Back to Bermuda: how is science best served? (2009)
Church, Deanna M, Hillier, LaDeana W
Abstract The independent announcements of two bovine genome assemblies from the same data suggest it is time to revisit the spirit of the Bermuda and Fort Lauderdale agreements and determine the...
A burst of segmental duplications in the genome of the African great ape ancestor (2009)
Marqués-Bonet, Tomàs, Kidd, Jeffrey M., Ventura, Mario, Graves, Tina A., Cheng, Ze, Hillier, LaDeana W., ...
5 pages, 4 figures.-- Supplementary information (3 files) available at: http://www.nature.com/nature/journal/v457/n7231/suppinfo/nature07744.html
Massively parallel sequencing of the polyadenylated transcriptome of C. elegans (2009)
Hillier, LaDeana W., Reinke, Valerie, Green, Philip, Hirst, Martin, Marra, Marco A., Waterston, Robert H.
Using massively parallel sequencing by synthesis methods, we have surveyed the polyA+ transcripts from four stages of the nematode Caenorhabditis elegans to an unprecedented depth. Using novel...
Article Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes (2008)
Adam Siepel, Gill Bejerano, Jakob S. Pedersen, Angie S. Hinrichs, Minmei Hou, Kate Rosenbloom, ...
We have conducted a comprehensive search for conserved elements in vertebrate genomes, using genome-wide multiple alignments of five vertebrate species (human, mouse, rat, chicken, and Fugu...
Loss of genes implicated in gastric function during platypus evolution (2008)
Ordoñez, Gonzalo R, Hillier, LaDeana W, Warren, Wesley C, Grützner, Frank, López-Otín, Carlos, Puente, Xose S
Abstract Background The duck-billed platypus ( Ornithorhynchus anatinus ) belongs to the mammalian subclass Prototheria, which diverged from the Theria line early in mammalian evolution. The platypus...
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...
Loss of genes implicated in gastric function during platypus evolution (2008)
Ordonez, Gonzalo R., Hillier, LaDeana W., Warren, Wesley, Grutzner, Frank, Lopez-Otin, Carlos, Puente, Xose S.
© 2008 Ordoñez et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License...
Loss of genes implicated in gastric function during platypus evolution (2008)
Ordonez, Gonzalo R., Hillier, LaDeana W., Warren, Wesley, Grutzner, Frank, Lopez-Otin, Carlos, Puente, Xose S.
© 2008 Ordoñez et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License...
Begun, David J, Holloway, Alisha K, Stevens, Kristian, Hillier, Ladeana W, Poh, Yu-Ping, Hahn, Matthew W, ...
The population genetic perspective is that the processes shaping genomic variation can be revealed only through simultaneous investigation of sequence polymorphism and divergence within and between...
David J. Begun, Alisha K. Holloway, Kristian Stevens, LaDeana W. Hillier, Yu-Ping Poh, Matthew W. Hahn, ...
The population genetic perspective is that the processes shaping genomic variation can be revealed only through simultaneous investigation of sequence polymorphism and divergence within and between...
Design and implementation of a generalized laboratory data model (2007)
Wendl, Michael C, Smith, Scott, Pohl, Craig S, Dooling, David J, Chinwalla, Asif T, Crouse, Kevin, ...
Abstract Background Investigators in the biological sciences continue to exploit laboratory automation methods and have dramatically increased the rates at which they can generate data. In many...
LaDeana W. Hillier, Raymond D. Miller, Scott E. Baird, Asif Chinwalla, Lucinda A. Fulton, Daniel C. Koboldt, ...
To determine whether the distinctive features of Caenorhabditis elegans chromosomal organization are shared with the C. briggsae genome, we constructed a single nucleotide polymorphism–based...
Principles of Genome Evolution in the Drosophila melanogaster Species Group (2007)
José M. Ranz, Damien Maurin, Yuk S. Chan, Marcin Von Grotthuss, LaDeana W. Hillier, John Roote, ...
That closely related species often differ by chromosomal inversions was discovered by Sturtevant and Plunkett in 1926. Our knowledge of how these inversions originate is still very limited, although...
Design and implementation of a generalized laboratory data model (2007)
Michael C Wendl, Scott Smith, Craig S Pohl, David J Dooling, Asif T Chinwalla, Kevin Crouse, ...
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...
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....
Genomics in C. elegans: So many genes, such a little worm (2005)
Hillier, LaDeana W., Coulson, Alan, Murray, John I., Bao, Zhirong, Sulston, John E., Waterston, Robert H.
The Caenorhabditis elegans genome sequence is now complete, fully contiguous telomere to telomere and totaling 100,291,840 bp. The sequence has catalyzed the collection of systematic data sets and...
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes (2005)
Siepel, Adam, Bejerano, Gill, Pedersen, Jakob S., Hinrichs, Angie S., Hou, Minmei, Rosenbloom, Kate, ...
