Assisted assembly: how to improve a de novogenome assembly by using related species (2009)
Gnerre, Sante, Lander, Eric S, Lindblad-Toh, Kerstin, Jaffe, David B
Abstract We describe a new assembly algorithm, where a genome assembly with low sequence coverage, either throughout the genome or locally, due to cloning bias, is considerably improved through an...
And The Canine Genome Mapping Community: (2008)
Elaine A. Ostr, Kerstin Lindblad-toh, Eric S. L, Gregory M. Acl, Gustavo D. Aguirre, Matthew M. Binns, ...
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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,...
Wiik, Anne Caroline, Wade, Claire, Biagi, Tara, Ropstad, Ernst-Otto, Bjerkås, Ellen, Lindblad-Toh, Kerstin, ...
Cone-rod dystrophy is a retinal degenerative disorder occurring naturally in man and dog. Here we identify a novel gene for early-onset cone-rod dystrophy in the wire-haired dachshund. For the first...
Kerstin Lindblad-toh, Petteri Sevon, John D. Rioux, Anu Villapakkam, Lauri A. Laitinen, ...
We have analyzed a dense set of single-nucleotide polymorphisms (SNPs) and microsatellites spanning the T-helper cytokine gene cluster (interleukins 3, 4, 5, 9, and 13, interferon regulatory...
Initial sequence and comparative analysis of the cat genome (2007)
Pontius, Joan U., Mullikin, James C., Smith, Douglas R., Lindblad-Toh, Kerstin, Gnerre, Sante, ...
The genome sequence (1.9-fold coverage) of an inbred Abyssinian domestic cat was assembled, mapped, and annotated with a comparative approach that involved cross-reference to annotated genome...
Thomas, Rachael, Duke, Shannon E., Bloom, Stephanie K., Breen, Tessa E., Young, Andrea C., Feiste, Erika, ...
The generation of a 7.5× dog genome assembly provides exciting new opportunities to interpret tumor-associated chromosome aberrations at the biological level. We present a genomic microarray for...
Margulies, Elliott H., Cooper, Gregory M., Asimenos, George, Thomas, Daryl J., Dewey, Colin N., Siepel, Adam, ...
A key component of the ongoing ENCODE project involves rigorous comparative sequence analyses for the initially targeted 1% of the human genome. Here, we present orthologous sequence generation,...
Baker, Michelle L, Indiviglio, Sandra, Nyberg, April M, Rosenberg, George H, Lindblad-Toh, Kerstin, Miller, Robert D, ...
Abstract Background Expressed sequence tags (ESTs) have been used for rapid gene discovery in a variety of organisms and provide a valuable resource for whole genome annotation. Although the genome...
28-Way vertebrate alignment and conservation track in the UCSC Genome Browser (2007)
Miller, Webb, Rosenbloom, Kate, Hardison, Ross C., Hou, Minmei, Taylor, James, Raney, Brian, ...
This article describes a set of alignments of 28 vertebrate genome sequences that is provided by the UCSC Genome Browser. The alignments can be viewed on the Human Genome Browser (March 2006...
Identification and classification of conserved RNA secondary structures in the human genome (2006)
Pedersen, Jakob Skou, Bejerano, Gill, Siepel, Adam, Rosenbloom, Kate, Lindblad-Toh, Kerstin, Lander, Eric S, ...
The discoveries of microRNAs and riboswitches, among others, have shown functional RNAs to be biologically more important and genomically more prevalent than previously anticipated. We have developed...
Identification and Classification of Conserved RNA Secondary Structures in the Human Genome (2006)
Jakob Skou Pedersen, Gill Bejerano, Adam Siepel, Kate Rosenbloom, Kerstin Lindblad-Toh, Eric S. Lander, ...
The discoveries of microRNAs and riboswitches, among others, have shown functional RNAs to be biologically more important and genomically more prevalent than previously anticipated. We have developed...
Identification and Classification of Conserved RNA Secondary Structures in the Human Genome (2006)
Jakob Skou Pedersen, Gill Bejerano, Adam Siepel, Kate R. Rosenbloom, Kerstin Lindblad-Toh, Eric S Lander, ...
The discovery of, e.g., microRNAs and riboswitches have shown functional RNAs to be biologically more important and genomically more prevalent than previously anticipated. We have developed a general...
The dog and rat olfactory receptor repertoires (2005)
Quignon, Pascale, Giraud, Mathieu, Rimbault, Maud, Lavigne, Patricia, Tacher, Sandrine, Morin, Emmanuelle, ...
