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Book ; Online: Diagrammatic Rules for Triad Census

Borriello, Enrico

2024

Abstract: In network theory, a triad census is a method designed to categorize and enumerate the various types of subgraphs with three nodes and their connecting edges within a network. Triads serve as fundamental building blocks for comprehending the structure ... ...

Abstract	In network theory, a triad census is a method designed to categorize and enumerate the various types of subgraphs with three nodes and their connecting edges within a network. Triads serve as fundamental building blocks for comprehending the structure and dynamics of networks, and the triad census offers a systematic approach to their classification. Typically, triad counts are obtained numerically, but lesser-known methods have been developed to precisely evaluate them without the need for sampling. In our study, we build upon Moody's matrix approach, presenting general diagrammatic rules that systematically and intuitively generate closed formulas for the occurrence numbers of triads in a network. Comment: 15 pages, 1 figures
Keywords	Physics - Physics and Society ; Computer Science - Social and Information Networks
Publishing date	2024-01-14
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: The basis of easy controllability in Boolean networks.

Borriello, Enrico / Daniels, Bryan C

Nature communications

2021 Volume 12, Issue 1, Page(s) 5227

Abstract: Effective control of biological systems can often be achieved through the control of a surprisingly small number of distinct variables. We bring clarity to such results using the formalism of Boolean dynamical networks, analyzing the effectiveness of ... ...

Abstract	Effective control of biological systems can often be achieved through the control of a surprisingly small number of distinct variables. We bring clarity to such results using the formalism of Boolean dynamical networks, analyzing the effectiveness of external control in selecting a desired final state when that state is among the original attractors of the dynamics. Analyzing 49 existing biological network models, we find strong numerical evidence that the average number of nodes that must be forced scales logarithmically with the number of original attractors. This suggests that biological networks may be typically easy to control even when the number of interacting components is large. We provide a theoretical explanation of the scaling by separating controlling nodes into three types: those that act as inputs, those that distinguish among attractors, and any remaining nodes. We further identify characteristics of dynamics that can invalidate this scaling, and speculate about how this relates more broadly to non-biological systems.
MeSH term(s)	Algorithms ; Models, Biological ; Models, Genetic
Language	English
Publishing date	2021-09-01
Publishing country	England
Document type	Journal Article
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-021-25533-3
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Evolution of default genetic control mechanisms.

Bains, William / Borriello, Enrico / Schulze-Makuch, Dirk

PloS one

2021 Volume 16, Issue 5, Page(s) e0251568

Abstract: We present a model of the evolution of control systems in a genome under environmental constraints. The model conceptually follows the Jacob and Monod model of gene control. Genes contain control elements which respond to the internal state of the cell ... ...

Abstract	We present a model of the evolution of control systems in a genome under environmental constraints. The model conceptually follows the Jacob and Monod model of gene control. Genes contain control elements which respond to the internal state of the cell as well as the environment to control expression of a coding region. Control and coding regions evolve to maximize a fitness function between expressed coding sequences and the environment. The model was run 118 times to an average of 1.4∙106 'generations' each with a range of starting parameters probed the conditions under which genomes evolved a 'default style' of control. Unexpectedly, the control logic that evolved was not significantly correlated to the complexity of the environment. Genetic logic was strongly correlated with genome complexity and with the fraction of genes active in the cell at any one time. More complex genomes correlated with the evolution of genetic controls in which genes were active ('default on'), and a low fraction of genes being expressed correlated with a genetic logic in which genes were biased to being inactive unless positively activated ('default off' logic). We discuss how this might relate to the evolution of the complex eukaryotic genome, which operates in a 'default off' mode.
MeSH term(s)	Animals ; Evolution, Molecular ; Gene Expression Regulation ; Gene-Environment Interaction ; Genome ; Humans ; Models, Genetic
Language	English
Publishing date	2021-05-13
Publishing country	United States
Document type	Journal Article
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0251568
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Book ; Online: The basis of easy controllability in Boolean networks

Borriello, Enrico / Daniels, Bryan C.

