References to Gene Logic Databases

With the 15 years of being in existence, there have been several references to the Gene Logic databases in publications and in books.  I am pretty amazed at the different kinds of research work being done with our databases and the services that we have been performing for our partners.

I will be annotating these in the coming few days so this is not an exhaustive list by any means.

 

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Articles in 2011

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1. Therapeutic Targeting the Loss of the Birt-Hogg-Dubé Suppressor Gene

Xiaohong Lu1,  Wenbin Wei3, Janine Fenton1,2, Michael S. Nahorski1,2, Erzsebet Rabai2,4, Anne Reiman1,2, Laurence Seabra1,2, Zsuzsanna Nagy2,4, Farida Latif1,2,3 andEamonn R. Maher1,2,3

+Author Affiliations Authors’ Affiliations:¹Medical and Molecular Genetics, School of Clinical and Experimental Medicine, ²Centre for Rare Diseases and Personalised Medicine, ³The Cancer Research UK Cancer Centre, and ⁴Division of Neuropharmacology and Neurobiology Section, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom

Corresponding Author: Eamonn R. Maher, Department of Medical and Molecular Genetics, School of Clinical and Experimental Medicine, University of Birmingham; Edgbaston, Birmingham B15 2TT

…….To identify candidate anticancer agents that might differentially affect cancer cell lines with differing
levels of FLCN expression, drugs with GI 50 positively correlated with the FLCN expression values
as measured using Affymetrix U133 array and U95 array by Gene Logic, Inc

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2.  An antibody-drug conjugate targeting the endothelin B receptor for the treatment of melanoma.

Jyoti Asundi1, Chae Reed2, Jennifer Arca3, Krista McCutcheon4, Ronald Ferrando5, Suzanna Clark6, Elizabeth Luis7, Janet Tien8, Ron Firestein9, and Paul Polakis10,*

+Author Affiliations

¹Cancer Targets, Genentech,Inc ²BioAnalytical Sciences, Genentech,Inc ³Translational Oncology, Genentech,Inc ⁴Research, Trellis Bioscience ⁵Pathology, Genentech, Inc ⁶Translational Oncology & Cancer Signaling, Genentech Inc ⁷Proetin Chemistry, Genentech Inc. ⁸Translation Oncology, Genentech, Inc. ⁹Pathology, Genentech ¹⁰Cancer Targets, Genentech, Inc

* Corresponding Author:Paul Polakis, Cancer Targets, Genentech, Inc, 1 DNA Way, South San Francisco, CA, 94080, United States ppolakis@gene.com

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3. Chronic Suppression of Phosphodiesterase 10A Alters Striatal Expression of Genes Responsible for Neurotransmitter Synthesis, Neurotransmission, and Signaling Pathways Implicated in Huntington’s Disease

Robin J. Kleiman, Lida H. Kimmel, Susan E. Bove,Thomas A. Lanz,John F. Harms,Alison Romegialli,Kenneth S. Miller, Amy Willis, Shelley des Etages, Max Kuhn and Christopher J. Schmidt

+Author Affiliations

1. Neuroscience Research Unit (R.J.K., L.H.K., S.E.B., T.A.L., J.F.H., A.R., A.W., C.J.S.), Genetically Modified Animals Unit (K.S.M.), Cardiovascular and Metabolic Disease Research Unit (S.d.E.), and Biostatistics Unit (M.K.), Pfizer Global Research and Development, Pfizer, Inc., Groton, Connecticut

1. Address correspondence to:Dr. Robin J. Kleiman, Neuroscience Research Unit, Eastern Point Road, Pfizer Global Research and Development, Groton, CT 06379. E-mail:robin.j.kleiman@pfizer.comAffymetrix Chip Profiling and Data Analysis. RNA isolation and
   hybridizations to mouse 430 2.0 whole genome Affymetrix (Santa Clara, CA) chips
   were performed by GeneLogic (Gaithersburg, MD)

4. Telomerase-deficient mice exhibit bone loss due to defects in osteoblasts and increased osteoclastogenesis by inflammatory microenvironment^†

Hamid Saeed¹, Basem M. Abdallah¹, Nicholas Ditzel¹, Philip Catala-Lehnen², Weimin Qiu¹, Michael Amling², Moustapha Kassem^1,3,*DOI: 10.1002/jbmr.349

