Lead Bioinformatics Engineer
About the job
- An M.S. or Ph.D. in Bioinformatics, Computational Biology, Genomics, Computer Science, or a closely related field is required.
- At least 7 years of hands-on bioinformatics engineering experience, including production-grade pipeline development and deployment, is required.
- Deep expertise in genomic data types and file formats such as FASTQ, BAM/CRAM, VCF, BED, HDF5, and AnnData, and in the computational tools used to process them, is required.
- Demonstrated experience building and operating cloud-native bioinformatics workflows using AWS, Azure, or GCP and workflow managers such as Nextflow, Snakemake, or WDL is required; AWS is preferred.
- Strong programming proficiency in Python and/or R, plus experience in shell scripting for pipeline automation, is required.
- Familiarity with public genomic data repositories and their access and compliance frameworks, such as dbGaP, UK Biobank, and TCGA, is required.
- The candidate must be able to manage complex external relationships and data access processes, including data use agreements, Data Access Committee applications, and compliance reporting.
- The candidate must be comfortable engaging with both scientific and technical audiences.
- Own and operate Flagship's portfolio bioinformatics platform stack, including CodeOcean, Sequera (Nextflow Tower), Tamarind.bio, and adjacent tools, serving as primary administrator, configurator, and first point of escalation for platform-level issues.
- Build and maintain reusable, production-quality pipeline templates and starter deployments for portfolio companies and Pioneering Medicines teams to adopt without bespoke engineering for each use case.
- Translate Pioneering Intelligence's open-source bioinformatics library contributions into deployable, documented workflows that scientists and informatics teams can operate independently.
- Establish and maintain standards for bioinformatics data formats, pipeline documentation, and code contribution guidelines to ensure internally developed and contributed workflows meet consistent reproducibility and portability standards.
- Guide portfolio company scientists and informatics teams in building and adapting pipelines within the platform framework, enabling scientific self-sufficiency at the company level.
- Partner with Scientific Cloud Engineering to align bioinformatics platform infrastructure with enterprise cloud architecture standards, including identity management, security controls, and cost governance.
- Serve as Flagship's primary contact with external genomic and biomedical data consortia and repositories, including UK Biobank, the Francis Crick Institute, dbGaP, GTEx, and ENCODE.
- Manage the lifecycle of data access agreements, including Data Access Committee applications, data use agreements, renewals, and compliance reporting, in coordination with legal and compliance teams.
- Monitor consortium partners' roadmaps and emerging datasets, surfacing data access opportunities aligned with portfolio scientific needs.
- Coordinate onboarding of consortium-sourced datasets into Flagship's data environment, working with data engineering teammates on ingestion, governance metadata, and access controls.
- Build relationships with data operations and scientific leads at partner institutions to streamline access and deepen collaboration.
- Work with Data & Informatics Engineering teammates, including data architects, data engineers, and software engineers, to integrate bioinformatics workloads into shared data platforms, pipelines, and catalogs.
- Collaborate with Research Systems, Lab Systems, and informatics counterparts across Flagship and portfolio companies to translate scientific requirements into platform capabilities.
- Partner with Pioneering Intelligence data science and machine learning teams to format, annotate, and make processed omics datasets accessible for downstream analytical and artificial intelligence workflows.
- Participate in cross-team technical reviews, architecture discussions, and sprint ceremonies as a contributing member of the Scientific Cloud team.
- Contribute to shared standards, playbooks, and documentation for the broader Scientific Cloud organization and portfolio.
- Act as an internal subject matter expert on genomics, transcriptomics, and multi-omics data ecosystems, advising portfolio company scientists and IT counterparts on best practices.
- Evaluate and recommend computational resources, including high-performance computing, cloud batch, and spot instances, for large-scale genomic workloads.
- Stay current with bioinformatics tooling, reference datasets, and public database standards, contributing to platform evolution.
- Contribute to technical documentation, onboarding materials, and knowledge-sharing forums to build institutional bioinformatics capability.
- Experience administering or deploying managed bioinformatics platforms such as CodeOcean, Sequera/Nextflow Tower, Tamarind.bio, or similar cloud-native workflow environments.
