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...
AUTOMATED IMAGE ANALYSIS FOR DNA FINGERPRINTING (2007)
Daniel R. Fuhrmann, Readman Chiu, Jacqueline E. Schein, Robert H. Waterston, John D. Mcpherson, Marco A. Marra
Methods for automated detection of DNA restriction fragments resolved on agarose fingerprinting gels are described. We present a mathematical model for the location and shape of the restriction...
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...
Mitreva, Makedonka, Wendl, Michael C, Martin, John, Wylie, Todd, Yin, Yong, Larson, Allan, ...
Abstract Background Codon usage has direct utility in molecular characterization of species and is also a marker for molecular evolution. To understand codon usage within the diverse phylum Nematoda,...
AceTree: a tool for visual analysis of Caenorhabditis elegansembryogenesis (2006)
Boyle, Thomas J, Bao, Zhirong, Murray, John I, Araya, Carlos L, Waterston, Robert H
Abstract Background The invariant lineage of the nematode Caenorhabditis elegans has potential as a powerful tool for the description of mutant phenotypes and gene expression patterns. We previously...
2006 Mitreva et Volume al. 7, Issue 8, Article R75 Open Access (2006)
Makedonka Mitreva, John Martin, Todd Wylie, Yong Yin, Allan Larson, John Parkinson, ...
Codon usage patterns in Nematoda: analysis based on over 25 million codons in thirty-two species
Fukushige, Tetsunari, Brodigan, Thomas M., Schriefer, Lawrence A., Waterston, Robert H., Krause, Michael
Myogenic regulatory factors (MRFs) are required for mammalian skeletal myogenesis. In contrast, bodywall muscle is readily detectable in Caenorhabditis elegans embryos lacking activity of the lone...
Fukushige, Tetsunari, Brodigan, Thomas M., Schriefer, Lawrence A., Waterston, Robert H., Krause, Michael
Myogenic regulatory factors (MRFs) are required for mammalian skeletal myogenesis. In contrast, bodywall muscle is readily detectable in Caenorhabditis elegans embryos lacking activity of the lone...
Investigating hookworm genomes by comparative analysis of two Ancylostomaspecies (2005)
Mitreva, Makedonka, McCarter, James P, Arasu, Prema, Hawdon, John, Martin, John, Dante, Mike, ...
Abstract Background Hookworms, infecting over one billion people, are the mostly closely related major human parasites to the model nematode Caenorhabditis elegans . Applying genomics techniques to...
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...
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...
Kirsch, Stefan, Weiß, Birgit, Miner, Tracie L., Waterston, Robert H., Clark, Royden A., Eichler, Evan E., ...
Basic medical research critically depends on the finished human genome sequence. Two types of gaps are known to exist in the human genome: those associated with heterochromatic sequences and those...
Kirsch, Stefan, Weiß, Birgit, Miner, Tracie L., Waterston, Robert H., Clark, Royden A., Eichler, Evan E., ...
Basic medical research critically depends on the finished human genome sequence. Two types of gaps are known to exist in the human genome: those associated with heterochromatic sequences and those...
Mitreva, Makedonka, McCarter, James P., Martin, John, Dante, Mike, Wylie, Todd, Chiapelli, Brandi, ...
Although developmental timing of gene expression is used to infer potential gene function, studies have yet to correlate this information between species. We analyzed 10,921 ESTs in 3311 clusters...
Novel transcription regulatory elements in Caenorhabditis elegans muscle genes (2004)
GuhaThakurta, Debraj, Schriefer, Lawrence A., Waterston, Robert H., Stormo, Gary D.
We report the identification of three new transcription regulatory elements that are associated with muscle gene expression in the nematode Caenorhabditis elegans. Starting from a subset of...
Nematode.net: a tool for navigating sequences from parasitic and free-living nematodes (2004)
Wylie, Todd, Martin, John C., Dante, Michael, Mitreva, Makedonka Dautova, Clifton, Sandra W., Chinwalla, Asif, ...
Nematode.net (www.nematode.net) is a web‐ accessible resource for investigating gene sequences from nematode genomes. The database is an outgrowth of the parasitic nematode EST project at...
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...
Analysis and functional classification of transcripts from the nematode Meloidogyne incognita (2003)
McCarter, James P, Dautova Mitreva, Makedonka, Martin, John, Dante, Mike, Wylie, Todd, Rao, Uma, ...
Abstract Background Plant parasitic nematodes are major pathogens of most crops. Molecular characterization of these species as well as the development of new techniques for control can benefit from...
Robert H. Waterston, Sean Eddy, Richard K. Wilson, Genome Sequencing
The value of Caenorhabditis elegans as a model organism for biomedical research is unquestioned. The interpretation of its 100.2 Mb complete genome sequence has been enhanced by a high quality, 98 %...
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...
Li, Li, Brunk, Brian P., Kissinger, Jessica C., Pape, Deana, Tang, Keliang, Cole, Robert H., ...
