Senior Scientist in Computational Genomics

Company Summary:At FL122, we are at the forefront of pioneering genomic technologies that redefine human health and assisted reproduction. Founded by the innovative Flagship Pioneering, we are dedicated to creating, funding, and nurturing first-in-category life sciences companies. Our portfolio includes over 100 groundbreaking companies developed over the past two decades, such as Moderna (MRNA), Generate Biomedicines, Tessera Therapeutics, and Quotient Therapeutics. We pride ourselves on being an equal opportunity employer.Position Summary:We are in search of our inaugural Computational Genomics Scientist to spearhead vital research that will underpin our scientific platform. As an early-stage team member, you will enjoy significant ownership of your work, shaping our analytical strategy from the ground up by integrating genomics, statistical genetics, and advanced modeling techniques. Your responsibilities will encompass the comprehensive delivery of computational research projects, including design, execution, interpretation, and communication of results to senior leadership. We seek a resourceful individual who thrives in a fast-paced, agile environment and possesses a proactive mindset. The ideal candidate will combine technical expertise with a growth-oriented approach, meticulous attention to detail, and a relentless drive for excellence. Collaboration is essential in our startup environment, where all team members work closely to push the boundaries of scientific discovery.

Join us as a Senior Scientist in Computational Biology at Flagship Pioneering, Inc. In this pivotal role, you will leverage your expertise to drive innovative research and development in computational biology, contributing to groundbreaking discoveries and advancements in the field.

ABOUT PIONEERING INTELLIGENCE Pioneering Intelligence is a forward-thinking initiative that builds upon Flagship Pioneering's rich history of establishing groundbreaking scientific and computational enterprises. By leveraging cutting-edge advancements in artificial intelligence, machine learning, and data science, we aim to accelerate fundamental research and cultivate a dynamic portfolio of AI-first companies. As an integral part of Flagship's unique model that intertwines science, entrepreneurship, and investment, we transform revolutionary concepts into impactful companies, enhancing AI innovations that contribute to human health, sustainability, and more. THE ROLE We are on the lookout for a Principal Scientist specializing in Embedded Machine Learning and Computational Methods to spearhead various AI/ML and computational initiatives across early-stage ventures within our company origination framework. Your responsibilities will include defining and executing practical AI strategies, overseeing the development of methodologies and platforms (including systems design, drug design, molecular modeling, systems biology, protein design, and LLM-based workflows), and ensuring a high standard of rigor in model development, benchmarking, scaling, and reporting. You will also manage cross-functional teams as necessary, influence the strategic direction of our initiatives, and represent Pioneering Intelligence to venture teams and external collaborators. The ideal candidate is a self-motivated individual with a diverse skill set, capable of transitioning seamlessly from protein design to mass spectrometry or docking pipelines, and then creating LLM-based agents to streamline scientific workflows.

Role overview Bicycle Therapeutics seeks a Senior Scientist specializing in Computational Chemistry to join the team in Cambridge. The position focuses on using computational methods to design and optimize new therapeutic candidates, directly supporting the company’s goal of developing new medicines. What you will do Lead molecular modeling studies for ongoing drug discovery projects. Use advanced simulation techniques to analyze and predict molecular behavior. Collaborate with scientists from various disciplines to integrate computational insights into laboratory research. Share research findings through publications and presentations at scientific meetings and conferences. Requirements Extensive experience with computational chemistry methods and tools. Strong foundation in molecular modeling and simulation. Proven ability to work effectively within cross-functional teams. Drive to advance drug discovery using computational science.

Charles River Analytics, a proud member of the GRVTY family, is at the forefront of developing innovative solutions and advanced technologies designed to address some of the most challenging issues faced globally. Our dynamic team of tech entrepreneurs collaborates to enhance AI, robotics, intelligent sensing, and human-centered computing. The research and technology we develop not only propel government initiatives but also unveil new opportunities in the commercial sector. At Charles River, we take immense pride in cultivating a workplace that attracts and retains top-tier talent and creative problem-solvers in the industry. Join us as we strive to accelerate our mission-driven innovations!We are currently seeking a dedicated Senior/Principal Scientist with expertise in Human-Systems Integration, Human Factors, or Human-Computer Interaction. In this role, you will spearhead the development of cutting-edge tools and interfaces that empower users to effectively collaborate with technology in demanding environments.Your responsibilities will include leading and expanding teams of researchers, designers, and engineers to assess work domains and user needs, create novel human-AI interaction concepts, and evaluate interactive prototypes. You will also be responsible for defining and directing technical projects, while fostering robust relationships with clients, sponsors, and collaborators. As a subject matter expert in Human Systems, you will work alongside multidisciplinary teams to explore and pursue research opportunities across various technical domains.

