Updated: November 9th 2012.
ToxExpress® Program was a collaborative program with several large Pharma companies and Gene Logic. Of late, there has been interest in this program by several companies in the Chemical, Environmental, Tobacco and Cosmetic Industry. For those trying to evaluate this program this list of references may be very helpful to see how others have used this program effectively.
http://www.genelogic.com/knowledge-suites/toxexpress-program
2012, 2011, 2010, 2009, 2008, 2007, 2006, 2005, 2004, 2003, 2002, 2001, 2000
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2012
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Predictive modeling of chemical hazard by integrating numerical descriptors of chemical structures and short-term toxicity assay data
I Rusyn, A Sedykh, Y Low, KZ Guyton… – Toxicological …, 2012 – Soc Toxicology
… (2011) reported a similar outcome when gene expression data … Evaluation System
[http://toxico.nibio.go.jp/], Chemical Effects in Biological Systems Database [http://www.niehs.
nih.gov/research/resources/databases/cebs/], ToxExpress [http://www.genelogic.com/knowledge …
[http://toxico.nibio.go.jp/], Chemical Effects in Biological Systems Database [http://www.niehs.
nih.gov/research/resources/databases/cebs/], ToxExpress [http://www.genelogic.com/knowledge …
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2011
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Quantitative knowledge-based analysis in compound safety assessment
S Bureeva… – Expert Opinion on Drug Metabolism …, 2011 – ingentaconnect.com
… Two compa- nies, GeneLogic and Iconix, developed commercial databases of gene expression
profiles and ‘drug signatures’ for dozens of toxicity end points and hundreds of drugs, known,
respec- tively, as ToxExpress Ò Program [26] and DrugMatrix [18]. …
profiles and ‘drug signatures’ for dozens of toxicity end points and hundreds of drugs, known,
respec- tively, as ToxExpress Ò Program [26] and DrugMatrix [18]. …
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2010
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State-of-the-art genomics approaches in toxicology
P Van Hummelen… – Mutation Research/Reviews in Mutation …, 2010 – Elsevier
… for hepatotoxicity based on raw microarray data within ToxExpress ® data base of Gene Logic. …
Japanese Toxicogenomics Project in which they developed a 112 gene classifier to … GeneLogic’s
ToxExpress ® Program contains a database comprised of over 14,000 drug treated …
Japanese Toxicogenomics Project in which they developed a 112 gene classifier to … GeneLogic’s
ToxExpress ® Program contains a database comprised of over 14,000 drug treated …
15 Toxicogenomic and pathway analysis
B Lu, Y Jiang… – Predictive Toxicology in Drug Safety, 2010 – books.google.com
… In the commercial arena, GeneLogic’s ToxExpress and Entelo’s DrugMatrix are the two major …
DrugMatrix also come from two main data- base vendors Genelogic and Entelos. … toxicity15
DrugMatrix; 5 -day signatures predict 30-day nephrotoxicity10 Gene Logic ToxShield R&D …
DrugMatrix also come from two main data- base vendors Genelogic and Entelos. … toxicity15
DrugMatrix; 5 -day signatures predict 30-day nephrotoxicity10 Gene Logic ToxShield R&D …
[PDF] Toxicogenomics revolution in the optimisation of pharmaceutical drug development and drug safety evaluations
CN Fokunang, EA Tembe-Fokunang… – African Journal of …, 2010 – academicjournals.org
… Gaithersburg, MD, USA) has built a reference database called the ToxExpress™ Module (Wen …
However, gene expression for certain genes might be switched on or off, rather … Finally,
toxicogenomics DB providers such as GeneLogic, CuraGen and Iconix supply software tools …
However, gene expression for certain genes might be switched on or off, rather … Finally,
toxicogenomics DB providers such as GeneLogic, CuraGen and Iconix supply software tools …
Predicting hepatotoxicity using cell based assays
LC Mattheakis, JK Trautman, GP Solar… – US Patent …, 2010 – Google Patents
… Med. Biol. 41:523-537, 1996. R. Pepperkok et al., “System for quantitation of gene expression
in single cells by computerized microimaging: Application to c-fos expression after microinjection
of anti-casein kinase II antibody”, Experimental Cell Research 204:278-285, 1993. …
in single cells by computerized microimaging: Application to c-fos expression after microinjection
of anti-casein kinase II antibody”, Experimental Cell Research 204:278-285, 1993. …
Drug development from natural products: Exploiting synergistic effects
G Ulrich-Merzenich, D Panek, H Zeitler… – Indian journal of …, 2010 – nopr.niscair.res.in
… 200 validated gene signature sets Gene Logic www.genelogic.com ToxExpress™
ToxExpress™ reference data base predictive system with in in vivo+in vitro models.
Extensive liver toxicity database. Exonhit http://www.exonhit.com …
ToxExpress™ reference data base predictive system with in in vivo+in vitro models.
