About.

you’re an innovator. So are we.

See, we already have something in common.

We speak Biology. We build bioinformatics tools, pipelines, and systems.  We apply and invent cutting-edge scientific methods and algorithms. Your success is our success.

Bioinformaticians who understand you.

Generating insights from the data can be a source of pride and identity, but it can also be a source of frustration and anxiety. Those insights can drive the success of your business.  Providing those key insights to advance the understanding of disease and biology is what we do.

By the Numbers

We’re proud of the clients we serve, the team we’ve built, and the projects completed.  Here are the summary statistics.

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5+ Year Clients

We deliver value and insights consistently over the long haul and evolve to meet your needs over time.

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Projects Completed

From small high-value projects, to long-term on-going engagements, we've done them all.

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Clients Served

From single-person startups and small R&D teams, to the largest pharma, life science, and diagnostic companies in the world

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Team Members

We’ve assembled a team of world-class bioinformaticians so you don’t have to.

Our People

We are bioinformaticians, computational biologists, and software engineers with experience in basic research, technology development, diagnostics, therapeutics and beyond.

Tim Fennell

Founding Partner

Tim Fennell

Founding Partner
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Molecular Biology Debugger
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Nils Homer

Founding Partner

Nils Homer

Founding Partner
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Has the need for Bioinformatics speed
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Clint Valentine

Vice President of Operations

Clint Valentine

Vice President of Operations
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The precision engineer for precision health assays
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Charlotte Tolonen

Chief of Staff

Charlotte Tolonen

Chief of Staff
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Brings the savoir-faire
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John Didion

Director of Engineering

John Didion

Director of Engineering
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Has seen too much, so you don’t have to
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Jeff Gentry

Distinguished Bioinformatics Engineer

Jeff Gentry

Distinguished Bioinformatics Engineer
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Software, as a service
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Yossi Farjoun

Principal Bioinformatics Scientist

Yossi Farjoun

Principal Bioinformatics Scientist
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Recovering Mathematician, Data Spelunker
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Ted Brookings

Staff Bioinformatics Scientist

Ted Brookings

Staff Bioinformatics Scientist
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Reformed Physicist, Productive Member of Society
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Jess Smith

Staff Bioinformatics Scientist

Jess Smith

Staff Bioinformatics Scientist
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Always practical, usually knowledgeable, ultimately compostable
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Matt Stone

Staff Bioinformatics Scientist

Matt Stone

Staff Bioinformatics Scientist
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Sweats the small stuff
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Alison Meynert

Staff Bioinformatics Scientist

Alison Meynert

Staff Bioinformatics Scientist
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Swimming in the deep data sea
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Jason Fan

Senior Bioinformatics Engineer

Jason Fan

Senior Bioinformatics Engineer
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Making your bits and bases go vroom
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Erin McAuley

Senior Bioinformatics Engineer

Erin McAuely

Senior Bioinformatics Scientist
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Coming May 2024

Senior Bioinformatics Scientist

Coming May 28 2024
CAREERS

Coming June 2024

Senior Bioinformatics Scientist

Coming June 3 2024
CAREERS

Let’s talk.

Send us an email or fill out the form below contact@fulcrumgenomics.com.

Tim Fennell

Founding Partner

Tim Fennell is a Founding Partner at Fulcrum Genomics LLC, with over a decade of experience in genomics and bioinformatics. He combines a background in computer science and large-scale software engineering with a passion for molecular biology, genetics, and statistics in order to rapidly solve challenging problems in genomics. Prior to founding Fulcrum Genomics, Tim served as Director of Bioinformatics at the Broad Institute where he led the development and operation of pipelines for the institute’s Next Generation Sequencing (NGS) data, the bioinformatics strategy for the creation of a CLIA licensed clinical sequencing lab, and was the lead author of the industry standard Picard suite of programs for working with NGS data. Before moving into the life sciences, Tim was a business and technology consultant at Sapient Corporation where he developed innovative process and technological solutions to solve business challenges for clients in the Energy Services, Financial Services and Healthcare industries.

