Pacific BioSciences of California, Inc. vs THE CHINESE UNIVERSITY OF HONG KONG et al.

Termination Decision: Post-DI Settlement

Joint Motion to Terminate IPR2024-00028

Joint Request 317(b) IPR2024-00028

Updated Exhibit List

EX2061 - CONFIDENTIAL Assignment and Settlement Agreement

EX2062 - CONFIDENTIAL Mutual Release

Other: Hearing transcript

Petitioner's Objections to Evidence filed with Reply to Motion to Exclude

Petitioner's Updated Exhibit List

Petitioner's Demonstratives

Patent Owner Demonstratives

Patent Owner Reply re Motion to Exclude

EX2058 - Page not found - GitHub

EX2059 - Page not found - PacBio

EX2060 - Candeloro Declaration to Reply re Motion to Exclude

Patent Owner Updated Exhibit List

Petitioner's Reply in Support of Motion to Exclude

ORDER Setting Oral Argument

Petitioner's Opposition to Patent Owner’s Motion to Exclude

Patent Owner's Opp to Motion to Exclude

Petitioner's Motion to Exclude

Patent Owner's Motion to Exclude

Patent Owner's Request for Oral Argument

Petitioner's Request for Oral Argument

Patent Owner Sur-Reply

Patent Owner's Objections to Petitioner's Evidence

Petitioner's Reply to Patent Owner's Response

DNA Modification Detection Using R

Pacific Biosciences Press Release

Deposition Transcript of Dr. Peter Koo

Updated Notice of Deposition of Dr. Koo

Notice of Deposition of Dr. Koo

Petitioner's Second Objections to Evidence

EX2033 - Dessimoz Notice of Deposition

EX2034 - Novbakhtian Notice of Deposition

EX2035 - Measuring DNA Methylation

EX2036 - Novbakhtian LinkedIn Profile

EX2037 - Dessimoz Transcript 2024-06-21

EX2038 - Beaulaurier Nat Rev Genet 2019

EX2039 - Birknerova Cancers 2022

EX2040 - Gouil Essays in Biochem 2019

EX2041 - Koo Supplemental Declaration

EX2042 - Sang Methods Mol Biol 2021

EX2043 - Wang Biomolecules 2023

EX2044 - Cheung Nat Commun 2023

EX2045 - How nanopore sequencing works

EX2046 - What is Oxford Nanopore Technology sequencing

EX2047 - ESHG-2022 Blethrow-Poster

EX2048 - ESHG Conference 2022 Website

EX2049 - ESHG 2022 PacBio team

EX2050 - Searle Nucleic Acids 2023

EX2051 - Gigante Nucleic Acids Res 2019

EX2052 - Koo CV 2024-07-26

EX2053 - PacBio Press Release

EX2054 - Claim Chart 794 Patent Claim 1

EX2055 - List of materials reviewed for Koo Supplemental Decl

EX2056 - Candeloro Declaration

Patent Owner Response IPR2024-00028

Joint Stipulation to Extend Deadlines

Notice of Deposition - Dessimoz

Notice of Deposition - Novbakhtian

PO Objections to Petitioner's Evidence IPR2024-00028

Petitioner's Objections to Evidence

Institution Decision: Grant

SCHEDULING ORDER

Petitioner's Updated Exhibit List

U.S. Patent No. 11,091,794 to Lo (“the ’794 patent”)

U.S. Patent No. 11,844,666 to Flusberg et al. (“Flusberg-666”)

U.S. Patent Application No. 17/891,899 File History (Part 1)

U.S. Patent Application No. 17/891,899 File History (Part 2)

U.S. Patent Application No. 17/891,899 File History (Part 3)

U.S. Patent Application No. 17/891,899 File History (Part 4)

U.S. Patent Application No. 17/891,899 File History (Part 5)

U.S. Patent Application No. 17/891,899 File History (Part 6)

EX2001 - US11091794 Color Drawings_part_1

EX2001 - US11091794 Color Drawings_part_2

EX2002 - Koo Declaration re 794 IPR2024-00028

EX2003 - Peter Koo CV

EX2004 - Li BAM paper

EX2005 - Suzuki

EX2006 - Zheng and Casari, Feature Engineering EXCERPTS

EX2007 - Web page - ccb.jhu.edu-StringTie

EX2008 - Web page - gatk.broadinstitute.org-GATK

EX2009 - Web page - gatk.broadinstitute.org-HaplotypeCaller

EX2010 - Web page - Genome Browser BAM Track Format

EX2011 - Web page - hbctraining.github.io-Peak calling with MACS2

EX2012 - YouTube PacBio Data Deep Dive 1Aqnlq-Nwyk

EX2013 - Screencapture YouTube PacBio Structures Deep Dive 1aqnLQ-nwYk

EX2014 - Screencapture PacBio Video Data Deep Dive

EX2015 - Transcript - PacBio Data Deep Dive

EX2016 - Redacted Version of Complaint

EX2017 - Motley Fool Earnings Call Transcript (Complaint Ex. C)

EX2018 - PacBio Children's Mercy Press Release (Complaint Ex. E)

