On the public citation graph

Synthesizing Signaling Pathways from Temporal Phosphoproteomic Data

https://doi.org/10.1101/209676
0 signed · 133 inferred · view as graph

Inferred edges come from two machine sources: sweeps of open repository metadata (mostly SSRN and Zenodo), and a bulk OpenAlex citation snapshot. Every row below is labelled with the one it came from. Neither is a complete citation index — absence here is not evidence of absence.

Is this your work? Sign in with ORCID and put your name on the claims that are yours.
Claim with ORCID
Reference health. See whether every reference in this work resolves to a known work and none has been retracted — and get a dated CiteStamped badge you can embed.
See reference health

What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/cam4.314openalex-snapshot
Inhibition of epidermal growth factor signaling by the cardiac glycoside ouabain in medulloblastoma
inferredcites →https://doi.org/10.1002/pmic.200900375openalex-snapshot
A guided tour of the Trans‐Proteomic Pipeline
inferredcites →https://doi.org/10.1002/pmic.201200439openalex-snapshot
Comet: An open‐source MS / MS sequence database search tool
inferredcites →https://doi.org/10.1007/11691372_29openalex-snapshot
PRISM: A Tool for Automatic Verification of Probabilistic Systems
inferredcites →https://doi.org/10.1007/978-1-4899-3035-4openalex-snapshot
Practical Data Analysis for Designed Experiments
inferredcites →https://doi.org/10.1007/978-3-540-78800-3_24openalex-snapshot
Z3: An Efficient SMT Solver
inferredcites →https://doi.org/10.1007/978-3-642-22438-6_30openalex-snapshot
Scala to the Power of Z3: Integrating SMT and Programming
inferredcites →https://doi.org/10.1007/978-94-017-9041-3_10openalex-snapshot
Model Checking in Biology
inferredcites →https://doi.org/10.1007/s00018-004-4258-xopenalex-snapshot
C-peptide stimulates Na+, K+-ATPase via activation of ERK1/2 MAP kinases in human renal tubular cells
inferredcites →https://doi.org/10.1007/s00018-012-1039-9openalex-snapshot
Na+,K+-ATPase as a docking station: protein–protein complexes of the Na+,K+-ATPase
inferredcites →https://doi.org/10.1016/j.cell.2006.09.026openalex-snapshot
Global, In Vivo, and Site-Specific Phosphorylation Dynamics in Signaling Networks
inferredcites →https://doi.org/10.1016/j.cellsig.2011.05.004openalex-snapshot
Akt signalling in health and disease
inferredcites →https://doi.org/10.1016/j.celrep.2014.07.036openalex-snapshot
Ultradeep Human Phosphoproteome Reveals a Distinct Regulatory Nature of Tyr and Ser/Thr-Based Signaling
inferredcites →https://doi.org/10.1016/j.celrep.2015.01.052openalex-snapshot
A Cell-Signaling Network Temporally Resolves Specific versus Promiscuous Phosphorylation
inferredcites →https://doi.org/10.1016/j.cels.2016.11.005openalex-snapshot
Elucidation of Signaling Pathways from Large-Scale Phosphoproteomic Data Using Protein Interaction Networks
inferredcites →https://doi.org/10.1016/j.cels.2016.11.013openalex-snapshot
Context Specificity in Causal Signaling Networks Revealed by Phosphoprotein Profiling
inferredcites →https://doi.org/10.1016/j.febslet.2010.04.019openalex-snapshot
Oncogenic mutant forms of EGFR: Lessons in signal transduction and targets for cancer therapy
inferredcites →https://doi.org/10.1016/j.febslet.2012.07.034openalex-snapshot
The p38 and Hog1 SAPKs control cell cycle progression in response to environmental stresses
inferredcites →https://doi.org/10.1016/j.sbi.2013.07.005openalex-snapshot
Towards a detailed atlas of protein–protein interactions
inferredcites →https://doi.org/10.1038/msb.2008.72openalex-snapshot
Linear combinations of docking affinities explain quantitative differences in RTK signaling
inferredcites →https://doi.org/10.1038/msb.2009.3openalex-snapshot
Toward accurate reconstruction of functional protein networks
inferredcites →https://doi.org/10.1038/msb.2009.47openalex-snapshot
Pathway databases and tools for their exploitation: benefits, current limitations and challenges
inferredcites →https://doi.org/10.1038/msb4100014openalex-snapshot
A comprehensive pathway map of epidermal growth factor receptor signaling
inferredcites →https://doi.org/10.1038/msb4100094openalex-snapshot
Effects of HER2 overexpression on cell signaling networks governing proliferation and migration