- Experience in a multi-company or portfolio environment supporting scientific teams with varying computational needs.
- Familiarity with single-cell omics platforms such as 10x Genomics, Seurat, Scanpy, and scVelo, and with spatial transcriptomics workflows.
- Experience with containerization using Docker or Singularity and container orchestration for HPC/cloud hybrid environments.
- Knowledge of data governance frameworks, catalog tools such as DataHub and Collibra, and lineage tracking for scientific data.
- Experience contributing to or maintaining open-source bioinformatics libraries or shared code repositories.
- Prior experience in a biotechnology, pharmaceutical, or life sciences technology organization.
About the company
Flagship Pioneering funds and incubates life-sciences ventures by creating bioplatform companies, forming early-stage NewCos and guiding them to GrowthCos. It identifies broad scientific platforms that can generate multiple products, builds companies around these platforms, and moves them from inception to growth to assemble a multi-product portfolio. Unlike traditional investors, it creates new ventures from scratch and shepherds them through staged development, building a pipeline of category-leading biotech and life-science companies. Its goal is to develop a diverse portfolio of platform-based companies that advance human health and sustainability by delivering multiple products.
Company Size
501-1,000
Company Stage
N/A
Total Funding
$11B
Headquarters
Cambridge, Maryland
Founded
2000
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Simplify's Take
What believers are saying
- Sept. 23, 2026 ONTARGET gives up to $47 million over five years.
- Apr. 1, 2026 AWS partnership gives companies cloud credits, support, and AI infrastructure.
- Apr. 21, 2026 Serif launched with $50 million for modified DNA medicines.
What critics are saying
- Sept. 28, 2026 Inari settled Corteva litigation, surrendered IP, and faces licensing costs.
- Mar. 6, 2026 Alltrna cut 19 workers, and CEO Michelle Werner exited.
- If Lila or Serif disappoint, Flagship's platform premium collapses and LP fundraising stalls.
What makes Flagship Pioneering unique
- Sept. 23, 2026 DoW contract proves Flagship sells a platform, not single startups.
- Flagship's 40-plus-company ecosystem bundles AI, translational science, and drug development under one roof.
- Aug. 3, 2026 leadership hires add global partnerships and fundraising firepower.
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Benefits
Professional Development Budget
Flexible Work Hours
Company News
Flagship Pioneering awarded first-of-its-kind contract by Department of War to advance next-generation medical countermeasure technologies against evolving biological threats. Sep 23, 2026, 06:30 ET Agreement marks strategic shift in how Department of War partners with the private sector, with Flagship providing access to broad range of innovative platforms against evolving threats Award of up to $47 million over a five-year period; initial projects include Flagship-founded Apriori Bio and Prologue Medicines CAMBRIDGE, Mass., Sept. 23, 2026 /PRNewswire/ - Flagship Pioneering, a scientific innovation engine for transformative platforms and products, has been awarded a first-of-its-kind contract by the Department of War (DoW) under the ONTARGET - Operationalizing Novel Technologies for Advanced Rapid Generation of Effective Medical Countermeasures (MCM) - program. The award of up to $47 million will be executed over a five-year period, beginning with a select set of initial projects and allowing for additional projects to be initiated throughout the contract term. The strategic partnership will leverage Flagship's unique ecosystem of more than 40 pioneering companies and technological capabilities across translational science, platform engineering, drug development, enabling technologies, and AI/machine learning to support the rapid testing of tailored solutions across a broad range of DoW MCM priorities and evolving threats. The initial projects include Flagship-founded companies Apriori Bio and Prologue Medicines. The award will be administered by Flagship Health Security Corporation, a new subsidiary of Flagship Pioneering created specifically to facilitate government partnerships. "Through the ONTARGET program, we can harness our nation's greatest strength - its unmatched capacity to invent and scale breakthrough technologies - to stay ahead of evolving threats and safeguard national security," said Noubar Afeyan, Ph.D., Founder and CEO of Flagship Pioneering. "By mobilizing Flagship's ecosystem of first-in-category, AI-enabled biotechnologies, we are not only advancing next-generation countermeasures, we will also be building the innovation infrastructure to define America's strategic advantage for decades ahead." The agreement marks a strategic shift in how DoW partners with the private sector, establishing a new, more agile model for defense solutions. Instead of contracting for a specific product, DoW and Flagship will evaluate a broad range of cutting-edge platform technologies from Flagship's ecosystem of companies for their potential to accelerate and optimize medical countermeasure development and address an evolving range of DoW