Large-scale EST sequencing projects for several important parasites within the phylum Apicomplexa were undertaken for the purpose of gene discovery. Included were several parasites of medical...
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., ...
The construction and analysis of M13 libraries prepared from YAC DNA (1995)
Vaudin, Mark, Hillier, LaDeana, Brinkman, Ryan, Sulston, John, Wilson, Richard K., Waterston, Robert H.
Yeast artificial chromosomes (YACs) provide a powerful way to isolate and map large regions of genomlc DNA and their use In genome analysis is now extensive. We modified a series of procedures to...
Low pressure DNA shearing: a method for random DNA sequence analysis (1990)
Schriefer, Lawrence A., Gebauer, Beth K., Qiu, Lisa Q.Q., Waterston, Robert H., Wilson, Richard K.
Antigen competition--[microform]. (1972)
Thesis (Ph. D.)--University of Chicago, 1972.
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...
On the sequencing of the human genome
Waterston, Robert H., Lander, Eric S., Sulston, John E.
Two recent papers using different approaches reported draft sequences of the human genome. The international Human Genome Project (HGP) used the hierarchical shotgun approach, whereas Celera Genomics...
Analysis and functional classification of transcripts from the nematode Meloidogyne incognita
McCarter, James P, Dautova Mitreva, Makedonka, Martin, John, Dante, Mike, Wylie, Todd, Rao, Uma, ...
As an entrée to characterizing plant parasitic nematode genomes, 5,700 expressed sequence tags (ESTs) from the infective second-stage larvae (L2) of the root-knot nematode Meloidogyne incognita have...
Wendl, Michael C., Waterston, Robert H.
We develop an extension to the Lander-Waterman theory for characterizing gaps in bacterial artificial chromosome fingerprint mapping and shotgun sequencing projects. It supports a larger set 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...
Nematode.net: a tool for navigating sequences from parasitic and free-living nematodes
Wylie, Todd, Martin, John C., Dante, Michael, Mitreva, Makedonka Dautova, Clifton, Sandra W., Chinwalla, Asif, ...
Nematode.net (www.nematode.net) is a web- accessible resource for investigating gene sequences from nematode genomes. The database is an outgrowth of the parasitic nematode EST project at Washington...
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...
Mitreva, Makedonka, McCarter, James P., Martin, John, Dante, Mike, Wylie, Todd, Chiapelli, Brandi, ...
Although developmental timing of gene expression is used to infer potential gene function, studies have yet to correlate this information between species. We analyzed 10,921 ESTs in 3311 clusters...
Li, Li, Brunk, Brian P., Kissinger, Jessica C., Pape, Deana, Tang, Keliang, Cole, Robert H., ...
Large-scale EST sequencing projects for several important parasites within the phylum Apicomplexa were undertaken for the purpose of gene discovery. Included were several parasites of medical...
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...
Novel transcription regulatory elements in Caenorhabditis elegans muscle genes
GuhaThakurta, Debraj, Schriefer, Lawrence A., Waterston, Robert H., Stormo, Gary D.
We report the identification of three new transcription regulatory elements that are associated with muscle gene expression in the nematode Caenorhabditis elegans. Starting from a subset of...
Interchromosomal segmental duplications of the pericentromeric region on the human Y chromosome
Kirsch, Stefan, Weiß, Birgit, Miner, Tracie L., Waterston, Robert H., Clark, Royden A., Eichler, Evan E., ...
Basic medical research critically depends on the finished human genome sequence. Two types of gaps are known to exist in the human genome: those associated with heterochromatic sequences and those...
Investigating hookworm genomes by comparative analysis of two Ancylostoma species
Mitreva, Makedonka, McCarter, James P, Arasu, Prema, Hawdon, John, Martin, John, Dante, Mike, ...
AceTree: a tool for visual analysis of Caenorhabditis elegans embryogenesis
Boyle, Thomas J, Bao, Zhirong, Murray, John I, Araya, Carlos L, Waterston, Robert H
Automated cell lineage tracing in Caenorhabditis elegans
Bao, Zhirong, Murray, John I., Boyle, Thomas, Ooi, Siew Loon, Sandel, Matthew J., Waterston, Robert H.
The invariant cell lineage and cell fate of Caenorhabditis elegans provide a unique opportunity to decode the molecular mechanisms of animal development. To exploit this opportunity, we have...
A Second Informational Suppressor, SUP-7 X, in CAENORHABDITIS ELEGANS
More than 30 independent suppressor mutations have been obtained in the nematode C. elegans through reversion analysis of two unc-13 mutants. Many of the new isolates map to the region of the...
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...
On the sequencing of the human genome
Waterston, Robert H., Lander, Eric S., Sulston, John E.
Two recent papers using different approaches reported draft sequences of the human genome. The international Human Genome Project (HGP) used the hierarchical shotgun approach, whereas Celera Genomics...
