Cyrus solves difficult protein engineering and structure prediction problems using the most scientifically advanced, powerful, and laboratory-proven software tools available. Cyrus’ work is based primarily on the Rosetta molecular modeling and design toolkit first developed at the lab of co-founder David Baker. We are passionate about scientific excellence, operational excellence, and customer success.

OUR STORY

Computational biology has made huge leaps forward in the last decade, with the first designs of biologically active proteins by software. This software, Rosetta, was named one of the top-10 scientific breakthroughs of 2016. Rosetta-designed proteins can treat brain cancer, break down gluten in Celiac Disease patients, and block a broad range of flu strains. The Cyrus founders gained experience in using and developing Rosetta at David Baker’s lab. While trying to help others who struggled to learn how to use these powerful tools, they realized that a new organization was needed to bring Rosetta to the thousands of scientists and companies who need it.

Thus Cyrus was born. We sought a name to signify the fact that Cyrus software carries out tasks that were historically thought to be impossible. Cyrus Levinthal’s paradox pointed out that protein structure prediction appears to be an impossible problem to compute – Cyrus offerings shows a way out of the paradox, allowing our customers to do the impossible.

OUR GOALS

Scientific Excellence

Cyrus was founded by scientists and driven by our desire to constantly be at the leading edge of computational biology, with experimentally proven computational tools, like homology modeling. This means that we implement algorithms from a variety of sources, starting with the Rosetta software toolkit and its associated software dependencies, and that we focus on constant methodological improvement and rigorous, peer-reviewed scientific benchmarking.

Operational Excellence

Cyrus is committed to providing the most powerful and reliable bio-molecular computation resource available. We partner with industry-leading firms to provide vast amounts of compute, high uptime, data security, and efficient use of computational resources for our customers. Our team is up-to-the-minute on modern cloud operations, and we are passionate about continued improvement as these tools and resources develop.

User Success

The most powerful algorithms and hundreds of thousands of computers are useless without a set of support resources to help our customers achieve their scientific goals. Our ultimate aim is not only to provide a beautiful rosetta interface, but to create customer success by delivering powerful and delightful tools and supporting their use.

Cyrus was created in part to provide these support resources efficiently and professionally. That means a custom-designed GUI, instructional videos, telephone support, and on-site coaching by industry-leading scientists. Your scientific success — solving new protein structures, creating more active mutants, designing novel protein binding activities, and more — is our goal.

OUR TEAM

Lucas Nivon

Chief Executive Officer

Lucas is trained in computational biophysics and protein engineering. Prior to Cyrus he was a Translational Investigator & Senior Fellow at the Baker lab at UW, developing small-molecule binding proteins and protein design algorithms. Lucas is the founder of PedalAnywhere, an online-only bicycle rental company. Lucas’ scientific work includes a patented computationally designed enzyme, an RNA-dynamics-modeling software toolkit (built during his Ph.D. with Eugene Shakhnovich and Xiaowei Zhuang at Harvard), and algorithm optimization for automation of computational protein design. Harvard A.B., Biochemical Sciences (summa cum laude and Goldwater Scholar) and Ph.D., Biophysics; Hertz Fellow.

Yifan Song

Chief Science Officer

Yifan has been at the forefront of computational protein modeling and biophysics in a variety of fields. Yifan was the lead developer on core Rosetta protein modeling functionality, and the project manager at CCNY for an electrostatics calculation software package, MCCE. He pioneered a number of technical refinements in protein structure energy evaluation currently used in Rosetta. Yifan is a leader in computational protein modeling, with experience ranging from ab initio protein structure prediction to crystallography to protein-protein interaction design and over 20 scientific publications in leading journals. He is a former Translational Investigator & Research Scientist at the Baker lab at the University of Washington. Yifan completed a B.S. in Physics at Fudan University and earned his Ph.D. in Physics at CCNY.

David Baker

Scientific Co-Founder & Advisor

David is a Professor at the University of Washington and an HHMI Investigator. David is the originator of the Rosetta software package and is responsible for numerous scientific breakthroughs and “firsts” in computational modeling of protein structures and design of novel proteins. Highlights include:
1) The first reliable prediction of small-protein 3D structures.
2) The design of the first fully de novo protein structure in a computer.
3) The design of the first protein-protein binding interactions in a computer
4) The creation of a specific ligand-binding protein by computational methods.
5) David has published over 330 peer-reviewed scientific papers, including over 20 in Science and Nature alone.