warfighter protection priorities. The ONTARGET program is managed by the Joint Science and Technology Office (JSTO) within the Department of War's Chemical and Biological Defense Program. The ONTARGET program aims to stay ahead of evolving threats - adaptive and engineered - by partnering with the private sector in unique and powerful ways to enhance medical countermeasure performance, accelerate development timelines, and strengthen response effectiveness. "Ultimately, our goal is to get the best technology into the hands of our warfighters as quickly as possible. The ONTARGET agreement provides a new pathway to do just that, by identifying and maturing the most promising biotechnologies the private sector has to offer," said Robert Kristovich, Ph.D., Director of JSTO at the Defense Threat Reduction Agency. "This keeps our military personnel equipped to face any biological challenge." The program targets several priority capability areas essential for national defense preparedness: * Broad-spectrum countermeasures against emerging threats * Precision delivery technologies to improve efficacy and reduce side effects * Toxin-neutralizing platforms for enhanced protection * Novel approaches to immune enhancement and viral pathway disruption * Integration of AI/ML to optimize medical countermeasure discovery and development Initial Research Projects The award will provide proof-of-concept funding for a select set of cutting-edge projects, each leveraging distinct Flagship technologies. The Department of War will have the opportunity to advance additional projects throughout the five-year agreement with Flagship. Apriori Bio - Broadly Protective Medical Countermeasures Apriori Bio will apply its Octavia(TM) platform, a biology-enabled AI platform for the design of variant-resilient countermeasures, to rapidly generate one or more stable, cross-protective candidates. By anticipating viral evolution, the platform can enable faster, more resilient countermeasure development, reducing response timelines, and strengthening biological threat readiness against evolving and engineered threats. Prologue Medicines - Immunomodulatory Protein Discovery Prologue Medicines' DELVE platform applies advanced AI approaches to mine millions of viral proteins and identify evolutionarily-optimized functions that can modulate and enhance human immune responses. This project seeks to leverage DELVE to strengthen immune resilience and enable rapid, adaptable countermeasures that can be deployed across a broad range of emerging and engineered threats. About Flagship Pioneering Flagship Pioneering invents and builds platform companies, each with the potential for multiple products that transform human health, sustainability and beyond. Since its launch in 2000, Flagship has originated and fostered more than 100 scientific ventures, operating with $14 billion of assets under its direction as of its latest capital raise, announced in July 2024. The current Flagship ecosystem comprises more than 40 companies, including Generate Biomedicines, Inari, Lila Sciences, Moderna, Sana Biotechnology, Tessera Therapeutics and Valo Health. Flagship Health Security Corporation is a subsidiary of Flagship Pioneering created specifically to facilitate government partnerships. Media contact SOURCE Flagship Pioneering
Chiesi appoints David Khougazian as Group CEO. Khougazian most recently served as Executive Partner, Growth, and Head of Global Engagement at Flagship Pioneering Chiesi Group has appointed David Khougazian as Group Chief Executive Officer (CEO). Khougazian joins Chiesi following an international career spanning more than 25 years across the global healthcare and life sciences sectors. Most recently, he served as Executive Partner, Growth, and Head of Global Engagement at Flagship Pioneering, where he supported the growth and development of science-driven healthcare companies and worked closely with leadership teams on long-term value creation, partnerships, financing and organisational development. Following a thorough selection process led by the Board of Directors, Khougazian will succeed Interim Group CEO Jean-Marc Bellemin, who has successfully led the Group since 15 May 2026, while also continuing in his permanent role as Group CFO. Maria Paola Chiesi, Chiesi Group Chair, commented: "Innovation has always been at the heart of Chiesi's mission and long-term vision. David's appointment reflects our ambition to accelerate this journey and strengthen Chiesi's ability to innovate in a healthcare environment that is changing faster than ever. "David brings a unique combination of global healthcare leadership, operational experience and exposure to some of the most dynamic areas of biotech innovation, which makes him exceptionally well positioned to guide Chiesi through this next chapter. Khougazian commented: "The healthcare landscape is evolving rapidly, creating extraordinary opportunities to advance innovation and transform patient outcomes. I look forward to working alongside Chiesi colleagues around the world to further strengthen the Group's innovation capabilities, advance its pipeline and partnerships, and create lasting value for patients, healthcare systems and society." 16th September 2026 Latest intelligence.
