Microsatellites Are Molecular Clocks That Support Accurate Inferences about History (2009)
Sun, James X., Mullikin, James C., Patterson, Nick, Reich, David E.
Microsatellite length mutations are often modeled using the generalized stepwise mutation process, which is a type of random walk. If this model is sufficiently accurate, one can estimate the...
The ClinSeq Project: Piloting large-scale genome sequencing for research in genomic medicine (2009)
Biesecker, Leslie G., Mullikin, James C., Facio, Flavia M., Turner, Clesson, Cherukuri, Praveen F., Blakesley, Robert W., ...
ClinSeq is a pilot project to investigate the use of whole-genome sequencing as a tool for clinical research. By piloting the acquisition of large amounts of DNA sequence data from individual human...
ssahaSNP – A Polymorphism Detection Tool on a Whole Genome Scale (2008)
Zemin Ning, Mario Caccamo, James C. Mullikin
We present a software package which can detect homozygous SNPs and indels on a eukaryotic genome scale from millions of shotgun reads. Matching seeds of a few kmer words are found to locate the...
Kim, HyeRan, Hurwitz, Bonnie, Yu, Yeisoo, Collura, Kristi, Gill, Navdeep, SanMiguel, Phillip, ...
Abstract We describe the establishment and analysis of a genus-wide comparative framework composed of 12 bacterial artificial chromosome fingerprint and end-sequenced physical maps representing the...
Accurate whole human genome sequencing using reversible terminator chemistry (2008)
Bentley, David R., Balasubramanian, Shankar, Swerdlow, Harold P., Smith, Geoffrey P., Milton, John, Brown, Clive G., ...
DNA sequence information underpins genetic research, enabling discoveries of important biological or medical benefit. Sequencing projects have traditionally used long (400-800 base pair) reads, but...
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...
A second generation human haplotype map of over 3.1 million SNPs (2007)
Frazer, Kelly A., Ballinger, Dennis G., Cox, David R., Hinds, David A., Stuve, Laura L., Gibbs, Richard A., ...
We describe the Phase II HapMap, which characterizes over 3.1 million human single nucleotide polymorphisms (SNPs) genotyped in 270 individuals from four geographically diverse populations and...
Clark, Taane G, Andrew, Toby, Cooper, Gregory M, Margulies, Elliott H, Mullikin, James C, Balding, David J
Abstract Background We describe the distribution of indels in the 44 Encyclopedia of DNA Elements (ENCODE) regions (about 1% of the human genome) and evaluate the potential contributions of small...
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,...
Ryan, Joseph F, Burton, Patrick M, Mazza, Maureen E, Kwong, Grace K, Mullikin, James C, Finnerty, John R
Abstract Background Homeodomain transcription factors are key components in the developmental toolkits of animals. While this gene superclass predates the evolutionary split between animals, plants,...
StellaBase: The Nematostella vectensis Genomics Database (2006)
Sullivan, James C., Ryan, Joseph F., Watson, James A., Webb, Jeramy, Mullikin, James C., Rokhsar, Daniel, ...
StellaBase, the Nematostella vectensis Genomics Database, is a web-based resource that will facilitate desktop and bench-top studies of the starlet sea anemone. Nematostella is an emerging model...
An intermediate grade of finished genomic sequence suitable for comparative analyses (2004)
Blakesley, Robert W., Hansen, Nancy F., Mullikin, James C., Thomas, Pamela J., McDowell, Jennifer C., Maskeri, Baishali, ...
Although the cost of generating draft-quality genomic sequence continues to decline, refining that sequence by the process of “sequence finishing” remains expensive. Near-perfect finished...
An intermediate grade of finished genomic sequence suitable for comparative analyses (2004)
Blakesley, Robert W., Hansen, Nancy F., Mullikin, James C., Thomas, Pamela J., McDowell, Jennifer C., Maskeri, Baishali, ...
Although the cost of generating draft-quality genomic sequence continues to decline, refining that sequence by the process of “sequence finishing” remains expensive. Near-perfect finished...
