The theory of discovering rare variants via DNA sequencing (2009)
Wendl, Michael C, Wilson, Richard K
Abstract Background Rare population variants are known to have important biomedical implications, but their systematic discovery has only recently been enabled by advances in DNA sequencing. The...
Statistical aspects of discerning indel-type structural variation via DNA sequence alignment (2009)
Wendl, Michael C, Wilson, Richard K
Abstract Background Structural variations in the form of DNA insertions and deletions are an important aspect of human genetics and especially relevant to medical disorders. Investigations have shown...
Somatic mutations affect key pathways in lung adenocarcinoma (2008)
Ding, Li, Getz, Gad, Wheeler, David A., Mardis, Elaine R., McLellan, Michael D., Cibulskis, Kristian, ...
Determining the genetic basis of cancer requires comprehensive analyses of large collections of histopathologically well- classified primary tumours. Here we report the results of a collaborative...
Aspects of coverage in medical DNA sequencing (2008)
Wendl, Michael C, Wilson, Richard K
Abstract Background DNA sequencing is now emerging as an important component in biomedical studies of diseases like cancer. Short-read, highly parallel sequencing instruments are expected to be used...
Somatic mutations affect key pathways in lung adenocarcinoma (2008)
Ding, Li, Getz, Gad, Wheeler, David A., Mardis, Elaine R., McLellan, Michael D., Cibulskis, Kristian, ...
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...
Chen, Ken, McLellan, Michael D., Ding, Li, Wendl, Michael C., Kasai, Yumi, Wilson, Richard K., ...
Small insertions and deletions (indels) and single nucleotide polymorphisms (SNPs) are common genetic variants that are thought to be associated with a wide variety of human diseases. Owing to the...
Abstract Background The Sulston score is a well-established, though approximate metric for probabilistically evaluating postulated clone overlaps in DNA fingerprint mapping. It is known to...
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, ...
This is an Open Access article distribut... (2007)
Bmc Bioinformatics, Michael C Wendl, Michael C Wendl
Algebraic correction methods for computational assessment of
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,...
Extension of Lander-Waterman theory for sequencing filtered DNA libraries (2005)
Wendl, Michael C, Barbazuk, W Brad
Abstract Background The degree to which conventional DNA sequencing techniques will be successful for highly repetitive genomes is unclear. Investigators are therefore considering various filtering...
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...
Michael C Wendl, W Brad, Barbazuk Open Access, Michael C Wendl, W Brad Barbazuk
which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Background: The degree to which conventional DNA sequencing techniques will...
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...
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.
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.
Brent Ewing, Ladeana Hillier, Michael C. Wendl, Phil Green
The availability of massive amounts of DNA sequence information has begun to revolutionize the practice of biology. As a result, current large-scale sequencing output, while impressive, is not...
Base-Calling of Automated Sequencer Traces Using Phred. I. Accuracy Assessment (1998)
Ewing, Brent, Hillier, LaDeana, Wendl, Michael C., Green, Phil
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...
Automated Sequence Preprocessing in a Large-Scale Sequencing Environment
Wendl, Michael C., Dear, Simon, Hodgson, Dave, Hillier, LaDeana
A software system for transforming fragments from four-color fluorescence-based gel electrophoresis experiments into assembled sequence is described. It has been developed for large-scale processing...
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...
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...
Automated Sequence Preprocessing in a Large-Scale Sequencing Environment
Wendl, Michael C., Dear, Simon, Hodgson, Dave, Hillier, LaDeana
A software system for transforming fragments from four-color fluorescence-based gel electrophoresis experiments into assembled sequence is described. It has been developed for large-scale processing...
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...
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.
PolyScan: An automatic indel and SNP detection approach to the analysis of human resequencing data
Chen, Ken, McLellan, Michael D., Ding, Li, Wendl, Michael C., Kasai, Yumi, Wilson, Richard K., ...
Small insertions and deletions (indels) and single nucleotide polymorphisms (SNPs) are common genetic variants that are thought to be associated with a wide variety of human diseases. Owing to the...
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, ...
Collision probability between sets of random variables
We develop the collision probability for a canonical collision problem using a counting procedure based on signed graphs. The result involves Stirling numbers of the second kind and is...