Mark David Welch

US Patent:

6436675, Aug 20, 2002

Filed:

Sep 28, 1999

Appl. No.:

09/408393

Inventors:

Mark Welch - Fremont CA
Jon Ness - Sunnyvale CA
Claes Gustafsson - Belmont CA
Willem P. C. Stemmer - Los Gatos CA
Jeremy Minshull - Menlo Park CA

Assignee:

Maxygen, Inc. - Redwood City CA

International Classification:

C12Q 168

US Classification:

435 911, 435 6, 536 253

Abstract:

Methods of providing shuffling libraries that include codon-varied oligonucleotide sequences are described. Codon-varied oligonucleotides are synthesized using trinucleotide or mononucleotide phosphoramidite sequences, and are derived from homologous or non-homologous nucleic acid sequences, or combinations of such sequences. Various methods of recombining codon-varied oligonucleotide sequences to expedite artificial evolution are also described. The present invention additionally relates to various integrated systems that are optionally used to automate these recombination methods.

US Patent:

6777218, Aug 17, 2004

Filed:

Mar 23, 2000

Appl. No.:

09/533480

Inventors:

Frank Mikkelsen - Valby, DK
Tina Sejersgård Fanø - Kobenhavn O, DK
Jon E. Ness - Redwood City CA
Mark D. Welch - Fremont CA
Lorraine J. Giver - Sunnyvale CA
Jeremy S. Minshull - Los Altos CA
Torben V. Borchert - Birkeroed, DK
Joel Cherry - Davis CA

Assignee:

Novozymes A/S - Bagsvaerd
Maxygen, Inc - Redwood City CA

International Classification:

C12N 952

US Classification:

435220, 435 691, 435221, 4352523, 435 3201, 435471, 536 232, 510350

Abstract:

The present invention relates to novel subtilases having an improved wash performance on egg stains. The present invention also relates to isolated nucleic acid sequences encoding the subtilases, nucleic acid constructs, recombinant expression vectors, host cells comprising the nucleic acid construct, and methods for producing and using the subtilases of the invention. Further, the present invention relates to cleaning and detergent compositions comprising the subtilase enzymes of the invention as well as to use of such enzymes in detergent compositions and for removal of egg stains.

US Patent:

7462469, Dec 9, 2008

Filed:

May 23, 2002

Appl. No.:

10/154936

Inventors:

Steven H. Bass - Hillsborough CA, US
S. Christopher Davis - San Francisco CA, US
Phillip A. Patten - Menlo Park CA, US
Matthew Tobin - San Carlos CA, US
Jeremy Minshull - Los Altos CA, US
Mark Welch - Fremont CA, US
Claes Gustafsson - Belmont CA, US
Brian Carr - Raleigh NC, US
Stephane Jenne - Foster City CA, US
Sun Ai Raillard - Mountain View CA, US
Andreas Crameri - Mountain View CA, US
Willem P. C. Stemmer - Los Gatos CA, US
Robin Emig - Belmont CA, US
Pascal Longchamp - Allschwil, CH
Stanley Goldman - Walnut Creek CA, US
Lorraine J. Giver - Sunnyvale CA, US
Joseph A. Affholter - Lake Village Zephyr Cove NV, US

Assignee:

Maxygen, Inc. - Redwood City CA

International Classification:

C12P 19/34
C12Q 1/68

US Classification:

435 912, 435 6, 435 911

Abstract:

Integrated systems and methods for diversity generation and screening are provided. The systems use common fluid and array handling components to provide nucleic acid diversification, transcription, translation, product screening and subsequent diversification reactions.

US Patent:

7561972, Jul 14, 2009

Filed:

Jul 31, 2008

Appl. No.:

12/184234

Inventors:

Mark Welch - Fremont CA, US
Claes Gustafsson - Belmont CA, US

Assignee:

DNA Twopointo, Inc. - Menlo Park CA

International Classification:

G01N 33/48
C12Q 1/00
C12Q 1/48
C07H 21/02

US Classification:

702 19, 702 20, 435 4, 435 6, 435 15, 536 231, 536 241

Abstract:

A method of designing a polynucleotide sequence encoding a polypeptide sequence of a predetermined polypeptide is provided. A frequency lookup table corresponding to an expression system is obtained. The table comprises a plurality of sequence elements and a plurality of frequency ranges, each frequency range for a corresponding sequence element. Each frequency range is a range of frequencies with which a corresponding sequence element can occur in a polynucleotide. The polynucleotide sequence is defined using the frequency lookup table by determining, for each respective sequence element in the frequency lookup table, whether the respective sequence element encodes a portion of the polypeptide sequence. When the respective sequence element encodes a portion of the polypeptide sequence, the sequence element is incorporated into the polynucleotide at a frequency of occurrence that is within the frequency range specified for the respective sequence element in the lookup table. The polynucleotide sequence is then outputted.

