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[Pittsburgh, 03/13/2024] – We are delighted to announce that Dr. Carl Kingsford, Ocean Genomics co-founder and CEO, and Herbert A. Simon Professor of Computer Science in the Ray and Stephanie Lane Computational Biology Department at Carnegie Mellon University, has been elected as a Fellow of the International Society of Computational Biology (ISCB). This prestigious recognition underscores Carl’s exceptional contributions to the field and his continued advancements in scalable algorithmic approaches.

Carl’s journey in computational molecular biology has been nothing short of remarkable. His tireless pursuit of knowledge has led to groundbreaking advancements that resonate across academia and industry. From deciphering gene expression patterns to unraveling the intricacies of chromatin regions, Carl’s work exemplifies excellence. Carl’s has been essential in the development of Ocean Genomics’ technologies including: TxomeAI®, DiscoverAI™ and DeepSea™, and his leadership remains pivotal.

His academic research is focused on developing efficient algorithms and AI methods for extracting knowledge from large biological datasets. With contributions including accurate gene expression quantification, identification of compact chromatin regions, and enhancing large-scale sequence search efficiency. Carl’s lab continues to explore the frontiers of computer science’s role in scientific discovery, including recent advancements in pan-genomic analysis algorithms, reinforcement learning for experimental optimization, and meta-learning techniques for adapting deep neural networks to new tasks with limited data.

The ISCB has recognized Carl’s contributions which include transformative methods for gene expression quantification, k-mer-based computational methodologies, and efficient algorithms for searching unassembled sequence data. Adding “Kingsford’s theoretical understanding of algorithmic challenges and leadership in conferences further solidify his impactful role in shaping computational biology.”

The ISCB Fellows Program is a rare distinction. Introduced in 2009, it honors outstanding members who have significantly impacted computational biology. Carl now joins the ranks of visionaries who have shaped the field. Only 0.5% of last year’s ISCB membership receives this honor—a testament to Carl’s influence.

See Carnegie Mellon’s announcement of Dr. Kingsford’s election to ISCB Fellow Here

For more information on the ISCB and this year’s fellows, please visit the ISCB’s website

Our deeply integrated multi-omics analysis of a patient’s DNA and RNA together identifies critical genomic variants missed using DNA alone.

[Pittsburgh, 7/26/2023] – Ocean Genomics, the transcriptomics AI company, and Geneyx, a leading genomic analysis company, announced they were awarded a grant from the BIRD Foundation to develop and commercialize a cutting-edge, multi-omic software method. This joint effort aims to combine DNA and RNA technologies, revolutionizing the detection of genomic variants and significantly advancing disease diagnosis and drug target identification.

“Improved identification of structural variants in cancer can lead to more targeted and effective treatment options as well as advance our basic understanding of the disease and its progression. New computational algorithms and tools that can improve the sensitivity and specificity of identifying variants are clearly needed.”
Ayesha N. Shajahan-Haq, PhD, Assistant Professor of Oncology at Georgetown University’s Lombardi Comprehensive Cancer Center, and a collaborator on the project.

“Many diseases are caused by structural variants, but they can be difficult to detect, and many are missed in testing only DNA or RNA alone. By deeply integrated analysis of a patient’s DNA and RNA together, we can identify more of these variants, improve diagnosis, and determine targets for new therapies. Many thanks to the BIRD Foundation for recognizing the importance of this innovation and supporting us to develop and bring this solution to market in collaboration with Geneyx.”
Carl Kingsford, CEO Ocean Genomics

“We are thrilled to receive the grant from the BIRD Foundation and collaborate with Ocean Genomics on this groundbreaking project. Integrating DNA and RNA technologies to create a multi-omic software method holds tremendous potential for improving disease diagnosis and identifying drug targets. This advancement will pave the way for personalized medicine, enabling us to develop tailored treatment plans based on individual genetic profiles.”
David Yizhar, CEO of Geneyx

“Congratulations to Geneyx and Ocean Genomics on receiving the grant from the BIRD Foundation to support their joint project. Their innovative multi-omic software technique has the potential to revolutionize the field of genomics and significantly contribute to the diagnosis of diseases and identification of drug targets.”
Jaron Lotan, Executive Director of the BIRD Foundation

About Ocean Genomics: Ocean Genomics provides its AI platform and compute-ready data assets for advancing drug discovery and development. Its Intelligent Transcriptome™ hosts over 100,000 transcriptomic samples, many pre-trained models, and a vast and growing molecular knowledge graph. The Intelligent Transcriptome™ enables biopharma partners to discover new targets, signatures, and biomarkers, determine biological impact and MoA, and enable drug rescue and repurposing.

