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Papers of Note: Aug 25, 2009


Sequencing-Related Papers of Note, July 2009

A DNA barcode for land plants.
CBOL Plant Working Group.
Proc Natl Acad Sci U S A. 2009 Aug 4;106(31):12794-7. Epub 2009 Jul 30.

Partial sequencing of a single DNA molecule with a scanning tunnelling microscope.
Tanaka H, Kawai T.
Nat Nanotechnol. 2009 Aug;4(8):518-22. Epub 2009 Jul 5.

RNA-MATE: A recursive mapping strategy for high-throughput RNA-sequencing data.
Cloonan N, Xu Q, Faulkner GJ, Taylor DF, Tang DT, Kolle G, Grimmond SM.
Bioinformatics. 2009 Jul 30. [Epub ahead of print]

Characterization of the Zoarces viviparus liver transcriptome using massively parallel pyrosequencing.
Kristiansson E, Asker N, Förlin L, Larsson DG.
BMC Genomics. 2009 Jul 31;10:345.

DNA strands from denatured duplexes are translocated through engineered protein nanopores at alkaline pH.
Maglia G, Henricus M, Wyss R, Li Q, Cheley S, Bayley H.
Nano Lett. 2009 Jul 31. [Epub ahead of print]

Dissection of gene regulatory networks in embryonic stem cells by means of high-throughput sequencing.
Beisel C, Paro R.
Biol Chem. 2009 Jul 30. [Epub ahead of print]

Reduced matrix viscosity in DNA sequencing by CE and microchip electrophoresis using a novel thermo-responsive copolymer.
Wan F, He W, Zhang J, Chu B.
Electrophoresis. 2009 Jul;30(14):2488-98.

Sequence variant discovery in DNA repair genes from radiosensitive and radiotolerant prostate brachytherapy patients.
Pugh TJ, Keyes M, Barclay L, Delaney A, Krzywinski M, et al.
Clin Cancer Res. 2009 Aug 1;15(15):5008-16. Epub 2009 Jul 28.

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Microarray-based multicycle-enrichment of genomic subsets for targeted next-generation sequencing.
Summerer D, Wu H, Haase B, Cheng Y, Schracke N, Stähler CF et al.
Genome Res. 2009 Jul 28. [Epub ahead of print]

Mapping accuracy of short reads from massively parallel sequencing and the implications for quantitative expression profiling.
Palmieri N, Schlötterer C.
PLoS One. 2009 Jul 28;4(7):e6323.

Direct multiplex sequencing (DMPS): A novel method for targeted high-throughput sequencing of ancient and highly degraded DNA.
Stiller M, Knapp M, Stenzel U, Hofreiter M, Meyer M.
Genome Res. 2009 Jul 27. [Epub ahead of print]

Community-wide response of gut microbiota to enteropathogenic Citrobacter infection revealed by deep sequencing.
Hoffmann C, Hill DA, Minkah N, Kirn T, Troy A, Artis D, Bushman F.
Infect Immun. 2009 Jul 27. [Epub ahead of print]

BSMAP: whole genome bisulfite sequence MAPping program.
Xi Y, Li W.
BMC Bioinformatics. 2009 Jul 27;10:232.

A method for studying protistan diversity using massively parallel sequencing of V9 hypervariable regions of small-subunit ribosomal RNA genes.
Amaral-Zettler LA, McCliment EA, Ducklow HW, Huse SM.
PLoS One. 2009 Jul 27;4(7):e6372.

Deep sequencing of the zebrafish transcriptome response to mycobacterium infection.
Hegedűs Z, Zakrzewska A, Agoston VC, Ordas A, Rácz P, Mink M, Spaink HP, Meijer AH.
Mol Immunol. 2009 Jul 23. [Epub ahead of print]

Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data.
Balwierz PJ, Carninci P, Daub CO, Kawai J, Hayashizaki Y, Van Belle W, Beisel C, van Nimwegen E.
Genome Biol. 2009 Jul 22;10(7):R79. [Epub ahead of print]

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Enhancement of charged macromolecule capture by nanopores in a salt gradient.
Chou T.
J Chem Phys. 2009 Jul 21;131(3):034703.

Quantitative phenotyping via deep barcode sequencing.
Smith AM, Heisler LE, Mellor J, Kaper F, Thompson MJ, Chee M, Roth FP, Giaever G, Nislow C.
Genome Res. 2009 Jul 21. [Epub ahead of print]

Virtual terminator nucleotides for next-generation DNA sequencing.
Bowers J, Mitchell J, Beer E, Buzby PR, Causey M, Efcavitch JW, et al.
Nat Methods. 2009 Aug;6(8):593-5. Epub 2009 Jul 20.

