Publications
B. Weigle, R. Ebner, A.Temme, S. Schwind, A. Kiessling, M. Schmitz, M.A. Rieger, G lexapro online. Schackert, H wellbutrin sr online.K . Schackert & E .P . Rieber . "Selective Overexpression of the Transcription Factor SOX11 in Human Malignant Gliomas." Oncology Reports 13: 139-44, 2005.
L.A. Kunz-Schughart, J.P. Freyer, F. Hofstaedter, R.Ebner. "The Use of 3-D Culture for High-Throughput Screening: The Multicellular Spheroid Model." Journal of Biomolecular Screening 9(4): 273-285, 2004.
B. Weigle, S. Fuessel, R. Ebner, A. Temme, M. Schmitz, S. Schwind, A. Kiessling, M.A. Rieger, A. Meye, M.P. Wirth, & E.P. Rieber. "D-GPCR: A Novel Putative G Protein-Coupled Receptor Overexpressed in Prostate Cancer and Prostate." Biochem. Biophys. Res. Commun. 322(1): 239-249, 2004.
B.H. Mecham, G.T. Klus, J. Strovel, M. Augustus, D. Byrne, P. Bozso, D.Z. Wetmore, T.J. Mariani, I.S. Kohane, Z. Szallasi. "Sequence-Matched Probes Produce Increased Cross-Platform Consistency and More Reproducible Biological Results in Microarray-Based Gene Expression Measurements." Nucleic Acids Res. 32(9): e74, May 2004.
T. Takahashi, N. Shivapurkar, H. Shigematsu, J. Reddy, M. Suzuki, M. Augustus, K. Miyajima, J. Yin, S. Meltzer, A.F. Gazdar. "DNA Methylation Profiles of Colorectal Cancers, Colon Polyps and Non-Malignant Colon Tissues." Proc. Am. Assoc. Cancer Res. 45(2): #4999 1154, March 2004.
S.D. Pack, O.M. Alper, K. Stromberg, M. Augustus, M. Ozdemirli, A.M. Miermont, G. Klus, M. Rusin, R. Slack, N.F. Hacker, T. Ried, Z. Szallasi, O. Alper. "Simultaneous Suppression of Epidermal Growth Factor Receptor and C-erbB-2 Reverses Aneuploidy and Malignant Phenotype of a Human Ovarian Carcinoma Cell Line." Cancer Res. 64(3):789-794, February 2004.
B. Weigle, R. Ebner, S. Schwind, P. Rieber. "GPCR-PCa: A Novel Putative G-Protein-Coupled Receptor Overexpressed in Prostate Cancer." Proc. Am. Assoc. Cancer Res. 45(2): #2708 625, March 2004.
B. Weigle, A. Kiessling, R. Ebner, S. Fussel, A. Temme, A. Meye, M. Schmitz, M.A. Rieger, D. Ockert, M.P. Wirth, & E.P. Rieber. "D-PCa-2: A Novel Transcript Specifically Expressed in Human Normal Prostate and Prostate Cancer." Intl. J. Cancer 109(6): May 2004.
R.Ebner. "Cancer Obeys Universal Law of Growth Study." The Times of India (interview), November 2003.
M.A. Rieger, R. Ebner, A. Kiessling, J. Rohayem, M. Schmitz, A. Temme, E.P. Rieber, & B. Weigle. "Identification of a Novel Mammary Gland Restricted Cytochrome P450, CYP4Z1, with Overexpression in Breast Carcinoma." Cancer Res. 64(7): 2357-2364, November 2004.
R. Ebner. "Cancer Obeys Law." Interview with Philip Cohen, New Scientist 180(2421): 14, November 2003.
R. Ebner. "Researchers Suggest That Universal 'Law' Governs Tumor Growth." J. Natl. Cancer Inst. 95(10): 704-705 (interview with Mike Martin), May 2003.
D.K. Bol, D.R. Soppet, A. Glodek. "The Changing Landscape of Drug Discovery Screening." Current Drug Discovery, 17-21, July 2003.
P. Stafford, P. Liu. "Microarray Technology Comparison, Statistical Analysis, and Experimental Design, Microarrays Methods and Applications: Nuts & Bolts," Ed. Gary Hardiman. DNA Press, June 2003.
P.E. Young, D.K. Bol. "High-Throughput Transcriptional Profiling for Drug Discovery and Lead Development." Genetic Engineering News, Vol. 23. January 2003.