The Genome Sequence of Caenorhabditis briggsae: A Platform for Comparative Genomics (2003)
Lincoln D. Stein, Zhirong Bao, Darin Blasiar, Thomas Blumenthal, Michael R. Brent, Nansheng Chen, ...
With the Caenorhabditis briggsae genome now in hand, C. elegans biologists have a powerful new research tool to refine their knowledge of gene function in C. elegans and to study the path of genome...
The Genome Sequence of Caenorhabditis briggsae: A Platform for Comparative Genomics (2003)
Lincoln D. Stein, Zhirong Bao, Darin Blasiar, Thomas Blumenthal, Michael R. Brent, Nansheng Chen, ...
The soil nematodes Caenorhabditis briggsae and Caenorhabditis elegans diverged from a common ancestor roughly 100 million years ago and yet are almost indistinguishable by eye. They have the same...
Mullikin, James C., Ning, Zemin
The Phusion assembler has assembled the mouse genome from the whole-genome shotgun (WGS) dataset collected by the Mouse Genome Sequencing Consortium, at ∼7.5× sequence coverage, producing a...
Revisiting the mouse mitochondrial DNA sequence (2003)
Bayona-Bafaluy, María Pilar, Acín-Pérez, Rebeca, Mullikin, James C., Park, Jeong Soon, Moreno-Loshuertos, Raquel, Hu, Peiqing, ...
The existence of reliable mtDNA reference sequences for each species is of great relevance in a variety of fields, from phylogenetic and population genetics studies to pathogenetic determination of...
Revisiting the mouse mitochondrial DNA sequence
Bayona-Bafaluy, María Pilar, Acín-Pérez, Rebeca, Mullikin, James C., Park, Jeong Soon, Moreno-Loshuertos, Raquel, Hu, Peiqing, ...
The existence of reliable mtDNA reference sequences for each species is of great relevance in a variety of fields, from phylogenetic and population genetics studies to pathogenetic determination of...
The Genome Sequence of Caenorhabditis briggsae: A Platform for Comparative Genomics
Stein, Lincoln D, Bao, Zhirong, Blasiar, Darin, Blumenthal, Thomas, Brent, Michael R, Chen, Nansheng, ...
The soil nematodes Caenorhabditis briggsae and Caenorhabditis elegans diverged from a common ancestor roughly 100 million years ago and yet are almost indistinguishable by eye. They have the same...
SSAHA: A Fast Search Method for Large DNA Databases
Ning, Zemin, Cox, Anthony J., Mullikin, James C.
We describe an algorithm, SSAHA (Sequence Search and Alignment by Hashing Algorithm), for performing fast searches on databases containing multiple gigabases of DNA. Sequences in the database are...
Identifying gene regulatory elements by genome-wide recovery of DNase hypersensitive sites
Crawford, Gregory E., Holt, Ingeborg E., Mullikin, James C., Tai, Denise, Green, Eric D., Wolfsberg, Tyra G., ...
Analysis of the human genome sequence has identified ≈25,000–30,000 protein-coding genes, but little is known about how most of these are regulated. Mapping DNase I hypersensitive (HS) sites has...
Mullikin, James C., Ning, Zemin
The Phusion assembler has assembled the mouse genome from the whole-genome shotgun (WGS) dataset collected by the Mouse Genome Sequencing Consortium, at ∼7.5× sequence coverage, producing a...
An intermediate grade of finished genomic sequence suitable for comparative analyses
Blakesley, Robert W., Hansen, Nancy F., Mullikin, James C., Thomas, Pamela J., McDowell, Jennifer C., Maskeri, Baishali, ...
Although the cost of generating draft-quality genomic sequence continues to decline, refining that sequence by the process of “sequence finishing” remains expensive. Near-perfect finished...
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...
StellaBase: The Nematostella vectensis Genomics Database
Sullivan, James C., Ryan, Joseph F., Watson, James A., Webb, Jeramy, Mullikin, James C., Rokhsar, Daniel, ...