About Geneyx: An AI platform for human genetic analysis and interpretation. Geneyx provides advanced solutions for genomic data interpretation and analysis, empowering researchers, clinicians, and healthcare providers to gain valuable insights from genomic information.

About The BIRD Foundation: The BIRD Foundation is a renowned organization dedicated to promoting collaboration and innovation between Israeli and American companies in various industries. It provides grants and funding opportunities to support joint research and development projects, fostering technological advancements and business partnerships. With a focus on promoting cross-border cooperation, the BIRD Foundation plays a crucial role in driving economic growth and knowledge exchange between Israel and the United States.

 

Media Contacts:
Anja Taylor, Director of Marketing, Ocean Genomics
anja@oceangenomics.com

Raviv Itzhaky, CMO, Geneyx
Hq@geneyx.com

Anja Taylor
Ocean Genomics
anja@oceangenomics.com
Visit us on social media:
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PITTSBURGH, Pa. — Ocean Genomics presented our poster for their AI-driven combined transcriptomic and genomic analysis titled “Molecular Predictors and Immunomodulatory Role of Dual Checkpoint Inhibitor Blockade Using ipilimumab/nivolumab in Patients with Extensive Stage Small Cell Lung Cancer” at the American Society of Clinical Oncologists (ASCO) Annual Meeting 2023, on June 2 – June 6, 2023 at the McCormick Place Convention Center in Chicago, Illinois, and has been published in the 2023 ASCO Annual Meeting Proceedings.

Session Title: Lung Cancer—Non-Small Cell Local-Regional/Small Cell/Other Thoracic Cancers

Abstract Title: Molecular predictors and immunomodulatory role of dual checkpoint inhibitor blockade using ipilimumab/nivolumab in patients with extensive stage small cell lung cancer.

Abstract Presentation Number: 8597
Poster Board Number: 224

We had the pleasure of working with two outstanding partners at Yale University School of Medicine/Yale Cancer Center, Anne Chiang, MD, PhD (Associate Cancer Center Director for Clinical Initiatives), and Kurt Schalper, MD, PhD (Director, Translational Immuno-oncology Laboratory), in analysis of their novel single-arm, phase-2 clinical trial (NCT03670056).

The analysis combined whole exome DNA, and RNA-sequencing and was conducted using Ocean Genomics’ Intelligent Transcriptome Platform including our TxomeAI® data analysis pipeline, by members of our computational biology team.

About Ocean Genomics

Ocean Genomics is the transcriptomics AI company. We develop software, data and models and enable our partners to leverage advanced transcriptomic information with other related data and AI to advantage their discovery and development programs. We partner with cutting-edge drug developers to supply insights and evidence that enable data-driven decisions, provide confidence in the underlying biology, and increase the probability of technical and clinical success at every step. Our founders are recognized as leading experts in the fields of computational biology and AI, and developers of many of the most widely used software methods in gene expression analysis.

Our Intelligent Transcriptome computing platforms extract extensive gene expression features and analyses from raw RNA-Seq files (TxomeAI®), and automatically integrate those features with clinical and other -omics to produce accurate, actionable models, and discover drug targets and biomarkers (DiscoverAI™). Our vast database (DeepSea™) provides deeply characterized transcriptomes, curated metadata, and pre-trained AI models to add power to discovery and analyses.

For more information, please visit oceangenomics.com and connect with us on Twitter and LinkedIn.

PITTSBURGH, Pa. — Ocean Genomics’ abstract for their AI-driven transcriptome analysis titled “Novel Expression Biomarkers via Prediction of Response to FOLFIRINOX (FFX) Treatment for Pancreatic Ductal Adenocarcinoma” has been presented as a poster at the American Association for Cancer Research (AACR) Annual Meeting 2023, and has been published in the online Proceedings of the AACR.

