From The MarthLab
[edit] Mutational profiling with next-generation DNA sequencers.
Rapid whole-genome mutational profiling using next-generation sequencing technologies. Douglas R. Smith, Aaron R. Quinlan, Heather E. Peckham, Kathryn Makowsky , Wei Tao, Betty Woolf, Lei Shen, William F. Donahue, and Nadeem Tusneem , Michael P. Stromberg, Donald A. Stewart, Lu Zheng, Swati S. Ranade, Jason B. Warner, Clarence C. Lee, Brittney E. Coleman, Zheng Zhang, Stephen F. McLaughlin , Joel A. Malek, Jon M. Sorenson, Alan P. Blanchard, Jarrod Chapman, David Hillman , Feng Chen, Daniel S. Rokhsar, Kevin J. McKernan, Thomas W. Jeffries, Gabor T. Marth, and Paul M. Richardson. Genome Research. 2008 Sep 4. [Epub ahead of print]
[edit] A next-generation sequence assembly viewer program
EagleView: A genome assembly viewer for next-generation sequencing technologies. Huang W, Marth G. Genome Research. 2008;18(9):1538-43. Epub 2008 Jun 11.
[edit] Whole-genome SNP calling in Illumina reads.
Whole-genome sequencing and variant discovery in C. elegans. Hillier LW, Marth GT, Quinlan AR, Dooling D, Fewell G, Barnett D, Fox P, Glasscock JI, Hickenbotham M, Huang W, Magrini VJ, Richt RJ, Sander SN, Stewart DA, Stromberg M, Tsung EF, Wylie T, Schedl T, Wilson RK, Mardis ER. Nature Methods. 2008;5:183-8.
[edit] A base caller program for 454 reads.
PYROBAYES: An improved base-caller for SNP discovery in pyrosequences. Quinlan AR, Stewart DA, Strömberg MP, Marth GT. Nature Methods. 2008;5:179-81.
[edit] Missing SNPs because of heterozygosity in PCR primer binding sites
Primer-site SNPs mask mutations. Quinlan, AR, Marth, G.T. Nature Methods 4, 192 (Mar, 2007)
[edit] Reconstruction of demographic history from the SNP allele frequency spectrum of three world populations
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 by the Human Genome Project. Population genetic inference from polymorphism density distributions
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] A review 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
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
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] 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 algorithm
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 (CAF)
Sequence assembly with CAFTOOLS. Dear, S., Durbin, R., Hillier, L., Marth, G., Thierry-Mieg, J. & Mott, R.. Genome Research 8, 260-7 (1998)
