CellMiner: a relational database and query tool for the NCI-60 cancer cell lines (2009)
Shankavaram, Uma T, Varma, Sudhir, Kane, David, Sunshine, Margot, Chary, Krishna K, Reinhold, William C, ...
Abstract Background Advances in the high-throughput omic technologies have made it possible to profile cells in a large number of ways at the DNA, RNA, protein, chromosomal, functional, and...
Philip L. Lorenzi, William C. Reinhold, Martina Rudelius, Michele Gunsior, Uma Shankavaram, Kimberly J. Bussey, ...
synthetase as a causal, predictive biomarker
Ryan, Michael C, Zeeberg, Barry R, Caplen, Natasha J, Cleland, James A, Kahn, Ari B, Liu, Hongfang, ...
Abstract Background Over 60% of protein-coding genes in vertebrates express mRNAs that undergo alternative splicing. The resulting collection of transcript isoforms poses significant challenges for...
Molecular Pathways Chk2 Molecular Interaction Map and Rationale for Chk2 Inhibitors (2008)
Yves Pommier, John N. Weinstein, Mirit I. Aladjem, Kurt W. Kohn
Abstract To organize the rapidly accumulating information on bioregulatory networks related to the histone g-H2AX-ATM-Chk2-p53-Mdm2 pathways in concise and unambiguous diagrams, we used the molecular...
Harry B. Burke, Ph. D. Background, The Tnm, John N. Weinstein, Ph. D, Frank E. Harrell, ...
Philip H. Goodman, M.D., M.S. an accurate, consistent, universal cancer outcome prediction system. Since the
Affymetrix Probe Sets, Hongfang Liu, Barry R Zeeberg, Qu Gang, A Gunes Koru, Ro Ferrucci, ...
$ Contributed equally Motivation: Affymetrix microarrays are widely used to measure global expression of mRNA transcripts. That technology is based on the concept of a probe set. Individual probes...
VennMaster: Area-proportional Euler diagrams for functional GO analysis of microarrays (2008)
Kestler, Hans A, Müller, André, Kraus, Johann M, Buchholz, Malte, Gress, Thomas M, Liu, Hongfang, ...
Abstract Background Microarray experiments generate vast amounts of data. The functional context of differentially expressed genes can be assessed by querying the Gene Ontology (GO) database via...
Hans A Kestler, André Müller, Johann M Kraus, Malte Buchholz, Hongfang Liu, Barry R Zeeberg, ...
This is an Open Access article distributed under the terms of the Creative Commons Attribution License
EDGAR: Extraction of Drugs, Genes And Relations from the Biomedical Literature (2007)
Thomas C. Rindfleisch, Lorraine Tanabe, John N . Weinstein
This paper reports on the
Liu, Hongfang, Zeeberg, Barry R., Qu, Gang, Koru, A. Gunes, Ferrucci, Alessandro, Kahn, Ari, ...
Motivation: Affymetrix microarrays are widely used to measure global expression of mRNA transcripts. That technology is based on the concept of a probe set. Individual probes within a probe set were...
Eichler, Gabriel S, Reimers, Mark, Kane, David, Weinstein, John N
Abstract Interpretation of microarray data remains a challenge, and most methods fail to consider the complex, nonlinear regulation of gene expression. To address that limitation, we introduce...
Multiplexing siRNAs to compress RNAi-based screen size in human cells (2007)
Martin, Scott E., Jones, Tamara L., Thomas, Cheryl L., Lorenzi, Philip L., Nguyen, Dac A., Runfola, Timothy, ...
Here we describe a novel strategy using multiplexes of synthetic small interfering RNAs (siRNAs) corresponding to multiple gene targets in order to compress RNA interference (RNAi) screen size....
Kahn, Ari B, Ryan, Michael C, Liu, Hongfang, Zeeberg, Barry R, Jamison, D Curtis, Weinstein, John N
Abstract Background There are many fewer genes in the human genome than there are expressed transcripts. Alternative splicing is the reason. Alternatively spliced transcripts are often specific to...
Detailed DNA methylation profiles of the E-cadherin promoter in the NCI-60 cancer cells (2007)
Reinhold, William C., Reimers, Mark A., Maunakea, Alika K., Kim, Sohyoung, Lababidi, Samir, Scherf, Uwe, ...
