Data reporting standards: making the things we use better (2009)
Abstract Genomic data often persist far beyond the initial study in which they were generated. But the true value of the data is tied to their being both used and useful, and the usefulness of the...
Data-driven normalization strategies for high-throughput quantitative RT-PCR (2009)
Mar, Jessica C, Kimura, Yasumasa, Schroder, Kate, Irvine, Katharine M, Hayashizaki, Yoshihide, Suzuki, Harukazu, ...
Abstract Background High-throughput real-time quantitative reverse transcriptase polymerase chain reaction (qPCR) is a widely used technique in experiments where expression patterns of genes are to...
The promise of the genome project was that a complete sequence would provide us with information that would transform biology and medicine. But the ‘parts list ’ that has emerged from the genome...
Papers on normalization, variable selection, classification or clustering of microarray data (2009)
Rocke, David M., Ideker, Trey, Troyanskaya, Olga, Quackenbush, John, Dopazo, Joaquin
Taylor, Chris, Field, Dawn, Sansone, Susanna-Assunta, Apweiler, Rolf, Ashburner, Michael, Ball, Cathy, ...
The Minimum Information for Biological and Biomedical Investigations (MIBBI) project aims to foster the coordinated development of minimum-information checklists and provide a resource for those...
Taylor, Chris F., Field, Dawn, Sansone, Susanna-Assunta, Aerts, Jan, Apweiler, Rolf, Asburner, Michael, ...
The Minimum Information for Biological and Biomedical Investigations (MIBBI) project provides a resource for those exploring the range of extant minimum information checklists and fosters coordinated...
Seeded Bayesian Networks: Constructing genetic networks from microarray data (2008)
Djebbari, Amira, Quackenbush, John
Abstract Background DNA microarrays and other genomics-inspired technologies provide large datasets that often include hidden patterns of correlation between genes reflecting the complex processes...
Boedigheimer, Michael J, Wolfinger, Russell D, Bass, Michael B, Bushel, Pierre R, Chou, Jeff W, Cooper, Matthew, ...
Abstract Background The use of gene expression profiling in both clinical and laboratory settings would be enhanced by better characterization of variance due to individual, environmental, and...
BIOINFORMATICS ORIGINAL PAPER doi:10.1093/bioinformatics/btm043 Gene (2008)
Jun S. Song, Kaveh Maghsoudi, Wei Li, Edward Fox, John Quackenbush, X. Shirley Liu
Motivation: New generation Affymetrix oligonucleotide microarrays often have blob-like image defects that will require investigators to either repeat their hybridization assays or analyze their data...
BIOINFORMATICS Estimating p-values in small microarray experiments (2008)
Hyuna Yang A, Gary Churchill A, John Quackenbush
Motivation: Microarray data typically have small numbers of observations per gene which can result in low power for statistical tests. Test statistics that borrow information from data across all of...
Jaebum Kim, Saurabh Sinha, John Quackenbush
Motivation: A quantitative study of molecular evolutionary events such as substitutions, insertions and deletions from closely related genomes requires (i) an accurate multiple sequence alignment...
Jinwook Seo, Heather Gordish-dressman, Eric P. Hoffman, John Quackenbush
Motivation: Human clinical projects typically require a priori statistical power analysis. Towards this end, we sought to build a flexible and interactive power analysis tool for microarray studies...
Nak-kyeong Kim, Kannan Tharakaraman, John L. Spouge, John Quackenbush
Motivation: Many computational methods for identifying regulatory elements use a likelihood ratio between motif and background models. Often, the methods use a background model of independent bases....
[9] TM4 Microarray Software Suite (2008)
I. Saeed, Nirmal K. Bhagabati, John C. Braisted, Wei Liang, Vasily Sharov, Eleanor A. Howe, ...
Tusher, V. G., Tibshirani, R., and Chu, G. (2001). Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl. Acad. Sci. USA 98, 5116–5121. Zhang, L., Miles, M....
Guillaume Achaz A, Frédéric Boyer C, Alain Viari C, Eric Coissac C, John Quackenbush
Repseek, a tool to retrieve approximate repeats from
Priti Hegde, Rong Qi, Kristie Abernathy, Cheryl Gay, Sonia Dharap, Renee Gaspard, ...
Microarray expression analysis has become one of the most widely used functional genomics tools. Efficient application of this technique requires the development of robust and reproducible protocols....
BIOINFORMATICS ORIGINAL PAPER Data and text mining (2008)
Rainer Malik, Lude Franke, Arno Siebes, John Quackenbush
Combination of text-mining algorithms increases the performance
Category Microarray Blob-Defect Removal Improves Array Analysis (2008)
Jun S. Song, Kaveh Maghsoudi, Wei Li, Edward Fox, John Quackenbush, X. Shirley, ...
† These authors contributed equally.
Deforche K A, Er T B, Camacho R C, Grossman Z D, Soares Ma E, Laethem K A, ...
Human Immunodeficiency Virus-1 (HIV-1) antiviral resistance is a major cause of antiviral therapy failure and compromises future treatment options. As a consequence, resistance testing is the...
BIOINFORMATICS EDITORIAL (2008)
John Quackenbush, Steven L. Salzberg
It is time to end the patenting of software
Deutsch, Eric W, Ball, Catherine A, Berman, Jules J, Bova, G Steven, Brazma, Alvis, Bumgarner, Roger E, ...
One purpose of the biomedical literature is to report results in sufficient detail that the methods of data collection and analysis can be independently replicated and verified. Here we present...
Herschkowitz, Jason I, Simin, Karl, Weigman, Victor J, Mikaelian, Igor, Usary, Jerry, Hu, Zhiyuan, ...
Abstract Background Although numerous mouse models of breast carcinomas have been developed, we do not know the extent to which any faithfully represent clinically significant human phenotypes. To...
Microarray blob-defect removal improves array analysis (2007)
Song, Jun S., Maghsoudi, Kaveh, Li, Wei, Fox, Edward, Quackenbush, John, Shirley Liu, X.
Motivation: New generation Affymetrix oligonucleotide microarrays often have blob-like image defects that will require investigators to either repeat their hybridization assays or analyze their data...