Chiesi appoints David Khougazian as Group Chief Executive Officer to lead the next phase of innovation-driven growth. Business Wire Published Sep 15, 2026 Highlights * David Khougazian appointed Group Chief Executive Officer to lead Chiesi's next phase of innovation-driven growth, effective 15 October 2026. * Bringing over 25 years of international healthcare leadership experience and a strong track record in innovation and transformation, David joins Chiesi from Flagship Pioneering. PARMA, Italy - Chiesi Group (Chiesi) today announced the appointment of David Khougazian as Group Chief Executive Officer (CEO), effective 15 October 2026. David joins Chiesi following a distinguished international career spanning more than 25 years across the global healthcare and life sciences sectors. Most recently, he served as Executive Partner, Growth, and Head of Global Engagement at Flagship Pioneering, where he supported the growth and development of science-driven healthcare companies and worked closely with leadership teams on long-term value creation, partnerships, financing and organizational development. Top Stories Interested in more newsletters? Browse here. Following a thorough selection process led by the Board of Directors, David will succeed Interim Group CEO Jean-Marc Bellemin, who has successfully led the Group since 15 May 2026, while also continuing in his permanent role as Group CFO. Maria Paola Chiesi , Chiesi Group Chair, commented: "We are delighted to welcome David to Chiesi at a time of strong momentum for the company. Innovation has always been at the heart of Chiesi's mission and long-term vision. David's appointment reflects our ambition to accelerate this journey and strengthen Chiesi's ability to innovate in a healthcare environment that is changing faster than ever. He brings a unique combination of global healthcare leadership, operational experience and exposure to some of the most dynamic areas of biotech innovation, which makes him exceptionally well positioned to guide Chiesi through this next chapter. On behalf of the Board, I would like to express my sincere gratitude to Jean-Marc Bellemin for his commitment and stewardship during this transition period. I would also like to thank the entire Group Executive Leadership Team for their dedication and collective leadership, which have been instrumental in maintaining the Group's focus and preparing the organization for the next steps." David Khougazian commented: "I am honored and excited to join Chiesi, a company widely recognized for its strong values, scientific excellence, entrepreneurial mindset and commitment to patients. The healthcare landscape is evolving rapidly, creating extraordinary opportunities to advance innovation and transform patient outcomes. Chiesi has built an impressive foundation, combining scientific expertise and a clear commitment to sustainable growth across generations. I look forward to working alongside Chiesi colleagues around the world to further strengthen the Group's innovation capabilities, advance its pipeline and partnerships, and create lasting value for patients, healthcare systems and society." Chiesi remains firmly committed to executing its patient-centric strategy, advancing innovation across its therapeutic areas, and delivering sustainable growth for the benefit of patients, healthcare systems, communities and the planet. About Chiesi Group Chiesi is a research-oriented international biopharmaceutical group that develops and markets innovative therapeutic solutions in respiratory health, rare diseases, and specialty care. The company's mission is to improve people's quality of life and act responsibly towards both the community and the environment. By adopting the legal form of Benefit Corporation in Italy, the US, France and Colombia, Chiesi's commitment to creating shared value for society as a whole is legally binding and central to company-wide decision-making. As a certified B Corp since 2019, Chiesi meets verified standards for social and environmental business practices. The company aims to reach Net-Zero greenhouse gases (GHG) emissions by 2035. With 90 years of experience, Chiesi is headquartered in Parma (Italy), with 31 affiliates worldwide, and counts more than 7,900 employees. The Group's research and development center in Parma works alongside 6 other important R&D hubs in France, the US, Canada, China, the UK, and Sweden. For further information please visit or the website of your local Chiesi affiliate. View source version on businesswire.com: Press Info: Anna Bonisoli Alquati, Head of Global External Communications: Michela Lijoi, Global External Communications Sr. Manager: mobile +39 328.6353044, e-mail: Davide Paterlini, Global External Communications Sr. Manager: mobile +39 345.7983132, e-mail:
AI integration in Single-Use Technologies reshapes biopharmaceutical manufacturing as global corporate AI investment reaches $252.3 billion. "AI-enabled bioprocessing can reduce costs and development timelines by 30% to 50% as adoption of intelligent single-use systems expands." Boston, Aug. 21, 2026 (GLOBE NEWSWIRE) - As corporate AI investment surpasses $252 billion globally and biopharmaceutical manufacturers accelerate their adoption of intelligent manufacturing systems, the convergence of artificial intelligence and single-use technologies (SUTs) is emerging as one of the most consequential strategic inflection points in bioprocessing. BCC Research's latest intelligence offering, AI Impact on Single-Use Technologies for Biopharmaceuticals Market - BCC Pulse Report, provides a comprehensive qualitative assessment of how AI is fundamentally restructuring upstream and downstream biomanufacturing operations - and where capital is flowing as a result. Key Findings - Global corporate AI investment reached $252.3 billion in 2024, with private investment surging 44.5% and M&A activity increasing 12.1%, according to the Stanford AI Index Report 2025. The U.S. led all nations with $109.1 billion in private AI investment, compared to China's $9.3 billion. Overall AI investment has grown more than 13-fold since 2014, signaling a sustained structural commitment across sectors including biopharmaceuticals. - Asia-Pacific is rapidly emerging as a global leader in biopharmaceutical innovation, driven by government-led digital transformation initiatives including Singapore's National Precision Medicine Strategy and Thailand 4.0, accelerating AI adoption across R&D, manufacturing, and commercialization - with CDMOs and Global Capability Centers (GCCs) at the forefront. - AI integration in bioprocessing is delivering measurable operational gains, with AI and IoT-enabled solutions reducing costs and development timelines by up to 30% to 50% through optimized upstream and downstream processing. More than 60% of biopharmaceutical manufacturers are already incorporating AI and IoT-enabled solutions for process monitoring and control. - Digital twins, AI-powered single-use bioreactors, and Process Analytical Technology (PAT) integrated with machine learning are redefining real-time quality control - replacing traditional daily sampling with continuous in-line monitoring. AI-enabled single-use chromatography systems are demonstrating deviation rate reductions of 50% or greater, while ML models are optimizing transmembrane pressure and flux rates in single-use filtration to reduce membrane fouling. - Emerging technologies reshaping the sector include autonomous manufacturing systems with AI agents controlling processes in real time, hybrid AI models combining machine learning with mechanistic understanding of fluid dynamics and cell biology, and AI-powered automated labs - so-called "AI science factories" - accelerating process development at scale. - Key players driving adoption include Pfizer, Thermo Fisher Scientific Inc., Sartorius, Roche, Novartis, Sanofi, Eli Lilly, and Accenture, alongside specialized AI bioprocessing innovators such as Basetwo, DataHow, Lemnisca, Lila Sciences, PostEra, Isomorphic Labs, Insilico Medicine, CytoReason, Turbine, and NVIDIA. Strategic Implications The convergence of AI and single-use technologies is being driven by structural forces that extend well beyond individual company strategy. Growing demand for biologics and vaccines requires faster, contamination-free production environments - precisely the conditions that single-use systems are designed to support and that AI is positioned to optimize. The shift toward data-centric manufacturing is critical here: SUTs generate high-resolution process data that, when unlocked by AI-powered analytics and predictive maintenance platforms, create compounding operational advantages across the production lifecycle. Regulatory flexibility in the U.S. is accelerating adoption, with American universities developing 40 AI models in 2024 alone - surpassing China's 15 and Europe's 3. By contrast, the EU AI Act's strict risk-based framework and a documented 