Serafim Batzoglou, Lior Pachter, Jill P. Mesirov, Bonnie Berger, Eric S. L
We describe a novel analytical approach to gene recognition based on cross-species comparison. We first undertook a comparison of orthologous genomic loci from human and mouse, studying the extent of...
Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1 (2009)
Barbie, David A., Tamayo, Pablo, Boehm, Jesse S., Kim, So Young, Moody, Susan E., Dunn, Ian F., ...
Methods Whole-Genome Sequence Assembly for Mammalian Genomes: Arachne 2 (2008)
David B. Jaffe, Jonathan Butler, Sante Gnerre, Evan Mauceli, Kerstin Lindblad-toh, Jill P. Mesirov, ...
We previously described the whole-genome assembly program Arachne, presenting assemblies of simulated data for small to mid-sized genomes. Here we describe algorithmic adaptations to the program,...
BioMed Central Open Access (2008)
Gul S Dalgin, Gabriela Alexe, Daniel Scanfeld, Pablo Tamayo, Jill P Mesirov, Shridar Ganesan, ...
This is an Open Access article distributed under the terms of the Creative Commons Attribution License
BIOINFORMATICS APPLICATIONS NOTE Gene expression Comparative gene marker selection suite (2008)
Joshua Gould, Gad Getz, Stefano Monti, Michael Reich, Jill P. Mesirov
Motivation: An important step in analyzing expression profiles from microarray data is to identify genes that can discriminate between distinct classes of samples. Many statistical approaches for...
BIOINFORMATICS APPLICATIONS NOTE Genome analysis Combo: a whole genome comparative browser (2008)
Reinhard Engels, Tamara Yu, Chris Burge, Jill P. Mesirov, David Decaprio, James E. Galagan
Summary: Combo is a comparative genome browser that provides a dynamic view of whole genome alignments along with their associated annotations. Combo provides two different visualization...
Abstract Class Prediction and Discovery Using Gene Expression Data (2008)
Donna K. Slonim, Pablo Tamayo, Jill P. Mesirov, Todd R. Golub, Eric S. L
Classification of patient samples is a crucial aspect of cancer diagnosis and treatment. We present a method for classifying samples by computational analysis of gene expression data. We consider the...
Portraits of breast cancer progression (2007)
Dalgin, Gul S, Alexe, Gabriela, Scanfeld, Daniel, Tamayo, Pablo, Mesirov, Jill P, Ganesan, Shridar, ...
Abstract Background Clustering analysis of microarray data is often criticized for giving ambiguous results because of sensitivity to data perturbation or clustering techniques used. In this paper,...
GSEA-P: a desktop application for Gene Set Enrichment Analysis (2007)
Subramanian, Aravind, Kuehn, Heidi, Gould, Joshua, Tamayo, Pablo, Mesirov, Jill P.
Gene Set Enrichment Analysis (GSEA) is a computational method that assesses whether an a priori defined set of genes shows statistically significant, concordant differences between two biological...
Comparative gene marker selection suite (2006)
Gould, Joshua, Getz, Gad, Monti, Stefano, Reich, Michael, Mesirov, Jill P.
Motivation: An important step in analyzing expression profiles from microarray data is to identify genes that can discriminate between distinct classes of samples. Many statistical approaches for...
Combo: a whole genome comparative browser (2006)
Engels, Reinhard, Yu, Tamara, Burge, Chris, Mesirov, Jill P., DeCaprio, David, Galagan, James E.
Summary: Combo is a comparative genome browser that provides a dynamic view of whole genome alignments along with their associated annotations. Combo provides two different visualization...
GeneCruiser: a web service for the annotation of microarray data (2005)
Liefeld, Ted, Reich, Michael, Gould, Joshua, Zhang, Peili, Tamayo, Pablo, Mesirov, Jill P.
Summary: GeneCruiser is a web service allowing users to annotate their genomic data by mapping microarray feature identifiers to gene identifiers from databases, such as UniGene, while providing...
Assembly of polymorphic genomes: Algorithms and application to Ciona savignyi (2005)
Vinson, Jade P., Jaffe, David B., O'Neill, Keith, Karlsson, Elinor K., Stange-Thomann, Nicole, Anderson, Scott, ...
Whole-genome assembly is now used routinely to obtain high-quality draft sequence for the genomes of species with low levels of polymorphism. However, genome assembly remains extremely challenging...
GeneCruiser: a web service for the annotation of microarray data (2005)
Liefeld, Ted, Reich, Michael, Gould, Josh, Zhang, Peili, Tamayo, Pablo, Mesirov, Jill P.
Summary: GeneCruiser is a web service allowing users to annotate their genomic data by mapping microarray feature identifiers to gene identifiers from databases such as UniGene, while providing links...
Improving genome annotations using phylogenetic profile anomaly detection (2004)
Mikkelsen, Tarjei S., Galagan, James E., Mesirov, Jill P.
