Adam Paul Arkin

US Patent:

59148918, Jun 22, 1999

Filed:

Jun 11, 1997

Appl. No.:

8/860585

Inventors:

Harley H. McAdams - Stanford CA
Adam P. Arkin - Half Moon Bay CA
Lucille Shapiro - Stanford CA

Assignee:

Board of Trustees, The Leland Stanford Junior University - Palo Alto CA

International Classification:

G06F 1718

US Classification:

364578

Abstract:

A system and method for simulating the operation of biochemical networks includes a computer having a computer memory used to store a set of objects, each object representing a biochemical mechanism in the biochemical network to be simulated. Most objects have one or more associated signals, representing quantities or concentrations of associated proteins, positions of associated molecules, or other information concerning the state of a biochemical network. Each object has an associated set of methods. These methods include methods for determining reaction probabilities for biochemical reactions associated with the objects, and reaction simulation methods for simulating performance of those biochemical reactions. For a specified simulation time period, the operation of the biochemical network is simulated by executing at least a subset of the probability determination methods to determine reaction probabilities for at a subset of the biochemical reactions associated with the objects, selecting ones of the reaction simulation methods to execute in accordance with the determined reaction probabilities, and executing the selected ones of said reaction simulation methods. Execution of the selected reaction simulation methods causes associated ones of the signals to be updated.

US Patent:

20210403995, Dec 30, 2021

Filed:

Sep 13, 2021

Appl. No.:

17/473968

Inventors:

- Oakland CA, US
Adam P. Arkin - San Francisco CA, US
Adam M. Deutschbauer - Berkeley CA, US

International Classification:

C12Q 1/6869
C12N 15/10

Abstract:

The present invention provides for a method for screening for gene function for a bacteriophage, the method comprising: (1) (a) providing one or more host organism, such as a species or strain, libraries, (b) providing randomly barcoded transposon sequencing (such as RB-TnSeq), and (c) screening for loss-of-function (LOF) mutant phenotypes; or (2) (a) providing one or more DNA barcoded overexpression strain libraries (such as Dub-seq) using DNA of the host organism and/or phage, and (b) screening for gain-of-function (GOF).

US Patent:

20210254048, Aug 19, 2021

Filed:

Feb 6, 2021

Appl. No.:

17/169442

Inventors:

- Oakland CA, US
Denish Piya - El Cerrito CA, US
Adam P. Arkin - San Francisco CA, US

International Classification:

C12N 15/10
C12N 7/00
C12Q 1/70
A61K 35/76

Abstract:

The present invention provides for a nucleic acid encoding a bacteriophage genome comprising a unique n-mer barcode inserted in a non-essential location or gene location within the bacteriophage genome, or a bacteriophage comprising the nucleic acid thereof

US Patent:

20180127796, May 10, 2018

Filed:

Nov 8, 2017

Appl. No.:

15/807498

Inventors:

- Oakland CA, US
Adam P. Arkin - San Francisco CA, US

International Classification:

C12Q 1/02
C12Q 1/68
G06F 19/24

Abstract:

Disclosed herein are methods, compositions, and systems for determining specific microbial taxa, within a complex consortia of mixed taxa, which are interacting with each other in an environment of interest. In some embodiments, after diluting a sample comprising multiple different taxa of microorganisms, dilutions of the sample are cultivated for determining taxonomic information and interactions of multiple taxa of microorganisms in the sample.

US Patent:

20180030435, Feb 1, 2018

Filed:

Jul 31, 2017

Appl. No.:

15/665226

Inventors:

- Oakland CA, US
Adam Deutschbauer - Berkeley CA, US
Adam P. Arkin - San Francisco CA, US
Pavel Novichkov - Walnut Creek CA, US

International Classification:

C12N 15/10

Abstract:

Disclosed herein are barcoded expression libraries comprising a plurality of expression vectors, wherein each expression vector comprises a nucleic acid fragment flanked by a first barcode and a second barcode. Further disclosed herein are methods of making the barcoded expression libraries and methods of conducting functional analysis using the barcoded expression libraries.

US Patent:

20150011007, Jan 8, 2015

Filed:

Sep 27, 2012

Appl. No.:

14/346263

Inventors:

- Oakland CA, US
Adam P. Arkin - San Francisco CA, US
Lei S. Qi - El Cerrito CA, US

International Classification:

C12N 15/72

US Classification:

435471, 536 241, 43525233, 4353201

Abstract:

Provided herein are nucleic acid constructs that contain a synthetic control element that includes a cis-regulator of translation, and an adapter translation-coupled regulator of transcription. Further provided herein are nucleic acid constructs that contain nucleic acid sequences under the control of the synthetic control elements. Also provided are compositions and methods related to the nucleic acid constructs.