Copyright © 2011 American Society for Bone and Mineral Research

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Articles in 2010

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1. Upregulation of Poly (ADP-Ribose) Polymerase-1 (PARP1) in Triple-Negative Breast Cancer and Other Primary Human Tumor Types

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2. Mutated genes in cancer research

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3. Performance of PCR based assays targeting bacteriodales genetic markers of human fecal pollution in sewage and fecal samples

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4. Molecular Biomarker Analyses Using Circulating Tumor Cells

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5. Fetal malformations and early embryonic gene expression response in cynomolgus monkeys maternally exposed to thalidomide

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6. Gene expression profiling studies of three SERMs and their conjugated estrogen combinations in human breast cancer cells: Insights into the unique antagonistic effects of bazedoxifene on conjugated estrogens

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7. Research Gene expression profiles help identify the Tissue of Origin for metastatic brain cancers

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8. Implication of synapse-related genes in bipolar disorder by linkage and gene expression analyses

Catalina Lopez de Lara^a1a2, Iris Jaitovich-Groisman^a1, Cristiana Cruceanu^a1, Firoza Mamdani^a1, Véronique Lebel^a1, Volodymyr Yerko^a1, Angus Beck^a3, L. Trevor Young^a4, Guy Rouleau^a5, Paul Grof^a6, Martin Alda^a2a7 c2 and Gustavo Turecki^a1 c1

this one references Genesis 2.0 , which is one of the most comprehensive gene expression analysis packages you can find. This allows users to completely view their data from Bioexpress or their own data and slice and dice the data in any manner they choose to. Very powerful indeed say most of the users who do use this product.

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9. Toxicogenomics revolution in the optimisation ofpharmaceutical drug development and drug safetyevaluations

Fokunang C. N.1*, Tembe-Fokunang E. A.1, Ngameni B.1, Barkwan S. S.2, Tomkins P. T.2,Asongalem E. A.1, Ngadjui B. T.1, Ngogang J. Y.1, Abena O. M. T.1and Asonganyi T.11Department of Pharmacy and African Pharmacotherapeutics, Faculty of Medicine and Biomedical Sciences,University of Yaoundé 1, P.O. Box 33032, Yaoundé, Centre Region, Cameroon.2Athlone Institute of Technology, Centre for Biopolymer and Bio–molecular Research, County Westmeath,Republic of Ireland.

this full length paper addresses the new high throughput means of assessing toxicity using toxicogenomics.  Toxicogenomics investigate the changes in gene expression profile following exposure to a toxicant. This paper referes to the ToxExpress database created by Gene Logic and also looks at the field in general. Good reading material

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10 . State-of-the-art genomics approaches in toxicology

Paul Van Hummelen^a, b, ,  and Jennifer Sasaki^c

^a MicroArray Facility, VIB, Herestraat 18, 3000 Leuven, Belgium

^b Bionomics Research & Technology Center (BRTC), Environmental and Occupational Health Science Institute (EOHSI), University of Medicine and Dentistry of New Jersey, 170 Frelinghuysen Road, Piscataway, NJ 08854, United States

^c Johnson & Johnson Pharmaceutical Research and Development, 1000 Route 202 South, Raritan, NJ 08869, United States

this paper addresses the new state of the art genomics techniques in the field of toxicology.

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11  A novel adipokine GM2AP impairs insulin signaling

Kiyoshi Higashi^a, , , Toshiyuki Mikami^b, Toru Yamada^b, Hitoshi Kawashima^b, Toru Kimura^b and Hideo Kaneko^a

^a Environmental Health Science Laboratory, Sumitomo Chemical Co. Ltd., Oaka 554-8558, Japan

^b Genomic Science Laboratories, Dainippon Sumitomo Pharma Co. Ltd., Oaka 554-8558, Japan

this references the Ascenta database.

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Articles in 2009

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1.

Global Brain Gene Expression Analysis Links Glutamatergic and GABAergic Alterations to Suicide and Major Depression

Adolfo Sequeira^1¤, Firoza Mamdani¹, Carl Ernst¹, Marquis P. Vawter⁴, William E. Bunney⁴, Veronique Lebel¹, Sonia Rehal¹, Tim Klempan¹, Alain Gratton¹, Chawki Benkelfat², Guy A. Rouleau³, Naguib Mechawar¹, Gustavo Turecki^1*

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Articles in 2008

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1. From pharmacogenomics to translational biomarkers.Mendrick DL.Department of Toxicogenomics, Gene Logic Inc., Gaithersburg, Maryland, USA.

