Barrière, Antoine, Yang, Shiaw-Pyng, Pekarek, Elizabeth, Thomas, Cristel G., Haag, Eric S., Ruvinsky, Ilya
The majority of nematodes are gonochoristic (dioecious) with distinct male and female sexes, but the best-studied species, Caenorhabditis elegans, is a self-fertile hermaphrodite. The sequencing of...
Genome analysis of the platypus reveals unique signatures of evolution (2008)
Wesley C. Warren, LaDeana W. Hillier, Jennifer A. Marshall Graves, Ewan Birney, Chris P. Ponting, Frank Grützner, ...
Genome analysis of the platypus reveals unique signatures of evolution (2008)
Warren, Wesley C., Hillier, LaDeana W., Marshall Graves, Jennifer A., Birney, Ewan, Ponting, Chris P., Grützner, Frank, ...
We present a draft genome sequence of the platypus, Ornithorhynchus anatinus. This monotreme exhibits a fascinating combination of reptilian and mammalian characters. For example, platypuses have a...
Application of a superword array in genome assembly (2006)
Huang, Xiaoqiu, Yang, Shiaw-Pyng, Chinwalla, Asif T., Hillier, LaDeana W., Minx, Patrick, Mardis, Elaine R., ...
We introduce a data structure called a superword array for finding quickly matches between DNA sequences. The superword array possesses some desirable features of the lookup table and suffix array....
Physical map-assisted whole-genome shotgun sequence assemblies (2006)
Warren, René L., Varabei, Dmitry, Platt, Darren, Huang, Xiaoqiu, Messina, David, Yang, Shiaw-Pyng, ...
We describe a targeted approach to improve the contiguity of whole-genome shotgun sequence (WGS) assemblies at run-time, using information from Bacterial Artificial Chromosome (BAC)-based physical...
Generation and annotation of the DNA sequences of human chromosomes 2 and 4 (2005)
LaDeana W. Hillier, Tina A. Graves, Robert S. Fulton, Lucinda A. Fulton, Kymberlie H. Pepin, Patrick Minx, ...
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...
Application of a superword array in genome assembly (2005)
Xiaoqiu Huang, Shiaw-pyng Yang, Asif T. Chinwalla, Ladeana W. Hillier, Patrick Minx, Elaine R. Mardis, ...
We introduce a data structure called a superword array for finding quickly matches between DNA sequences. The superword array possesses some desirable features of the lookup table and suffix array....
A physical map of the chicken genome (2004)
John W. Wallis, Jan Aerts, Martien A. M. Groenen, Richard P. M. A. Crooijmans, Dan Layman, Tina A. Graves, ...
A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms (2004)
Wong, Gane Ka-Shu ; JFA; CORA, Liu, Bin, Wang, Jun, Zhang, Yong, Yang, Xu, Zhang, Zengjin, ...
We describe a genetic variation map for the chicken genome containing 2.8 million single-nucleotide polymorphisms (SNPs). This map is based on a comparison of the sequences of three domestic chicken...
A physical map of the chicken genome (2004)
Wallis, John W, Aerts, Jan, Groenen, Martien A M, Crooijmans, Richard P M A, Layman, Dan, Graves, Tina A, ...
Strategies for assembling large, complex genomes have evolved to include a combination of whole-genome shotgun sequencing and hierarchal map-assisted sequencing. Whole-genome maps of all types can...
Gap statistics for whole genome shotgun DNA sequencing projects (2004)
Wendl, Michael C., Yang, Shiaw-Pyng
Motivation: Investigators utilize gap estimates for DNA sequencing projects. Standard theories assume sequences are independently and identically distributed, leading to appreciable under-prediction...
Gap statistics for whole genome shotgun DNA sequencing projects (2004)
Wendl, Michael C., Yang, Shiaw-Pyng
Motivation: Investigators utilize gap estimates for DNA sequencing projects. Standard theories assume sequence is independently and identically distributed, leading to appreciable under-prediction of...
