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Recent Sequencing-Related Papers of Note: Jun 10, 2014

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Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication.
Wu GA, Prochnik S, Jenkins J, Salse J, et al.
Nat Biotechnol. 2014 Jun 8. [Epub ahead of print]


A reference genome for common bean and genome-wide analysis of dual domestications.
Schmutz J, McClean PE, Mamidi S, Wu GA, et al.
Nat Genet. 2014 Jun 8. [Epub ahead of print]


ABRA: improved coding indel detection via assembly based re-alignment.
Mose LE, Wilkerson MD, Hayes DN, Perou CM, Parker JS.
Bioinformatics. 2014 Jun 6. [Epub ahead of print]


Efficient de novo assembly of large and complex genomes by massively parallel sequencing of fosmid pools.
Alexeyenko A, Nystedt B, Vezzi F, Sherwood E, et al.
BMC Genomics. 2014 Jun 6;15(1):439.


Construction and analysis of high-density linkage map using high-throughput sequencing data.
Liu D, Ma C, Hong W, Huang L, et al.
PLoS One. 2014 Jun 6;9(6):e98855.


The sheep genome illuminates biology of the rumen and lipid metabolism.
Jiang Y, Xie M, Chen W, Talbot R, et al.
Science. 2014 Jun 6;344(6188):1168-73.


Genomic mapping of phosphorothioates reveals partial modification of short consensus sequences.
Cao B, Chen C, DeMott MS, Cheng Q, et al.
Nat Commun. 2014 Jun 5;5:3951. doi: 10.1038/ncomms4951.


CloudDOE: a user-friendly tool for deploying Hadoop clouds and analyzing high-throughput sequencing data with MapReduce.
Chung WC, Chen CC, Ho JM, Lin CY, et al.
PLoS One. 2014 Jun 4;9(6):e98146.


Genome at juncture of early human migration: a systematic analysis of two whole genomes and thirteen exomes from Kuwaiti population subgroup of inferred Saudi Arabian tribe ancestry.
Alsmadi O, John SE, Thareja G, Hebbar P, et al.
PLoS One. 2014 Jun 4;9(6):e99069.


Use of stereotypical mutational motifs to define resolution limits for the ultra-deep resequencing of mitochondrial DNA.
Gardner K, Payne BA, Horvath R, Chinnery PF.
Eur J Hum Genet. 2014 Jun 4. [Epub ahead of print]


Comprehensive massive parallel DNA sequencing strategy for the genetic diagnosis of the neuro-cardio-facio-cutaneous syndromes.
Justino A, Dias P, João Pina M, Sousa S, et al.
Eur J Hum Genet. 2014 Jun 4. [Epub ahead of print]


CAP-miRSeq: a comprehensive analysis pipeline for microRNA sequencing data.
Sun Z, Evans J, Bhagwate A, Middha S, et al.
BMC Genomics. 2014 Jun 3;15(1):423.


PVT: an efficient computational procedure to speed up next-generation sequence analysis.
Maji RK, Sarkar A, Khatua S, Dasgupta S, Ghosh Z.
BMC Bioinformatics. 2014 Jun 4;15(1):167.


PePr: A peak-calling prioritization pipeline to identify consistent or differential peaks from replicated ChIP-seq data.
Zhang Y, Lin YH, Johnson TD, Rozek LS, Sartor MA.
Bioinformatics. 2014 Jun 3. [Epub ahead of print]


Efficient and sensitive identification and quantification of airborne pollen using next-generation DNA sequencing.
Kraaijeveld K, de Weger LA, Ventayol García M, Buermans H, et al.
Mol Ecol Resour. 2014 Jun 4. [Epub ahead of print]


Second generation sequencing of three STRs D3S1358, D12S391 and D21S11 in Danes and a new nomenclature for sequenced STR alleles.
Gelardi C, Rockenbauer E, Dalsgaard S, Børsting C, Morling N.
Forensic Sci Int Genet. 2014 May 10;12C:38-41.


Genome-wide adaptive complexes to underground stresses in blind mole rats Spalax.
Fang X, Nevo E, Han L, Levanon EY, et al.
Nat Commun. 2014 Jun 3;5:3966.