2020

Abstract	Effective control of biological systems can often be achieved through the control of a surprisingly small number of distinct variables. We bring clarity to such results using the formalism of Boolean dynamical networks, analyzing the effectiveness of external control in selecting a desired final state when that state is among the original attractors of the dynamics. Analyzing 49 existing biological network models, we find strong numerical evidence that the average number of nodes that must be forced scales logarithmically with the number of original attractors. This suggests that biological networks may be typically easy to control even when the number of interacting components is large. We provide a theoretical explanation of the scaling by separating controlling nodes into three types: those that act as inputs, those that distinguish among attractors, and any remaining nodes. We further identify characteristics of dynamics that can invalidate this scaling, and speculate about how this relates more broadly to non-biological systems. Comment: 44 pages, 17 figures, 2 table
Keywords	Quantitative Biology - Molecular Networks
Subject code	612
Publishing date	2020-10-22
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Cell phenotypes as macrostates of the GRN dynamics.

Borriello, Enrico / Walker, Sara I / Laubichler, Manfred D

Journal of experimental zoology. Part B, Molecular and developmental evolution

2020 Volume 334, Issue 4, Page(s) 213–224

Abstract: The two most fundamental processes describing change in biology, development, and evolution, occur over drastically different timescales. Development involves temporal sequences of cell states controlled by hierarchies of regulatory structures. It occurs ...

Abstract	The two most fundamental processes describing change in biology, development, and evolution, occur over drastically different timescales. Development involves temporal sequences of cell states controlled by hierarchies of regulatory structures. It occurs over the lifetime of a single individual and is associated with gene expression level change of a given genotype. Evolution, by contrast, entails genotypic change through mutation, the acquisition/loss of genes and changes in the network topology of interactions among genes. It involves the emergence of new, environmentally selected phenotypes over the lifetimes of many individuals. We start by reviewing the most limiting aspects of the theoretical modeling of gene regulatory networks (GRNs) which prevent the study of both timescales in a common, mathematical language. We then consider the simple framework of Boolean network models of GRNs and point out its inadequacy to include evolutionary processes. As opposed to one-to-one maps to specific attractors, we adopt a many-to-one map which makes each phenotype correspond to multiple attractors. This definition no longer requires a fixed size for the genotype and opens the possibility for modeling the phenotypic change of a genotype, which is itself changing over evolutionary timescales. At the same time, we show that this generalized framework does not interfere with established numerical techniques for the identification of the kernel of controlling nodes responsible for cell differentiation through external signals.
MeSH term(s)	Animals ; Biological Evolution ; Gene Expression Regulation/physiology ; Gene Regulatory Networks ; Models, Biological ; Signal Transduction
Language	English
Publishing date	2020-03-10
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	2103823-5
ISSN	1552-5015 ; 0022-104X ; 1552-5007
ISSN (online)	1552-5015
ISSN	0022-104X ; 1552-5007
DOI	10.1002/jez.b.22938
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Book ; Online: Evolution of default genetic control mechanisms

Bains, William / Borriello, Enrico / Schulze-Makuch, Dirk

2021

Abstract	We present a model of the evolution of control systems in a genome under environmental constraints. The model conceptually follows the Jacob and Monod model of gene control. Genes contain control elements which respond to the internal state of the cell as well as the environment to control expression of a coding region. Control and coding regions evolve to maximize a fitness function between expressed coding sequences and the environment. 118 runs of the model run to an average of 1.4 x 10^6 `generations' each with a range of starting parameters probed the conditions under which genomes evolved a `default style' of control. Unexpectedly, the control logic that evolved was not significantly correlated to the complexity of the environment. Genetic logic was strongly correlated with genome complexity and with the fraction of genes active in the cell at any one time. More complex genomes correlated with the evolution of genetic controls in which genes were active (`default on'), and a low fraction of genes being expressed correlated with a genetic logic in which genes were biased to being inactive unless positively activated (`default off' logic). We discuss how this might relate to the evolution of the complex eukaryotic genome, which operates in a `default off' mode. Comment: 25 pages, 8 figures, 1 table
Keywords	Quantitative Biology - Genomics
Subject code	612
Publishing date	2021-01-08
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Book ; Online: A unified formal framework for developmental andevolutionary change in gene regulatory network models

Borriello, Enrico / Walker, Sara I. / Laubichler, Manfred D.

2018

Abstract: The two most fundamental processes describing change in biology, development and evolu-tion, occur over drastically different timescales, difficult to reconcile within a unified framework. Development involves temporal sequences of cell states controlled ...