Nils Homer

Founding Partner

Nils Homer is a Founding Partner at Fulcrum Genomics LLC and has over a decade of cutting-edge experience developing methods and software for the analysis of next-generation sequencing data. He has led high-pace technology and product development efforts at both industry and academic positions, and has directed teams of software developers to support the largest academic genome sequencing facility in the world for both research and clinical applications. Nils has also participated in the technology development and subsequent commercial launch of multiple sequencing assays and technologies, providing critical understanding for technical improvements in chemistry, molecular biology, and software. He combines his skill in developing novel methods, algorithms, and software with his understanding of the data produced to provide key insights into biological research and discovery. Nils holds a Masters and PhD in Computer Science from UCLA investigating methods applied to genomics, including alignment and variant detection for whole genome sequencing. He received his BA (Computer Science and Mathematics) from Colgate University. Nils previously served on the Scientific Advisory Board for Edico Genome until acquisition by Illumina.

Clint Valentine

VP of Operations

Clint Valentine leads operations at Fulcrum Genomics and supports a team of bioinformatics scientists, software engineers, and technology professionals. Previously, Clint was the VP of Data Sciences at TwinStrand Biosciences, Inc., where he spearheaded the growth of multiple successful R&D and technology teams responsible for developing new RUO and clinical NGS software products, analytical professional services, IT, and clinical data management. Throughout his career, Clint has pioneered innovative NGS methods that are now disrupting the fields of genetic toxicology and cancer minimal residual disease monitoring. He is passionate about making discoveries that advance our understanding of the early initiating events of cancer and how to ultimately prevent disease, as well as modern software development and its potential to improve human health outcomes. Clint holds a BS in Biology, a BS in Environmental Science, and an MS in Bioinformatics from Northeastern University. He also serves on national leadership committees for genetic toxicology and provides advisory support to Northeastern University as a member of the Bioengineering Industrial Advisory Board.

Charlotte Tolonen

Chief of Staff

Charlotte has more than 20 years’ varied experience in genomics operations management. Most recently she designed technical relationships and strategy for large-scale genomic collaborations within the AnVIL. Previously she founded and then led the Broad Institute Genome Sequencing Center’s Data Operations team, which managed efficient processing and data management strategy for high-throughput genomics data. Prior to that she implemented operations at the Whitehead Institute Center for Genome Research under the CIO as the team became the Broad Institute’s Computational Biology group. Charlotte earned a BA in Environmental, Population, and Organismic Biology from the University of Colorado, Boulder and an MSc in Systems and Synthetic Biology from Université Paris-Saclay.

John Didion

Director of Engineering

John has over 20 years of experience as a professional software engineer, including more than 10 years applying his skills to the life sciences. Most recently, he was the Senior Director of Bioinformatics at Apton Biosciences, where he led a cross-functional team supporting the development of an ultra-high throughput sequencing instrument, until it was acquired by PacBio in 2023. Previously he was a Director of Engineering at DNAnexus, where he led the development of industry-standard cloud-based bioinformatics workflows, as well as the company’s flagship dxCompiler product, which automates the execution of Workflow Description Language (WDL) and Common Workflow Language (CWL) pipelines on the cloud. He also held roles in academia and industry, applying multi-omic data analysis to challenges in oncology and common disease. John is passionate about bringing good software engineering practices to the life sciences, and he actively maintains and contributes to a variety of open-source projects that benefit from his experience and skills. John holds a PhD in Bioinformatics and Computational Biology from the University of North Carolina at Chapel Hill, and a BS in Computer Science from Northwestern University. He currently serves as a member of the OpenWDL core team.

Jeff Gentry

Distinguished Bioinformatics Engineer

Jeff Gentry has over two decades of experience applying software engineering to the life sciences. His focus has been democratizing large scale data analytics. Most recently he served as Director of Engineering at Foundation Medicine overseeing software development for their Real World Data / Real World Evidence (RWD/RWE) data products. Before that Jeff led the Batch Data Analytics group at the Broad Institute. This included the creation of the Cromwell workflow system, the Workflow Description Language (WDL), and workflow support in Terra. His prior roles include application & tool development and partnering with scientists to develop high quality software for their project. He is a member of the leadership teams for both WDL and the Common Workflow Language (CWL). 

