-
P.
Bamborough,
D.
Drewry,
G.
Harper,
Gary
Smith,
K.
Schneider
(2008)
Assessment of chemical coverage of kinome space and its implications for kinase drug discovery.
Journal of medicinal chemistry, 51 24
-
D.
Parkin,
F.
Bray,
J.
Ferlay,
P.
Pisani
(2005)
Global Cancer Statistics, 2002
CA: A Cancer Journal for Clinicians, 55
-
B.
Fuchs,
T.
Fujii,
J.
Dorfman,
Jonathan
Goodwin,
A.
Zhu,
M.
Lanuti,
K.
Tanabe
(2008)
Epithelial-to-mesenchymal transition and integrin-linked kinase mediate sensitivity to epidermal growth factor receptor inhibition in human hepatoma cells.
Cancer research, 68 7
-
M.
Cusick,
Haiyuan
Yu,
A.
Smolyar,
K.
Venkatesan,
Anne-Ruxandra
Carvunis,
Nicolas
Simonis,
Jean-François
Rual,
Heather
Borick,
P.
Braun,
Matija
Dreze,
M.
Galli,
J.
Yazaki,
D.
Hill,
J.
Ecker,
F.
Roth,
M.
Vidal
(2009)
Literature-curated protein interaction datasets
Nature methods, 6
-
Annalisa
Petrelli,
Silvia
Giordano
(2008)
From single- to multi-target drugs in cancer therapy: when aspecificity becomes an advantage.
Current medicinal chemistry, 15 5
-
(2009)
BMC Systems Biology BioMed Central Methodology article
-
Haluk
Yuzugullu,
K.
Benhaj,
Nuri
Ozturk,
S.
Senturk,
Emine
Celik,
A.
Toylu,
Nilgun
Tasdemir,
Mustafa
Yilmaz,
E.
Erdal,
K.
Akcali,
N.
Atabey,
M.
Ozturk
(2009)
Canonical Wnt signaling is antagonized by noncanonical Wnt5a in hepatocellular carcinoma cells
Molecular Cancer, 8
-
J.
Schwacke,
Eberhard
Voit,
Email
John,
O.
Voit
(2004)
Theoretical Biology and Medical Modelling Open Access Improved Methods for the Mathematically Controlled Comparison of Biochemical Systems
-
M.
Cusick,
Niels
Klitgord,
M.
Vidal,
D.
Hill
(2005)
Interactome: gateway into systems biology.
Human molecular genetics, 14 Spec No. 2
-
C.
Jørgensen,
Andrew
Sherman,
Ginny
Chen,
A.
Pasculescu,
A.
Poliakov,
Marilyn
Hsiung,
B.
Larsen,
D.
Wilkinson,
R.
Linding,
T.
Pawson
(2009)
Cell-Specific Information Processing in Segregating Populations of Eph Receptor Ephrin–Expressing Cells
Science, 326
-
A.
Hopkins,
C.
Groom
(2002)
The druggable genome
Nature Reviews Drug Discovery, 1
-
A.
Jemal,
F.
Bray,
Melissa
Center,
J.
Ferlay,
Elizabeth
Ward,
D.
Forman
(2011)
Global cancer statistics
CA: A Cancer Journal for Clinicians, 61
-
T.
Przytycka,
Mona
Singh,
D.
Slonim
(2010)
Toward the dynamic interactome: it's about time
Briefings in bioinformatics, 11 1
-
(2011)
Cancer Res Cancer Research
-
L.
Alexopoulos,
J.
Sáez-Rodríguez,
B.
Cosgrove,
D.
Lauffenburger,
P.
Sorger
(2010)
Networks Inferred from Biochemical Data Reveal Profound Differences in Toll-like Receptor and Inflammatory Signaling between Normal and Transformed Hepatocytes*
Molecular & Cellular Proteomics : MCP, 9
-
J.
Sáez-Rodríguez,
Arthur
Goldsipe,
Jeremy
Muhlich,
L.
Alexopoulos,
Bjorn
Millard,
D.
Lauffenburger,
P.
Sorger
(2008)
Flexible informatics for linking experimental data to mathematical models via DataRail
Bioinformatics, 24 6
-
R.
Prill,
D.
Marbach,
J.
Sáez-Rodríguez,
P.
Sorger,
L.
Alexopoulos,
Xiaowei
Xue,
N.
Clarke,
G.
Altan-Bonnet,
G.
Stolovitzky
(2010)
Towards a Rigorous Assessment of Systems Biology Models: The DREAM3 Challenges
PLoS ONE, 5
-
Han-Yu
Chuang,
Eunjung
Lee,
Yu-Tsueng
Liu,
Doheon
Lee,
T.
Ideker
(2007)
Network-based classification of breast cancer metastasis
Molecular Systems Biology, 3
-
E.
Bonnet,
T.