Motivation: A promising strategy for refining genome annotations is to detect features that conflict with known functional or evolutionary relationships between groups of genes. Previous work in this...
Improving genome annotations using phylogenetic profile anomaly detection (2004)
Mikkelsen, Tarjei S., Galagan, James E., Mesirov, Jill P.
Motivation: A promising strategy for refining genome annotations is to detect features that conflict with known functional or evolutionary relationships between groups of genes. Previous work in this...
Estimating dataset size requirements for classifying DNA Microarray data (2003)
Sayan Mukherjee, Pablo Tamayo, Simon Rogers, Ryan Rifkin, Anna Engle, Colin Campbell, ...
A statistical methodology for estimating dataset size requirements for classifying microarray data using learning curves is introduced. The goal is to use existing classi � cation results to...
An analytical method for multiclass molecular cancer classification (2003)
Ryan Rifkin, Sayan Mukherjee, Pablo Tamayo, Sridhar Ramaswamy, Chen-hsiang Yeang, Michael Angelo, ...
Abstract. Modern cancer treatment relies upon microscopic tissue examination to classify tumors according to anatomical site of origin. This approach is effective but subjective and variable even...
Whole-Genome Sequence Assembly for Mammalian Genomes: Arachne 2 (2003)
Jaffe, David B., Butler, Jonathan, Gnerre, Sante, Mauceli, Evan, Lindblad-Toh, Kerstin, Mesirov, Jill P., ...
We previously described the whole-genome assembly program Arachne, presenting assemblies of simulated data for small to mid-sized genomes. Here we describe algorithmic adaptations to the program,...
ARACHNE: A Whole-Genome Shotgun Assembler (2002)
Batzoglou, Serafim, Jaffe, David B., Stanley, Ken, Butler, Jonathan, Gnerre, Sante, Mauceli, Evan, ...
Class Prediction and Discovery Using Gene Expression Data (2000)
Donna K. Slonim, Pablo Tamayo, Jill P. Mesirov, Todd R. Golub, Eric S. Lander, Eric S. L
Classification of patient samples is a crucial aspect of cancer diagnosis and treatment. We present a method for classifying samples by computational analysis of gene expression data. We consider the...
Human and Mouse Gene Structure: Comparative Analysis and Application to Exon Prediction (2000)
Batzoglou, Serafim, Pachter, Lior, Mesirov, Jill P., Berger, Bonnie, Lander, Eric S.
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...
Multiclass cancer diagnosis using tumor gene expression signatures
Ramaswamy, Sridhar, Tamayo, Pablo, Rifkin, Ryan, Mukherjee, Sayan, Yeang, Chen-Hsiang, Angelo, Michael, ...
The optimal treatment of patients with cancer depends on establishing accurate diagnoses by using a complex combination of clinical and histopathological data. In some instances, this task is...
Human and Mouse Gene Structure: Comparative Analysis and Application to Exon Prediction
Batzoglou, Serafim, Pachter, Lior, Mesirov, Jill P., Berger, Bonnie, Lander, Eric S.
We describe a novel analytical approach to gene recognition based on cross-species comparison. We first undertook a comparison of orthologous genomic loci from human and mouse, studying the extent of...
Metagenes and molecular pattern discovery using matrix factorization
Brunet, Jean-Philippe, Tamayo, Pablo, Golub, Todd R., Mesirov, Jill P.
We describe here the use of nonnegative matrix factorization (NMF), an algorithm based on decomposition by parts that can reduce the dimension of expression data from thousands of genes to a handful...
Whole-Genome Sequence Assembly for Mammalian Genomes: Arachne 2
Jaffe, David B., Butler, Jonathan, Gnerre, Sante, Mauceli, Evan, Lindblad-Toh, Kerstin, Mesirov, Jill P., ...
We previously described the whole-genome assembly program Arachne, presenting assemblies of simulated data for small to mid-sized genomes. Here we describe algorithmic adaptations to the program,...
Assembly of polymorphic genomes: Algorithms and application to Ciona savignyi
Vinson, Jade P., Jaffe, David B., O'Neill, Keith, Karlsson, Elinor K., Stange-Thomann, Nicole, Anderson, Scott, ...
Whole-genome assembly is now used routinely to obtain high-quality draft sequence for the genomes of species with low levels of polymorphism. However, genome assembly remains extremely challenging...
ARACHNE: A Whole-Genome Shotgun Assembler
Batzoglou, Serafim, Jaffe, David B., Stanley, Ken, Butler, Jonathan, Gnerre, Sante, Mauceli, Evan, ...
We describe a new computer system, called ARACHNE, for assembling genome sequence using paired-end whole-genome shotgun reads. ARACHNE has several key features, including an efficient and sensitive...
Subramanian, Aravind, Tamayo, Pablo, Mootha, Vamsi K., Mukherjee, Sayan, Ebert, Benjamin L., Gillette, Michael A., ...