inferredcites →https://doi.org/10.1038/nature13302openalex-snapshot
A draft map of the human proteome
inferredcites →https://doi.org/10.1038/nbt.3154openalex-snapshot
Decoding the regulatory network of early blood development from single-cell gene expression measurements
inferredcites →https://doi.org/10.1038/nbt.3327openalex-snapshot
High-throughput phosphoproteomics reveals in vivo insulin signaling dynamics
inferredcites →https://doi.org/10.1038/nbt0302-301openalex-snapshot
Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae
inferredcites →https://doi.org/10.1038/ncb1174openalex-snapshot
Hog1 mediates cell-cycle arrest in G1 phase by the dual targeting of Sic1
inferredcites →https://doi.org/10.1038/ncomms3171openalex-snapshot
Genome-scale proteome quantification by DEEP SEQ mass spectrometry
inferredcites →https://doi.org/10.1038/ncomms9033openalex-snapshot
Large-scale models of signal propagation in human cells derived from discovery phosphoproteomic data
inferredcites →https://doi.org/10.1038/ng.235openalex-snapshot
Structure and function of a transcriptional network activated by the MAPK Hog1
inferredcites →https://doi.org/10.1038/ng.337openalex-snapshot
Bridging high-throughput genetic and transcriptional data reveals cellular responses to alpha-synuclein toxicity
inferredcites →https://doi.org/10.1038/ng0704-664openalex-snapshot
A gene network for navigating the literature
inferredcites →https://doi.org/10.1038/nmeth.1418openalex-snapshot
Systems analysis of EGF receptor signaling dynamics with microwestern arrays
inferredcites →https://doi.org/10.1038/nmeth.3773openalex-snapshot
Inferring causal molecular networks: empirical assessment through a community-based effort
inferredcites →https://doi.org/10.1038/npjsba.2015.18openalex-snapshot
Network analyses based on comprehensive molecular interaction maps reveal robust control structures in yeast stress response pathways
inferredcites →https://doi.org/10.1038/npjsba.2016.2openalex-snapshot
Pathways on demand: automated reconstruction of human signaling networks
inferredcites →https://doi.org/10.1038/nrg1637openalex-snapshot
Synthetic biology
inferredcites →https://doi.org/10.1038/nrg3244openalex-snapshot
Studying and modelling dynamic biological processes using time-series gene expression data
inferredcites →https://doi.org/10.1038/nrm1962openalex-snapshot
EGF–ERBB signalling: towards the systems level
inferredcites →https://doi.org/10.1038/nrm2900openalex-snapshot
Decoding signalling networks by mass spectrometry-based proteomics
inferredcites →https://doi.org/10.1038/nrmicro2419openalex-snapshot
Advantages and limitations of current network inference methods
inferredcites →https://doi.org/10.1038/sj.cdd.4402179openalex-snapshot
Akt phosphorylation of zyxin mediates its interaction with acinus-S and prevents acinus-triggered chromatin condensation
inferredcites →https://doi.org/10.1038/sj.emboj.7601095openalex-snapshot
Phosphorylation of Hsl1 by Hog1 leads to a G2 arrest essential for cell survival at high osmolarity
inferredcites →https://doi.org/10.1038/sj.emboj.7601756openalex-snapshot
The Sch9 kinase is a chromatin‐associated transcriptional activator of osmostress‐responsive genes
inferredcites →https://doi.org/10.1038/sj.onc.1204265openalex-snapshot
Reverse phase protein microarrays which capture disease progression show activation of pro-survival pathways at the cancer invasion front
inferredcites →https://doi.org/10.1038/sj.onc.1210255openalex-snapshot
Oncogenic re-wiring of cellular signaling pathways
inferredcites →https://doi.org/10.1039/c5ib00065copenalex-snapshot
The DIONESUS algorithm provides scalable and accurate reconstruction of dynamic phosphoproteomic networks to reveal new drug targets
inferredcites →https://doi.org/10.1073/pnas.0809822106openalex-snapshot
Modeling the temporal interplay of molecular signaling and gene expression by using dynamic nested effects models
inferredcites →https://doi.org/10.1073/pnas.091610798openalex-snapshot
Rck2, a member of the calmodulin-protein kinase family, links protein synthesis to high osmolarity MAP kinase signaling in budding yeast
inferredcites →https://doi.org/10.1073/pnas.1004751108openalex-snapshot
Finding undetected protein associations in cell signaling by belief propagation
inferredcites →https://doi.org/10.1073/pnas.1521288113openalex-snapshot
