A 200-MHz 64-bit Dual-Issue CMOS Microprocessor. - Daniel W. Dobberpuhl; Richard T. Witek; Randy L. Allmon; Robert Anglin; David Bertucci; Sharon M. Britton; Linda Chao; Robert A. Conrad; Daniel E. Dever; Bruce Gieseke; Soha Hassoun; Gregory W. Hoeppner; et al. (Digit. Tech. J., 1992)

A 200-MHz 64-b dual-issue CMOS microprocessor. - Daniel W. Dobberpuhl; Richard T. Witek; Randy L. Allmon; Robert Anglin; David Bertucci; Sharon M. Britton; Linda Chao; Robert A. Conrad; Daniel E. Dever; Bruce Gieseke; Soha Hassoun; Gregory W. Hoeppner; et al. (IEEE J. Solid State Circuits, 1992)

The chaos router chip: design and implementation of an adaptive router. - Kevin Bolding; Sen-Ching S. Cheung; Sung-Eun Choi; Carl Ebeling; Soha Hassoun; Ton Anh Ngo; Robert Wille (VLSI, 1993)

Architectural Retiming: Pipelining Latency-Constrained Circuts. - Soha Hassoun; Carl Ebeling (DAC, 1996)

Using precomputation in architecture and logic resynthesis. - Soha Hassoun; Carl Ebeling (ICCAD, 1998)

Architecture of a Message-Driven Processor. - William J. Dally; Linda Chao; Andrew A. Chien; Soha Hassoun; Waldemar Horwat; Jon Kaplan; Paul Song; Brian Totty; D. Scott Wills (25 Years ISCA: Retrospectives and Reprints, 1998)

Fine Grain Incremental Rescheduling Via Architectural Retiming. - Soha Hassoun (ISSS, 1998)

Regularity extraction via clan-based structural circuit decomposition. - Soha Hassoun; Carolyn McCreary (ICCAD, 1999)

Critical path analysis using a dynamically bounded delay model. - Soha Hassoun (DAC, 2000)

A Transaction-Based Unified Simulation/Emulation Architecture for Functional Verification. - Murali Kudlugi; Soha Hassoun; Charles Selvidge; Duaine Pryor (DAC, 2001)

Practices for Recruiting and Retaining Graduate Women Students in Computer Science and Engineering. - Soha Hassoun; Soheila Bana (MSE, 2001)

Verifying Clock Schedules in the Presence of Cross Talk. - Soha Hassoun; Eduardo H. Calvillo Gámez; Christopher Cromer (DATE, 2002)

Optimal buffered routing path constructions for single and multiple clock domain systems. - Soha Hassoun; Charles J. Alpert; Meera Thiagarajan (ICCAD, 2002)

Robust SAT-Based Search Algorithm for Leakage Power Reduction. - Fadi A. Aloul; Soha Hassoun; Karem A. Sakallah; David T. Blaauw (PATMOS, 2002)

Hardware Scheduling for Dynamic Adaptability using External Profiling and Hardware Threading. - Brian Swahn; Soha Hassoun (ICCAD, 2003)

Optimal use of 2-phase transparent latches in buffered maze routing. - Soha Hassoun (ISCAS (4), 2003)

First CADathlon Programming Contest held at 2002 ICCAD. - Soha Hassoun; Geert Janssen (IEEE Des. Test Comput., 2003)

Guest Editors' Introduction: Clockless VLSI Systems. - Soha Hassoun; Yong-Bin Kim; Fabrizio Lombardi (IEEE Des. Test Comput., 2003)

Guest Editors' Introduction: On-Chip Power Distribution Networks. - Sani R. Nassif; Soha Hassoun (IEEE Des. Test Comput., 2003)

Optimal path routing in single- and multiple-clock domain systems. - Soha Hassoun; Charles J. Alpert (IEEE Trans. Comput. Aided Des. Integr. Circuits Syst., 2003)

Static timing analysis for level-clocked circuits in the presence of crosstalk. - Soha Hassoun; Christopher Cromer; Eduardo H. Calvillo Gámez (IEEE Trans. Comput. Aided Des. Integr. Circuits Syst., 2003)