Reinhard Ebner, John Hartwell, and Jeffrey Cossman. "Mining Integrated Genome, Microarray and Pathology Data for Genome-Wide Drug Target Discovery in silico." BioExpress™ and GX™ GenCarta: Rapid Disease Gene Discovery, Diagnostic Marker Selection and Therapeutic Target Prioritization." Genetic Engineering News 22(15): 54-97, September 2002.
TALKS
D.R. Soppet. "The Road Less Traveled: Expression Driven Drug Discovery." Cambridge Health Institute Chips to Hits Meeting. Boston. September 2004.
R. Ebner. "Genomics-Derived Targets for Antibody-Based Cancer Therapeutics." SRI's Antibody World Summit 2004. Philadelphia. July 2004.
S. Pikul. "Gene Expression Guided Discovery of Novel Anti-Cancer Agents." Cambridge Health Institute Intelligent Drug Discovery Development, Emerging Technologies Session of the Hit-To-Lead Track, (ID3) The World Pharmaceutical Congress. Philadelphia. May 2004.
D.R. Soppet. "Use of Molecular Signature Systems to Identify, Characterize and Develop New Anticancer Medicines." Cambridge Health Institute's 5th Annual, Microarrays in Medicine, Arrays of Possibilities. World Trade Center. Boston. April 2004.
P.E. Young. "Expression Profiling of Target Disruption by RNAi and Incorporation Into Drug Screening" (oral presentation. Cambridge Health Institute's RNAi for Pathway Analysis Meeting. Boston. April 2004.
S. Horrigan, J. Strovel, P. Young, B. Weigle, M. Augustus & R. Ebner. "Novel Candidate Small Molecule Drug or Therapeutic Antibody Targets and Diagnostic Cancer Markers from Disease Tissue Molecular Profiling." Cambridge Health Institute's Eleventh Annual Molecular Medicine Tri-Conference, Track 4 - Molecular Diagnostics: Utilizing Biomarkers in Diagnostic Research. San Francisco. March 2004.
D. Bol. "Driving the Complete Drug Discovery Process with Genomics Technologies." IBC Systems Biology. Boston. October 2003.
R. Ebner, M. Augustus, D.K. Bol, J. Castaneda, W.M. Cholody, S.J. Horrigan, P.Liu, S. Pikul, M.J. Shea, D.R. Soppet, J.W. Strovel, J.W.H.Watthey, Z. Weaver, Q. Zong, K. Carter, P.E. Young. "Forward Chemical Genomics: Selection of Preclinical Lead Compounds Using Transcriptional Profiling In Every Stage of The Drug Discovery Process." Second International Symposium on Signal Transduction Modulators in Cancer Therapy (STM-2003), Proffered Paper Session (oral presentation). Amsterdam. October 2003.
P.E. Young. "Target and Pathway Profiling: Using Expression Analysis to Define the Biology of Cancer." Cambridge Health Institute Genomics on Target; From Function to Validation, Target Validation Genomics. Boston. October 2003.
R. Ebner, K.C. Carter. "High-Throughput Transcriptional Profiling for Novel Drug Discovery and Optimization." Nobel Pauling Biotech Symposium: Biotech vs. Big Pharma. Cambridge. July 2003.
P.E. Young. "Transcriptional Fingerprints In Drug Discovery." 94th Annual Meeting, American Association for Cancer Research, Educational Session: Pharmacogenomics in Drug Development and Clinical Trials. Washington, D.C. July 2003.
R. Ebner, D.K. Bol, S. Pikul, D.R. Soppet, S.J. Horrigan, P.E. Young, & K.C. Carter. "High-Throughput Transcriptional Profiling for Novel Drug Discovery and Optimization." Biochips 2003. Woodbridge Sheraton Place. Iselin. July 2003.
J. Padia. "Modern Drug Discovery Process Using Combinatorial Medicinal Chemistry and Gene Transcriptional Profiling." International Pharmaceutical Industry Congress (IPIC). New York. March 2003.
P.E. Young. "Focus on The Effect, Not on the Target: Using Forward Chemical Genomics and Transcriptional Fingerprinting to Discover and Optimize New Drugs." Marcus Evans High-Throughput Screening for Drug Discovery Meeting. Boston. February 2003.