Session Category: Molecular/Cellular Biology and Genetics
Session Title: Biomarker Discovery
Location: Section 9
Poster Board Number: 9
Abstract Presentation Number: 1400

A team of computational biologists at Ocean Genomics used the company’s Intelligent Transcriptome AI platform to discover the biomarker.

Roby A. Thomas, MD, co-author, is a medical oncologist and assistant director of medical information systems for UPMC Hillman Cancer Center.

About Ocean Genomics

Ocean Genomics is the transcriptomics AI company. We develop software, data and models and enable our partners to leverage advanced transcriptomic information with other related data and AI to advantage their discovery and development programs. We partner with cutting-edge drug developers to supply insights and evidence that enable data-driven decisions, provide confidence in the underlying biology, and increase the probability of technical and clinical success at every step. Our founders are recognized as leading experts in the fields of computational biology and AI, and developers of many of the most widely used software methods in gene expression analysis.

Our Intelligent Transcriptome computing platforms extract extensive gene expression features and analyses from raw RNA-Seq files (TxomeAI®), and automatically integrate those features with clinical and other -omics to produce accurate, actionable models, and discover drug targets and biomarkers (DiscoverAI™). Our vast database (DeepSea™) provides deeply characterized transcriptomes, curated metadata, and pre-trained AI models to add power to discovery and analyses.

For more information, please visit oceangenomics.com and connect with us on Twitter and LinkedIn.

NEW YORK; Feb. 16 , 2023 – Accenture (NYSE: ACN) has made a strategic investment, through
Accenture Ventures, in Ocean Genomics, a technology and AI company that has developed advanced
computational platforms to assist biopharma companies to discover and develop more effective
diagnostics and therapeutics.

Based in Pittsburgh, Ocean Genomics creates software that provides modeling and an understanding of
changes and variants in mRNA to enable a more accurate prediction of a patient’s biological response to
a drug. The expression of mRNA is a central biological process that occurs in every cell and helps govern
nearly all aspects of normal functioning and is often disrupted in disease. In collaboration with Ocean
Genomics, biopharma companies use the technology in in-silico drug discovery to develop treatments
based on an individual's personal biology. The global personalized medicine market size is expected to
reach more than $796 billion by 2028.

Petra Jantzer, Ph.D., a senior managing director and global lead of Accenture’s Life Sciences practice,
said, “The growth of in-silico in the discovery of individualized treatments and disease interventions will
change how we care for people around the world. We made this strategic investment in Ocean Genomics
to help biopharma companies better utilize genomic and transcriptomic data and AI in drug discovery to
develop targeted therapeutics at a higher pace and bring them to market faster.”

Scientific and technological advancements are creating breakthroughs for patient health, resulting in more
complex and personalized therapies. This New Science, a dynamic combination of the best in science
and health technology, is expected to drive 81 percent of biopharma revenue growth.

“As biopharma companies move to increasingly precise and effective therapies, they seek the talent,
technology and insights to enable more personalized, data-driven drug discovery,” said Carl Kingsford,
Ph.D., co-founder and CEO of Ocean Genomics. “With the support of, and collaboration with, Accenture,
we will be even better positioned to help the biopharma industry develop more effective diagnostics and
therapeutics.”

Ocean Genomics is now a part of Accenture Ventures’ Project Spotlight, an engagement and investment
program that connects emerging technology startups with the Global 2000 to fill strategic innovation gaps.
Project Spotlight offers extensive access to Accenture’s domain expertise and its enterprise clients,
helping startups harness human creativity and deliver on the promise of their technology.

“Ocean Genomics’ technology platform integrates gene expression, molecular features, clinical and
genomics data and advanced AI algorithms to better understand and predict the biological impact of
diseases and therapies,” said Tom Lounibos, managing director, Accenture Ventures. “With Ocean
Genomics now part of Project Spotlight, we will look to collaborate with our clients in the Life Sciences
industry and beyond on new ways to combine RNA, AI and other emerging technologies to advance drug
development, personalized medicine, and human health.”

Terms of the transaction were not disclosed.