EX2019 - Screencapture PacBio Products - Epigenetics (Complaint Ex. F)

EX2020 - YouTube PacBio HiFi Sequencing - See What Youve Been Missing d2an7LXhPSU

EX2021 - Screencapture YouTube PacBio HiFi Sequencing - See What Youve Been Missing

EX2022 - Screencapture PacBio HiFi Sequencing - See What Youve Been Missing

EX2023 - Transcript - PacBio HiFi Sequencing See What You've Been Missing

EX2024 - YouTube PacBio Methylation Detection rT231BCp6Ro

EX2025 - Screencapture YouTube PacBio Methylation Detection

EX2026 - Transcript - PacBio Methylation Detection with PacBio HiFi Sequencing

EX2027 - Screencapture PacBio pacb.com-blog-smrt-cell

EX2028 - SMRT Link Release Notes (Complaint Exhibit D)

EX2029 - US20100221716A1 (Flusberg)

EX2030 - Candeloro Declaration

EX2031 - Baker Declaration

EX2032 - Koo List of Materials Considered

Patent Owner Preliminary Response

Notice : Power of Attorney

Notice : Mandatory Notice

Notice: Notice filing date accorded

Curriculum Vitae of Christophe Dessimoz, Ph.D.

U.S. Patent Application No. 16/995,607 File History - Part 1

U.S. Patent Application No. 16/995,607 File History - Part 2

U.S. Patent Application No. 16/995,607 File History - Part 3

U.S. Patent Application No. 17/379,544 File History - Part 1

U.S. Patent Application No. 17/379,544 File History - Part 2

U.S. Patent Application No. 17/379,544 File History - Part 4

Flusberg, et al., “Direct Detection of DNA Methylation During Single-molecu

Clark, et al. “Direct Detection and Sequencing of Damaged DNA Bases” Genome

Loomis et al., “Sequencing the Unsequenceable: Expanded CGG-repeat Alleles

Schadt, et al., “Modeling Kinetic Rate Variation in Third Generation DNA Se

BAM Format Specification for PacBio, PacBioFileFormats 5.0 Documentation, h

SAM/BAM Specification Working Group, Sequence Alignment/Map Format Specific

Davis et al., “Entering the Era of Bacterial Epigenomics with Single Molecu

Take2 Tech, Ltd. v. Pac. Biosciences of Cal., Inc., DDE-1-22-cv-01595, Infr

Feng, et al, “Detecting DNA modifications from SMRT Sequencing Data by Mode

“Detecting DNA Base Modifications Using Single Molecule, Real-Time Sequenci

Zou et al., “A Primer on Deep Learning in Genomics” Nature Genetics, 51(1)

Pacific Biosciences Template Preparation and Sequencing Guide, https://www.

Pacific Biosciences kineticsTools Manual, http://web.archive.org/web/201708

Jonas Korlach & Stephen W. Turner, “Single-Molecule Sequencing” in Encyclop

GenomeWeb, “PacBio Reveals Beta System Specs for RS; Says Commercial Releas

Jacob Schreiber et al., “Error Rates for Nanopore Discrimination among Cyto

Langlotz, A Roadmap for Foundational Research on Artificial Intelligence in

Miotto et al., “Deep Learning for Healthcare: Review, Opportunities and Cha

Tse et al., “Genome-wide Detection of Cytosine Methylation by Single Molecu

Tiernan Ray, “AI is Changing the Entire Nature of Compute,” ZDNet, http://w

Wenger et al., “Accurate Circular Consensus Long-read Sequencing Improves V

Pacific Biosciences, PacBioFileFormats Documentation (Feb. 2022) (“PacBioFi

Lau et al., “LongISLND: in silico Sequencing of Lengthy and Noisy Datatypes

Tahir et al., “iRNA-PseKNC(2methyl): Identify RNA 2’-O-methylation Sites by

DeepVariant Usage Guide, https://github.com/google/deepvariant/blob/42b9c77

U.S. Patent Application No. 18/189,084 File History

Liu et al., “Accurate Detection of m6A RNA Modifications in Native RNA Sequ

First Declaration of Nathaniel E. Frank-White

Second Declaration of Nathaniel E. Frank-White

Declaration of Mozhgan Novbakhtian

GitHub, PacBio BAM 3.0, https://github.com/PacificBiosciences/PacBioFileFor

GitHub, PacBio BAM 5.0, https://github.com/PacificBiosciences/PacBioFileFor

EX1005 - 17379544 File History - Part 3.pdf

Liu et al., “Detection of DNA Base Nodifications by Deep Recurrent Neural N

EXPUNGED

U.S. Patent No. 9,175,338 to Flusberg et al. (“Flusberg-338”)

U.S. Patent Pub. No. 2016/0326593 to Clement et al. (“Clement”)

U.S. Patent Publication No. 2016/0208241 to Tsai et al. (“Tsai”)

Int. Appl. Publ. No. WO 2012/065043 (“Flusberg PCT”)

Eid et al., “Real-time DNA sequencing from single polymerase molecules,” Sc

PacBio Sequencing – How it Works video file

Declaration of Dr. Christophe Dessimoz

Petitioner's Power of Attorney

Petition : as filed