Pipeliner: software to evaluate the performance of bioinformatics pipelines for next generation re-sequencing.
Nevado B, Perez-Enciso M.
Mol Ecol Resour. 2014 May 28. [Epub ahead of print]


Biological ingredient analysis of traditional Chinese medicine preparation based on high-throughput sequencing: the story for Liuwei Dihuang Wan.
Cheng X, Su X, Chen X, Zhao H, et al.
Sci Rep. 2014 Jun 3;4:5147.


Comparison of RNA-seq by poly (A) capture, ribosomal RNA depletion, and DNA microarray for expression profiling.
Zhao W, He X, Hoadley KA, Parker JS, et al.
BMC Genomics. 2014 Jun 2;15(1):419.


Direct observation of genomic heterogeneity through local haplotyping analysis.
Gulukota K, Helseth DL Jr, Khandekar JD.
BMC Genomics. 2014 Jun 2;15(1):418.


4sUDRB-seq: measuring genomewide transcriptional elongation rates and initiation frequencies within cells.
Fuchs G, Voichek Y, Benjamin S, Gilad S, Amit I, Oren M.
Genome Biol. 2014 May 16;15(5):R69.


Direct sequencing from the minimal number of DNA molecules needed to fill a 454 picotiterplate.
Džunková M, Garcia-Garcerà M, Martínez-Priego L, D'Auria G, et al.
PLoS One. 2014 Jun 2;9(6):e97379.


Selective and flexible depletion of problematic sequences from RNA-seq libraries at the cDNA stage.
Archer SK, Shirokikh NE, Preiss T.
BMC Genomics. 2014 May 26;15(1):401.


Comparison of next-generation sequencing samples using compression-based distances and its application to phylogenetic reconstruction.
Tran NH, Chen X.
BMC Res Notes. 2014 May 29;7(1):320.


GAP-seq: a method for identification of DNA palindromes.
Yang H, Volfovsky N, Rattray A, Chen X, et al.
BMC Genomics. 2014 May 22;15(1):394.


A method for generating highly multiplexed ChIP-seq libraries.
Ford E, Nikopoulou C, Kokkalis A, Thanos D.
BMC Res Notes. 2014 May 22;7(1):312.


RNA-seq: Impact of RNA degradation on transcript quantification.
Gallego Romero I, Pai AA, Tung J, Gilad Y.
BMC Biol. 2014 May 30;12(1):42.


HECTOR: a parallel multistage homopolymer spectrum based error corrector for 454 sequencing data.
Wirawan A, Harris RS, Liu Y, Schmidt B, Schröder J.
BMC Bioinformatics. 2014 May 6;15(1):131.


Sequence artefacts in a prospective series of formalin-fixed tumours tested for mutations in hotspot regions by massively parallel sequencing.
Wong SQ, Li J, Tan AY, Vedururu R, et al.
BMC Med Genomics. 2014 May 13;7(1):23.


Sequence and assembly of the DUF1220-rich 1q21 region using a haploid human genome.
O Bleness M, Searles VB, Dickens CM, Astling D, et al.
BMC Genomics. 2014 May 20;15(1):387.


Discovery of transgene insertion sites by high throughput sequencing of mate pair libraries.
Srivastava A, Philip VM, Greenstein I, Rowe LB, et al.
BMC Genomics. 2014 May 14;15(1):367.


Effective filtering strategies to improve data quality from population-based whole exome sequencing studies.
Carson AR, Smith EN, Matsui H, Brækkan SK, et al.
BMC Bioinformatics. 2014 May 2;15(1):125.


Population genetic analysis of bi-allelic structural variants from low-coverage sequence data with an expectation-maximization algorithm.
Lucas-Lledó JI, Vicente-Salvador D, Aguado C, Cáceres M.
BMC Bioinformatics. 2014 May 29;15(1):163.


EXPRSS: an Illumina based high-throughput expression-profiling method to reveal transcriptional dynamics.
Rallapalli G, Kemen EM, Robert-Seilaniantz A, Segonzac C, et al.
BMC Genomics. 2014 May 6;15:341.

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