Michoel,
Y.
Peer
(2010)
Prediction of a gene regulatory network linked to prostate cancer from gene expression, microRNA and clinical data
Bioinformatics, 26
-
J.
Uhm
(2010)
The transcriptional network for mesenchymal transformation of brain tumours
Yearbook of Neurology and Neurosurgery, 2010
-
Eiichi
Araki,
M.
Miralpeix
(1992)
Regulation of insulin receptor substrate-1 in liver and muscle of animal models of insulin resistance.
The Journal of clinical investigation, 90 5
-
A.
Bauer-Mehren,
L.
Furlong,
F.
Sanz
(2009)
Pathway databases and tools for their exploitation: benefits, current limitations and challenges
Molecular Systems Biology, 5
-
M.
Gstaiger,
R.
Aebersold
(2009)
Applying mass spectrometry-based proteomics to genetics, genomics and network biology
Nature Reviews Genetics, 10
-
Siân
Jones,
Xiaosong
Zhang,
D.
Parsons,
Jimmy
Lin,
R.
Leary,
P.
Angenendt,
P.
Mankoo,
H.
Carter,
H.
Kamiyama,
A.
Jimeno,
Seung‐Mo
Hong,
Baojin
Fu,
Ming-Tseh
Lin,
E.
Calhoun,
M.
Kamiyama,
K.
Walter,
T.
Nikolskaya,
Y.
Nikolsky,
James
Hartigan,
Douglas
Smith,
M.
Hidalgo,
S.
Leach,
A.
Klein,
E.
Jaffee,
M.
Goggins,
A.
Maitra,
C.
Iacobuzio-Donahue,
J.
Eshleman,
S.
Kern,
R.
Hruban,
R.
Karchin,
N.
Papadopoulos,
G.
Parmigiani,
B.
Vogelstein,
V.
Velculescu,
K.
Kinzler
(2008)
Core Signaling Pathways in Human Pancreatic Cancers Revealed by Global Genomic Analyses
Science, 321
-
Sven
Nelander,
Weiqing
Wang,
B.
Nilsson,
Q.
She,
C.
Pratilas,
N.
Rosen,
P.
Gennemark,
C.
Sander
(2008)
Models from experiments: combinatorial drug perturbations of cancer cells
Molecular Systems Biology, 4
-
S.
Gaudet,
K.
Janes,
J.
Albeck,
E.
Pace,
D.
Lauffenburger,
P.
Sorger
(2005)
A Compendium of Signals and Responses Triggered by Prodeath and Prosurvival Cytokines*S
Molecular & Cellular Proteomics, 4
-
(2011)
Comparative Networks of Normal and Transformed Hepatocytes
-
Harold
Kim,
T.
Shay,
E.
O’Shea,
A.
Regev
(2009)
Transcriptional Regulatory Circuits: Predicting Numbers from Alphabets
Science, 325
-
M.
Birrell,
E.
Hardaker,
Sissie
Wong,
K.
McCluskie,
M.
Catley,
J.
Alba,
R.
Newton,
S.
Haj‐Yahia,
K.
Pun,
Clarissa
Watts,
Robert
Shaw,
Tony
Savage,
M.
Belvisi
(2005)
Ikappa-B kinase-2 inhibitor blocks inflammation in human airway smooth muscle and a rat model of asthma.
American journal of respiratory and critical care medicine, 172 8
-
J.
Llovet,
J.
Bruix
(2008)
Molecular targeted therapies in hepatocellular carcinoma
Hepatology, 48
-
E.
Yasuda,
T.
Kumada,
S.
Takai,
A.
Ishisaki,
Takahiro
Noda,
R.
Matsushima-Nishiwaki,
N.
Yoshimi,
Kanefusa
Kato,
H.
Toyoda,
Y.
Kaneoka,
A.
Yamaguchi,
O.
Kozawa
(2005)
Attenuated phosphorylation of heat shock protein 27 correlates with tumor progression in patients with hepatocellular carcinoma.
Biochemical and biophysical research communications, 337 1
-
D.
Goldberg
(1988)
Genetic Algorithms in Search Optimization and Machine Learning
-
B.
Aldridge,
J.
Sáez-Rodríguez,
Jeremy
Muhlich,
P.
Sorger,
D.
Lauffenburger
(2007)
Fuzzy Logic Analysis of Kinase Pathway Crosstalk in TNF/EGF/Insulin-Induced Signaling
PLoS Computational Biology, 5
-
J.
Sáez-Rodríguez,
L.
Alexopoulos,
J.
Epperlein,
Regina
Samaga,
D.
Lauffenburger,
Steffen
Klamt,
P.
Sorger
(2009)
Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction
Molecular Systems Biology, 5
-
B.
Aldridge,
J.
Burke,
D.
Lauffenburger,
P.