Abstract Background Dogs and rats have a highly developed capability to detect and identify odorant molecules, even at minute concentrations. Previous analyses have shown that the olfactory receptors...
Initial sequence of the chimpanzee genome and comparison with the human genome (2005)
Mikkelsen, Tarjei S., Hillier, LaDeana W., Eichler, Evan E., Zody, Michael C., Jaffe, David B., Yang, Shiaw-Pyng, ...
Here we present a draft genome sequence of the common chimpanzee (Pan troglodytes). Through comparison with the human genome, we have generated a largely complete catalogue of the genetic differences...
Construction of a 2-Mb resolution BAC microarray for CGH analysis of canine tumors (2005)
Thomas, Rachael, Scott, Allyson, Langford, Cordelia F., Fosmire, Susan P., Jubala, Cristan M., Lorentzen, Travis D., ...
Recognition of the domestic dog as a model for the comparative study of human genetic traits has led to major advances in canine genomics. The pathophysiological similarities shared between many...
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,...
SBE-TAGS: An array-based method for efficient single-nucleotide polymorphism genotyping
Hirschhorn, Joel N., Sklar, Pamela, Lindblad-Toh, Kerstin, Lim, Yin-Mei, Ruiz-Gutierrez, Melisa, Bolk, Stacey, ...
Generating human single-nucleotide polymorphisms (SNPs) is no longer a rate-limiting step for genetic studies of disease. The number of SNPs in public databases already exceeds 200,000, and the total...
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,...
Margulies, Elliott H., Vinson, Jade P., Miller, Webb, Jaffe, David B., Lindblad-Toh, Kerstin, Chang, Jean L., ...
With the recent completion of a high-quality sequence of the human genome, the challenge is now to understand the functional elements that it encodes. Comparative genomic analysis offers a powerful...
The dog and rat olfactory receptor repertoires
Quignon, Pascale, Giraud, Mathieu, Rimbault, Maud, Lavigne, Patricia, Tacher, Sandrine, Morin, Emmanuelle, ...
An almost complete list of odorant receptor genes in the dog (1,094 genes) and the rat (1,493 genes) is described. A comparison of odorant receptor repertoires in rat, dog, mouse and human is also...
Identification and Classification of Conserved RNA Secondary Structures in the Human Genome
Pedersen, Jakob Skou, Bejerano, Gill, Siepel, Adam, Rosenbloom, Kate, Lindblad-Toh, Kerstin, Lander, Eric S, ...
The discoveries of microRNAs and riboswitches, among others, have shown functional RNAs to be biologically more important and genomically more prevalent than previously anticipated. We have developed...
Construction of a 2-Mb resolution BAC microarray for CGH analysis of canine tumors
Thomas, Rachael, Scott, Allyson, Langford, Cordelia F., Fosmire, Susan P., Jubala, Cristan M., Lorentzen, Travis D., ...
Recognition of the domestic dog as a model for the comparative study of human genetic traits has led to major advances in canine genomics. The pathophysiological similarities shared between many...
SBE-TAGS: An array-based method for efficient single-nucleotide polymorphism genotyping
Hirschhorn, Joel N., Sklar, Pamela, Lindblad-Toh, Kerstin, Lim, Yin-Mei, Ruiz-Gutierrez, Melisa, Bolk, Stacey, ...
Generating human single-nucleotide polymorphisms (SNPs) is no longer a rate-limiting step for genetic studies of disease. The number of SNPs in public databases already exceeds 200,000, and the total...
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,...
Margulies, Elliott H., Vinson, Jade P., Miller, Webb, Jaffe, David B., Lindblad-Toh, Kerstin, Chang, Jean L., ...
With the recent completion of a high-quality sequence of the human genome, the challenge is now to understand the functional elements that it encodes. Comparative genomic analysis offers a powerful...
The dog and rat olfactory receptor repertoires
Quignon, Pascale, Giraud, Mathieu, Rimbault, Maud, Lavigne, Patricia, Tacher, Sandrine, Morin, Emmanuelle, ...
An almost complete list of odorant receptor genes in the dog (1,094 genes) and the rat (1,493 genes) is described. A comparison of odorant receptor repertoires in rat, dog, mouse and human is also...
Construction of a 2-Mb resolution BAC microarray for CGH analysis of canine tumors
Thomas, Rachael, Scott, Allyson, Langford, Cordelia F., Fosmire, Susan P., Jubala, Cristan M., Lorentzen, Travis D., ...
Recognition of the domestic dog as a model for the comparative study of human genetic traits has led to major advances in canine genomics. The pathophysiological similarities shared between many...