Yossi Farjoun

Principal Bioinformatics Scientist

With a background in applied mathematics and over a decade of experience with analyzing genomic data in various contexts, Yossi applies his analytical skill and programming expertise to bioinformatic challenges. Yossi enjoys exploring complex data, learning about new technologies and improving analysis methods. His favorite work-related activities are developing models and algorithms, and learning about new technologies and ideas. Pet peeves include p-hacking and post-hoc statistical analysis. His non-work activities include rock-climbing, ceramics, glass-blowing, yoga, and swimming. 

Ted Brookings

Staff Bioinformatics Scientist

Ted Brookings has 5 years of experience developing algorithms and cloud pipelines for structural variant discovery. He received his PhD in physics from UC Santa Barbara for work in the intersection of theoretical neuroscience and complex systems. He then spent ten years analyzing and developing models of electrophysiology data as a postdoc in a wet lab at Brandeis, and then as a software engineer at Q-State Biosciences. Subsequently he joined the structural variants group at the Broad Data Sciences Platform, and helped stand up the experimental structural variant pipeline.

Jess Smith

Staff Bioinformatics Scientist

Jess Smith has worked in bioinformatics for the last decade following completion of her doctorate at UC Berkeley. Trained in the physical sciences, she is always excited to learn about new sequencing platforms and to consider the physical processes and molecular mechanisms involved in generating sequencing data. Her experience spans a wide variety of data types including both short-read and long-read data, with a particular emphasis on small genomes and low-complexity assays. She has experience in early stage biotechnology companies and non-profit research institutions in and adjacent to immuno-oncology, antibody discovery, molecular diagnostics, and core sequencing technology improvements. She has a high tolerance for ambiguous scientific questions or messy data and a low tolerance for complicated solutions to simple problems.

Matt Stone

Staff Bioinformatics Scientist

Matt has 8 years of experience engineering bioinformatics solutions and completing novel genomics analysis. His expertise spans a diverse range of biological contexts, including immunotherapy, spatial and single-cell transcriptomics, and structural variant discovery. Matt was most recently the bioinformatics lead at Modulus Therapeutics in Seattle, where he developed pipelines and analyses to support CAR NK therapeutic discovery. Prior to his role at Modulus, Matt was the lead data scientist for the Fred Hutch Innovation Lab where he managed collaborations with industry partners to incubate novel single-cell RNA, spatial RNA, and TCR sequencing technologies. Matt excels as the interface between the wet and dry lab; he cares deeply about collaborating with lab scientists to understand the data they generate and how to advance scientific discovery with a mind for translational applications and improving human health outcomes. He is passionate about best practices in software engineering and has a keen eye for details in data. Matt has a BA in Computer Science from Dartmouth College and an MS in Biomedical Data Science from the University of Wisconsin-Madison.

Jason Fan

Senior Bioinformatics Engineer

Jason is passionate about building performant solutions and practicing good engineering principles in the life sciences.  In 2023, Jason received his PhD in Computer Science from University of Maryland, College Park where his work was funded by the National Science Foundation Graduate Research Fellowship Program and the Chan-Zuckerberg Initiative.  At UMD, Jason built fast and accurate indexes for analyzing huge reference sequence collections. He has also developed matrix factorization algorithms for data imputation, and mutational signature analysis in cancer.  Away from his desk, you might find Jason climbing on large rocks or swinging at tennis balls.

Erin McAuley

Senior Bioinformatics Scientist

Erin is interested in solving difficult bioinformatics challenges in order to advance scientific discovery and benefit human health outcomes. She received her PhD from the University of Chicago, where she studied adult epithelial stem cells and their contribution to tissue homeostasis, regeneration, and tumorigenesis. She has previously worked with federal agencies like the CDC to develop and standardize workflows for processing genomic sequencing data. Prior to Fulcrum Genomics, Erin worked in the clinical genetics space at Invitae. As a bioinformatics engineer, she supported production-level Nextflow pipelines for hybrid capture NGS analysis and optimized variant calling algorithms for hard-to-sequence genes.