Opentrons Publications and Citations

At Opentrons, we began making robots for biologists so they can conduct their research faster and more reproducibly.

And it’s working.

We’ve seen nearly two dozen citations over the last two years from scientists using our platform, and we're seeing more every day. Biologists are citing Opentrons in publications, preprints, conference papers, articles, and even in their graduate thesis projects! We are thrilled to be a part of these projects, and we are thrilled to share them with you.

Here’s a sample of some of the ways Opentrons is being cited:


Microbiology

PAPER: Mice Fed an Obesogenic Western Diet, Administered Antibiotics, and Subjected to a Sterile Surgical Procedure Develop Lethal Septicemia with Multidrug-Resistant Pathobionts
A paper describing the effects of an obesogenic Western diet on post-surgical infection outcomes. The international research team led by the University of Chicago used Opentrons for library pooling in their 16s rRNA sequencing pipeline. Here’s an excerpt:

The results of the quantification were used to normalize the amount of DNA from the PCR product to use for sequencing and to ensure that each amplicon was represented evenly during sequencing. These volumes were then sequentially consolidated into a single tube using an OpenTrons liquid-handler running a custom Python script.

Read the paper in mBio


DIY Bio

ARTICLE: A DIY Approach to Automating Your Lab
An article from Mike May describing how using flexible research equipment solutions like Opentrons helps biologists save time and money, and empowers them with increased customization. Here’s an excerpt:

[Researchers] intimidated by building instruments from scratch can take a middle-ground approach and modify existing hardware. Greenwald, for instance, tweaked the OT-One, a robotic pipetting system made by Opentrons in New York City, to automate reagent addition and sample imaging in cell-signalling studies.

Read the article in Nature


Synthetic Biology

PREPRINT: DNA-BOT: A Low-Cost, Automated DNA Assembly Platform For Synthetic Biology
A preprint from researchers at Imperial College London detailing how they created a fully automated DNA assembly method for a variety of synthetic biology applications. Here’s an excerpt:

Automating DNA assembly enables larger builds using less researcher time, increasing the accessible design space. However, these benefits currently incur high costs for both equipment and consumables. Here, we address this limitation by introducing low-cost DNA assembly with BASIC on Opentrons (DNA-BOT).

Read the preprint on bioRxiv

ARTICLE: Improving Reproducibility in Synthetic Biology
An article from researchers at the Novo Nordisk Foundation Center for Biosustainability in Denmark describing ways to alleviate the problems of reproducibility in synthetic biology - and citing Opentrons as a key part of building that future. Here’s an excerpt:

A recent Kickstarter campaign from Opentrons has aimed to address both the demand for a low cost and flexible liquid handler. The resulting OT-One robot has proved popular in both academia and industry, enabling Opentrons to establish itself in the field of lab automation.

Read the article in Frontiers in Bionengineering and Biotechnology

PAPER: Rapid Production and Recovery of Cell Spheroids by Automated Droplet Microfluidics
A preprint from researchers at Sweden's SciLifeLab describing ways to streamline loading of microfluidics using an Opentrons liquid handling robot. Here’s an excerpt:

As a continuous phase a hydrofluoroether (HFE, 3M™ Novec™ 7500 Engineered Fluid) with 1% PEG-PFPE amphiphilic block copolymer surfactant (Ran Biotechnologies) was used. 1ml of HFE with 1% of the surfactant was added to the continuous phase reservoir with the aid of a pipetting robot (Opentrons OT-One-S Hood). This primes the micro-channels, limiting to the minimum the amount of air trapped inside the network of microfluidic channels.

Read the paper in SLAS Technology OR the NCBI abstract

POSTER: Flexible Automated Platform for the Assembly and Test of Recombinase State Machine-Based Genetic Circuits
A poster from Boston University’s DAMP Lab detailing how to create better, easy-to-use, scalable recombinase state machine (RSM) based genetic circuits with automation. Here’s an excerpt:

Our standardized RSM assembly pipeline explores both Gibson (Synthetic Genomics) and BASIC (Imperial College-REF) methodologies utilizing the OT-2 (Opentrons) low-cost liquid handling robot.

View the poster online


Genetics & Gene Editing

PREPRINT: Synthetic Genetic Codes Designed to Hinder Evolution
A preprint from researchers at [Stanford University] (https://engineering.stanford.edu/people/drew-endy) describing the creation and testing of point mutations of protein-coding sequences in E.coli. Here’s an excerpt:

We show by in vitro experiments that a reduced set of 21 tRNA is capable of expressing a protein whose coding sequence is recoded to use a fail-safe code, whereas a standard-code encoding is not expressed.

Read the preprint on biorXiv

PREPRINT: PlasmoTron: an Open-Source Platform For Automated Culture of Malaria Parasites
A preprint from researchers at the Sanger Institute describing an inexpensive open-source lab automation system to automate malaria parasite culture. Here’s an excerpt:

The mere concept of parasitaemia, and the need to maintain the correct ratio of two different culture components, blood and media, is unique to parasitology and so can be difficult to implement in commercial systems which were not intended for this relatively niche purpose. A potential solution is the OpenTrons system, which is considerably cheaper than any other liquid-handling system, and also very flexible, meaning that it could potentially be adapted to the unique requirements of Plasmodium culture.

Read the preprint on biorXiv

PAPER: FusX: A Rapid One-Step Transcription Activator-Like Effector Assembly System for Genome Science
A paper from researchers at the Mayo Clinic describing a novel, low-cost, automated, and streamlined Golden Gate TALE assembly system called FusX, along with its applications in zebrafish gene editing. Here’s an excerpt:

We show that the FusX system can be readily adapted using a laboratory automation tool, the OpenTrons liquid-handling robot, enabling the rapid scaling of this protocol from in silico TALEN design tools.

Read the paper in Human Gene Therapy


Endocrinology

PAPER: Measuring Luteinising Hormone Pulsatility with a Robotic Aptamer-Enabled Electrochemical Reader
A paper from researchers at the University of Hong Kong describing a novel approach to automating luteinising hormone pulsatility for rapid clinical diagnosis of reproductive disorders. Here’s an excerpt:

We report the development and application of a Robotic APTamer-enabled Electrochemical Reader (RAPTER) electrochemical analysis system to determine luteinising hormone pulsatility.

Read the paper in Nature Communications


Thesis

THESIS: Robot-Trifle: A Robotic System for Automated Combinatorial Growth Phenotyping
A master's thesis from Jeremy Kimball at the University of Illinois describing a streamlined, automated analysis pipeline to create microorganism growth phenotypes. Here’s an excerpt:

This project, robot-trifle, is an analysis pipeline for streamlining the automated construction of minimal chemically-defined media for microorganisms known to grow in culture. [...] The robot itself used for this project is an open hardware autopipettor [sic] available from Opentrons.

Read Jeremy's thesis


Again, these are only a sample of some of the ways Opentrons is being used. We already know of some really exciting research our community is working on with papers coming in the fall, so stay tuned! We’ll share those when they become public.

We’ll be updating this list regularly. Please come and check it out!

Current Opentrons users: have you cited us? Are you planning to? We’d love to know! Email us at community@opentrons.com so we can share your work with the rest of our community.