E-cadherin (E-cad) is a transmembrane adhesion glycoprotein, the expression of which is often reduced in invasive or metastatic tumors. To assess E-cad's distribution among different types of cancer...
Ari B Kahn, Michael C Ryan, Hongfang Liu, Barry R Zeeberg, Curtis Jamison, John N Weinstein
© 2007 Kahn et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License
Major, Sylvia M, Nishizuka, Satoshi, Morita, Daisaku, Rowland, Rick, Sunshine, Margot, Shankavaram, Uma, ...
Abstract Background Monoclonal antibodies are used extensively throughout the biomedical sciences for detection of antigens, either i n vitro or in vivo . We, for example, have used them for...
Morin, Ryan D., Chang, Elbert, Petrescu, Anca, Liao, Nancy, Griffith, Malachi, Kirkpatrick, Robert, ...
Sequencing of full-insert clones from full-length cDNA libraries from both Xenopus laevis and Xenopus tropicalis has been ongoing as part of the Xenopus Gene Collection Initiative. Here we present...
Morin, Ryan D., Chang, Elbert, Petrescu, Anca, Liao, Nancy, Griffith, Malachi, Kirkpatrick, Robert, ...
Sequencing of full-insert clones from full-length cDNA libraries from both Xenopus laevis and Xenopus tropicalis has been ongoing as part of the Xenopus Gene Collection Initiative. Here we present...
Zeeberg, Barry R, Qin, Haiying, Narasimhan, Sudarshan, Sunshine, Margot, Cao, Hong, Kane, David W, ...
Abstract Background We previously developed GoMiner, an application that organizes lists of 'interesting' genes (for example, under-and overexpressed genes from a microarray experiment) for...
Reimers, Mark, Weinstein, John N
Abstract Background Quality-control is an important issue in the analysis of gene expression microarrays. One type of problem is regional bias, in which one region of a chip shows artifactually high...
Mark Reimers, John N Weinstein, Mark Reimers, John N Weinstein
Background: Quality-control is an important issue in the analysis of gene expression microarrays. One type of problem is regional bias, in which one region of a chip shows artifactually high or low...
Zeeberg, Barry R, Riss, Joseph, Kane, David W, Bussey, Kimberly J, Uchio, Edward, Linehan, W Marston, ...
Abstract Background When processing microarray data sets, we recently noticed that some gene names were being changed inadvertently to non-gene names. Results A little detective work traced the...
Lee, Jae K, Bussey, Kimberly J, Gwadry, Fuad G, Reinhold, William, Riddick, Gregory, Pelletier, Sandra L, ...
Abstract Microarray gene-expression profiles are generally validated one gene at a time by real-time RT-PCR. We describe here a different approach based on simultaneous mutual validation of large...
MatchMiner: a tool for batch navigation among gene and gene product identifiers (2003)
Bussey, Kimberly J, Kane, David, Sunshine, Margot, Narasimhan, Sudar, Nishizuka, Satoshi, Reinhold, William C, ...
Abstract MatchMiner is a freely available program package for batch navigation among gene and gene product identifier types commonly encountered in microarray studies and other forms of 'omic'...
GoMiner: a resource for biological interpretation of genomic and proteomic data (2003)
Zeeberg, Barry R, Feng, Weimin, Wang, Geoffrey, Wang, May D, Fojo, Anthony T, Sunshine, Margot, ...
Abstract We have developed GoMiner, a program package that organizes lists of 'interesting' genes (for example, under- and overexpressed genes from a microarray experiment) for biological...
Software GoMiner: a resource for biological interpretation of genomic and proteomic data (2003)
Barry R Zeeberg, Weimin Feng, Geoffrey Wang, May D Wang, T Fojo, Margot Sunshine, ...
electronic version of this article is the complete one and can be found online at
Edgar: Extraction of drugs, genes and relations from the biomedical literature (2000)
Thomas C. Rindflesch, Lorraine Tanabe, John N. Weinstein, Lawrence Hunter
EDGAR (Extraction of Drugs, Genes and Relations) is a natural language processing system that extracts information about drugs and genes relevant to cancer from the biomedical literature. This...
Edgar: Extraction of drugs, genes and relations from the biomedical literature (2000)
Thomas C. Rindflesch, Lorraine Tanabe, John N. Weinstein, Lawrence Hunter
EDGAR (Extraction of Drugs, Genes and Relations) is a natural language processing system that extracts information about drugs and genes relevant to cancer from the biomedical literature. This...
