Contact and support
Need help, have a question, or want to contact the ResearchHub team?
© 2026 ResearchHub. Built for responsible scholarly connection.
Research graph
References from Proteomics for systems toxicology. Local targets link to admitted publications; unresolved targets remain external evidence.
FutureTox: building the road for 21st century toxicology and risk assessment practices
10.1093/toxsci/kft252 · 2014 · External reference
Unresolved reference
2007 · External reference
t4 workshop report: pathways of toxicity
10.14573/altex.1309261 · 2014 · External reference
10.1021/tx400410s
10.1021/tx400410s · External reference
10.1038/nrg3185
10.1038/nrg3185 · External reference
10.1016/j.cell.2009.04.050
10.1016/j.cell.2009.04.050 · External reference
10.1016/j.molcel.2010.09.022
10.1016/j.molcel.2010.09.022 · External reference
10.1016/j.molcel.2010.09.028
10.1016/j.molcel.2010.09.028 · External reference
10.1038/nrm3311
10.1038/nrm3311 · External reference
10.1038/nrm3546
10.1038/nrm3546 · External reference
10.1089/ars.2010.3733
10.1089/ars.2010.3733 · External reference
Double standards in quantitative proteomics: direct comparative assessment of difference in gel electrophoresis and metabolic stable isotope labeling
10.1074/mcp.m400121-mcp200 · 2005 · External reference
2D-electrophoresis and multiplex immunoassay proteomic analysis of different body fluids and cellular components reveal known and novel markers for extended fasting
10.1186/1755-8794-4-24 · 2011 · External reference
Proteomic methodological recommendations for studies involving human plasma, platelets, and peripheral blood mononuclear cells
10.1021/pr700714x · 2008 · External reference
10.1038/nbt.1658
10.1038/nbt.1658 · External reference
10.1073/pnas.0800788105
10.1073/pnas.0800788105 · External reference
A perspective on the use of iTRAQ reagent technology for protein complex and profiling studies
10.1093/jxb/erj168 · 2006 · External reference
Using PeptideAtlas, SRMAtlas, and PASSEL: comprehensive resources for discovery and targeted proteomics
10.1002/0471250953.bi1325s46 · 2014 · External reference
Selected reaction monitoring for quantitative proteomics: a tutorial
10.1038/msb.2008.61 · 2008 · External reference
10.1038/nmeth.2015
10.1038/nmeth.2015 · External reference
10.1074/mcp.o112.020131
10.1074/mcp.o112.020131 · External reference
10.1002/pmic.200900398
10.1002/pmic.200900398 · External reference
10.1126/scisignal.2001314
10.1126/scisignal.2001314 · External reference
Metastatic castration-resistant prostate cancer reveals intrapatient similarity and interpatient heterogeneity of therapeutic kinase targets
10.1073/pnas.1319948110 · 2013 · External reference
10.1002/elps.200305795
10.1002/elps.200305795 · External reference
10.1002/pmic.200800454
10.1002/pmic.200800454 · External reference
10.1016/j.cell.2009.01.041
10.1016/j.cell.2009.01.041 · External reference
10.1038/nrm3099
10.1038/nrm3099 · External reference
10.1016/0955-0674(95)80031-x
10.1016/0955-0674(95)80031-x · External reference
10.1038/nrd3321
10.1038/nrd3321 · External reference
10.1038/nature07960
10.1038/nature07960 · External reference
A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles
10.1074/mcp.m111.013284 · 2011 · External reference
A guided tour of the trans‐proteomic pipeline
10.1002/pmic.200900375 · 2010 · External reference
Computational Proteomics Analysis System (CPAS): an extensible, open-source analytic system for evaluating and publishing proteomic data and high throughput biological experiments
10.1021/pr0503533 · 2006 · External reference
OpenMS—an open-source software framework for mass spectrometry
10.1186/1471-2105-9-163 · 2008 · External reference
10.1038/nbt.1511
10.1038/nbt.1511 · External reference
10.1074/mcp.r112.025163
10.1074/mcp.r112.025163 · External reference
Unresolved reference
2012 · External reference
pyOpenMS: a Python‐based interface to the OpenMS mass‐spectrometry algorithm library
