Single Molecule DNA Sequencing

Harris, TD et al. (2008). Single-molecule DNA sequencing of a viral genome. Science 320, 106-109.

Bowers, J et al. (2009). Virtual terminator nucleotides for next-generation DNA sequencing. Nat Methods 6, 593-595.

Thompson, JF and Milos, PM (2011). The properties and applications of single molecule DNA sequencing. Genome Biology 12, 217.

Kahvejian A, Quackenbush J, Thompson JF. (2008). What would you do if you could sequence everything? Nat Biotechnol. 26: 1125-33.

Milos, P.M. (2009). Emergence of single-molecule sequencing and potential for molecular diagnostic applications. Expert Rev Mol Diagn 9, 659-666.

Efcavitch, JW., and Thompson, JF (2010). Single-molecule DNA analysis. Annu Rev Anal Chem (Palo Alto Calif) 3, 109-128.

Kapranov P et al. (2011). Native molecular state of AAV vectors revealed by single molecule sequencing. Human Gene Therapy. Online Ahead of Editing: August 29, 2011

ChIP-Seq

Goren, A et al. (2010). Chromatin profiling by directly sequencing small quantities of immunoprecipitated DNA. Nat Methods 7, 47-49.

Davies BW, Bogard RW, Mekalanos JJ. (2011). Mapping the regulon of Vibrio cholerae ferric uptake regulator expands its known network of gene regulation. Proc Natl Acad Sci U S A. Jul 26;108(30):12467-72. Epub 2011 Jul 12.

Methyl-Seq

Pastor WA et al. (2011). Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells. Nature. May 19;473(7347):394-7. Epub 2011 May 8.

Direct RNA Sequencing

Ozsolak, F et al. (2010). Comprehensive polyadenylation site maps in yeast and human reveal pervasive alternative polyadenylation. Cell 143, 1018-1029.

Ozsolak, F and Milos, PM (2010). Direct RNA Sequencing. Experimental Medicine 28: 2574-2580.

Ozsolak, F et al. (2009). Direct RNA sequencing. Nature 461, 814-818.

Ozsolak, F and Milos, PM (2010). RNA sequencing: advances, challenges and opportunities.  Nat Rev Genet. 2011 Feb;12(2):87-98. Epub 2010 Dec 30.

Gurumurthy S et al. (2010). The Lkb1 metabolic sensor maintains haematopoietic stem cell survival. Nature. Dec 2;468(7324):659-63.

cDNA-Based DGE, RNA-Seq and Small RNA Sequencing

Sam, LT et al.  (2011). A Comparison of Single Molecule and Amplification Based Sequencing of Cancer Transcriptomes. PLoS ONE 6(3): e17305.

Ting, DT et al. (2011). Aberrant overexpression of satellite repeats in pancreatic and other epithelial cancers.  Science 331, 593-6.

Kapranov, P et al. (2010). The majority of total nuclear-encoded non-ribosomal RNA in a human cell is "dark matter" unannotated RNA. BMC Biology 8,149.

Lipson, D et al. (2009). Quantification of the yeast transcriptome by single-molecule sequencing. Nat Biotechnol 27, 652-658.

Kapranov, P et al. (2010). New class of gene-termini-associated human RNAs suggests a novel RNA copying mechanism. Nature 466, 642-646.

Ozsolak, F et al. (2010). Digital transcriptome profiling from attomole-level RNA samples. Genome Res 20, 519-525.

Ozsolak, F et al. (2010). Amplification-free digital gene expression profiling from minute cell quantities. Nat Methods. 7 :619-21.

Raz T et al. (2011). Protocol dependence of sequencing-based gene expression measurements. PLoS One. May 6;6(5):e19287.

Kapranov P. (2009). Studying chromosome-wide transcriptional networks: new insights into disease? Genome Med. May 11;1(5):50.

Ancient DNA Sequencing

Orlando L et al. (2011) True single-molecule DNA sequencing of a Pleistocene horse bone. Genome Res. Jul 29. [Epub ahead of print]

Single Step Target Selection and Sequencing

Thompson JF et al. (2011). Single-step capture and sequencing of natural DNA for detection of BRCA1 mutations. Genome Res. Jul 15. [Epub ahead of print]

Methods

Hart, C et al. (2010). Single-molecule sequencing: sequence methods to enable accurate quantitation. Methods Enzymol 472, 407-430.

Thompson, JF, and Steinmann, KE (2010). Single molecule sequencing with a HeliScope genetic analysis system. Curr Protoc Mol Biol Chapter 7, Unit7 10.

Informatics

Giladi E et al. (2010). Error tolerant indexing and alignment of short reads with covering template families. J Comput Biol. 17: 1279-93.

Protein Quantification

Tessler L, Reifenberger J, and Mitra R.  (2009). Protein Quantification in Complex Mixtures by Solid Phase Single-Molecule Counting.  Analytical Chemistry.  81: 7141–7148.