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Publications

Peer-reviewed papers, patents, and citations from the TeselaGen team and the broader scientific community.

Papers by TeselaGen

Research authored or co-authored by members of the TeselaGen team.

A Procedural Framework for Benchmarking Biofoundry Capabilities

Nathan J. Hillson

2023ACS Synthetic Biology, 12.12, 3778–3782

Perspectives for self-driving labs in synthetic biology

Hector G. Martin, et al.

2023Current Opinion in Biotechnology, 79, 102881

Ten simple rules for managing laboratory information

Casey-Tyler Berezin, et al.

2023PLoS Computational Biology, 19.12, e1011652

Automated platform for the plasmid construction process

Alberto A. Nava, et al.

2023ACS Synthetic Biology, 12.12, 3506–3513

Engineering Biology for Climate and Sustainability: A research roadmap for a cleaner future

Engineering Biology Research Consortium

2022NSF Report

Making security viral: shifting engineering biology culture and publishing

Rebecca Mackelprang, et al.

2022ACS Synthetic Biology, 11.2, 522–527

Multiomics data collection, visualization, and utilization for guiding metabolic engineering

Somtirtha Roy, et al.

2021Frontiers in Bioengineering and Biotechnology, 9, 612893

BioParts—a biological parts search portal and updates to the ICE parts registry software platform

Hector A. Plahar, et al.

2021ACS Synthetic Biology, 10.10, 2649–2660

Synthetic biology: at the crossroads of genetic engineering and human therapeutics

Jennifer Cable, et al.

2021Annals of the New York Academy of Sciences, 1506.1, 98–117

An integrated computer-aided design and manufacturing workflow for synthetic biology

Ernst Oberortner, et al.

2020Springer US

Combining mechanistic and machine learning models for predictive engineering and optimization of tryptophan metabolism

Jie Zhang, et al.

2020Nature Communications, 11.1, 4880

Combinatorial-hierarchical DNA library design using the TeselaGen DESIGN Module with j5

Michael J. Fero, et al.

2020Springer US

DNA Scanner: a web application for comparing DNA synthesis feasibility, price and turnaround time across vendors

Gledon Doci, et al.

2020Synthetic Biology, ysaa011

Repurposing a microfluidic formulation device for automated DNA construction

Garima Goyal, et al.

2020PLoS ONE, 15.11, e0242157

Building a global alliance of biofoundries

Nathan Hillson, et al.

2019Nature Communications, 10.1, 2040

SBOL visual: a graphical language for genetic designs

Jacqueline Y. Quinn, et al.

2015PLoS Biology, 13.12, e1002310

PR-PR: cross-platform laboratory automation system

Gregory Linshiz, et al.

2014ACS Synthetic Biology, 3.8, 515–524

The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology

Michal Galdzicki, et al.

2014Nature Biotechnology, 32.6, 545–550

j5 DNA assembly design automation

Nathan J. Hillson

2014DNA Cloning and Assembly Methods, 245–269

Proposed design of distributed macroalgal biorefineries: thermodynamics, bioconversion technology, and sustainability implications

Alexander Golberg, et al.

2014Biofuels, Bioproducts and Biorefining, 8.1, 67–82

PaR-PaR laboratory automation platform

Gregory Linshiz, et al.

2013ACS Synthetic Biology, 2.5, 216–222

Synthetic Biology Open Language Visual: An Open-Source Graphical Notation for Synthetic Biology

Jacqueline Quinn, et al.

20135th International Workshop on Bio-Design Automation

Synthetic biology open language (SBOL) version 1.1.0

Michal Galdzicki, et al.

2012MIT DSpace

Publications Citing TeselaGen

Independent research that references or builds upon TeselaGen technology.

Atypical contribution of caspase-3 to melanoma cancer cell motility by regulation of coronin 1B activity

Kevin Berthenet, et al.

2024bioRxiv, 2024-06

The Convergence of AI and Synthetic Biology: The Looming Deluge

Cindy Vindman, et al.

