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3 results on '"John Stephen West"'

1. CCDs for spectroscopy

Author

Morley M. Blouke, Taner Dosluoglu, Mark D. Nelson, Yair Talmi, Raymond W. Simpson, and John Stephen West

Subjects
Imaging spectroscopy, Materials science, Fabrication, Spectrometer, Pixel, business.industry, Optical engineering, Amplifier, Electronic engineering, Optoelectronics, Field-effect transistor, business, Characterization (materials science)
Abstract

CCDs have been used in spectroscopy for a number of years and for all the obvious reasons. Unfortunately most scientific CCDs are square arrays and are not ideally formatted for spectroscopic applications. This paper discuses the design and fabrication of two CCD arrays specifically intended for use in spectroscopic applications. The devices have 1100 X 330 and 1752 X 532 pixel formats, and are fabricated using the three phase, overlapping polysilicon gate technology and they are available in both front-illuminated as well as back- illuminated versions. In addition, devices with enhanced UV sensitivity are being fabricated. Characterization data are presented. The architecture of these devices leads to some interesting applications which we discuss briefly.© (1995) COPYRIGHT SPIE--The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only.

Published
1995
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2. New camera for high-speed, high-dynamic-range digital imaging at 4,000 frames/second (burst rate) and 14-16 bits/pixel

Author

Raymond W. Simpson, John Stephen West, and Sam Khoo

Subjects
Engineering, Pixel, Dynamic range, business.industry, ComputingMethodologies_IMAGEPROCESSINGANDCOMPUTERVISION, Digital imaging, Image intensifier, Frame rate, law.invention, law, Shutter, Computer vision, Artificial intelligence, Image sensor, business, High dynamic range
Abstract

A novel combination of techniques with a proprietary masked CCD allows economical commercial realization of a fast framing camera which can acquire images at 4,000 frames per second while maintaining the low readout noise of a slow scan scientific grade CCD system. A 16 bit gray scale dynamic range has been achieved in production with this system and even higher dynamic ranges appear possible in the near future with this technique. This imaging system can also be combined with a gated image intensifier to provide shutter times in the nanosecond domain.

Published
1994
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3. Accurate whole human genome sequencing using reversible terminator chemistry

