TB database: an integrated platform for tuberculosis research (2009)
Reddy, T. B. K., Riley, Robert, Wymore, Farrell, Montgomery, Phillip, DeCaprio, Dave, Engels, Reinhard, ...
The effective control of tuberculosis (TB) has been thwarted by the need for prolonged, complex and potentially toxic drug regimens, by reliance on an inefficient vaccine and by the absence of...
Short-term genome evolution of Listeria monocytogenesin a non-controlled environment (2008)
Orsi, Renato H, Borowsky, Mark L, Lauer, Peter, Young, Sarah K, Nusbaum, Chad, Galagan, James E, ...
Abstract Background While increasing data on bacterial evolution in controlled environments are available, our understanding of bacterial genome evolution in natural environments is limited. We thus...
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...
Short-term genome evolution of Listeria monocytogenes in a non-controlled environment (2008)
Orsi, Renato H., Borowsky, Mark L., Lauer, Peter, Young, Sarah K., Nusbaum, Chad, Galagan, James E., ...
Background: While increasing data on bacterial evolution in controlled environments are available, our understanding of bacterial genome evolution in natural environments is limited. We thus...
Cross-kingdom patterns of alternative splicing and splice recognition (2008)
McGuire, Abigail M, Pearson, Matthew D, Neafsey, Daniel E, Galagan, James E
Abstract Background Variations in transcript splicing can reveal how eukaryotes recognize intronic splice sites. Retained introns (RIs) commonly appear when the intron definition (ID) mechanism of...
Jade P. Vinson, Stacey Luoma, David Decaprio, Matthew D. Pearson, James E. Galagan
Computational gene prediction using generative models has reached a plateau, with several groups converging to a generalized hidden Markov model (GHMM) incorporating phylogenetic models of nucleotide...
Mechanisms of intron gain and loss in Cryptococcus (2008)
Sharpton, Thomas J, Neafsey, Daniel E, Galagan, James E, Taylor, John W
Abstract Background Genome comparisons across deep phylogenetic divergences have revealed that spliceosomal intron gain and loss are common evolutionary events. However, because of the deep...
Dual Modes of Natural Selection on Upstream Open Reading Frames (2007)
Neafsey, Daniel E., Galagan, James E.
Upstream open reading frames (uORFs) are common features of eukaryotic genes, occurring in 10%–25% of 5′ leader sequences. Upstream ORFs that have been subjected to experimental analysis have...
Positive selection for unpreferred codon usage in eukaryotic genomes (2007)
Neafsey, Daniel E, Galagan, James E
Abstract Background Natural selection has traditionally been understood as a force responsible for pushing genes to states of higher translational efficiency, whereas lower translational efficiency...
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...
Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae (2005)
Galagan, James E., Calvo, Sarah E., Cuomo, Christina, Ma, Li-Jun, Wortman, Jennifer R., Batzoglou, Serafim, ...
The aspergilli comprise a diverse group of filamentous fungi spanning over 200 million years of evolution. Here we report the genome sequence of the model organism Aspergillus nidulans, and a...
Genomics of the fungal kingdom: Insights into eukaryotic biology (2005)
Galagan, James E., Henn, Matthew R., Ma, Li-Jun, Cuomo, Christina A., Birren, Bruce
The last decade has witnessed a revolution in the genomics of the fungal kingdom. Since the sequencing of the first fungus in 1996, the number of available fungal genome sequences has increased by an...
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...
Patterns of Intron Gain and Loss in Fungi (2004)
Cydney B. Nielsen, Brad Friedman, Bruce Birren, Christopher B. Burge, James E. Galagan
A comparative study of four fungal genomes reveals the patterns of intron gain and loss over several hundred million years of evolution.
Patterns of Intron Gain and Loss in Fungi (2004)
Cydney B. Nielsen, Brad Friedman, Bruce Birren, Christopher B. Burge, James E. Galagan
Little is known about the patterns of intron gain and loss or the relative contributions of these two processes to gene evolution. To investigate the dynamics of intron evolution, we analyzed...
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...
The Genome of M. acetivorans Reveals Extensive Metabolic and Physiological Diversity
Galagan, James E., Nusbaum, Chad, Roy, Alice, Endrizzi, Matthew G., Macdonald, Pendexter, FitzHugh, Will, ...
Methanogenesis, the biological production of methane, plays a pivotal role in the global carbon cycle and contributes significantly to global warming. The majority of methane in nature is derived...
Borkovich, Katherine A., Alex, Lisa A., Yarden, Oded, Freitag, Michael, Turner, Gloria E., Read, Nick D., ...
We present an analysis of over 1,100 of the ∼10,000 predicted proteins encoded by the genome sequence of the filamentous fungus Neurospora crassa. Seven major areas of Neurospora genomics and...