Abstract	The two most fundamental processes describing change in biology, development and evolu-tion, occur over drastically different timescales, difficult to reconcile within a unified framework. Development involves temporal sequences of cell states controlled by hierarchies of regulatory structures. It occurs over the lifetime of a single individual, and is associated to the gene expression level change of a given genotype. Evolution, by contrast entails genotypic change through the acquisition/loss of genes and changes in the network topology of interactions among genes. It involves the emergence of new, environmentally selected phenotypes over the lifetimes of many individuals. Here we present a model of regulatory network evolution that accounts for both timescales. We extend the framework of Boolean models of gene regulatory networks (GRN)-currently only applicable to describing development to include evolutionary processes. As opposed to one-to-one maps to specific attractors, we identify the phenotypes of the cells as the relevant macrostates of the GRN. A phenotype may now correspond to multiple attractors, and its formal definition no longer requires a fixed size for the genotype. This opens the possibility for a quantitative study of the phenotypic change of a genotype, which is itself changing over evolutionary timescales. We show how the realization of specific phenotypes can be controlled by gene duplication events (used here as an archetypal evolutionary event able to change the genotype), and how successive events of gene duplication lead to new regulatory structures via selection. At the same time, we show that our generalized framework does not inhibit network controllability and the possibility for network control theory to describe epigenetic signaling during development. Comment: 13 pages, 4 figures, 1 table
Keywords	Physics - Biological Physics ; Quantitative Biology - Populations and Evolution
Subject code	612
Publishing date	2018-09-07
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Book ; Online: The mass-hierarchy and CP-violation discovery reach of the LBNO long-baseline neutrino experiment

Collaboration, LAGUNA-LBNO / : / Agarwalla, S. K. / Agostino, L. / Aittola, M. / Alekou, A. / Andrieu, B. / Angus, D. / Antoniou, F. / Ariga, A. / Ariga, T. / Asfandiyarov, R. / Autiero, D. / Ballett, P. / Bandac, I. / Banerjee, D. / Barker, G. J. / Barr, G. / Bartmann, W. /

Bay, F. / Berardi, V. / Bertram, I. / Bésida, O. / Blebea-Apostu, A. M. / Blondel, A. / Bogomilov, M. / Borriello, E. / Boyd, S. / Brancus, I. / Bravar, A. / Buizza-Avanzini, M. / Cafagna, F. / Calin, M. / Calviani, M. / Campanelli, M. / Cantini, C. / Caretta, O. / Cata-Danil, G. / Catanesi, M. G. / Cervera, A. / Chakraborty, S. / Chaussard, L. / Chesneanu, D. / Chipesiu, F. / Christodoulou, G. / Coleman, J. / Crivelli, P. / Davenne, T. / Dawson, J. / De Bonis, I. / De Jong, J. / Déclais, Y. / Sanchez, P. Del Amo / Delbart, A. / Densham, C. / Di Lodovico, F. / Di Luise, S. / Duchesneau, D. / Dumarchez, J. / Efthymiopoulos, I. / Eliseev, A. / Emery, S. / Enqvist, K. / Enqvist, T. / Epprecht, L. / Ereditato, A. / Erykalov, A. N. / Esanu, T. / Finch, A. J. / Fitton, M. D. / Franco, D. / Galymov, V. / Gavrilov, G. / Gendotti, A. / Giganti, C. / Goddard, B. / Gomez, J. J. / Gomoiu, C. M. / Gornushkin, Y. A. / Gorodetzky, P. / Grant, N. / Haesler, A. / Haigh, M. D. / Hasegawa, T. / Haug, S. / Hierholzer, M. / Hissa, J. / Horikawa, S. / Huitu, K. / Ilic, J. / Ioannisian, A. N. / Izmaylov, A. / Jipa, A. / Kainulainen, K. / Kalliokoski, T. / Karadzhov, Y. / Kawada, J. / Khabibullin, M. / Khotjantsev, A. / Kokko, E. / Kopylov, A. N. / Kormos, L. L. / Korzenev, A. / Kosyanenko, S. / Kreslo, I. / Kryn, D. / Kudenko, Y. / Kudryavtsev, V. A. / Kumpulainen, J. / Kuusiniemi, P. / Lagoda, J. / Lazanu, I. / Levy, J. -M. / Litchfield, R. P. / Loo, K. / Loveridge, P. / Maalampi, J. / Magaletti, L. / Margineanu, R. M. / Marteau, J. / Martin-Mari, C. / Matveev, V. / Mavrokoridis, K. / Mazzucato, E. / McCauley, N. / Mercadante, A. / Mineev, O. / Mirizzi, A. / Mitrica, B. / Morgan, B. / Murdoch, M. / Murphy, S. / Mursula, K. / Narita, S. / Nesterenko, D. A. / Nguyen, K. / Nikolics, K. / Noah, E. / Novikov, Yu. / O'Keeffe, H. / Odell, J. / Oprima, A. / Palladino, V. / Papaphilippou, Y. / Pascoli, S. / Patzak, T. / Payne, D. / Pectu, M. / Pennacchio, E. / Periale, L. / Pessard, H. / Pistillo, C. / Popov, B. / Przewlocki, P. / Quinto, M. / Radicioni, E. / Ramachers, Y. / Ratoff, P. N. / Ravonel, M. / Rayner, M. / Resnati, F. / Ristea, O. / Robert, A. / Rondio, E. / Rubbia, A. / Rummukainen, K. / Sacco, R. / Saftoiu, A. / Sakashita, K. / Sarkamo, J. / Sato, F. / Saviano, N. / Scantamburlo, E. / Sergiampietri, F. / Sgalaberna, D. / Shaposhnikova, E. / Slupecki, M. / Sorel, M. / Spooner, N. J. C. / Stahl, A. / Stanca, D. / Steerenberg, R. / Sterian, A. R. / Sterian, P. / Still, B. / Stoica, S. / Strauss, T. / Suhonen, J. / Suvorov, V. / Szeptycka, M. / Terri, R. / Thompson, L. F. / Toma, G. / Tonazzo, A. / Touramanis, C. / Trzaska, W. H. / Tsenov, R. / Tuominen, K. / Vacheret, A. / Valram, M. / Vankova-Kirilova, G. / Vanucci, F. / Vasseur, G. / Velotti, F. / Velten, P. / Viant, T. / Vincke, H. / Virtanen, A. / Vorobyev, A. / Wark, D. / Weber, A. / Weber, M. / Wiebusch, C. / Wilson, J. R. / Wu, S. / Yershov, N. / Zalipska, J. / Zito, M.