Sorger
(2006)
Physicochemical modelling of cell signalling pathways
Nature Cell Biology, 8
-
Paul
Shannon,
Andrew
Markiel,
Owen
Ozier,
N.
Baliga,
Jonathan
Wang,
Daniel
Ramage,
Nada
Amin,
Benno
Schwikowski,
T.
Ideker
(2003)
Cytoscape: a software environment for integrated models of biomolecular interaction networks.
Genome research, 13 11
-
E.
Pieroni,
Sergio
de la Fuente van Bentem,
G.
Mancosu,
E.
Capobianco,
H.
Hirt,
Alberto
de la Fuente
(2008)
Protein networking: insights into global functional organization of proteomes
PROTEOMICS, 8
-
Á.
Száz
(2007)
Minimal structures , generalized topologies , and ascending systems should not be studied without generalized uniformities
-
J.
Sáez-Rodríguez,
S.
Mirschel,
R.
Hemenway,
Steffen
Klamt,
E.
Gilles,
Martin
Ginkel
(2006)
Visual setup of logical models of signaling and regulatory networks with ProMoT
BMC Bioinformatics, 7
-
Haiyuan
Yu,
A.
Smolyar,
K.
Venkatesan,
Anne-Ruxandra
Carvunis,
Nicolas
Simonis,
Jean-François
Rual,
Heather
Borick,
P.
Braun,
Matija
Dreze,
J.
Vandenhaute,
M.
Galli,
J.
Yazaki,
D.
Hill,
J.
Ecker,
F.
Roth,
M.
Vidal
(2009)
Literature-curated protein interaction
-
Luis
Mendoza,
Ioannis
Xenarios
(2005)
Theoretical Biology and Medical Modelling Open Access a Method for the Generation of Standardized Qualitative Dynamical Systems of Regulatory Networks
-
P.
Podolin,
James
Callahan,
B.
Bolognese,
Yue
Li,
K.
Carlson,
T.
Davis,
Geoff
Mellor,
Christopher
Evans,
A.
Roshak
(2005)
Attenuation of Murine Collagen-Induced Arthritis by a Novel, Potent, Selective Small Molecule Inhibitor of IκB Kinase 2, TPCA-1 (2-[(Aminocarbonyl)amino]-5-(4-fluorophenyl)-3-thiophenecarboxamide), Occurs via Reduction of Proinflammatory Cytokines and Antigen-Induced T Cell Proliferation
Journal of Pharmacology and Experimental Therapeutics, 312
-
H.
Lee,
B.
Tian,
J.
Sedivy,
J.
Wands,
Miran
Kim
(2006)
Loss of Raf kinase inhibitor protein promotes cell proliferation and migration of human hepatoma cells.
Gastroenterology, 131 4
-
(2011)
www.aacrjournals.org Cancer Res
-
Mark
Ciaccio,
Joel
Wagner,
Chih-Pin
Chuu,
D.
Lauffenburger,
R.
Jones
(2010)
Systems Analysis of EGF Receptor Signaling Dynamics with Micro-Western Arrays
Nature methods, 7
-
S.
Frame,
P.
Cohen
(2001)
GSK3 takes centre stage more than 20 years after its discovery.
The Biochemical journal, 359 Pt 1
-
R.
Prill,
D.
Marbach,
J.
Saez-Rodriguez,
P.
Sorger,
L.
Alexopoulos,
Xiaowei
Xue,
N.
Clarke,
G.
Altan-Bonnet,
G.
Stolovitzky
(2010)
Correction: Towards a Rigorous Assessment of Systems Biology Models: The DREAM3 Challenges
PLoS ONE, 5
-
K.
Sachs,
D.
Gifford,
T.
Jaakkola,
P.
Sorger,
D.
Lauffenburger
(2002)
Bayesian Network Approach to Cell Signaling Pathway Modeling
Science's STKE, 2002
-
C.
Taniguchi,
J.
Winnay,
Tatsuya
Kondo,
R.
Bronson,
A.
Guimaraes,
J.
Alemán,
Ji
Luo,
G.
Stephanopoulos,
R.
Weissleder,
L.
Cantley,
C.
Kahn
(2010)
The phosphoinositide 3-kinase regulatory subunit p85alpha can exert tumor suppressor properties through negative regulation of growth factor signaling.
Cancer research, 70 13
-
Ju-Seog
Lee,
S.
Thorgeirsson
(2002)
Functional and genomic implications of global gene expression profiles in cell lines from human hepatocellular cancer
Hepatology, 35
-
Seth
Berger,
R.
Iyengar
(2009)
Network analyses in systems pharmacology
Bioinformatics, 25 19
-
L.
Khamzina,
P.
Gruppuso,
J.
Wands
(2003)
Insulin signaling through insulin receptor substrate 1 and 2 in normal liver development.
Gastroenterology, 125 2