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The structure and function of complex networks

by M. E. J. Newman - SIAM REVIEW , 2003
"... Inspired by empirical studies of networked systems such as the Internet, social networks, and biological networks, researchers have in recent years developed a variety of techniques and models to help us understand or predict the behavior of these systems. Here we review developments in this field, ..."
Abstract - Cited by 2600 (7 self) - Add to MetaCart
Inspired by empirical studies of networked systems such as the Internet, social networks, and biological networks, researchers have in recent years developed a variety of techniques and models to help us understand or predict the behavior of these systems. Here we review developments in this field

Apoptosis: a Basic Biological Phenomenon with Wide-ranging Implications in Tissue Kinetics

by J. F. R. Kerr, A. H. Wyllie, A. R. Curriet - Br. J. Cancer , 1972
"... Summary.-The term apoptosis is proposed for a hitherto little recognized mechanism of controlled cell deletion, which appears to play a complementary but opposite role to mitosis in the regulation of animal cell populations. Its morphological features suggest that it is an active, inherently program ..."
Abstract - Cited by 641 (6 self) - Add to MetaCart
programmed phenomenon, and it has been shown that it can be initiated or inhibited by a variety of environmental stimuli, both physiological and pathological. The structural changes take place in two discrete stages. The first comprises nuclear and cytoplasmic condensation and breaking up of the cell into a

Hidden Markov models in computational biology: applications to protein modeling

by Anders Krogh, Michael Brown, I. Saira Mian, Kimmen Sjölander, David Haussler - JOURNAL OF MOLECULAR BIOLOGY , 1994
"... Hidden.Markov Models (HMMs) are applied t.0 the problems of statistical modeling, database searching and multiple sequence alignment of protein families and protein domains. These methods are demonstrated the on globin family, the protein kinase catalytic domain, and the EF-hand calcium binding moti ..."
Abstract - Cited by 655 (39 self) - Add to MetaCart
protein family, or contain the given domain. The Hi " produces multiple alignments of good quality that agree closely with the alignments produced by programs that incorporate three-dimensional structural information. When employed in discrimination tests (by examining how closely the sequences in a

Large margin methods for structured and interdependent output variables

by Ioannis Tsochantaridis, Thorsten Joachims, Thomas Hofmann, Yasemin Altun - JOURNAL OF MACHINE LEARNING RESEARCH , 2005
"... Learning general functional dependencies between arbitrary input and output spaces is one of the key challenges in computational intelligence. While recent progress in machine learning has mainly focused on designing flexible and powerful input representations, this paper addresses the complementary ..."
Abstract - Cited by 624 (12 self) - Add to MetaCart
the complementary issue of designing classification algorithms that can deal with more complex outputs, such as trees, sequences, or sets. More generally, we consider problems involving multiple dependent output variables, structured output spaces, and classification problems with class attributes. In order

Deformable models in medical image analysis: A survey

by Tim Mcinerney, Demetri Terzopoulos - Medical Image Analysis , 1996
"... This article surveys deformable models, a promising and vigorously researched computer-assisted medical image analysis technique. Among model-based techniques, deformable models offer a unique and powerful approach to image analysis that combines geometry, physics, and approximation theory. They hav ..."
Abstract - Cited by 591 (7 self) - Add to MetaCart
the significant variability of biological structures over time and across different individuals. Furthermore, they support highly intuitive interaction mechanisms that, when necessary, allow medical scientists and practitioners to bring their expertise to bear on the model-based image interpretation task

The SWISS-MODEL Workspace: A web-based environment for protein structure homology modelling

by Konstantin Arnold, Lorenza Bordoli, Torsten Schwede, et al. - BIOINFORMATICS , 2005
"... Motivation: Homology models of proteins are of great interest for planning and analyzing biological experiments when no experimental three-dimensional structures are available. Building homology models requires specialized programs and up-to-date sequence and structural databases. Integrating all re ..."
Abstract - Cited by 575 (5 self) - Add to MetaCart
Motivation: Homology models of proteins are of great interest for planning and analyzing biological experiments when no experimental three-dimensional structures are available. Building homology models requires specialized programs and up-to-date sequence and structural databases. Integrating all

The Protein Data Bank

by Helen M. Berman, John Westbrook, Zukang Feng, Gary Gilliland, T. N. Bhat, Helge Weissig, Ilya N. Shindyalov, Philip E. Bourne - Nucleic Acids Res , 2000
"... The Protein Data Bank (PDB; http://www.rcsb.org/pdb/ ) is the single worldwide archive of structural data of biological macromolecules. This paper describes the goals of the PDB, the systems in place for data deposition and access, how to obtain further information, and near-term plans for the futur ..."
Abstract - Cited by 1387 (24 self) - Add to MetaCart
The Protein Data Bank (PDB; http://www.rcsb.org/pdb/ ) is the single worldwide archive of structural data of biological macromolecules. This paper describes the goals of the PDB, the systems in place for data deposition and access, how to obtain further information, and near-term plans

Edge Detection

by Ellen C. Hildreth , 1985
"... For both biological systems and machines, vision begins with a large and unwieldy array of measurements of the amount of light reflected from surfaces in the environment. The goal of vision is to recover physical properties of objects in the scene, such as the location of object boundaries and the s ..."
Abstract - Cited by 1287 (1 self) - Add to MetaCart
For both biological systems and machines, vision begins with a large and unwieldy array of measurements of the amount of light reflected from surfaces in the environment. The goal of vision is to recover physical properties of objects in the scene, such as the location of object boundaries

Evolving Neural Networks through Augmenting Topologies

by Kenneth O. Stanley, Risto Miikkulainen - Evolutionary Computation
"... An important question in neuroevolution is how to gain an advantage from evolving neural network topologies along with weights. We present a method, NeuroEvolution of Augmenting Topologies (NEAT), which outperforms the best fixed-topology method on a challenging benchmark reinforcement learning task ..."
Abstract - Cited by 536 (112 self) - Add to MetaCart
task. We claim that the increased efficiency is due to (1) employing a principled method of crossover of different topologies, (2) protecting structural innovation using speciation, and (3) incrementally growing from minimal structure. We test this claim through a series of ablation studies

Modeling and simulation of genetic regulatory systems: A literature review

by Hidde De Jong - JOURNAL OF COMPUTATIONAL BIOLOGY , 2002
"... In order to understand the functioning of organisms on the molecular level, we need to know which genes are expressed, when and where in the organism, and to which extent. The regulation of gene expression is achieved through genetic regulatory systems structured by networks of interactions between ..."
Abstract - Cited by 738 (14 self) - Add to MetaCart
In order to understand the functioning of organisms on the molecular level, we need to know which genes are expressed, when and where in the organism, and to which extent. The regulation of gene expression is achieved through genetic regulatory systems structured by networks of interactions between
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