2024arXiv preprint, 2404.18973

Data-driven learning of structure augments quantitative prediction of biological responses

Yuanchi Ha, et al.

2024PLOS Computational Biology, 20.6, e1012185

AutoESDCas: A Web-Based Tool for the Whole-Workflow Editing Sequence Design Based on CRISPR/Cas

Chunhe Yang, et al.

2024ACS Synthetic Biology

Designing a synthetic moss genome using GenoDesigner

Wenfei Yu, et al.

2024Nature Plants, 1–9

teemi: An open-source literate programming approach for iterative design-build-test-learn cycles

Søren D. Petersen, et al.

2024PLOS Computational Biology, 20.3, e1011929

Synthetic biology open language (SBOL) version 3.1.0

Lukas Buecherl, Chris J. Myers

2023Journal of Integrative Bioinformatics, 20.1, 20220058

Literate programming for iterative design-build-test-learn cycles in bioengineering

Søren Petersen, et al.

2023bioRxiv, 2023-06

Biological and Environmental Research network requirements review final report

Jason Zurawski, et al.

2023eScholarship, UC

Identification of optimal sgRNA candidates for mutagenesis of the ALS1 gene in Ipomoea batatas

Neda Kianpour

2023MS thesis, Inland Norway University

Tracking of plasmodesmata localization with the use of fluorescently labelled VAP27 protein

Irina Kulamikhina, Natalia Kanunnikova, Olga Selezneva

2023BIO Web of Conferences, 78

Accelerating engineered microbe optimization through machine learning and multi-omics datasets

Hector Garcia Martin

2023Lawrence Berkeley National Laboratory

Carbon-negative production of acetone and isopropanol by gas fermentation at industrial pilot scale

Fungmin Eric Liew, et al.

2022Nature Biotechnology, 40.3, 335–344

Engineering genetic circuits: advancements in genetic design automation tools and standards

Lukas Buecherl, Chris J. Myers

2022Current Opinion in Microbiology, 68, 102155

Bioinformational trends in grape and wine biotechnology

Thomas A. Dixon, Thomas C. Williams, Isak S. Pretorius

2022Trends in Biotechnology, 40.1, 124–135

Automation and analysis of high-dimensionality experiments in biocatalytic reaction screening

Shama Chilakwad

2022Dissertation, UCL

New synthetic biology tools for metabolic control

Xueqin Lv, et al.

2022Current Opinion in Biotechnology, 76, 102724

Machine learning guided batched design of a bacterial Ribosome Binding Site

Mengyan Zhang, et al.

2022ACS Synthetic Biology, 11.7, 2314–2326

Genetic Circuit Design Principles

Jing Wui Yeoh, et al.

2022Handbook of Cell Biosensors, 339–381

Construction of multiscale genome-scale metabolic models: Frameworks and challenges

Xinyu Bi, et al.

2022Biomolecules, 12.5, 721

The mitochondrial genome and Epigenome of the Golden lion Tamarin from fecal DNA using Nanopore adaptive sequencing

Nicole Wanner, et al.

2021BMC Genomics, 22, 1–11

Thailand Synthetic Biology Ecosystem Assessment and Recommendations

Innovation Policy Council

2021NXPO Report

Setting up an automated biomanufacturing laboratory

Marilene Pavan

2021Synthetic Gene Circuits: Methods and Protocols, 137–155

Developing Novel Methods for Co-translational Studies of Membrane Protein Folding

Grant Pellowe

2021Dissertation, King’s College London

Aquarium: open-source laboratory software for design, execution and data management

Justin Vrana, et al.

2021Synthetic Biology, 6.1, ysab006

CDMOs Embrace Industry 4.0 to Satisfy Customer Demand

Gareth John Macdonald

2021Genetic Engineering & Biotechnology News, 41.4, 43–45

SynBiopython: an open-source software library for Synthetic Biology

Jing Wui Yeoh, et al.

