Soha Hassoun

Justin J. J. van der Hooft

Ewy A. Mathé

Haley Chatelaine

Dagstuhl Reports, 2024

MassSpecGym: A benchmark for the discovery and identification of molecules.

[BibT_eX]

[DOI]

CoRR, 2024

2023

CSI: Contrastive data Stratification for Interaction prediction and its application to compound-protein interaction prediction.

[BibT_eX]

[DOI]

Apurva Kalia

Dilip Krishnan

Bioinform., August, 2023

Using graph neural networks for site-of-metabolism prediction and its applications to ranking promiscuous enzymatic products.

[BibT_eX]

[DOI]

Vladimir Porokhin

Bioinform., March, 2023

On Separate Normalization in Self-supervised Transformers.

[BibT_eX]

[DOI]

Proceedings of the Advances in Neural Information Processing Systems 36: Annual Conference on Neural Information Processing Systems 2023, 2023

2022

Ensemble Spectral Prediction (ESP) Model for Metabolite Annotation.

[BibT_eX]

[DOI]

CoRR, 2022

Boost-RS: boosted embeddings for recommender systems and its application to enzyme-substrate interaction prediction.

[BibT_eX]

[DOI]

Bioinform., 2022

Few-Shot Link Prediction with Domain-Agnostic Graph Embedding.

[BibT_eX]

[DOI]

Proceedings of the 21st IEEE International Conference on Machine Learning and Applications, 2022

2021

Contrastive Multiview Coding for Enzyme-Substrate Interaction Prediction.

[BibT_eX]

[DOI]

Apurva Kalia

Dilip Krishnan

CoRR, 2021

Learning graph representations of biochemical networks and its application to enzymatic link prediction.

[BibT_eX]

[DOI]

Julie Jiang

Bioinform., 2021

Stochastic Iterative Graph Matching.

[BibT_eX]

[DOI]

Proceedings of the 38th International Conference on Machine Learning, 2021

2020

ASAP-SML: An antibody sequence analysis pipeline using statistical testing and machine learning.

[BibT_eX]

[DOI]

James Van Deventer

PLoS Comput. Biol., 2020

Using Graph Neural Networks for Mass Spectrometry Prediction.

[BibT_eX]

[DOI]

Hao Zhu

CoRR, 2020

Hierarchical Classification of Enzyme Promiscuity Using Positive, Unlabeled, and Hard Negative Examples.

[BibT_eX]

[DOI]

Gian Marco Visani

Michael C. Hughes

CoRR, 2020

Towards scaling elementary flux mode computation.

[BibT_eX]

[DOI]

Mona Yosafshahi

Briefings Bioinform., 2020

2019

Pathway Activity Analysis and Metabolite Annotation for Untargeted Metabolomics using Probabilistic Modeling.

[BibT_eX]

[DOI]

CoRR, 2019

Workshop on Microbiomics, Metagenomics, and Metabolomics.

[BibT_eX]

[DOI]

Proceedings of the 10th ACM International Conference on Bioinformatics, 2019

2017

Pathway Enrichment Analysis for Untargeted Metabolomics.

[BibT_eX]

[DOI]

Vladimir Porokhin

Proceedings of the 8th ACM International Conference on Bioinformatics, 2017

A Tool for Predicting the Dark Side of Enzymes.

[BibT_eX]

[DOI]

Linfeng Liu

Proceedings of the 8th ACM International Conference on Bioinformatics, 2017

Towards the Design of Matrix Metalloproteinases (MMP) Antibody Sequences.

[BibT_eX]

[DOI]

James Van Deventer

Proceedings of the 8th ACM International Conference on Bioinformatics, 2017

A Workshop on Microbiomics, Metagenomics, and Metabolomics.

[BibT_eX]

[DOI]

Venkatesh Endalur Gopinarayanan

Curtis Huttenhower

Proceedings of the 8th ACM International Conference on Bioinformatics, 2017

An Advanced Workflow for Metabolite Annotation.

[BibT_eX]

[DOI]

Proceedings of the 8th ACM International Conference on Bioinformatics, 2017

ProSol DB: A Protein Solubility Database.

[BibT_eX]

[DOI]

Sara A. Amin

Nikhil U. Nair

Proceedings of the 8th ACM International Conference on Bioinformatics, 2017

2016

gEFM: An Algorithm for Computing Elementary Flux Modes Using Graph Traversal.

[BibT_eX]

[DOI]

Shuchin Aeron

IEEE ACM Trans. Comput. Biol. Bioinform., 2016

Steven P. Levitan (1950-2016).

[BibT_eX]

[DOI]

Mary Jane Irwin

IEEE Des. Test, 2016

2015

Simulation Methodology and Evaluation of Through Silicon Via (TSV)-FinFET Noise Coupling in 3-D Integrated Circuits.