Leming M. Shi, Timothy G. Myers, Yi Fan, Patrick M. O’connor, Kenneth D. Paull, Stephen H. Friend, ...
The United States National Cancer Institute conducts an anticancer drug discovery program in which �10,000 compounds are screened every year in vitro against a panel of 60 human cancer cell lines...
Growth and Chemotherapeutic Response of Cells in a Hollow-Fiber In Vitro Solid Tumor Model (1994)
Casciari, Joseph J., Hollingshead, Melinda G., Alley, Michael C., Mayo, Joseph G., Malspeis, Louis, Miyauchi, Seiji, ...
Background: Cancer treatments that appear promising in tissue culture are often less effective in solid tumors, in part because of the proliferative and microenvironmental heterogeneity that develops...
Chemosensitivity prediction by transcriptional profiling
Staunton, Jane E., Slonim, Donna K., Coller, Hilary A., Tamayo, Pablo, Angelo, Michael J., Park, Johnny, ...
In an effort to develop a genomics-based approach to the prediction of drug response, we have developed an algorithm for classification of cell line chemosensitivity based on gene expression profiles...
Gadd45, a p53-Responsive Stress Protein, Modifies DNA Accessibility on Damaged Chromatin
Carrier, France, Georgel, Philippe T., Pourquier, Philippe, Blake, Mellissa, Kontny, H. Udo, Antinore, Michael J., ...
This report demonstrates that Gadd45, a p53-responsive stress protein, can facilitate topoisomerase relaxing and cleavage activity in the presence of core histones. A correlation between reduced...
MatchMiner: a tool for batch navigation among gene and gene product identifiers
Bussey, Kimberly J, Kane, David, Sunshine, Margot, Narasimhan, Sudar, Nishizuka, Satoshi, Reinhold, William C, ...
MatchMiner is a freely available program package for batch navigation among gene and gene product identifier types commonly encountered in microarray studies and other forms of 'omic' research.
GoMiner: a resource for biological interpretation of genomic and proteomic data
Zeeberg, Barry R, Feng, Weimin, Wang, Geoffrey, Wang, May D, Fojo, Anthony T, Sunshine, Margot, ...
GoMiner, a program package that organizes lists of 'interesting' genes for biological interpretation in the context of the Gene Ontology, has been developed.
Nishizuka, Satoshi, Charboneau, Lu, Young, Lynn, Major, Sylvia, Reinhold, William C., Waltham, Mark, ...
Because most potential molecular markers and targets are proteins, proteomic profiling is expected to yield more direct answers to functional and pharmacological questions than does transcriptional...
Lee, Jae K, Bussey, Kimberly J, Gwadry, Fuad G, Reinhold, William, Riddick, Gregory, Pelletier, Sandra L, ...
Microarray gene-expression profiles are generally validated one gene at a time by real-time RT-PCR. A different approach is described, based on simultaneous mutual validation of large numbers of...
Kohn, Kurt W., Riss, Joseph, Aprelikova, Olga, Weinstein, John N., Pommier, Yves, Barrett, J. Carl
A complex bioregulatory network could be more easily comprehended if its essential function could be described by a small “core” subsystem, and if its response characteristics were switch-like....
Zeeberg, Barry R, Riss, Joseph, Kane, David W, Bussey, Kimberly J, Uchio, Edward, Linehan, W Marston, ...
Karyotypic “state” as a potential determinant for anticancer drug discovery
Roschke, Anna V., Lababidi, Samir, Tonon, Giovanni, Gehlhaus, Kristen S., Bussey, Kimberly, Weinstein, John N., ...
Cancer is a genetic disease caused by genomic instability. In many cancers, this instability is manifested by chromosomal reconfigurations and karyotypic complexity. These features are particular...
Zeeberg, Barry R, Qin, Haiying, Narasimhan, Sudarshan, Sunshine, Margot, Cao, Hong, Kane, David W, ...
Molecular Interaction Maps of Bioregulatory Networks: A General Rubric for Systems Biology
Kohn, Kurt W., Aladjem, Mirit I., Weinstein, John N., Pommier, Yves
A standard for bioregulatory network diagrams is urgently needed in the same way that circuit diagrams are needed in electronics. Several graphical notations have been proposed, but none has become...