Transcriptome analysis by strand-specific sequencing of complementary DNA.
Parkhomchuk D, Borodina T, Amstislavskiy V, Banaru M, Hallen L, Krobitsch S, Lehrach H, Soldatov A.
Nucleic Acids Res. 2009 Jul 20. [Epub ahead of print]

High-throughput sequencing reveals suppressors of Vibrio cholerae rpoE mutations: one fewer porin is enough.
Davis BM, Waldor MK.
Nucleic Acids Res. 2009 Jul 20. [Epub ahead of print]

Transcriptome of embryonic and neonatal mouse cortex by high-throughput RNA sequencing.
Han X, Wu X, Chung WY, Li T, Nekrutenko A, Altman NS, Chen G, Ma H.
Proc Natl Acad Sci U S A. 2009 Aug 4;106(31):12741-6. Epub 2009 Jul 17.

Identification and characterization of novel amphioxus microRNAs by Solexa sequencing.
Chen X, Li Q, Wang J, Guo X, Jiang X, Ren Z, Weng C, Sun G, Wang X, Liu Y, Ma L, et al.
Genome Biol. 2009 Jul 17;10(7):R78. [Epub ahead of print]

A strand-specific RNA-Seq analysis of the transcriptome of the typhoid bacillus Salmonella typhi.
Perkins TT, Kingsley RA, Fookes MC, Gardner PP, James KD, Yu L, Assefa SA, He M, et al.
PLoS Genet. 2009 Jul;5(7):e1000569. Epub 2009 Jul 17.

Targeted retrieval and analysis of five Neandertal mtDNA genomes.
Briggs AW, Good JM, Green RE, Krause J, Maricic T, Stenzel U, Lalueza-Fox C, Rudan P, et al.
Science. 2009 Jul 17;325(5938):318-21.

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The genome of the blood fluke Schistosoma mansoni.
Berriman M, Haas BJ, LoVerde PT, Wilson RA, Dillon GP, Cerqueira GC, et al.
Nature. 2009 Jul 16;460(7253):352-8.

The Schistosoma japonicum genome reveals features of host-parasite interplay.
Schistosoma japonicum Genome Sequencing and Functional Analysis Consortium
Nature. 2009 Jul 16;460(7253):345-51.

Probabilistic resolution of multi-mapping reads in massively parallel sequencing data using MuMRescueLite.
Hashimoto T, de Hoon MJ, Grimmond SM, Daub CO, Hayashizaki Y, Faulkner GJ.
Bioinformatics. 2009 Jul 15. [Epub ahead of print]

PIQA: Pipeline for Illumina G1 Genome Analyzer data quality assessment.
Martínez-Alcántara A, Ballesteros E, Feng C, Rojas M, Koshinsky H, Fofanov VY, Havlak P, Fofanov Y.
Bioinformatics. 2009 Jul 14. [Epub ahead of print]

Integrating sequencing technologies in personal genomics: optimal low cost reconstruction of structural variants.
Du J, Bjornson RD, Zhang ZD, Kong Y, Snyder M, Gerstein MB.
PLoS Comput Biol. 2009 Jul;5(7):e1000432. Epub 2009 Jul 10.

Chimeric transcript discovery by paired-end transcriptome sequencing.
Maher CA, Palanisamy N, Brenner JC, Cao X, Kalyana-Sundaram S, Luo S, Khrebtukova I, et al.
Proc Natl Acad Sci U S A. 2009 Jul 28;106(30):12353-8. Epub 2009 Jul 10.

RazerS — fast read mapping with sensitivity control.
Weese D, Emde AK, Rausch T, Döring A, Reinert K.
Genome Res. 2009 Jul 10. [Epub ahead of print]

Investigation of archaeal and bacterial diversity in fermented seafood using barcoded pyrosequencing.
Roh SW, Kim KH, Nam YD, Chang HW, Park EJ, Bae JW.
ISME J. 2009 Jul 9. [Epub ahead of print]

A highly annotated whole-genome sequence of a Korean individual.
Kim JI, Ju YS, Park H, Kim S, Lee S, Yi JH, Mudge J, Miller NA, Hong D, et al.
Nature. 2009 Jul 8. [Epub ahead of print]

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Chemical synthesis, DNA incorporation and biological study of a new photocleavable 2'-deoxyadenosine mimic.
Berthet N, Crey-Desbiolles C, Kotera M, Dumy P.
Nucleic Acids Res. 2009 Jul 8. [Epub ahead of print]

DNA profiling using solid-state nanopores: detection of DNA-binding molecules.
Wanunu M, Sutin J, Meller A.
Nano Lett. 2009 Jul 8. [Epub ahead of print]

Evidence for human microRNA-offset RNAs in small RNA sequencing data.
Langenberger D, Bermudez-Santana C, Hertel J, Hoffmann S, Khaitovich P, Stadler PF.
Bioinformatics. 2009 Jul 6. [Epub ahead of print]

Improved protocols for the Illumina Genome Analyzer sequencing system.
Quail MA, Swerdlow H, Turner DJ.
Curr Protoc Hum Genet. 2009 Jul;Chapter 18:Unit 18.2.

