Computational biology
Branch of biology
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We include updates on John M. Jumper, Folding@home, Protein Data Bank, DNA digital data storage, K-mer, UniProt, Human Microbiome Project, Foldit, UCSC Genome Browser, Ensembl genome database project, Pfam, Flux balance analysis, Statistical potential, MODELLER, AIDA interactive educational freeware diabetes simulator, Fluxomics ... and more.
| 2025 |
Jian Ma
Received the Allen Newell Award for Research Excellence, highlighting his outstanding contributions to computational research.
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| 2025 |
Matt Thomson
Published research paper on 'Dynamic flow control through an active matter programming language' in Nature Materials.
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| 2024 | Begins serving as a scientific advisory board member of Arc Institute. |
| 2024 | Elected as a foreign member of the Royal Society and an associate member of the European Molecular Biology Organization. |
| 2024 | Awarded the Nobel Prize in Chemistry alongside Demis Hassabis for groundbreaking work in protein structure prediction using AlphaFold. |
| 2024 |
Jian Ma
Served as the Program Chair for the RECOMB 2024 conference, a significant role in the computational biology research community.
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| 2024 |
Matt Thomson
Published two research papers: 'Engineering flexible machine learning systems by traversing functionally invariant paths' in Nature Machine Intelligence, and 'Automated construction of cognitive maps with visual predictive coding' (co-authored with J. Gornet) in the same journal.
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| 2024 |
Jian Ma
Served as the Program Chair for the RECOMB (Research in Computational Molecular Biology) conference.
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| 2024 |
Jian Ma
Published 'scGHOST: Identifying single-cell 3D genome subcompartments' in Nature Methods.
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| 2024 |
Jian Ma
Published 'Computational methods for analysing multiscale 3D genome organization' in Nature Reviews Genetics.
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| 2024 |
Jian Ma
Published 'Applying interpretable machine learning in computational biology - pitfalls, recommendations and opportunities for new developments' in Nature Methods.
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| 2024 |
Jian Ma
Launched the Center for AI-Driven Biomedical Research (AI4BIO) at Carnegie Mellon University, aiming to drive innovations at the intersection of AI and biomedicine.
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| February 2024 | Appointed as a university professor, taking the chair of data analytics and bioinformatics at the Martin Luther University of Halle-Wittenberg while maintaining research group connections with the German National Center for Infection Research (DZIF) at the University of Tübingen. |
| 2023 | Delivered a TED AI talk on 'Can AI Help Develop New Medicines' and received the 25th L'Oréal-UNESCO For Women in Science Awards (Laureate for North America). |
| 2023 | Jumper was awarded the Breakthrough Prize in Life Sciences for developing AlphaFold, which accurately predicts protein structures. |
| 2023 | Jumper was awarded the Albert Lasker Award for Basic Medical Research. |
| 2023 | Jumper received the Canada Gairdner International Award for his contributions to protein structure prediction. |
| 2023 | Elected a Fellow of the Royal Society. |
| 2023 |
Matt Thomson
Granted the NIH Transformative R01 award, further acknowledging his groundbreaking research in computational and systems biology.
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| 2023 |
Jian Ma
Published 'SPICEMIX enables integrative single-cell spatial modeling of cell identity' in Nature Genetics, which was selected as a Cover Article.
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| 2022 | Jumper received the Wiley Prize in Biomedical Sciences for his work on protein structure prediction. |
| 2022 | Stepped down from his role as de facto chairman of the SysMod community meeting within ISCB. |
| 2022 |
Matt Thomson
Matt Thomson co-founded Yurts with his former PhD student Guruprasad Raghavan, expanding his work beyond academic research into entrepreneurial ventures in computational biology.
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| 2022 |
Jian Ma
Published 'Multiscale and integrative single-cell Hi-C analysis with Higashi' in Nature Biotechnology.
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| 2022 |
Jian Ma
Published 'Ultrafast and interpretable single-cell 3D genome analysis with Fast-Higashi' in Cell Systems, which was selected as a Cover Article.
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| 2022 |
Jian Ma
Published 'Nucleome Browser', an integrative and multimodal data navigation platform for 4D Nucleome in Nature Methods.
