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Books and Theses
- 2016
[b1]Ali Ebrahim:
Development and Dissemination of Computational Methods for Genome-scale Modeling. University of California, San Diego, USA, 2016
Journal Articles
- 2023
- [j17]Ali Ebrahim
, Jalal Khalifat:
Fast approximation of the top-k items in data streams using FPGAs. IET Comput. Digit. Tech. 17(2): 60-73 (2023) - 2022
- [j16]Jalal Khalifat, Ali Ebrahim:
Design and Implementation of a Reliable Reconfigurable Imaging System. Int. J. Embed. Real Time Commun. Syst. 13(1): 1-17 (2022) - 2021
- [j15]Colton J. Lloyd, Jonathan Monk, Laurence Yang, Ali Ebrahim, Bernhard O. Palsson:
Computation of condition-dependent proteome allocation reveals variability in the macro and micro nutrient requirements for growth. PLoS Comput. Biol. 17(6) (2021) - 2019
- [j14]Laurence Yang, Ali Ebrahim, Colton J. Lloyd, Michael A. Saunders, Bernhard O. Palsson:
DynamicME: dynamic simulation and refinement of integrated models of metabolism and protein expression. BMC Syst. Biol. 13(1): 2:1-2:15 (2019) - [j13]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:
Predicting proteome allocation, overflow metabolism, and metal requirements in a model acetogen. PLoS Comput. Biol. 15(3) (2019) - 2018
- [j12]Colton J. Lloyd, Ali Ebrahim, Laurence Yang, Zachary A. King, Edward Catoiu, Edward J. O'Brien, Joanne K. Liu, Bernhard O. Palsson:
COBRAme: A computational framework for genome-scale models of metabolism and gene expression. PLoS Comput. Biol. 14(7) (2018) - 2016
- [j11]Laurence Yang, Ding Ma, Ali Ebrahim, Colton J. Lloyd, Michael A. Saunders, Bernhard O. Palsson:
solveME: fast and reliable solution of nonlinear ME models. BMC Bioinform. 17: 391 (2016) - [j10]Zachary A. King, Justin Lu, Andreas Dräger, Philip Miller, Stephen Federowicz, Joshua A. Lerman, Ali Ebrahim, Bernhard O. Palsson, Nathan E. Lewis:
BiGG Models: A platform for integrating, standardizing and sharing genome-scale models. Nucleic Acids Res. 44(Database-Issue): 515-522 (2016) - 2015
- [j9]Zachary A. King, Andreas Dräger, Ali Ebrahim, Nikolaus Sonnenschein, Nathan E. Lewis, Bernhard O. Palsson:
Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways. PLoS Comput. Biol. 11(8) (2015) - [j8]Xabier Iturbe, Khaled Benkrid, Chuan Hong, Ali Ebrahim, Raul Torrego, Tughrul Arslan:
Microkernel Architecture and Hardware Abstraction Layer of a Reliable Reconfigurable Real-Time Operating System (R3TOS). ACM Trans. Reconfigurable Technol. Syst. 8(1): 5:1-5:35 (2015) - 2014
- [j7]Xabier Iturbe, Ali Ebrahim, Khaled Benkrid, Chuan Hong, Tughrul Arslan, Jon Pérez, Didier Keymeulen, Marco D. Santambrogio:
R3TOS-Based Autonomous Fault-Tolerant Systems. IEEE Micro 34(6): 20-30 (2014) - 2013
- [j6]Brian J. Schmidt, Ali Ebrahim, Thomas O. Metz, Joshua N. Adkins, Bernhard Ø. Palsson, Daniel R. Hyduke:
GIM3E: condition-specific models of cellular metabolism developed from metabolomics and expression data. Bioinform. 29(22): 2900-2908 (2013) - [j5]Ali Ebrahim, Joshua A. Lerman, Bernhard Ø. Palsson, Daniel R. Hyduke:
