Snake: An Efficient Strategy for the Reuse of Circuitry and Partial Computation Results in High-Performance Reconfigurable Computing. - Xabier Iturbe; Khaled Benkrid; Ali Ebrahim; Chuan Hong; Tughrul Arslan; Imanol Martinez (ReConFig, 2011)

Efficient On-Chip Task Scheduler and Allocator for Reconfigurable Operating Systems. - Chuan Hong; Khaled Benkrid; Xabier Iturbe; Ali Ebrahim; Tughrul Arslan (IEEE Embed. Syst. Lett., 2011)

A novel high-performance fault-tolerant ICAP controller. - Ali Ebrahim; Khaled Benkrid; Xabier Iturbe; Chuan Hong (AHS, 2012)

Online clock routing in Xilinx FPGAs for high-performance and reliability. - Xabier Iturbe; Khaled Benkrid; Raul Torrego; Ali Ebrahim; Tughrul Arslan (AHS, 2012)

Design and implementation of fault-tolerant soft processors on FPGAs. - Chuan Hong; Khaled Benkrid; Xabier Iturbe; Ali Ebrahim (FPL, 2012)

Novel Dynamic Partial Reconfiguration Implementation of K-Means Clustering on FPGAs: Comparative Results with GPPs and GPUs. - Hanaa M. Hussain; Khaled Benkrid; Ali Ebrahim; Ahmet T. Erdogan; Huseyin Seker (Int. J. Reconfigurable Comput., 2012)

Multiple-clone configuration of relocatable partial bitstreams in Xilinx Virtex FPGAs. - Ali Ebrahim; Khaled Benkrid; Xabier Iturbe; Chuan Hong (AHS, 2013)

A platform for secure IP integration in Xilinx Virtex FPGAs. - Ali Ebrahim; Khaled Benkrid; Jalal Khalifat; Chuan Hong (ReConFig, 2013)

GIM3E: condition-specific models of cellular metabolism developed from metabolomics and expression data. - Brian J. Schmidt; Ali Ebrahim; Thomas O. Metz; Joshua N. Adkins; Bernhard Ø. Palsson; Daniel R. Hyduke (Bioinform., 2013)

COBRApy: COnstraints-Based Reconstruction and Analysis for Python. - Ali Ebrahim; Joshua A. Lerman; Bernhard Ø. Palsson; Daniel R. Hyduke (BMC Syst. Biol., 2013)

Runtime Scheduling, Allocation, and Execution of Real-Time Hardware Tasks onto Xilinx FPGAs Subject to Fault Occurrence. - Xabier Iturbe; Khaled Benkrid; Chuan Hong; Ali Ebrahim; Tughrul Arslan; Imanol Martinez (Int. J. Reconfigurable Comput., 2013)

R3TOS: A Novel Reliable Reconfigurable Real-Time Operating System for Highly Adaptive, Efficient, and Dependable Computing on FPGAs. - Xabier Iturbe; Khaled Benkrid; Chuan Hong; Ali Ebrahim; Raul Torrego; Imanol Martinez; Tughrul Arslan; Jon Pérez 001 (IEEE Trans. Computers, 2013)

On enhancing the reliability of internal configuration controllers in FPGAs. - Ali Ebrahim; Tughrul Arslan; Xabier Iturbe (AHS, 2014)

An Efficient Implementation of the Adams-Hamilton's Demosaicing Algorithm in FPGAs. - Jalal Khalifat; Ali Ebrahim; Tughrul Arslan (ARC, 2014)

A fast and scalable FPGA damage diagnostic service for R3TOS using BIST cloning technique. - Ali Ebrahim; Tughrul Arslan; Xabier Iturbe (FPL, 2014)

R3TOS-Based Autonomous Fault-Tolerant Systems. - Xabier Iturbe; Ali Ebrahim; Khaled Benkrid; Chuan Hong; Tughrul Arslan; Jon Pérez 001; Didier Keymeulen; Marco D. Santambrogio (IEEE Micro, 2014)

A dynamic partial reconfiguration design for camera systems. - Jalal Khalifat; Ali Ebrahim; Adewale Adetomi; Tughrul Arslan (AHS, 2015)

Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways. - Zachary A. King; Andreas Dräger; Ali Ebrahim; Nikolaus Sonnenschein; Nathan E. Lewis; Bernhard O. Palsson (PLoS Comput. Biol., 2015)

Microkernel Architecture and Hardware Abstraction Layer of a Reliable Reconfigurable Real-Time Operating System (R3TOS). - Xabier Iturbe; Khaled Benkrid; Chuan Hong; Ali Ebrahim; Raul Torrego; Tughrul Arslan (ACM Trans. Reconfigurable Technol. Syst., 2015)

solveME: fast and reliable solution of nonlinear ME models. - Laurence Yang 001; Ding Ma 003; Ali Ebrahim; Colton J. Lloyd; Michael A. Saunders; Bernhard O. Palsson (BMC Bioinform., 2016)

BiGG Models: A platform for integrating, standardizing and sharing genome-scale models. - Zachary A. King; Justin Lu; Andreas Dräger; Philip Miller; Stephen Federowicz; Joshua A. Lerman; Ali Ebrahim; Bernhard O. Palsson; Nathan E. Lewis (Nucleic Acids Res., 2016)

Development and Dissemination of Computational Methods for Genome-scale Modeling. - Ali Ebrahim (2016)

COBRAme: A computational framework for genome-scale models of metabolism and gene expression. - Colton J. Lloyd; Ali Ebrahim; Laurence Yang 001; Zachary A. King; Edward Catoiu; Edward J. O'Brien; Joanne K. Liu; Bernhard O. Palsson (PLoS Comput. Biol., 2018)

DynamicME: dynamic simulation and refinement of integrated models of metabolism and protein expression. - Laurence Yang 001; Ali Ebrahim; Colton J. Lloyd; Michael A. Saunders; Bernhard O. Palsson (BMC Syst. Biol., 2019)

Predicting proteome allocation, overflow metabolism, and metal requirements in a model acetogen. - Joanne K. Liu; Colton J. Lloyd; Mahmoud M. Al-Bassam; Ali Ebrahim; Ji-Nu Kim; Connor A. Olson; Alexander Aksenov; Pieter C. Dorrestein; Karsten Zengler (PLoS Comput. Biol., 2019)

An Efficient Hardware Architecture for Finding Frequent Items in Data Streams. - Ali Ebrahim; Jalal Khlaifat (ICCD, 2020)

Fast Approximation of the Top-k Items in Data Streams Using a Reconfigurable Accelerator. - Ali Ebrahim; Jalal Khalifat (ARC, 2021)

Computation of condition-dependent proteome allocation reveals variability in the macro and micro nutrient requirements for growth. - Colton J. Lloyd; Jonathan Monk; Laurence Yang 001; Ali Ebrahim; Bernhard O. Palsson (PLoS Comput. Biol., 2021)

Design and Implementation of a Reliable Reconfigurable Imaging System. - Jalal Khalifat; Ali Ebrahim (Int. J. Embed. Real Time Commun. Syst., 2022)

Fast approximation of the top-k items in data streams using FPGAs. - Ali Ebrahim; Jalal Khalifat (IET Comput. Digit. Tech., 2023)

Counting Heavy Items in Filtered Data Streams Using an HLS-Generated FPGA Kernel. - Ali Ebrahim (ARC, 2025)