Extensive liver toxicity database. Exonhit http://www.exonhit.com …
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2009
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Methods for determining hepatotoxins
D Mendrick, M Porter, K Johnson, B Higgs… – US Patent …, 2009 – Google Patents
… DL, ToxExpress, FDA-DIA Pharmacogenomics Work- shop May 2002, (2002). Mendrick, D.,
“Discovery of Relevant biomarkers for Nonclinical and Clinical Applications,” American College
of Toxicology Mtg. Nov. 8, 2004, (2004). Mendrick, D., “Rold of Gene Expression Studies …
“Discovery of Relevant biomarkers for Nonclinical and Clinical Applications,” American College
of Toxicology Mtg. Nov. 8, 2004, (2004). Mendrick, D., “Rold of Gene Expression Studies …
H Toyoshiba, H Sawada, I Naeshiro… – Toxicology letters, 2009 – Elsevier
… Tong et al., 2003), ArrayExpress at the EBI (Parkinson et al., 2007), the Toxicogenomics Project
(TGP) (Takashima et al., 2006), Iconix DrugMatrix, the GeneLogic ToxExpress and BioExpress,
and the NCBI microarray data repository Gene Expression Omnibus (GEO) (www.ncbi …
(TGP) (Takashima et al., 2006), Iconix DrugMatrix, the GeneLogic ToxExpress and BioExpress,
and the NCBI microarray data repository Gene Expression Omnibus (GEO) (www.ncbi …
[PDF] Toxicogenomics and Cell-based Assays for Toxicology
… For example, ToxExpress® (http://www.genelogic.com/) and DrugMatrix®
(http://www.iconixbiosciences.com/) are two of the most comprehensive reference
databases available, devel- oped by Gene Logic and Iconix, respectively. …
(http://www.iconixbiosciences.com/) are two of the most comprehensive reference
databases available, devel- oped by Gene Logic and Iconix, respectively. …
Toxicogenomics Application to Oncology Drug Development
L Calzolai… – … in Anticancer Drug Development and Clinical …, 2009 – Springer
… ToxExpress Gene Logic Inc.: ToxExpress Module www.genelogic.com PTS CuraGen
Corporation: Predictive http://www.curagen.com/rnd/pts.asp Toxicogenomic Screen GeneMatrix
Iconix Biosciences, Inc.: GeneMatrix http://www.iconixbiosciences.com …
Corporation: Predictive http://www.curagen.com/rnd/pts.asp Toxicogenomic Screen GeneMatrix
Iconix Biosciences, Inc.: GeneMatrix http://www.iconixbiosciences.com …
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2008
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Key Aspects of Toxicogenomic Data Analysis and Interpretation as a Safety Assessment Tool to Identify and Understand Drug‐Induced Toxicity
A Vladimirova… – Toxicogenomics, 2008 – Wiley Online Library
… These include databases from commercial sources, such as Gene– Logic’s ToxExpress R
с System (Castle et al., 2002) (http://www.genelogic.com/genomics/ toxexpress/system.cfm),
and Entelos (formerly Iconix Biosciences) DrugMatrix R с (http:// …
с System (Castle et al., 2002) (http://www.genelogic.com/genomics/ toxexpress/system.cfm),
and Entelos (formerly Iconix Biosciences) DrugMatrix R с (http:// …
Microarray analysis in rat liver slices correctly predicts in vivo hepatotoxicity
MGL Elferink, P Olinga, AL Draaisma… – Toxicology and applied …, 2008 – Elsevier
… TM (Suite v1.0 and the liver V toxicity prediction model)(Gene Logic, an Ocimum … models to assess
the potential for human hepatotoxicity based on rat gene expression data. … Affymetrix CEL files
for the appropriate treated samples and controls (GeneLogic, www.genelogic.com …
the potential for human hepatotoxicity based on rat gene expression data. … Affymetrix CEL files
for the appropriate treated samples and controls (GeneLogic, www.genelogic.com …
SA Barros… – METHODS IN MOLECULAR BIOLOGY-CLIFTON …, 2008 – Springer
… This chapter describes our internal efforts to develop and evaluate predictive in vitro and in vivo
toxicogenomic models for hepatotoxicity based on the raw microarray data within the ToxExpress®
database (Gene Logic, Inc., Gaithersburg, MD), with the goal of leveraging this …
toxicogenomic models for hepatotoxicity based on the raw microarray data within the ToxExpress®
database (Gene Logic, Inc., Gaithersburg, MD), with the goal of leveraging this …
Toxicogenomics and classic toxicology: how to improve prediction and mechanistic understanding of human toxicity
DL Mendrick – … IN MOLECULAR BIOLOGY-CLIFTON THEN TOTOWA-, 2008 – Springer
… Genomic analysis can detect such events as shown in Fig. 3 and Fig. 4. Studies in Gene
Logic’s (Gaithersburg, MD) ToxExpress® database were used for the analysis. InFig. … A study
was performed using data in Gene Logic’s ToxExpress database. …
