Hamid Bolouri

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Systems Biology Workbench Delphi/Kylix Programmer's Manual

Michael Hucka, Andrew Finney, Herbert M. Sauro, 2002 .

Rotation, Translation, and Scaling Tolerant Recognition of Complex Shapes Using a Hierarchical Self-Organising Neural Network

Hamid Bolouri, Theo Sabisch, Alistair Ferguson, 1997, ICONIP.

1996 proceedings, Eighth Annual IEEE International Conference on Innovative Systems in Silicon, Austin, Texas, USA

Donatella Sciuto, Hamid Bolouri, Laurence LaForge, 1996 .

An Overview of the ERATO Systems Biology Workbench Project

Hiroaki Kitano, Michael Hucka, Andrew Finney, 2001 .

Integrative network modeling reveals mechanisms underlying T cell exhaustion

Lu Huang, Paul Shannon, Hamid Bolouri, 2019, Scientific Reports.

Automatic registration of complex images using a self organizing neural system

Hamid Bolouri, Theo Sabisch, Alistair Ferguson, 1998, 1998 IEEE International Joint Conference on Neural Networks Proceedings. IEEE World Congress on Computational Intelligence (Cat. No.98CH36227).

The Relationship between Logic and Bayesian Networks

Hamid Bolouri, 2008 .

Artificial evolution: modelling the development of the retina

Roger Adams, Hamid Bolouri, S. George, 1996 .

Developmental artificial neural networks for shape recognition: a model of the retina

Roger Adams, Hamid Bolouri, S. George, 1996 .

Menu-driven cloud computing and resource sharing for R and Bioconductor

Hamid Bolouri, Rajiv Dulepet, Michael Angerman, 2011, Bioinform..

Image redundancy reduction for neural network classification using discrete cosine transforms

Alistair G. Rust, Hamid Bolouri, Zhengjun Pan, 2000, Proceedings of the IEEE-INNS-ENNS International Joint Conference on Neural Networks. IJCNN 2000. Neural Computing: New Challenges and Perspectives for the New Millennium.

Simplified Models: Bayesian Networks

Hamid Bolouri, 2008 .

Learning algorithms for RAM-based neural networks

Hamid Bolouri, Alistair Ferguson, L. C. W. Dixon, 1997 .

Systems Biology Workbench C++ Programmer's Manual

Michael Hucka, Andrew Finney, Herbert M. Sauro, 2002 .

Towards Computational Neural Systems through Developmental Evolution

Rod Adams, Alistair G. Rust, Hamid Bolouri, 2001, Emergent Neural Computational Architectures Based on Neuroscience.

A logical model of cis-regulatory control in a eukaryotic system

James M. Bower, Hamid Bolouri, Eric H. Davidson, 2001 .

Designing Development Rules for Artificial Evolution

Hamid Bolouri, S. George, Alistair G. Rust, 1997, ICANNGA.

Book Review: Neural and Automata Networks — dynamical behaviour and applications

Hamid Bolouri, 1991 .

Model Selection Theory

Hamid Bolouri, 2008 .

Systems Biology Workbench Standard Modules and Menus

Michael Hucka, Andrew Finney, Herbert M. Sauro, 2002 .

Object-oriented regression for building predictive models with high dimensional omics data from translational studies

Hamid Bolouri, Lue Ping Zhao, L. Zhao, 2016, J. Biomed. Informatics.

Notes on Data Processing for GRN Modeling

Hamid Bolouri, 2008 .

Staged training of Neocognitron by evolutionary algorithms

Hamid Bolouri, Zhengjun Pan, T. Sabisch, 1999, Proceedings of the 1999 Congress on Evolutionary Computation-CEC99 (Cat. No. 99TH8406).

Proposal for a Minimal SBML Level 2 Definition

Hiroaki Kitano, V. Gor, Michael Hucka, 2002 .

Book Review: Pattern Recognition: statistical, structural and neural approaches

Hamid Bolouri, 1992 .

Book Review: Fundamentals of Neural Networks — Architectures, Algorithms, and Applications: L. FAUSETT

Hamid Bolouri, 1995 .

Graphical Representations of Gene Regulatory Networks

Hamid Bolouri, 2008 .

High-Speed Airborne Particle Monitoring Using Artificial Neural Networks

Hamid Bolouri, Theo Sabisch, Alistair Ferguson, 1995, NIPS.

Network Inference in Practice

Hamid Bolouri, 2008 .

Molecular self-organisation in a developmental model for the evolution of large-scale artificial neural networks

Roger Adams, Alistair G. Rust, Hamid Bolouri, 1998 .

Molecular Self-Organization in the Development Model for the Evolution of Large-scale Artificial Neural Networks

Rod Adams, Alistair G. Rust, Hamid Bolouri, 1998, ICONIP.

Implicit Modeling via Interaction Network Maps

Hamid Bolouri, 2008 .

Simplified Models — GRN State Signatures in Data

Hamid Bolouri, 2008 .

Programmer's Manual

Michael Hucka, Andrew Finney, Herbert M. Sauro, 2004 .

A finite state automaton model for multi-neuron simulations

Rod Adams, Alistair G. Rust, Hamid Bolouri, 2002, Neurocomputing.

