Helicos Biosciences Corporation

Lucent Technologies Inc.

Fluidigm Corporation

Praelux Incorporated

At+t Corp.

At&t Bell Laboratories

Ge Healthcare Bio-sciences Corp.

Timothy D Harris

Stanley N Lapidus

Philip Richard Buzby

Richard L Hansen

William Karsh

Jay K Trautman

Neal A Nicklaus

Mirna Jarosz

James Joseph Dimeo

Phillip Richard Buzby

Jaime Gill

John E Cunningham

Loren Neil Pfeiffer

Erdmann F Schubert

Kenneth William West

Jan P Van Der Ziel

Joel Hasen

Robert D Grober

David Gershoni

David Novak

John J Boyce, Iv

Qing Wang

Jamie Gill

The invention provides methods for sequencing a polynucleotide comprising stopping an extension cycle in a sequence by synthesis reaction before the reaction has run to near or full completion.

Short cycle methods for sequencing polynucleotides

Methods of the invention comprise methods and devices for nucleic acid sequence determination. Generally, the invention relates to preparing a substrate for sequencing a target nucleic acid.

Methods and devices for nucleic acid sequence determination

Methods and apparatus for screening large numbers of chemical compounds and performing a wide variety of fluorescent assays, including live cell assays. The methods utilize a laser linescan confocal microscope with high speed, high resolution and multi-wavelength capabilities and real time data-processing. Imaging may be done at video-rates and with use of ultraviolet illumination.

Method and apparatus for screening chemical compounds

The invention provides methods for sequencing a polynucleotide comprising stopping an extension cycle in a sequence by synthesis reaction before the reaction has run to near or fill completion.

The disclosure provides methods of reducing the range of representation levels of nucleic acid targets. The methods are particularly useful for multi-target analyses benefiting from a low variance of target representations, such as, e.g., single molecule sequencing and/or heterozygous genotyping, and pathogen diagnosis. Two general methods are provided. In Method 1, starting concentrations of probes are adjusted. In Method 2, target-specific probes are 'binned,' i.e., several subsets of probes are selected based on similar representation levels. Thereafter, each subset of corresponding targets is extracted, with or without amplification, using a separate portion of the sample (i.e., separate vessels).

Methods of equalizing representation levels of nucleic acid targets

The disclosure provides methods of generating paired reads in sequencing-by-synthesis process, particularly, in systems with relatively short read lengths (e.g., 15-35bases), such as for example, in single molecule sequencing by synthesis. Several implementations of the methods are provided. Of particular advantage are the methods that permit re-sequencing of the template, which yields lower error rates. The invention further provides methods of using paired reads, for example, for positioning them over repeats or for assembly into large sequences, including whole genome assembly.

Paired-end reads in sequencing by synthesis

The invention provides methods for improving the accuracy of a sequencing-by-synthesis reaction by sequencing at least a portion of a template and at least a portion of template complementary sequence.

Methods for increasing accuracy of nucleic acid sequencing

A system for analyzing a sample is disclosed. The system includes a light-transmitting probe with a light emitting tip having a diameter that is less than one-wavelength of light. The system is adapted to place the probe in close proximity to the sample without physically contacting the sample with the probe, and to move the sample relative to the probe such that light transmitted from the probe is directed onto the desired portion of the sample surface. The system further include a light source which transmits light into the probe tip. The system also includes a detector which detects a portion of the light transmitted through the sample. The detector is configured to detect that portion of the light that was incident on the sample surface at an angle greater than the critical angle. The detector is equipped with an aperture through which passes substantially all of the light that was incident on the surface at an angle less than the critical angle and which was transmitted through the sample. The system further analyzes the light received by the detector to determine the relative index of refraction of a material at one point on the surface of the sample relative to the index of refraction of the material at another point on the surface of the sample.

Manufacturing method including near-field optical microscopic

Quantum carrier confinement in a wire-like region defined by intersecting layers is significantly enhanced by various structural modifications of a conventional quantum wire device. In that way, operation of the device at room temperature and above is made feasible.

Quantum wire lasers

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Toms River, NJ, United States of America

Timothy D Harris