Logic’s (Gaithersburg, MD) ToxExpress® database were used for the analysis. InFig. … A study
was performed using data in Gene Logic’s ToxExpress database. …
Methods for determining renal toxins
D Mendrick, M Porter, K Johnson, B Higgs… – US Patent …, 2008 – Google Patents
… CI. G06F 19/00 (2006.01) The present invention is based on the elucidation of the global
changes in gene expression and the identification of toxicity markers in tissues or cells exposed
to a knownrenal toxin. … Kawamoto, etal., Gene, 174:151-158 (1996). …
changes in gene expression and the identification of toxicity markers in tissues or cells exposed
to a knownrenal toxin. … Kawamoto, etal., Gene, 174:151-158 (1996). …
Molecular cardiotoxicology modeling
DL Mendrick, MW Porter, KR Johnson… – US Patent …, 2008 – Google Patents
… Pharmacol, 45: 2289-2294 (1993). (Continued) Primary Examiner—Carolyn L. Smith (74) Attorney,
Agent, or Firm—Cooley Godward Kronish LLP (57) ABSTRACT The present invention is based
on the elucidation of the global changes in gene expression and the identification …
Agent, or Firm—Cooley Godward Kronish LLP (57) ABSTRACT The present invention is based
on the elucidation of the global changes in gene expression and the identification …
W Lin, G Shen, TO Khor… – Hepatotoxicity – Wiley Online Library
… There are some commercial companies, such as ‘GeneLogic ToxExpress‘ and ‘CuraGen’, which
provide commercially available toxicogenomic databases, aiming to improve the prediction of
hep- atotoxicants and human-specific toxicants through gene expression profile …
provide commercially available toxicogenomic databases, aiming to improve the prediction of
hep- atotoxicants and human-specific toxicants through gene expression profile …
Use of Toxicogenomics as an Early Predictive Tool for Hepatotoxicity
L Suter – Toxicogenomics, 2008 – Wiley Online Library
… nomics databases such as DrugMatrix R с by Iconix/Entelos (Fielden and Kolaja, 2006) and
ToxExpress R с by Genelogic, and several … Experimental evidence using gene expression profiling
of monkeys treated with ciprofibrate, a PPAR α agonist, revealed clear species …
ToxExpress R с by Genelogic, and several … Experimental evidence using gene expression profiling
of monkeys treated with ciprofibrate, a PPAR α agonist, revealed clear species …
From Pharmacogenomics to Translational Biomarkers
DL Mendrick – … IN MOLECULAR BIOLOGY-CLIFTON THEN TOTOWA-, 2008 – Springer
… Examination of Kim-1 in human renal diseases was performed using the BioExpress® database
at Gene Logic (Gaithersburg, MD). … Studies from the ToxExpress database were selected to
examine the time course of gene expression change and the results from three …
at Gene Logic (Gaithersburg, MD). … Studies from the ToxExpress database were selected to
examine the time course of gene expression change and the results from three …
In Vivo Predictive Toxicogenomics
MW Porter – … IN MOLECULAR BIOLOGY-CLIFTON THEN TOTOWA-, 2008 – Springer
… For commercial predictive service providers such as Gene Logic Inc. (Gaithersburg, MD, USA)
and Iconix Pharmaceuticals Inc. … There is no single way to treat multiple time point data in building
models. Gene Logic has attempted to build models by two methods. …
and Iconix Pharmaceuticals Inc. … There is no single way to treat multiple time point data in building
models. Gene Logic has attempted to build models by two methods. …
Pathway analysis tools and toxicogenomics reference databases for risk assessment
B Ganter, N Zidek, PR Hewitt, D Müller… – …, 2008 – Future Medicine
… database of the NIH/NIEHS [64,65,123], ArrayTrack from the FDA/NCTR [66,124], ArrayExpress
at the EBI [67,125] and the NCBI microarray data repository Gene Expression Omnibus (GEO)
[126]. The commercial databases include GeneLogic’s ToxExpress ® System [22,127 …
at the EBI [67,125] and the NCBI microarray data repository Gene Expression Omnibus (GEO)
[126]. The commercial databases include GeneLogic’s ToxExpress ® System [22,127 …
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2007
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From the bench to the clinic and back again: translational biomarker discovery using in silico mining of pharmacogenomic data
DL Mendrick… – Biomarkers, 2007 – Future Medicine
… translational biomarker. Using Gene Logic’s BioExpress and ToxExpress databases,
the expression of FETUB in multiple species was explored. In Figure 4, the expression
of FETUB in various liver diseases in humans is shown. The …