We have conducted a comprehensive search for conserved elements in vertebrate genomes, using genome-wide multiple alignments of five vertebrate species (human, mouse, rat, chicken, and Fugu...
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes (2005)
Siepel, Adam, Bejerano, Gill, Pedersen, Jakob S., Hinrichs, Angie S., Hou, Minmei, Rosenbloom, Kate, ...
We have conducted a comprehensive search for conserved elements in vertebrate genomes, using genome-wide multiple alignments of five vertebrate species (human, mouse, rat, chicken, and Fugu...
A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms (2004)
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...
Furey, Terrence S., Diekhans, Mark, Lu, Yontao, Graves, Tina A., Oddy, Lachlan, Randall-Maher, Jennifer, ...
The NCBI Reference Sequence (RefSeq) project and the NIH Mammalian Gene Collection (MGC) together define a set of ∼30,000 nonredundant human mRNA sequences with identified coding regions...
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...
Software for Automated Analysis of DNA Fingerprinting Gels (2003)
Fuhrmann, Daniel R., Krzywinski, Martin I., Chiu, Readman, Saeedi, Parvaneh, Schein, Jacqueline E., Bosdet, Ian E., ...
Here we describe software tools for the automated detection of DNA restriction fragments resolved on agarose fingerprinting gels. We present a mathematical model for the location and shape of the...
Theories and Applications for Sequencing Randomly Selected Clones (2001)
Wendl, Michael C., Marra, Marco A., Hillier, LaDeana W., Chinwalla, Asif T., Wilson, Richard K., Waterston, Robert H.
Theories and Applications for Sequencing Randomly Selected Clones (2001)
Wendl, Michael C., Marra, Marco A., Hillier, LaDeana W., Chinwalla, Asif T., Wilson, Richard K., Waterston, Robert H.
Cliften, Paul F., Hillier, LaDeana W., Fulton, Lucinda, Graves, Tina, Miner, Tracie, Gish, Warren R., ...
Theories and Applications for Sequencing Randomly Selected Clones (2001)
Wendl, Michael C., Marra, Marco A., Hillier, LaDeana W., Chinwalla, Asif T., Wilson, Richard K., Waterston, Robert H.
High Throughput Fingerprint Analysis of Large-Insert Clones (1997)
Marra, Marco A., Kucaba, Tamara A., Dietrich, Nicole L., Green, Eric D., Brownstein, Buddy, Wilson, Richard K., ...
Ellsworth, Rachel E., Jamison, D. Curtis, Touchman, Jeffrey W., Chissoe, Stephanie L., Braden Maduro, Valerie V., Bouffard, Gerard G., ...
The identification of the cystic fibrosis transmembrane conductance regulator gene (CFTR) in 1989 represents a landmark accomplishment in human genetics. Since that time, there have been numerous...
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...
High Throughput Fingerprint Analysis of Large-Insert Clones
Marra, Marco A., Kucaba, Tamara A., Dietrich, Nicole L., Green, Eric D., Brownstein, Buddy, Wilson, Richard K., ...
As part of the Human Genome Project, the Washington University Genome Sequencing Center has commenced systematic sequencing of human chromsome 7. To organize and supply the effort, we have undertaken...
Theories and Applications for Sequencing Randomly Selected Clones
Wendl, Michael C., Marra, Marco A., Hillier, LaDeana W., Chinwalla, Asif T., Wilson, Richard K., Waterston, Robert H.
Theory is developed for the process of sequencing randomly selected large-insert clones. Genome size, library depth, clone size, and clone distribution are considered relevant properties and perfect...
Software for Automated Analysis of DNA Fingerprinting Gels
Fuhrmann, Daniel R., Krzywinski, Martin I., Chiu, Readman, Saeedi, Parvaneh, Schein, Jacqueline E., Bosdet, Ian E., ...
Here we describe software tools for the automated detection of DNA restriction fragments resolved on agarose fingerprinting gels. We present a mathematical model for the location and shape of the...
Furey, Terrence S., Diekhans, Mark, Lu, Yontao, Graves, Tina A., Oddy, Lachlan, Randall-Maher, Jennifer, ...
The NCBI Reference Sequence (RefSeq) project and the NIH Mammalian Gene Collection (MGC) together define a set of ∼30,000 nonredundant human mRNA sequences with identified coding regions...
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
Siepel, Adam, Bejerano, Gill, Pedersen, Jakob S., Hinrichs, Angie S., Hou, Minmei, Rosenbloom, Kate, ...
We have conducted a comprehensive search for conserved elements in vertebrate genomes, using genome-wide multiple alignments of five vertebrate species (human, mouse, rat, chicken, and Fugu...
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...
Ellsworth, Rachel E., Jamison, D. Curtis, Touchman, Jeffrey W., Chissoe, Stephanie L., Braden Maduro, Valerie V., Bouffard, Gerard G., ...