COBRApy: COnstraints-Based Reconstruction and Analysis for Python. BMC Syst. Biol. 7: 74 (2013) - [j4]Xabier Iturbe, Khaled Benkrid, Chuan Hong, Ali Ebrahim, Tughrul Arslan, Imanol Martinez:
Runtime Scheduling, Allocation, and Execution of Real-Time Hardware Tasks onto Xilinx FPGAs Subject to Fault Occurrence. Int. J. Reconfigurable Comput. 2013: 905057:1-905057:32 (2013) - [j3]Xabier Iturbe, Khaled Benkrid, Chuan Hong, Ali Ebrahim, Raul Torrego, Imanol Martinez, Tughrul Arslan, Jon Pérez:
R3TOS: A Novel Reliable Reconfigurable Real-Time Operating System for Highly Adaptive, Efficient, and Dependable Computing on FPGAs. IEEE Trans. Computers 62(8): 1542-1556 (2013) - 2012
- [j2]Hanaa M. Hussain, Khaled Benkrid, Ali Ebrahim, Ahmet T. Erdogan, Huseyin Seker:
Novel Dynamic Partial Reconfiguration Implementation of K-Means Clustering on FPGAs: Comparative Results with GPPs and GPUs. Int. J. Reconfigurable Comput. 2012: 135926:1-135926:15 (2012) - 2011
- [j1]Chuan Hong, Khaled Benkrid, Xabier Iturbe, Ali Ebrahim, Tughrul Arslan:
Efficient On-Chip Task Scheduler and Allocator for Reconfigurable Operating Systems. IEEE Embed. Syst. Lett. 3(3): 85-88 (2011)
Conference and Workshop Papers
- 2021
- [c12]Ali Ebrahim, Jalal Khalifat:
Fast Approximation of the Top-k Items in Data Streams Using a Reconfigurable Accelerator. ARC 2021: 3-17 - 2020
- [c11]Ali Ebrahim, Jalal Khlaifat:
An Efficient Hardware Architecture for Finding Frequent Items in Data Streams. ICCD 2020: 113-119 - 2015
- [c10]Jalal Khalifat, Ali Ebrahim, Adewale Adetomi, Tughrul Arslan:
A dynamic partial reconfiguration design for camera systems. AHS 2015: 1-7 - 2014
- [c9]Ali Ebrahim, Tughrul Arslan, Xabier Iturbe:
On enhancing the reliability of internal configuration controllers in FPGAs. AHS 2014: 83-88 - [c8]Jalal Khalifat, Ali Ebrahim, Tughrul Arslan:
An Efficient Implementation of the Adams-Hamilton's Demosaicing Algorithm in FPGAs. ARC 2014: 205-212 - [c7]Ali Ebrahim, Tughrul Arslan, Xabier Iturbe:
A fast and scalable FPGA damage diagnostic service for R3TOS using BIST cloning technique. FPL 2014: 1-4 - 2013
- [c6]Ali Ebrahim, Khaled Benkrid, Xabier Iturbe, Chuan Hong:
Multiple-clone configuration of relocatable partial bitstreams in Xilinx Virtex FPGAs. AHS 2013: 178-183 - [c5]Ali Ebrahim, Khaled Benkrid, Jalal Khalifat, Chuan Hong:
A platform for secure IP integration in Xilinx Virtex FPGAs. ReConFig 2013: 1-6 - 2012
- [c4]Xabier Iturbe, Khaled Benkrid, Raul Torrego, Ali Ebrahim, Tughrul Arslan:
Online clock routing in Xilinx FPGAs for high-performance and reliability. AHS 2012: 85-91 - [c3]Ali Ebrahim, Khaled Benkrid, Xabier Iturbe, Chuan Hong:
A novel high-performance fault-tolerant ICAP controller. AHS 2012: 259-263 - [c2]Chuan Hong, Khaled Benkrid, Xabier Iturbe, Ali Ebrahim:
Design and implementation of fault-tolerant soft processors on FPGAs. FPL 2012: 683-686 - 2011
- [c1]Xabier Iturbe, Khaled Benkrid, Ali Ebrahim, Chuan Hong, Tughrul Arslan, Imanol Martinez:
Snake: An Efficient Strategy for the Reuse of Circuitry and Partial Computation Results in High-Performance Reconfigurable Computing. ReConFig 2011: 182-189
Coauthor Index
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