Bionano Brand Guidelines: BioNanomatrix, Nanochannels & Optical Genome Mapping

Princeton nanochannels and a Philadelphia start-up.

Bionano began as BioNanomatrix. The company’s annual report for 2025 says it was formed in January 2003 as BioNanomatrix LLC, became BioNanomatrix Inc. in August 2007, changed its name to BioNano Genomics in October 2011 and adopted its current spelling, Bionano Genomics, in July 2018 — the change was a single lower-case n, which gave the brand the one-word form it uses today.

Its technology came from Princeton University. In March 2009 The Daily Princetonian described a method for stretching out DNA in extremely narrow channels, developed by the physics professor Robert Austin and the engineering professor Stephen Chou. Long, tangled DNA molecules could be threaded into the channels and gently pulled straight, Austin explained, “like threading string through the eye of a needle.” The paper reported that the method had been licensed since 2003 by the Philadelphia-based company BioNanomatrix, founded by Han Cao, a biologist in Chou’s laboratory, who was its chief scientific officer. The article added that the nanofluidics approach had been named one of the Ten Emerging Technologies of 2009 by MIT’s Technology Review.

The aim was not to read DNA letter by letter. Cao told the paper the technology would most likely be used to look at large-scale rearrangements of the genome — how many copies of a gene a person carries, or whether sections have been flipped — and Austin said its use would “not be sequencing per se.” The advantage, the paper explained, was that the method does not shred the genetic material into tens of thousands of pieces before reading it. Edward Cox, a Princeton professor of molecular biology, had also contributed to the early development, the paper said.

Saphyr, Stratys and a listing.

By the time it went public the company was based in San Diego. In June 2018 Renaissance Capital reported that Bionano Genomics, a San Diego company founded in 2003, had filed to list on Nasdaq under the symbol BNGO, and described it as developing the Saphyr system for next-generation genome mapping; Roth Capital was the sole bookrunner on the offering.

The method is called optical genome mapping. As the company describes it, very long DNA molecules are isolated, fluorescent labels are attached at a short sequence that recurs across the genome, and the labelled molecules are straightened in nanochannel arrays on a chip and imaged; software then looks for changes in the pattern of labels that point to structural variants. The company says its labelling step recognises a six-letter sequence that occurs roughly 14 to 17 times in every 100,000 bases of human DNA. Bionano says Saphyr works with molecules from 150,000 base pairs to several million in length.

A newer, higher-throughput instrument, Stratys, followed. The company’s 2025 annual report says it has been placing the system selectively since the end of 2022; the website says it can hold twelve sample chips at once, loaded individually or in batches, with space reserved for three priority samples so urgent runs can “jump the queue.” Both instruments are sold, the site’s footer states, “For Research Use Only.”

On manufacturing, the annual report is specific. Saphyr is built by a third-party medical-device manufacturer; the first Stratys units were made in-house, with production due to move to the same contract maker. The chip consumables are produced by third-party manufacturers at their facilities, and Bionano completes final assembly and quality-control checks of the chips at its headquarters in San Diego.

Instruments, flow cells and data.

DNA sequencing and genomics-tools companies sell to scientists, yet their pictures tend to repeat a small set of scenes: a benchtop instrument with a glowing panel in a clean, bright laboratory; a flow cell or chip held between gloved fingers; a colourful double helix or a data visualisation; a researcher studying results on a screen. Because the chemistry itself is invisible, the hardware, the consumables and the data become the main images.

Conferences are where many of these companies meet their customers. The Advances in Genome Biology and Technology meeting, known as AGBT, and the annual meeting of the American Society of Human Genetics, known as ASHG, are regular venues for news. Oxford Nanopore says it presented its first nanopore sequencing data at AGBT in February 2012, and Genetic Engineering & Biotechnology News reported in November 2024 that PacBio introduced its Vega benchtop sequencer at ASHG with a concert. Some companies run their own events too: Oxford Nanopore says it held the first London Calling conference for its users in May 2015.

Names and colours do much of the identity work. Instruments carry short, memorable product names, and some companies give their hardware one recognisable colour; GEN reported that PacBio’s new look, introduced with its Revio sequencer, came with a commitment to pink. The palettes in these guides are our own interpretations, not official colour standards.

This guide sets out what can be checked about each company — who founded it, who owns it, and which platforms it sells — and marks clearly what rests only on the company’s own word. Where a company describes its instruments as for research use only, or says they are not intended for diagnosis, as PacBio and Oxford Nanopore do, we report that as the company states it.

Acquisitions, cutbacks and a reverse split.

After the listing, Bionano grew by acquisition. Its annual report records the purchase of Lineagen in August 2020, BioDiscovery in October 2021 and Purigen in November 2022. Alongside its mapping systems, the website now sells the Ionic purification system, which uses a technique called isotachophoresis to isolate DNA and RNA, and the VIA analysis software. The Ionic system, the company says, works without columns, beads or repeated washing steps, separating nucleic acids from impurities with an electric field along the channels of a chip.

The years since have been leaner. The 2025 annual report refers to cost-saving initiatives and headcount reductions announced in 2023 and 2024, and to several rounds of workforce reductions. The same report says the company’s Bionano Laboratories unit phased out certain testing services during 2024 and 2025, and that Bionano is no longer investing in three multicentre studies it had supported. In a release dated 22 January 2025, filed with the US Securities and Exchange Commission, the company announced a 1-for-60 reverse stock split, effective on 24 January 2025, with split-adjusted trading on Nasdaq from 27 January. The 2025 annual report gives the company’s headquarters as San Diego.

The company’s own language stays close to the method. Its website speaks of revealing “all classes of structural variants” and states a mission to “transform the way the world sees the genome.”

For a design guide, Bionano shows how a company can build an identity around a way of seeing rather than a way of reading. Compare PacBio, another company built around long DNA molecules, and Illumina, its San Diego neighbour in sequencing. For this guide we use indigo, violet and silver with a sans, an unofficial interpretation; no product or logo is reproduced.

Keep Bionano’s identity on hand — save it to a board in the Made Good inspiration library.