Author

Zoya Kingsbury, Marc Laurent, Jason Bryant, Konstantinos D. Diakoumakos, Klaus Maisinger, Louise Fraser, Jean Ernest Sohna Sohna, Adrian Horgan, Patrick Mccauley, Jane Rogers, David W. Elmore, Mark A. Osborne, Juying Yan, Mark Smith, Milan Fedurco, Gary P. Schroth, Belen Dominguez-Fernandez, Heng Li, Andrea Sabot, Suzanne Wakelin, Cindy Lawley, Carole Anastasi, David Klenerman, David George, Daniel P. Pliskin, Mohammed D. Alam, Svilen S. Tzonev, Mark T. Reed, Xiaohai Liu, Asha Boodhun, Lu Zhang, Aylwyn Scally, T. A. Huw Jones, Ugonna C. Egbujor, Tzvetana H. Kerelska, George Stefan Golda, Shankar Balasubramanian, Lukasz Szajkowski, Mitch Lok, Mitch K. Shiver, Paul McNitt, Simon Chang, Maria Q. Johnson, Gyoung-Dong Kang, Victor J. Quijano, Sarah E. Lee, Mike Zuerlein, Maria Candelaria Rogert Bacigalupo, Alan D. Kersey, Selena G. Barbour, Dirk J. Evers, Andrew C. Pike, Stephen Rawlings, Karin Fuentes Fajardo, Mirian S. Karbelashvili, Matthew E. Hurles, Sonia M. Novo, Xavier Lee, James C. Burrows, John Stephen West, Jingwen Wang, Ify C. Aniebo, Natasha R. Crake, Christian D. Haudenschild, Richard Shaw, Come Raczy, W. Scott Furey, Wu Xiaolin, Lambros L. Paraschos, Josefina M. Seoane, John W. Martin, Katya Hoschler, Raquel Maria Sanches-Kuiper, Nick J. McCooke, Colin Barnes, Johannes P. Sluis, Abass A. Bundu, John Milton, R. Keira Cheetham, Nancy F. Hansen, Clive Gavin Brown, Nigel P. Carter, Richard J. Carter, Chiara Rodighiero, Kim B. Stevens, Shujun Luo, Radhika M. Mammen, Phyllida M. Roe, Melanie Anne Smith, Bojan Obradovic, Johnny T. Ho, Jennifer A. Loch, Terena James, Harold Swerdlow, Dale Buermann, David E. Green, Steve Hurwitz, Joe W. Mullens, Ning Sizto, Frank L. Oaks, Eli Rusman, Natalie J. Rourke, Nikolai Romanov, Anthony J. Smith, Claire Bevis, Selene M. Virk, Ling Yau, Yuli Verhovsky, D. Chris Pinkard, Stephanie Vandevondele, Vincent Peter Smith, Rob C. Brown, Eric J. Spence, Joe Podhasky, Ana Chiva Rodriguez, Michael Lawrence Parkinson, Anthony Romieu, Joe S. Brennan, Rithy K. Roth, David Mark Dunstan Bailey, Roberto Rigatti, Anil Kumar, Phillip J. Black, Primo Baybayan, Saibal Banerjee, Matthew M. Hims, Arnold Liao, R. Neil Cooley, Omead Ostadan, Vincent A. Benoit, Andrew A. Brown, Silke Ruediger, Leslie J. Irving, Parul Mehta, James C. Mullikin, Klaudia Walter, John Rogers, Jonathan Mark Boutell, Alex P. Kindwall, Paula Kokko-Gonzales, Alger C. Pike, Michael J. O'Neill, Eric Vermaas, Subramanian V. Sankar, Sean Humphray, Steven W. Short, Gerardo Turcatti, Helen Bignell, Kimberley J. Gietzen, Peta E. Torrance, Narinder I. Heyer, David James Earnshaw, Kevin Hall, Martin R. Schenker, Richard Durbin, Philip A. Granieri, Tobias William Barr Ost, Iain R. Bancarz, Lea Pickering, David L. Gustafson, Peter Lundberg, Niall Anthony Gormley, John Bridgham, Andrew Osnowski, Scott M. Kirk, Mark R. Ewan, Keith W. Moon, Bee Ling Ng, Graham John Worsley, Anthony J. Cox, Olubunmi O. Dada, Gregory C. Walcott, Sergey Etchin, Irina Khrebtukova, Kevin Benson, Vicki H. Rae, Zemin Ning, Carolyn Tregidgo, Nestor Castillo, Colin P. Goddard, Taksina Newington, Denis V. Ivanov, Anastassia Spiridou, Maria Chiara E. Catenazzi, Neil Sutton, Kevin Harnish, Darren James Ellis, Lisa Murray, Geoffrey Paul Smith, Mark T. Ross, David R. Bentley, M. R. Pratt, Isabelle Rasolonjatovo, and Michael R. Flatbush

Subjects
Male, Genotype, 2 base encoding, Nigeria, Sequence assembly, Hybrid genome assembly, Genomics, Computational biology, Biology, Polymorphism, Single Nucleotide, Sensitivity and Specificity, Deep sequencing, Article, 03 medical and health sciences, 0302 clinical medicine, Consensus Sequence, Humans, Paired-end tag, 030304 developmental biology, Genetics, Whole genome sequencing, Chromosomes, Human, X, 0303 health sciences, Multidisciplinary, Genome, Human, DNA sequencing theory, Sequence Analysis, DNA, 030220 oncology & carcinogenesis
Abstract

DNA sequence information underpins genetic research, enabling discoveries of important biological or medical benefit. Sequencing projects have traditionally used long (400-800 base pair) reads, but the existence of reference sequences for the human and many other genomes makes it possible to develop new, fast approaches to re-sequencing, whereby shorter reads are compared to a reference to identify intraspecies genetic variation. Here we report an approach that generates several billion bases of accurate nucleotide sequence per experiment at low cost. Single molecules of DNA are attached to a flat surface, amplified in situ and used as templates for synthetic sequencing with fluorescent reversible terminator deoxyribonucleotides. Images of the surface are analysed to generate high-quality sequence. We demonstrate application of this approach to human genome sequencing on flow-sorted X chromosomes and then scale the approach to determine the genome sequence of a male Yoruba from Ibadan, Nigeria. We build an accurate consensus sequence from >30x average depth of paired 35-base reads. We characterize four million single-nucleotide polymorphisms and four hundred thousand structural variants, many of which were previously unknown. Our approach is effective for accurate, rapid and economical whole-genome re-sequencing and many other biomedical applications.

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