Danley, Patrick D, Mullen, Sean P, Liu, Fenglong, Nene, Vishvanath, Quackenbush, John, Shaw, Kerry L
Abstract Background As the developmental costs of genomic tools decline, genomic approaches to non-model systems are becoming more feasible. Many of these systems may lack advanced genetic tools but...
Microarray Blob-Defect Removal Improves Array Analysis (2007)
Song, Jun S., Maghsoudi, Kaveh, Li, Wei, Fox, Edward, Quackenbush, John, Shirley Liu, X.
Motivation: New generation Affymetrix oligonucleotide microarrays often have blob-like image defects that will require investigators to either repeat their hybridization assays or analyze their data...
Mar, Jessica C, Rubio, Renee, Quackenbush, John
Abstract Background A great deal of interest has been generated by systems biology approaches that attempt to develop quantitative, predictive models of cellular processes. However, the starting...
A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB (2006)
Rayner, Tim F, Rocca-Serra, Philippe, Spellman, Paul T, Causton, Helen C, Farne, Anna, Holloway, Ele, ...
Abstract Background Sharing of microarray data within the research community has been greatly facilitated by the development of the disclosure and communication standards MIAME and MAGE-ML by the...
Hu, Valerie W, Frank, Bryan C, Heine, Shannon, Lee, Norman H, Quackenbush, John
Abstract Background The autism spectrum encompasses a set of complex multigenic developmental disorders that severely impact the development of language, non-verbal communication, and social skills,...
Transcript Annotation in FANTOM3: Mouse Gene Catalog Based on Physical cDNAs (2006)
Norihiro Maeda, Takeya Kasukawa, Rieko Oyama, Julian Gough, Martin Frith, Pär G. Engström, ...
The international FANTOM consortium aims to produce a comprehensive picture of the mammalian transcriptome, based upon an extensive cDNA collection and functional annotation of full-length enriched...
Transcript Annotation in FANTOM3: Mouse Gene Catalog Based on Physical cDNAs (2006)
Maeda, Norihiro, Kasukawa, Takeya, Oyama, Rieko, Gough, Julian, Frith, Martin, Engstrom, Par G., ...
The international FANTOM consortium aims to produce a comprehensive picture of the mammalian transcriptome, based upon an extensive cDNA collection and functional annotation of full-length enriched...
Transcript Annotation in FANTOM3: Mouse Gene Catalog Based on Physical cDNAs (2006)
Maeda, Norihiro, Kasukawa, Takeya, Oyama, Rieko, Gough, Julian, Frith, Martin, Engstrom, Par G., ...
The international FANTOM consortium aims to produce a comprehensive picture of the mammalian transcriptome, based upon an extensive cDNA collection and functional annotation of full-length enriched...
Transcript Annotation in FANTOM3: Mouse Gene Catalog Based on Physical cDNAs (2006)
Maeda, Norihiro, Kasukawa, Takeya, Oyama, Rieko, Gough, Julian, Frith, Martin, Engstrom, Par G., ...
The international FANTOM consortium aims to produce a comprehensive picture of the mammalian transcriptome, based upon an extensive cDNA collection and functional annotation of full-length enriched...
Transcript Annotation in FANTOM3: Mouse Gene Catalog Based on Physical cDNAs (2006)
Maeda, Norihiro, Kasukawa, Takeya, Oyama, Rieko, Gough, Julian, Frith, Martin, Engstrom, Par, ...
The international FANTOM consortium aims to produce a comprehensive picture of the mammalian transcriptome, based upon an extensive cDNA collection and functional annotation of full-length enriched...
Transcript Annotation in FANTOM3: Mouse Gene Catalog Based on Physical cDNAs (2006)
Maeda, Norihiro, Kasukawa, Takeya, Oyama, Rieko, Gough, Julian, Frith, Martin, Engstrom, Par, ...
The international FANTOM consortium aims to produce a comprehensive picture of the mammalian transcriptome, based upon an extensive cDNA collection and functional annotation of full-length enriched...
Transcript Annotation in FANTOM3: Mouse Gene Catalog Based on Physical cDNAs (2006)
Maeda, Norihiro, Kasukawa, Takeya, Oyama, Rieko, Gough, Julian, Frith, Martin, Engstrom, Par, ...
The international FANTOM consortium aims to produce a comprehensive picture of the mammalian transcriptome, based upon an extensive cDNA collection and functional annotation of full-length enriched...
Rosetta error model for gene expression analysis (2006)
Lee Weng, Hongyue Dai, Yihui Zhan, Yudong He, Sergey B. Stepaniants, E. Bassett, ...
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for...
* Corresponding authors (2006)
Tim F Rayner, Paul T Spellman, Helen C Causton, Anna Farne, Ele Holloway, Rafael A Irizarry, ...
A simple spreadsheet-based, MIAME-supportive format for
microarray gene expression data using weighted Chinese restaurant
Transcript Annotation in FANTOM3: Mouse Gene Catalog Based on Physical cDNAs (2006)
Maeda, Norihiro, Kasukawa, Takeya, Oyama, Rieko, Gough, Julian, Frith, Martin, Engstrom, Par G., ...
The international FANTOM consortium aims to produce a comprehensive picture of the mammalian transcriptome, based upon an extensive cDNA collection and functional annotation of full-length enriched...
Chan, Vera S. F., Chau, Suk-yi, Tian, Lina, Chen, Yan, Kwong, Simon K. Y., Quackenbush, John, ...
Sonic hedgehog (Shh) is a crucial morphogen in the development of numerous tissues and organs, including the nervous system, gastrointestinal tract and lung. Recent findings suggest that Shh plays an...
Uneven chromosome contraction and expansion in the maize genome (2006)
Bruggmann, Rémy, Bharti, Arvind K., Gundlach, Heidrun, Lai, Jinsheng, Young, Sarah, Pontaroli, Ana C., ...
Maize (Zea mays or corn), both a major food source and an important cytogenetic model, evolved from a tetraploid that arose about 4.8 million years ago (Mya). As a result, maize has extensive...