Position Overview Join our innovative team at Apriori Bio, where we harness the power of computational and data-centric methods to craft groundbreaking antigens and assess vaccine efficacy. Our cutting-edge AI/ML platform, Octavia™, allows us to navigate viral fitness landscapes, anticipate immune evasion patterns, and engineer vaccines that prime the immune system for future challenges. In this role, you will leverage computational techniques—including structural modeling, machine learning, and statistical inference—to enhance our vaccine design initiatives based on insights from Octavia™. Proficiency in protein engineering and immunological datasets is advantageous, alongside a keen interest or background in high-throughput functional genomics, virology, or vaccinology. The Scientist will collaborate closely with both computational and experimental teams to analyze outcomes, formulate hypotheses, and aid in antigen development. This position is perfect for scientists who are eager to engage in a unique learning environment characterized by innovation and interdisciplinary collaboration within a fast-paced startup.

Charles River Analytics, a proud member of the GRVTY family, is dedicated to developing innovative solutions and cutting-edge technology to address some of the world’s most pressing challenges. Our dynamic team of tech entrepreneurs collaborates to lead advancements in artificial intelligence, robotics, smart sensing, and human-centered computing. Our research and development initiatives not only enhance government programs but also unlock new opportunities within the commercial sector. As part of GRVTY, we are excited to expand our capabilities while maintaining our commitment to excellence in national security domains. Are you ready to join us in accelerating our mission-driven innovations? We would love to hear from you! We are currently seeking a motivated and experienced senior researcher who specializes in Human-Systems Integration, Human Factors, or Human-Computer Interaction. In this role, you will create groundbreaking tools and interfaces that enable users to effectively collaborate with technology in demanding work environments. As a leader, you will guide and expand teams of researchers, designers, and engineers to analyze work contexts and user requirements, develop innovative human-AI interaction concepts, and demonstrate and evaluate interactive prototypes. Your role will involve defining and directing technical projects, fostering strong partnerships with customers, sponsors, and collaborators. Additionally, you will share your expertise in Human Systems, working alongside cross-disciplinary teams to explore new research opportunities in exciting technical fields.

FL122, a new venture from Flagship Pioneering based in Cambridge, MA, is building genomic technologies aimed at advancing human health and assisted reproduction. Flagship Pioneering has launched over 100 life sciences companies in the past two decades, including Moderna, Generate Biomedicines, and Tessera Therapeutics. The team addresses complex challenges in human health and sustainability. Role overview The Scientist in Reproductive and Molecular Biology will play a key part in establishing FL122’s scientific platform. This role focuses on developing and standardizing laboratory workflows that involve handling human gametes and performing molecular characterization. As part of the early scientific team, the Scientist will work closely with senior scientists and company leadership to define technical standards and carry out experimental strategies. What you will do Develop and improve laboratory workflows for handling human gametes and conducting molecular analysis Work directly with sensitive human samples in an IVF or embryology laboratory setting Use molecular biology techniques to support experimental goals Collaborate with colleagues and leadership to establish technical standards Help plan and execute experimental strategies Requirements Background in reproductive biology and molecular biology Hands-on experience in IVF or embryology laboratory environments Proficiency in molecular biology techniques Strong attention to detail and ability to work with sensitive human samples Adaptable and comfortable working across different scientific areas Collaborative approach suited to an early-stage startup team

Join our innovative team as a Senior Scientist where you'll drive critical research projects and make a significant impact in the field. We are seeking a highly motivated individual with a passion for scientific discovery and a strong background in relevant disciplines.

