Jian Peng

US Patent:

20210297090, Sep 23, 2021

Filed:

Jun 8, 2021

Appl. No.:

17/342231

Inventors:

Bonnie Berger Leighton - Newtonville MA, US
Deniz Yorukoglu - Cambridge MA, US
Jian Peng - Cambridge MA, US

International Classification:

H03M 7/30

Abstract:

A method of compressive read mapping. A high-resolution homology table is created for the reference genomic sequence, preferably by mapping the reference to itself. Once the homology table is created, the reads are compressed to eliminate full or partial redundancies across reads in the dataset. Preferably, compression is achieved through self-mapping of the read dataset. Next, a coarse mapping from the compressed read data to the reference is performed. Each read link generated represents a cluster of substrings from one or more reads in the dataset and stores their differences from a locus in the reference. Preferably, read links are further expanded to obtain final mapping results through traversal of the homology table, and final mapping results are reported. As compared to prior techniques, substantial speed-up gains are achieved through the compressive read mapping technique due to efficient utilization of redundancy within read sequences as well as the reference.

US Patent:

20210118097, Apr 22, 2021

Filed:

Feb 8, 2019

Appl. No.:

16/968364

Inventors:

- Urbana IL, US
Jian Peng - Champaign IL, US
Yunan Luo - Urbana IL, US

Assignee:

THE BOARD OF TRUSTEES OF THE UNIVERSITY OF ILLINOIS - Urbana IL

International Classification:

G06T 5/00
G06T 5/50
G06T 7/10

Abstract:

Aspects of the subject disclosure may include, for example, performing, by a processing system, image fusion using two or more groups of images to generate predicted images, wherein each group of the two or more groups has one of a different resolution, a different frequency temporal pattern or a combination thereof than another of the two or more groups. Gap filling can be performed by the processing system to correct images of the two or more groups. Additional embodiments are disclosed.

US Patent:

20200265917, Aug 20, 2020

Filed:

Jan 25, 2018

Appl. No.:

16/481061

Inventors:

- Cambridge MA, US
Susan Lindquist - Brookline MA, US
Bonnie A. Berger - Newtonville MA, US
Ernest Fraenkel - Newton MA, US
Jian Peng - Champaign IL, US

International Classification:

G16B 5/00
G16B 30/10
G01N 33/50
C12Q 1/02

Abstract:

Disclosed are methods, systems, cells and compositions directed to modeling a physiologic or pathologic process in an animal using a set of yeast genes analogous to a set of animal genes and augmenting the physiologic or pathologic process in the animal with predicted gene interactions based on the interactions between the set of yeast genes. Also disclosed are methods of screening for and using therapeutics for neurodegenerative proteinopathies.

US Patent:

20190348998, Nov 14, 2019

Filed:

Mar 12, 2019

Appl. No.:

16/299263

Inventors:

Bonnie Berger Leighton - Newtonville MA, US
Deniz Yorukoglu - Cambridge MA, US
Jian Peng - Cambridge MA, US

International Classification:

H03M 7/30

Abstract:

A method of compressive read mapping. A high-resolution homology table is created for the reference genomic sequence, preferably by mapping the reference to itself. Once the homology table is created, the reads are compressed to eliminate full or partial redundancies across reads in the dataset. Preferably, compression is achieved through self-mapping of the read dataset. Next, a coarse mapping from the compressed read data to the reference is performed. Each read link generated represents a cluster of substrings from one or more reads in the dataset and stores their differences from a locus in the reference. Preferably, read links are further expanded to obtain final mapping results through traversal of the homology table, and final mapping results are reported. As compared to prior techniques, substantial speed-up gains are achieved through the compressive read mapping technique due to efficient utilization of redundancy within read sequences as well as the reference.

US Patent:

20190171625, Jun 6, 2019

Filed:

Feb 5, 2019

Appl. No.:

16/267778

Inventors:

Bonnie Berger Leighton - Newtonville MA, US
Deniz Yorukoglu - Cambridge MA, US
Yun William Yu - Cambridge MA, US
Jian Peng - Cambridge MA, US

International Classification:

G06F 16/174
G16B 30/00
G16C 99/00
G16B 50/00

Abstract:

This disclosure provides for a highly-efficient and scalable compression tool that compresses quality scores, preferably by capitalizing on sequence redundancy. In one embodiment, compression is achieved by smoothing a large fraction of quality score values based on k-mer neighborhood of their corresponding positions in read sequences. The approach exploits the intuition that any divergent base in a k-mer likely corresponds to either a single-nucleotide polymorphism (SNP) or sequencing error; thus, a preferred approach is to only preserve quality scores for probable variant locations and compress quality scores of concordant bases, preferably by resetting them to a default value. By viewing individual read datasets through the lens of k-mer frequencies in a corpus of reads, the approach herein ensures that compression “lossiness” does not affect accuracy in a deleterious way.

US Patent:

20170147597, May 25, 2017

Filed:

Apr 27, 2015

Appl. No.:

14/697114

Inventors:

Bonnie Berger Leighton - Newtonville MA, US
Deniz Yorukoglu - Cambridge MA, US
Y. William Yu - Cambridge MA, US
Jian Peng - Cambridge MA, US

International Classification:

G06F 17/30
G06F 19/28
G06F 19/22

Abstract:

This disclosure provides for a highly-efficient and scalable compression tool that compresses quality scores, preferably by capitalizing on sequence redundancy. In one embodiment, compression is achieved by smoothing a large fraction of quality score values based on k-mer neighborhood of their corresponding positions in read sequences. The approach exploits the intuition that any divergent base in a k-mer likely corresponds to either a single-nucleotide polymorphism (SNP) or sequencing error; thus, a preferred approach is to only preserve quality scores for probable variant locations and compress quality scores of concordant bases, preferably by resetting them to a default value. By viewing individual read datasets through the lens of k-mer frequencies in a corpus of reads, the approach herein ensures that compression “lossiness” does not affect accuracy in a deleterious way.

US Patent:

20160191076, Jun 30, 2016

Filed:

Aug 27, 2015

Appl. No.:

14/837567

Inventors:

Bonnie Berger Leighton - Newtonville MA, US
Deniz Yorukoglu - Cambridge MA, US
Jian Peng - Cambridge MA, US

International Classification:

H03M 7/30
G06F 17/30

Abstract:

A method of compressive read mapping. A high-resolution homology table is created for the reference genomic sequence, preferably by mapping the reference to itself. Once the homology table is created, the reads are compressed to eliminate full or partial redundancies across reads in the dataset. Preferably, compression is achieved through self-mapping of the read dataset. Next, a coarse mapping from the compressed read data to the reference is performed. Each read link generated represents a cluster of substrings from one or more reads in the dataset and stores their differences from a locus in the reference. Preferably, read links are further expanded to obtain final mapping results through traversal of the homology table, and final mapping results are reported. As compared to prior techniques, substantial speed-up gains are achieved through the compressive read mapping technique due to efficient utilization of redundancy within read sequences as well as the reference.