the expression of FETUB in multiple species was explored. In Figure 4, the expression
of FETUB in various liver diseases in humans is shown. The …
NOVEL METHODS FOR FUNCTIONAL ANALYSIS OF HIGH-THROUGHPUT EXPERIMENTAL DATA AND GENE GROUPS IDENTIFIED THEREFROM
Y Nikolsky, A Bugrim… – US Patent App. 12/520,441, 2007 – Google Patents
… a microarray platform. Current analytical software and empirical gene expression
reference databases include Iconix DrugMatrix and GeneLogic’s ToxExpress. This
software has relatively low predictive power. However, this …
reference databases include Iconix DrugMatrix and GeneLogic’s ToxExpress. This
software has relatively low predictive power. However, this …
E Szeto – US Patent 7,251,642, 2007 – Google Patents
… 31, 2007 (56) ANALYSIS ENGINE AND WORK SPACE MANAGER FOR USE WITH GENE
EXPRESSION DATA Inventor: Ernest Szeto, Berkeley, CA (US) Assignee: Gene Logic Inc.,
Gaithersburg, MD (US) Notice: Subject to any disclaimer, the term of this patent is extended or …
EXPRESSION DATA Inventor: Ernest Szeto, Berkeley, CA (US) Assignee: Gene Logic Inc.,
Gaithersburg, MD (US) Notice: Subject to any disclaimer, the term of this patent is extended or …
Predicting hepatotoxicity using cell based assays
LC Mattheakis, JK Trautman, GP Solar… – US Patent …, 2007 – Google Patents
… Med. Biol. 41:523-537, 1996. R. Pepperkok et al., “System for quantitation of gene expression
in single cells by computerized microimaging: Application to c-fos expression after microinjection
of anti-casein kinase II antibody”, Experimental Cell Research 204:278-285, 1993. …
in single cells by computerized microimaging: Application to c-fos expression after microinjection
of anti-casein kinase II antibody”, Experimental Cell Research 204:278-285, 1993. …
Incorporating genome-based technologies into toxicology and safety assessments for drug discovery and development
LG Yengi – International Journal of Pharmaceutical Medicine, 2007 – ingentaconnect.com
… field was Gene Logic Inc. (Gaithersburg, throughput screening and the human genome project,
which made MD, USA) which, in partnership with a group of pharmaceutical it possible for newly
sequenced clones and transcripts to be easily companies, developed ToxExpress® 1 …
which made MD, USA) which, in partnership with a group of pharmaceutical it possible for newly
sequenced clones and transcripts to be easily companies, developed ToxExpress® 1 …
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2006
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Predictive models of hepatotoxicity using gene expression data from primary rat hepatocytes
L Hultin-Rosenberg, S Jagannathan… – …, 2006 – informahealthcare.com
… Expression profiles Expression profiles were obtained by performing directed queries
on the ToxExpress database from Gene Logic (http://www.genelogic.com; Castle et
al. 2002). Profiles were obtained from treatments of hepatocytes …
on the ToxExpress database from Gene Logic (http://www.genelogic.com; Castle et
al. 2002). Profiles were obtained from treatments of hepatocytes …
Toxicogenomics strategies for predicting drug toxicity
R Martin, D Rose, K Yu… – Pharmacogenomics, 2006 – Future Medicine
… Samples for the two knowledge bases were subsets of those available from the
ToxExpress ® database (Gene Logic, Inc., MD, USA). The in vitro knowledgebase
consisted of data derived from rat primary hepatocytes, while …
ToxExpress ® database (Gene Logic, Inc., MD, USA). The in vitro knowledgebase
consisted of data derived from rat primary hepatocytes, while …
[CITATION] The ToxExpress™ Module*: applying gene expression data to predictive toxicology
Application of data mining approaches to drug delivery
S Ekins, J Shimada… – Advanced drug delivery reviews, 2006 – Elsevier
… several hundred marketed drugs and toxicants using different array platforms (the Iconix Drug
Matrix™ [60], GeneLogic ToxExpress™ [61] and … connected with molecule bioactivity databases
such as BioPrint, which would combine molecular interactions at the gene level with …
Matrix™ [60], GeneLogic ToxExpress™ [61] and … connected with molecule bioactivity databases
such as BioPrint, which would combine molecular interactions at the gene level with …
Toxicogenomics and cross-species biomarker discovery: applications in drug discovery and safety assessment
MS Orr – Toxicology Mechanisms and Methods, 2006 – informahealthcare.com
… At Gene Logic Inc., Affymetrix GeneChips® microarrays were used to identify dysregulated