Company Overview Flagship Labs 110 Inc. (FL110) is an innovative, privately held technology company at the forefront of developing a fully integrated, end-to-end platform that revolutionizes proteomics. Our cutting-edge platform combines advanced bioengineering, machine learning, and bespoke microelectronics to deliver unparalleled precision and insights. Backed by Flagship Pioneering, we possess the vision, courage, and resources to achieve extraordinary results. Our culture fosters collaboration and creativity, making it essential for team members to embrace diverse perspectives and an inclusive mindset. If you are excited by the prospect of working in such an environment and possess some of the qualifications listed below, we encourage you to apply. Position Overview: We are looking for a passionate and skilled (Senior) Scientist, Nanopore to become part of our dynamic team. The level for this position is flexible based on experience. Your primary focus will be on the advancement of nanopore sensing technologies, contributing to the development of a nanopore-based protein reading system. As a key member of a cross-functional team, you will collaborate closely with chemists, bioinformaticians, software developers, and hardware engineers. The ideal candidate will have a robust background in nanopore technology, particularly in protein translocation, along with either relevant experience in the biotechnology sector or a proven record of scientific accomplishment.

Join Artech Information Systems LLC as a Scientist in Cambridge, where you will contribute to groundbreaking research and innovative solutions in a collaborative environment. Your expertise will help drive scientific advancements and enhance our projects.

Are you passionate about advancing the field of machine learning? Join our team at Altos Labs as a Machine Learning Scientist or Senior Machine Learning Scientist. In this role, you will leverage your expertise to drive innovation and development in cutting-edge research projects. Collaborate with a multidisciplinary team to push the boundaries of machine learning technology.

ABOUT PIONEERING INTELLIGENCEPioneering Intelligence extends Flagship Pioneering's tradition of launching innovative scientific and computational initiatives. By leveraging the latest advancements in AI, machine learning, and data analytics, we aim to expedite fundamental research and build a diverse portfolio of AI-first companies. As a key player in Flagship's integrated approach to science, entrepreneurship, and investment, we transform groundbreaking concepts into transformative enterprises that enhance AI innovations in human health, sustainability, and more.THE ROLEWe are on the lookout for a Principal Scientist specializing in Embedded Machine Learning and Computational Techniques to spearhead various AI/ML and computational initiatives across early-stage ventures in our company origination process. You will be responsible for defining and executing practical AI strategies, overseeing the development of methodologies and platforms such as systems design, drug design, molecular modeling, systems biology, protein design, and LLM-driven workflows while ensuring the utmost rigor in model development, benchmarking, scaling, and reporting. You will manage cross-functional contributors as necessary, influence the strategic direction of the company, and represent Pioneering Intelligence to venture teams and external partners. The ideal candidate is a proactive, deep thinker who can seamlessly transition between protein design one week and mass spectrometry or docking pipelines the next, while also developing LLM-based agents to automate scientific workflows.

Your Impact at LilaThe Senior Scientist in Analytical Chemistry will spearhead the development and application of cutting-edge analytical and characterization techniques to bolster Discovery Chemistry initiatives across Lila’s innovative platform. This role is pivotal in facilitating the swift design, synthesis, screening, and optimization of small molecules and related molecular entities. You will be instrumental in producing high-quality, informative experimental data that guides chemistry decisions and enhances platform learning.By collaborating closely with teams in Discovery Chemistry, automation, AI/computational fields, and screening, you will establish and scale multimodal characterization workflows that surpass conventional analytical chemistry methodologies. Your expertise will help create an integrated analytical framework that includes compound characterization, reaction monitoring, molecular profiling, and rapid data generation to support fast-paced design–make–test–analyze cycles.Your contributions will be vital in molding Lila’s next-generation discovery engine, merging profound analytical chemistry knowledge with high-throughput experimentation and AI-driven workflows.

Company Overview: At Flagship Labs 103, Inc., we are revolutionizing healthcare by shifting the paradigm of disease diagnosis and intervention. Our innovative technological and computational platforms are designed to detect cellular dynamics from minimally invasive biospecimens, allowing us to connect individuals with the most effective interventions to prevent the onset and progression of diseases. We are dedicated to enhancing patient outcomes through advanced research methodologies. Position Summary: We are looking for a dynamic and experienced Senior Scientist to lead our bioconjugation initiatives and propel FL103’s programs to new heights. The ideal candidate is a self-starter with a strong commitment to producing high-quality data in a fast-paced, innovative research environment. You will play a pivotal role in supporting our ongoing bioconjugation projects across various research and development domains. Key Responsibilities: Design, synthesize, purify, and analyze oligonucleotide-conjugates for antibodies and other modalities, while developing and optimizing conjugation protocols utilizing both established and novel chemistries and technologies as part of our assay development platform. Work collaboratively with the assay development team to refine and enhance conjugates to support FL103’s scientific endeavors. Participate in a cross-functional team to oversee project timelines, deliver regular updates, and communicate progress effectively within the team. Establish and nurture strong working relationships with key collaborators across the company to further discovery research activities toward pre-clinical development. Contribute to the creation of research reports and presentations for internal project teams, leadership, and external stakeholders. Maintain organized and detailed lab notebooks and batch records.