Identification and Classification of Conserved RNA Secondary Structures in the Human Genome
Pedersen, Jakob Skou, Bejerano, Gill, Siepel, Adam, Rosenbloom, Kate, Lindblad-Toh, Kerstin, Lander, Eric S, ...
The discoveries of microRNAs and riboswitches, among others, have shown functional RNAs to be biologically more important and genomically more prevalent than previously anticipated. We have developed...
Baker, Michelle L, Indiviglio, Sandra, Nyberg, April M, Rosenberg, George H, Lindblad-Toh, Kerstin, Miller, Robert D, ...
Xie, Xiaohui, Mikkelsen, Tarjei S., Gnirke, Andreas, Lindblad-Toh, Kerstin, Kellis, Manolis, Lander, Eric S.
Conserved noncoding elements (CNEs) constitute the majority of sequences under purifying selection in the human genome, yet their function remains largely unknown. Experimental evidence suggests that...
Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome
Margulies, Elliott H., Cooper, Gregory M., Asimenos, George, Thomas, Daryl J., Dewey, Colin N., Siepel, Adam, ...
A key component of the ongoing ENCODE project involves rigorous comparative sequence analyses for the initially targeted 1% of the human genome. Here, we present orthologous sequence generation,...
A unique T cell receptor discovered in marsupials
Parra, Zuly E., Baker, Michelle L., Schwarz, Ryan S., Deakin, Janine E., Lindblad-Toh, Kerstin, Miller, Robert D.
T cells recognize antigens by using T cell receptors (TCRs) encoded by gene segments, called variable (V), diversity (D), and joining (J), that undergo somatic recombination to create diverse binding...
Initial sequence and comparative analysis of the cat genome
Pontius, Joan U., Mullikin, James C., Smith, Douglas R., Lindblad-Toh, Kerstin, Gnerre, Sante, Clamp, Michele, ...
The genome sequence (1.9-fold coverage) of an inbred Abyssinian domestic cat was assembled, mapped, and annotated with a comparative approach that involved cross-reference to annotated genome...
28-Way vertebrate alignment and conservation track in the UCSC Genome Browser
Miller, Webb, Rosenbloom, Kate, Hardison, Ross C., Hou, Minmei, Taylor, James, Raney, Brian, ...
This article describes a set of alignments of 28 vertebrate genome sequences that is provided by the UCSC Genome Browser. The alignments can be viewed on the Human Genome Browser (March 2006...
Distinguishing protein-coding and noncoding genes in the human genome
Clamp, Michele, Fry, Ben, Kamal, Mike, Xie, Xiaohui, Cuff, James, Lin, Michael F., ...
Although the Human Genome Project was completed 4 years ago, the catalog of human protein-coding genes remains a matter of controversy. Current catalogs list a total of ≈24,500 putative...
Wiik, Anne Caroline, Wade, Claire, Biagi, Tara, Ropstad, Ernst-Otto, Bjerkås, Ellen, Lindblad-Toh, Kerstin, ...
Cone-rod dystrophy is a retinal degenerative disorder occurring naturally in man and dog. Here we identify a novel gene for early-onset cone-rod dystrophy in the wire-haired dachshund. For the first...
Lineage-Specific Biology Revealed by a Finished Genome Assembly of the Mouse
Church, Deanna M., Goodstadt, Leo, Hillier, LaDeana W., Zody, Michael C., Goldstein, Steve, She, Xinwe, ...
A finished clone-based assembly of the mouse genome reveals extensive recent sequence duplication during recent evolution and rodent-specific expansion of certain gene families. Newly assembled...
Awano, Tomoyuki, Johnson, Gary S., Wade, Claire M., Katz, Martin L., Johnson, Gayle C., Taylor, Jeremy F., ...
Canine degenerative myelopathy (DM) is a fatal neurodegenerative disease prevalent in several dog breeds. Typically, the initial progressive upper motor neuron spastic and general proprioceptive...
A Missense Mutation in the SERPINH1 Gene in Dachshunds with Osteogenesis Imperfecta
Drögemüller, Cord, Becker, Doreen, Brunner, Adrian, Haase, Bianca, Kircher, Patrick, Seeliger, Frank, ...
Osteogenesis imperfecta (OI) is a hereditary disease occurring in humans and dogs. It is characterized by extremely fragile bones and teeth. Most human and some canine OI cases are caused by...
Assisted assembly: how to improve a de novo genome assembly by using related species
Gnerre, Sante, Lander, Eric S, Lindblad-Toh, Kerstin, Jaffe, David B
A method is described for improving low sequence coverage genome assemblies