Uneven chromosome contraction and expansion in the maize genome (2006)
Bruggmann, Rémy, Bharti, Arvind K., Gundlach, Heidrun, Lai, Jinsheng, Young, Sarah, Pontaroli, Ana C., ...
Maize (Zea mays or corn), both a major food source and an important cytogenetic model, evolved from a tetraploid that arose about 4.8 million years ago (Mya). As a result, maize has extensive...
Chan, Vera S. F., Chau, Suk-yi, Tian, Lina, Chen, Yan, Kwong, Simon K. Y., Quackenbush, John, ...
Sonic hedgehog (Shh) is a crucial morphogen in the development of numerous tissues and organs, including the nervous system, gastrointestinal tract and lung. Recent findings suggest that Shh plays an...
The TIGR Maize Database (2006)
Chan, Agnes P., Pertea, Geo, Cheung, Foo, Lee, Dan, Zheng, Li, Whitelaw, Cathy, ...
Maize is a staple crop of the grass family and also an excellent model for plant genetics. Owing to the large size and repetitiveness of its genome, we previously investigated two approaches to...
Hackl, Hubert, Burkard, Thomas, Sturn, Alexander, Rubio, Renee, Schleiffer, Alexander, Tian, Sun, ...
Abstract Background Large-scale transcription profiling of cell models and model organisms can identify novel molecular components involved in fat cell development. Detailed characterization of the...
A robust method for the amplification of RNA in the sense orientation (2005)
Marko, Nicholas F, Frank, Bryan, Quackenbush, John, Lee, Norman H
Abstract Background Small quantities of RNA (1–4 μg total RNA) available from biological samples frequently require a single round of amplification prior to analysis, but current amplification...
Gene Expression, Amira Djebbari, Svetlana Karamycheva, Eleanor Howe, John Quackenbush
Vol. 21 no. 15 2005, pages 3324–3326 doi:10.1093/bioinformatics/bti503 MeSHer: identifying biological concepts in microarray assays
Amira Djebbari, Svetlana Karamycheva, Eleanor Howe, John Quackenbush
Summary: MeSHer uses a simple statistical approach to identify biological concepts in the form of Medical Subject Headings (MeSH terms) obtained from the PubMed database that are significantly...
Margolin, Adam A., Greshock, Joel, Naylor, Tara L., Mosse, Yael, Maris, John M., Bignell, Graham, ...
Summary: This synopsis provides an overview of array-based comparative genomic hybridization data display, abstraction and analysis using CGHAnalyzer, a software suite, designed specifically for this...
Djebbari, Amira, Karamycheva, Svetlana, Howe, Eleanor, Quackenbush, John
Summary: MeSHer uses a simple statistical approach to identify biological concepts in the form of Medical Subject Headings (MeSH terms) obtained from the PubMed database that are significantly...
Margolin, Adam A., Greshock, Joel, Naylor, Tara L., Mosse, Yael, Maris, John M., Bignell, Graham, ...
Summary: This synopsis provides an overview of array-based comparative genomic hybridization (aCGH) data display, abstraction and analysis using CGHAnalyzer, a software suite, designed specifically...
Djebbari, Amira, Karamycheva, Svetlana, Howe, Eleanor, Quackenbush, John
Summary: MeSHer uses a simple statistical approach to identify biological concepts in the form of Medical Subject Headings (MeSH terms) obtained from the PubMed database that are significantly...
Submission of Microarray Data to Public Repositories (2004)
Catherine A. Ball, Alvis Brazma, Helen Causton, Steve Chervitz, Ron Edgar, Pascal Hingamp, ...
The Microarray Gene Expression Data Society believe that the time is right for journals to require that microarray data be deposited in public repositories, as a condition for publication.
Submission of Microarray Data to Public Repositories (2004)
Catherine A. Ball, Alvis Brazma, Helen Causton, Steve Chervitz, Ron Edgar, Pascal Hingamp, ...
Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones (2004)
Tadashi Imanishi, Takeshi Itoh, Yutaka Suzuki, Claire O'Donovan, Satoshi Fukuchi, Kanako O. Koyanagi, ...
An international team has systematically validated and annotated just over 21,000 human genes using full-length cDNA, thereby providing a valuable new resource for the human genetics community.
Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones (2004)
Tadashi Imanishi, Takeshi Itoh, Yutaka Suzuki, Claire O'Donovan, Satoshi Fukuchi, Kanako O. Koyanagi, ...
The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this...
Ghedin, Elodie, Pumfery, Anne, De La Fuente, Cynthia, Yao, Karen, Miller, Naomi, Lacoste, Vincent, ...
Abstract Background Since the discovery of human immunodeficiency virus (HIV-1) twenty years ago, AIDS has become one of the most studied diseases. A number of viruses have subsequently been...
Orthologous gene-expression profiling in multi-species models: search for candidate genes (2004)
Grigoryev, Dmitry N, Ma, Shwu-Fan, Irizarry, Rafael A, Ye, Shui, Quackenbush, John, Garcia, Joe GN
Abstract Microarray-driven gene-expression profiles are generally produced and analyzed for a single specific experimental model. We have assessed an analytical approach that simultaneously evaluates...
The limits of log-ratios (2004)
Sharov, Vasily, Kwong, Ka, Frank, Bryan, Chen, Emily, Hasseman, Jeremy, Gaspard, Renee, ...
Abstract Background DNA microarray assays typically compare two biological samples and present the results of those comparisons gene-by-gene as the logarithm base two of the ratio of the measured...
Maureen Cronin, Krishna Ghosh, Frank Sistare, John Quackenbush, Vincent Vilker
Standards ” was held in March of this year to define the requirements for standardizing RNA-based molecular assays, specifically microarray and quantitative reversetranscriptase-PCR technologies....
Open-source software accelerates bioinformatics (2003)
Abstract A report on the Wellcome Trust/Cold Spring Harbor Genome Informatics meeting, Cold Spring Harbor, USA, 7-11 May 2003.
Joseph M. Merrick, Ahmed Osman, Jennifer Tsai, John Quackenbush, Philip T. LoVerde, Norman H. Lee
Expressed sequence tag (EST) sequencing and analysis is a primary research tool to identify and characterize the Schistosoma mansoni transcriptome. As part of our gene discovery effort, a total of...