20% loss of top EU AI research talent to U.S. institutions are creating meaningful adoption gaps. Data silos, fragmented pharmaceutical data platforms, and low AI penetration in biotech patent applications - still approximately 3.5% in 2020 compared to 17.5% across all sectors - further underscore that this transformation remains early-stage, even as momentum builds rapidly. Investment Considerations For investors, the AI-SUT convergence presents a compelling but differentiated opportunity. Anchor commitments signal strong conviction at the top of the market: Novartis committed $3 billion with Isomorphic Labs, Sanofi committed $1.2 billion with Insilico Medicine, Eli Lilly co-invested $1 billion with NVIDIA on an AI supercomputing and digital twin initiative, and Lila Sciences raised $350 million in a Series A backed by Flagship Pioneering, NVIDIA, and General Catalyst. Earlier-stage opportunities are also active, with Basetwo raising $11.5 million for AI-driven process optimization and Lemnisca securing pre-seed funding for AI-driven fermentation scale-up - consistent with the $0.5 million to $1.5 million pre-seed norms typical of early AI bioprocessing ventures. Key risks include infrastructure and standardization challenges inherent to single-use systems, regulatory headwinds in Europe, and persistent data integration barriers that could constrain AI model performance across fragmented pharmaceutical platforms. About the Report AI Impact on Single-Use Technologies for Biopharmaceuticals Market - BCC Pulse Report provides a qualitative strategic analysis of AI adoption trends, emerging technologies, investment activity, competitive dynamics, and regional adoption patterns across the single-use biopharmaceutical manufacturing landscape. About BCC Research BCC Research provides objective, unbiased measurement and assessment of market opportunities with detailed market research reports. Our experienced industry analysts assess growth trends, identify and evaluate new and changing market opportunities, and provide critical information and innovative decision support tools to help inform the strategic decision-making process. For media inquiries, email [email protected] or visit our media page for access to our market research library. Any data and analysis extracted from this press release must be accompanied by a statement identifying BCC Research LLC as the source and publisher. BCC Research LLC 50 Milk St., Ste. 16, Boston, MA 02109 [email protected] | +1 781-489-7301 www.bccresearch.com Legal Disclaimer: EIN Presswire provides this news content "as is" without warranty of any kind. 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AWS becomes Novo Nordisk's preferred AI partner for drug discovery. Novo Nordisk names AWS its preferred cloud and AI partner, opening a London hub to speed drug discovery. Published: August 10, 2026 AWS will anchor Novo Nordisk's cloud and AI strategy as the Danish pharma moves to speed new medicines to market under a pact unveiled Monday. The deal opens a co-innovation hub inside Novo's existing London facility where engineers from both sides will work on speeding up development of new medicines. Novo CEO Mike Doustdar said the collaboration is about "making AI a driver of innovation" across the Danish pharma, which focuses on serious chronic diseases. Novo gains access to Amazon Bio Discovery, a service offering AI models trained on biological datasets, plus Amazon Bedrock for building AI applications. The tools are meant to identify drug targets, design therapies and combine clinical, genomic and imaging data. Novo will also deploy Bedrock AgentCore, a managed platform for scaling AI agents, to make operations more efficient. Executives said the work is already paying off. Clinical documentation time has fallen, and 25,000 Novo employees have become more productive under the current setup. AWS CEO Matt Garman said forward deployed engineers and Novo's science teams can "compress drug discovery timelines" and process complex datasets securely. The agreement extends an existing relationship spanning Amazon Pharmacy, Amazon Ads and Amazon One Medical. AWS has signed similar life-sciences pacts this year with Flagship Pioneering and Johnson & Johnson, while Novo has separately worked with OpenAI and Denmark's first national supercomputer. Financial terms were not disclosed. The London hub is the latest in a wave of cloud-pharma AI partnerships reshaping how medicines get discovered.