Analysis and functional classification of transcripts from the nematode Meloidogyne incognita
McCarter, James P, Dautova Mitreva, Makedonka, Martin, John, Dante, Mike, Wylie, Todd, Rao, Uma, ...
As an entrée to characterizing plant parasitic nematode genomes, 5,700 expressed sequence tags (ESTs) from the infective second-stage larvae (L2) of the root-knot nematode Meloidogyne incognita have...
Wendl, Michael C., Waterston, Robert H.
We develop an extension to the Lander-Waterman theory for characterizing gaps in bacterial artificial chromosome fingerprint mapping and shotgun sequencing projects. It supports a larger set 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...
Nematode.net: a tool for navigating sequences from parasitic and free-living nematodes
Wylie, Todd, Martin, John C., Dante, Michael, Mitreva, Makedonka Dautova, Clifton, Sandra W., Chinwalla, Asif, ...
Nematode.net (www.nematode.net) is a web- accessible resource for investigating gene sequences from nematode genomes. The database is an outgrowth of the parasitic nematode EST project at Washington...
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...
Mitreva, Makedonka, McCarter, James P., Martin, John, Dante, Mike, Wylie, Todd, Chiapelli, Brandi, ...
Although developmental timing of gene expression is used to infer potential gene function, studies have yet to correlate this information between species. We analyzed 10,921 ESTs in 3311 clusters...
Li, Li, Brunk, Brian P., Kissinger, Jessica C., Pape, Deana, Tang, Keliang, Cole, Robert H., ...
Large-scale EST sequencing projects for several important parasites within the phylum Apicomplexa were undertaken for the purpose of gene discovery. Included were several parasites of medical...
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...
Novel transcription regulatory elements in Caenorhabditis elegans muscle genes
GuhaThakurta, Debraj, Schriefer, Lawrence A., Waterston, Robert H., Stormo, Gary D.
We report the identification of three new transcription regulatory elements that are associated with muscle gene expression in the nematode Caenorhabditis elegans. Starting from a subset of...
Interchromosomal segmental duplications of the pericentromeric region on the human Y chromosome
Kirsch, Stefan, Weiß, Birgit, Miner, Tracie L., Waterston, Robert H., Clark, Royden A., Eichler, Evan E., ...
Basic medical research critically depends on the finished human genome sequence. Two types of gaps are known to exist in the human genome: those associated with heterochromatic sequences and those...
Investigating hookworm genomes by comparative analysis of two Ancylostoma species
Mitreva, Makedonka, McCarter, James P, Arasu, Prema, Hawdon, John, Martin, John, Dante, Mike, ...
A Second Informational Suppressor, SUP-7 X, in CAENORHABDITIS ELEGANS
More than 30 independent suppressor mutations have been obtained in the nematode C. elegans through reversion analysis of two unc-13 mutants. Many of the new isolates map to the region of the...
Automated cell lineage tracing in Caenorhabditis elegans
Bao, Zhirong, Murray, John I., Boyle, Thomas, Ooi, Siew Loon, Sandel, Matthew J., Waterston, Robert H.
The invariant cell lineage and cell fate of Caenorhabditis elegans provide a unique opportunity to decode the molecular mechanisms of animal development. To exploit this opportunity, we have...
AceTree: a tool for visual analysis of Caenorhabditis elegans embryogenesis
Boyle, Thomas J, Bao, Zhirong, Murray, John I, Araya, Carlos L, Waterston, Robert H
Codon usage patterns in Nematoda: analysis based on over 25 million codons in thirty-two species
Mitreva, Makedonka, Wendl, Michael C, Martin, John, Wylie, Todd, Yin, Yong, Larson, Allan, ...
A codon usage table for 32 nematode species is presented and suggests that total genomic GC content drives codon usage.
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., ...
Fukushige, Tetsunari, Brodigan, Thomas M., Schriefer, Lawrence A., Waterston, Robert H., Krause, Michael
Myogenic regulatory factors (MRFs) are required for mammalian skeletal myogenesis. In contrast, bodywall muscle is readily detectable in Caenorhabditis elegans embryos lacking activity of the lone...
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...
Myotactin, a Novel Hypodermal Protein Involved in Muscle–Cell Adhesion inCaenorhabditis elegans
Hresko, Michelle Coutu, Schriefer, Lawrence A., Shrimankar, Paresh, Waterston, Robert H.
In C. elegans, assembly of hypodermal hemidesmosome-like structures called fibrous organelles is temporally and spatially coordinated with the assembly of the muscle contractile apparatus, suggesting...
Nematode Gene Sequences: Update for December 2003
McCarter, James P., Mitreva, Makedonka, Clifton, Sandra W., Bird, David McK., Waterston, Robert H.
Nematode Gene Sequences, December 2000 Update
McCarter, James P., Bird, David McK., Clifton, Sandra W., Waterston, Robert H.
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...