secreted genes in human or rat samples. Comparisons of the dysregulated genes identified in
either the human (BioExpress® database) or rat studies (ToxExpress® database) were …
secreted genes in human or rat samples. Comparisons of the dysregulated genes identified in
either the human (BioExpress® database) or rat studies (ToxExpress® database) were …
MOLECULAR CARDIOTOXICOLOGY MODELING
DL Mendrick… – US Patent App. 12/064,933, 2006 – Google Patents
… CI. C12Q 1/68 (2006.01) (52) US CI 435/6 (57) ABSTRACT The present invention includes
methods of predicting car- diotoxicity of test agents and methods of generating car- diotoxicity
prediction models using algorithms for analyzing quantitative gene expression information. …
methods of predicting car- diotoxicity of test agents and methods of generating car- diotoxicity
prediction models using algorithms for analyzing quantitative gene expression information. …
Toxicogenomics in drug discovery and development: mechanistic analysis of compound/class-dependent effects using the DrugMatrix® database
B Ganter, RD Snyder, DN Halbert… – Pharmacogenomics, 2006 – Future Medicine
… Since the most effective application of toxicogenomics requires generation of high content gene
expression data on large numbers of reference compounds, and therefore … Commercial
toxicogenomic databases include GeneLogic’s (MD, USA) ToxExpress™ Module [47,205 …
expression data on large numbers of reference compounds, and therefore … Commercial
toxicogenomic databases include GeneLogic’s (MD, USA) ToxExpress™ Module [47,205 …
Predicting hepatotoxicity using cell based assays
LC Mattheakis, JK Trautman, GP Solar… – US Patent App. 11/ …, 2006 – Google Patents
… See “Serious liver injury: leading reasons for drug removals, restrictions” http://www.fda.gov/fdac/
features/ 2001/301_liver.html; and ToxExpress™ Application Note, GeneExpress ToxExpress
Predictive System™, Gene Logic, Gaithersburg, Md. (2002). …
features/ 2001/301_liver.html; and ToxExpress™ Application Note, GeneExpress ToxExpress
Predictive System™, Gene Logic, Gaithersburg, Md. (2002). …
Tissue and species distribution of the glutathione pathway transcriptome
WB Mattes, KK Daniels, M Summan, ZA Xu… – …, 2006 – informahealthcare.com
… arrays. Rat and canine gene expression data are resident in Gene Logic’s ToxExpress®
System Database, whereas mouse gene expression data are found within Gene Logic’s
BioExpress® System Database. Affymetrix probesets …
System Database, whereas mouse gene expression data are found within Gene Logic’s
BioExpress® System Database. Affymetrix probesets …
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2005
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The use of toxicogenomic data in risk assessment: a regulatory perspective
VSW Chan, MD Theilade – Clinical Toxicology, 2005 – informahealthcare.com
… GeneLogic ToxExpress is a consortium of more than seven pharmaceutical companies that
examines samples from rats, dogs, and humans using microarray and traditional toxicity
assessment methods. The group aims to collect data on gene expression changes …
examines samples from rats, dogs, and humans using microarray and traditional toxicity
assessment methods. The group aims to collect data on gene expression changes …
Hepatotoxicity Molecular Models
M Porter, B Higgs, D Mendrick… – US Patent App. 11/ …, 2005 – Google Patents
… Each elec- tronic copy of the Sequence Listing was created on Mar. 28, 2005 with a file size of
5995 KB. The file names are as follows: Copy 1—gene logic 5134-wo.txt; Copy 2—gene logic
5134-wo.txt; Copy 3—gene logic 5134-wo.txt.; and CRF—gene logic 5134-wo.txt. …
5995 KB. The file names are as follows: Copy 1—gene logic 5134-wo.txt; Copy 2—gene logic
5134-wo.txt; Copy 3—gene logic 5134-wo.txt.; and CRF—gene logic 5134-wo.txt. …
Techniques: application of systems biology to absorption, distribution, metabolism, excretion and toxicity
S Ekins, Y Nikolsky… – Trends in pharmacological sciences, 2005 – Elsevier
… Several companies market content databases of gene-expression profiles, histopathology,
multi-parameter clinical chemistry tests and … These include Iconix (Drug Matrix™;
http://www.iconixpharm.com/), GeneLogic (ToxExpress™; http://www.genelogic.com/) [55], …
multi-parameter clinical chemistry tests and … These include Iconix (Drug Matrix™;
http://www.iconixpharm.com/), GeneLogic (ToxExpress™; http://www.genelogic.com/) [55], …
Toxicogenomics in the pharmaceutical industry: Hollow promises or real benefit?
