1. Benchmarking plant single cell RNA-sequencing sample processing strategies
   2026/05/09 by Thomas Eekhout, Lindsy De Veirman, Jolien De Block +6 · 2 voices
   Agricultural and Biological Sciences · Biochemistry, Genetics and Molecular Biology · #Arabidopsis #Cell #Cell Image Analysis Techniques #Cell sorting #Flow cytometry #Genomics #Plant Molecular Biology Research #Plant cell #Single-cell analysis #Single-cell and spatial transcriptomics #Transcriptome #Workflow
2. copick: An open dataset interface and toolkit for collaborative annotation and analysis of cryo‐electron tomography data
   2026/04/17 by Utz H. Ermel, Jonathan Schwartz, Zhuowen Zhao +7 · 1 voice · 1 citation
   Biochemistry, Genetics and Molecular Biology · Materials Science · #Advanced Electron Microscopy Techniques and Applications #Annotation #Application programming interface #Cloud computing #Context (archaeology) #Electron and X-Ray Spectroscopy Techniques #Enzyme Structure and Function #Interface (matter) #Plug-in #Suite #Visualization #Workflow
3. BIEN : A biodiversity informatics ecosystem advancing open and reproducible workflows for plant observation, plot and trait data
   2026/03/24 by Brian J. Enquist, Brad Boyle, Brian S. Maitner +36 · 2 voices
   Agricultural and Biological Sciences · Computer Science · Environmental Science · #Biodiversity #Biosphere #Citizen science #Ecosystem services #Geographic information system #Geospatial analysis #Health informatics tools #Mediterranean and Iberian flora and fauna #Plot (graphics) #Research Data Management Practices #Species Distribution and Climate Change #Workflow
4. Smart microscopy: current implementations and a roadmap for interoperability
   2026/02/21 by Lucien Hinderling, Hannah S. Heil, Alfredo Rates +33 · 2 voices · 5 citations
   Biochemistry, Genetics and Molecular Biology · Engineering · #Adaptation (eye) #Advanced Fluorescence Microscopy Techniques #Cell Image Analysis Techniques #Field (mathematics) #Image Processing Techniques and Applications #Implementation #Interoperability #Modular design #Software #Workflow
5. Compartment‐guided assembly of large‐scale molecular models with Bentopy
   2026/02/12 by M. S. S. Westendorp, J. A. Stevens, C. M. Brown +4 · 2 voices · 3 citations
   Biochemistry, Genetics and Molecular Biology · Engineering · Physics and Astronomy · #Advanced Electron Microscopy Techniques and Applications #Bottleneck #Computational model #Force Microscopy Techniques and Applications #Modular design #Molecular model #Nanopore and Nanochannel Transport Studies #Organelle #Representation (politics) #Systems biology #Workflow
6. Cookbook for plant genome sequences
   2026/02/06 by Julie Anne Vieira Salgado de Oliveira, Nancy Choudhary, Samuel Nestor Meckoni +3 · 4 voices · 3 citations
   Agricultural and Biological Sciences · Biochemistry, Genetics and Molecular Biology · #Chromosomal and Genetic Variations #DNA sequencing #Genetics, Bioinformatics, and Biomedical Research #Genome #Genome Biology #Genomics #Genomics and Phylogenetic Studies #Nanopore sequencing #Personal genomics #Phylogenetic tree #Whole genome sequencing #Workflow
7. HEPTAPOD: Orchestrating High Energy Physics Workflows Towards Autonomous Agency
   2025/12/17 by Tony Menzo, Menzo, Tony, Alexander Roman +13 · 1 voice · 3 citations
   Computer Science · Decision Sciences · Social Sciences · #Agency (philosophy) #Artificial Intelligence in Law #Construct (python library) #Event (particle physics) #Interface (matter) #Multi-Agent Systems and Negotiation #Orchestration #Pipeline (software) #Scientific Computing and Data Management #Software deployment #Workflow #hep-ex #hep-ph
8. xcms in Peak Form: Now Anchoring a Complete Metabolomics Data Preprocessing and Analysis Software Ecosystem
