Bos taurusgenome assembly (2009)
Liu, Yue, Qin, Xiang, Song, Xing-Zhi, Jiang, Huaiyang, Shen, Yufeng, Durbin, K James, ...
Abstract Background We present here the assembly of the bovine genome. The assembly method combines the BAC plus WGS local assembly used for the rat and sea urchin with the whole genome shotgun (WGS)...
Improving Phrap-Based Assembly of the Rat Using “Reliable” Overlaps (2008)
Roberts, Michael, Zimin, Aleksey V., Hayes, Wayne, Hunt, Brian R., Ustun, Cevat, White, James R., ...
The assembly methods used for whole-genome shotgun (WGS) data have a major impact on the quality of resulting draft genomes. We present a novel algorithm to generate a set of “reliable” overlaps...
Insights into social insects from the genome of the honeybee Apis mellifera (2006)
Robinson, Gene E, Gibbs, Richard A, Worley, Kim C, Evans, Jay D, Maleszka, Ryszard, ...
Here we report the genome sequence of the honeybee Apis mellifera, a key model for social behaviour and essential to global ecology through pollination. Compared with other sequenced insect genomes,...
The DNA sequence, annotation and analysis of human chromosome 3 (2006)
Muzny, Donna M., Scherer, Steven E., Kaul, Rajinder, Wang, Jing, Yu, Jun, ...
The DNA sequence, annotation and analysis of human chromosome 3 (2006)
Muzny, Donna M., Scherer, Steven E., Kaul, Rajinder, Wang, Jing, Yu, Jun, ...
The DNA sequence, annotation and analysis of human chromosome 3 (2006)
Muzny, Donna M., Scherer, Steven E., Kaul, Rajinder, Wang, Jing, Yu, Jun, ...
Richards, Stephen, Liu, Yue, Bettencourt, Brian R., Hradecky, Pavel, Letovsky, Stan, Nielsen, Rasmus, ...
We have sequenced the genome of a second Drosophila species, Drosophila pseudoobscura, and compared this to the genome sequence of Drosophila melanogaster, a primary model organism. Throughout...
Richards, Stephen, Liu, Yue, Bettencourt, Brian R., Hradecky, Pavel, Letovsky, Stan, Nielsen, Rasmus, ...
The genome sequence of a second fruit fly, D. pseudoobscura, presents an opportunity for comparative analysis of a primary model organism D. melanogaster. The vast majority of Drosophila genes have...
The Atlas Genome Assembly System (2004)
Havlak, Paul, Chen, Rui, Durbin, K. James, Egan, Amy, Ren, Yanru, Song, Xing-Zhi, ...
Atlas is a suite of programs developed for assembly of genomes by a “combined approach” that uses DNA sequence reads from both BACs and whole-genome shotgun (WGS) libraries. The BAC clones afford...
Index array flattening through program transformation (1995)
Raja Das, Paul Havlak, Joel Saltz, Ken Kennedy
This paper presents techniques for compiling loops with complex, indirect array accesses into loops whose array references have at most one level of indirection. The transformation allows prefetching...
Interprocedural Symbolic Analysis (1994)
Paul Havlak, Paul Havlak, Paul Havlak
Compiling for efficient execution on advanced computer architectures requires extensive program analysis and transformation. Most compilers limit their analysis to simple phenomena within single...
Construction of Thinned Gated Single-Assignment Form (1993)
. Analysis of symbolic expressions benefits from a suitable program representation. We show how to build thinned gated singleassignment (TGSA) form, a value-oriented program representation which is...
An implementation of interprocedural bounded regular section analysis (1991)
Paul Havlak, Paul Havlak, Ken Kennedy, Ken Kennedy
Optimizing compilers should produce efficient code even in the presence of high-level language constructs. However, current programming support systems are significantly lacking in their ability to...
An Implementation of Interprocedural Bounded Regular Section Analysis (1991)
Paul Havlak, Paul Havlak, Ken Kennedy, Ken Kennedy
Optimizing compilers should produce efficient code even in the presence of high-level language constructs. However, current programming support systems are significantly lacking in their ability to...
The Atlas Genome Assembly System
Havlak, Paul, Chen, Rui, Durbin, K. James, Egan, Amy, Ren, Yanru, Song, Xing-Zhi, ...
Atlas is a suite of programs developed for assembly of genomes by a “combined approach” that uses DNA sequence reads from both BACs and whole-genome shotgun (WGS) libraries. The BAC clones afford...
Richards, Stephen, Liu, Yue, Bettencourt, Brian R., Hradecky, Pavel, Letovsky, Stan, Nielsen, Rasmus, ...
We have sequenced the genome of a second Drosophila species, Drosophila pseudoobscura, and compared this to the genome sequence of Drosophila melanogaster, a primary model organism. Throughout...
The Atlas Genome Assembly System
Havlak, Paul, Chen, Rui, Durbin, K. James, Egan, Amy, Ren, Yanru, Song, Xing-Zhi, ...
Atlas is a suite of programs developed for assembly of genomes by a “combined approach” that uses DNA sequence reads from both BACs and whole-genome shotgun (WGS) libraries. The BAC clones afford...
Richards, Stephen, Liu, Yue, Bettencourt, Brian R., Hradecky, Pavel, Letovsky, Stan, Nielsen, Rasmus, ...
We have sequenced the genome of a second Drosophila species, Drosophila pseudoobscura, and compared this to the genome sequence of Drosophila melanogaster, a primary model organism. Throughout...
Scale-invariant structure of strongly conserved sequence in genomic intersections and alignments
Salerno, William, Havlak, Paul, Miller, Jonathan
A power-law distribution of the length of perfectly conserved sequence from mouse/human whole-genome intersection and alignment is exhibited. Spatial correlations of these elements within the mouse...
Improving Phrap-Based Assembly of the Rat Using “Reliable” Overlaps
Roberts, Michael, Zimin, Aleksey V., Hayes, Wayne, Hunt, Brian R., Ustun, Cevat, White, James R., ...
The assembly methods used for whole-genome shotgun (WGS) data have a major impact on the quality of resulting draft genomes. We present a novel algorithm to generate a set of “reliable” overlaps...