From systems to biology: A computational analysis of the research articles on systems biology from 1992 to 2013

Zou, Yawen; Laubichler, Manfred D.

doi:10.1371/journal.pone.0200929

Cited by 9 publications

(6 citation statements)

References 36 publications

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“…Our framework presents a general approach to connect the molecular scale to the cell population scale. It is noteworthy that cancer cells have similar multi scale features in low scale (production of molecules from genes), intermediate scale (interaction of gene with its cellular environment) and high scale (collective behavior of cells) [42][43][44][45]. Our framework can incorporate these hallmarks to study the nature and phenotype of cancer cells.…”

Section: Discussionmentioning

confidence: 99%

Multicellular Models Bridging Intracellular Signaling and Gene Transcription to Population Dynamics

et al. 2018

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Cell signaling and gene transcription occur at faster time scales compared to cellular death, division, and evolution. Bridging these multiscale events in a model is computationally challenging. We introduce a framework for the systematic development of multiscale cell population models. Using message passing interface (MPI) parallelism, the framework creates a population model from a single-cell biochemical network model. It launches parallel simulations on a single-cell model and treats each stand-alone parallel process as a cell object. MPI mediates cell-to-cell and cell-to-environment communications in a server-client fashion. In the framework, model-specific higher level rules link the intracellular molecular events to cellular functions, such as death, division, or phenotype change. Cell death is implemented by terminating a parallel process, while cell division is carried out by creating a new process (daughter cell) from an existing one (mother cell). We first demonstrate these capabilities by creating two simple example models. In one model, we consider a relatively simple scenario where cells can evolve independently. In the other model, we consider interdependency among the cells, where cellular communication determines their collective behavior and evolution under a temporally evolving growth condition. We then demonstrate the framework’s capability by simulating a full-scale model of bacterial quorum sensing, where the dynamics of a population of bacterial cells is dictated by the intercellular communications in a time-evolving growth environment.

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Section: Discussionmentioning

confidence: 99%

Multicellular Models Bridging Intracellular Signaling and Gene Transcription to Population Dynamics

et al. 2018

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“…In practice, system biology is simply the application of dynamical complex system concepts to the molecular metabolism using a sophisticated computerized approach, named the computational model ( Baitaluk, 2009 ; Tavassoly et al, 2018 ; Zou and Laubichler, 2018 ). The theory of self-organized systems means the possibility to understand the internal logic of life, through the manifestations of cellular metabolism ( Schrodinger, 1944 ).…”

Section: Semantic Nihilism and The Turing Machinementioning

confidence: 99%

Bionetworks, system biology, and superorganisms

Nicoletti¹

2020

Insect-Borne Diseases in the 21st Century

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“…The scientometric analysis and knowledge mapping was conducted with the software Citespace (v5.0 R2, Drexel University, Pennsylvania, USA). It is a Java-based, user friendly software that allows for knowledge mapping by visualization of bibliographic data [33][34][35][36][37][38]. The knowledge mapping in present study was predominantly based on the theory of co-citation analysis which considers a significant relationship between two or more articles when they are cited together in another publication [22,23].…”

Section: Scientometric Analysismentioning

confidence: 99%

A scientometric analysis of birth cohorts in South Asia: Way forward for Pakistan

Waqas

Zafar²,

Lawlor

et al. 2020

PLoS ONE

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The present study aims to: a) systematically map the of birth cohort studies from the South Asian region b) examine the major research foci and landmark contributions from these cohorts using reproducible scientometric techniques and c) offer recommendations on establishing new birth cohorts in Pakistan, building upon the strengths, weaknesses and gaps of previous cohorts. Bibliographic records for a total of 260 articles, published during through December 2018, were retrieved from the Web of Science (core database). All data were analysed using Microsoft Excel (2013), Web of Science platform and CiteSpace. A series of network analysis were then run for each time-period using the link reduction method and pathfinder network scaling. The co-cited articles were clustered into their homogeneous research clusters. The clusters were named using the Latent Semantic Indexing (LSI) method that utilized author keywords as source of names for these clusters. The scientometric analyses of original research output from these birth cohorts also paint a pessimistic landscape in Pakistan-where Pakistani sites for birth cohorts contributed only 31 publications; a majority of these utilized the MAL-ED birth cohort data. A majority of original studies were published from birth cohorts in India (156), Bangladesh (63), and Nepal (15). Out of these contributions, 31 studies reported data from multiple countries. The three major birth cohorts include prospective and multi-country MAL-ED birth cohort and The Pakistan Early Childhood Development Scale Up Trial, and a retrospective Maternal and infant nutrition intervention cohort. In addition to these, a few small-scale birth cohorts reported findings pertaining to neonatal sepsis, intrauterine growth retardation and its effects on linear growth of children and environmental enteropathy.

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From systems to biology: A computational analysis of the research articles on systems biology from 1992 to 2013

Cited by 9 publications

References 36 publications

Multicellular Models Bridging Intracellular Signaling and Gene Transcription to Population Dynamics

Multicellular Models Bridging Intracellular Signaling and Gene Transcription to Population Dynamics

Bionetworks, system biology, and superorganisms

A scientometric analysis of birth cohorts in South Asia: Way forward for Pakistan

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