[BibT_eX]

[DOI]

Brad D. Gaynor

IEEE Trans. Very Large Scale Integr. Syst., 2015

PreProPath: An Uncertainty-Aware Algorithm for Identifying Predictable Profitable Pathways in Biochemical Networks.

[BibT_eX]

[DOI]

IEEE ACM Trans. Comput. Biol. Bioinform., 2015

PROXIMAL: a method for Prediction of Xenobiotic Metabolism.

[BibT_eX]

[DOI]

BMC Syst. Biol., 2015

Discovery of substrate cycles in large scale metabolic networks using hierarchical modularity.

[BibT_eX]

[DOI]

Gautham Vivek Sridharan

BMC Syst. Biol., 2015

2014

Guest Editors' Introduction: Highlights of the 50th DAC.

[BibT_eX]

[DOI]

Yervant Zorian

IEEE Des. Test, 2014

2013

Designing TSVs for 3D Integrated Circuits

[BibT_eX]

[DOI]

Springer Briefs in Electrical and Computer Engineering, Springer, ISBN: 978-1-4614-5508-0, 2013

MC<sup>3</sup>: a steady-state model and constraint consistency checker for biochemical networks.

[BibT_eX]

[DOI]

BMC Syst. Biol., 2013

Probabilistic strain optimization under constraint uncertainty.

[BibT_eX]

[DOI]

BMC Syst. Biol., 2013

New topic session 2B: Why (Re-)Designing Biology is ∗Slightly∗ more challenging than designing electronics.

[BibT_eX]

[DOI]

Bozena Kaminska

Bernard Courtois

Proceedings of the 31st IEEE VLSI Test Symposium, 2013

Gene modification identification under flux capacity uncertainty.

[BibT_eX]

[DOI]

Proceedings of the 50th Annual Design Automation Conference 2013, 2013

Decomposing Biochemical Networks Into Elementary Flux Modes Using Graph Traversal.

[BibT_eX]

[DOI]

Proceedings of the ACM Conference on Bioinformatics, 2013

Abstraction of Kinetic Models For Biochemical Networks.

[BibT_eX]

[DOI]

Calvin Hopkins

Proceedings of the ACM Conference on Bioinformatics, 2013

2012

Design Automation for Synthetic Biological Systems.

[BibT_eX]

[DOI]

Douglas Densmore

IEEE Des. Test Comput., 2012

Guest Editors' Introduction: Synthetic Biology.

[BibT_eX]

[DOI]

Douglas Densmore

IEEE Des. Test Comput., 2012

Metabolic Flux-Based Modularity using Shortest Retroactive distances.

[BibT_eX]

[DOI]

Gautham Vivek Sridharan

Michael Yi

BMC Syst. Biol., 2012

Genetic/bio design automation for (re-)engineering biological systems.

[BibT_eX]

[DOI]

Proceedings of the 2012 Design, Automation & Test in Europe Conference & Exhibition, 2012

The feasibility of Carbon Nanotubes for power delivery in 3-D Integrated Circuits.

[BibT_eX]

[DOI]

Proceedings of the 17th Asia and South Pacific Design Automation Conference, 2012

2011

Power Delivery Design for 3-D ICs Using Different Through-Silicon Via (TSV) Technologies.

[BibT_eX]

[DOI]

IEEE Trans. Very Large Scale Integr. Syst., 2011

Identification of Biochemical Network Modules Based on Shortest Retroactive Distances.

[BibT_eX]

[DOI]

Gautham Vivek Sridharan

PLoS Comput. Biol., 2011

Mitigating TSV-induced substrate noise in 3-D ICs using GND plugs.

[BibT_eX]

[DOI]

Proceedings of the 12th International Symposium on Quality Electronic Design, 2011

2010

Fast, accurate a priori routing delay estimation.

[BibT_eX]

[DOI]

Jinhai Qiu

Sherief Reda

Proceedings of the International Workshop on System Level Interconnect Prediction Workshop, 2010

Joint DAC/IWBDA special session engineering biology: fundamentals and applications.

[BibT_eX]

[DOI]

J. Christopher Anderson

Richard M. Murray

Proceedings of the 47th Design Automation Conference, 2010

Early estimation of TSV area for power delivery in 3-D integrated circuits.

[BibT_eX]

[DOI]

Sherief Reda

Proceedings of the IEEE International Conference on 3D System Integration, 2010

2009

An algorithm for identifying dominant-edge metabolic pathways.

[BibT_eX]

[DOI]

Proceedings of the 2009 International Conference on Computer-Aided Design, 2009

Evolving soft robotic locomotion in PhysX.

[BibT_eX]

[DOI]

Proceedings of the Genetic and Evolutionary Computation Conference, 2009

System-level comparison of power delivery design for 2D and 3D ICs.