Abstract :There is a need for new biomarkers to enable faster detection of adverse events due to drugs and disease processes. One would prefer biomarkers that are useful in multiple species (i.e., translational or bridging biomarkers) so that it would be possible to directly link responses between species and follow such injury in both preclinical and clinical settings. This chapter will explore some of the issues surrounding the use of pharmacogenomics to identify and qualify such biomarkers, and examples will be provided.

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2. In vivo predictive toxicogenomics.

Porter MW.

Department of Toxicogenomics, Gene Logic Inc., Gaithersburg, Maryland, USA.

Abstract

Reference databases consisting of large sample numbers and high-dimensional microarray data are now available for the investigation of adverse events in animal model systems such as the rat. This large volume of data, accompanied by appropriate study designs, compound and dose selection procedure, and minimization of technical and biological confounding effects, can yield successful predictive models for a variety of hypotheses. The process of training, validating, and implementing predictive models is cyclical and complex. This chapter highlights individual decisions that need to be made before, during, and after a model or set of models has been trained, with an emphasis on proper statistical methods and suitable interpretation of the results.

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3. Toxicogenomics and classic toxicology: how to improve prediction and mechanistic understanding of human toxicity.

Mendrick DL.

Department of Toxicogenomics, Gene Logic Inc., Gaithersburg, Maryland, USA.

Abstract

The field of toxicogenomics has been advancing during the past decade or so since its origin. Most pharmaceutical companies are using it in one or more ways to improve their productivity and supplement their classic toxicology studies. Acceptance of toxicogenomics will continue to grow as regulatory concerns are addressed, proof of concept studies are disseminated more fully, and internal case studies show value for the use of this new technology in concert with classic testing.

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4.  New markers of pancreatic cancer identified through differential gene expression analyses: claudin 18 and annexin A8.

Karanjawala ZE, Illei PB, Ashfaq R, Infante JR, Murphy K, Pandey A, Schulick R, Winter J, Sharma R, Maitra A, Goggins M, Hruban RH.The Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, The Johns Hopkins Medical Institutions, Baltimore, MD 21231-2410, USA.

Abstract

The gene expression patterns of 24 surgically resected primary infiltrating ductal adenocarcinomas of the pancreas were compared with 18 non-neoplastic samples using the Affymetrix U133 Plus 2.0 Arrays and the Gene Logic GeneExpress Software System. Gene fragments from 4 genes (annexin A8, claudin 18, CXCL5, and S100 A2) were selected from the fragments found to be highly expressed in infiltrating adenocarcinomas when compared with normal tissues. The protein expression of these genes was examined using immunohistochemical labeling of tissue microarrays.

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5. Differential Expression of Multiple Genes in Association with MADH4/DPC4/SMAD4 Inactivation in Pancreatic Cancer

Dengfeng Cao,¹ Raheela Ashfaq,³ Michael G. Goggins,¹ Ralph H. Hruban,^1,2 Scott E. Kern,² and Christine A. Iacobuzio-Donahue^1,2

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6. New Markers of Pancreatic Cancer Identified Through Differential Gene Expression Analyses: Claudin 18 and Annexin A8

Zarir E. Karanjawala, MD, PhD,^* Peter B. Illei, MD,^* Raheela Ashfaq, MD,^† Jeffrey R. Infante, MD,^*‡ Kathleen Murphy, PhD,^* Akhilesh Pandey, MD, PhD,^*‡§ Richard Schulick, MD,^|| Jordan Winter, MD,^|| Rajni Sharma, PhD,^*Anirban Maitra, MBBS,^*‡§ Michael Goggins, MD,^*‡ and Ralph H. Hruban, MD^*‡

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7. Empirical Bayes models for multiple probe type microarrays at the probe level

Magnus Åstrand, Petter Mostad and Mats Rudemo

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Articles in 2007

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1. Fisher’s combined p-value for detecting differentially expressed genes using Affymetrix expression arrays

Ann Hess and Hari Iyer

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2. Liver-specific Activities of FGF19 Require Klotho beta

