A fully open access, peer-reviewed journal published jointly by Oxford University Press and the International Society for Computational Biology.
Joined April 2021
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🧮 Recently published in Bioinformatics Advances: “1100 synthetic benchmark problems for dynamic modeling of cellular processes ”
Read more: doi.org/10.1093/bioadv/vbag3…
The synthetic problems reproduce the statistical characteristics of their templates while spanning a broader, more continuous range of optimization difficulty and parameter identifiability.
💾 Benchmark problems and the generation algorithm are available at github.com/niklasneubrand/11…, archived at doi.org/10.5281/zenodo.23211…
🧬 New in Bioinformatics Advances: “RT-SRFM: A transport-growth-fate latent dynamical framework for developmental single-cell time series ”
Access it here: doi.org/10.1093/bioadv/vbag2…
On zebrafish and sea urchin datasets, it outperformed optimal-transport and neural-dynamics baselines in mass calibration and fate prediction.
💻 RT-SRFM’s source code and datasets are available at github.com/typical666/RT-SRF…
In Memoriam in Bioinformatics Advances: “Peer Bork (1963–2026): Pioneer of computational biology, architect of bioinformatics resources, and visionary microbiome researcher”
Read the tribute here: doi.org/10.1093/bioadv/vbag2…
Author: @Alexbateman1
Over three decades, Peer pioneered protein domain discovery (WW, HEAT, BRCT), built foundational resources including SMART, STRING, eggNOG, and iTOL, and transformed microbiome science with the 2011 discovery of human gut enterotypes, cited nearly 10,000 times.
His influence spans more than 600 publications, a citation count exceeding 460,000, and over 50 trainees who now lead their own research groups. Tributes can be shared at peerbork.muchloved.com/.
🔬 New study in Bioinformatics Advances: "Bridging LLM-based agents and workflow languages for automated multi-perspective analysis of scRNA-seq data"
Find it here: doi.org/10.1093/bioadv/vbag3…
Validation raised the executable analysis intent fulfillment rate from 0.061 to 0.378, with parallel execution achieving up to a 29.9-fold speedup over sequential runs.
💻 Source code for the framework is available at github.com/bioinfo-tsukuba/m… under the MIT license.
🧬 New paper in Bioinformatics Advances: "DistPCA: Tera-scale genomic PCA via out-of-core distributed parallelism"
Read it here: doi.org/10.1093/bioadv/vbag3…
On a 500K-genome dataset it cut wall-clock time from 12.1 to 2.3 hours against the state-of-the-art PCAone, a 5.26x speedup, while preserving near-identical PC accuracy.
🖥️ DistPCA is available at github.com/CEID-HPCLAB/DistP…, with an archived release at doi.org/10.5281/zenodo.20392…
🦠 Latest research in Bioinformatics Advances: "Computational characterization of three conserved pathogenicity-associated genomic regions in Fusobacterium nucleatum ATCC 25586"
Explore the paper: doi.org/10.1093/bioadv/vbag3…
Iron proved essential for growth, with complete deprivation abolishing it entirely, supporting a proposed hemolysin–iron–ROS–Hippo pathway potentially relevant to colorectal cancer progression.
💻 Code, supplementary data, and analysis scripts are available at github.com/exporterdream/fn-… and Zenodo at doi.org/10.5281/zenodo.23091…