About Accenture
Accenture is a leading global professional services company that helps the world’s leading businesses,
governments and other organizations build their digital core, optimize their operations, accelerate revenue
growth and enhance citizen services—creating tangible value at speed and scale. We are a talent and
innovation led company with 738,000 people serving clients in more than 120 countries. Technology is at
the core of change today, and we are one of the world’s leaders in helping drive that change, with strong
ecosystem relationships. We combine our strength in technology with unmatched industry experience,
functional expertise and global delivery capability. We are uniquely able to deliver tangible outcomes

because of our broad range of services, solutions and assets across Strategy & Consulting, Technology,
Operations, Industry X and Accenture Song. These capabilities, together with our culture of shared
success and commitment to creating 360° value, enable us to help our clients succeed and build trusted,
lasting relationships. We measure our success by the 360° value we create for our clients, each other,
our shareholders, partners and communities. Visit us at www.accenture.com.

About Ocean Genomics 
Ocean Genomics is the Intelligent Transcriptome company. We make the software and provide services
that enable our partners to leverage advanced transcriptomic information and AI to advantage their
discovery and development programs. We partner with cutting-edge drug developers to supply insights
and evidence that enable data-driven decisions, provide confidence in the underlying biology, and
increase the probability of technical and clinical success at every step. Our founders are recognized as
leading experts in the fields of computational biology and AI, and developers of many of the most widely
used software methods in gene expression analysis. Our Intelligent Transcriptome computing platforms
extract extensive gene expression features and analyses from raw RNA-Seq files (TxomeAI®), and
automatically integrate those features with clinical and other -omics to produce accurate, actionable
models, and discover drug targets and biomarkers (DiscoverAI™). Our vast database (DeepSea™)
provides deeply characterized transcriptomes, curated metadata, and pre-trained AI models to add power
to discovery and analyses. For more information, please visit oceangenomics.com and connect with us
on Twitter and LinkedIn.

# # #

Contacts:
Maggie Nolan
Accenture
+1.917.452.3964
margaret.d.nolan@accenture.com

Christian Harper
Accenture
+1 917.452.4417
christian.harper@accenture.com

Copyright © 2023 Accenture. All rights reserved. Accenture and its logo are trademarks of Accenture.

PITTSBURGH, Pa. — Ocean Genomics’ abstract for their AI-driven transcriptome analysis titled “Novel Expression Biomarkers via Prediction of Response to FOLFIRINOX (FFX) Treatment for Pancreatic Ductal Adenocarcinoma” has been accepted as a poster at the American Association for Cancer Research (AACR) Annual Meeting 2023, scheduled for April 14-19 in Orlando, Florida, and will be published in the online Proceedings of the AACR.

Session Category: Molecular/Cellular Biology and Genetics
Session Title: Biomarker Discovery
Session Date and Time: Monday Apr 17, 2023 9:00 AM – 12:30 PM
Location: Section 9
Poster Board Number: 9
Abstract Presentation Number: 1400

A team of computational biologists at Ocean Genomics used the company’s Intelligent Transcriptome AI platform to discover the biomarker.

Roby A. Thomas, MD, co-author, is a medical oncologist and assistant director of medical information systems for UPMC Hillman Cancer Center.

About Ocean Genomics
Ocean Genomics is the transcriptomics AI company. We make the software and provide services that enable our partners to leverage advanced transcriptomic information and AI to advantage their discovery and development programs. We partner with cutting-edge drug developers to supply insights and evidence that enable data-driven decisions, provide confidence in the underlying biology, and increase the probability of technical and clinical success at every step. Our founders are recognized as leading experts in the fields of computational biology and AI, and developers of many of the most widely used software methods in gene expression analysis.

Our Intelligent Transcriptome computing platforms extract extensive gene expression features and analyses from raw RNA-Seq files (TxomeAI®), and automatically integrate those features with clinical and other -omics to produce accurate, actionable models, and discover drug targets and biomarkers (DiscoverAI™). Our vast database (DeepSea™) provides deeply characterized transcriptomes, curated metadata, and pre-trained AI models to add power to discovery and analyses.

For more information, please visit oceangenomics.com and connect with us on Twitter and LinkedIn.

Ocean Genomics is seeking candidates for an internship program for students interested in
computer science, machine learning, computational biology, and genomics.