Quantification of the yeast transcriptome by single-molecule sequencing.
Lipson D, Raz T, Kieu A, Jones DR, Giladi E, Thayer E, Thompson JF, Letovsky S, Milos P, Causey M.
Nat Biotechnol. 2009 Jul;27(7):652-8. Epub 2009 Jul 5.

Deep sampling of the Palomero maize transcriptome by a high throughput strategy of pyrosequencing.
Vega-Arreguín JC, Ibarra-Laclette E, Jiménez-Moraila B, Martínez O, Vielle-Calzada JP, et al.
BMC Genomics. 2009 Jul 6;10:299.

Parametric complexity of sequence assembly: theory and applications to next generation sequencing.
Nagarajan N, Pop M.
J Comput Biol. 2009 Jul;16(7):897-908.

The genomics of speciation in Drosophila: diversity, divergence, and introgression estimated using low-coverage genome sequencing.
Kulathinal RJ, Stevison LS, Noor MA.
PLoS Genet. 2009 Jul;5(7):e1000550. Epub 2009 Jul 3.

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Combining microarray-based genomic selection (MGS) with the Illumina Genome Analyzer platform to sequence diploid target regions.
Okou DT, Locke AE, Steinberg KM, Hagen K, Athri P, Shetty AC, Patel V, Zwick ME.
Ann Hum Genet. 2009 Jul 1. [Epub ahead of print]

A method for preparing DNA sequencing templates using a DNA-binding microplate.
Yang Y, Hebron HR, Hang J.
J Biomol Tech. 2009 Jul;20(3):165-71.

The complete genome of Teredinibacter turnerae T7901: an intracellular endosymbiont of marine wood-boring bivalves (shipworms).
Yang JC, Madupu R, Durkin AS, Ekborg NA, Pedamallu CS, Hostetler JB, Radune D, et al.
PLoS One. 2009 Jul 1;4(7):e6085.

Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding.
McKernan KJ, Peckham HE, Costa GL, McLaughlin SF, Fu Y, Tsung EF, Clouser CR, et al.
Genome Res. 2009 Jul 27. [Epub ahead of print]

Filter-based hybridization capture of subgenomes enables resequencing and copy-number detection.
Herman DS, Hovingh GK, Iartchouk O, Rehm HL, Kucherlapati R, Seidman JG, Seidman CE.
Nat Methods. 2009 Jul;6(7):507-10. Epub 2009 Jun 21.

Mining the x-chromosome for disease genes by deep resequencing.
McCabe ER.
Pediatr Res. 2009 Jul;66(1):2. No abstract available.

Profiling the T-cell receptor beta-chain repertoire by massively parallel sequencing.
Freeman JD, Warren RL, Webb JR, Nelson BH, Holt RA.
Genome Res. 2009 Jul 13. [Epub ahead of print]

Next-generation tag sequencing for cancer gene expression profiling.
Morrissy AS, Morin RD, Delaney A, Zeng T, McDonald H, Jones S, Zhao Y, Hirst M, Marra MA.
Genome Res. 2009 Jul 10. [Epub ahead of print]

Multiplex padlock targeted sequencing reveal human hypermutable CpG variations.
Li JB, Gao Y, Aach J, Zhang K, Kryukov GV, Xie B, Ahlford A, Yoon JK, Rosenbaum AM, et al.
Genome Res. 2009 Jul 13. [Epub ahead of print]
PMID: 19525355 [PubMed - as supplied by publisher

Deep sequencing of Salmonella RNA associated with heterologous Hfq proteins in vivo reveals small RNAs as a major target class and identifies RNA processing phenotypes.
Sittka A, Sharma CM, Rolle K, Vogel J.
RNA Biol. 2009 Jul 3;6(3). [Epub ahead of print]

The Scan

Purnell Choppin Dies

Purnell Choppin, a virologist who led the Howard Hughes Medical Institute, has died at 91, according to the Washington Post.

Effectiveness May Decline, Data From Israel Suggests

The New York Times reports that new Israeli data suggests a decline in Pfizer-BioNTech SARS-CoV-2 vaccine effectiveness against Delta variant infection, though protection against severe disease remains high.

To See Future Risk

Slate looks into the use of polygenic risk scores in embryo screening.

PLOS Papers on Methicillin-Resistant Staphylococcus, Bone Marrow Smear Sequencing, More

In PLOS this week: genomic analysis of methicillin-resistant Staphylococcus pseudintermedius, archived bone marrow sequencing, and more.