From The MarthLab
[edit] Primer-site SNPs mask mutations.
We describe the negative effects of heterozygosity within PCR primer binding sites on SNP discovery. Quinlan, AR, Marth, G.T. Nat Methods 4, 192 (Mar, 2007)
[edit] Reconstruction of demographic history from the relative SNP allele frequencies in three world populations. General, statistically rigorous analytical methods for allele frequency data.
The allele frequency spectrum in genome-wide human variation data reveals signals of differential demographic history in three large world populations. Marth, G.T., Czabarka, E., Murvai, J., Sherry, S.T. Genetics 166, 351-372 (2004)
[edit] A high-density, high-quality microsatellite map of the human genome.
STRP screening sets for the human genome at 5 cM density. Ghebranious N., Vaske D., Yu A, Zhao .C, Marth G., Weber J.L.BMC Genomics 4, (2003)
[edit] SNP discovery in overlapping sections of BAC clones sequenced for the construction of the public human genome reference sequence, in the Pui Kwok lab and at the NCBI. Population-genetic inferences based on SNP marker density distributions observed in the overlap SNP data.
Sequence variations in the public human genome data reflect a bottlenecked population history. Marth, G.T., Cutler, D., Wooding, S., Schuler, G., Yeh, R., Davenport, R., Agarwala, R., Church, D., Wheelan, S., Baker, J., Ward, M., Kholodov, M., Phan, L., Czabarka, E., Murvai, J., Cutler, D., Wooding, S., Rogers, A., Chakravarti, A., Harpending, H.C., Kwok, P-Y., Sherry, S.T. PNAS 100, 376-381 (2003)
[edit] Description of SNP mining methods and data sources.
Computational SNP discovery in DNA sequence data. Gabor T. Marth. In: Single Nucleotide Polymorphisms: Methods and Protocols (ed. Kwok, P.Y.), Humana Press (2002)
[edit] Discovery and characterization of short diallelic insertions and deletions, mainly from genome BAC overlap data, in Jim Weber's lab at the Marshfield Medical and Research Foundation.
Human diallelic insertion/deletion polymorphisms. American Journal of Human Genetics. Weber, J.L., David, D., Heil, J., Fan, Y., Zhao, C. & Marth, G.T. American Journal of Human Genetics 71, 854-62 (2002)
[edit] Validation and population-specific allele frequency estimation for hundreds of SNPs found by The SNP Consortium in whole-genome shotgun data aligned to the genome reference, and those found in BAC overlaps, in Pui Kwok's lab at Washington University.
Single-nucleotide polymorphisms in the public domain: how useful are they?. Marth, G, Yeh, R, Minton, M, Donaldson, R, Li, Q, Duan, S., Davenport R, Miller RD, Kwok PY. Nature Genetics 27, 371-2 (2001)
[edit] Collaborative work between the various groups in The SNP Consortium, and Steve Sherry and me at the NCBI for the generation of the first high-density SNP map of the Human genome.
A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Sachidanandam, R, Weissman, D, Schmidt, SC, Kakol, JM, Stein, LD, Marth, G, Sherry S, Mullikin JC, Mortimore BJ, Willey DL, Hunt SE, Cole CG, Coggill PC, Rice CM, Ning Z, Rogers J, Bentley DR, Kwok PY, Mardis ER, Yeh RT, Schultz B, Cook L, Davenport R, Dante M, Fulton L, Hillier L, Waterston RH, McPherson JD, Gilman B, Schaffner S, Van Etten WJ, Reich D, Higgins J, Daly MJ, Blumenstiel B, Baldwin J, Stange-Thomann N, Zody MC, Linton L, Lander ES, Altshuler D; The International SNP Map Working Group. Nature 409, 928-33 (2001)
[edit] The PolyBayes SNP discovery method, and its application to SNP mining in human ESTs anchored to genomic clone sequences
A general approach to single-nucleotide polymorphism discovery. Gabor T. Marth, Mark D. Yandell, Ian Korf, Zhijie Gu, Raymond T. Yeh, Hamideh Zakeri, Nathan O. Stitziel, LaDeana Hillier, Pui-Yan Kwok and Warren Gish. Nature Genetics 23, 452-456 (1999)
[edit] The Common Assembly Format developed for data representation in the genome sequence assembly process. Also a brief description of CAF-related tools.
Sequence assembly with CAFTOOLS. Dear, S., Durbin, R., Hillier, L., Marth, G., Thierry-Mieg, J. & Mott, R.. Genome Research 8, 260-7 (1998)
[edit] Progress of the Human genome sequencing as of 1998. Molecular and informatics methods and tools.
Toward a complete human genome sequence. The Sanger Center and the Washington University Genome Sequencing Center. Genome Research 8, 1097-108 (1998)
[edit] The complete C. elegans genome sequence.
Genome sequence of the nematode C. elegans: a platform for investigating biology. The C. elegans Sequencing Consortium. Science 282, 2012-8 (1998)