[BibT_eX]

[DOI]

Proceedings of the IEEE International Conference on 3D System Integration, 2009

Through-Silicon Via (TSV)-induced noise characterization and noise mitigation using coaxial TSVs.

[BibT_eX]

[DOI]

Proceedings of the IEEE International Conference on 3D System Integration, 2009

2008

Electro-Thermal Analysis of Multi-Fin Devices.

[BibT_eX]

[DOI]

IEEE Trans. Very Large Scale Integr. Syst., 2008

2006

METS: A Metric for Electro-Thermal Sensitivity, and Its Application To FinFETs.

[BibT_eX]

[DOI]

Proceedings of the 7th International Symposium on Quality of Electronic Design (ISQED 2006), 2006

Gate sizing: finFETs vs 32nm bulk MOSFETs.

[BibT_eX]

[DOI]

Proceedings of the 43rd Design Automation Conference, 2006

2005

A transaction-based unified architecture for simulation and emulation.

[BibT_eX]

[DOI]

IEEE Trans. Very Large Scale Integr. Syst., 2005

2003

Guest Editorial.

[BibT_eX]

[DOI]

Steven M. Nowick

Leon Stok

IEEE Trans. Comput. Aided Des. Integr. Circuits Syst., 2003

Static timing analysis for level-clocked circuits in the presence of crosstalk.

[BibT_eX]

[DOI]

Eduardo H. Calvillo Gámez

Christopher Cromer

IEEE Trans. Comput. Aided Des. Integr. Circuits Syst., 2003

Optimal path routing in single- and multiple-clock domain systems.

[BibT_eX]

[DOI]

Charles J. Alpert

IEEE Trans. Comput. Aided Des. Integr. Circuits Syst., 2003

Guest Editors' Introduction: On-Chip Power Distribution Networks.

[BibT_eX]

Sani R. Nassif

IEEE Des. Test Comput., 2003

Guest Editors' Introduction: Clockless VLSI Systems.

[BibT_eX]

[DOI]

Yong-Bin Kim

Fabrizio Lombardi

IEEE Des. Test Comput., 2003

First CADathlon Programming Contest held at 2002 ICCAD.

[BibT_eX]

Geert Janssen

IEEE Des. Test Comput., 2003

Optimal use of 2-phase transparent latches in buffered maze routing.

[BibT_eX]

[DOI]

Proceedings of the 2003 International Symposium on Circuits and Systems, 2003

Hardware Scheduling for Dynamic Adaptability using External Profiling and Hardware Threading.

[BibT_eX]

[DOI]

Proceedings of the 2003 International Conference on Computer-Aided Design, 2003

2002

Robust SAT-Based Search Algorithm for Leakage Power Reduction.

[BibT_eX]

[DOI]

Proceedings of the Integrated Circuit Design. Power and Timing Modeling, 2002

Optimal buffered routing path constructions for single and multiple clock domain systems.

[BibT_eX]

[DOI]

Charles J. Alpert

Meera Thiagarajan

Proceedings of the 2002 IEEE/ACM International Conference on Computer-aided Design, 2002

Verifying Clock Schedules in the Presence of Cross Talk.

[BibT_eX]

[DOI]

Eduardo H. Calvillo Gámez

Christopher Cromer

Proceedings of the 2002 Design, 2002

2001

Practices for Recruiting and Retaining Graduate Women Students in Computer Science and Engineering.

[BibT_eX]

[DOI]

Soheila Bana

Proceedings of the 2001 International Conference on Microelectronics Systems Education, 2001

A Transaction-Based Unified Simulation/Emulation Architecture for Functional Verification.

[BibT_eX]

[DOI]

Proceedings of the 38th Design Automation Conference, 2001

2000

Critical path analysis using a dynamically bounded delay model.

[BibT_eX]

[DOI]

Proceedings of the 37th Conference on Design Automation, 2000

1999

Regularity extraction via clan-based structural circuit decomposition.

[BibT_eX]

[DOI]

Carolyn McCreary

Proceedings of the 1999 IEEE/ACM International Conference on Computer-Aided Design, 1999

1998

Fine Grain Incremental Rescheduling Via Architectural Retiming.

[BibT_eX]

[DOI]

Proceedings of the 11th International Symposium on System Synthesis, 1998

Architecture of a Message-Driven Processor.

[BibT_eX]

[DOI]

Proceedings of the 25 Years of the International Symposia on Computer Architecture (Selected Papers)., 1998

Using precomputation in architecture and logic resynthesis.

[BibT_eX]

[DOI]

Carl Ebeling

Proceedings of the 1998 IEEE/ACM International Conference on Computer-Aided Design, 1998

1996

Architectural Retiming: Pipelining Latency-Constrained Circuts.

[BibT_eX]

[DOI]