Full-Time

Senior Software Engineer and Project Lead

Biology

Simons Foundation

Simons Foundation

201-500 employees

Philanthropic funder advancing mathematics and sciences

Compensation Overview

$190k - $235k/yr

New York, NY, USA

In Person

Category
Biology & Biotech (2)
,
Software Engineering (1)
Required Skills
Python
Machine Learning
DevOps
Requirements
  • B.S. in Computer Science, Software Engineering, or a related technical field
  • At least 10 years of professional software experience in software engineering, including leading teams and direct involvement in the planning, design, and development of software
  • Experience collaborating daily with other key team members of different technical and scientific backgrounds
  • Proficiency in full stack software development
  • Extensive experience in Python, including developing data pipelines and software libraries
  • Demonstrated experience with the full software development lifecycle, including testing, CI/CD, version control, and deployment
  • Experience building and maintaining web-based interfaces and applications
  • Background in computational biology, bioinformatics, or a related field, with experience developing software in support of biological research
  • Experience working with large, heterogeneous biological datasets—ideally in genomics or biomedical contexts
  • Effective technical leadership and mentorship abilities
  • Excellent communication skills, especially when working across disciplinary boundaries
  • Deep curiosity about science and a passion for building tools that empower scientific discovery
  • Strong sense of ownership and drive for continuous improvement
Responsibilities
  • Serve as technical lead for HumanBase, guiding the design, architecture, and implementation of new features and major infrastructure upgrades
  • Lead and mentor a team of full stack software engineers, ensuring high-quality code, efficient workflows, and continuous professional development
  • Plan, develop, and optimize scalable genomics data processing pipelines
  • Integrate machine learning methods into production pipelines to analyze heterogeneous biological datasets
  • Establish and enforce software engineering best practices, including coding standards, version control, documentation, testing, and deployment workflows
  • Collaborate cross-functionally with computational biologists, data scientists, and external partners to align engineering efforts with scientific goals
  • Stay current with emerging technologies in cloud infrastructure, bioinformatics, and scientific computing and assess their relevance for HumanBase
  • Perform additional duties or projects as assigned

The Simons Foundation funds basic science and mathematics research to advance knowledge. It provides grants, fellowships, programs, and events by using endowments and donations; researchers submit proposals and the foundation reviews and awards funding for projects and collaborations. Unlike many funders, it concentrates on math, physical sciences, life sciences, autism, and nanofluidics, supporting long‑term work and scientific gatherings rather than services or products. Its goal is to push the boundaries of knowledge in basic science and mathematics by enabling researchers to pursue important ideas and partnerships.

Company Size

201-500

Company Stage

N/A

Total Funding

N/A

Headquarters

New York City, New York

Founded

1994

Simplify Jobs

Simplify's Take

What believers are saying

  • Hopi Hoekstra joined board in 2026 enhancing life sciences strategy.
  • Amanda Hallberg Greenwell starts October 13, 2025 boosting external relations.
  • New collaborations on black holes and neural computation drive breakthroughs.

What critics are saying

  • Endowment loses $50-150M from 20-30% equity correction in 12-24 months.
  • Musk and Altman poach talent with larger AI and physics budgets in 12-18 months.
  • Visa delays shrink graduate fellowship pool 30-40% in 6-12 months.

What makes Simons Foundation unique

  • Simons Foundation uniquely funds Simons Collaborations uniting multidisciplinary teams on quantum field theory.
  • Pioneers nanofluidics research for water purification and nanoscale machines.
  • Launched Flatiron Institute advancing science via computational methods.

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Benefits

Relocation Assistance

Company News

Simons Foundation
Mar 25th, 2026
Hopi Hoekstra joins Simons Foundation board of trustees.