The identification of the cystic fibrosis transmembrane conductance regulator gene (CFTR) in 1989 represents a landmark accomplishment in human genetics. Since that time, there have been numerous...
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...
High Throughput Fingerprint Analysis of Large-Insert Clones
Marra, Marco A., Kucaba, Tamara A., Dietrich, Nicole L., Green, Eric D., Brownstein, Buddy, Wilson, Richard K., ...
As part of the Human Genome Project, the Washington University Genome Sequencing Center has commenced systematic sequencing of human chromsome 7. To organize and supply the effort, we have undertaken...
Theories and Applications for Sequencing Randomly Selected Clones
Wendl, Michael C., Marra, Marco A., Hillier, LaDeana W., Chinwalla, Asif T., Wilson, Richard K., Waterston, Robert H.
Theory is developed for the process of sequencing randomly selected large-insert clones. Genome size, library depth, clone size, and clone distribution are considered relevant properties and perfect...
Software for Automated Analysis of DNA Fingerprinting Gels
Fuhrmann, Daniel R., Krzywinski, Martin I., Chiu, Readman, Saeedi, Parvaneh, Schein, Jacqueline E., Bosdet, Ian E., ...
Here we describe software tools for the automated detection of DNA restriction fragments resolved on agarose fingerprinting gels. We present a mathematical model for the location and shape of the...
Furey, Terrence S., Diekhans, Mark, Lu, Yontao, Graves, Tina A., Oddy, Lachlan, Randall-Maher, Jennifer, ...
The NCBI Reference Sequence (RefSeq) project and the NIH Mammalian Gene Collection (MGC) together define a set of ∼30,000 nonredundant human mRNA sequences with identified coding regions...
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
Siepel, Adam, Bejerano, Gill, Pedersen, Jakob S., Hinrichs, Angie S., Hou, Minmei, Rosenbloom, Kate, ...
We have conducted a comprehensive search for conserved elements in vertebrate genomes, using genome-wide multiple alignments of five vertebrate species (human, mouse, rat, chicken, and Fugu...
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...
Molecular Profiling of Clinical Tissue Specimens : Feasibility and Applications
Emmert-Buck, Michael R., Strausberg, Robert L., Krizman, David B., Bonaldo, M. Fatima, Bonner, Robert F., Bostwick, David G., ...
Principles of Genome Evolution in the Drosophila melanogaster Species Group
Ranz, José M, Maurin, Damien, Chan, Yuk S, Von Grotthuss, Marcin, Hillier, LaDeana W, Roote, John, ...
That closely related species often differ by chromosomal inversions was discovered by Sturtevant and Plunkett in 1926. Our knowledge of how these inversions originate is still very limited, although...
Molecular Profiling of Clinical Tissue Specimens: Feasibility and Applications
Emmert-Buck, Michael R., Strausberg, Robert L., Krizman, David B., Bonaldo, M. Fatima, Bonner, Robert F., Bostwick, David G., ...
Hillier, LaDeana W, Miller, Raymond D, Baird, Scott E, Chinwalla, Asif, Fulton, Lucinda A, Koboldt, Daniel C, ...
To determine whether the distinctive features of Caenorhabditis elegans chromosomal organization are shared with the C. briggsae genome, we constructed a single nucleotide polymorphism–based...
Population Genomics: Whole-Genome Analysis of Polymorphism and Divergence in Drosophila simulans
Begun, David J, Holloway, Alisha K, Stevens, Kristian, Hillier, LaDeana W, Poh, Yu-Ping, Hahn, Matthew W, ...
The population genetic perspective is that the processes shaping genomic variation can be revealed only through simultaneous investigation of sequence polymorphism and divergence within and between...
Design and implementation of a generalized laboratory data model
Wendl, Michael C, Smith, Scott, Pohl, Craig S, Dooling, David J, Chinwalla, Asif T, Crouse, Kevin, ...
Loss of genes implicated in gastric function during platypus evolution
Ordoñez, Gonzalo R, Hillier, LaDeana W, Warren, Wesley C, Grützner, Frank, López-Otín, Carlos, Puente, Xose S
Several genes implicated in food digestion have been deleted or inactivated in platypus. This loss perhaps explains the anatomical and physiological differences in the gastrointestinal tract between...
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...
Back to Bermuda: how is science best served?
Church, Deanna M, Hillier, LaDeana W
Two bovine genome assemblies from the same data suggest it is time to revisit the spirit of the Bermuda and Fort Lauderdale agreements.
Massively parallel sequencing of the polyadenylated transcriptome of C. elegans
Hillier, LaDeana W., Reinke, Valerie, Green, Philip, Hirst, Martin, Marra, Marco A., Waterston, Robert H.
Using massively parallel sequencing by synthesis methods, we have surveyed the polyA+ transcripts from four stages of the nematode Caenorhabditis elegans to an unprecedented depth. Using novel...