Benjamin C. Lin, Manping Wang, Craig Blackmore and Luc R. Desnoyers 1

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3. Identification of Hepatocyte Growth Factor Activator Inhibitor-1B as a Potential Physiological Inhibitor of Prostasin

Bin Fan^‡, Thomas D. Wu^§, Wei Li^‡ and Daniel Kirchhofer^‡,1

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4. The use of logic relationships to model colon cancer gene expression networks with mRNA microarray data

Xiaogang Ruan^a, Jinlian Wang^a, Hui Li^b, Rhoda E. Perozzi^c, and Edmund F. Perozzi^c,

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Articles in 2006

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1. A summarization approach for Affymetrix GeneChip data using a reference training set from a large, biologically diverse database

Simon Katz¹, Rafael A Irizarry², Xue Lin ³, Mark Tripputi¹ and Mark W Porter¹

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2.Complementary new approaches enable repositioning of failed drug candidates

Louis A Tartaglia^†

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3.Multiregional Gene Expression Profiling Identifies MRPS6 as a Possible Candidate Gene for Parkinson’s Disease

PAPAPETROPOULOS, SPIRIDON¹; FFRENCH-MULLEN, JARLATH²; MCCORQUODALE, DONALD¹; QIN, YUJING¹; PABLO, JOHN¹; MASH, DEBORAH C.¹

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4.Uncovering potential biomarkers in ovarian carcinoma via biclustering of DNA microarray data

Tchagang,A.B. Tewfik,A.H. Skubitz,A.P.N. Skubitz,K.M.;

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5. Notch signaling is required for normal prostatic epithelial cell proliferation and differentiation

Xi-De Wang^a, Ching Ching Leow^a, Jiping Zha^b, Zhijun Tang^c, Zora Modrusan^a, Freddy Radtke^d, Michel Aguet^e, Frederic J. de Sauvage^aand Wei-Qiang Gao^a

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6. TTLL7 Is a Mammalian β-Tubulin Polyglutamylase Required for Growth of MAP2-positive Neurites

Koji Ikegami^‡ , Masahiro Mukai ^‡, Jun-ichi Tsuchida ^§, Robb L. Heier ^¶, Grant R. MacGregor ^¶ and Mitsutoshi Setou ^{‡ ∥ ** 1}

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7.  Pharmacogenomics and regulatory decision making: an international perspective

D L Mendrick¹, C Brazell², E A Mansfield³, R Pietrusko⁴, I Barilero⁵, J Hackett⁶, S Stürzebecher⁷ and D Jacobson-Kram⁸

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8.

Intracranial drug-delivery scaffolds: Biocompatibility evaluation of sucrose acetate isobutyrate gels

 

James Lee^a, George I. Jallo^a, Margaret B. Penno^b, Kathleen L. Gabrielson^c, G. David Young^d, Randolph M. Johnson^{e, 1}, Edward M. Gillis^e, 2, Charles Rampersaud^e, 2, Benjamin S. Carson^a and Michael Guarnieri^a

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9.

Clusters of Adjacent and Similarly Expressed Genes across Normal Human Tissues Complicate Comparative Transcriptomic Discovery

Chang Liu¹, Sujoy Ghosh¹, David B. Searls¹, Ann M. Saunders¹, Jeffrey Cossman² and Dr. Allen D. Roses¹

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10.

Implication of SSAT by Gene Expression and Genetic Variation in Suicide and Major Depression

Adolfo Sequeira, MSc; Fuad G. Gwadry, PhD; Jarlath M. H. ffrench-Mullen, PhD; Lilian Canetti; Yves Gingras, MSc; Robert A. Casero, Jr, PhD; Guy Rouleau, MD, PhD; Chawki Benkelfat, MD; Gustavo Turecki, MD, PhD

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11. Therapeutic Implications of a Human Neutralizing Antibody to the Macrophage-Stimulating Protein Receptor Tyrosine Kinase (RON), a c-MET Family Member

Jennifer M. O’Toole¹, Karen E. Rabenau¹, Kerri Burns¹, Dan Lu², Venkat Mangalampalli³, Paul Balderes⁴, Nicole Covino⁴, Rajiv Bassi⁵, Marie Prewett⁵, Kimberly J. Gottfredsen⁶, Megan N. Thobe⁷, Yuan Cheng¹, Yiwen Li⁵, Daniel J. Hicklin⁵, Zhenping Zhu², Susan E. Waltz⁷, Michael J. Hayman⁶, Dale L. Ludwig³, and Daniel S. Pereira¹