Hopi Hoekstra joins Simons Foundation board of trustees. Pioneering evolutionary biologist Danielle "Hopi" Hoekstra has joined the Simons Foundation's board of trustees. As a board member, she will provide strategic vision, oversight and stewardship to the foundation in support of its mission to advance the frontiers of research in mathematics and the basic sciences. Hoekstra is the Edgerley Family Dean of the Faculty of Arts and Sciences and a professor in organismic and molecular biology at Harvard University. She previously served as the curator of mammals at Harvard's Museum of Comparative Zoology. Her research focuses on the genetic basis of adaptation - from morphology to behavior - in vertebrates, including wild mice. Hoekstra holds a B.A. in integrative biology from the University of California, Berkeley and a Ph.D. from the University of Washington. Before stepping into her role as dean at Harvard, she was a Howard Hughes Medical Institute investigator. She is a member of the American Academy of Arts and Sciences, the American Philosophical Society and the National Academy of Sciences. She previously served on the advisory board of Quanta Magazine, an editorially independent publication of the Simons Foundation. Hoekstra joins fellow Simons Foundation trustees Cori Bargmann, a neurobiologist and geneticist; physician-scientist Emery Brown; mathematician and physicist Ingrid Daubechies; mathematical physicist Robbert Dijkgraaf; mathematician David Eisenbud; investor and business leader Bill Ford; organizational advisor and investment professional Andrew Golden; mathematician Jill Pipher; computer scientist William H. Press; investor and philanthropist Nat Simons; financial executive Ellen Taus; molecular biologist and vice chair Shirley M. Tilghman; and co-founder and chair Marilyn H. Simons. The Simons Foundation also expresses its heartfelt thanks to physicist and emeritus trustee Peter Littlewood, who recently retired from the board of trustees following nine years of invaluable leadership, insight and commitment to the foundation's mission.

Help Net Security
Nov 12th, 2025
IBM pushes toward quantum advantage by 2026 with new Nighthawk processor

IBM pushes toward quantum advantage by 2026 with new Nighthawk processor. IBM is taking another major step toward its goal of achieving quantum advantage by 2026 and fault-tolerant quantum computing by 2029, unveiling its most advanced quantum processor yet, IBM Quantum Nighthawk. IBM Quantum Nighthawk processor. The new processor, revealed today, is built on a redesigned architecture meant to pair with high-performance quantum software. IBM says this combination could enable Nighthawk to deliver quantum advantage as soon as next year, the point when a quantum computer can outperform every classical-only method on a specific problem. Expected to reach IBM users by the end of 2025, Nighthawk packs 120 qubits linked by 218 next-generation tunable couplers arranged in a square lattice, offering more than 20% greater connectivity than the company's previous Heron processor. That extra interconnection, IBM says, allows users to execute circuits with 30% greater complexity while keeping error rates low. The architecture is designed to handle workloads of up to 5,000 two-qubit gates, a critical measure of quantum computational capacity. Future iterations are projected to hit 7,500 gates by 2026, 10,000 by 2027, and as many as 15,000 two-qubit gates by 2028, when IBM expects systems could scale to 1,000 or more interconnected qubits using long-range couplers first tested last year. "There are many pillars to bringing truly useful quantum computing to the world," said Jay Gambetta, Director of IBM Research and IBM Fellow. "We believe that IBM is the only company that is positioned to rapidly invent and scale quantum software, hardware, fabrication, and error correction to unlock transformative applications. We are thrilled to announce many of these milestones today." Community validation on the road to advantage. IBM expects the first verified cases of quantum advantage to be confirmed by the broader research community by the end of 2026. To help track and validate those claims, IBM has joined forces with Algorithmiq, the Flatiron Institute, and BlueQubit to launch an open, community-led quantum advantage tracker. The tracker currently hosts three experiments covering observable estimation, variational problems, and classically verifiable challenges, and invites contributions from researchers across the quantum and classical computing worlds. IBM says it hopes the initiative will encourage rigorous benchmarking and healthy competition between classical and quantum approaches. "I'm proud that our team at Algorithmiq is leading one of the three projects in the new quantum advantage tracker. The model we designed explores regimes so complex that it challenges all state-of-the-art classical methods tested so far," said Sabrina Maniscalco, CEO, Algorithmiq. "We are seeing promising experimental results, and independent simulations from researchers at the Flatiron Institute validate its classical hardness. These are only the first steps - quantum advantage will take time to verify, and the tracker will let everyone follow that journey."

Simons Foundation
Oct 1st, 2025
Announcing the Recipients of the Autism and Neuroscience Conferences and Courses Awards

The Simons Foundation's Autism & Neuroscience division is pleased to announce the recipients of its 2025 Autism and Neuroscience Conferences and Courses Awards.

Simons Foundation
Sep 16th, 2025
Amanda Hallberg Greenwell to Join Simons Foundation as Senior Vice President, External Relations

The Simons Foundation is pleased to announce that on October 13, 2025, Amanda Hallberg Greenwell will join the foundation as senior vice president, external relations.

Clival Private Limited
Aug 22nd, 2025
Allos Pharma Advances Arbaclofen Program for Autism and Fragile X

Allos has also secured non-dilutive funding from the Simons Foundation.