Mark Benjamin

President and EVP Business Development

Mark is a trained scientist and seasoned business development professional. Prior to joining Cyrus, Mark was Chief Business Officer at Q-State Biosciences, a Harvard University company focusing on neuroscience drug discovery. Mark served as CEO of Galenea, an MIT spin out from the lab of Nobel laureate Susumu Tonegawa, which – through partnerships with Otsuka, CHDI, Novartis, Eisai and Janssen, worked on drug discovery for a number of neurodegenerative and neuropsychiatric disorders. Prior to Galenea, he was Chief Business Officer at Nura, a company formed out of Nobel Laureate Linda Buck’s GPCR work at the Fred Hutchinson Cancer Research Center. Mark spent some time in Geneva helping to build and eventually sell a Serono spin-out DNA-sequencing company – Manteia - the core of which forms part of the Illumina sequencing platform, and he was an early employee at Rosetta Inpharmatics – a gene expression profiling and microarray company founded by a Seattle-based team including Nobel laureate Lee Hartwell and systems biology pioneer, Lee Hood, where he headed up Business Development. He has a D.Sc. in Cancer Biology from Harvard University and a B.Sc. (First class, with honors) in Genetics from the University of London.

Sam DeLuca

Director of Engineering

Sam is both an accomplished scientific developer in molecular modeling with a specialty in Rosetta, as well as an experienced software engineer in cloud infrastructure for high throughput systems. Sam developed a version of the RosettaLigand small molecule docking algorithm suitable for high throughput screening while a graduate student in the Meiler lab at Vanderbilt. In addition to his scientific research, Sam was also a core contributor to RosettaCommons infrastructure. Prior to Cyrus, Sam worked at CloudLock (later acquired by Cisco), where he was a Senior software engineer who designed and implemented a high throughput system for analyzing large numbers of documents stored in the cloud. Sam completed a B.S. in Bioinformatics at Rensselaer Polytechnic University and a Ph.D. in chemical and physical biology at Vanderbilt University.

Gus Tai

Board Member

Gus Tai is a general partner at Trinity Ventures, where he specializes in funding early-stage companies and supporting entrepreneurs at the time of company formation. A Forbes Midas List recipient, Gus has backed a number of pioneering companies including Blue Nile (IPO), Bulletproof Coffee, Callisto Media, Markforged, 10% Happier, MaxPoint (IPO), Photobucket (acquired by Fox Interactive Media), Trion Worlds, Truaxis (acquired by MasterCard) and Zulily (IPO). Gus holds a BA in Applied Mathematics from Harvard University and a MS and MBA from MIT’s Department of Materials Science and Engineering and Sloan School of Management, respectively.

Eric Bell

Board Member

Eric is Managing Director of SpringRock Ventures. Before co-founding SpringRock, Eric headed the health care investment effort for the Invention Development Fund at Intellectual Ventures (IV). Prior to IV, Eric had spent most of his career in venture capital; he was an investment professional responsible for early and mid-stage health care investments at Vulcan Capital and at Tredegar Investments. Eric has also been Director of Business Development with Corixa Corporation, a biotechnology company in Seattle, WA. Prior to business school, Eric had worked for a start-up medical device company developing a home hemodialysis machine, Aksys, Ltd. (AKSY). Eric has an M.B.A. from the Wharton School at the University of Pennsylvania, an M.S.E. in Biomedical Engineering from the University of Pennsylvania, and a B.S. in Mechanical Engineering from Worcester Polytechnic Institute.

Chad Waite

Board Member

Chad is a Managing Director at OVP Venture Partners, where he has raised seven funds, with $750M currently under management. Chad has 28 years of experience investing across sectors as diverse as IT, clean tech, and digital biology. The firm has invested in over 130 companies, with 53 exits, including 23 IPOs. Notable successes include WatchGuard, Seattle Genetics, and Rosetta Inpharmatics.
Chad‘s additional investments include Accelerator, Adapx, Airgo Networks, Boston Beer, CellPro, Complete Genomics, Corixa, Loudeye Technologies, NanoString, SignalSoft, Verdezyne, Verity. He currently serves on the Board of Directors of Adapx, NanoString, NexGenia, Talyst and Verdezyne. Prior to joining OVP in 1987, Chad was a General Partner at Hambrecht & Quist Venture Partners where he focused on investments in IT and life sciences. Prior to H&Q, he was in marketing and sales management at Cobe Laboratories, Inc. in its cardiovascular medical products division. Chad is a member of the Oregon Health Sciences University (OHSU) BSIF Advisory Board and a member of the University of Washington’s Technology Transfer Advisory Board.

Carl Gordon

Board Observer

Carl L. Gordon, Ph.D., CFA, is a founding Partner and Co-Head of Global Private Equity at OrbiMed. He was a senior biotechnology analyst at Mehta and Isaly from 1995 to 1997. He was a Fellow at The Rockefeller University from 1993 to 1995. Carl received a Ph.D. in Molecular Biology from the Massachusetts Institute of Technology (1993) and a Bachelor of Arts Degree from Harvard College (1987). Carl was included on the Forbes Midas List of top venture capital investors numerous times from 2014 to 2018.