Funded by a grant from the Chan Zuckerberg Initiative, this program is focused on providing
opportunities for unrepresented groups in open-source scientific software development.
Selected interns will work with the Ocean team on the development and improvement of the
Salmon application suite.
Interns will have the opportunity to work directly with both the original developers and current
active contributors of the Salmon gene expression software family. As well as receiving
personal mentorship in working with open-source projects, machine learning, and computational
biology.

During this 16-week internship interns will gain experience in the biotech industry, improve their
professional and academic networks, contribute to the improvement of open science initiatives,
and be paid for their time and contributions.

The successful candidate will have experience coding in Python or R, C++ or Rust, and
familiarity with UNIX shell and tools.

This program will give preference to anyone who self-identifies as a woman, BIPOC, and/or
LGBTQ+. It is primarily designed for undergraduate US residents, but we encourage anyone
interested to apply regardless of age, education status, or residency.

To apply, please email your resume and cover letter to jobs@oceangenomics.com

Over the last year Ocean Genomics has, with the help of a grant from the Chan Zuckerberg Initiative, developed several new features and applications for the open-source Salmon application and ecosystem. These features include enhancements to single cell analysis, ONT Long Reads, Soft Clipping support, and additional BAM format support. For full details, and documentation, see below: 

Single Cell Enhancements: 

• SciSeq – Use salmon and alevin-fry to process 3-level single cell combinatorial indexing RNA sequencing (sci-RNA-seq3) reads. View Tutorial 
• SPLiT-Seq – Analyze SPLiT-pool ligation-based transcriptome sequencing (SPLiT-seq) reads using Alevin-fry. View Tutorial 
• Custom Protocols – Salmon and alevin-fry now support most single-cell RNA-seq protocols using the custom geometry flag. COMING SOON! 

NEW Quantification from Genomic Alignments Support: Mudskipper, a new addition to the Salmon ecosystem that converts genomic alignments in BAM/SAM formats to transcriptomic alignments in BAM format or RAD format. This is done by projecting alignment coordinates based on the transcript annotations passed as input in GTF format. Mudskipper is available on Github, Bioconda and Cargo. View Tutorials 

Soft Clipping and Accurate CIGAR: With Salmon’s new soft-clipping functionality, you con align read sequences to short targets or remove extraneous adapters with high precision to achieve more accurate transcript quantification results. COMING SOON! 

ONT Long Read Support: Use Salmon to quantify Oxford Nanopore Technologies (ONT) long-reads (both cDNA and direct RNA) which now has an enhanced alignment error model specially designed to work with long-reads. View Tutorial

 For more information, documentation, tutorials or to download the latest version of Salmon visit https://combine-lab.github.io/salmon/  

PITTSBURGH, Pa. — Ocean Genomics has been awarded a grant by the Chan Zuckerberg Initiative (CZI) for the implementation of an internship program designed to increase the accessibility, inclusion and diversity of underrepresented communities in genomic and transcriptomic open-source biotechnology projects.

The award will allow Ocean Genomics to provide opportunities to women, BIPOC, and LGBTQ+ individuals to participate in improving open-source projects used for quantifying gene expression. Gene expression analysis compares the RNA expression levels of multiple genes in samples under various conditions. Such analyses can provide insight into variations in gene expression between healthy and diseased samples and enable the discovery and validation of multidimensional biomarkers for disease. Interns supported by this award will extend and develop new use cases for software called Salmon and Alevin, which are two widely used packages for quantifying the amount of expression from bulk RNA-seq and single-cell RNA-seq, respectively.

“These internships provide the opportunity to develop deep scientific coding skills while gaining practical experience in a biotech organization and developing stronger professional networks, and at the same time they strengthening our work advancing transcriptomic analysis software with new skills and perspectives.” said Carl Kingsford, CEO, Ocean Genomics.
The award will directly support the creation of several paid internship opportunities for undergraduates in computational biology, software engineering, and machine learning. The internship program will provide the mentoring necessary to enable selected candidates to participate in making significant contributions to these popular open-source RNA-seq analysis tools. Interns will have opportunities to develop their academic and professional networks while working at Ocean Genomics and interacting with partners and collaborators.

“We are thrilled to have the opportunity to develop this internship program. This means a lot to me personally, and I look forward to helping create opportunities and representation that ripple out long past the life of any single project.” said Maya Bishop, Project Manager at Ocean Genomics.