Guest Editorial. - Soha Hassoun; Steven M. Nowick; Leon Stok (IEEE Trans. Comput. Aided Des. Integr. Circuits Syst., 2003)

A transaction-based unified architecture for simulation and emulation. - Soha Hassoun; Murali Kudlugi; Duaine Pryor; Charles Selvidge (IEEE Trans. Very Large Scale Integr. Syst., 2005)

Gate sizing: finFETs vs 32nm bulk MOSFETs. - Brian Swahn; Soha Hassoun (DAC, 2006)

METS: A Metric for Electro-Thermal Sensitivity, and Its Application To FinFETs. - Brian Swahn; Soha Hassoun (ISQED, 2006)

Electro-Thermal Analysis of Multi-Fin Devices. - Brian Swahn; Soha Hassoun (IEEE Trans. Very Large Scale Integr. Syst., 2008)

Through-Silicon Via (TSV)-induced noise characterization and noise mitigation using coaxial TSVs. - Nauman H. Khan; Syed M. Alam; Soha Hassoun (3DIC, 2009)

System-level comparison of power delivery design for 2D and 3D ICs. - Nauman H. Khan; Syed M. Alam; Soha Hassoun (3DIC, 2009)

Evolving soft robotic locomotion in PhysX. - John Rieffel; Frank Saunders; Shilpa Nadimpalli; Harvey Zhou; Soha Hassoun; Jason H. Rife; Barry Trimmer (GECCO (Companion), 2009)

An algorithm for identifying dominant-edge metabolic pathways. - Ehsan Ullah; Kyongbum Lee; Soha Hassoun (ICCAD, 2009)

Early estimation of TSV area for power delivery in 3-D integrated circuits. - Nauman H. Khan; Sherief Reda; Soha Hassoun (3DIC, 2010)

Joint DAC/IWBDA special session engineering biology: fundamentals and applications. - Marc D. Riedel; Soha Hassoun; Ron Weiss; Pamela Silver; J. Christopher Anderson; Richard M. Murray (DAC, 2010)

Fast, accurate a priori routing delay estimation. - Jinhai Qiu; Sherief Reda; Soha Hassoun (SLIP, 2010)

Mitigating TSV-induced substrate noise in 3-D ICs using GND plugs. - Nauman H. Khan; Syed M. Alam; Soha Hassoun (ISQED, 2011)

Identification of Biochemical Network Modules Based on Shortest Retroactive Distances. - Gautham Vivek Sridharan; Soha Hassoun; Kyongbum Lee (PLoS Comput. Biol., 2011)

Power Delivery Design for 3-D ICs Using Different Through-Silicon Via (TSV) Technologies. - Nauman H. Khan; Syed M. Alam; Soha Hassoun (IEEE Trans. Very Large Scale Integr. Syst., 2011)

The feasibility of Carbon Nanotubes for power delivery in 3-D Integrated Circuits. - Nauman H. Khan; Soha Hassoun (ASP-DAC, 2012)

Genetic/bio design automation for (re-)engineering biological systems. - Soha Hassoun (DATE, 2012)

Metabolic Flux-Based Modularity using Shortest Retroactive distances. - Gautham Vivek Sridharan; Michael Yi; Soha Hassoun; Kyongbum Lee (BMC Syst. Biol., 2012)

Guest Editors' Introduction: Synthetic Biology. - Douglas Densmore; Soha Hassoun (IEEE Des. Test Comput., 2012)

Design Automation for Synthetic Biological Systems. - Douglas Densmore; Soha Hassoun (IEEE Des. Test Comput., 2012)

Abstraction of Kinetic Models For Biochemical Networks. - Calvin Hopkins; Soha Hassoun (BCB, 2013)

Decomposing Biochemical Networks Into Elementary Flux Modes Using Graph Traversal. - Ehsan Ullah; Calvin Hopkins; Shuchin Aeron; Soha Hassoun (BCB, 2013)

