MacCallum, Iain, Przybylski, Dariusz, Gnerre, Sante, Burton, Joshua, Shlyakhter, Ilya, Gnirke, Andreas, ...
Abstract We demonstrate that genome sequences approaching finished quality can be generated from short paired reads. Using 36 base (fragment) and 26 base (jumping) reads from five microbial genomes...
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...
Assisted assembly: how to improve a de novo genome assembly by using related species (2009)
Gnerre, Sante, Lander, Eric S., Lindbald-Toh, Kerstin, Jaffe, David B.
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 assisting...
Closing gaps in the human genome using sequencing by synthesis (2009)
Garber, Manuel, Zody, Michael C, Arachchi, Harindra M, Berlin, Aaron, Gnerre, Sante, Green, Lisa M, ...
Abstract The most recent release of the finished human genome contains 260 euchromatic gaps (excluding chromosome Y). Recent work has helped explain a large number of these unresolved regions as...
Closing gaps in the human genome using sequencing by synthesis (2009)
Arachchi, Harindra M., Green, Lisa M., Zody, Michael C., Lennon, Niall, Gnerre, Sante, Berlin, Aaron, ...
The most recent release of the finished human genome contains 260 euchromatic gaps (excluding chromosome Y). Recent work has helped explain a large number of these unresolved regions as 'structural'...
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,...
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...
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,...
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...
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,...
Free composition of paragroups / (1997)
Thesis (Ph. D. in Mathematics)--University of California, Berkeley, May 1997.
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,...
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...
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...
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,...
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,...
Analysis of Chimpanzee History Based on Genome Sequence Alignments
Caswell, Jennifer L., Mallick, Swapan, Richter, Daniel J., Neubauer, Julie, Schirmer, Christine, Gnerre, Sante, ...
Population geneticists often study small numbers of carefully chosen loci, but it has become possible to obtain orders of magnitude for more data from overlaps of genome sequences. Here, we generate...
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...
Closing gaps in the human genome using sequencing by synthesis
Garber, Manuel, Zody, Michael C, Arachchi, Harindra M, Berlin, Aaron, Gnerre, Sante, Green, Lisa M, ...
A novel method for closing non-structural gaps in the human genome assembly using 454 sequencing is presented here.
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
The difficulty of avoiding false positives in genome scans for natural selection
Mallick, Swapan, Gnerre, Sante, Muller, Paul, Reich, David
Several studies have found evidence for more positive selection on the chimpanzee lineage compared with the human lineage since the two species split. A potential concern, however, is that these...