Zhu, Yunxia, King, Benjamin L, Parvizi, Babak, Brunk, Brian P, Stoeckert, Christian J, Quackenbush, John, ...
Abstract Databases of experimentally generated and computationally derived transcript sequences are valuable resources for genome analysis and annotation. The utility of such databases is enhanced...
Assessing unmodified 70-mer oligonucleotide probe performance on glass-slide microarrays (2003)
Wang, Hong-Ying, Malek, Renae L, Kwitek, Anne E, Greene, Andrew S, Luu, Truong V, Behbahani, Babak, ...
Abstract Background Long oligonucleotide microarrays are potentially more cost- and management-efficient than cDNA microarrays, but there is little information on the relative performance of these...
Wells, Christine, Ravasi, Timothy, Sultana, Razvan, Yagi, Ken, Carninci, Piero, Bono, Hidemasa, ...
The current RIKEN transcript set represents a significant proportion of the mouse transcriptome but transcripts expressed in the innate and acquired immune systems are poorly represented. In the...
Wells, Christine, Ravasi, Timothy, Sultana, Razvan, Yagi, Ken, Carninci, Piero, Bono, Hidemasa, ...
The current RIKEN transcript set represents a significant proportion of the mouse transcriptome but transcripts expressed in the innate and acquired immune systems are poorly represented. In the...
Wells, Christine, Ravasi, Timothy, Sultana, Razvan, Yagi, Ken, Carninci, Piero, Bono, Hidemasa, ...
The current RIKEN transcript set represents a significant proportion of the mouse transcriptome but transcripts expressed in the innate and acquired immune systems are poorly represented. In the...
Wells, Christine A., Ravasi, Timothy, Sultana, Razvan, Yagi, Ken, Carninci, Piero, Bono, Hidemasa, ...
The current RIKEN transcript set represents a significant proportion of the mouse transcriptome but transcripts expressed in the innate and acquired immune systems are poorly represented. In the...
Development and Evaluation of an Automated Annotation Pipeline and cDNA Annotation System (2003)
Kasukawa, Takeya, Furuno, Masaaki, Nikaido, Itoshi, Bono, Hidemasa, Hume, David A., Bult, Carol, ...
Manual curation has long been held to be the “gold standard” for functional annotation of DNA sequence. Our experience with the annotation of more than 20,000 full-length cDNA sequences revealed...
Pertea, Geo, Huang, Xiaoqiu, Liang, Feng, Antonescu, Valentin, Sultana, Razvan, Karamycheva, Svetlana, ...
TGICL is a pipeline for analysis of large Expressed Sequence Tags (EST) and mRNA databases in which the sequences are first clustered based on pairwise sequence similarity, and then assembled by...
Yuan, Qiaoping, Ouyang, Shu, Liu, Jia, Suh, Bernard, Cheung, Foo, Sultana, Razvan, ...
Rice is not only a major food staple for the world's population but it also is a model species for a major group of flowering plants, the monocotyledonous plants. Draft genomic sequence of two...
Gene Expression Analyses of Arabidopsis Chromosome 2 Using a Genomic DNA Amplicon Microarray (2003)
Kim, Heenam, Snesrud, Erik C., Haas, Brian, Cheung, Foo, Town, Christopher D., Quackenbush, John
The gene predictions and accompanying functional assignments resulting from the sequencing and annotation of a genome represent hypotheses that can be tested and used to develop a more complete...
Yang, Ivana V, Chen, Emily, Hasseman, Jeremy P, Liang, Wei, Frank, Bryan C, Wang, Shuibang, ...
Abstract Background 'Fold-change' cutoffs have been widely used in microarray assays to identify genes that are differentially expressed between query and reference samples. More accurate measures of...
Deepak Agrawal, Tingan Chen, Rosalyn Irby, John Quackenbush, Ann F. Chambers, Marianna Szabo, ...
Background: New tumor markers and markers of tumor progression are needed for improved staging and for better assessment of treatment of many cancers. Gene expression profiling techniques offer the...
Cross-Referencing Eukaryotic Genomes: TIGR Orthologous Gene Alignments (TOGA) (2002)
Lee, Yuandan, Sultana, Razvan, Pertea, Geo, Cho, Jennifer, Karamycheva, Svetlana, Tsai, Jennifer, ...
Genesis: cluster analysis of microarray data (2002)
Sturn, Alexander, Quackenbush, John, Trajanoski, Zlatko
Summary: A versatile, platform independent and easy to use Java suite for large-scale gene expression analysis was developed. Genesis integrates various tools for microarray data analysis such as...
Agrawal, Deepak, Chen, Tingan, Irby, Rosalyn, Quackenbush, John, Chambers, Ann F., Szabo, Marianna, ...
Background: New tumor markers and markers of tumor progression are needed for improved staging and for better assessment of treatment of many cancers. Gene expression profiling techniques offer the...
An open letter to the scientific journals (2002)
Ball, Catherine A., Sherlock, Gavin, Parkinson, Helen, Rocca-Sera, Philippe, Brooksbank, Catherine, Causton, Helen C., ...
Tsai, Jennifer, Sultana, Razvan, Lee, Yudan, Pertea, Geo, Karamycheva, Svetlana, Antonescu, Valentin, ...
Abstract Microarray expression analysis is providing unprecedented data on gene expression in humans and mammalian model systems. Although such studies provide a tremendous resource for understanding...
Quackenbush, John, Cho, Jennifer, Lee, Daniel, Liang, Feng, Holt, Ingeborg, Karamycheva, Svetlana, ...
While genome sequencing projects are advancing rapidly, EST sequencing and analysis remains a primary research tool for the identification and categorization of gene sequences in a wide variety of...
Smith, Timothy P.L., Grosse, William M., Freking, Brad A., Roberts, Andrew J., Stone, Roger T., Casas, Eduardo, ...
A concise guide to cDNA microarray analysis (2000)
Priti Hegde, Rong Qi, Kristie Abernathy, Cheryl Gay, Sonia Dharap, Renee Gaspard, ...