Although genomewide RNA expression analysis has become a routine tool in biomedical research, extracting biological insight from such information remains a major challenge. Here, we describe a...
Isakoff, Michael S., Sansam, Courtney G., Tamayo, Pablo, Subramanian, Aravind, Evans, Julia A., Fillmore, Christine M., ...
Snf5 (Ini1/Baf47/Smarcb1), a core member of the Swi/Snf chromatin remodeling complex, is a potent tumor suppressor whose mechanism of action is largely unknown. Biallelic loss of Snf5 leads to the...
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...
Multiclass cancer diagnosis using tumor gene expression signatures
Ramaswamy, Sridhar, Tamayo, Pablo, Rifkin, Ryan, Mukherjee, Sayan, Yeang, Chen-Hsiang, Angelo, Michael, ...
The optimal treatment of patients with cancer depends on establishing accurate diagnoses by using a complex combination of clinical and histopathological data. In some instances, this task is...
ARACHNE: A Whole-Genome Shotgun Assembler
Batzoglou, Serafim, Jaffe, David B., Stanley, Ken, Butler, Jonathan, Gnerre, Sante, Mauceli, Evan, ...
We describe a new computer system, called ARACHNE, for assembling genome sequence using paired-end whole-genome shotgun reads. ARACHNE has several key features, including an efficient and sensitive...
Human and Mouse Gene Structure: Comparative Analysis and Application to Exon Prediction
Batzoglou, Serafim, Pachter, Lior, Mesirov, Jill P., Berger, Bonnie, Lander, Eric S.
We describe a novel analytical approach to gene recognition based on cross-species comparison. We first undertook a comparison of orthologous genomic loci from human and mouse, studying the extent of...
Metagenes and molecular pattern discovery using matrix factorization
Brunet, Jean-Philippe, Tamayo, Pablo, Golub, Todd R., Mesirov, Jill P.
We describe here the use of nonnegative matrix factorization (NMF), an algorithm based on decomposition by parts that can reduce the dimension of expression data from thousands of genes to a handful...
Whole-Genome Sequence Assembly for Mammalian Genomes: Arachne 2
Jaffe, David B., Butler, Jonathan, Gnerre, Sante, Mauceli, Evan, Lindblad-Toh, Kerstin, Mesirov, Jill P., ...
We previously described the whole-genome assembly program Arachne, presenting assemblies of simulated data for small to mid-sized genomes. Here we describe algorithmic adaptations to the program,...
Assembly of polymorphic genomes: Algorithms and application to Ciona savignyi
Vinson, Jade P., Jaffe, David B., O'Neill, Keith, Karlsson, Elinor K., Stange-Thomann, Nicole, Anderson, Scott, ...
Whole-genome assembly is now used routinely to obtain high-quality draft sequence for the genomes of species with low levels of polymorphism. However, genome assembly remains extremely challenging...
Subramanian, Aravind, Tamayo, Pablo, Mootha, Vamsi K., Mukherjee, Sayan, Ebert, Benjamin L., Gillette, Michael A., ...
Although genomewide RNA expression analysis has become a routine tool in biomedical research, extracting biological insight from such information remains a major challenge. Here, we describe a...
Isakoff, Michael S., Sansam, Courtney G., Tamayo, Pablo, Subramanian, Aravind, Evans, Julia A., Fillmore, Christine M., ...
Snf5 (Ini1/Baf47/Smarcb1), a core member of the Swi/Snf chromatin remodeling complex, is a potent tumor suppressor whose mechanism of action is largely unknown. Biallelic loss of Snf5 leads to the...
Portraits of breast cancer progression
Dalgin, Gul S, Alexe, Gabriela, Scanfeld, Daniel, Tamayo, Pablo, Mesirov, Jill P, Ganesan, Shridar, ...
Tamayo, Pablo, Scanfeld, Daniel, Ebert, Benjamin L., Gillette, Michael A., Roberts, Charles W. M., Mesirov, Jill P.
The high dimensionality of global transcription profiles, the expression level of 20,000 genes in a much small number of samples, presents challenges that affect the sensitivity and general...
Subclass Mapping: Identifying Common Subtypes in Independent Disease Data Sets
Hoshida, Yujin, Brunet, Jean-Philippe, Tamayo, Pablo, Golub, Todd R., Mesirov, Jill P.
Whole genome expression profiles are widely used to discover molecular subtypes of diseases. A remaining challenge is to identify the correspondence or commonality of subtypes found in multiple,...
Automated high-dimensional flow cytometric data analysis
Pyne, Saumyadipta, Hu, Xinli, Wang, Kui, Rossin, Elizabeth, Lin, Tsung-I, Maier, Lisa M., ...
Flow cytometric analysis allows rapid single cell interrogation of surface and intracellular determinants by measuring fluorescence intensity of fluorophore-conjugated reagents. The availability of...