2021Synthetic Biology, ysab001

Commercial Biomolecules

Basanta Kumara Bahera, Ram Prasad, Shyambhavee Behera

2021Life Sciences Industry, Springer, 1–27

The grey zone of cyber-biological security

Thom Dixon

2021International Affairs, 97.3, 685–702

Synthetic biology open language (SBOL) version 3.0.0

Hasan Baig, et al.

2020Journal of Integrative Bioinformatics, 17.2-3, 20200017

Cell-free biocatalysis for the production of platform chemicals

Peter L. Bergquist, Sana Siddiqui, Anwar Sunna

2020Frontiers in Energy Research, 8, 193

Domain interactions determine the conformational ensemble of the periplasmic chaperone SurA

Dagan C. Marx, et al.

2020Protein Science, 29.10, 2043–2053

Drawing on the past to shape the future of synthetic yeast research

Thomas A. Dixon, Isak S. Pretorius

2020International Journal of Molecular Sciences, 21.19, 7156

Innovation ecosystems in the bioeconomy

Jim Philp, David Winickoff

2019OECD Publishing

Better research by efficient sharing: evaluation of free management platforms for synthetic biology designs

Uriel Urquiza-García, et al.

2019Synthetic Biology, 4.1, ysz016

Definitive demonstration by synthesis of genome annotation completeness

Paul R. Jaschke, et al.

2019PNAS, 116.48, 24206–24213

Microsoft makes splash in AI-enabled lab solutions

Eric Smalley

2019Nature Biotechnology, 37.8, 832–835

Cyberbiosecurity for biopharmaceutical products

Jennifer L. Mantle, et al.

2019Frontiers in Bioengineering and Biotechnology, 7, 116

Life Formed: Evolutionary Design and the Futures of a Political Biology

Aubrey M. Yee

2019Dissertation, University of Hawai'i

Models for DNA design tools: The trouble with metaphors in synthetic biology

Erika Szymanski

2019ACS Synthetic Biology, 8.12, 2635–2641

Methods for predictable and accelerated engineering of metabolism in eukaryotes

Søren Dalsgård Petersen

2019Dissertation, DTU

Gene design goes automatic

Anna Nowogrodzki

2018Nature, 564.7735, 291–292

Genetics and Genetic Engineering

Tomas Cannon

2018Scientific e-Resources

US Department of Energy Bioenergy Research Centers: 10-Year Retrospective

N. Kent Peters, et al.

2018DOE/SC-0193

A standard-enabled workflow for synthetic biology

Chris J. Myers, et al.

2017Biochemical Society Transactions, 45.3, 793–803

Design automation in synthetic biology

Evan Appleton, et al.

2017Cold Spring Harbor Perspectives in Biology, 9.4, a023978

Genetic constructor: an online DNA design platform

Maxwell Bates, et al.

2017ACS Synthetic Biology, 6.12, 2362–2365

Software Compliance Testing For The Synthetic Biology Open Language

Meher Samineni

2017Dissertation, University of Utah

Genotype specification language

Erin H. Wilson, et al.

2016ACS Synthetic Biology, 5.6, 471–478

Design for the modern prometheus: towards an integrated biodesign workflow

Sunanda Sharma

2016Dissertation, MIT

An Investigation of Innovative Energy Technologies Entering the Market between 2009-2015

Lindsay M. Steele

2016PNNL-31017

The synthetic biology open language

Chris Myers, et al.

2015Computational Methods in Synthetic Biology, 323–336

DNA assembly tools and strategies for the generation of plasmids

Chang-Ho Baek, et al.

2015Plasmids: Biology and Impact in Biotechnology and Discovery, 599–613

Seeking Better Biofuels

Melody M. Bomgardner

2015Chemical & Engineering News, 93.42, 8–10

Molecular genetic techniques for algal bioengineering

Kenan Jijakli, et al.

2015Biomass and Biofuels from Microalgae, 155–171

PrecisePrimer: an easy-to-use web server for designing PCR primers for DNA library cloning

Cyrille Pauthenier, Jean-Loup Faulon

2014Nucleic Acids Research, 42.W1, W205–W209

Platforms for genetic design automation

Chris J. Myers

2013Methods in Microbiology, 40, 177–202

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