Gap statistics for whole genome shotgun DNA sequencing projects (2004)
Wendl, Michael C., Yang, Shiaw-Pyng
Motivation: Investigators utilize gap estimates for DNA sequencing projects. Standard theories assume sequence is independently and identically distributed, leading to appreciable under-prediction of...
The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes (2003)
Helen Skaletsky, Tomoko Kuroda-Kawaguchi, Patrick J. Minx, Holland S. Cordum, LaDeana Hillier, Laura G. Brown, ...
PCAP: A Whole-Genome Assembly Program (2003)
Huang, Xiaoqiu, Wang, Jianmin, Aluru, Srinivas, Yang, Shiaw-Pyng, Hillier, LaDeana
We describe a whole-genome assembly program named PCAP for processing tens of millions of reads. The PCAP program has several features to address efficiency and accuracy issues in assembly. Multiple...
Vita.
Dept. of Electrical Engineering.
PCAP: A Whole-Genome Assembly Program
Huang, Xiaoqiu, Wang, Jianmin, Aluru, Srinivas, Yang, Shiaw-Pyng, Hillier, LaDeana
We describe a whole-genome assembly program named PCAP for processing tens of millions of reads. The PCAP program has several features to address efficiency and accuracy issues in assembly. Multiple...
Application of a superword array in genome assembly
Huang, Xiaoqiu, Yang, Shiaw-Pyng, Chinwalla, Asif T., Hillier, LaDeana W., Minx, Patrick, Mardis, Elaine R., ...
We introduce a data structure called a superword array for finding quickly matches between DNA sequences. The superword array possesses some desirable features of the lookup table and suffix array....
Physical map-assisted whole-genome shotgun sequence assemblies
Warren, René L., Varabei, Dmitry, Platt, Darren, Huang, Xiaoqiu, Messina, David, Yang, Shiaw-Pyng, ...
We describe a targeted approach to improve the contiguity of whole-genome shotgun sequence (WGS) assemblies at run-time, using information from Bacterial Artificial Chromosome (BAC)-based physical...
PCAP: A Whole-Genome Assembly Program
Huang, Xiaoqiu, Wang, Jianmin, Aluru, Srinivas, Yang, Shiaw-Pyng, Hillier, LaDeana
We describe a whole-genome assembly program named PCAP for processing tens of millions of reads. The PCAP program has several features to address efficiency and accuracy issues in assembly. Multiple...
Application of a superword array in genome assembly
Huang, Xiaoqiu, Yang, Shiaw-Pyng, Chinwalla, Asif T., Hillier, LaDeana W., Minx, Patrick, Mardis, Elaine R., ...
We introduce a data structure called a superword array for finding quickly matches between DNA sequences. The superword array possesses some desirable features of the lookup table and suffix array....
Physical map-assisted whole-genome shotgun sequence assemblies
Warren, René L., Varabei, Dmitry, Platt, Darren, Huang, Xiaoqiu, Messina, David, Yang, Shiaw-Pyng, ...
We describe a targeted approach to improve the contiguity of whole-genome shotgun sequence (WGS) assemblies at run-time, using information from Bacterial Artificial Chromosome (BAC)-based physical...
A Catalog of Neutral and Deleterious Polymorphism in Yeast
Doniger, Scott W., Kim, Hyun Seok, Swain, Devjanee, Corcuera, Daniella, Williams, Morgan, Yang, Shiaw-Pyng, ...
The abundance and identity of functional variation segregating in natural populations is paramount to dissecting the molecular basis of quantitative traits as well as human genetic diseases. Genome...
Detecting heterozygosity in shotgun genome assemblies: Lessons from obligately outcrossing nematodes
Barrière, Antoine, Yang, Shiaw-Pyng, Pekarek, Elizabeth, Thomas, Cristel G., Haag, Eric S., Ruvinsky, Ilya
The majority of nematodes are gonochoristic (dioecious) with distinct male and female sexes, but the best-studied species, Caenorhabditis elegans, is a self-fertile hermaphrodite. The sequencing of...