US Patent:

7561973, Jul 14, 2009

Filed:

Jul 31, 2008

Appl. No.:

12/184240

Inventors:

Mark Welch - Fremont CA, US
Claes Gustafsson - Belmont CA, US

Assignee:

DNA Twopointo, Inc. - Menlo Park CA

International Classification:

G01N 33/48
C12Q 1/00
C12Q 1/48
C12Q 1/68
C07H 21/02
C07H 21/04
C12Q 1/08

US Classification:

702 19, 702 20, 435 4, 435 6, 435 15, 435 912, 536 231, 536 241

Abstract:

A method of determining a property that affects expression of polynucleotides in an expression system. A plurality of polynucleotides, each encoding a polypeptide sequence, is constructed. An amino acid is encoded a plurality of times in both a first and second polynucleotide in the plurality. The amino acid is encodable by a plurality of synonymous codons including a first codon. The first codon is in the first polynucleotide at a first frequency relative to other synonymous codons, and is in the second polynucleotide at a second frequency relative to other synonymous codons. The first and second frequencies are different. Each polynucleotide is individually expressed in the expression system to measure an expression property value of the polynucleotides, thereby determining a property that affects expression of polynucleotides. The property is an effect that a frequency of use of one or more codons has on expression of polynucleotides in the expression system.

US Patent:

8014961, Sep 6, 2011

Filed:

Feb 21, 2007

Appl. No.:

11/677505

Inventors:

Steven H. Bass - Hillsborough CA, US
Simon Christopher Davis - San Francisco CA, US
Phillip A. Patten - Portola Valley CA, US
Matthew Tobin - San Carlos CA, US
Jeremy S. Minshull - Los Altos CA, US
Mark Welch - Fremont CA, US
Claus Gustafsson - Belmont CA, US
Brian Carr - Raleigh NC, US
Stephan J. Jenne - Foster City CA, US
Sun Ai Raillard - Mountain View CA, US
Andreas Crameri - Mountain View CA, US
Willem P. C. Stemmer - Los Gatos CA, US
Robin Emig - Belmont CA, US
Pascal Longchamp - Lausanne, CH
Stanley Goldman - Walnut Creek CA, US
Lorraine J. Giver - Sunnyvale CA, US
Joseph A. Affholter - Zephyr Cove NV, US

Assignee:

Codexis Mayflower Holdings, LLC - Redwood City CA

International Classification:

G01N 33/48

US Classification:

702 20

Abstract:

Integrated systems and methods for diversity generation and screening are provided. The systems use common fluid and array handling components to provide nucleic acid diversification, transcription, translation, product screening and subsequent diversification reactions.

US Patent:

8126653, Feb 28, 2012

Filed:

Jul 31, 2008

Appl. No.:

12/184230

Inventors:

Mark Welch - Fremont CA, US
Claes Gustafsson - Belmont CA, US

Assignee:

DNA Twopointo, Inc. - Menlo Park CA

International Classification:

G01N 33/48
C12Q 1/68
G06G 7/58

US Classification:

702 19, 435 6, 702 20, 703 11

Abstract:

A method of determining a property that affects expression of polynucleotides in an expression system. A plurality of polynucleotides, each encoding a polypeptide sequence, is constructed. An amino acid is encoded a plurality of times in both a first and second polynucleotide in the plurality. The amino acid is encodable by a plurality of synonymous codons including a first codon. The first codon is in the first polynucleotide at a first frequency relative to other synonymous codons, and is in the second polynucleotide at a second frequency relative to other synonymous codons. The first and second frequencies are different. Each polynucleotide is individually expressed in the expression system to measure an expression property value of the polynucleotides, thereby determining a property that affects expression of polynucleotides. The property is an effect that a frequency of use of one or more codons has on expression of polynucleotides in the expression system.

US Patent:

8401798, Mar 19, 2013

Filed:

Jul 31, 2008

Appl. No.:

12/184233

Inventors:

Mark Welch - Fremont CA, US
Claes Gustafsson - Belmont CA, US

Assignee:

DNA Twopointo, Inc. - Menlo Park CA

International Classification:

G01N 33/34
G06F 19/00

US Classification:

702 19, 702 20

Abstract:

Methods for determining a property that affects expression of polynucleotides are provided. A plurality of polynucleotides each encoding a polypeptide sequence is constructed. A frequency that a sequence element is used in a first polynucleotide is different than in a second polynucleotide. Each polynucleotide is expressed in an expression system to obtain an expression property value thereby constructing a dataset that contains, for each respective polynucleotide, sequence element occurrence in the respective polynucleotide and the measured expression property value of the respective polynucleotide. A model is computed that describes variation in the measured expression property values as a function of a plurality of variables and weights. From the model, a property that affects expression of polynucleotides in the expression system is determined, where the property is an effect that the frequency of occurrence of one or more sequence elements has on the expression property of polynucleotides in the expression system.