Gene modification identification under flux capacity uncertainty. - Mona Yousofshahi; Michael Orshansky; Kyongbum Lee; Soha Hassoun (DAC, 2013)

New topic session 2B: Why (Re-)Designing Biology is ∗Slightly∗ more challenging than designing electronics. - Bozena Kaminska; Bernard Courtois; Soha Hassoun (VTS, 2013)

Probabilistic strain optimization under constraint uncertainty. - Mona Yousofshahi; Michael Orshansky; Kyongbum Lee; Soha Hassoun (BMC Syst. Biol., 2013)

MC3: a steady-state model and constraint consistency checker for biochemical networks. - Mona Yousofshahi; Ehsan Ullah; Russell Stern; Soha Hassoun (BMC Syst. Biol., 2013)

Designing TSVs for 3D Integrated Circuits - Nauman H. Khan; Soha Hassoun (Springer, 2013)

Guest Editors' Introduction: Highlights of the 50th DAC. - Yervant Zorian; Soha Hassoun (IEEE Des. Test, 2014)

Discovery of substrate cycles in large scale metabolic networks using hierarchical modularity. - Gautham Vivek Sridharan; Ehsan Ullah; Soha Hassoun; Kyongbum Lee (BMC Syst. Biol., 2015)

PROXIMAL: a method for Prediction of Xenobiotic Metabolism. - Mona Yousofshahi; Sara Manteiga; Charmian Wu; Kyongbum Lee; Soha Hassoun (BMC Syst. Biol., 2015)

PreProPath: An Uncertainty-Aware Algorithm for Identifying Predictable Profitable Pathways in Biochemical Networks. - Ehsan Ullah; Mark Walker; Kyongbum Lee; Soha Hassoun (IEEE ACM Trans. Comput. Biol. Bioinform., 2015)

Simulation Methodology and Evaluation of Through Silicon Via (TSV)-FinFET Noise Coupling in 3-D Integrated Circuits. - Brad D. Gaynor; Soha Hassoun (IEEE Trans. Very Large Scale Integr. Syst., 2015)

Steven P. Levitan (1950-2016). - Mary Jane Irwin; Soha Hassoun (IEEE Des. Test, 2016)

gEFM: An Algorithm for Computing Elementary Flux Modes Using Graph Traversal. - Ehsan Ullah; Shuchin Aeron; Soha Hassoun (IEEE ACM Trans. Comput. Biol. Bioinform., 2016)

ProSol DB: A Protein Solubility Database. - Sara A. Amin; Venkatesh Endalur Gopinarayanan; Nikhil U. Nair; Soha Hassoun (BCB, 2017)

An Advanced Workflow for Metabolite Annotation. - Neda Hassanpour; Nicholas Alden; Kyongbum Lee; Soha Hassoun (BCB, 2017)

A Workshop on Microbiomics, Metagenomics, and Metabolomics. - Soha Hassoun; Curtis Huttenhower (BCB, 2017)

Towards the Design of Matrix Metalloproteinases (MMP) Antibody Sequences. - Xinmeng Li; James Van Deventer; Soha Hassoun (BCB, 2017)

A Tool for Predicting the Dark Side of Enzymes. - Linfeng Liu 004; Soha Hassoun (BCB, 2017)

Pathway Enrichment Analysis for Untargeted Metabolomics. - Vladimir Porokhin; Xinmeng Li; Soha Hassoun (BCB, 2017)

Workshop on Microbiomics, Metagenomics, and Metabolomics. - Soha Hassoun; Yasser El-Manzalawy; Georg Gerber; David Koslicki; Gail Rosen (BCB, 2019)

Pathway Activity Analysis and Metabolite Annotation for Untargeted Metabolomics using Probabilistic Modeling. - Ramtin Hosseini; Neda Hassanpour; Li-Ping Liu 001; Soha Hassoun (CoRR, 2019)

Towards scaling elementary flux mode computation. - Ehsan Ullah; Mona Yosafshahi; Soha Hassoun (Briefings Bioinform., 2020)

Hierarchical Classification of Enzyme Promiscuity Using Positive, Unlabeled, and Hard Negative Examples. - Gian Marco Visani; Michael C. Hughes; Soha Hassoun (CoRR, 2020)