A Lühe, L Suter, S Ruepp, T Singer… – Mutation Research/ …, 2005 – Elsevier
… In addition to the non-commercial resources, commercial providers, such as Gene Logic,
Inc. (ToxExpress ® ) or Iconix Pharmaceuticals, Inc. (DrugMatrix ® ) offer comprehensive
instruments for assessment of the toxic potential of a compound. …
Inc. (ToxExpress ® ) or Iconix Pharmaceuticals, Inc. (DrugMatrix ® ) offer comprehensive
instruments for assessment of the toxic potential of a compound. …
The role of transcriptome analysis in pre-clinical toxicology
GH Searfoss, TP Ryan… – Current Molecular Medicine, 2005 – ingentaconnect.com
… Prediction of 10 different liver toxicities. Gene Logic www.genelogic.com ToxExpress™
Gaithersburg, MD ToxExpress™ reference database predictive system with in vivo and in vitro
models. Extensive liver toxicity database. Multifaceted tools and services. …
Gaithersburg, MD ToxExpress™ reference database predictive system with in vivo and in vitro
models. Extensive liver toxicity database. Multifaceted tools and services. …
Expression genomics and drug development: towards predictive pharmacology
ET Liu – Briefings in functional genomics & proteomics, 2005 – bfg.oxfordjournals.org
… Keywords: transcription, cDNAs, expression signatures, gene regulation, drug effects … It
demonstrated a hierarchy of transcriptional impact, with cell lineage making a greater impact
than biochemical pathways, and, in turn, greater than individual gene effects. …
demonstrated a hierarchy of transcriptional impact, with cell lineage making a greater impact
than biochemical pathways, and, in turn, greater than individual gene effects. …
Prediction methods and databases within chemoinformatics: emphasis on drugs and drug candidates
SÓ Jónsdóttir, FS Jørgensen… – Bioinformatics, 2005 – Oxford Univ Press
… The ToxExpress Reference Database is a toxicogenomic database, which contains gene
expression profiles from known toxicants. This database is built on in vivo and in vitro studies
of exposure to toxicants, and around 110 compounds have been profiled. …
expression profiles from known toxicants. This database is built on in vivo and in vitro studies
of exposure to toxicants, and around 110 compounds have been profiled. …
P1 Altered Expression of Gene Products Involved as a Complex in the Endogenous Hepatocarcinogenesis of Rats Fed a Choline-Deficient, L-Amino Acid-Defined …
D Nakae, F Uematsu, Y Hatanaka… – Toxicologic …, 2005 – tpx.sagepub.com
… P1 Altered Expression of Gene Products Involved as a Complex in the Endogenous
Hepatocarcinogenesis of Rats Fed a Choline-Deficient, L-Amino Acid-Defined Diet. … P11 Gene
Expression in Regenerating Rat Liver Following Partial Hepatectomy: A Detailed Time Course. …
Hepatocarcinogenesis of Rats Fed a Choline-Deficient, L-Amino Acid-Defined Diet. … P11 Gene
Expression in Regenerating Rat Liver Following Partial Hepatectomy: A Detailed Time Course. …
N Fletcher, D Wahlström, R Lundberg… – Toxicology and applied …, 2005 – Elsevier
… Clinical chemistry and pathological examination was carried out at Gene Logic Inc. … Dose selection
was designed to encompass the dose at which gene changes were observed using microarray
analyses. … Data are contained within GeneLogic’s Toxexpress database. …
was designed to encompass the dose at which gene changes were observed using microarray
analyses. … Data are contained within GeneLogic’s Toxexpress database. …
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2004
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Methods for enhancing gene expression analysis
U Scherf, GD Hoke, DJ Wilson… – US Patent App. 10/ …, 2004 – Google Patents
… MD (US); Daniel J. Wilson, Mississauga (CA); Debra A. Barnes, Frederick, MD (US)
Correspondence Address: MORGAN LEWIS & BOCKIUS LLP 1111 PENNSYLVANIA AVENUE
NW WASHINGTON, DC 20004 (US) (73) Assignee: Gene Logic, Inc., Gaithersburg, MD (21) Appl. …
Correspondence Address: MORGAN LEWIS & BOCKIUS LLP 1111 PENNSYLVANIA AVENUE
NW WASHINGTON, DC 20004 (US) (73) Assignee: Gene Logic, Inc., Gaithersburg, MD (21) Appl. …
Gene expression alterations during HGF-induced dedifferentiation of a renal tubular epithelial cell line (MDCK) using a novel canine DNA microarray
DF Balkovetz, ER Gerrard Jr, S Li… – American Journal of …, 2004 – Am Physiological Soc
… The cRNA products were fragmented to 200 nucleotides or less, heated at 99°C for 5 min, and
hybridized for 16 h at 45°C to the ToxExpress GeneChip Canine Array, which was developed
as a custom array by Gene Logic and Pfizer, using Affymetrix standard design …
hybridized for 16 h at 45°C to the ToxExpress GeneChip Canine Array, which was developed