Microarray expression analysis has become one of the most widely used functional genomics tools. Efficient application of this technique requires the development of robust and reproducible protocols....
An optimized protocol for analysis of est sequences (2000)
Feng Liang, Ingeborg Holt, Geo Pertea, Svetlana Karamycheva, Steven L. Salzberg, John Quackenbush
The vast body of Expressed Sequence Tag (EST) data in the public databases provide an important resource for comparative and functional genomics studies and an invaluable tool for the annotation of...
Anchoring of rice BAC clones to the rice genetic map in silico (2000)
Yuan, Qiaoping, Liang, Feng, Hsiao, Joseph, Zismann, Victoria, Benito, Maria-Ines, Quackenbush, John, ...
A wealth of molecular resources have been developed for rice genomics, including dense genetic maps, expressed sequence tags (ESTs), yeast artificial chromosome maps, bacterial artificial chromosome...
An optimized protocol for analysis of EST sequences (2000)
Liang, Feng, Holt, Ingeborg, Pertea, Geo, Karamycheva, Svetlana, Salzberg, Steven L., Quackenbush, John
The vast body of Expressed Sequence Tag (EST) data in the public databases provide an important resource for comparative and functional genomics studies and an invaluable tool for the annotation of...
The TIGR Gene Indices: reconstruction and representation of expressed gene sequences (2000)
Quackenbush, John, Liang, Feng, Holt, Ingeborg, Pertea, Geo, Upton, Jonathan
Expressed sequence tags (ESTs) have provided a first glimpse of the collection of transcribed sequences in a variety of organisms. However, a careful analysis of this sequence data can provide...
An STS-Based Radiation Hybrid Map of the Human Genome (1997)
Stewart, Elizabeth A., McKusick, Kathleen B., Aggarwal, Amita, Bajorek, Ewa, Brady, Shannon, Chu, Angela, ...
Thesis (M.A.)--State University of New York at Binghamton, Department of Biological Sciences, 1991.
The TIGR Gene Indices: analysis of gene transcript sequences in highly sampled eukaryotic species
Quackenbush, John, Cho, Jennifer, Lee, Daniel, Liang, Feng, Holt, Ingeborg, Karamycheva, Svetlana, ...
While genome sequencing projects are advancing rapidly, EST sequencing and analysis remains a primary research tool for the identification and categorization of gene sequences in a wide variety of...
Exploring the transcriptome of the malaria sporozoite stage
Kappe, Stefan H. I., Gardner, Malcolm J., Brown, Stuart M., Ross, Jessica, Matuschewski, Kai, Ribeiro, Jose M., ...
Most studies of gene expression in Plasmodium have been concerned with asexual and/or sexual erythrocytic stages. Identification and cloning of genes expressed in the preerythrocytic stages lag far...
The TIGR Gene Indices: reconstruction and representation of expressed gene sequences
Quackenbush, John, Liang, Feng, Holt, Ingeborg, Pertea, Geo, Upton, Jonathan
Expressed sequence tags (ESTs) have provided a first glimpse of the collection of transcribed sequences in a variety of organisms. However, a careful analysis of this sequence data can provide...
An optimized protocol for analysis of EST sequences
Liang, Feng, Holt, Ingeborg, Pertea, Geo, Karamycheva, Svetlana, Salzberg, Steven L., Quackenbush, John
The vast body of Expressed Sequence Tag (EST) data in the public databases provide an important resource for comparative and functional genomics studies and an invaluable tool for the annotation of...
Anchoring of rice BAC clones to the rice genetic map in silico
Yuan, Qiaoping, Liang, Feng, Hsiao, Joseph, Zismann, Victoria, Benito, Maria-Ines, Quackenbush, John, ...
A wealth of molecular resources have been developed for rice genomics, including dense genetic maps, expressed sequence tags (ESTs), yeast artificial chromosome maps, bacterial artificial chromosome...
Within the fold: assessing differential expression measures and reproducibility in microarray assays
Yang, Ivana V, Chen, Emily, Hasseman, Jeremy P, Liang, Wei, Frank, Bryan C, Wang, Shuibang, ...
Fold-change' cutoffs have been widely used in microarray assays to identify genes that are differentially expressed. More accurate measures are required to identify high-confidence sets of genes with...
RESOURCERER: a database for annotating and linking microarray resources within and across species
Tsai, Jennifer, Sultana, Razvan, Lee, Yudan, Pertea, Geo, Karamycheva, Svetlana, Antonescu, Valentin, ...
Microarray expression analysis is providing unprecedented data on gene expression in humans and mammalian model systems. Although such studies provide a tremendous resource for understanding human...
Assessing unmodified 70-mer oligonucleotide probe performance on glass-slide microarrays
Wang, Hong-Ying, Malek, Renae L, Kwitek, Anne E, Greene, Andrew S, Luu, Truong V, Behbahani, Babak, ...
Long oligonucleotide microarrays are potentially more cost- and management efficient than cDNA microarrays. Unmodified sense and antisense 70-mer oligonucleotides were synthesized and compared with...
Zhu, Yunxia, King, Benjamin L, Parvizi, Babak, Brunk, Brian P, Stoeckert, Christian J, Quackenbush, John, ...
The analysis and results are presented of a semi-automated process of connecting transcript assemblies with highly curated biological information for mouse genes that is available through the Mouse...
Yuan, Qiaoping, Ouyang, Shu, Liu, Jia, Suh, Bernard, Cheung, Foo, Sultana, Razvan, ...
Rice is not only a major food staple for the world's population but it also is a model species for a major group of flowering plants, the monocotyledonous plants. Draft genomic sequence of two...
Comparative Analyses of Potato Expressed Sequence Tag Libraries1
Ronning, Catherine M., Stegalkina, Svetlana S., Ascenzi, Robert A., Bougri, Oleg, Hart, Amy L., Utterbach, Teresa R., ...
The cultivated potato (Solanum tuberosum) shares similar biology with other members of the Solanaceae, yet has features unique within the family, such as modified stems (stolons) that develop into...
