Perturbation biology: inferring signaling networks in cellular systems (Q28537769)

16

0 references

Martin L Miller

Martin L Miller

4

0 references

Alfredo Braunstein

Alfredo Braunstein

13

0 references

Andrea Pagnani

Andrea Pagnani

14

0 references

Martin Weigt

Martin Weigt

12

0 references

Riccardo Zecchina

Riccardo Zecchina

15

0 references

Christine A Pratilas

11

Christine A Pratilas

0 references

Gordon B. Mills

9

Gordon Mills

0 references

author name string

Evan J Molinelli

1

0 references

Anil Korkut

2

0 references

Weiqing Wang

3

0 references

Nicholas P Gauthier

5

0 references

Xiaohong Jing

6

0 references

Poorvi Kaushik

7

0 references

Qin He

8

0 references

David B Solit

PLOS Computational Biology

10

0 references

language of work or name

English

0 references

publication date

2013

0 references

published in

0 references

volume

9

0 references

issue

12

0 references

page(s)

e1003290

0 references

copyright license

Creative Commons Attribution 4.0 International

start time

19 December 2013

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

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Rb-Raf-1 interaction disruptor RRD-251 induces apoptosis in metastatic melanoma cells and synergizes with dacarbazine

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A mitotic phosphorylation feedback network connects Cdk1, Plk1, 53BP1, and Chk2 to inactivate the G(2)/M DNA damage checkpoint

19 March 2017

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Extended kalman filter for estimation of parameters in nonlinear state-space models of biochemical networks

19 March 2017

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Survival of the sparsest: robust gene networks are parsimonious

19 March 2017

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Computationally derived points of fragility of a human cascade are consistent with current therapeutic strategies

19 March 2017

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Roles of the Raf/MEK/ERK pathway in cell growth, malignant transformation and drug resistance

19 March 2017

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Chemogenomic profiling on a genome-wide scale using reverse-engineered gene networks

19 March 2017

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Genetic interaction between Rb and K-ras in the control of differentiation and tumor suppression

19 March 2017

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EGF receptor gene mutations are common in lung cancers from "never smokers" and are associated with sensitivity of tumors to gefitinib and erlotinib

19 March 2017

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EGFR mutations in lung cancer: correlation with clinical response to gefitinib therapy

19 March 2017

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Activating mutations in the epidermal growth factor receptor underlying responsiveness of non-small-cell lung cancer to gefitinib

19 March 2017

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Inferring genetic networks and identifying compound mode of action via expression profiling

19 March 2017

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Structural basis for the autoinhibition of c-Abl tyrosine kinase

19 March 2017

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Automated modelling of signal transduction networks

19 March 2017

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The phosphoinositide 3-kinase pathway

19 March 2017

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Efficacy and safety of a specific inhibitor of the BCR-ABL tyrosine kinase in chronic myeloid leukemia

19 March 2017

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COT drives resistance to RAF inhibition through MAP kinase pathway reactivation

7 April 2017

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PI3K pathway alterations in cancer: variations on a theme

7 April 2017

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BRAF mutation predicts sensitivity to MEK inhibition

7 April 2017

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Abiraterone and increased survival in metastatic prostate cancer

7 April 2017

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7 April 2017

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Drug synergy screen and network modeling in dedifferentiated liposarcoma identifies CDK4 and IGF1R as synergistic drug targets.

7 April 2017

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Crowdsourcing network inference: the DREAM predictive signaling network challenge

29 September 2017

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Concurrent loss of the PTEN and RB1 tumor suppressors attenuates RAF dependence in melanomas harboring (V600E)BRAF

29 September 2017

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AKT inhibition relieves feedback suppression of receptor tyrosine kinase expression and activity

29 September 2017

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Gene regulatory networks from multifactorial perturbations using Graphical Lasso: application to the DREAM4 challenge

29 September 2017

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Multifaceted polo-like kinases: drug targets and antitargets for cancer therapy

29 September 2017

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29 September 2017

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Ligand-specific c-Fos expression emerges from the spatiotemporal control of ErbB network dynamics

29 September 2017

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Protein dynamics in drug combinations: a linear superposition of individual-drug responses