   2025/12/08 by Philippine Louail, Carl Brunius, Mar Garcia‐Aloy +8 · 1 voice · 3 citations
   Biochemistry, Genetics and Molecular Biology · Chemistry · #Advanced Proteomics Techniques and Applications #Bioconductor #Cell Image Analysis Techniques #Component (thermodynamics) #Data pre-processing #Data processing #Interoperability #Metabolomics and Mass Spectrometry Studies #Modular design #Preprocessor #Software #Visualization #Workflow
9. Quick Analysis of Sedimentary Ancient DNA Using quicksand
   2025/11/24 by Merlin Szymanski, Johann Visagie, Frédéric Romagné +2 · 2 voices · 3 citations
   Biochemistry, Genetics and Molecular Biology · Environmental Science · Social Sciences · #Ancient DNA #DNA sequencing #Environmental DNA in Biodiversity Studies #Forensic and Genetic Research #Pipeline (software) #Pleistocene-Era Hominins and Archaeology #Sedimentary rock #Taxonomic rank #Workflow
10. Strategies for community-sourced biocuration in bioinformatics: a case study on MIBiG 4.0
    2025/11/01 by Kai Blin, Catarina Loureiro, Nico L L Louwen +10 · 1 voice · 1 citation
    Biochemistry, Genetics and Molecular Biology · Computer Science · #Annotation #Bioinformatics and Genomic Networks #Biological database #Biomedicine #Computational Drug Discovery Methods #Data curation #Genomics and Phylogenetic Studies #Metadata #Usability #Workflow
11. CLINB: A Climate Intelligence Benchmark for Foundational Models
    2025/10/29 by Michelle Chen Huebscher, Huebscher, Michelle Chen, Katharine Mach +24 · 1 voice
    Computer Science · Social Sciences · #Benchmark (surveying) #Bridging (networking) #Computational and Text Analysis Methods #Domain (mathematical analysis) #Domain knowledge #Multimodal Machine Learning Applications #Process (computing) #Quality (philosophy) #Rubric #Topic Modeling #Workflow #cs.AI #cs.CL
12. Computational Approaches for Pathway‐Centric Analysis of Protein Post‐Translational Modifications
    2025/10/18 by Julian Müller, Bernhard Küster, Matthew The · 1 voice · 3 citations
    Biochemistry, Genetics and Molecular Biology · Computer Science · Medicine · #Bioinformatics and Genomic Networks #Computational Drug Discovery Methods #Context (archaeology) #Function (biology) #Microbial Natural Products and Biosynthesis #Protein function #Proteomics #State (computer science) #Variety (cybernetics) #Visualization #Workflow
13. fluxible: An R package to process ecosystem gas fluxes from closed‐loop chambers in an automated and reproducible way
    2025/09/25 by Joseph Gaudard, Richard J. Telford, Julia Chacón‐Labella +12 · 2 voices
    Environmental Science · #Atmospheric and Environmental Gas Dynamics #Automation #Climate variability and models #Comparability #Data processing #Ecosystem #Homogeneity (statistics) #Limiting #Plant Water Relations and Carbon Dynamics #Process (computing) #Workflow
14. Hunyuan3D Studio: End-to-End AI Pipeline for Game-Ready 3D Asset Generation
    2025/09/16 by Li Yang, Lei, Biwen, Li, Yang +185 · 2 voices · 5 citations
    Computer Science · Decision Sciences · #Asset (computer security) #Bridge (graph theory) #Computer Graphics and Visualization Techniques #Computer Vision and Pattern Recognition (cs.CV) #FOS: Computer and information sciences #Image Processing and 3D Reconstruction #Pipeline (software) #Semantics (computer science) #Simulation Techniques and Applications #Studio #Suite #Video game #Visualization #Workflow
15. Computational design of intrinsically disordered proteins
    2025/09/15 by Giulio Tesei, Francesco Pesce, Tesei, Giulio +4 · 4 voices · 2 citations
    Biochemistry, Genetics and Molecular Biology · Materials Science · #Computational model #Intrinsically disordered proteins #Protein Structure and Dynamics #Protein design #Protein stability #Scalability #Workflow #q-bio.BM