Innovate and Create Models from Scratch! At Flagship Pioneering, we are dedicated to launching pioneering companies that challenge the status quo. Within our Flagship Labs, small, agile teams develop new technical theses, rigorously test them, and build ventures around groundbreaking concepts. We are assembling an exceptional machine learning team within our newly established venture, Flagship Labs 120. Our focus is on uncovering hidden structures from complex measurement data of intricate physical systems, often necessitating mechanism-informed modeling, carefully designed inductive biases, and principled methodologies for inverse problems. This is a pioneering role dedicated to innovative modeling, moving beyond standard optimization tasks. You will have the opportunity to design, prototype, test, and refine novel approaches that establish the technical foundation of our platform starting from day one.

Join our innovative team at Flagship Pioneering, Inc., where we are dedicated to advancing biopharmaceutical technologies. We are seeking a Senior Scientist in LNP Formulations who will play a key role in the development of lipid nanoparticle (LNP) formulations. This position offers the opportunity to work on cutting-edge research and contribute to the creation of next-generation therapeutics.

About Serif Biomedicines, Inc. Serif Biomedicines, Inc. is a privately held biotechnology company in Cambridge, MA. The team is developing new approaches to gene therapy for diseases that current medical solutions cannot address. Serif Biomedicines was founded by Flagship Pioneering, known for launching over 100 innovative life sciences organizations focused on human health and sustainability. Role Overview The Senior Scientist, Molecular Biology will design and develop next-generation DNA constructs for programmable medicine. This position suits scientists experienced in synthetic biology, high-throughput cloning, and computational sequence engineering. The role centers on building scalable platforms for plasmid DNA design, construction, and optimization, using automation, algorithm-driven sequence design, and data-centric workflows. This scientist will report to the Director of Molecular Biology and may supervise a direct report. Collaboration with other scientists and group leaders across the R&D team is a key part of the job. What You Will Do Lead the design and construction of plasmid DNA constructs, including vector architecture, gene synthesis strategies, and high-efficiency cloning (such as Gibson, Golden Gate, and recombination-based methods). Advance automated and computational sequence design by applying advanced tools and pipelines for codon optimization, regulatory element tuning, and multi-parameter construct optimization. Establish and manage vendor relationships to support both internal and external capabilities, helping projects move forward efficiently and minimizing disruptions.

Join AbbVie, a global biopharmaceutical company, as a Senior Scientist I in our Neuroscience division specializing in Biologics Screening. In this role, you will lead innovative research efforts to develop therapies that address unmet medical needs in the field of neuroscience.

ABOUT PIONEERING INTELLIGENCE Pioneering Intelligence continues the legacy of Flagship Pioneering by creating innovative scientific and computational ventures. Utilizing advancements in AI, machine learning, and data analytics, our mission is to expedite fundamental research and establish a diverse portfolio of AI-first companies. We integrate science, entrepreneurship, and capital to transform groundbreaking concepts into impactful companies, furthering AI advancements in human health, sustainability, and more. THE ROLE We are on the lookout for a Principal Scientist in Embedded Machine Learning/Computational to spearhead multiple AI/ML and computational projects within early-stage ventures as part of Flagship’s origination process. Your responsibilities will include defining and executing effective AI strategies, leading method and platform advancements (such as systems design, drug design, molecular modeling, systems biology, protein design, and LLM/agentic workflows), and ensuring excellence in model development, benchmarking, scaling, and reporting. You'll collaborate with cross-functional teams, shape the direction of the company, and represent Pioneering Intelligence to both venture teams and external partners. The ideal candidate is a proactive deep diver, capable of transitioning from protein design to mass spectrometry or docking pipelines, and then developing LLM-based agents to streamline scientific workflows.