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| 2022 | First Asian Student Council Symposium (ASCS) held, preceding the ISCB-Asia Conference. |
| 2021 | Became a fellow of the American Association for Cancer Research (AACR). |
| 2021 | Recognized by Nature as one of the ten 'people who mattered' in science in Nature's annual Natures 10 listing. |
| 2021 | Jumper was awarded the BBVA Foundation Frontiers of Knowledge Award in the category of Biology and Biomedicine. |
| 2021 | Received the Los Alamos Medal for changing the course of science. |
| 2021 | Elected a Fellow of the Academy of Medical Sciences. |
| 2020 | Became the Head and Executive Vice President of Genentech Research and Early Development, located in South San Francisco, and joined the extended Corporate Executive Committee of Roche. |
| 2020 | Elected as a member of the US National Academy of Medicine (NAM). |
| 2020 |
Folding@home cores
Gromacs 2020.5 version released, implemented in Core a8 for Folding@home, supporting Windows, Linux, macOS, and ARM platforms.
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| 2020 | Appointed as Professor of Bioinformatics at AUTH (Aristotle University of Thessaloniki). |
| 2020 | Acknowledged by MIT's Technology Review as one of their 35 Innovators under 35, highlighting her significant contributions to biotechnology. |
| 2020 | Won multiple funding rounds in prestigious competitions including StartMIT, StartIAP, MIT100K, and the Sandbox Innovation Fund Program for her groundbreaking biotechnology research. |
| 2020 |
Matt Thomson
Received the Okawa Research Award, highlighting his significant contributions to research in his field.
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| 2020 |
Serratus
Serratus research team analyzed 5.7 million freely available sequencing datasets (20.4 petabytes of raw data) in the Sequence Read Archive (SRA) in just 11 days, with a computing cost of US$23,900. This analysis discovered 132,000 novel viral RNA-dependent RNA polymerase (RdRp) sequences, dramatically expanding the known genetic diversity of RNA viruses from approximately 15,000 distinct sequences to a significantly larger number.
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| 2020 |
Jian Ma
Awarded a Guggenheim Fellowship in Computer Science, highlighting his significant research achievements.
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| 2020 |
Sergey Piletsky
Filed patent for Methods and Kits for determining binding sites, with co-inventors Elena Piletska, Francesco Canfarotta, and Don Jones.
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| 2020 |
Source attribution
A study in Taiwan investigated HIV transmission using phylogenetic analysis, though the branches with low support did not conclusively support transmission from the defendant to the plaintiff.
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| November 2020 | AlphaFold, led by John M. Jumper, won the 14th Critical Assessment of Structure Prediction (CASP) competition, outperforming other algorithms by scoring above 90 for around two-thirds of the proteins in the global distance test. |
| July 2020 | Joined the faculty of St. Jude Children's Research Hospital as the endowed chair in biological data science in the structural biology department and director of the center of excellence for data-driven discovery. |
| April 12 2020 |
Folding@home
Folding@home becomes the world's first exaflop computing system, reaching a peak performance of 2.43 exaflops.
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| March 2020 |
Folding@home
Project achieves a computing speed of approximately 1.22 exaflops, driven by heightened interest during the COVID-19 pandemic.
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| March 2020 |
Folding@home
Folding@home launched a program to assist researchers worldwide in studying the coronavirus pandemic, initially focusing on simulating potentially druggable protein targets from SARS-CoV-2 and SARS-CoV viruses.
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| March 25 2020 |
Folding@home
Folding@home reached 768 petaFLOPS, or 1.5 x86 exaFLOPS, becoming the first exaFLOP computing system.
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| March 20 2020 |
Folding@home
Folding@home announced via Twitter that it was running with over 470 native petaFLOPS, equivalent to 958 x86 petaFLOPS, due to increased participation during the coronavirus pandemic.
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This contents of the box above is based on material from the Wikipedia articles Christos Ouzounis, John M. Jumper, M. Madan Babu, Jian Ma (computational biologist), List of Folding@home cores, Leila Pirhaji, International Society for Computational Biology Student Council, Source attribution, Serratus (virology), Aviv Regev, Bette Korber, Sergey Piletsky, Folding@home, Matt Thomson & Andreas Dräger, which are released under the Creative Commons Attribution-ShareAlike 4.0 International License.