Open-source software accelerates bioinformatics
A report on the Wellcome Trust/Cold Spring Harbor Genome Informatics meeting, Cold Spring Harbor, USA, 7-11 May 2003.
Smith, Timothy P.L., Grosse, William M., Freking, Brad A., Roberts, Andrew J., Stone, Roger T., Casas, Eduardo, ...
An essential component of functional genomics studies is the sequence of DNA expressed in tissues of interest. To provide a resource of bovine-specific expressed sequence data and facilitate this...
Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones
Imanishi, Tadashi, Itoh, Takeshi, Suzuki, Yutaka, O'Donovan, Claire, Fukuchi, Satoshi, Koyanagi, Kanako O, ...
The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this...
Wells, Christine A., Ravasi, Timothy, Sultana, Razvan, Yagi, Ken, Carninci, Piero, Bono, Hidemasa, ...
The current RIKEN transcript set represents a significant proportion of the mouse transcriptome but transcripts expressed in the innate and acquired immune systems are poorly represented. In the...
Development and Evaluation of an Automated Annotation Pipeline and cDNA Annotation System
Kasukawa, Takeya, Furuno, Masaaki, Nikaido, Itoshi, Bono, Hidemasa, Hume, David A., Bult, Carol, ...
Manual curation has long been held to be the “gold standard” for functional annotation of DNA sequence. Our experience with the annotation of more than 20,000 full-length cDNA sequences revealed...
Orthologous gene-expression profiling in multi-species models: search for candidate genes
Grigoryev, Dmitry N, Ma, Shwu-Fan, Irizarry, Rafael A, Ye, Shui Qing, Quackenbush, John, Garcia, Joe GN
An analytical approach that simultaneously evaluates multi-species experimental models is presented. This approach may be a useful tool in the selection of process-related candidate genes.
Gene Expression Analyses of Arabidopsis Chromosome 2 Using a Genomic DNA Amplicon Microarray
Kim, Heenam, Snesrud, Erik C., Haas, Brian, Cheung, Foo, Town, Christopher D., Quackenbush, John
The gene predictions and accompanying functional assignments resulting from the sequencing and annotation of a genome represent hypotheses that can be tested and used to develop a more complete...
Ghedin, Elodie, Pumfery, Anne, De La Fuente, Cynthia, Yao, Karen, Miller, Naomi, Lacoste, Vincent, ...
Submission of Microarray Data to Public Repositories
Ball, Catherine A, Brazma, Alvis, Causton, Helen, Chervitz, Steve, Edgar, Ron, Hingamp, Pascal, ...
The Microarray Gene Expression Data Society believe that the time is right for journals to require that microarray data be deposited in public repositories, as a condition for publication
Murine Macrophage Transcriptional Responses to Bacillus anthracis Infection and Intoxication
Bergman, Nicholas H., Passalacqua, Karla D., Gaspard, Renee, Shetron-Rama, Lynne M., Quackenbush, John, Hanna, Philip C.
Interactions between Bacillus anthracis and host macrophages represent critical early events in anthrax pathogenesis, but their details are not clearly understood. Here we report the first genomewide...
A robust method for the amplification of RNA in the sense orientation
Marko, Nicholas F, Frank, Bryan, Quackenbush, John, Lee, Norman H
Liu, Fenglong, VanToai, Tara, Moy, Linda P., Bock, Geoffrey, Linford, Lara D., Quackenbush, John
Plants have evolved adaptation mechanisms to sense oxygen deficiency in their environments and make coordinated physiological and structural adjustments to enhance their hypoxic tolerance. To gain...
Microarray Data Standards: An Open Letter
Ball, Catherine, Brazma, Alvis, Causton, Helen, Chervitz, Steve, Edgar, Ron, Hingamp, Pascal, ...
Chan, Agnes P., Pertea, Geo, Cheung, Foo, Lee, Dan, Zheng, Li, Whitelaw, Cathy, ...
Maize is a staple crop of the grass family and also an excellent model for plant genetics. Owing to the large size and repetitiveness of its genome, we previously investigated two approaches to...
Hackl, Hubert, Burkard, Thomas Rainer, Sturn, Alexander, Rubio, Renee, Schleiffer, Alexander, Tian, Sun, ...
In-depth bioinformatics analyses of expressed sequence tags found to be differentially expressed during differentiation of 3T3-L1 pre-adipocyte cells were combined with de novo functional annotation...
Cross-Referencing Eukaryotic Genomes: TIGR Orthologous Gene Alignments (TOGA)
Lee, Yuandan, Sultana, Razvan, Pertea, Geo, Cho, Jennifer, Karamycheva, Svetlana, Tsai, Jennifer, ...
Comparative genomics promises to rapidly accelerate the identification and functional classification of biologically important human genes. We developed the TIGR Orthologous Gene Alignment (TOGA;...
Transcript Annotation in FANTOM3: Mouse Gene Catalog Based on Physical cDNAs
Maeda, Norihiro, Kasukawa, Takeya, Oyama, Rieko, Gough, Julian, Frith, Martin, Engström, Pär G, ...
The international FANTOM consortium aims to produce a comprehensive picture of the mammalian transcriptome, based upon an extensive cDNA collection and functional annotation of full-length enriched...
A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB
Rayner, Tim F, Rocca-Serra, Philippe, Spellman, Paul T, Causton, Helen C, Farne, Anna, Holloway, Ele, ...
The TIGR Gene Indices: analysis of gene transcript sequences in highly sampled eukaryotic species
Quackenbush, John, Cho, Jennifer, Lee, Daniel, Liang, Feng, Holt, Ingeborg, Karamycheva, Svetlana, ...
While genome sequencing projects are advancing rapidly, EST sequencing and analysis remains a primary research tool for the identification and categorization of gene sequences in a wide variety of...
Exploring the transcriptome of the malaria sporozoite stage
Kappe, Stefan H. I., Gardner, Malcolm J., Brown, Stuart M., Ross, Jessica, Matuschewski, Kai, Ribeiro, Jose M., ...
Most studies of gene expression in Plasmodium have been concerned with asexual and/or sexual erythrocytic stages. Identification and cloning of genes expressed in the preerythrocytic stages lag far...