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Articles in 2005

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1. Differential Gene Expression in Liposarcoma, Lipoma, and Adipose Tissue

Dr.Keith M Skubitz^1,4, Edward Y Cheng², Denis R Clohisy², Roby C Thompson² and Amy P. N Skubitz³

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2. Iterative Reconstruction of Transcriptional Regulatory Networks: An Algorithmic Approach

Christian L. Barrett, Bernhard O. Palsson^*

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3.Altered patterns of transcription of the septin gene, SEPT9, in ovarian tumorigenesis

Michael Scott¹, W. Glenn McCluggage², Kenneth J. Hillan³, Peter A. Hall¹, S.E. Hilary Russell^1,*,†

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4.An Exploration of Affymetrix Probe-Set Intensities in Spike-In Experiments

Karla V. Ballman, Terry M. Therneau

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5.

A comparison of match-only algorithms for the analysis of Plasmodium falciparum oligonucleotide arrays

K.M. Simpson^a, J. Baum^a, R.T. Good^a, E.A. Winzeler^b, A.F. Cowman^a and T.P. Speed^a,c

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Articles in 2004

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1. Gene expression in aggressive fibromatosis

Keith M Skubitz^ac, Amy P.N Skubitz^b

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2. Characterization of sarcomas by means of gene expression

Keith M Skubitz^ac, Amy P.N Skubitz^b

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3. Gene expression in giant-celltumors

Keith M. Skubitz^ad, Edward Y. Cheng^bd,Denis R. Clohisy^bd,Roby C. Thompson^bd,Amy P.N. Skubitz^cd

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4. Hath1, Down-Regulated in Colon Adenocarcinomas, Inhibits Proliferation and Tumorigenesis of Colon Cancer Cells

Ching Ching Leow, Maria S. Romero, Sarajane Ross, Paul Polakis, and Wei-Qiang Gao

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5. Identification and Validation of Novel Androgen-Regulated Genes in Prostate Cancer

Anne Marie Velasco, Kimberly A. Gillis, Yizheng Li, Eugene L. Brown, Tammy M. Sadler, Maria Achilleos, Lee M. Greenberger, Philip Frost, Wenlong Bai and Yixian Zhang

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6. Gene expression profiles of circulating leukocytes correlate with renal disease activity in IgA nephropathy

GLORIA A PRESTON¹, IWAO WAGA¹, DAVID A ALCORTA, HITOSHI SASAI, WILLIAM E MUNGER, PAMELA SULLIVAN, BRIAN PHILLIPS, J CHARLES JENNETTE and RONALD J FALK

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7. Today’s drug discovery unlocking greater potential

J King

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8.

Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset

Sung E Choe^1,2, Michael Boutros^6,1, Alan M Michelson^1,2,3, George M Church¹ and Marc S Halfon^4,2,5*

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9. Toxicogenomics Data: The Road to Acceptance

Kris Freeman

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Articles in 2003

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1. A high performance test of differential gene expression for oligonucleotide arrays

William J Lemon^*, Sandya Liyanarachchi^† and Ming You^*†

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2. Exploration, normalization, and summaries of high density oligonucleotide array probe level data

Rafael A. Irizarry^*, Bridget Hobbs, Francois Collin, Yasmin D. BeazerBarclay, Kristen J. Antonellis, Uwe Scherf and Terence P. Speed

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3. Expression Profiling Identifies a Novel α-Methylacyl-CoA Racemase Exon with Fumarate Hydratase Homology

Grace L. Shen-Ong², Yun Feng, and Dean A. Troyer

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4. Differential gene expression in leiomyosarcoma

Keith M. Skubitz M.D.^1,*,†, Amy P. N. Skubitz Ph.D.²

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5. Heterogeneity of Variance in Gene Expression Microarray Data

Davidm. Rocke

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6. Highly Expressed Genes in Pancreatic Ductal Adenocarcinomas