as a custom array by Gene Logic and Pfizer, using Affymetrix standard design …
Molecular cardiotoxicology modeling
DL Mendrick, MW Porter, KR Johnson… – US Patent App. 10/ …, 2004 – Google Patents
… CI. C12Q 1/68 G06F 19/00 (52) US CI (57) (2006.01) (2006.01) ABSTRACT 435/6; 702/20 The
present invention is based on the elucidation of the global changes in gene expression and the
identification of toxicity markers in tissues or cells exposed to a known cardiotoxin. …
present invention is based on the elucidation of the global changes in gene expression and the
identification of toxicity markers in tissues or cells exposed to a known cardiotoxin. …
K SUMIDA… – ww.sumitomo-chem.co.jp
… Treatment Rat Hepatocyte (Human, Rat) Bioinformatics CuraGen Gene Logic Iconix Company
GeneCalling® Affymetrix GeneChip Amersham CodeLink Gene Expression Platform Predictive
Toxicogenomics Screen (PTS) ToxExpress/ ToxSuite/ ToxScreen DrugMatrix …
GeneCalling® Affymetrix GeneChip Amersham CodeLink Gene Expression Platform Predictive
Toxicogenomics Screen (PTS) ToxExpress/ ToxSuite/ ToxScreen DrugMatrix …
Primary rat hepatocyte toxicity modeling
D Mendrick, M Porter, K Johnson… – US Patent App. 10/ …, 2004 – Google Patents
… S. Orr, Gaithersburg, MD (US); Michael Elashoff, Gaithersburg, MD (US) Correspondence Address:
COOLEY GODWARD LLP THE BROWN BUILDING – 875 15TH STREET, NW SUITE 800
WASHINGTON, DC 20005-2221 (US) (73) Assignee: Gene Logic Inc., Gaithersburg, MD …
COOLEY GODWARD LLP THE BROWN BUILDING – 875 15TH STREET, NW SUITE 800
WASHINGTON, DC 20005-2221 (US) (73) Assignee: Gene Logic Inc., Gaithersburg, MD …
Methods For Molecular Toxicology Modeling
JC Diggans… – US Patent App. 10/580,423, 2004 – Google Patents
… In a preferred embodiment, the database is a ToxExpress® or BioExpress® database marketed
by Gene Logic Inc., Gaithersburg, Md. [0061] The databases of the invention may be linked
to an outside or external database such as GenBank (www ncbi. …
by Gene Logic Inc., Gaithersburg, Md. [0061] The databases of the invention may be linked
to an outside or external database such as GenBank (www ncbi. …
[BOOK] Analyzing microarray gene expression data
GJ McLachlan, KA Do… – 2004 – books.google.com
Page 1. Analyzing Microarray Gene Expression Data Page 2. This Page Intentionally
Left Blank Page 3. Analyzing Microarray Gene Expression Data Page 4. WILEY
SERIES IN PROBABILITY AND STATISTICS Established …
Left Blank Page 3. Analyzing Microarray Gene Expression Data Page 4. WILEY
SERIES IN PROBABILITY AND STATISTICS Established …
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2003
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[CITATION] An introduction to toxicogenomics
ME Burczynski – 2003 – Informa HealthCare
Toxicogenomics takes center stage
J Lehmann – Drug News Perspect, 2003 – journals.prous.com
… Standardization of experimental methods was and continues to be pushed to the extreme limit
to optimize precision and reproducibility in the ToxExpress project led by Gene Logic. … URLs cited.
Society of Toxicology: http://www.toxicology.org. Gene Logic: www.genelogic.com. …
to optimize precision and reproducibility in the ToxExpress project led by Gene Logic. … URLs cited.
Society of Toxicology: http://www.toxicology.org. Gene Logic: www.genelogic.com. …
[CITATION] 12 Predictive Toxicogenomics
MW Porter, AL Castle, MS Orr… – An introduction to …, 2003 – Informa HealthCare
Predicting hepatotoxicity using cell based assays
LC Mattheakis, JK Trautman, GP Solar… – US Patent App. 10/ …, 2003 – Google Patents
… See “Serious liver injury: leading reasons for drug removals, restrictions” http://www.fda.gov/fdac/
features/ 2001/301_liver.html; and ToxExpress™ Application Note, GeneExpress ToxExpress
Predictive System™, Gene Logic, Gaithersburg, Md. (2002). …
features/ 2001/301_liver.html; and ToxExpress™ Application Note, GeneExpress ToxExpress
Predictive System™, Gene Logic, Gaithersburg, Md. (2002). …
Molecular nephrotoxicology modeling
DL Mendrick, MW Porter, KR Johnson… – US Patent App. 10/ …, 2003 – Google Patents
… CI. G06F 19/00 (2006.01) (52) US CI 702/20 (57) ABSTRACT The present invention is based
on the elucidation of the global changes in gene expression and the identification of toxicity
markers in kidney tissues or cells exposed to a known renal toxin. …
on the elucidation of the global changes in gene expression and the identification of toxicity
markers in kidney tissues or cells exposed to a known renal toxin. …
[CITATION] The future of Toxicogenomics
JC Rockett – An introduction to toxicogenomics, 2003 – Informa HealthCare
