R. Elwasif; Shantenu Jha (JSSPP, 2022)

RADICAL-Pilot and Parsl: Executing Heterogeneous Workflows on HPC Platforms. - Aymen Alsaadi; Logan T. Ward; André Merzky; Kyle Chard; Ian T. Foster; Shantenu Jha; Matteo Turilli (WORKS@SC, 2022)

A Scalable Solution for Running Ensemble Simulations for Photovoltaic Energy. - Weiming Hu; Guido Cervone; Matteo Turilli; André Merzky; Shantenu Jha (CoRR, 2022)

Workflows Community Summit: Tightening the Integration between Computing Facilities and Scientific Workflows. - Rafael Ferreira da Silva; Kyle Chard; Henri Casanova; Dan Laney; Dong H. Ahn; Shantenu Jha; William E. Allcock; Gregory Bauer; Dmitry Duplyakin; Bjoern Enders; Todd M. Heer; Eric Lancon; et al. (CoRR, 2022)

Asynchronous Execution of Heterogeneous Tasks in AI-coupled HPC Workflows. - Vincent R. Pascuzzi; Matteo Turilli; Shantenu Jha (CoRR, 2022)

AI-coupled HPC Workflows. - Shantenu Jha; Vincent R. Pascuzzi; Matteo Turilli (CoRR, 2022)

FAIR for AI: An interdisciplinary, international, inclusive, and diverse community building perspective. - Eliu A. Huerta; Ben Blaiszik; L. Catherine Brinson; Kristofer E. Bouchard; Daniel Diaz 003; Caterina Doglioni; Javier M. Duarte; Murali Emani; Ian T. Foster; Geoffrey C. Fox; Philip C. Harris; Lukas Heinrich; et al. (CoRR, 2022)

High-Throughput Virtual Screening and Validation of a SARS-CoV-2 Main Protease Noncovalent Inhibitor. - Austin Clyde; Stephanie Galanie; Daniel W. Kneller; Heng Ma; Yadu N. Babuji; Ben Blaiszik; Alexander Brace; Thomas S. Brettin; Kyle Chard; Ryan Chard; Leighton Coates; Ian T. Foster; et al. (J. Chem. Inf. Model., 2022)

Design and Performance Characterization of RADICAL-Pilot on Leadership-Class Platforms. - André Merzky; Matteo Turilli; Mikhail Titov; Aymen Al-Saadi; Shantenu Jha (IEEE Trans. Parallel Distributed Syst., 2022)

PSI/J: A Portable Interface for Submitting, Monitoring, and Managing Jobs. - Mihael Hategan-Marandiuc; André Merzky; Nicholson T. Collier; Ketan Maheshwari; Jonathan Ozik; Matteo Turilli; Andreas Wilke; Justin M. Wozniak; Kyle Chard; Ian T. Foster; Rafael Ferreira da Silva; Shantenu Jha; et al. (e-Science, 2023)

Building the I (Interoperability) of FAIR for Performance Reproducibility of Large-Scale Composable Workflows in RECUP. - Bogdan Nicolae; Tanzima Z. Islam; Robert B. Ross; Huub J. J. Van Dam; Kevin Assogba; Polina Shpilker; Mikhail Titov; Matteo Turilli; Tianle Wang 001; Ozgur O. Kilic; Shantenu Jha; Line C. Pouchard (e-Science, 2023)

A Parallel Machine Learning Workflow for Neutron Scattering Data Analysis. - Tianle Wang 001; Sudip K. Seal; Ramakrishnan Kannan; Cristina Garcia-Cardona; Thomas Proffen; Shantenu Jha (IPDPS Workshops, 2023)

Asynchronous Execution of Heterogeneous Tasks in ML-Driven HPC Workflows. - Vincent R. Pascuzzi; Ozgur O. Kilic; Matteo Turilli; Shantenu Jha (JSSPP, 2023)

A Conceptual Architecture for a Quantum-HPC Middleware. - Nishant Saurabh; Shantenu Jha; André Luckow (QSW, 2023)

Novel Approaches Toward Scalable Composable Workflows in Hyper-Heterogeneous Computing Environments. - Jonathan Bader; Jim Belak; Matthew T. Bement; Matthew Berry; Robert Carson; Daniela Cassol; Stephen Chan; John Coleman; Kastan Day; Alejandro Duque; Kjiersten Fagnan; Jeff Froula; et al. (SC Workshops, 2023)

Workflows Community Summit 2022: A Roadmap Revolution. - Rafael Ferreira da Silva; Rosa M. Badia; Venkat Bala; Debbie Bard; Peer-Timo Bremer; Ian Buckley; Silvina Caíno-Lores; Kyle Chard; Carole A. Goble; Shantenu Jha; Daniel S. Katz; Daniel E. Laney; et al. (CoRR, 2023)

#COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol. - Abigail C. Dommer; Lorenzo Casalino; Fiona L. Kearns; Mia A. Rosenfeld; Nicholas Wauer; Surl-Hee Ahn; John Russo 003; A. Sofia F. Oliveira; Clare Morris; Anthony T. Bogetti; Anda Trifan; Alexander Brace; et al. (Int. J. High Perform. Comput. Appl., 2023)

Data for manuscript "Adaptive Ensemble Refinement of Protein Structures in High Resolution Electron Microscopy Density Maps with Radical Augmented Molecular Dynamics Flexible Fitting". - Daipayan Sarkar; Hyungro Lee; John W. Vant; Matteo Turilli; Josh Vincent Vermaas; Shantenu Jha; Abhishek Singharoy (Zenodo, 2023)

Adaptive Ensemble Refinement of Protein Structures in High Resolution Electron Microscopy Density Maps with Radical Augmented Molecular Dynamics Flexible Fitting. - Daipayan Sarkar; Hyungro Lee; John W. Vant; Matteo Turilli; Josh Vincent Vermaas; Shantenu Jha; Abhishek Singharoy (J. Chem. Inf. Model., 2023)

Optimal decision-making in high-throughput virtual screening pipelines. - Hyun-Myung Woo; Xiaoning Qian; Li Tan; Shantenu Jha; Francis J. Alexander; Edward R. Dougherty; Byung-Jun Yoon (Patterns, 2023)

An Active Learning-Based Streaming Pipeline for Reduced Data Training of Structure Finding Models in Neutron Diffractometry. - Tianle Wang 001; Jorge Ramirez; Cristina Garcia-Cardona; Thomas Proffen; Shantenu Jha; Sudip K. Seal (IEEE Big Data, 2024)

Workflow Mini-Apps: Portable, Scalable, Tunable & Faithful Representations of Scientific Workflows. - Ozgur O. Kilic; Tianle Wang 001; Matteo Turilli; Mikhail Titov; André Merzky; Line Pouchard; Shantenu Jha (CCGrid, 2024)

Hydra: Brokering Cloud and HPC Resources to Support the Execution of Heterogeneous Workloads at Scale. - Aymen Alsaadi; Matteo Turilli; Shantenu Jha (FlexScience@HPDC, 2024)

Enabling Performance Observability for Heterogeneous HPC Workflows with SOMA. - Dewi Yokelson; Mikhail Titov; Srinivasan Ramesh; Ozgur O. Kilic; Matteo Turilli; Shantenu Jha; Allen D. Malony (ICPP, 2024)

Radical-Cylon: A Heterogeneous Data Pipeline for Scientific Computing. - Arup Kumar Sarker; Aymen Alsaadi; Niranda Perera; Mills Staylor; Gregor von Laszewski; Matteo Turilli; Ozgur Ozan Kilic; Mikhail Titov; André Merzky; Shantenu Jha; Geoffrey C. Fox (JSSPP, 2024)

Design and Implementation of an Analysis Pipeline for Heterogeneous Data. - Arup Kumar Sarker; Aymen Alsaadi; Niranda Perera; Mills Staylor; Gregor von Laszewski; Matteo Turilli; Ozgur Ozan Kilic; Mikhail Titov; André Merzky; Shantenu Jha; Geoffrey C. Fox (CoRR, 2024)

Quantum Mini-Apps: A Framework for Developing and Benchmarking Quantum-HPC Applications. - Nishant Saurabh; Pradeep Kumar Mantha; Florian J. Kiwit; Shantenu Jha; André Luckow (CoRR, 2024)

AI-coupled HPC Workflow Applications, Middleware and Performance. - Wes Brewer; Ana Gainaru; Frédéric Suter; Feiyi Wang; Murali Emani; Shantenu Jha (CoRR, 2024)

Scaling on Frontier: Uncertainty Quantification Workflow Applications using ExaWorks to Enable Full System Utilization. - Mikhail Titov; Robert Carson; Matthew Rolchigo; John Coleman; James F. Belak; Matthew T. Bement; Daniel E. Laney; Matteo Turilli; Shantenu Jha (CoRR, 2024)

Feasibility Study on Active Learning of Smart Surrogates for Scientific Simulations. - Pradeep Bajracharya; Javier Quetzalcóatl Toledo-Marín; Geoffrey C. Fox; Shantenu Jha; Linwei Wang (CoRR, 2024)

ExaWorks Software Development Kit: A Robust and Scalable Collection of Interoperable Workflow Technologies. - Matteo Turilli; Mihael Hategan-Marandiuc; Mikhail Titov; Ketan Maheshwari; Aymen Alsaadi; André Merzky; Ramon Arambula; Mikhail Zakharchanka; Matt Cowan; Justin M. Wozniak; Andreas Wilke; Ozgur Ozan Kilic; et al. (CoRR, 2024)

Workflows Community Summit 2024: Future Trends and Challenges in Scientific Workflows. - Rafael Ferreira da Silva; Deborah Bard; Kyle Chard; Shaun De Witt; Ian T. Foster; Tom Gibbs; Carole A. Goble; William F. Godoy; Johan Gustafsson 001; Utz-Uwe Haus; Stephen Hudson; Shantenu Jha; et al. (CoRR, 2024)