M. Augustus. "High Throughput Technologies and Therapeutic Advances:
Molecular Genetics and Gene Expression Approaches to Therapeutic Targets." The Cellular and Molecular Biology of Cancer Course, Imperial College, Hammersmith Hospital. London. February 2003.
R. Ebner. "Drug Discovery Process: The Changing Needs of a Rapidly Expanding Operation." Cambridge Health Institute Data Visualization and Interpretation Meeting. Washington, D.C. September 2002.
D. Soppet. "High Throughput Screening For Drug Discovery: Avalon's Expression Based Approach." Marcus Evans High Throughput Screening Meeting. Boston July 2002.
POSTERS
P.E. Young, J. Castaneda, M. Chakiath, K. Evans, S.K. Horrigan, S. Pikul, M.J. Shea, D.R. Soppet, J.W. Strovel, Q. Zong. High-Throughput Screening Against Intractable Targets: The Use of Target Disruption Gene Signatures for Rapid Cancer Drug Discovery. Poster presented at the EORTC-NCI-AACR 2004 Meeting in Geneva Switzerland. September 2004.
P.E. Young, J. Castaneda, M. Chakiath, K. Evans, S.K. Horrigan, S. Pikul, M.J. Shea, D.R. Soppet, J.W. Strovel, Q.Zong. Expression Profiling of Target Disruption by RNAi and Incorporation Into High-Throughput Drug Screening. Poster presented at the IBC's Annual World Congress, Drug Discovery Technology in Boston. August 2004.
Q. Zong, Z. Weaver, D. Liu, J. Bullard, P. Natarajan, D.R. Soppet. Establishing an In Vivo Efficacy Predictor and Its Application in High-Throughput Drug Discovery. Poster presented at the Cambridge Healthtech Institute's Beyond Genome Meeting in San Francisco. June 2004.
T.Takahashi, N. Shivapurkar, H. Shigematsu, J. Reddy, M. Suzuki, M. Augustus, K. Miyajima, J. Yin, S. Meltzer, A.F. Gazdar. DNA Methylation Profiles of Colorectal Cancers, Colon Polyps and Non-Malignant Colon Tissues. (poster) Proc. Am. Assoc. Cancer Res. 45(2): #4999, 1154. March 2004.
D.K. Bol, Z. Weaver, Q. Zong, J.W. Strovel, P.E. Young, S. J. Garvey, T. Perry, Y. Knight, D. Liu, P. Natarajan, J.R. Bullard, S. Pikul, J. Padia, S. O'Brien, J. Lu. Identification of a Predictive Efficacy Signature from Microarray Analysis of Human Tumor Xenografts Treated with Anticancer Compounds (poster). Proc. Am. Assoc. Cancer Res. 45 #2017, 464. March 2004.
J.W. Strovel, Q. Zong, P.E. Young, Z. Weaver, S. Pikul, W.M. Cholody, V. Petukhova, N.E. Ohler, D.K. Bol. Use of Compound-Responsive Gene Signatures to Predict for Sensitivity and Resistance to Experimental Therapeutics (poster). Proc. Am. Assoc. Cancer Res. 45 #2034, 468. March 2004.
M. Augustus, R. Ebner, H. Khalak, P. Young, Q. Zong. Expression Biomarkers as Predictors of In-Vivo Efficacy: Enabling Improved Cancer Treatments. Poster presented at the Cambridge Health Institute's 11th Annual Molecular Medicine Tri-Conference, Track 4 - MOLECULAR DIAGNOSTICS: Utilizing Biomarkers in Diagnostic Research in San Francisco. March 2004.
R. Ebner, S. Horrigan, J. Strovel, P. Young, B. Weigle, M. Augustus. Novel Candidate Small Molecule Drug or Therapeutic Antibody Targets and Diagnostic Cancer Markers from Disease Tissue Molecular Profiling. Poster presented at the Cambridge Health Institute's 11th Annual Molecular Medicine Tri-Conference, Track 4 - Molecular Diagnostics: Utilizing Biomarkers in Diagnostic Research in San Francisco. March 2004.
