Affymetrix, Inc.

Nautilus Subsidiary, Inc.

Twist Bioscience Corporation

Cellular Research, Inc.

Pacific Biosciences of California, Inc.

Perlegen Sciences, Inc.

Apton Biosystems, Inc.

Affymetrix Technologies, N.v.

Becton Dickinson and Company Limited

David Stern

Peter J Fiekowsky

Pierre F Indermuhle

Chuan Gao

Melvin Yamamoto

Devin Nguyen

Richard P Rava

Parag Mallick

Mark O Trulson

Ian Walton

Eugene P Marsh

Stephen P A Fodor

Andres Fernandez

Stephen P Fodor

Bill James Peck

Sujal M Patel

Jarrett D Egertson

Vadim Lobanov

Ryan Kempston Seghers

Calvin F Quate

Glenn K Fu

Bryan P Staker

Geoffrey Richard Facer

Paul Heilman

Elliott Sorelle

Jean I Montagu

Christina Fan

Windsor Owens

Edvinas Zizminskas

George T Wu

Ezra Van Gelder

Philipp S Spuhler

Torri Elise Rinker

Elisabeth Marie Walczak

Roger Rudoff

Joshua Simon Klein

Geoff Facer

Sonal Tonapi

Robert Hartlage

Pengyu Hao

Daniel Horner

Janice H Lai

Maryam Jouzi

Rob Hartlage

Kevin Chen

Abdullah Ozer

Minyong Chung

Tracy Chan

Ari Chaney

Xiaohua Chen Huang

Kimberly R Metzler

Sixing Li

The present disclosure provides systems and methods for detecting components of an array of biological, chemical, or physical entities. In an aspect, the present disclosure provides a method for detecting an array of biological, chemical, or physical entities, comprising: (a) using one or more light sensing devices, acquiring pixel information from sites in an array, wherein the sites comprise biological, chemical, or physical entities that produce light; (b) processing the pixel information to identify a set of regions of interest (ROIs) corresponding to the sites in the array that produce the light; (c) classifying the pixel information for the ROIs into a categorical classification from among a plurality of distinct categorical classifications, thereby producing a plurality of pixel classifications; and (d) identifying one or more components of the array of biological, chemical, or physical entities based at least in part on the plurality of pixel classifications.

Methods and systems for computational decoding of biological, chemical, and physical entities

The present disclosure provides methods and systems for performing single-molecule detection using fabricated integrated on-chip devices. Provided herein is a composition, comprising: (a) a substrate; (b) a structured nucleic acid particle coupled to the substrate, wherein a biological entity is coupled to the structured nucleic acid particle; and (c) a fluorescent detection agent, wherein the fluorescent detection agent comprises an affinity reagent attached to another structured nucleic acid particle, wherein the affinity reagent is bound to the biological entity.

Methods and systems for integrated on-chip single-molecule detection

Disclosed herein is a high throughput optical scanning device and methods of use. The optical scanning device and methods of use provided herein can allow high throughput scanning of a continuously moving object with a high resolution despite fluctuations in stage velocity. This can aid in high throughput scanning of a substrate, such as a biological chip comprising fluorophores. Also provided herein are improved optical relay systems and scanning optics.

High speed scanning system with acceleration tracking

Compositions, systems, and methods are disclosed for preparing and utilizing arrays, such as single-analyte arrays containing a plurality of fiducial elements with random spatial distributions. Arrays may be prepared with pluralities of fiducial elements comprising optically active or passive moieties. Arrays containing random spatial distributions of fiducial elements may be utilized for various array-based processes that require spatial information.

Integrated arrays for single-analyte processes

Methods and systems are provided herein for selecting an affinity reagent which binds a desired peptide epitope in a plurality of sequence contexts. The method relies on obtaining a peptide library, each peptide having the sequence αXβ, wherein X is the desired peptide epitope, wherein each of α and β comprise an amino acid, using the peptide library to select an affinity reagent.

Selection of affinity reagents

Compositions, devices, methods and systems are provided for differential functionalization of a surface of a structure to support biopolymer synthesis. Provided herein are processes which include use of lamps, lasers, and/or microcontact printing to add functional groups to surfaces for the efficient and uniform synthesis of oligonucleic acids.

Functionalized surfaces and preparation thereof

In one embodiment of the invention, a method to image a probe array is described that includes focusing on a plurality of fiducials on a surface of an array. The method utilizes obtaining the best z position of the fiducials and using a surface fitting algorithm to produce a surface fit profile. One or more surface non-flatness parameters can be adjusted to improve the flatness image of the array surface to be imaged.

Methods and devices for reading microarrays

Methods, systems and platforms for digital imaging of multiple regions of an array, and detection and counting of the labeled features thereon, are described.

Methods and systems for digitally counting features on arrays

Growing community of inventors

Mountain View, CA, United States of America

David Stern