Eric Larsen

Board Observer

Eric Larsen is an experienced entrepreneur and executive in finance, technology, and business operations. He began his career at Andersen Consulting, led the technology team at Quellos , and subsequently held a senior role in the Aladdin Product Group at BlackRock. He is currently an active investor and Entrepreneur in Residence at the UW. He works as an advisor with emerging Northwest companies seeking to scale and has led multiple fund raising rounds.
At Quellos he built the world-class research, operations and customer management system Quasar, a key strategic advantage for Quellos, scaling from 17 employees with $324M in assets to 350 employees and $25B. He also led Financial Risk Management and advised emerging hedge funds via Quellos Financial Ventures. BlackRock, the largest asset manager in the world with over $4 trillion in AUM, acquired Quellos’ hedge fund business in 2007 and Eric lead the development of Quasar into BlackRock’s internal core Aladdin CRM with over 5000 users. At BlackRock Eric served on the Global Operating Committee, oversaw the global redesign of BlackRock’s websites, and launched the Client Analytics group in 2014.
Eric earned CFA designation in 2001, his MBA with honors in Finance from DePaul University, and his undergraduate degree at University of Illinois in Electrical Engineering.

SCIENTIFIC ADVISORY BOARD

Jeff Gray

Scientific Advisor

Jeffrey J. Gray is a professor of chemical and biomolecular engineering at Johns Hopkins University. Prof. Gray‘s research focuses on computational protein structure prediction and design, and he leads the development of RosettaDock, RosettaAntibody, the ROSIE web server, and the PyRosetta interactive platform for protein structure prediction and design. Gray is a member of the College of Fellows of the American Institute of Medical and Biological Engineering (AIMBE), and he has won AIChE’s David Himmelblau Award for Innovations in Computer-Based Chemical Engineering Education. Gray has received the Beckman Young Investigator Award, the Johns Hopkins Alumni Association Excellence in Teaching Award, and the National Science Foundation‘s CAREER Award. He serves on the editorial board of Proteins and the scientific advisory board of the Rosetta Design Group, and from 2005-2015 he served on the board of directors of the Ingenuity Project. He is a champion of broadening participation in science and engineering, serving as a member of the Johns Hopkins Diversity Leadership Council, the chair of the Homewood Council for Inclusive Excellence, and as the Diversity Chair of the Rosetta Commons. He is also the Director of the NSF-supported Rosetta Commons Summer Intern Program. Gray received his B.S.E. at the University of Michigan (’94), his Ph.D. at the University of Texas at Austin, and his post-doctoral training at the University of Washington.

Will Chen

Scientific Advisor

Will Chen is a leader and innovator in target validation using combined computational and experimental approaches. He was a junior faculty member at Harvard Medical School heading an effort in systems pharmacology before moving to industry to work on neurology and immunology drug discovery. Currently he is a Senior Director at Biogen in the Translational Biology group. His work relates to the systematic integration of human genetics and genomics, molecular and clinical data through advanced analytics and disease pathways to generate novel understanding of disease biology and patient outcomes. Will has also been part of the multi-partner private-public consortium Open Targets that counts a number of biotech and pharmaceutical companies as members including Biogen, GSK, Takeda, Sanofi and Celgene. Will completed his bachelors in physics at UC Berkeley and his PhD at Harvard University in biophysics working on protein folding and soft matter systems.

CYRUS EMPLOYEES

Karen Khar

Computation Protein Scientist

Ben Baker

Software Development Engineer

Steven Lewis

Scientist

Indigo King

Scientist

Brandon Frenz

Scientific Software Developer

Aaron Aguhob

Jr. Scientific Software Developer

Ryan Pavlovicz

Scientist

Amanda Duran

Protein Engineer Scientist

Toni Stamper

Sales Operation Specialist

Joe Ylagan

Software Development Engineer

Alex Bustillos

Office Administrator

Jenna Bogen

Project Manager

Amanda Loshbaugh

Protein Engineer Scientist

Kui Chan

Scientist IV

Erik Procko

Grace DeVane

Research Assistant II

Ragul Gowthaman

Protein Engineer Scientist

Dan Farrell

Protein Engineer Scientist

David Thieker

Protein Engineer Scientist

Thomas Tuong

IT Support / Junior System Administrator

Andy Jerome

Program & Business Development Manager

OUR STORY

OUR GOALS

Scientific Excellence

Operational Excellence

User Success

OUR TEAM

Lucas Nivon

Yifan Song

David Baker

Mark Benjamin

Sam DeLuca

Gus Tai

Eric Bell

Chad Waite

Carl Gordon

Eric Larsen

SCIENTIFIC ADVISORY BOARD

Jeff Gray

Will Chen

CYRUS EMPLOYEES

Karen Khar

Ben Baker

Steven Lewis

Indigo King

Brandon Frenz

Aaron Aguhob

Ryan Pavlovicz

Amanda Duran

Toni Stamper

Joe Ylagan

Alex Bustillos

Jenna Bogen

Amanda Loshbaugh

Kui Chan

Erik Procko

Grace DeVane

Ragul Gowthaman

Dan Farrell

David Thieker

Thomas Tuong

Andy Jerome

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