Exascale Workflow Applications and Middleware: An ExaWorks Retrospective. - Aymen Alsaadi; Mihael Hategan-Marandiuc; Ketan Maheshwari; André Merzky; Mikhail Titov; Matteo Turilli; Andreas Wilke; Justin M. Wozniak; Kyle Chard; Rafael Ferreira da Silva; Shantenu Jha; Daniel E. Laney (CoRR, 2024)

Envisioning National Resources for Artificial Intelligence Research: NSF Workshop Report. - Shantenu Jha; Yolanda Gil (CoRR, 2024)

Pilot-Quantum: A Quantum-HPC Middleware for Resource, Workload and Task Management. - Pradeep Kumar Mantha; Florian J. Kiwit; Nishant Saurabh; Shantenu Jha; André Luckow (CoRR, 2024)

Pathway-based analyses of gene expression profiles at low doses of ionizing radiation. - Xihaier Luo; Seyednami Niyakan; Patrick R. Johnstone; Sean McCorkle; Gilchan Park; Vanessa López-Marrero; Shinjae Yoo; Edward R. Dougherty; Xiaoning Qian; Francis J. Alexander; Shantenu Jha; Byung-Jun Yoon (Frontiers Bioinform., 2024)

Quantum-centric supercomputing for materials science: A perspective on challenges and future directions. - Yuri Alexeev; Maximilian Amsler; Marco Antonio Barroca; Sanzio Bassini; Torey Battelle; Daan Camps; David Casanova; Young Jay Choi; Frederic T. Chong; Charles Chung; Christopher Codella; Antonio D. Córcoles; et al. (Future Gener. Comput. Syst., 2024)

radical-collaboration/PaleoSTeHM: PaleoSTeHM v1.0-rc: a modern, scalable spatio-temporal hierarchical modeling framework for paleo-environmental data. - Yucheng Lin; AHReedy; Kopp Robert; Matteo Turilli; Shantenu Jha (Zenodo, 2024)

Frontiers in Scientific Workflows: Pervasive Integration With High-Performance Computing. - Rafael Ferreira da Silva; Rosa M. Badia; Deborah Bard; Ian T. Foster; Shantenu Jha; Frédéric Suter (Computer, 2024)

Pareto Prompt Optimization. - Guang Zhao; Byung-Jun Yoon; Gilchan Park; Shantenu Jha; Shinjae Yoo; Xiaoning Qian (ICLR, 2025)

Adaptive Protein Design Protocols and Middleware. - Aymen Alsaadi; Jonathan Ash; Mikhail Titov; Matteo Turilli; André Merzky; Shantenu Jha; Sagar Khare (IPDPS (Workshops), 2025)

Scalable Runtime Architecture for Data-driven, Hybrid HPC and ML Workflow Applications. - André Merzky; Mikhail Titov; Matteo Turilli; Ozgur O. Kilic; Tianle Wang 001; Shantenu Jha (IPDPS (Workshops), 2025)

Compositional Execution Motifs for Quantum-HPC Systems. - Nishant Saurabh; Pradeep Kumar Mantha; Shantenu Jha; André Luckow (IPDPS (Workshops), 2025)

Comparative Performance Evaluation of Large Language Models for Extracting Molecular Interactions and Pathway Knowledge. - Gilchan Park; Byung-Jun Yoon; Xihaier Luo; Vanessa López-Marrero; Shinjae Yoo; Shantenu Jha (J. Comput. Biol., 2025)

Deep RC: A Scalable Data Engineering and Deep Learning Pipeline. - Arup Kumar Sarker; Aymen Alsaadi; Alexander James Halpern; Prabhath Tangella; Mikhail Titov; Gregor von Laszewski; Shantenu Jha; Geoffrey C. Fox (CoRR, 2025)

Improved Dimensionality Reduction for Inverse Problems in Nuclear Fusion and High-Energy Astrophysics. - Jonathan Gorard; Ammar Hakim; Hong Qin 002; Kyle Parfrey; Shantenu Jha (CoRR, 2025)

A Grassroots Network and Community Roadmap for Interconnected Autonomous Science Laboratories for Accelerated Discovery. - Rafael Ferreira da Silva; Milad Abolhasani; Dionysios A. Antonopoulos; Laura Biven; Ryan N. Coffee; Ian T. Foster; Leslie Hamilton; Shantenu Jha; Theresa Mayer; Benjamin Mintz; Robert G. Moore; Salahudin Nimer; et al. (CoRR, 2025)

A terminology for scientific workflow systems. - Frédéric Suter; Tainã Coleman; Ilkay Altintas; Rosa M. Badia; Bartosz Balis; Kyle Chard; Iacopo Colonnelli; Ewa Deelman; Paolo Di Tommaso; Thomas Fahringer; Carole A. Goble; Shantenu Jha; et al. (Future Gener. Comput. Syst., 2026)