StellaBase, the Nematostella vectensis Genomics Database, is a web-based resource that will facilitate desktop and bench-top studies of the starlet sea anemone. Nematostella is an emerging model...
Revisiting the mouse mitochondrial DNA sequence
Bayona-Bafaluy, María Pilar, Acín-Pérez, Rebeca, Mullikin, James C., Park, Jeong Soon, Moreno-Loshuertos, Raquel, Hu, Peiqing, ...
The existence of reliable mtDNA reference sequences for each species is of great relevance in a variety of fields, from phylogenetic and population genetics studies to pathogenetic determination of...
The Genome Sequence of Caenorhabditis briggsae: A Platform for Comparative Genomics
Stein, Lincoln D, Bao, Zhirong, Blasiar, Darin, Blumenthal, Thomas, Brent, Michael R, Chen, Nansheng, ...
The soil nematodes Caenorhabditis briggsae and Caenorhabditis elegans diverged from a common ancestor roughly 100 million years ago and yet are almost indistinguishable by eye. They have the same...
SSAHA: A Fast Search Method for Large DNA Databases
Ning, Zemin, Cox, Anthony J., Mullikin, James C.
We describe an algorithm, SSAHA (Sequence Search and Alignment by Hashing Algorithm), for performing fast searches on databases containing multiple gigabases of DNA. Sequences in the database are...
Identifying gene regulatory elements by genome-wide recovery of DNase hypersensitive sites
Crawford, Gregory E., Holt, Ingeborg E., Mullikin, James C., Tai, Denise, Green, Eric D., Wolfsberg, Tyra G., ...
Analysis of the human genome sequence has identified ≈25,000–30,000 protein-coding genes, but little is known about how most of these are regulated. Mapping DNase I hypersensitive (HS) sites has...
Mullikin, James C., Ning, Zemin
The Phusion assembler has assembled the mouse genome from the whole-genome shotgun (WGS) dataset collected by the Mouse Genome Sequencing Consortium, at ∼7.5× sequence coverage, producing a...
An intermediate grade of finished genomic sequence suitable for comparative analyses
Blakesley, Robert W., Hansen, Nancy F., Mullikin, James C., Thomas, Pamela J., McDowell, Jennifer C., Maskeri, Baishali, ...
Although the cost of generating draft-quality genomic sequence continues to decline, refining that sequence by the process of “sequence finishing” remains expensive. Near-perfect finished...
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...
StellaBase: The Nematostella vectensis Genomics Database
Sullivan, James C., Ryan, Joseph F., Watson, James A., Webb, Jeramy, Mullikin, James C., Rokhsar, Daniel, ...
StellaBase, the Nematostella vectensis Genomics Database, is a web-based resource that will facilitate desktop and bench-top studies of the starlet sea anemone. Nematostella is an emerging model...
Ryan, Joseph F, Burton, Patrick M, Mazza, Maureen E, Kwong, Grace K, Mullikin, James C, Finnerty, John R
The first near-complete set of homeodomains from a non-bilaterian animal is described.
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,...
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...
Kim, HyeRan, Hurwitz, Bonnie, Yu, Yeisoo, Collura, Kristi, Gill, Navdeep, SanMiguel, Phillip, ...
Bacterial artificial chromosome (BAC) fingerprint and end-sequenced physical maps representing the ten genome types of Oryza are presented
Functional constraint and small insertions and deletions in the ENCODE regions of the human genome
Clark, Taane G, Andrew, Toby, Cooper, Gregory M, Margulies, Elliott H, Mullikin, James C, Balding, David J
Indel rates were observed to be reduced approximately twenty-fold in exonic ENCODE regions, five-fold in sequence that exhibits high evolutionary constraint in mammals and up to two-fold in some...
Yuhki, Naoya, Mullikin, James C., Beck, Thomas, Stephens, Robert, O'Brien, Stephen J.
Two sequences of major histocompatibility complex (MHC) regions in the domestic cat, 2.976 and 0.362 Mbps, which were separated by an ancient chromosome break (55–80 MYA) and followed by a...