29 September 2017

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Identification of crosstalk between phosphoprotein signaling pathways in RAW 264.7 macrophage cells

29 September 2017

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Reconstructing nonlinear dynamic models of gene regulation using stochastic sampling

29 September 2017

1 reference

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Computational modeling of the EGFR network elucidates control mechanisms regulating signal dynamics

29 September 2017

1 reference

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Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction

29 September 2017

1 reference

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(V600E)BRAF is associated with disabled feedback inhibition of RAF-MEK signaling and elevated transcriptional output of the pathway

29 September 2017

1 reference

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A factor graph nested effects model to identify networks from genetic perturbations

29 September 2017

1 reference

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Single-agent and combination therapeutic strategies to inhibit hepatocyte growth factor/MET signaling in cancer

29 September 2017

1 reference

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Models from experiments: combinatorial drug perturbations of cancer cells

29 September 2017

1 reference

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Clustering by soft-constraint affinity propagation: applications to gene-expression data

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3868523

Clustering by passing messages between data points

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3868523

Using the principle of entropy maximization to infer genetic interaction networks from gene expression patterns

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3868523

Physicochemical modelling of cell signalling pathways.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3868523

Reverse phase protein array: validation of a novel proteomic technology and utility for analysis of primary leukemia specimens and hematopoietic stem cells

29 September 2017

1 reference

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Parameter estimation using Simulated Annealing for S-system models of biochemical networks

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3868523

Applying computational modeling to drug discovery and development

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3868523

The application of systems biology to drug discovery

29 September 2017

1 reference

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Multiple signaling pathways must be targeted to overcome drug resistance in cell lines derived from melanoma metastases

29 September 2017

1 reference

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The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3868523

Histone deacetylase 3 localizes to the plasma membrane and is a substrate of Src.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3868523

Disruption of the Rb--Raf-1 interaction inhibits tumor growth and angiogenesis

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3868523

Data-driven computer simulation of human cancer cell

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3868523

SRC gene expression in human cancer: the role of transcriptional activation

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3868523

Rb and N-ras function together to control differentiation in the mouse

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3868523

Reverse engineering gene networks using singular value decomposition and robust regression

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3868523

Computational modeling of the dynamics of the MAP kinase cascade activated by surface and internalized EGF receptors

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3868523

Genetic network inference: from co-expression clustering to reverse engineering

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3868523

Systems biology and combination therapy in the quest for clinical efficacy.

29 September 2017

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Combinatorial complexity of pathway analysis in metabolic networks.

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Analytic and algorithmic solution of random satisfiability problems.

21 January 2018

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Polynomial iterative algorithms for coloring and analyzing random graphs.

21 January 2018

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Genetic network identification using convex programming.

21 January 2018

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On the sparse reconstruction of gene networks.

21 January 2018

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Time-varying modeling of gene expression regulatory networks using the wavelet dynamic vector autoregressive method

21 January 2018

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Inferring gene regulatory networks from multiple microarray datasets

21 January 2018

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Solvable Model of a Spin-Glass

21 January 2018

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Factor graphs and the sum-product algorithm

21 January 2018

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Survey propagation: An algorithm for satisfiability

21 January 2018

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Learning by message passing in networks of discrete synapses.

21 January 2018

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GeNGe: systematic generation of gene regulatory networks

21 January 2018

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Causal inference in statistics: An overview

21 January 2018

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An error model for protein quantification

21 January 2018

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Inference algorithms for gene networks: a statistical mechanics analysis

21 January 2018

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Modeling regulatory networks with weight matrices

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3868523

Generalization of back-propagation to recurrent neural networks

27 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24367245

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Nras loss induces metastatic conversion of Rb1-deficient neuroendocrine thyroid tumor

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24367245

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Bayesian Learning for Neural Networks

1 reference

31 March 2022

https://opencitations.net/index/coci/api/v1/references/10.1371/JOURNAL.PCBI.1003290

Identifiers

DOI

10.1371/JOURNAL.PCBI.1003290

1 reference

journals/ploscb/MolinelliKWMGJKHMSPWBPZS13

1 reference

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1593150

1 reference

1 reference

1593150

PubMed publication ID

24367245

1 reference