10.1002/pmic.201300246 · 2014 · External reference
Unresolved reference
2008 · External reference
Unresolved reference
2005 · External reference
10.1016/1044-0305(94)80016-2
10.1016/1044-0305(94)80016-2 · External reference
Probability-based protein identification by searching sequence databases using mass spectrometry data
10.1002/(sici)1522-2683(19991201)20:18<3551::aid-elps3551>3.0.co;2-2 · 1999 · External reference
10.1093/bioinformatics/bth092
10.1093/bioinformatics/bth092 · External reference
10.1021/pr0499491
10.1021/pr0499491 · External reference
Probability-based validation of protein identifications using a modified SEQUEST algorithm
10.1021/ac025826t · 2002 · External reference
Target–decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry
10.1038/nmeth1019 · 2007 · External reference
Assigning significance to peptides identified by tandem mass spectrometry using decoy databases
10.1021/pr700600n · 2007 · External reference
10.1021/pr801109k
10.1021/pr801109k · External reference
When target–decoy false discovery rate estimations are inaccurate and how to spot instances
10.1021/pr301063v · 2013 · External reference
Computational proteomics pitfalls and challenges: HavanaBioinfo 2012 Workshop report
10.1016/j.jprot.2013.01.019 · 2013 · External reference
Generic comparison of protein inference engines
10.1074/mcp.o110.007088 · 2012 · External reference
iProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates
10.1074/mcp.m111.007690 · 2011 · External reference
A non-parametric cutout index for robust evaluation of identified proteins
10.1074/mcp.o112.022863 · 2013 · External reference
Improving sensitivity in proteome studies by analysis of false discovery rates for multiple search engines
10.1002/pmic.200800473 · 2009 · External reference
Development and validation of a spectral library searching method for peptide identification from MS/MS
10.1002/pmic.200600625 · 2007 · External reference
Using annotated peptide mass spectrum libraries for protein identification
10.1021/pr0602085 · 2006 · External reference
Building consensus spectral libraries for peptide identification in proteomics
10.1038/nmeth.1254 · 2008 · External reference
Understanding the improved sensitivity of spectral library searching over sequence database searching in proteomics data analysis
10.1002/pmic.201000492 · 2011 · External reference
Algorithms for the de novo sequencing of peptides from tandem mass spectra
10.1586/epr.11.54 · 2011 · External reference
10.1089/106652799318300
10.1089/106652799318300 · External reference
10.1089/10665270152530872
10.1089/10665270152530872 · External reference
10.1002/rcm.1196
10.1002/rcm.1196 · External reference
PEAKS DB: de novo sequencing assisted database search for sensitive and accurate peptide identification
10.1074/mcp.m111.010587 · 2012 · External reference
Current challenges in software solutions for mass spectrometry-based quantitative proteomics
10.1007/s00726-012-1289-8 · 2012 · External reference
Normalization approaches for removing systematic biases associated with mass spectrometry and label-free proteomics
10.1021/pr050300l · 2006 · External reference
Development and evaluation of normalization methods for label-free relative quantification of endogenous peptides
10.1074/mcp.m800514-mcp200 · 2009 · External reference
Normalyzer: a tool for rapid evaluation of normalization methods for omics datasets
10.1021/pr401264n · 2014 · External reference
Quantitative accuracy in mass spectrometry based proteomics of complex samples: the impact of labeling and precursor interference
10.1016/j.jprot.2013.10.035 · 2013 · External reference
10.1021/pr400098r
10.1021/pr400098r · External reference
Statistical inference from multiple iTRAQ experiments without using common reference standards
10.1021/pr300624g · 2013 · External reference
An adaptive alignment algorithm for quality-controlled label-free LC–MS
10.1074/mcp.o112.021907 · 2013 · External reference