16. Paper2Agent: Reimagining Research Papers As Interactive and Reliable AI Agents
    2025/09/08 by Jiacheng Miao, Miao, Jiacheng, Joe R. Davis +7 · 14 voices · 11 citations
    Computer Science · Decision Sciences · #Codebase #Construct (python library) #Context (archaeology) #Exploit #Multi-agent system #Protocol (science) #Scientific Computing and Data Management #Semantic Web and Ontologies #Workflow #cs.AI #cs.CL #cs.LG
17. A causal framework for the drivers of animal social network structure
    2025/09/08 by Ben Kawam, Julia Ostner, Richard McElreath +2 · 1 voice · 2 citations
    Agricultural and Biological Sciences · Psychology · Social Sciences · #Animal Behavior and Reproduction #Bayesian network #Bayesian probability #Causal inference #Causal model #Causal structure #Estimator #Evolutionary Game Theory and Cooperation #Inference #Primate Behavior and Ecology #Set (abstract data type) #Statistical inference #Workflow
18. Cookbook for Plant Genome Sequences
    2025/09/08 by Julie Anne Vieira Salgado de Oliveira, Nancy Choudhary, Samuel Nestor Meckoni +3 · 2 voices
    Agricultural and Biological Sciences · Biochemistry, Genetics and Molecular Biology · #Chromosomal and Genetic Variations #DNA sequencing #Genome #Genomics #Genomics and Phylogenetic Studies #Hybrid genome assembly #Nanopore sequencing #Phylogenetic tree #Whole genome sequencing #Workflow
19. L-MARS: Legal Multi-Agent System with Agentic Search and Citation-Faithfulness Audit
    2025/08/31 by Boqin Yuan, Ziqi Wang, Wang, Ziqi +1 · 4 citations
    Computer Science · Social Sciences · #Artificial Intelligence in Law #Benchmark (surveying) #Blueprint #Inference #Multi-Agent Systems and Negotiation #Preference #Scalability #Toolbox #Topic Modeling #Work (physics) #Workflow #cs.AI #cs.CL
20. Simulation-Based Inference: A Practical Guide
    2025/08/18 by Michael Deistler, Jan Boelts, Deistler, Michael +27 · 3 voices · 13 citations
    Computer Science · Decision Sciences · Mathematics · #Artificial neural network #Bayesian inference #Causal inference #Frequentist inference #Inference #Process (computing) #Simulation Techniques and Applications #Suite #Workflow #cs.LG #stat.ML
21. OdysseyBench: Evaluating LLM Agents on Long-Horizon Complex Office Application Workflows
    2025/08/12 by W. Wang, Wang, Weixuan, Han, Dongge +8 · 12 citations
    Computer Science · Medicine · #Artificial Intelligence in Healthcare and Education #Benchmark (surveying) #Computation and Language (cs.CL) #FOS: Computer and information sciences #Focus (optics) #Multimodal Machine Learning Applications #Resource (disambiguation) #Scalability #Task (project management) #Topic Modeling #Workflow
22. Real‐Time, Inline Quantitative MRI Enabled by Scanner‐Integrated Machine Learning: A Proof of Principle With NODDI
    2025/07/16 by Samuel Rot, Rot, Samuel, Iulius Dragonu +29 · 2 citations
    Medicine · Neuroscience · #Advanced Neuroimaging Techniques and Applications #Artificial intelligence #Artificial neural network #Computer science #Computer vision #DICOM #Estimation theory #Functional Brain Connectivity Studies #Ground truth #MRI in cancer diagnosis #Operating system #Orientation (vector space) #Parametric statistics #Pipeline (software) #Proof of concept #Scanner #Translation (biology) #Workflow
23. Coral Protocol: Open Infrastructure Connecting The Internet of Agents
    2025/04/30 by Roman J. Georgio, Georgio, Roman J., Caelum Forder +10 · 6 voices · 3 citations
    Computer Science · Engineering · #Communications protocol #Interoperability #Modular design #Payment #Protocol (science) #The Internet #Underwater Vehicles and Communication Systems #Vendor #Workflow #cs.AI #cs.MA