Christine A. Iacobuzio-Donahue¹³,Raheela Ashfaq⁵, Anirban Maitra¹, N. Volkan Adsay ⁶ , Grace L. Shen-Ong ⁷ , Karin Berg ¹ , Michael A. Hollingsworth ⁸ , John L. Cameron ² , Charles J. Yeo ² , Scott E. Kern ¹³ , Michael Goggins ¹⁴ , and Ralph H. Hruban ¹³

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7. Molecular Cloning, Genomic Structure, and Expression Analysis of MUC20, a Novel Mucin Protein, Up-regulated in Injured Kidney

Toshio Higuchi^‡§, Takuya Orita^‡§, Setsuko Nakanishi^‡, Ken Katsuya^‡, Hirotaka Watanabe^‡, Yoshiki Yamasaki^‡, Iwao Waga^‡, Toyomichi Nanayama^¶, Yoshihisa Yamamoto^¶, William Munger^∥, Hong-Wei Sun^∥, Ronald J. Falk^**, J. Charles Jennette^**,David A. Alcorta^**, Huiping Li^‡‡, Tadashi Yamamoto^‡‡, Yutaka Saito^‡ and Motonao Nakamura^‡§§

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8. Altered mRNA expression in renal biopsy tissue from patients with IgA nephropathy

Iwao Waga, Jun Yamamoto, Hitoshi Sasai, William E Munger, Susan L Hogan, Gloria A Preston, Hong-Wei Sun, J Charles Jennette, Ronald J Falk and David A Alcorta

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9. Data Management Challenges for Molecular and Cell Biology: An Industry Perspective

Victor M. Markowitz

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Articles in 2002

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1. Large-scale gene expression analysis in molecular target discovery.

 

 

Orr MS, Scherf U.

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2. Toxicogenomics: a new revolution in drug safety

 

Arthur L. Castle^a, Michael P. Carver^b and Donna L. Mendrick

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3. Biochemical programs and enzyme-pattern-targeted chemotherapy in cancer cells

George Weber^a, Edith Olah^a, May S. Lui^a and Diana Tzeng^a

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4.

Gene Expression Data Management: A Case Study

Victor M. Markowitz, I-Min A. Chen and Anthony Kosky

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Articles in 2001

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1. Applying data warehouse concepts to gene expression data management

 

 

Markowitz, V.M., Topaloglou, T.

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2. An inherited p53 mutation that contributes in a tissue-specific manner to pediatric adrenal cortical carcinoma

 

Raul C. Ribeiro ^a,b,c,d, Fabiano Sandrini ^e, Bonald Figueiredo ^e,f, Gerard P. Zambetti^g,h, Edson Michalkiewicz^b, Antony R. Lafferty ⁱ, Luiz DeLacerda ^e,f, Mark Rabin ^j,k, Craig Cadwell ^g, Gilberto Sampaio ^f,l, Israil Cat ^e,Constantine A. Stratakis ⁱ, and Romolo Sandrini ^e,f

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3. Reproducible gene expression measurement among multiple laboratories obtained in a blinded study using standardized RT (StaRT)-PCR

 

 

Erin L. Crawford MS^*, Godfridus J. Peters PhD^[dagger], Paul Noordhuis ^[dagger], Marianne G. Rots PhD^[dagger], Martin Vondracek MS^[Dagger], Roland C. Grafstr^[ouml]m DrMEDSc^[Dagger], Kimberly Lieuallen BS^[sect], Gregory Lennon PhD^[par], Robert J. Zahorchak PhD^[para], Melanie J. Georgeson BS^[para], Anil Wali PhD^[num], John F. Lechner PhD^**, Pan Sheng Fan MD^*, M. Bashar Kahaleh MD^*, Sadik A. Khuder DDS, PhD^*, Kristy A. Warner PhD^*, David A. Weaver DDS, PhD^* and James C. Willey MD^*

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4. Molecular genetics of small cell lung carcinoma

Ignacio I Wistuba^abc,Adi F Gazdar^abc1,John D Minna^abc1

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5.