Staib, Frank, Robles, Ana I., Varticovski, Lyuba, Wang, Xin W., Zeeberg, Barry R., Sirotin, Michail, ...
Activation of the p53 network plays a central role in the inflammatory stress response associated with ulcerative colitis and may modulate cancer risk in patients afflicted with this chronic disease....
Major, Sylvia M, Nishizuka, Satoshi, Morita, Daisaku, Rowland, Rick, Sunshine, Margot, Shankavaram, Uma, ...
Development of Gene Ontology Tool for Biological Interpretation of Genomic and Proteomic Data
Feng, Weimin, Wang, Geoffrey, Zeeberg, Barry R., Guo, Kejiao, Fojo, Anthony T., Kane, David W., ...
We have designed and developed a Gene Ontology based navigation tool, GoMiner, which organizes lists of interesting genes from a microarray or a protein array experiment for biological...
Morin, Ryan D., Chang, Elbert, Petrescu, Anca, Liao, Nancy, Griffith, Malachi, Kirkpatrick, Robert, ...
Sequencing of full-insert clones from full-length cDNA libraries from both Xenopus laevis and Xenopus tropicalis has been ongoing as part of the Xenopus Gene Collection Initiative. Here we present...
Chemosensitivity prediction by transcriptional profiling
Staunton, Jane E., Slonim, Donna K., Coller, Hilary A., Tamayo, Pablo, Angelo, Michael J., Park, Johnny, ...
In an effort to develop a genomics-based approach to the prediction of drug response, we have developed an algorithm for classification of cell line chemosensitivity based on gene expression profiles...
Gadd45, a p53-Responsive Stress Protein, Modifies DNA Accessibility on Damaged Chromatin
Carrier, France, Georgel, Philippe T., Pourquier, Philippe, Blake, Mellissa, Kontny, H. Udo, Antinore, Michael J., ...
This report demonstrates that Gadd45, a p53-responsive stress protein, can facilitate topoisomerase relaxing and cleavage activity in the presence of core histones. A correlation between reduced...
MatchMiner: a tool for batch navigation among gene and gene product identifiers
Bussey, Kimberly J, Kane, David, Sunshine, Margot, Narasimhan, Sudar, Nishizuka, Satoshi, Reinhold, William C, ...
MatchMiner is a freely available program package for batch navigation among gene and gene product identifier types commonly encountered in microarray studies and other forms of 'omic' research.
GoMiner: a resource for biological interpretation of genomic and proteomic data
Zeeberg, Barry R, Feng, Weimin, Wang, Geoffrey, Wang, May D, Fojo, Anthony T, Sunshine, Margot, ...
GoMiner, a program package that organizes lists of 'interesting' genes for biological interpretation in the context of the Gene Ontology, has been developed.
Nishizuka, Satoshi, Charboneau, Lu, Young, Lynn, Major, Sylvia, Reinhold, William C., Waltham, Mark, ...
Because most potential molecular markers and targets are proteins, proteomic profiling is expected to yield more direct answers to functional and pharmacological questions than does transcriptional...
Lee, Jae K, Bussey, Kimberly J, Gwadry, Fuad G, Reinhold, William, Riddick, Gregory, Pelletier, Sandra L, ...
Microarray gene-expression profiles are generally validated one gene at a time by real-time RT-PCR. A different approach is described, based on simultaneous mutual validation of large numbers of...
Kohn, Kurt W., Riss, Joseph, Aprelikova, Olga, Weinstein, John N., Pommier, Yves, Barrett, J. Carl
A complex bioregulatory network could be more easily comprehended if its essential function could be described by a small “core” subsystem, and if its response characteristics were switch-like....
Zeeberg, Barry R, Riss, Joseph, Kane, David W, Bussey, Kimberly J, Uchio, Edward, Linehan, W Marston, ...
Karyotypic “state” as a potential determinant for anticancer drug discovery
Roschke, Anna V., Lababidi, Samir, Tonon, Giovanni, Gehlhaus, Kristen S., Bussey, Kimberly, Weinstein, John N., ...
Cancer is a genetic disease caused by genomic instability. In many cancers, this instability is manifested by chromosomal reconfigurations and karyotypic complexity. These features are particular...
Zeeberg, Barry R, Qin, Haiying, Narasimhan, Sudarshan, Sunshine, Margot, Cao, Hong, Kane, David W, ...