24. EvANI benchmarking workflow for evolutionary distance estimation
    2025/05/01 by Sina Majidian, Stephen Hwang, Mohsen Zakeri +1 · 1 voice · 1 citation
    Biochemistry, Genetics and Molecular Biology · Engineering · #Artificial intelligence #Benchmarking #Business #Computer science #Data mining #Database #Engineering #Estimation #Evolution and Genetic Dynamics #Genomics and Phylogenetic Studies #RNA and protein synthesis mechanisms #Systems engineering #Workflow
25. Semantic Commit: Helping Users Update Intent Specifications for AI Memory at Scale
    2025/04/12 by Priyan Vaithilingam, M. Kim, Vaithilingam, Priyan +12 · 1 voice · 2 citations
    Computer Science · #Affordance #Artificial Intelligence (cs.AI) #Context-Aware Activity Recognition Systems #D.2.1 #Explainable Artificial Intelligence (XAI) #FOS: Computer and information sciences #H.5.2 #Human-Computer Interaction (cs.HC) #I.2.11 #I.2.7 #I.7.0 #Intelligent agent #Natural language #Parallel Computing and Optimization Techniques #Pipeline (software) #Process (computing) #Semantic memory #User interface #Workflow #cs.AI #cs.HC
26. Scholar Inbox: Personalized Paper Recommendations for Scientists
    2025/04/11 by Markus Flicke, Flicke, Markus, Glenn Angrabeit +25 · 2 voices · 3 citations
    Computer Science · Decision Sciences · #Focus (optics) #Personalization #Quality (philosophy) #Recommender system #Research Data Management Practices #Selection (genetic algorithm) #User experience design #User modeling #Workflow #scientometrics and bibliometrics research
27. MCP Safety Audit: LLMs with the Model Context Protocol Allow Major Security Exploits
    2025/04/02 by Brandon Radosevich, John Halloran, Radosevich, Brandon +2 · 1 voice · 34 citations
    Computer Science · #Adversarial Robustness in Machine Learning #Artificial Intelligence (cs.AI) #Audit #Context (archaeology) #Credential #Cryptographic protocol #Cryptography and Security (cs.CR) #Exploit #FOS: Computer and information sciences #Machine Learning (cs.LG) #Protocol (science) #Security and Verification in Computing #Set (abstract data type) #Software System Performance and Reliability #Vulnerability (computing) #Workflow #cs.AI #cs.CR #cs.LG
28. LLM-AutoDiff: Auto-Differentiate Any LLM Workflow
    2025/01/28 by Li Yin, Yin Li, Zhangyang Wang +2 · 3 voices · 7 citations
    Computer Science · Engineering · Psychology · Social Sciences · #Artificial Intelligence in Law #Computer science #Database #Natural Language Processing Techniques #Psychology #Tunneling and Rock Mechanics #Workflow #cs.CL
29. Droplet microfluidics for single-cell studies: a frontier in ecological understanding of microbiomes
    2025/01/01 by Wannes Nauwynck, Karoline Faust, Nico Boon · 1 voice · 4 citations
    Engineering · #Bioinformatics #Biology #Cell #Computational biology #Computer science #Ecology #Electrowetting and Microfluidic Technologies #Evolutionary biology #Functional diversity #Gene #Genetics #Innovative Microfluidic and Catalytic Techniques Innovation #Metagenomics #Microbial ecology #Microbiome #Microfluidics #Nanotechnology #Single-cell analysis #Workflow
30. Deep-Learning Based Docking Methods: Fair Comparisons to Conventional Docking Workflows
    2024/12/03 by Ajay N. Jain, Jain, Ajay N., Ann E. Cleves +3 · 10 voices · 1 citation
    Biochemistry, Genetics and Molecular Biology · Chemistry · Computer Science · Decision Sciences · #Artificial intelligence #Chemistry #Cloud Computing and Resource Management #Computational chemistry #Computer science #Database #Docking (animal) #Machine learning #Molecular dynamics #Protein–ligand docking #Scientific Computing and Data Management #Virtual screening #Workflow #cs.AI #q-bio.BM

more