Emerald Therapeutics, Inc.

Emerald Cloud Lab, Inc.

Daniel J Kleinbaum

Brian M Frezza

Jonathan K Leung

George W Fraser

Brad Bond

Courtney E Webster

Bradley M Bond

Shayna L Hilburg

Alex M Yoshikawa

Catherine L Hofler

Ruben E Valas

George N Stanley

Sergio I Villarreal

Robert M Teed

Cheri Y Li

Sean M Fitzgerald

Ben C Kline

Shivani S Baisiwala

Anand V Sastry

Srikant Vaithilingam

Guillaume Robichaud

Wyatt J Woodson

Yang Choo

Hayley E Buchman

Yidan Y Cong

Cameron R Lamoureux

James R McKernan

Asuka Ota

Paul R Zurek

Collin A Melton

Eric Shyr

Kyla N Velaer

The disclosure provides systems and methods for conducting and managing integrated laboratory experiments. The system includes a variety of laboratory instruments that are connected to conduct a large number of different types of experiments, and an interface for a user to design experiments and adjust parameters for the experiments. Given the integration, the system can further take data from related samples and instruments for determining or adjusting certain experimental parameters for optimized experimental efficiency and results.

System and method for management, execution, and analysis of laboratory experiments

Provided are nucleic acid translators capable of carrying out logic operations with improved efficiency, maximized output and reduced off-target effects, in particular in a biological system. Methods of using these translators to transduce signal are also provided.

Rotationally sequestered translators

The disclosure provides systems and methods for data analysis of experimental data. The analysis can include reference data that are not directly generated from the present experiment, which reference data may be values of the experimental parameters that were either provided by a user, computed by the system with input from a user, or computed by the system without using any input from a user. Another example of such reference data may be information about the instrument, such as the calibration method of the instrument.

Laboratory experiment data exploration and visualization

An approach to designing a polynucleotide probe to hybridize selectively to a target polynucleotide sequence involves calculating the final concentration of the intended binding product between a candidate probe and the target sequence. The calculation takes into consideration the binding reaction between the candidate probe and the target fragment on the target sequence, as well as various other binding reactions, involving either the probe or the target fragment, that interfere with the intended binding reaction. In contrast to the conventional technology, which attempts to determine the entire structure of the target polynucleotide, this approach only needs to determine the binding dynamics that impact on the intended probe-target fragment binding. The approach does not require determination of the structure of the involved sequences.

Polynucleotide probe design

Improvement is effected for a nucleic acid-based molecular computing system that is comprised of (i) a nucleic acid structure, (ii) at least one polynucleotide displacement molecule that can bind with the nucleic acid structure under hybridizing conditions, and (iii) a clashing polynucleotide molecule that competes with the polynucleotide displacement molecule for binding the nucleic acid structure under the hybridizing conditions. The method for such improvement entails incorporating chemical modification that inhibits the binding of the clashing molecule and the nucleic acid structure or facilitating the binding of the displacement molecule and the nucleic structure.

System and method for propagating information using modified nucleic acids

A fabrication process for producing, annealing, and conjugating nucleic acid molecules is implemented, under the direction of one or more computer programs, on two or more instruments, for carrying out the process. The process can include: (a) synthesizing, on a solid support and in a plurality of reactions, at least one of a nucleic acid and a peptide nucleic acid, and cleaving the synthesized biomolecule product from the support, providing a sample of synthesized biomolecule product from each reaction of the plurality; (b) measuring, for each sample, the volume of the sample and/or the concentration of the product; (c) subjecting the product from each reaction to chromatography under conditions suitable for achieving single-base-resolution for the product, the conditions being a function of the volume and/or concentration measured in (b); and then (d) collecting and pooling, from the chromatography of (c) for each sample, peaks that correspond to the product.

Systems and methods for automated preparation of nucleic acids

Conjugated molecules are prepared that comprise a predetermined number of oligo conjugation components. The conjugated molecules also may comprise one or more detectable labels. Preparation of these molecules can be implemented according to an asymmetric or a symmetric conjugation strategy.

Preparation of oligo conjugates

A method is provided for improving a nucleic acid-based molecular computing system comprised of (i) a nucleic acid structure, (ii) at least one polynucleotide displacement molecule that can bind with the nucleic acid structure under hybridizing conditions, and (iii) a clashing polynucleotide molecule that competes with the polynucleotide displacement molecule for binding the nucleic acid structure under the hybridizing conditions The method entails incorporation of chemical modification that inhibits the binding of the clashing molecule and the nucleic acid structure or facilitates the binding of the displacement molecule and the nucleic structure.

Growing community of inventors

Redwood City, CA, United States of America

Daniel J Kleinbaum