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Papers of Note: Aug 31, 2010


Transcriptome profiling in neurodegenerative disease.
Courtney E, Kornfeld S, Janitz K, Janitz M.
J Neurosci Methods. 2010 Aug 25. [Epub ahead of print]

HLA class I allele associations with HCV genetic variants in patients with chronic HCV genotypes 1a or 1b infection.
Lange CM, Roomp K, Dragan A, Nattermann J, et al.
J Hepatol. 2010 Aug 3. [Epub ahead of print]

Hepatic but not brain iron is rapidly chelated by deferasirox in aceruloplasminemia due to a novel gene mutation.
Finkenstedt A, Wolf E, Höfner E, Gasser BI, et al.
J Hepatol. 2010 Aug 4. [Epub ahead of print]

miRNAkey: a software for microRNA deep sequencing analysis.
Ronen R, Gan I, Modai S, Sukacheov A, et al.
Bioinformatics. 2010 Aug 27. [Epub ahead of print]

Comparative genomic characterization of Actinobacillus pleuropneumoniae.
Xu Z, Chen X, Li L, Li T, Wang S, Chen H, Zhou R.
J Bacteriol. 2010 Aug 27. [Epub ahead of print]

Computational analysis of genome-wide DNA methylation during the differentiation of human embryonic stem cells along the endodermal lineage.
Chavez L, Jozefczuk J, Grimm C, Dietrich J, et al.
Genome Res. 2010 Aug 27. [Epub ahead of print]

MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery.
Wang K, Singh D, Zeng Z, Coleman SJ, et al.
Nucleic Acids Res. 2010 Aug 27. [Epub ahead of print]

Identity-by-descent filtering of exome sequence data identifies PIGV mutations in hyperphosphatasia mental retardation syndrome.
Krawitz PM, Schweiger MR, Rödelsperger C, Marcelis C, et al.
Nat Genet. 2010 Aug 29. [Epub ahead of print]

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Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species.
Yassour M, Pfiffner J, Levin JZ, Adiconis X, et al.
Genome Biol. 2010 Aug 26;11(8):R87.

Direct measure of the de novo mutation rate in autism and schizophrenia cohorts.
Awadalla P, Gauthier J, Myers RA, Casals F, et al.
Am J Hum Genet. 2010 Aug 25. [Epub ahead of print]

A focal epilepsy and intellectual disability syndrome is due to a mutation in TBC1D24.
Corbett MA, Bahlo M, Jolly L, Afawi Z, et al.
Am J Hum Genet. 2010 Aug 25. [Epub ahead of print]

METAREP: JCVI Metagenomics Reports - an open source tool for high-performance comparative metagenomics.
Goll J, Rusch D, Tanenbaum DM, Thiagarajan M, et al.
Bioinformatics. 2010 Aug 26. [Epub ahead of print]

Genomic comparison of the ants Camponotus floridanus and Harpegnathos saltator.
Bonasio R, Zhang G, Ye C, Mutti NS, et al.
Science. 2010 Aug 27;329(5995):1068-71.

Nanopore DNA sequencing with MspA.
Derrington IM, Butler TZ, Collins MD, Manrao E, Pavlenok M, et al.
Proc Natl Acad Sci U S A. 2010 Aug 26. [Epub ahead of print]

Identification of novel FMR1 variants by massively parallel sequencing in developmentally delayed males.
Collins SC, Bray SM, Suhl JA, Cutler DJ, et al.
Am J Med Genet A. 2010 Aug 26. [Epub ahead of print]

GASSST: Global Alignment Short Sequence Search Tool.
Rizk G, Lavenier D.
Bioinformatics. 2010 Aug 24. [Epub ahead of print]

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Tracking the evolution of multiple in vitro HCV replicon variants under protease inhibitor selection pressure by 454 deep sequencing.
Verbinnen T, Van Marck H, Vandenbroucke I, Vijgen L, et al.
J Virol. 2010 Aug 25. [Epub ahead of print]

Multigene assays and isolated tumor cells for early breast cancer treatment: time for bionetworks.
Roukos DH, Ziogas DE, Katsios C.
Expert Rev Anticancer Ther. 2010 Aug;10(8):1187-95.

Reshaping the gut microbiome with bacterial transplantation and antibiotic intake.
Manichanh C, Reeder J, Gibert P, Varela E, et al.
Genome Res. 2010 Aug 24. [Epub ahead of print]

A ChIP-seq defined genome-wide map of vitamin D receptor binding: Associations with disease and evolution.
Ramagopalan SV, Heger A, Berlanga AJ, Maugeri NJ, et al.
Genome Res. 2010 Aug 24. [Epub ahead of print]

Deep and wide digging for binding motifs in ChIP-seq data.
Kulakovskiy IV, Boeva VA, Favorov AV, Makeev VJ.
Bioinformatics. 2010 Aug 24. [Epub ahead of print]

Role of postmortem genetic testing demonstrated in a case of glutaric aciduria type II.
Lee HC, Lai CK, Siu TS, Yuen YP, et al.
Diagn Mol Pathol. 2010 Sep;19(3):184-6.

Lung cancer genomic signatures.
Agulló-Ortuño MT, López-Ríos F, Paz-Ares L.
J Thorac Oncol. 2010 Aug 23. [Epub ahead of print]

Bisulphite sequencing of plant genomic DNA.
Aichinger E, Köhler C.
Methods Mol Biol. 2010;655:433-43.

Deep sequencing of the small RNA transcriptome of normal and malignant human B cells identifies hundreds of novel microRNAs.
Jima DD, Zhang J, Jacobs C, Richards KL, et al.
Blood. 2010 Aug 23. [Epub ahead of print]

Oligonucleotide indexing of DNA barcodes: identification of tuna and other scombrid species in food products.
Botti S, Giuffra E.
BMC Biotechnol. 2010 Aug 23;10(1):60. [Epub ahead of print]

Analysis of co-receptor usage of circulating viral and proviral HIV genome quasispecies by ultra-deep pyrosequencing in patients candidate to CCR5 antagonist treatment.
Abbate I, Rozera G, Tommasi C, Bruselles A, et al.
Clin Microbiol Infect. 2010 Aug 20. [Epub ahead of print]

The Scan

Study Links Genetic Risk for ADHD With Alzheimer's Disease

A higher polygenic risk score for attention-deficit/hyperactivity disorder is also linked to cognitive decline and Alzheimer's disease, a new study in Molecular Psychiatry finds.

Study Offers Insights Into Role of Structural Variants in Cancer

A new study in Nature using cell lines shows that structural variants can enable oncogene activation.

Computer Model Uses Genetics, Health Data to Predict Mental Disorders

A new model in JAMA Psychiatry finds combining genetic and health record data can predict a mental disorder diagnosis before one is made clinically.

Study Tracks Off-Target Gene Edits Linked to Epigenetic Features

Using machine learning, researchers characterize in BMC Genomics the potential off-target effects of 19 computed or experimentally determined epigenetic features during CRISPR-Cas9 editing.