Ocean Genomics is adamant about ensuring the biomedical open-source community is a welcoming and accessible space for all contributors. We understand that there are often systemic barriers for underrepresented communities to participate, and we are committed to actively making space for their voices and contributions to be recognized in this field.

About Ocean Genomics

Ocean Genomics’ AI-driven intelligent transcriptome platform and empower discovery and translational research. The company was founded by authors and inventors of several leading new-generation transcriptome analysis applications used by tens of thousands of researchers world-wide with over 1,500 citations. Ocean Genomics works to speed and improve drug development through its advanced transcriptome analysis methods.

About the Chan Zuckerberg Initiative

The Chan Zuckerberg Initiative was founded in 2015 to help solve some of society’s toughest challenges — from eradicating disease and improving education, to addressing the needs of our local communities. Our mission is to build a more inclusive, just, and healthy future for everyone. For more information, please visit www.chanzuckerberg.com

PITTSBURGH, PA, March 24, 2021 — (BUSINESS WIRE) — Ocean Genomics (Pittsburgh, PA), a world leader in AI-based gene expression analysis and RNA biomarker development, and Geninus (Seoul, South Korea), a leading full-service genomics laboratory, announce a strategic partnership for the purpose of co-developing RNA-based biomarkers and advancing research and clinical applications with hospital, academic and biotechnology clients.

The two companies will launch in Korea Ocean Genomics’ advanced AI-based transcriptome analysis and biomarker platform (txome.ai) as both a cloud-based and on-premises solution. Geninus will leverage the txome.ai platform to expand its CancerSCAN clinical diagnostics platform for its hospital customers, and for biomarker discovery services with academic and biotechnology clients. Ocean Genomics and Geninus will also partner on the co-development of a series of RNA-informed multidimensional biomarkers for research and clinical use.

“We are excited to embark on this partnership with Geninus” said Carl Kingsford, co-founder and CEO, Ocean Genomics. “Ocean Genomics’ expertise in AI and computational method development, together with Geninus’ translational experts and access to data is a powerful combination. Working together, we can advance the field and enhance the uses of RNA biomarkers in clinical and research applications – and provide essential insights for clinicians who care for cancer patients.”

Dr. Woong Yang Park, CEO, Geninus, said, “Genome analysis for precision cancer medicine is becoming an essential process in hospitals. Gene expression analysis on tumor tissue RNA can deliver critical information for targeted therapy and immunotherapy. We expect to advance precision medicine by incorporating Ocean Genomics’ txome.ai into Geninus’ clinical diagnostics platform, CancerSCAN. We look forward to working with Ocean Genomics in co-developing biomarkers and expanding services to our academic and biotechnology customers.”

About Ocean Genomics

Ocean Genomics’ mission is to enable drug development and personalized medicine by combining AI with advanced gene-expression analysis to determine rich gene expression signatures and develop RNA-informed multidimensional biomarkers. DNA is a predictor of what might happen in the future, while RNA reveals what’s happening now, making it an essential component in drug development, screening and monitoring, diagnosis and treatment selection. Analyzing RNA requires far more advanced software and computational methods than analyzing DNA.

Ocean Genomics provides the required specialized expertise in AI and transcriptomic analysis and advanced computational software solutions required to power discovery and development programs with life sciences companies and academic researchers. Ocean Genomics provides a self-service, fully configured, cloud-based platform, txome.ai, which provides advanced transcriptome analysis and biomarker generation.

For more information, please visit oceangenomics.com and connect with us on Twitter and LinkedIn.

About Geninus

Geninus provides clinical genome analysis solutions for precision medicine clinics. CancerSCAN, a cancer genome diagnostics platform, is used to inform personalized cancer treatment with targeted therapeutics and immunotherapy in major hospitals in Korea and Japan. CancerSCAN includes an information management system, a bioinformatics pipeline, variant annotation, clinical reports, and datacenter. OncoSTATION, a user interface for CancerSCAN, can be installed within hospital information systems. In addition, Geninus operates a single cell genome analysis platform called Celinus for biomarker discovery. Through collaborations with clinicians and pharmaceutical companies, Celinus can unearth new druggable targets or diagnostic markers in tumor microenvironment cells.

For more information, please visit kr-geninus.com.