Interactive Roundtable (TRI-session) Discussion (Table Ten). Improving Computational Predictive Tools at the Cambridge Health Institute's 11th Annual Molecular Medicine Tri-Conference in San Francisco. March 2004)
D.K. Bol, Q. Zong, M. Augustus, K.C. Carter, M. Chakiath, W.M. Cholody, J. DiCarlo, R. Ebner, K.L. Evans, S.J. Horrigan, J.S. Ireland, H.G. Khalak, D. Liu, P. Natarajan, S.A. O'Brien, N. Ohler, J. Padia, T.L. Adams, S. Pikul, K. Schifferli, J. Scott, J.R. Buchoff, M.J. Shea, J. Watthey, Z. Weaver, P.E. Young. Comprehensive Mechanism-of-Action Based Clustering of Anti-Cancer Drugs by Large- Scale Transcriptional Profiling. Poster presented at the AACR Japanese Cancer Association Joint Conference on Advances in Cancer Research in Hawaii. January 2004.
P.E. Young, M. Shea, Q. Zong, D.K. Bol, M. Chakiath, S.J. Horrigan, H.G. Khalak, D. Liu, J.W. Strovel, S. Pikul, & D.R. Soppet. High-Resolution Characterization of Kinase Inhibitors Through Transcriptional Profiling. Poster presented at the AACR-NCI-EORTC Meeting, International Conference - Molecular Targets and Cancer Therapeutics - Discovery, Biology and Clinical Applications in Boston. November 2004.
Z. Weaver, T. Perry, P. Young, S. Pikul, J. Strovel, J. Padia, S. O'Brien, J. Lu, S. Garvey, Q. Zong, D. Bol. Rapid Assessment of Compound Efficacy, Transcriptional Changes and Kinetics: Use of Genomics Technologies to Optimize Anti-Cancer Agents In-Vivo. Poster presented at the AACR/NCI/EORTC International Conference - Molecular Targets and Cancer Therapeutics - Discovery, Biology and Clinical Applications in Boston. November 2003.
H. Khalak, D.K. Bol, J. DiCarlo, S.J. Horrigan, M. Shea, D.R. Soppet Q. Zong, P.E. Young. (2003, September). Profiling on The Go: Molecular Signatures of Cellular Function. Poster presented at the Cambridge Healthtech Institute's Microarray Data Analysis Meeting in Baltimore. September 2003.
D.Soppet, J. Castaneda, S. Horrigan, M. Shea, T. Tatunchak, Q. Zong, P. Young, D. Bol. Constructing Gene Expression Based Screens Independent of Identified Targets. Poster presented at the Society for Bimolecular Screening in Portland. September 2003.
Q. Zong, P.E. Young, M. Augustus, D.K. Bol, K.C. Carter, M. Chakiath, W.M. Cholody, J. DiCarlo, R. Ebner, K.L. Evans, S.J. Horrigan, J.S. Ireland, H.G. Khalak, D. Liu, P. Natarajan, S.A. O'Brien, N. Ohler, J. Padia, T.L. Adams, S. Pikul, K. Schifferli, J. Scott, J.R. Buchoff, M.J. Shea, J. Watthey, Z. Weaver. Comprehensive Mechanism-of-Action Based Clustering of Anti-Cancer Drugs by Large-Scale Transcriptional Profiling. Poster presented at the Northwest Gene Expression Conference, Seattle. 2003
P.E. Young, M. Augustus, D.K. Bol, K.C. Carter, M. Chakiath, W.M. Cholody, J. DiCarlo, R. Ebner, K.L. Evans, S.J. Horrigan, J.S. Ireland, H.G. Khalak, D.Liu, P. Natarajan, S.A. O'Brien, N. Ohler, J. Padia, T.L. Adams, S. Pikul, K. Schifferli, J. Scott, J.R. Buchoff, M.J. Shea, J. Watthey, Z. Weaver, Q. Zong. Comprehensive Mechanism-of-Action Based Clustering of Anti-Cancer Drugs By Large-Scale Transcriptional Profiling. (poster). Proc. Am. Assoc. Cancer Res. 44(2): #951,190, July 2003.
D.R. Soppet, J. Castaneda, A. Majolagbe, T.L. Adams, J.R. Buchoff, M.Bu, C.B. Cargile, J. DiCarlo, K.L. Evans, J.S. Ireland, H.G. Khalak, T.D. Lawrence, J. Lu, R.F. Melhem, S.A. O'Brien, N.E. Ohler, J. Padia, V. Petukhova, J. Rick, K. Schifferli, M.J. Shea, K.J. Strand, T. Tatunchak, J. Watthey, Z. Weaver, L. White, J.W. Strovel, S.K. Horrigan, M. Cholody, S. Pikul, R. Ebner, P.E. Young, M.Augustus, K.C. Carter. Hits: A High-Throughput Integrated Transcriptional Screen For Identifying Potential Therapeutic Agents. (poster). Proc. Am. Assoc. Cancer Res. 44(2): #4562, 907, July 2003.
