Systems biology
Computational and mathematical modeling of complex biological systems
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We include updates on Cell signaling, Biopunk, Two-hybrid screening, Metabolomics, Biological network inference, Pollination network, Gene regulatory network, Metabolome, KEGG, WikiPathways, Regulome, Interactome, Human ecosystem, Bonini's paradox, Metallome, Dynamic energy budget theory ... and more.
| 2025 |
Immunome
The Mal-ID project successfully sequenced B and T cell receptors at scale across multiple diagnoses using three machine learning models, achieving a high area under the receiver operative characteristic curve value of 0.986.
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| 2024 | Anticipated first human clinical trial of engineered live yeast for treating Clostridioides difficile infection, to be sponsored by Fzata, Inc. |
| 2024 |
International Conference on Systems Biology
ICSB-2024 (International Conference on Systems Biology) scheduled to be held in Bombay, India at IIT (Indian Institute of Technology).
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| 2023 | Significant advancements in RNA therapeutics, including improved safety and efficiency in synthetic biology, with RNA-based systems showing faster and potentially safer genetic modification capabilities. |
| 2023 | Researchers successfully created the first synthetically made human embryos derived from stem cells. |
| 2023 |
International Conference on Systems Biology
ICSB-2023 conference held in Hartford, Connecticut, USA
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| 2022 |
International Conference on Systems Biology
ICSB-2022 conference held in-person in Berlin, Germany
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| 2021 |
Metabolome
First comprehensive brain metabolome atlas of the mouse brain was released online, representing a significant milestone in understanding metabolic changes across different brain regions and life stages of a mammalian model.
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| 2021 |
Metascape
Metascape for Bioinformaticians (MSBio) was released, providing a computational platform for automated batch analyses of gene lists using Docker container technology. The release enables academic users to perform offline analyses and commercial users to conduct secure computations with proprietary knowledge bases.
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| 2021 | Scientists report that xenobots can self-replicate by gathering loose cells from the environment to form new xenobots. |
| 2021 |
International Conference on Systems Biology
ICSB-2021 conference canceled due to COVID-19 pandemic
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| January 2021 |
BioGRID
BioGRID contained over 2.0 million biological interactions, 29,023 chemical-protein interactions, and 506,485 post-translational modifications, curated from 75,988 publications covering more than 80 species.
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| 2020 |
Cellular model
E-Cell Project was last updated, indicating ongoing maintenance or development of the cellular modeling platform.
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| 2020 | First xenobot created, a programmable synthetic organism derived from frog cells and designed by AI. Demis Hassabis and John M. Jumper also present AlphaFold2, an AI model capable of predicting structures for nearly all known proteins. |
| 2020 |
International Conference on Systems Biology
ICSB-2020 conference canceled due to COVID-19 pandemic
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| 2019 |
GeneNetwork
GN1 (GeneNetwork version 1) was actively maintained through this year, with subsequent focus shifting to GN2.
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| 2019 | Scientists at ETH Zurich report the creation of Caulobacter ethensis-2.0, the first bacterial genome made entirely by computer. |
| 2019 | European synthetic cell efforts were unified under the SynCellEU initiative. |
| 2019 | Researchers successfully implemented a perceptron in biological systems, opening new possibilities for machine learning within biological computational frameworks. |
| 2019 |
International Conference on Systems Biology
ICSB-2019 conference held in Okinawa, Japan at the Okinawa Institute of Science and Technology Graduate University
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| May 2019 | Researchers achieved a milestone by creating a new synthetic variant of Escherichia coli, reducing the natural number of genome codons from 64 to 59 to encode 20 amino acids. |
| April 26 2019 |
SBML
Final Release 2 specification for SBML Level 3 Version 2 Core was issued.
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| April 3 2019 |
Metascape
Published a paper titled 'Metascape provides a biologist-oriented resource for the analysis of systems-level datasets' in Nature Communications, detailing the software's capabilities and significance.
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| 2018 |
International Conference on Systems Biology
ICSB-2018 conference held in Lyon, France at the Université de Lyon
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| 2017 | The international Build-a-Cell large-scale open-source research collaboration for constructing synthetic living cells was initiated, followed by the establishment of national synthetic cell organizations like FabriCell, MaxSynBio, and BaSyC. |
| 2017 | The 'Boolean logic and arithmetic through DNA excision' (BLADE) system was developed to engineer digital computation in human cells, further advancing biological computing technologies. |
| 2017 |
International Conference on Systems Biology
ICSB-2017 conference held in Blacksburg, Virginia at Virginia Tech
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| 2016 | Researchers demonstrated how principles of computer engineering can be used to automate digital circuit design within bacterial cells, expanding the potential of biological computing. |
| 2016 |
International Conference on Systems Biology
ICSB-2016 conference held in Barcelona, Spain
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| 2016 |
Immunome
The Human Immunome Program was launched as a collaborative project between The Human Vaccines Project, Vanderbilt University Medical Center, and Illumina, Inc. The ten-year project aims to decipher the complete collection of human B and T immune cell receptors by studying thousands of individuals across diverse demographics.
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| 2015 |
International Conference on Systems Biology
ICSB-2015 conference originally planned for Shanghai, ultimately held in Singapore
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| December 9 2015 |
Metascape
The first Metascape application was published, marking an important milestone in the gene annotation and analysis software development.
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| October 8 2015 |
Metascape
Metascape was first released as a beta version by a team of scientists including Yingyao Zhou, Bin Zhou, Lars Pache, Max Chang, Christopher Benner, and Sumit Chanda.
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| 2014 | Researchers presented the first living organism with an 'artificial' expanded DNA code by modifying E. coli, extracting its genome and replacing it with a chromosome containing the nucleosides d5SICS and dNaM. |
| 2014 |
International Conference on Systems Biology
ICSB-2014 conference held in Melbourne, Australia
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| 2013 |
International Conference on Systems Biology
ICSB-2013 conference held in Copenhagen, Denmark
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| 2012 | Charpentier and Doudna labs publish the programming of CRISPR-Cas9 for DNA targeting, greatly simplifying and expanding eukaryotic gene editing. |
| 2012 |
International Conference on Systems Biology
ICSB-2012 conference held in Toronto, Canada
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| 2011 | A proof-of-concept therapy was developed using biological digital computation to detect and kill human cancer cells, showcasing a practical medical application of synthetic biology. |
| 2011 |
International Conference on Systems Biology
ICSB-2011 conference held in Mannheim, Germany
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| 2010 |
GeneNetwork
Original source code and compact database for GeneNetwork were made available on SourceForge.
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| 2010 | First synthetic bacterial genome, M. mycoides JCVI-syn1.0, published in Science, made from chemically-synthesized DNA using yeast recombination. |
| 2010 | Craig Venter and his team produced a completely synthetic bacterial chromosome and successfully introduced it to genomically emptied bacterial host cells, which were able to grow and replicate. This resulted in the creation of Mycoplasma laboratorium, the first living organism with a completely engineered genome. |
| 2010 |
International Conference on Systems Biology
ICSB-2010 conference held in Edinburgh, United Kingdom
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This contents of the box above is based on material from the Wikipedia articles BioGRID, SBML, Synthetic biology, Flux balance analysis, Immunome, International Conference on Systems Biology, GeneNetwork, Metascape, Metabolome, SPIKE (database) & Cellular model, which are released under the Creative Commons Attribution-ShareAlike 4.0 International License.