Nucleic acid detection assay control genes
A Castle, B Higgs, M Elashoff… – US Patent App. 10/620,765, 2003 – Google Patents
… Available databases include, but are not limited to, the Gene Logic ToxExpress® database, the
Gene Expression Omni- bus gene expression and hybridization array repository available through
NCBI (www.ncbi.nlm.nih.gov/entrez) and the SAGE™ gene expression database. …
Gene Expression Omni- bus gene expression and hybridization array repository available through
NCBI (www.ncbi.nlm.nih.gov/entrez) and the SAGE™ gene expression database. …
DL Mendrick – Toxicogenomics, 2003 – Springer Verlag
Methods for classification of biological data
AL Castle, MR Elashoff, KR Johnson… – US Patent App. 10/ …, 2003 – Google Patents
… Gaithersburg, MD (US); Kory R. Johnson, Gaithersburg, MD (US); Mark W. Porter, Gaithersburg,
MD (US) Correspondence Address: MORGAN LEWIS & BOCKIUS LLP 1111 PENNSYLVANIA
AVENUE NW WASHINGTON, DC 20004 (US) (73) Assignee: Gene Logic, Inc. …
MD (US) Correspondence Address: MORGAN LEWIS & BOCKIUS LLP 1111 PENNSYLVANIA
AVENUE NW WASHINGTON, DC 20004 (US) (73) Assignee: Gene Logic, Inc. …
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2002
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Toxicogenomics: a new revolution in drug safety
AL Castle, MP Carver… – Drug discovery today, 2002 – Elsevier
… The combination of READS™ and ToxExpress™ (Gene Logic) and GeneChip® (Affymetrix, Santa
Clara, CA, USA) enables the detection of both novel and known genes that respond to toxicants,
as well as validation of interesting genes using Q-RT-PCR. Predictive toxicology. …
Clara, CA, USA) enables the detection of both novel and known genes that respond to toxicants,
as well as validation of interesting genes using Q-RT-PCR. Predictive toxicology. …
System and method for managing gene expression data
V Markowitz, T Topaloglou… – US Patent App. 10/ …, 2002 – Google Patents
… 11,2003 (54) SYSTEM AND METHOD FOR MANAGING GENE EXPRESSION DATA (76) Inventors:
Victor Markowitz, Albany, CA (US); Thodoros Topaloglou, Menlo Park, CA (US); Kevin McLoughlin,
Oakland, CA (US); John Campbell, Gaithersburg, MD (US); Dmitry Krylov …
Victor Markowitz, Albany, CA (US); Thodoros Topaloglou, Menlo Park, CA (US); Kevin McLoughlin,
Oakland, CA (US); John Campbell, Gaithersburg, MD (US); Dmitry Krylov …
JD Thompson – Drug discovery today, 2002 – Elsevier
… affymetrix.com). Libraries of drug profiles from mammalian cells are also commercially
available from, for example, DrugMatrix (Incyte Genomics, http://www.incyte.com)
and ToxExpress (Gene Logic, http://www.genelogic.com). In …
available from, for example, DrugMatrix (Incyte Genomics, http://www.incyte.com)
and ToxExpress (Gene Logic, http://www.genelogic.com). In …
System and method for retrieving and using gene expression data from multiple sources
V Markowitz, T Topaloglou… – US Patent App. 10/096,645, 2002 – Google Patents
… 9,2003 (54) SYSTEM AND METHOD FOR RETRIEVING AND USING GENE EXPRESSION DATA
FROM MULTIPLE SOURCES (76) Inventors: Victor Markowitz, Albany, CA (US); Thodoros
Topaloglou, Menlo Park, CA (US); I-Min Amy Chen, El Cerrito, CA (US) Correspondence …
FROM MULTIPLE SOURCES (76) Inventors: Victor Markowitz, Albany, CA (US); Thodoros
Topaloglou, Menlo Park, CA (US); I-Min Amy Chen, El Cerrito, CA (US) Correspondence …
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2001
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VM Markowitz… – … and Bioengineering Conference …, 2001 – ieeexplore.ieee.org
… GeneExpress products are available as DataSuites, such as BioExpress and ToxExpress,
which contain data on disease or tissue specific samples (see http://www.genelogic.com/gexpress …
GeneExpress is notable for its size: it includes gene expression data on thousands of …
which contain data on disease or tissue specific samples (see http://www.genelogic.com/gexpress …
GeneExpress is notable for its size: it includes gene expression data on thousands of …
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2000
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[HTML] Toxico-Logic
A Francis – The Scientist, 2000 – f1000scientist.com
… Clontech 800-662-2566 http://www.clontech.com. Gene Logic 301-987-1700 www.genelogic.
com. Incyte 877-746-2983 http://www.incyte.com. … Gene Logic began developing its ToxExpress
database with Wyeth-Ayerst Research about 18 months ago. …
com. Incyte 877-746-2983 http://www.incyte.com. … Gene Logic began developing its ToxExpress
database with Wyeth-Ayerst Research about 18 months ago. …
Janampatri to Genomepatri - Anu Acharya 
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