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News 571 Publications 15 Members

Contrast Sensitivity With a Subretinal Prosthesis and Implications for Efficient Delivery of Visual Information.

Goetz, Georges Smith, Richard Lei, Xin Galambos, Ludwig Kamins, Theodore Mathieson, Keith Sher, Alexander Palanker, Daniel

Published in Investigative ophthalmology & visual science

To evaluate the contrast sensitivity of a degenerate retina stimulated by a photovoltaic subretinal prosthesis, and assess the impact of low contrast sensitivity on transmission of visual information. We measure ex vivo the full-field contrast sensitivity of healthy rat retina stimulated with white light, and the contrast sensitivity of degenerate ...

Transcriptome Profiling of Developing Murine Lens Through RNA Sequencing.

Khan, Shahid Y Hackett, Sean F Lee, Mei-Chong W Pourmand, Nader Talbot, C Conover Jr Riazuddin, S Amer

Published in Investigative ophthalmology & visual science

Transcriptome is the entire repertoire of transcripts present in a cell at any particular time. We undertook a next-generation whole transcriptome sequencing approach to gain insight into the transcriptional landscape of the developing mouse lens. We ascertained mouse lenses at six developmental time points including two embryonic (E15 and E18) and...

Optimized Protocol for Simple Extraction of High-Quality Genomic DNA from Clostridium difficile for Whole-Genome Sequenc...

Sim, James Heng Chiak Anikst, Victoria Lohith, Akshar Pourmand, Nader Banaei, Niaz

Published in Journal of clinical microbiology

Successful sequencing of the Clostridium difficile genome requires high-quality genomic DNA (gDNA) as the starting material. gDNA extraction using conventional methods is laborious. We describe here an optimized method for the simple extraction of C. difficile gDNA using the QIAamp DNA minikit, which yielded high-quality sequence reads on the Illum...

Analysis of nanopore data using hidden Markov models.

Schreiber, Jacob Karplus, Kevin

Published in Bioinformatics (Oxford, England)

The data, output, scripts and tutorials replicating the analysis are available at https://github.com/UCSCNanopore/Data/tree/master/Automation.

The Genome 10K Project: a way forward.

Koepfli, Klaus-Peter Paten, Benedict O'Brien, Stephen J

Published in Annual review of animal biosciences

The Genome 10K Project was established in 2009 by a consortium of biologists and genome scientists determined to facilitate the sequencing and analysis of the complete genomes of 10,000 vertebrate species. Since then the number of selected and initiated species has risen from ∼26 to 277 sequenced or ongoing with funding, an approximately tenfold in...

Comparative genomics reveals insights into avian genome evolution and adaptation.

Zhang, Guojie Li, Cai Li, Qiye Li, Bo Larkin, Denis M Lee, Chul Storz, Jay F Antunes, Agostinho Greenwold, Matthew J Meredith, Robert W ...

Published in Science (New York, N.Y.)

Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific...

Whole-genome analyses resolve early branches in the tree of life of modern birds.

Jarvis, Erich D Mirarab, Siavash Aberer, Andre J Li, Bo Houde, Peter Li, Cai Ho, Simon Y W Faircloth, Brant C Nabholz, Benoit Howard, Jason T ...

Published in Science (New York, N.Y.)

To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergen...

The birds of Genome10K

OBrien, Stephen J Haussler, David Ryder, Oliver

Published in GigaScience

Everyone loves the birds of the world. From their haunting songs and majesty of flight to dazzling plumage and mating rituals, bird watchers – both amateurs and professionals - have marveled for centuries at their considerable adaptations. Now, we are offered a special treat with the publication of a series of papers in dedicated issues of Science,...

Single-cell analyses of transcriptional heterogeneity during drug tolerance transition in cancer cells by RNA sequencing...

Lee, Mei-Chong Wendy Lopez-Diaz, Fernando J Khan, Shahid Yar Tariq, Muhammad Akram Dayn, Yelena Vaske, Charles Joseph Radenbaugh, Amie J Kim, Hyunsung John Emerson, Beverly M Pourmand, Nader ...

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

The acute cellular response to stress generates a subpopulation of reversibly stress-tolerant cells under conditions that are lethal to the majority of the population. Stress tolerance is attributed to heterogeneity of gene expression within the population to ensure survival of a minority. We performed whole transcriptome sequencing analyses of met...

You cannot tell a book by looking at the cover: Cryptic complexity in bacterial evolution.

Zhang, Qiucen Bos, Julia Tarnopolskiy, Grigory Sturm, James C Kim, Hyunsung Pourmand, Nader Austin, Robert H

Published in Biomicrofluidics

Do genetically closely related organisms under identical, but strong selection pressure converge to a common resistant genotype or will they diverge to different genomic solutions? This question gets at the heart of how rough is the fitness landscape in the local vicinity of two closely related strains under stress. We chose a Growth Advantage in S...

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