Data processing methods and quality control strategies for label-free LC–MS protein quantification
10.1016/j.bbapap.2013.03.026 · 2014 · External reference
Normalization and statistical analysis of quantitative proteomics data generated by metabolic labeling
10.1074/mcp.m800462-mcp200 · 2009 · External reference
Multiple hypothesis testing in proteomics: a strategy for experimental work
2011 · External reference
Controlling the false discovery rate: a practical and powerful approach to multiple testing
10.1111/j.2517-6161.1995.tb02031.x · 1995 · External reference
Toward objective evaluation of proteomic algorithms
10.1038/nmeth.1983 · 2012 · External reference
10.1016/j.jprot.2012.10.009
10.1016/j.jprot.2012.10.009 · External reference
Systematic comparison of label-free, metabolic labeling, and isobaric chemical labeling for quantitative proteomics on LTQ Orbitrap Velos
10.1021/pr200748h · 2012 · External reference
High performance computational analysis of large-scale proteome data sets to assess incremental contribution to coverage of the human genome
10.1021/pr400181q · 2013 · External reference
Low cost, scalable proteomics data analysis using Amazon's cloud computing services and open source search algorithms
10.1021/pr800970z · 2009 · External reference
Accelerating the scoring module of mass spectrometry-based peptide identification using GPUs
10.1186/1471-2105-15-121 · 2014 · External reference
Activities at the Universal Protein Resource (UniProt)
10.1093/nar/gkt1140 · 2014 · External reference
Unresolved reference
2011 · External reference
neXtProt: a knowledge platform for human proteins
10.1093/nar/gkr1179 · 2012 · External reference
10.1002/pmic.200300772
10.1002/pmic.200300772 · External reference
10.1126/scisignal.1159433
10.1126/scisignal.1159433 · External reference
STITCH 3: zooming in on protein–chemical interactions
10.1093/nar/gkr1011 · 2012 · External reference
T3DB: a comprehensively annotated database of common toxins and their targets
10.1093/nar/gkp934 · 2010 · External reference
10.1038/nrg3337
10.1038/nrg3337 · External reference
Combining literature text mining with microarray data: advances for system biology modeling
10.1093/bib/bbr018 · 2012 · External reference
10.1038/ng0704-664
10.1038/ng0704-664 · External reference
EBIMed—text crunching to gather facts for proteins from Medline
10.1093/bioinformatics/btl302 · 2007 · External reference
SciMiner: web-based literature mining tool for target identification and functional enrichment analysis
10.1093/bioinformatics/btp049 · 2009 · External reference
10.1093/nar/gkn296
10.1093/nar/gkn296 · External reference
10.1126/science.1073374
10.1126/science.1073374 · External reference
10.1038/nature04532
10.1038/nature04532 · External reference
10.1038/onc.2010.331
10.1038/onc.2010.331 · External reference
10.1002/jcp.10119
10.1002/jcp.10119 · External reference
10.1093/nar/gkt111
10.1093/nar/gkt111 · External reference
10.1093/bioinformatics/btr260
10.1093/bioinformatics/btr260 · External reference
10.1093/nar/gkt1076
10.1093/nar/gkt1076 · External reference
10.1093/nar/gkt1102
10.1093/nar/gkt1102 · External reference
Gene Ontology annotations and resources
10.1093/nar/gks1050 · 2013 · External reference
GeneSigDB: a manually curated database and resource for analysis of gene expression signatures
10.1093/nar/gkr901 · 2012 · External reference
PAGED: a pathway and gene-set enrichment database to enable molecular phenotype discoveries
10.1186/1471-2105-13-s15-s2 · 2012 · External reference
Liverome: a curated database of liver cancer-related gene signatures with self-contained context information
10.1186/1471-2164-12-s3-s3 · 2011 · External reference
10.1371/journal.pcbi.1002375
10.1371/journal.pcbi.1002375 · External reference
10.1038/nprot.2008.211
10.1038/nprot.2008.211 · External reference
Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool
10.1186/1471-2105-14-128 · 2013 · External reference