Early signaling dynamics of the epidermal growth factor receptor
inferredcites →https://doi.org/10.1074/jbc.271.23.13875openalex-snapshot
Purification and Characterization of Two Isoenzymes of DL-Glycerol-3-phosphatase from Saccharomyces cerevisiae
inferredcites →https://doi.org/10.1074/jbc.275.12.8290openalex-snapshot
The Transcriptional Response of Saccharomyces cerevisiae to Osmotic Shock
inferredcites →https://doi.org/10.1074/jbc.c800179200openalex-snapshot
Control of MAPK Specificity by Feedback Phosphorylation of Shared Adaptor Protein Ste50
inferredcites →https://doi.org/10.1074/jbc.m108848200openalex-snapshot
Transient Inhibition of Translation Initiation by Osmotic Stress
inferredcites →https://doi.org/10.1074/jbc.m312974200openalex-snapshot
High Osmolarity Glycerol (HOG) Pathway-induced Phosphorylation and Activation of 6-Phosphofructo-2-kinase Are Essential for Glycerol Accumulation and Yeast Cell Proliferation under Hyperosmotic Stress
inferredcites →https://doi.org/10.1074/jbc.m402152200openalex-snapshot
ERK1/2 Mediates Insulin Stimulation of Na,K-ATPase by Phosphorylation of the α-Subunit in Human Skeletal Muscle Cells
inferredcites →https://doi.org/10.1074/jbc.m910016199openalex-snapshot
The Transcriptional Response of Yeast to Saline Stress
inferredcites →https://doi.org/10.1074/mcp.m116.066233openalex-snapshot
Machine Learning of Global Phosphoproteomic Profiles Enables Discrimination of Direct versus Indirect Kinase Substrates
inferredcites →https://doi.org/10.1074/mcp.m400129-mcp200openalex-snapshot
Multiplexed Protein Quantitation in Saccharomyces cerevisiae Using Amine-reactive Isobaric Tagging Reagents
inferredcites →https://doi.org/10.1074/mcp.m500089-mcp200openalex-snapshot
Time-resolved Mass Spectrometry of Tyrosine Phosphorylation Sites in the Epidermal Growth Factor Receptor Signaling Network Reveals Dynamic Modules
inferredcites →https://doi.org/10.1074/mcp.m800186-mcp200openalex-snapshot
Temporal Perturbation of Tyrosine Phosphoproteome Dynamics Reveals the System-wide Regulatory Networks
inferredcites →https://doi.org/10.1074/mcp.o111.011064openalex-snapshot
Online Nanoflow Multidimensional Fractionation for High Efficiency Phosphopeptide Analysis
inferredcites →https://doi.org/10.1088/1478-3975/8/3/035008openalex-snapshot
Systematic computational prediction of protein interaction networks
inferredcites →https://doi.org/10.1089/1066527041410382openalex-snapshot
Physical Network Models
inferredcites →https://doi.org/10.1089/152791601750294344openalex-snapshot
BioCarta
inferredcites →https://doi.org/10.1089/cmb.2012.0092openalex-snapshot
Simultaneous Reconstruction of Multiple Signaling Pathways via the Prize-Collecting Steiner Forest Problem
inferredcites →https://doi.org/10.1089/cmb.2012.0241openalex-snapshot
Reconstructing Boolean Models of Signaling
inferredcites →https://doi.org/10.1091/mbc.e03-07-0521openalex-snapshot
Unique and Redundant Roles for HOG MAPK Pathway Components as Revealed by Whole-Genome Expression Analysis
inferredcites →https://doi.org/10.1093/bib/bbp057openalex-snapshot
Toward the dynamic interactome: it's about time
inferredcites →https://doi.org/10.1093/bioinformatics/btm170openalex-snapshot
SPINE: a framework for signaling-regulatory pathway inference from cause-effect experiments
inferredcites →https://doi.org/10.1093/bioinformatics/btm178openalex-snapshot
Nested effects models for high-dimensional phenotyping screens
inferredcites →https://doi.org/10.1093/bioinformatics/btq703openalex-snapshot
Cancer therapy design based on pathway logic
inferredcites →https://doi.org/10.1093/bioinformatics/bts211openalex-snapshot
How networks change with time
inferredcites →https://doi.org/10.1093/bioinformatics/bts514openalex-snapshot
Bayesian Inference of Signaling Network Topology in a Cancer Cell Line
inferredcites →https://doi.org/10.1093/bioinformatics/btt241openalex-snapshot
Identifying proteins controlling key disease signaling pathways
inferredcites →https://doi.org/10.1093/bioinformatics/btt393openalex-snapshot
Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming
inferredcites →https://doi.org/10.1093/bioinformatics/btu043openalex-snapshot
Network orientation via shortest paths
inferredcites →https://doi.org/10.1093/bioinformatics/btu383openalex-snapshot