Patterns of Intron Gain and Loss in Fungi
Nielsen, Cydney B, Friedman, Brad, Birren, Bruce, Burge, Christopher B, Galagan, James E
Little is known about the patterns of intron gain and loss or the relative contributions of these two processes to gene evolution. To investigate the dynamics of intron evolution, we analyzed...
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...
The Genome of M. acetivorans Reveals Extensive Metabolic and Physiological Diversity
Galagan, James E., Nusbaum, Chad, Roy, Alice, Endrizzi, Matthew G., Macdonald, Pendexter, FitzHugh, Will, ...
Methanogenesis, the biological production of methane, plays a pivotal role in the global carbon cycle and contributes significantly to global warming. The majority of methane in nature is derived...
Borkovich, Katherine A., Alex, Lisa A., Yarden, Oded, Freitag, Michael, Turner, Gloria E., Read, Nick D., ...
We present an analysis of over 1,100 of the ∼10,000 predicted proteins encoded by the genome sequence of the filamentous fungus Neurospora crassa. Seven major areas of Neurospora genomics and...
Patterns of Intron Gain and Loss in Fungi
Nielsen, Cydney B, Friedman, Brad, Birren, Bruce, Burge, Christopher B, Galagan, James E
Little is known about the patterns of intron gain and loss or the relative contributions of these two processes to gene evolution. To investigate the dynamics of intron evolution, we analyzed...
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...
Conrad: Gene prediction using conditional random fields
DeCaprio, David, Vinson, Jade P., Pearson, Matthew D., Montgomery, Philip, Doherty, Matthew, Galagan, James E.
We present Conrad, the first comparative gene predictor based on semi-Markov conditional random fields (SMCRFs). Unlike the best standalone gene predictors, which are based on generalized hidden...
Mechanisms of intron gain and loss in Cryptococcus
Sharpton, Thomas J, Neafsey, Daniel E, Galagan, James E, Taylor, John W
Comparison of five relatively closely related yeast Cryptococcus genomes suggests that recombination causes internal intron loss and that DNA repeat expansion can create new introns in a population.
Cross-kingdom patterns of alternative splicing and splice recognition
McGuire, Abigail M, Pearson, Matthew D, Neafsey, Daniel E, Galagan, James E
A comprehensive survey of alternate splicing across 42 eukaryotes so as to gain insight into how spliceosomal introns are recognized.
Dynamics of Pseudomonas aeruginosa genome evolution
Mathee, Kalai, Narasimhan, Giri, Valdes, Camilo, Qiu, Xiaoyun, Matewish, Jody M., Koehrsen, Michael, ...
One of the hallmarks of the Gram-negative bacterium Pseudomonas aeruginosa is its ability to thrive in diverse environments that includes humans with a variety of debilitating diseases or immune...
Hane, James K., Lowe, Rohan G.T., Solomon, Peter S., Tan, Kar-Chun, Schoch, Conrad L., Spatafora, Joseph W., ...
Stagonospora nodorum is a major necrotrophic fungal pathogen of wheat (Triticum aestivum) and a member of the Dothideomycetes, a large fungal taxon that includes many important plant pathogens...
Short-term genome evolution of Listeria monocytogenes in a non-controlled environment
Orsi, Renato H, Borowsky, Mark L, Lauer, Peter, Young, Sarah K, Nusbaum, Chad, Galagan, James E, ...
A High-Density Single Nucleotide Polymorphism Map for Neurospora crassa
Lambreghts, Randy, Shi, Mi, Belden, William J., DeCaprio, David, Park, Danny, Henn, Matthew R., ...
We report the discovery and validation of a set of single nucleotide polymorphisms (SNPs) between the reference Neurospora crassa strain Oak Ridge and the Mauriceville strain (FGSC 2555), of...
TB database: an integrated platform for tuberculosis research
Reddy, T. B. K., Riley, Robert, Wymore, Farrell, Montgomery, Phillip, DeCaprio, Dave, Engels, Reinhard, ...
The effective control of tuberculosis (TB) has been thwarted by the need for prolonged, complex and potentially toxic drug regimens, by reliance on an inefficient vaccine and by the absence of...
Colijn, Caroline, Brandes, Aaron, Zucker, Jeremy, Lun, Desmond S., Weiner, Brian, Farhat, Maha R., ...
Metabolism is central to cell physiology, and metabolic disturbances play a role in numerous disease states. Despite its importance, the ability to study metabolism at a global scale using genomic...
Large-scale identification of genetic design strategies using local search
Lun, Desmond S, Rockwell, Graham, Guido, Nicholas J, Baym, Michael, Kelner, Jonathan A, Berger, Bonnie, ...
In the past decade, computational methods have been shown to be well suited to unraveling the complex web of metabolic reactions in biological systems. Methods based on flux–balance analysis (FBA)...