10.1073/pnas.0506580102
10.1073/pnas.0506580102 · External reference
Assessment of network perturbation amplitudes by applying high-throughput data to causal biological networks
10.1186/1752-0509-6-54 · 2012 · External reference
Of mice and men: comparative proteomics of bronchoalveolar fluid
10.1183/09031936.00089409 · 2010 · External reference
Mitochondrial dysfunction, oxidative stress, and apoptosis revealed by proteomic and transcriptomic analyses of the striata in two mouse models of Parkinson's disease
10.1021/pr070546l · 2008 · External reference
10.1371/journal.pone.0013984
10.1371/journal.pone.0013984 · External reference
10.1002/pmic.200900412
10.1002/pmic.200900412 · External reference
Unresolved reference
2013 · External reference
10.1038/nrg1272
10.1038/nrg1272 · External reference
10.1038/nrg3552
10.1038/nrg3552 · External reference
Discovering regulatory and signalling circuits in molecular interaction networks
10.1093/bioinformatics/18.suppl_1.s233 · 2002 · External reference
Network based elucidation of drug response: from modulators to targets
10.1186/1752-0509-7-139 · 2013 · External reference
10.1016/j.cell.2011.02.016
10.1016/j.cell.2011.02.016 · External reference
STRING v9.1: protein–protein interaction networks, with increased coverage and integration
10.1093/nar/gks1094 · 2013 · External reference
10.1093/nar/gkq1018
10.1093/nar/gkq1018 · External reference
10.1186/gb-2010-11-5-r53
10.1186/gb-2010-11-5-r53 · External reference
10.1093/nar/28.1.27
10.1093/nar/28.1.27 · External reference
10.1038/nature03985
10.1038/nature03985 · External reference
Comparison of genomic and proteomic data in recurrent airway obstruction affected horses using ingenuity pathway analysis®
10.1186/1746-6148-7-48 · 2011 · External reference
Integrated redox proteomics and metabolomics of mitochondria to identify mechanisms of Cd toxicity
10.1093/toxsci/kfu018 · 2014 · External reference
10.1111/j.1600-065x.2011.01092.x
10.1111/j.1600-065x.2011.01092.x · External reference
Case study: the role of mechanistic network models in systems toxicology
10.1016/j.drudis.2013.07.023 · 2014 · External reference
A computable cellular stress network model for non-diseased pulmonary and cardiovascular tissue
10.1186/1752-0509-5-168 · 2011 · External reference
Construction of a computable network model for DNA damage, autophagy, cell death, and senescence
2013 · External reference
Construction of a computable cell proliferation network focused on non-diseased lung cells
10.1186/1752-0509-5-105 · 2011 · External reference
A modular cell-type focused inflammatory process network model for non-diseased pulmonary tissue
10.4137/bbi.s11509 · 2013 · External reference
Recent advances in modeling languages for pathway maps and computable biological networks
10.1016/j.drudis.2013.12.011 · 2014 · External reference
On crowd-verification of biological networks
2013 · External reference
10.1038/nbt.1968
10.1038/nbt.1968 · External reference
10.1093/bioinformatics/bts116
10.1093/bioinformatics/bts116 · External reference
10.1093/bioinformatics/btq675
10.1093/bioinformatics/btq675 · External reference
10.1038/nmeth.2212
10.1038/nmeth.2212 · External reference
10.1016/j.cell.2012.02.009
10.1016/j.cell.2012.02.009 · External reference
Network analysis of human in-stent restenosis
10.1161/circulationaha.106.637025 · 2006 · External reference
Proteomic and computational analysis of bronchoalveolar proteins during the course of the acute respiratory distress syndrome
10.1164/rccm.200712-1895oc · 2008 · External reference
Sense and nonsense of pathway analysis software in proteomics
10.1021/pr200654k · 2011 · External reference
10.1186/2050-6511-14-9
10.1186/2050-6511-14-9 · External reference
10.1038/msb4100180
10.1038/msb4100180 · External reference
10.1093/bioinformatics/btn161
10.1093/bioinformatics/btn161 · External reference
10.1093/bioinformatics/btq089
10.1093/bioinformatics/btq089 · External reference
