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The Sequencing Bead Array (SBA), a next-generation digital suspension array.

Akhras, Michael S Pettersson, Erik Diamond, Lisa Unemo, Magnus Okamoto, Jennifer Davis, Ronald W Pourmand, Nader

Published in PloS one

Here we describe the novel Sequencing Bead Array (SBA), a complete assay for molecular diagnostics and typing applications. SBA is a digital suspension array using Next-Generation Sequencing (NGS), to replace conventional optical readout platforms. The technology allows for reducing the number of instruments required in a laboratory setting, where ...

Modeling the impact of common noise inputs on the network activity of retinal ganglion cells

Vidne, Michael Ahmadian, Yashar Shlens, Jonathon Pillow, Jonathan W. Kulkarni, Jayant Litke, Alan M. Chichilnisky, E. J. Simoncelli, Eero Paninski, Liam

Published in Journal of Computational Neuroscience

Synchronized spontaneous firing among retinal ganglion cells (RGCs), on timescales faster than visual responses, has been reported in many studies. Two candidate mechanisms of synchronized firing include direct coupling and shared noisy inputs. In neighboring parasol cells of primate retina, which exhibit rapid synchronized firing that has been stu...

Polycyclic Aromatic Hydrocarbons as Plausible Prebiotic Membrane Components

Groen, Joost Deamer, David W. Kros, Alexander Ehrenfreund, Pascale

Published in Origins of Life and Evolution of Biospheres

Aromatic molecules delivered to the young Earth during the heavy bombardment phase in the early history of our solar system were likely to be among the most abundant and stable organic compounds available. The Aromatic World hypothesis suggests that aromatic molecules might function as container elements, energy transduction elements and templating...

Complete genome sequence of Pyrobaculum oguniense

Bernick, David L. Karplus, Kevin Lui, Lauren M. Coker, Joanna K. C. Murphy, Julie N. Chan, Patricia P. Cozen, Aaron E. Lowe, Todd M.

Published in Standards in Genomic Sciences

Pyrobaculum oguniense TE7 is an aerobic hyperthermophilic crenarchaeon isolated from a hot spring in Japan. Here we describe its main chromosome of 2,436,033 bp, with three large-scale inversions and an extra-chromosomal element of 16,887 bp. We have annotated 2,800 protein-coding genes and 145 RNA genes in this genome, including nine H/ACA-like sm...

Comprehensive genomic characterization of squamous cell lung cancers.

Published in Nature

Lung squamous cell carcinoma is a common type of lung cancer, causing approximately 400,000 deaths per year worldwide. Genomic alterations in squamous cell lung cancers have not been comprehensively characterized, and no molecularly targeted agents have been specifically developed for its treatment. As part of The Cancer Genome Atlas, here we profi...

Comprehensive molecular characterization of human colon and rectal cancer.

Published in Nature

To characterize somatic alterations in colorectal carcinoma, we conducted a genome-scale analysis of 276 samples, analysing exome sequence, DNA copy number, promoter methylation and messenger RNA and microRNA expression. A subset of these samples (97) underwent low-depth-of-coverage whole-genome sequencing. In total, 16% of colorectal carcinomas we...

Molecular probe technology detects bacteria without culture

Hyman, Richard W St Onge, Robert P Kim, Hyunsung Tamaresis, John S Miranda, Molly Aparicio, Ana Maria Fukushima, Marilyn Pourmand, Nader Giudice, Linda C Davis, Ronald W ...

Published in BMC Microbiology

BackgroundOur ultimate goal is to detect the entire human microbiome, in health and in disease, in a single reaction tube, and employing only commercially available reagents. To that end, we adapted molecular inversion probes to detect bacteria using solely a massively multiplex molecular technology. This molecular probe technology does not require...

Integrated molecular profiles of invasive breast tumors and ductal carcinoma in situ (DCIS) reveal differential vascular...

Kristensen, Vessela N Vaske, Charles J Ursini-Siegel, Josie Van Loo, Peter Nordgard, Silje H Sachidanandam, Ravi Sørlie, Therese Wärnberg, Fredrik Haakensen, Vilde D Helland, Åslaug ...

Published in Proceedings of the National Academy of Sciences of the United States of America

We use an integrated approach to understand breast cancer heterogeneity by modeling mRNA, copy number alterations, microRNAs, and methylation in a pathway context utilizing the pathway recognition algorithm using data integration on genomic models (PARADIGM). We demonstrate that combining mRNA expression and DNA copy number classified the patients ...

Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes

St John, John A Braun, Edward L Isberg, Sally R Miles, Lee G Chong, Amanda Y Gongora, Jaime Dalzell, Pauline Moran, Christopher Bed'Hom, Bertrand Abzhanov, Arkhat ...

Published in Genome Biology

The International Crocodilian Genomes Working Group (ICGWG) will sequence and assemble the American alligator (Alligator mississippiensis), saltwater crocodile (Crocodylus porosus) and Indian gharial (Gavialis gangeticus) genomes. The status of these projects and our planned analyses are described.

Gene isoform specificity through enhancer-associated antisense transcription.

Onodera, Courtney S Underwood, Jason G Katzman, Sol Jacobs, Frank Greenberg, David Salama, Sofie R Haussler, David

Published in PloS one

Enhancers and antisense RNAs play key roles in transcriptional regulation through differing mechanisms. Recent studies have demonstrated that enhancers are often associated with non-coding RNAs (ncRNAs), yet the functional role of these enhancer:ncRNA associations is unclear. Using RNA-Sequencing to interrogate the transcriptomes of undifferentiate...

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