Literome: PubMed-scale genomic knowledge base in the cloud
inferredcites →https://doi.org/10.1093/bioinformatics/btw254openalex-snapshot
Reconstructing the temporal progression of HIV-1 immune response pathways
inferredcites →https://doi.org/10.1093/bioinformatics/btw275openalex-snapshot
Influence maximization in time bounded network identifies transcription factors regulating perturbed pathways
inferredcites →https://doi.org/10.1093/nar/gkn653openalex-snapshot
PID: The Pathway Interaction Database
inferredcites →https://doi.org/10.1093/nar/gkq1207openalex-snapshot
Discovering pathways by orienting edges in protein interaction networks
inferredcites →https://doi.org/10.1093/nar/gkr988openalex-snapshot
KEGG for integration and interpretation of large-scale molecular data sets
inferredcites →https://doi.org/10.1093/nar/gkt1102openalex-snapshot
The Reactome pathway knowledgebase
inferredcites →https://doi.org/10.1093/nar/gku1267openalex-snapshot
PhosphoSitePlus, 2014: mutations, PTMs and recalibrations
inferredcites →https://doi.org/10.1093/nar/gkv1145openalex-snapshot
2016 update of the PRIDE database and its related tools
inferredcites →https://doi.org/10.1101/gad.229310.113openalex-snapshot
MAPK Hog1 closes the S. cerevisiae glycerol channel Fps1 by phosphorylating and displacing its positive regulators
inferredcites →https://doi.org/10.1101/gr.1239303openalex-snapshot
Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
inferredcites →https://doi.org/10.1101/gr.138628.112openalex-snapshot
Linking the signaling cascades and dynamic regulatory networks controlling stress responses
inferredcites →https://doi.org/10.1109/qest.2005.2openalex-snapshot
A Markov reward model checker
inferredcites →https://doi.org/10.1109/tbcas.2013.2288035openalex-snapshot
Time-Varying Causal Inference From Phosphoproteomic Measurements in Macrophage Cells
inferredcites →https://doi.org/10.1111/j.1749-6632.2002.tb04532.xopenalex-snapshot
Science's Signal Transduction Knowledge Environment
inferredcites →https://doi.org/10.1126/science.1172867openalex-snapshot
Global Analysis of Cdk1 Substrate Phosphorylation Sites Provides Insights into Evolution
inferredcites →https://doi.org/10.1126/science.1198704openalex-snapshot
Single-Cell Mass Cytometry of Differential Immune and Drug Responses Across a Human Hematopoietic Continuum
inferredcites →https://doi.org/10.1126/science.1248882openalex-snapshot
Defining an essential transcription factor program for naïve pluripotency
inferredcites →https://doi.org/10.1126/science.1250689openalex-snapshot
Conditional density-based analysis of T cell signaling in single-cell data
inferredcites →https://doi.org/10.1126/scisignal.2001699openalex-snapshot
A Directed Protein Interaction Network for Investigating Intracellular Signal Transduction
inferredcites →https://doi.org/10.1126/scisignal.2003994openalex-snapshot
Receptor Tyrosine Kinases Fall into Distinct Classes Based on Their Inferred Signaling Networks
inferredcites →https://doi.org/10.1126/scisignal.2004856openalex-snapshot
Time-resolved dissection of early phosphoproteome and ensuing proteome changes in response to TGF-β
inferredcites →https://doi.org/10.1126/scisignal.287re6openalex-snapshot
Oncogenic EGFR Signaling Networks in Glioma
inferredcites →https://doi.org/10.1126/scisignal.3139re6openalex-snapshot
ABL Tyrosine Kinases: Evolution of Function, Regulation, and Specificity
inferredcites →https://doi.org/10.1126/scisignal.aag2435openalex-snapshot
Identifying protein kinase–specific effectors of the osmostress response in yeast
inferredcites →https://doi.org/10.1128/mcb.00427-08openalex-snapshot
Serum-Induced Phosphorylation of the Serum Response Factor Coactivator MKL1 by the Extracellular Signal-Regulated Kinase 1/2 Pathway Inhibits Its Nuclear Localization
inferredcites →https://doi.org/10.1128/mcb.14.6.4135openalex-snapshot
GPD1, Which Encodes Glycerol-3-Phosphate Dehydrogenase, Is Essential for Growth under Osmotic Stress in Saccharomyces cerevisiae, and Its Expression Is Regulated by the High-Osmolarity Glycerol Response Pathway
inferredcites →https://doi.org/10.1128/mcb.20.11.3887-3895.2000openalex-snapshot
Rck2 Kinase Is a Substrate for the Osmotic Stress-Activated Mitogen-Activated Protein Kinase Hog1
inferredcites →https://doi.org/10.1145/1065010.1065045openalex-snapshot