Using Graph Neural Networks for Mass Spectrometry Prediction. - Hao Zhu; Li-Ping Liu 001; Soha Hassoun (CoRR, 2020)

ASAP-SML: An antibody sequence analysis pipeline using statistical testing and machine learning. - Xinmeng Li; James Van Deventer; Soha Hassoun (PLoS Comput. Biol., 2020)

Stochastic Iterative Graph Matching. - Linfeng Liu 004; Michael C. Hughes; Soha Hassoun; Liping Liu 001 (ICML, 2021)

Learning graph representations of biochemical networks and its application to enzymatic link prediction. - Julie Jiang; Li-Ping Liu 001; Soha Hassoun (Bioinform., 2021)

Contrastive Multiview Coding for Enzyme-Substrate Interaction Prediction. - Apurva Kalia; Dilip Krishnan; Soha Hassoun (CoRR, 2021)

Few-Shot Link Prediction with Domain-Agnostic Graph Embedding. - Hao Zhu; Mahashweta Das; Mangesh Bendre; Fei Wang 062; Hao Yang 007; Soha Hassoun (ICMLA, 2022)

Boost-RS: boosted embeddings for recommender systems and its application to enzyme-substrate interaction prediction. - Xinmeng Li; Li-Ping Liu 001; Soha Hassoun (Bioinform., 2022)

Ensemble Spectral Prediction (ESP) Model for Metabolite Annotation. - Xinmeng Li; Hao Zhu; Li-Ping Liu 001; Soha Hassoun (CoRR, 2022)

On Separate Normalization in Self-supervised Transformers. - Xiaohui Chen; Yinkai Wang; Yuanqi Du; Soha Hassoun; Liping Liu 001 (NeurIPS, 2023)

Using graph neural networks for site-of-metabolism prediction and its applications to ranking promiscuous enzymatic products. - Vladimir Porokhin; Li-Ping Liu 001; Soha Hassoun (Bioinform., 2023)

CSI: Contrastive data Stratification for Interaction prediction and its application to compound-protein interaction prediction. - Apurva Kalia; Dilip Krishnan; Soha Hassoun (Bioinform., 2023)

MassSpecGym: A benchmark for the discovery and identification of molecules. - Roman Bushuiev; Anton Bushuiev; Niek F. de Jonge; Adamo Young; Fleming Kretschmer; Raman Samusevich; Janne Heirman; Fei Wang 062; Luke Zhang; Kai Dührkop; Marcus Ludwig; Nils A. Haupt; et al. (NeurIPS, 2024)

JESTR: Joint Embedding Space Technique for Ranking Candidate Molecules for the Annotation of Untargeted Metabolomics Data. - Apurva Kalia; Dilip Krishnan; Soha Hassoun (CoRR, 2024)

Computational Metabolomics: Towards Molecules, Models, and their Meaning (Dagstuhl Seminar 24181). - Timothy M. D. Ebbels; Soha Hassoun; Ewy A. Mathé; Justin J. J. van der Hooft; Haley Chatelaine (Dagstuhl Reports, 2024)

MADGEN: Mass-Spec attends to De Novo Molecular generation. - Yinkai Wang; Xiaohui Chen; Liping Liu; Soha Hassoun (ICLR, 2025)

Graph Generative Pre-trained Transformer. - Xiaohui Chen; Yinkai Wang; Jiaxing He; Yuanqi Du; Soha Hassoun; Xiaolin Xu; Li-Ping Liu 001 (CoRR, 2025)

Large Language Model is Secretly a Protein Sequence Optimizer. - Yinkai Wang; Jiaxing He; Yuanqi Du; Xiaohui Chen; Jianan Canal Li; Liping Liu 001; Xiaolin Xu; Soha Hassoun (CoRR, 2025)

Protein-ligand co-design: a case for improving binding affinity between type II NADH:quinone oxidoreductase and quinones. - Vladimir Porokhin; Anne M. Brown; Soha Hassoun (J. Comput. Aided Mol. Des., 2025)