S.K. Horrigan, J.W. Strovel, C.B. Cargile, K. Strand, T. Lawrence, R. Melhem-Attieh, K.C. Carter & M. Augustus. Identification of TRIP13, a Putative Oncogene Involved in Mitotic Checkpoint Control in Epithelial Tumors, Using Integrated High-Resolution Amplicon Analysis and Genome-Wide Expression Profiling. (poster) Proc. Am. Assoc. Cancer Res. 44(2): #3254, 646, July 2003.
D. Bol, M. Bu, J. Castaneda, M. Chakiath, M. Cholody, M. Shea, D. Soppet, J. Padia, S. Pikul, J. Strovel, P. Young. Using Expression Technologies to Distinguish Subtle Differences in Activities of Anticancer Compounds - Transcriptional SAR. (poster). Proc. Am. Assoc. Cancer Res. 44 (2): #4580, 951, July 2003.
Q. Zong, P.E. Young, M. Augustus, D.K. Bol, K.C. Carter, M. Chakiath, W.M. Cholody, J. DiCarlo, R. Ebner, K.L. Evans, S.J. Horrigan, J.S. Ireland, H.G. Khalak, D.Liu, P. Natarajan, S.A. O'Brien, N. Ohler, J. Padia, T.L. Adams, S. Pikul, K. Schifferli, J. Scott, J.R. Buchoff, M.J. Shea, J. Watthey, Z. Weaver. Comprehensive Mechanism-Of-Action Based Clustering Of Anti-Cancer Drugs By Large-Scale Transcriptional Profiling. Poster presented at the Cambridge Health Institute's Beyond Genome 2003: RNA Interference Silencing Genes for Tools and Therapeutics, San Diego. June 2003
S. Pikul, T.L. Adams, M. Augustus, D.K. Bol, K.C. Carter, M. Chakiath, W.M. Cholody, J. DiCarlo, R. Ebner, K.L. Evans, S.J. Horrigan, J.S. Ireland, H.G. Khalak, D. Liu, P. Liu, P. Natarajan, S.A. O'Brien, N. Ohler, J. Padia, V. Petukhova, K. Schifferli, J. Scott, D.R. Soppet, J.R. Buchoff, M.J. Shea, J. Watthey, Z. Weaver, P.E. Young, & Q. Zong. Forward Chemical Genomics - A Novel Drug Discovery Process Based on Genomics Technologies. Poster presented at MipTech, The International Conference and Exhibition on Drug Discovery, Basel, Switzerland. May 2003.
Q. Zong, P.E. Young, M. Augustus, D.K. Bol, K.C. Carter, M. Chakiath, W.M. Cholody, J. DiCarlo, R. Ebner, K.L. Evans, S.J. Horrigan, J.S. Ireland, H.G. Khalak, D. Liu, P. Natarajan, S.A. O'Brien, N. Ohler, J. Padia, T.L. Adams, S. Pikul, K. Schifferli, J. Scott, J.R. Buchoff, M.J. Shea, J. Watthey, Z. Weaver. Comprehensive Mechanism-of-Action Based Clustering of Anti-Cancer Drugs by Large-Scale Transcriptional Profiling. Poster presented at the Cambridge Health Institute's 4th annual Macroresults for Microarrays: An Array of Possibilities, Boston. May 2003.
P. Liu, S. Bhattacharyya, J. Buchoff, J. DiCarlo, A. Glodek, J. Ireland, H. Khalak, J Scott, K. Sirotkin. Innovative Bioinformatics For an Early Stage Pharmaceutical Company: An Interactive Portal For Data Integration And Interpretation. Poster presented at the Genome Tri-Conference; CHI Molecular Medicine Marketplace, Track 4: Strategic Biocomputing, Santa Clara. March 2003.
P.E. Young, D. Soppet, S. Pikul, M. Augustus, Q. Zong, D. Bol, M. Shea, R. Ebner, S. Horrigan, Z. Weaver, & K.C. Carter. High-Throughput Transcriptional Profiling For Novel Drug Discovery And Optimization. Poster presented at the Cambridge Healthtech Institute's Genomics on Target Meeting; Chemogenomics/ Chemical Genomics, Boston. November 2002.
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