Opentrons Publications and Citations

Scientists have cited Opentrons nearly three dozen times over the past four years -- in peer-reviewed publications, preprints, conference papers, articles, and even in their graduate thesis projects -- and that's only the beginning! Here's a few examples.

At Opentrons, we began making robots for life scientists so they could conduct their research faster and more reproducibly.

And it’s working.

We’ve seen nearly three dozen citations over the last four years from scientists using our platform, and we're seeing more every day -- especially for our new Pandemic Response Lab. Biologists, chemists, and many other life scientists 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 are some of our citations:

We're constantly adding more, so keep checking this page! ___________________________________________________


PAPER: Automated Rational Strain Construction Based On High-Throughput Conjugation

A paper from researchers at Jülich Research Centre outlining an automated end-to-end molecular biology cloning procedure using the OT-2 as part of the genetic engineering workflow. Here's an excerpt:

*The decision to use two different liquid handling systems was motivated by the need to use lab equipment most efficiently: Whenever possible, the OT-2 was used to carry out a unit operation. This saved time compared to the more expensive EVO 200, which thus could be used for more demanding experiments…. To make the workflow as accessible as possible, it would be beneficial to only use the OT-2.

Read the paper in ACS

PAPER: Detection and characterization of the SARS-CoV-2 lineage B.1.526 in New York
A paper from researchers at California Institute of Technology detailing Opentrons’ Pandemic Response Lab (PRL)’s use of genome sequencing to detect the SARS-CoV-2 B.1.526 variant -- now known as the New York variant. Here’s an excerpt:

*As part of public health surveillance conducted by the New York City Public Health Laboratory (NYC PHL) and the Pandemic Response Lab (PRL) in New York, approximately 4.5 thousand SARS-CoV-2 genomes have been sequenced by NYC PHL and PRL from December 1, 2020 to February 28th, 2021.

Read the preprint in bioRxiv

PAPER: Evaluation Of Two Automated Low-Cost RNA Extraction Protocols For SARS-CoV-2 Detection

A paper from researchers at Hospital Universitario La Paz detailing two low-cost automated protocols for high-throughput RNA extraction in SARS-CoV-2 testing. Here's an excerpt:

*One hundred forty one SARS-CoV-2 positive samples were collected during a period of 10-days. In-house protocols were based on extraction with magnetic beads and designed to be used with either the Opentrons OT-2 liquid handling robot or the MagMAXTM Express-96 system.

Read the paper in PLOSOne

PAPER: Implementation Of An Efficient SARS-CoV-2 Specimen Pooling Strategy For High Throughput Diagnostic Testing

A paper from researchers at University of KwaZulu-Natal describing a low-cost high throughput method of RT-PCR pool testing for SARS-CoV-2 using the OT-2. Here’s an excerpt:

*To reduce these intensive demands on laboratory staff as well as the risk of human error, we have implemented an automated pipeline using a liquid-handling robot, Opentrons OT-2. This open source robotic platform lends itself to scalability and rapid deployment. The OT2 is modularly constructed and utilises widely available non-proprietary electronic components that are neither difficult nor expensive to repair or replace.

Read the paper in Nature

PAPER: Rapid Emergence and Epidemiologic Characteristics of the SARS-CoV-2 B.1.526 Variant
A summary from researchers at the Center for Disease Control and Prevention outlining the characteristics of the SARS-CoV-2 B.1.526 variant -- now known as the New York variant -- citing Opentrons’ Pandemic Response Lab (PRL)’s data. Here's an excerpt:

SARS-CoV-2 specimens were sequenced at the Public Health Laboratory (PHL) or the Pandemic Response Laboratory (PRL). During January 1–April 5, 2021, PHL received specimens primarily from NYC residents at nine COVID Express laboratories.

Read the report at the CDC

PAPER: ROBOCOV: An Affordable Open-Source Robotic Platform For SARS-CoV-2 Testing By RT-qPCR

A paper from researchers at Hospital Clinic de Barcelona demonstrating an automated reproducible workflow for RT-qPCR SARS-CoV-2 testing. Here's an excerpt:

The advent of the affordable OT-2 open-source liquid handling robots, developed by Opentrons, has opened the door to low-cost automated solutions. The stations, initially conceived to perform simple pipetting tasks in research labs, can be concatenated to produce more complex workflows.

Read the preprint in bioRxiv

PAPER: CONTAIN: An Open-Source Shipping Container Laboratory Optimised For Automated COVID-19 Diagnostics
A paper from scientists at OpenCell Bio and King's College London detailing how to create a modular biosafety level 2+ laboratory optimised for automated RT-qPCR COVID-19 testing based on a standard 40ft shipping container. Here's an excerpt:

We have developed automated protocols for RNA extraction and qPCR plate preparation for the open-source and low-cost Opentrons OT-2 liquid handlers... The use of open-source hardware and reagents allow labs to navigate around limited supply chains. The OT-2 liquid handling robot has a low initial cost relative to other liquid handling robots, can utilise generic plasticware and run protocols written in the coding language Python.

Read the preprint on bioRxiv

PAPER: Leveraging Open Hardware to Alleviate the Burden of COVID-19 on Global Health Systems
A paper summarizing free and open-source scientific and medical hardware developed and deployed for COVID-19 prevention, patient treatment and diagnostics. The research team led by the University of Sussex cites Opentrons' open-source hardware platform for COVID-19 surveillance testing system. Here’s an excerpt:

... open platforms for scaling reactions as exemplified by Opentrons, an open source lab automation platform that has been working with BP Genomics and the Open Medicine Institute to automate up to 2,400 tests per day and achieve US FDA EUA approval and is now automating COVID-19 testing at the Biomedical Diagnostic Center (CBD) of Hospital Clinic of Barcelona...