Programming by sketching for bit-streaming programs
inferredcites →https://doi.org/10.1145/2429069.2429125openalex-snapshot
Synthesis of biological models from mutation experiments
inferredcites →https://doi.org/10.1145/357084.357090openalex-snapshot
A Deductive Approach to Program Synthesis
inferredcites →https://doi.org/10.1177/1947601911407328openalex-snapshot
The ERK Cascade: Distinct Functions within Various Subcellular Organelles
inferredcites →https://doi.org/10.1186/1471-2105-10-322openalex-snapshot
Deterministic Effects Propagation Networks for reconstructing protein signaling networks from multiple interventions
inferredcites →https://doi.org/10.1186/1471-2105-11-154openalex-snapshot
TimeDelay-ARACNE: Reverse engineering of gene networks from time-course data by an information theoretic approach
inferredcites →https://doi.org/10.1186/1471-2105-15-250openalex-snapshot
Dynamic probabilistic threshold networks to infer signaling pathways from time-course perturbation data
inferredcites →https://doi.org/10.1186/1471-2105-5-147openalex-snapshot
Content-rich biological network constructed by mining PubMed abstracts
inferredcites →https://doi.org/10.1186/1471-2105-9-405openalex-snapshot
iRefIndex: A consolidated protein interaction database with provenance
inferredcites →https://doi.org/10.1186/1752-0509-8-s4-s2openalex-snapshot
TimeXNet: Identifying active gene sub-networks using time-course gene expression profiles
inferredcites →https://doi.org/10.1186/gb-2010-11-1-r3openalex-snapshot
NetPath: a public resource of curated signal transduction pathways
inferredcites →https://doi.org/10.1214/13-aoas696openalex-snapshot
Reconstructing evolving signalling networks by hidden Markov nested effects models
inferredcites →https://doi.org/10.1261/rna.864908openalex-snapshot
Yeast translational response to high salinity: Global analysis reveals regulation at multiple levels
inferredcites →https://doi.org/10.1371/journal.pcbi.1001099openalex-snapshot
Training Signaling Pathway Maps to Biochemical Data with Constrained Fuzzy Logic: Quantitative Analysis of Liver Cell Responses to Inflammatory Stimuli
inferredcites →https://doi.org/10.1371/journal.pcbi.1003290openalex-snapshot
Perturbation Biology: Inferring Signaling Networks in Cellular Systems
inferredcites →https://doi.org/10.1371/journal.pcbi.1003323openalex-snapshot
Linking Transcriptional Changes over Time in Stimulated Dendritic Cells to Identify Gene Networks Activated during the Innate Immune Response
inferredcites →https://doi.org/10.1371/journal.pcbi.1004879openalex-snapshot
Network-Based Interpretation of Diverse High-Throughput Datasets through the Omics Integrator Software Package
inferredcites →https://doi.org/10.1371/journal.pcbi.1005379openalex-snapshot
Data-driven reverse engineering of signaling pathways using ensembles of dynamic models
inferredcites →https://doi.org/10.1371/journal.pcbi.1006088openalex-snapshot
Network inference reveals novel connections in pathways regulating growth and defense in the yeast salt response
inferredcites →https://doi.org/10.1371/journal.pone.0046725openalex-snapshot
Quantitative Phosphoproteomics Reveals SLP-76 Dependent Regulation of PAG and Src Family Kinases in T Cells
inferredcites →https://doi.org/10.15252/msb.20145120openalex-snapshot
Pathway connectivity and signaling coordination in the yeast stress‐activated signaling network
inferredcites →https://doi.org/10.3389/fbioe.2014.00075openalex-snapshot
Toward Synthesizing Executable Models in Biology
inferredcites →https://doi.org/10.3389/fgene.2014.00263openalex-snapshot
Toward a systems-level view of dynamic phosphorylation networks
inferredcites →https://doi.org/10.3389/fmicb.2015.00730openalex-snapshot
Reconstruction of the temporal signaling network in Salmonella-infected human cells

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1016/j.patter.2021.100257openalex-snapshot
Causal interactions from proteomic profiles: Molecular data meet pathway knowledge
Editorial review for independent work. ICSAC — the Institute for Complexity Science and Advanced Computing — runs a structured editorial panel for researchers publishing outside journals, and publishes on CiteStamp rails. Submission is free and goes through ORCID: icsacinstitute.org/submit.