Bioinformatics

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41 papers9 papers in the last four weeks, against 1 the four weeks before. 0.1% of all new papers.

Biomedical systems biology workflow orchestration and execution with PoSyMed
Apr 21, 2026Simon Süwer, Zoe Chervontseva, Kester Bagemihl +3Scientific Reproducibility Scientific Workflow Automation
Institute for Computational Systems Biomedicine, University of Hamburg, Hamburg, Germany · Department for Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark · Faculty of Science, Computer Science, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
GenomeQA: Benchmarking General Large Language Models for Genome Sequence Understanding
Apr 7, 2026Weicai Long, Yusen Hou, Junning Feng +4LLM Evaluation Genomics
Hong Kong University of Science and Technology (Guangzhou) · The University of Hong Kong · Peking University
annbatch unlocks terabyte-scale training of biological data in anndata
Apr 2, 2026Ilan Gold, Felix Fischer, Lucas Arnoldt +2Bioinformatics Memory-Efficient Training
Department of Computational Health, Institute of Computational Biology, Helmholtz Munich, Germany · School of Computing, Information and Technology, Technical University of Munich, Munich, Germany · Munich Center for Machine Learning (MCML) +2
KGroups: A Versatile Univariate Max-Relevance Min-Redundancy Feature Selection Algorithm for High-dimensional Biological Data
Mar 30, 2026Malick Ebiele, Malika Bendechache, Rob BrennanBioinformatics Feature Selection
Computer Science, University College Dublin, Dublin, Dublin, Ireland. · ADAPT Centre, Dublin, Dublin, Ireland. · Computer Science, University of Galway, Galway, Galway, Ireland.
Central Dogma Transformer III: Interpretable AI Across DNA, RNA, and Protein
Mar 24, 2026Nobuyuki OtaBioinformatics Mechanistic Interpretability
Independent Researcher, Burlingame, CA, USA
Do Papers Tell the Whole Story? A Benchmark and Framework for Uncovering Hidden Implementation Gaps in Bioinformatics
Mar 23, 2026Tianxiang Xu, Xiaoyan Zhu, Xin Lai +4Software Engineering Benchmarks Scientific Reproducibility
Xi’an Jiaotong University
Beyond Expression Similarity: Contrastive Learning Recovers Functional Gene Associations from Protein Interaction Structure
Mar 21, 2026Jason DuryContrastive Learning Bioinformatics
Eridos AI
Reverse Distillation: Consistently Scaling Protein Language Model Representations
Mar 8, 2026Darius Catrina, Christian Bepler, Samuel Sledzieski +1Protein Language Models Protein Representation Learning
Department of Computer Science, Duke University, Durham, NC, USA · Depts of Biostats. and Bioinformatics; and Cell Biology, Duke University, Durham, NC, USA
Protein Language Models Diverge from Natural Language: Comparative Analysis and Improved Inference
Feb 24, 2026Anna Hart, Chi Han, Jeonghwan Kim +2Protein Language Models Protein Representation Learning
Siebel School of Data Science and Computing, University of Illinois Urbana-Champaign, 201 N Goodwin Ave, Urbana, IL 61801, USA · DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, 1206 W Gregory Drive, Urbana, IL 61801, USA · Chemical and Biomolecular Engineering, University of Illinois Urbana-Champaign, 600 S Matthews Ave, Urbana, IL 61801, USA
When do cheap embeddings beat protein language models? A theoretically-grounded hashing sketch for biological sequence classification
Dec 10, 2025Sarwan Ali, Taslim Murad, Imdadullah Khan +1Protein Language Models Randomized Sketching
Columbia University, NY, USA · Institute of Business Administration, Karachi, Pakistan · Lahore University of Management Sciences, Lahore, Pakistan +1
PUMA: Learning a Mutation-Aware Vocabulary of Protein Units
Mar 11, 2025Burak Suyunu, Özdeniz Dolu, Ibukunoluwa Abigail Olaosebikan +2Protein Language Models Protein Representation Learning
Department of Computer Engineering, Boaziçi University, 34342, Bebek, Istanbul, Turkey · C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26505, United States · Department of Pharmaceutical Chemistry, Istanbul Medipol University, Faculty of Pharmacy, 34815 Beykoz, Istanbul, Turkey +1

Apr 21, 2026J/K move · Enter open · S save

Biomedical systems biology workflow orchestration and execution with PoSyMed

Simon Süwer, Zoe Chervontseva, Kester Bagemihl, Jan Baumbach+2

Institute for Computational Systems Biomedicine, University of Hamburg, Hamburg, Germany · Department for Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark · Faculty of Science, Computer Science, Vrije Universiteit Amsterdam, Amsterdam, Netherlands

Scientific Reproducibility Scientific Workflow Automation Bioinformatics

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The rapid growth of scientific software has created practical barriers for bioinformatics research. Although powerful statistical, artificial intelligence (AI)-based methods are now widely available, their effective use is often hindered by fragmented distribution, inconsistent documentation, complex dependencies, and difficult-to-reproduce execution environments. As a result, reusing published tools and workflow adaptation to own date remains technically demanding and time-intensive, even for experienced users. Here, we present PoSyMed, an open and modular platform for the controlled integration, composition, and execution of bioinformatics tools and workflows. PoSyMed combines a backend-centered platform architecture with formal tool descriptions, controlled container-based build and execution processes, persistent workflow state, and a dialogue-based user interface. Large language models (LLM) are integrated not as autonomous decision-makers, but as human-computer interface with bounded semantic assistants that help identify tools, propose workflow steps, and support parameterization within a typed, validated, and human-supervised execution environment. PoSyMed is designed to improve reproducibility, traceability, and transparency in practical biomedical analysis within one platform. We describe the system architecture and evaluate its behavior across representative biological software scenarios with respect to workflow support, interaction design, and platform extensibility. PoSyMed is publicly available at https://apps.cosy.bio/posymed.