Extending traditional query-based integration approaches for functional characterization of post-genomic data

 

Barbara A. Eckman^1,*, Anthony S. Kosky² and Leonardo A. Laroco,^Jr1

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6. Identification of differentially expressed genes in hepatocellular carcinoma and metastatic liver tumors by oligonucleotide expression profiling

 

 

Darci Tackels-Horne M.S., M. David Goodman M.D., Amanda J. Williams M.S., Daniel J. Wilson M.S., Tara Eskandari M.S., Lisa M. Vogt M.S., Joseph F. Boland B.S., Uwe Scherf Ph.D., Joseph G. Vockley Ph.D.,^†

 

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7. Genomic and proteomic analysis of the myeloid differentiation program

Zheng Lian, Le Wang, Shigeru Yamaga, Wesley Bonds, Y. Beazer-Barclay, Yuval Kluger, Mark Gerstein, Peter E. Newburger, Nancy Berliner, and Sherman M. Weissman

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8. The end of the beginning for genomic medicine

David Bailey, Edward Zanders, and Philip Dean

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9.

Discovery of 830 candidate therapeutic targets and diagnostic markers for breast cancer using oligonucleotide microarray technology

Michael Orr, Amanda Williams, Lisa Vogt, Joseph Boland, Harry Yang, Jeffrey Cossman & Uwe Scherf

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Articles in 2000

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1. A gene expression database for the molecular pharmacology of cancer

Uwe Scherf^{1, 8}, Douglas T. Ross², Mark Waltham¹, Lawrence H. Smith¹, Jae K. Lee¹, Lorraine Tanabe¹, Kurt W. Kohn¹, William C. Reinhold¹, Timothy G. Myers⁴, Darren T. Andrews¹, Dominic A. Scudiero⁵, Michael B. Eisen³, Edward A. Sausville⁶, Yves Pommier¹, David Botstein³, Patrick O. Brown^2,7 & John N. Weinstein¹

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2.

Symptomatic and asymptomatic benign prostatic hyperplasia: Molecular differentiation by using microarrays

 

Kulkarni Prakash^*, Gregorio Pirozzi^*, Michael Elashoff^*,William Munger^*, Iwao Waga ^†, Rajiv Dhir ^‡, Yoshiyuki Kakehi ^§, and Robert H. Getzenberg ^‡,¶

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3. High-throughput gene expression analysis for drug discovery

 

Gregory G. Lennon

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4. A New Zinc Ribbon Gene (ZNRD1) Is Cloned from the Human MHC Class I Region

 

Wufang Fan^a,1, Zehou Wang^b, Fidelis Kyzysztof^c, Christa Prange^c and Greg Lennon^a

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5. Structure and Analysis of the Human Dimethylglycine Dehydrogenase Gene

Barbara A. Binzak^a, Joseph G. Vockley^b, 2, Robert B. Jenkins^c, a and Jerry Vockley^{d, a}

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6.Effects of c-erbB2 Overexpression on the Drug Sensitivities of Normal Human Mammary Epithelial Cells

Michael S. Orr, Patrick M. O’Connor and Kurt W. Kohn

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Articles in 1999

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1. READS: a method for display of 3′-end fragments of restriction enzyme-digested cDNAs for analysis of differential gene expression.

Prashar Y, Weissman SM.

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2. Ethical Issues in Human Gene Therapy

LeRoy Walters

 

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3. Immobilization of Nucleic Acids at Solid Surfaces: Effect of Oligonucleotide Length on Layer Assembly

A.B. Steel^*,R.L. Levicky^†,T.M. Herne^‡and M.J. Tarlov^‡

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4. Seamless Integration of Biological Applications within a Database Framework

 

Thodoros Topaloglou, Anthony Kosky and Victor Markowitz

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5.Protecting Genetic Privacy: Why It is So Hard to Do

Mark A. Rothstein

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Articles in 1998

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1. Manufacturing and quality control of plasmid-based gene expression systems.

Eastman EM, Durland RH.

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Articles in 1997

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1. Chimeric receptors as gene switches

Victoria E Allgood,^a and Eric M ^b

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Books

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And it doesn’t stop at journal articles, there are several books that reference Gene Logic databases.

1. Application of toxicogenomics to cross-species extrapolation

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2. Analyzing microarray gene expression data

By Geoffrey J. McLachlan, Kim-Anh Do, Christophe Ambroise

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3. Applications of toxicogenomic technologies to predictive toxicology and risk assessment

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4.  An introduction to toxicogenomics

By Michael E. Burczynski

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5. Genomics and Pharmacogenomics in Anticancer Drug Development and Clinical …

By Federico Innocenti