Read the paper in PLOS Biology


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

PAPER: Catalyzing rapid discovery of gold-precipitating bacterial lineages with university students
A paper from researchers at North Carolina State University describing an interdisciplinary program to engage students in genetic sampling, identification, and analysis of the microbe, Delftia spp. Here’s an excerpt:

Liquid handlers can be cost-prohibitive, but less expensive models such as the Opentrons OT-2 are available, and we are developing scripts for this instrument.

Read the preprint on PeerJ

Lab Automation

PAPER: Automated 3D Microphysiometry Facilitates High-Content And Highly Reproducible Oxygen Measurements Within 3D Cell Culture Models
A paper from researchers at Queensland University of Technology detailing a fully automated microphysiometry setup for viewing 3D cell culture models. Here's an excerpt:

Our data suggest that the microphysiometry setup enables highly reproducible measurements without human intervention, due to the high degree of automation and positional accuracy.

Read the paper in ACS

PAPER: Automation in the Life Science Research Laboratory
A paper from researchers at the University of Edinburgh outlining the difficulties of academic labs to adopt automation tools to augment or replace manual tasks for greater efficiency, time savings, and accuracy. Here's an excerpt:

Small-to medium-sized automation companies have often been most successful at innovative development of laboratory equipment, funded through grant schemes in cooperation with an academic institution or external venture capital funding. Examples include... OpenTrons (sic).

Read the article in Frontiers in Bioengineering and Biotechnology

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

PAPER: An Open-Source Technology Platform To Increase Reproducibility And Enable High-Throughput Production Of Tailorable Gelatin Methacryloyl (GelMA) - Based Hydrogels
A paper from researchers at Queensland University of Technology describing an open-source fully automated platform for high-throughput production of GelMA-based 3D constructs. Here's an excerpt:

An open-source pipetting robot (OT-One S Hood, Opentrons, Inc., NY, USA) was integrated with modified hardware and software components to accommodate the operation of two positive-displacement pipettes.

Read the paper in Science Direct

PAPER: An Open Source Technology Platform to Manufacture Hydrogel-Based 3D Culture Models in an Automated and Standardized Fashion
A paper from researchers at Queensland University of Technology detailing an open-source automation protocol to mix viscous materials. Here's an excerpt:

Manual-based workflows are limiting the advancement and widespread adoption of viscous materials, such as hydrogels used for biomedical applications. These challenges can be overcome by using automated workflows with standardized mixing processes to increase reproducibility.

View the paper in video journal JoVE

PAPER: OpenWorkstation: A Modular Open-Source Technology For Automated In Vitro Workflows
A paper from researchers at Queensland University of Technology outlining an assembly line style end to end fully automated lab platform consisting of customizable, open-source, off-the-shelf hardware. Here's an excerpt:

Opentrons API – A Python framework was designed to write protocol scripts for the pipetting module (OT-1).

Read the paper in Science Direct

PAPER: Unlocking The Efficiency of Genomics Laboratories With Robotic Liquid-Handling
A paper from researchers at the University of KwaZulu-Natal describing the increasing trend of genomics laboratories to invest in liquid-handling automation to make high-throughput next generation sequencing (NGS) workflows more efficient and cost effective. Here's an excerpt:

Open source programming robots boast at being the most flexible liquid-handling systems. Opentrons robots are fully modular in terms of protocol design and new protocols or labware can be easily coded into a versatile programmatic interface.

Read the paper at BMC Genomics

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: Drag-and-drop Genome Insertion without DNA Cleavage with CRISPR-Directed Integrases
A preprint from researchers at MIT describing drag-and-drop genome insertion without DNA cleavage with CRISPR-directed integrases. Here’s an excerpt:

Programmable and multiplexed genome integration of large, diverse DNA cargo independent of DNA repair remains an unsolved challenge of genome editing...We present Programmable Addition via Site-specific Targeting Elements, or PASTE, which achieves efficient and versatile gene integration at diverse loci by directing insertion with a CRISPR-Cas9 nickase fused to both a reverse transcriptase and serine integrase.

PREPRINT: Synthetic Genetic Codes Designed to Hinder Evolution
A preprint from researchers at Stanford University 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

Mass Spectometry

PAPER: A Semiautomated Paramagnetic Bead-Based Platform For Isobaric Tag Sample Preparation
A paper from researchers at Harvard Medical School detailing the performance of an OT-2 for isobaric tag sample preparation against manual pipetting. Here’s an excerpt:

We also provide the community with open-source templates for automating routine proteomics workflows on an opentrons OT-2 liquid handler.

Read the paper on Journal of the American Society for Mass Spectrometry

PAPER: Fully Automated Sample Processing and Analysis Workflow for Low-Input Proteome Profiling

A paper from researchers at the Brigham Young University describing a fully automated platform using only commercially available instrumentation for sample processing and analysis for protein profiling. Here’s an excerpt:

Of the many automated liquid handling systems available on the market today, the OT-2 is particularly attractive because of its low price (currently, $5000 plus the cost of accessories), which should be accessible to many laboratories.

Read the paper in Analytical Chemistry


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: 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, 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 so we can share your work with the rest of our community.

Related Readings