Molecular Interaction Maps of Bioregulatory Networks: A General Rubric for Systems Biology
Kohn, Kurt W., Aladjem, Mirit I., Weinstein, John N., Pommier, Yves
A standard for bioregulatory network diagrams is urgently needed in the same way that circuit diagrams are needed in electronics. Several graphical notations have been proposed, but none has become...
Morin, Ryan D., Chang, Elbert, Petrescu, Anca, Liao, Nancy, Griffith, Malachi, Kirkpatrick, Robert, ...
Sequencing of full-insert clones from full-length cDNA libraries from both Xenopus laevis and Xenopus tropicalis has been ongoing as part of the Xenopus Gene Collection Initiative. Here we present...
Development of Gene Ontology Tool for Biological Interpretation of Genomic and Proteomic Data
Feng, Weimin, Wang, Geoffrey, Zeeberg, Barry R., Guo, Kejiao, Fojo, Anthony T., Kane, David W., ...
We have designed and developed a Gene Ontology based navigation tool, GoMiner, which organizes lists of interesting genes from a microarray or a protein array experiment for biological...
Major, Sylvia M, Nishizuka, Satoshi, Morita, Daisaku, Rowland, Rick, Sunshine, Margot, Shankavaram, Uma, ...
Depicting combinatorial complexity with the molecular interaction map notation
Kohn, Kurt W, Aladjem, Mirit I, Kim, Sohyoung, Weinstein, John N, Pommier, Yves
To help us understand how bioregulatory networks operate, we need a standard notation for diagrams analogous to electronic circuit diagrams. Such diagrams must surmount the difficulties posed by...
Multiplexing siRNAs to compress RNAi-based screen size in human cells
Martin, Scott E., Jones, Tamara L., Thomas, Cheryl L., Lorenzi, Philip L., Nguyen, Dac A., Runfola, Timothy, ...
Here we describe a novel strategy using multiplexes of synthetic small interfering RNAs (siRNAs) corresponding to multiple gene targets in order to compress RNA interference (RNAi) screen size....
Lee, Jae K., Havaleshko, Dmytro M., Cho, HyungJun, Weinstein, John N., Kaldjian, Eric P., Karpovich, John, ...
The U.S. National Cancer Institute has used a panel of 60 diverse human cancer cell lines (the NCI-60) to screen >100,000 chemical compounds for anticancer activity. However, not all important cancer...
Chromatin Challenges during DNA Replication: A Systems Representation
Kohn, Kurt W., Aladjem, Mirit I., Weinstein, John N., Pommier, Yves
In a recent review, A. Groth and coworkers presented a comprehensive account of nucleosome disassembly in front of a DNA replication fork, assembly behind the replication fork, and the copying of...
VennMaster: Area-proportional Euler diagrams for functional GO analysis of microarrays
Kestler, Hans A, Müller, André, Kraus, Johann M, Buchholz, Malte, Gress, Thomas M, Liu, Hongfang, ...
Eichler, Gabriel S, Reimers, Mark, Kane, David, Weinstein, John N
The LeFE algorithm has been developed to address the complex, non-linear regulation of gene expression.
Ryan, Michael C, Zeeberg, Barry R, Caplen, Natasha J, Cleland, James A, Kahn, Ari B, Liu, Hongfang, ...
Roschke, Anna V, Glebov, Oleg K, Lababidi, Samir, Gehlhaus, Kristen S, Weinstein, John N, Kirsch, Ilan R
Chromosomal instability—a hallmark of epithelial cancers—is an ongoing process that results in aneuploidy and karyotypic heterogeneity of a cancer cell population. Previously, we stratified...
Delivery of Monoclonal Antibodies Through the Lymphatics: Characterization by Compartmental Modeling
Covell, David G., Steller, Michael A., Parker, Robert J., Weinstein, John N.
To investigate the effectiveness of subcutaneous administration for targeting antibody to lymph nodes we have used data on the kinetics of anti-H-2Kk antibody in Kk-positive and Kk-negative mice to...
MedMiner: An Internet Tool for Filtering and Organizing Biomedical Information
Uwe Scherf, Lawrence. H. Smith, Jae K. Lee, George S, George S. Michaels, Lawrence Hunter, ...
The trend toward high throughput techniques in molecular biology and the explosion of online scientific data threaten to overwhelm the ability of researchers to take full advantage of available...