Dizzy: Stochastic Simulation of Large-scale Genetic Regulatory Networks

Hamid Bolouri, David Orrell, Stephen Ramsey, 2005, J. Bioinform. Comput. Biol..

Improving reinforcement learning in stochastic RAM-based neural networks

Hamid Bolouri, Alistair Ferguson, 2004, Neural Processing Letters.

Integration of 198 ChIP-seq Datasets Reveals Human cis-Regulatory Regions

Walter L. Ruzzo, Hamid Bolouri, W. L. Ruzzo, 2012, J. Comput. Biol..

Dizzy: Stochastic Simulation of Large-scale Genetic Regulatory Networks (supplementary Material)

Hamid Bolouri, David Orrell, Stephen Ramsey, 2005, J. Bioinform. Comput. Biol..

From DNA sequence to network behavior: functional properties of genetic regulatory networks

Hamid Bolouri, 2004, Proceedings. 2004 IEEE Computational Systems Bioinformatics Conference, 2004. CSB 2004..

A method for estimating stochastic noise in large genetic regulatory networks

Hamid Bolouri, David Orrell, Pedro de Atauri, 2005, Bioinform..

Evolving computational neural systems using synthetic developmental mechanisms

Roger Adams, Hamid Bolouri, Maria J. Schilstra, 2003 .

Simplified Models: Boolean and Multi-valued Logic

Hamid Bolouri, 2008 .

Identification of complex shapes using a self organizing neural system

Hamid Bolouri, Theo Sabisch, Alistair Ferguson, 2000, IEEE Trans. Neural Networks Learn. Syst..

A structured approach to architectural yield optimisation for WSI

Hamid Bolouri, 1991 .

Why Make Computational Models of Gene Regulatory Networks

Hamid Bolouri, 2008 .

IMAGE RECOGNITION USING DISCRETE COSINE TRANSFORMS AS DIMENSIONALITY REDUCTION

Rod Adams, Hamid Bolouri, Zhengjun Pan, 2001 .

SBML Level 3: an extensible format for the exchange and reuse of biological models

Hiroaki Kitano, Aurélien Naldi, Denis Thieffry, 2020, Molecular systems biology.

Dissecting innate immune responses with the tools of systems biology.

Hamid Bolouri, Kelly D Smith, H. Bolouri, 2005, Current opinion in immunology.

Substantial interindividual and limited intraindividual genomic diversity among tumors from men with metastatic prostate cancer

Hamid Bolouri, Jay Shendure, Min Fang, 2016 .

The molecular landscape of pediatric acute myeloid leukemia reveals recurrent structural alterations and age-specific mutational interactions

Hamid Bolouri, Xiaotu Ma, Jinghui Zhang, 2017, Nature Medicine.

Is the regulation of galactose 1-phosphate tuned against gene expression noise?

Hamid Bolouri, Pedro de Atauri, David Orrell, 2005, The Biochemical journal.

Automatic Landmark Extraction using Self-Organising Maps 1

Hamid Bolouri, Theo Sabisch, Alistair Ferguson, 1997 .

Analysis and visualization of linked molecular and clinical cancer data by using Oncoscape

Emily Silgard, Paul Shannon, Hamid Bolouri, 2018, Nature Genetics.

The gene regulatory network basis of the "community effect," and analysis of a sea urchin embryo example.

Eric H Davidson, Hamid Bolouri, E. Davidson, 2010, Developmental biology.

The Logic of Gene Regulation

Hamid Bolouri, Maria J. Schilstra, 2005 .

New computational approaches for analysis of cis-regulatory networks.

Eric H Davidson, Hamid Bolouri, Alistair G Rust, 2002, Developmental biology.

Personal Genomics and Personalized Medicine

Hamid Bolouri, 2009 .

Control of internal and external noise in genetic regulatory networks.

Hamid Bolouri, David Orrell, H. Bolouri, 2004, Journal of theoretical biology.

Expression and functional profiling reveal distinct gene classes involved in fatty acid metabolism

Hamid Bolouri, John D Aitchison, Daehee Hwang, 2006, Molecular systems biology.

Evolutionary neural topiary: growing and sculpting artifical neurons to order

Alistair G. Rust, Hamid Bolouri, Roger Adams, 2000 .

The Innate Immune Database (IIDB)

Bin Li, Hamid Bolouri, Vesteinn Thorsson, 2008, BMC Immunology.

A provisional regulatory gene network for specification of endomesoderm in the sea urchin embryo.

Eric H Davidson, Hamid Bolouri, Lee Rowen, 2002, Developmental biology.

Developmental gene regulatory networks in the zebrafish embryo.

Hamid Bolouri, Hua-Ling Chen, William J. R. Longabaugh, 2009, Biochimica et biophysica acta.

Modeling DNA sequence-based cis-regulatory gene networks.

Eric H Davidson, Hamid Bolouri, E. Davidson, 2002, Developmental biology.

Embryonic pattern formation without morphogens.

Hamid Bolouri, H. Bolouri, 2008, BioEssays : news and reviews in molecular, cellular and developmental biology.

Modeling genomic regulatory networks with big data.

Hamid Bolouri, H. Bolouri, 2014, Trends in genetics : TIG.

A gene regulatory network armature for T lymphocyte specification

Hamid Bolouri, William J R Longabaugh, Constantin Georgescu, 2008, Proceedings of the National Academy of Sciences.