2013

Abstract: The next generation neutrino observatory proposed by the LBNO collaboration will address fundamental questions in particle and astroparticle physics. The experiment consists of a far detector, in its first stage a 20 kt LAr double phase TPC and a ... ...

Abstract	The next generation neutrino observatory proposed by the LBNO collaboration will address fundamental questions in particle and astroparticle physics. The experiment consists of a far detector, in its first stage a 20 kt LAr double phase TPC and a magnetised iron calorimeter, situated at 2300 km from CERN and a near detector based on a high-pressure argon gas TPC. The long baseline provides a unique opportunity to study neutrino flavour oscillations over their 1st and 2nd oscillation maxima exploring the $L/E$ behaviour, and distinguishing effects arising from $\delta_{CP}$ and matter. In this paper we have reevaluated the physics potential of this setup for determining the mass hierarchy (MH) and discovering CP-violation (CPV), using a conventional neutrino beam from the CERN SPS with a power of 750 kW. We use conservative assumptions on the knowledge of oscillation parameter priors and systematic uncertainties. The impact of each systematic error and the precision of oscillation prior is shown. We demonstrate that the first stage of LBNO can determine unambiguously the MH to $>5\sigma$C.L. over the whole phase space. We show that the statistical treatment of the experiment is of very high importance, resulting in the conclusion that LBNO has $\sim$ 100% probability to determine the MH in at most 4-5 years of running. Since the knowledge of MH is indispensable to extract $\delta_{CP}$ from the data, the first LBNO phase can convincingly give evidence for CPV on the $3\sigma$C.L. using today's knowledge on oscillation parameters and realistic assumptions on the systematic uncertainties. Comment: 35 pages, 22 figures, added authors
Keywords	High Energy Physics - Phenomenology
Subject code	621
Publishing date	2013-12-23
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Book: L' azimut Mezzogiorno

Borriello, Edoardo

Author's details	Edoardo Borriello
Keywords	Entwicklungspolitik ; Italien ; Süditalien
Size	143 S
Publisher	Ed. Sradapress
Publishing place	o. O
Document type	Book
Database	ECONomics Information System

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