Literature DB >> 21917716

Systems biology--biomedical modeling.

Eric A Sobie1, Young-Seon Lee, Sherry L Jenkins, Ravi Iyengar.   

Abstract

Because of the complexity inherent in biological systems, many researchers frequently rely on a combination of global analysis and computational approaches to gain insight into both (i) how interacting components can produce complex system behaviors, and (ii) how changes in conditions may alter these behaviors. Because the biological details of a particular system are generally not taught along with the quantitative approaches that enable hypothesis generation and analysis of the system, we developed a course at Mount Sinai School of Medicine that introduces first-year graduate students to these computational principles and approaches. We anticipate that such approaches will apply throughout the biomedical sciences and that courses such as the one described here will become a core requirement of many graduate programs in the biological and biomedical sciences.

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Year:  2011        PMID: 21917716      PMCID: PMC3188945          DOI: 10.1126/scisignal.2001989

Source DB:  PubMed          Journal:  Sci Signal        ISSN: 1945-0877            Impact factor:   8.192


  15 in total

Review 1.  The Virtual Cell: a software environment for computational cell biology.

Authors:  L M Loew; J C Schaff
Journal:  Trends Biotechnol       Date:  2001-10       Impact factor: 19.536

2.  Network motifs: simple building blocks of complex networks.

Authors:  R Milo; S Shen-Orr; S Itzkovitz; N Kashtan; D Chklovskii; U Alon
Journal:  Science       Date:  2002-10-25       Impact factor: 47.728

3.  ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments.

Authors:  Alexander Lachmann; Huilei Xu; Jayanth Krishnan; Seth I Berger; Amin R Mazloom; Avi Ma'ayan
Journal:  Bioinformatics       Date:  2010-08-13       Impact factor: 6.937

4.  A systems model of signaling identifies a molecular basis set for cytokine-induced apoptosis.

Authors:  Kevin A Janes; John G Albeck; Suzanne Gaudet; Peter K Sorger; Douglas A Lauffenburger; Michael B Yaffe
Journal:  Science       Date:  2005-12-09       Impact factor: 47.728

5.  AVIS: AJAX viewer of interactive signaling networks.

Authors:  Seth I Berger; Ravi Iyengar; Avi Ma'ayan
Journal:  Bioinformatics       Date:  2007-09-12       Impact factor: 6.937

6.  Mapping and quantifying mammalian transcriptomes by RNA-Seq.

Authors:  Ali Mortazavi; Brian A Williams; Kenneth McCue; Lorian Schaeffer; Barbara Wold
Journal:  Nat Methods       Date:  2008-05-30       Impact factor: 28.547

7.  Emergent properties of networks of biological signaling pathways.

Authors:  U S Bhalla; R Iyengar
Journal:  Science       Date:  1999-01-15       Impact factor: 47.728

Review 8.  Exploring the new world of the genome with DNA microarrays.

Authors:  P O Brown; D Botstein
Journal:  Nat Genet       Date:  1999-01       Impact factor: 38.330

9.  The response of human epithelial cells to TNF involves an inducible autocrine cascade.

Authors:  Kevin A Janes; Suzanne Gaudet; John G Albeck; Ulrik B Nielsen; Douglas A Lauffenburger; Peter K Sorger
Journal:  Cell       Date:  2006-03-24       Impact factor: 41.582

10.  Genes2Networks: connecting lists of gene symbols using mammalian protein interactions databases.

Authors:  Seth I Berger; Jeremy M Posner; Avi Ma'ayan
Journal:  BMC Bioinformatics       Date:  2007-10-04       Impact factor: 3.169

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  7 in total

Review 1.  The emerging paradigm of network medicine in the study of human disease.

Authors:  Stephen Y Chan; Joseph Loscalzo
Journal:  Circ Res       Date:  2012-07-20       Impact factor: 17.367

Review 2.  Systems Biology Approaches to Redox Metabolism in Stress and Disease States.

Authors:  Rui-Sheng Wang; William M Oldham; Bradley A Maron; Joseph Loscalzo
Journal:  Antioxid Redox Signal       Date:  2017-12-20       Impact factor: 8.401

Review 3.  Systems medicine: evolution of systems biology from bench to bedside.

Authors:  Rui-Sheng Wang; Bradley A Maron; Joseph Loscalzo
Journal:  Wiley Interdiscip Rev Syst Biol Med       Date:  2015-04-17

4.  Network modeling of TGFβ signaling in hepatocellular carcinoma epithelial-to-mesenchymal transition reveals joint sonic hedgehog and Wnt pathway activation.

Authors:  Steven Nathaniel Steinway; Jorge G T Zañudo; Wei Ding; Carl Bart Rountree; David J Feith; Thomas P Loughran; Reka Albert
Journal:  Cancer Res       Date:  2014-09-04       Impact factor: 12.701

Review 5.  Advanced systems biology methods in drug discovery and translational biomedicine.

Authors:  Jun Zou; Ming-Wu Zheng; Gen Li; Zhi-Guang Su
Journal:  Biomed Res Int       Date:  2013-09-19       Impact factor: 3.411

6.  Quantifying the relative importance of experimental data points in parameter estimation.

Authors:  Jenny E Jeong; Peng Qiu
Journal:  BMC Syst Biol       Date:  2018-11-22

Review 7.  Genomics, microbiomics, proteomics, and metabolomics in bronchopulmonary dysplasia.

Authors:  Charitharth Vivek Lal; Vineet Bhandari; Namasivayam Ambalavanan
Journal:  Semin Perinatol       Date:  2018-10-02       Impact factor: 3.300

  7 in total

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