The TIGR Gene Indices: reconstruction and representation of expressed gene sequences
Quackenbush, John, Liang, Feng, Holt, Ingeborg, Pertea, Geo, Upton, Jonathan
Expressed sequence tags (ESTs) have provided a first glimpse of the collection of transcribed sequences in a variety of organisms. However, a careful analysis of this sequence data can provide...
An optimized protocol for analysis of EST sequences
Liang, Feng, Holt, Ingeborg, Pertea, Geo, Karamycheva, Svetlana, Salzberg, Steven L., Quackenbush, John
The vast body of Expressed Sequence Tag (EST) data in the public databases provide an important resource for comparative and functional genomics studies and an invaluable tool for the annotation of...
Anchoring of rice BAC clones to the rice genetic map in silico
Yuan, Qiaoping, Liang, Feng, Hsiao, Joseph, Zismann, Victoria, Benito, Maria-Ines, Quackenbush, John, ...
A wealth of molecular resources have been developed for rice genomics, including dense genetic maps, expressed sequence tags (ESTs), yeast artificial chromosome maps, bacterial artificial chromosome...
Within the fold: assessing differential expression measures and reproducibility in microarray assays
Yang, Ivana V, Chen, Emily, Hasseman, Jeremy P, Liang, Wei, Frank, Bryan C, Wang, Shuibang, ...
Fold-change' cutoffs have been widely used in microarray assays to identify genes that are differentially expressed. More accurate measures are required to identify high-confidence sets of genes with...
RESOURCERER: a database for annotating and linking microarray resources within and across species
Tsai, Jennifer, Sultana, Razvan, Lee, Yudan, Pertea, Geo, Karamycheva, Svetlana, Antonescu, Valentin, ...
Microarray expression analysis is providing unprecedented data on gene expression in humans and mammalian model systems. Although such studies provide a tremendous resource for understanding human...
Assessing unmodified 70-mer oligonucleotide probe performance on glass-slide microarrays
Wang, Hong-Ying, Malek, Renae L, Kwitek, Anne E, Greene, Andrew S, Luu, Truong V, Behbahani, Babak, ...
Long oligonucleotide microarrays are potentially more cost- and management efficient than cDNA microarrays. Unmodified sense and antisense 70-mer oligonucleotides were synthesized and compared with...
Zhu, Yunxia, King, Benjamin L, Parvizi, Babak, Brunk, Brian P, Stoeckert, Christian J, Quackenbush, John, ...
The analysis and results are presented of a semi-automated process of connecting transcript assemblies with highly curated biological information for mouse genes that is available through the Mouse...
Cross-Referencing Eukaryotic Genomes: TIGR Orthologous Gene Alignments (TOGA)
Lee, Yuandan, Sultana, Razvan, Pertea, Geo, Cho, Jennifer, Karamycheva, Svetlana, Tsai, Jennifer, ...
Comparative genomics promises to rapidly accelerate the identification and functional classification of biologically important human genes. We developed the TIGR Orthologous Gene Alignment (TOGA;...
Yuan, Qiaoping, Ouyang, Shu, Liu, Jia, Suh, Bernard, Cheung, Foo, Sultana, Razvan, ...
Rice is not only a major food staple for the world's population but it also is a model species for a major group of flowering plants, the monocotyledonous plants. Draft genomic sequence of two...
Comparative Analyses of Potato Expressed Sequence Tag Libraries1
Ronning, Catherine M., Stegalkina, Svetlana S., Ascenzi, Robert A., Bougri, Oleg, Hart, Amy L., Utterbach, Teresa R., ...
The cultivated potato (Solanum tuberosum) shares similar biology with other members of the Solanaceae, yet has features unique within the family, such as modified stems (stolons) that develop into...
Open-source software accelerates bioinformatics
A report on the Wellcome Trust/Cold Spring Harbor Genome Informatics meeting, Cold Spring Harbor, USA, 7-11 May 2003.
Smith, Timothy P.L., Grosse, William M., Freking, Brad A., Roberts, Andrew J., Stone, Roger T., Casas, Eduardo, ...
An essential component of functional genomics studies is the sequence of DNA expressed in tissues of interest. To provide a resource of bovine-specific expressed sequence data and facilitate this...
Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones
Imanishi, Tadashi, Itoh, Takeshi, Suzuki, Yutaka, O'Donovan, Claire, Fukuchi, Satoshi, Koyanagi, Kanako O, ...
The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this...
Wells, Christine A., Ravasi, Timothy, Sultana, Razvan, Yagi, Ken, Carninci, Piero, Bono, Hidemasa, ...
The current RIKEN transcript set represents a significant proportion of the mouse transcriptome but transcripts expressed in the innate and acquired immune systems are poorly represented. In the...
Development and Evaluation of an Automated Annotation Pipeline and cDNA Annotation System
Kasukawa, Takeya, Furuno, Masaaki, Nikaido, Itoshi, Bono, Hidemasa, Hume, David A., Bult, Carol, ...
Manual curation has long been held to be the “gold standard” for functional annotation of DNA sequence. Our experience with the annotation of more than 20,000 full-length cDNA sequences revealed...
Orthologous gene-expression profiling in multi-species models: search for candidate genes
Grigoryev, Dmitry N, Ma, Shwu-Fan, Irizarry, Rafael A, Ye, Shui Qing, Quackenbush, John, Garcia, Joe GN
An analytical approach that simultaneously evaluates multi-species experimental models is presented. This approach may be a useful tool in the selection of process-related candidate genes.
Gene Expression Analyses of Arabidopsis Chromosome 2 Using a Genomic DNA Amplicon Microarray
Kim, Heenam, Snesrud, Erik C., Haas, Brian, Cheung, Foo, Town, Christopher D., Quackenbush, John
The gene predictions and accompanying functional assignments resulting from the sequencing and annotation of a genome represent hypotheses that can be tested and used to develop a more complete...
Ghedin, Elodie, Pumfery, Anne, De La Fuente, Cynthia, Yao, Karen, Miller, Naomi, Lacoste, Vincent, ...