Reverse engineering and analysis of large genome-scale gene networks
10.1093/nar/gks904 · 2013 · External reference
10.1093/nar/gks951
10.1093/nar/gks951 · External reference
Using random walks to identify cancer-associated modules in expression data
10.1186/1756-0381-6-17 · 2013 · External reference
NetWeAvers: an R package for integrative biological network analysis with mass spectrometry data
10.1093/bioinformatics/btt513 · 2013 · External reference
10.1093/nar/30.1.207
10.1093/nar/30.1.207 · External reference
ArrayExpress—a public repository for microarray gene expression data at the EBI
10.1093/nar/gkg091 · 2003 · External reference
Resilience in the proteomics data ecosystem: how the field cares for its data
10.1002/pmic.201300118 · 2013 · External reference
10.1093/nar/gks1262
10.1093/nar/gks1262 · External reference
MOPED enables discoveries through consistently processed proteomics data
10.1021/pr400884c · 2014 · External reference
Defining the transcriptome and proteome in three functionally different human cell lines
10.1038/msb.2010.106 · 2010 · External reference
10.1038/nature10098
10.1038/nature10098 · External reference
Sequence signatures and mRNA concentration can explain two‐thirds of protein abundance variation in a human cell line
10.1038/msb.2010.59 · 2010 · External reference
10.1371/journal.pbio.1000048
10.1371/journal.pbio.1000048 · External reference
Protein abundances are more conserved than mRNA abundances across diverse taxa
10.1002/pmic.201000327 · 2010 · External reference
10.1074/mcp.m300063-mcp200
10.1074/mcp.m300063-mcp200 · External reference
Dominant processes during human dendritic cell maturation revealed by integration of proteome and transcriptome at the pathway level
10.1021/pr9008546 · 2010 · External reference
Unresolved reference
1925 · External reference
Unresolved reference
1949 · External reference
400: a method for combining non-independent, one-sided tests of significance
1975 · External reference
Meta-analysis of pathway enrichment: combining independent and dependent omics data sets
10.1371/journal.pone.0089297 · 2014 · External reference
10.1371/journal.pcbi.1000639
10.1371/journal.pcbi.1000639 · External reference
Reconstructing targetable pathways in lung cancer by integrating diverse omics data
10.1038/ncomms3617 · 2013 · External reference
EU framework 6 project: predictive toxicology (PredTox)—overview and outcome
10.1016/j.taap.2010.10.008 · 2011 · External reference
10.1021/pr400219s
10.1021/pr400219s · External reference
10.1016/j.tiv.2012.01.012
10.1016/j.tiv.2012.01.012 · External reference
A 28-day rat inhalation study with an integrated molecular toxicology endpoint demonstrates reduced exposure effects for a prototypic modified risk tobacco product compared with conventional cigarettes
10.1016/j.fct.2014.02.034 · 2014 · External reference
Cigarette smoke induces an unfolded protein response in the human lung: a proteomic approach
10.1165/rcmb.2007-0221oc · 2008 · External reference
Cigarette smoke induces endoplasmic reticulum stress and the unfolded protein response in normal and malignant human lung cells
10.1186/1471-2407-8-229 · 2008 · External reference
10.1152/ajplung.00219.2012
10.1152/ajplung.00219.2012 · External reference
Reverse‐engineering human regulatory networks
10.1002/wsbm.1159 · 2012 · External reference
Cellular function and regulation of the translationally controlled tumour protein TCTP
10.2174/1874838401205010019 · 2012 · External reference
The Hsp90 inhibitor IPI-504 overcomes bortezomib resistance in mantle cell lymphoma in vitro and in vivo by down-regulation of the prosurvival ER chaperone BiP/Grp78
10.1182/blood-2010-04-278853 · 2011 · External reference
10.1016/j.taap.2014.01.002
10.1016/j.taap.2014.01.002 · External reference
Proteomic analysis of mismatch repair-mediated alkylating agent-induced DNA damage response
10.1186/2045-3701-3-37 · 2013 · External reference
10.1093/toxsci/kft145
10.1093/toxsci/kft145 · External reference
10.1146/annurev-pharmtox-011112-140248
10.1146/annurev-pharmtox-011112-140248 · External reference
Systems biology approaches and tools for analysis of interactomes and multi-target drugs
10.1007/978-1-60761-800-3_2 · 2010 · External reference
Utilizing toxicogenomic data to understand chemical mechanism of action in risk assessment
10.1016/j.taap.2011.01.017 · 2013 · External reference
10.1002/pmic.201270086
10.1002/pmic.201270086 · External reference
10.1021/pr3000249
10.1021/pr3000249 · External reference
Mass spectrometry-based proteomics using Q Exactive, a high-performance benchtop quadrupole Orbitrap mass spectrometer
10.1074/mcp.m111.011015 · 2011 · External reference
The quantitative proteome of a human cell line
10.1038/msb.2011.82 · 2011 · External reference
Targeted proteomic quantification on quadrupole-orbitrap mass spectrometer
10.1074/mcp.o112.019802 · 2012 · External reference
10.1038/nmeth.1408
10.1038/nmeth.1408 · External reference
10.1038/nmeth.2309
10.1038/nmeth.2309 · External reference
Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis
10.1074/mcp.o111.016717 · 2012 · External reference
10.1002/pmic.201000553
10.1002/pmic.201000553 · External reference
10.1074/mcp.e113.031658
10.1074/mcp.e113.031658 · External reference
Current standing and future prospects for the technologies proposed to transform toxicity testing in the 21st century
2011 · External reference
Deep proteome and transcriptome mapping of a human cancer cell line
10.1038/msb.2011.81 · 2011 · External reference
On marathons and Sprints: an integrated quantitative proteomics and transcriptomics analysis of differences between slow and fast muscle fibers
10.1074/mcp.m111.010801 · 2012 · External reference
The role of toxicoproteomics in assessing organ specific toxicity
2009 · External reference
Quantification of biological network perturbations for mechanistic insight and diagnostics using two-layer causal models
10.1186/1471-2105-15-238 · 2014 · External reference
The coming of age of phosphoproteomics—from large data sets to inference of protein functions
10.1074/mcp.r113.032862 · 2013 · External reference
Phosphoproteomics
10.1021/ac404019p · 2014 · External reference
Cross-species comparisons of transcriptomic alterations in human and rat primary hepatocytes exposed to 2, 3, 7, 8-tetrachlorodibenzo-p-dioxin
10.1093/toxsci/kfs069 · 2012 · External reference
The species translation challenge—a systems biology perspective on human and rat bronchial epithelial cells
10.1038/sdata.2014.9 · 2014 · External reference
Inter-species prediction of protein phosphorylation in the sbv IMPROVER species translation challenge
2014 · External reference
10.1016/j.jprot.2012.11.014
10.1016/j.jprot.2012.11.014 · External reference
10.1093/nar/gkp427
10.1093/nar/gkp427 · External reference
10.1093/bioinformatics/btn577
10.1093/bioinformatics/btn577 · External reference
10.1073/pnas.0508647102
10.1073/pnas.0508647102 · External reference
A comparative integrated transcript analysis and functional characterization of differential mechanisms for induction of liver hypertrophy in the rat
10.1016/j.taap.2011.01.021 · 2011 · External reference
Plasma and liver proteomic analysis of 3Z‐3‐[(1H‐pyrrol‐2‐yl)‐methylidene]‐1‐(1‐piperidinylmethyl)‐1, 3‐2H‐indol‐2‐one‐induced hepatotoxicity in Wistar rats
10.1002/pmic.200900699 · 2010 · External reference
Proteomic mapping of bezafibrate-treated human hepatocytes in primary culture using two-dimensional liquid chromatography
10.1016/j.toxlet.2010.12.015 · 2011 · External reference
Proteomics investigations of drug-induced hepatotoxicity in HepG2 cells
10.1093/toxsci/kfq380 · 2011 · External reference
Analysis of secreted proteins as an in vitro model for discovery of liver toxicity markers
10.1021/pr1005668 · 2010 · External reference
10.1002/pmic.200900674
10.1002/pmic.200900674 · External reference