Submission of Microarray Data to Public Repositories
Ball, Catherine A, Brazma, Alvis, Causton, Helen, Chervitz, Steve, Edgar, Ron, Hingamp, Pascal, ...
The Microarray Gene Expression Data Society believe that the time is right for journals to require that microarray data be deposited in public repositories, as a condition for publication
Murine Macrophage Transcriptional Responses to Bacillus anthracis Infection and Intoxication
Bergman, Nicholas H., Passalacqua, Karla D., Gaspard, Renee, Shetron-Rama, Lynne M., Quackenbush, John, Hanna, Philip C.
Interactions between Bacillus anthracis and host macrophages represent critical early events in anthrax pathogenesis, but their details are not clearly understood. Here we report the first genomewide...
A robust method for the amplification of RNA in the sense orientation
Marko, Nicholas F, Frank, Bryan, Quackenbush, John, Lee, Norman H
Liu, Fenglong, VanToai, Tara, Moy, Linda P., Bock, Geoffrey, Linford, Lara D., Quackenbush, John
Plants have evolved adaptation mechanisms to sense oxygen deficiency in their environments and make coordinated physiological and structural adjustments to enhance their hypoxic tolerance. To gain...
Microarray Data Standards: An Open Letter
Ball, Catherine, Brazma, Alvis, Causton, Helen, Chervitz, Steve, Edgar, Ron, Hingamp, Pascal, ...
Chan, Agnes P., Pertea, Geo, Cheung, Foo, Lee, Dan, Zheng, Li, Whitelaw, Cathy, ...
Maize is a staple crop of the grass family and also an excellent model for plant genetics. Owing to the large size and repetitiveness of its genome, we previously investigated two approaches to...
Hackl, Hubert, Burkard, Thomas Rainer, Sturn, Alexander, Rubio, Renee, Schleiffer, Alexander, Tian, Sun, ...
In-depth bioinformatics analyses of expressed sequence tags found to be differentially expressed during differentiation of 3T3-L1 pre-adipocyte cells were combined with de novo functional annotation...
Transcript Annotation in FANTOM3: Mouse Gene Catalog Based on Physical cDNAs
Maeda, Norihiro, Kasukawa, Takeya, Oyama, Rieko, Gough, Julian, Frith, Martin, Engström, Pär G, ...
The international FANTOM consortium aims to produce a comprehensive picture of the mammalian transcriptome, based upon an extensive cDNA collection and functional annotation of full-length enriched...
A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB
Rayner, Tim F, Rocca-Serra, Philippe, Spellman, Paul T, Causton, Helen C, Farne, Anna, Holloway, Ele, ...
Inferring steady state single-cell gene expression distributions from analysis of mesoscopic samples
Mar, Jessica C, Rubio, Renee, Quackenbush, John
A simple model for assessing transcript levels based on Poisson statistics is proposed and validated by estimating the variance on gene expression levels as a function of the number of cells surveyed.
Multi-Platform, Multi-Site, Microarray-Based Human Tumor Classification
Bloom, Greg, Yang, Ivana V., Boulware, David, Kwong, Ka Yin, Coppola, Domenico, Eschrich, Steven, ...
The introduction of gene expression profiling has resulted in the production of rich human data sets with potential for deciphering tumor diagnosis, prognosis, and therapy. Here we demonstrate how...
Uneven chromosome contraction and expansion in the maize genome
Bruggmann, Rémy, Bharti, Arvind K., Gundlach, Heidrun, Lai, Jinsheng, Young, Sarah, Pontaroli, Ana C., ...
Maize (Zea mays or corn), both a major food source and an important cytogenetic model, evolved from a tetraploid that arose about 4.8 million years ago (Mya). As a result, maize has extensive...
Danley, Patrick D, Mullen, Sean P, Liu, Fenglong, Nene, Vishvanath, Quackenbush, John, Shaw, Kerry L
Herschkowitz, Jason I, Simin, Karl, Weigman, Victor J, Mikaelian, Igor, Usary, Jerry, Hu, Zhiyuan, ...
Comparison of mammary tumor gene-expression profiles from thirteen murine models using microarrays and with that of human breast tumors showed that many of the defining characteristics of human...
Boedigheimer, Michael J, Wolfinger, Russell D, Bass, Michael B, Bushel, Pierre R, Chou, Jeff W, Cooper, Matthew, ...
Taoufik, Era, Petit, Edwige, Divoux, Didier, Tseveleki, Vivian, Mengozzi, Manuela, Roberts, Michael L., ...
CNS neurons use robust cytoprotective mechanisms to ensure survival and functioning under conditions of injury. These involve pathways induced by endogenous neuroprotective cytokines such as...
Nosho, Katsuhiko, Irahara, Natsumi, Shima, Kaori, Kure, Shoko, Kirkner, Gregory J., Schernhammer, Eva S., ...
Multistrain Genetic Comparisons Reveal CCR5 as a Receptor Involved in Airway Hyperresponsiveness
Walker, Julia K. L., Ahumada, Adriana, Frank, Bryan, Gaspard, Renee, Berman, Katherine, Quackenbush, John, ...
Asthma is a ubiquitous disease with a broad range of clinical phenotypes. To better understand the complex genetic and environmental interactions underlying asthma, we compared the gene–gene...
Data-driven normalization strategies for high-throughput quantitative RT-PCR
Mar, Jessica C, Kimura, Yasumasa, Schroder, Kate, Irvine, Katharine M, Hayashizaki, Yoshihide, Suzuki, Harukazu, ...
Kitami, Toshimori, Rubio, Renee, O'Brien, William, Quackenbush, John, Nadeau, Joseph H.
Dietary folate supplementation can dramatically reduce the severity and incidence of several common birth defects and adult diseases that are associated with anomalies in homocysteine and folate...
Gorgun, Gullu, Ramsay, Alan G., Holderried, Tobias A. W., Zahrieh, David, Le Dieu, Rifca, Liu, Fenglong, ...
Preclinical animal models have largely ignored the immune-suppressive mechanisms that are important in human cancers. The identification and use of such models should allow better predictions of...