Publications by authors named "Rolf Fagerberg"

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SynKit: A Graph-Based Python Framework for Rule-Based Reaction Modeling and Analysis.
Tieu-Long Phan, Marcos E González Laffitte, Klaus Weinbauer, Daniel Merkle, Jakob Lykke Andersen, Rolf Fagerberg

J Chem Inf Model· December 2025

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KGG: Knowledge-Guided Graph Self-Supervised Learning to Enhance Molecular Property Predictions.
Van-Thinh To, Phuoc-Chung Van Nguyen, Gia-Bao Truong, Tuyet-Minh Phan, Tieu-Long Phan, Rolf Fagerberg

J Chem Inf Model· September 2025

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Finding Thermodynamically Favorable Pathways in Chemical Reaction Networks Using Flows in Hypergraphs and Mixed-Integer Linear Programming.
Adittya Pal, Rolf Fagerberg, Jakob Lykke Andersen, Christoph Flamm, Peter Dittrich

J Chem Inf Model· July 2025

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SynTemp: Efficient Extraction of Graph-Based Reaction Rules from Large-Scale Reaction Databases.
Tieu-Long Phan, Klaus Weinbauer, Marcos E González Laffitte, Yingjie Pan, Daniel Merkle, Rolf Fagerberg

J Chem Inf Model· March 2025

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Pathway Realizability in Chemical Networks.
Jakob L Andersen, Sissel Banke, Rolf Fagerberg, Christoph Flamm, Daniel Merkle

J Comput Biol· February 2025

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Reaction rebalancing: a novel approach to curating reaction databases.
Tieu-Long Phan, Klaus Weinbauer, Thomas Gärtner, Daniel Merkle, Jakob L Andersen, Rolf Fagerberg

J Cheminform· July 2024

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Toward the Reconciliation of Inconsistent Molecular Structures from Biochemical Databases.
Casper Asbjørn Eriksen, Jakob Lykke Andersen, Rolf Fagerberg, Daniel Merkle

J Comput Biol· June 2024

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Representing Catalytic Mechanisms with Rule Composition.
Jakob L Andersen, Rolf Fagerberg, Christoph Flamm, Walter Fontana, Juri Kolčák

J Chem Inf Model· November 2022

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Graph transformation for enzymatic mechanisms.
Jakob L Andersen, Rolf Fagerberg, Christoph Flamm, Walter Fontana, Jurai Kolčák

Bioinformatics· July 2021

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Lipid molecular timeline profiling reveals diurnal crosstalk between the liver and circulation.
Richard R Sprenger, Martin Hermansson, Ditte Neess, Lena Sokol Becciolini, Signe Bek Sørensen, Rolf Fagerberg

Cell Rep· February 2021

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Finding the K best synthesis plans.
Rolf Fagerberg, Christoph Flamm, Rojin Kianian, Daniel Merkle, Peter F Stadler

J Cheminform· April 2018

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Algorithms for computing the triplet and quartet distances for binary and general trees.
Andreas Sand, Morten K Holt, Jens Johansen, Rolf Fagerberg, Gerth Stølting Brodal

Biology (Basel)· September 2013

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A practical O(n log2 n) time algorithm for computing the triplet distance on binary trees.
Andreas Sand, Gerth Stølting Brodal, Rolf Fagerberg, Christian N S Pedersen, Thomas Mailund

BMC Bioinformatics· September 2013

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Recrafting the neighbor-joining method.
Thomas Mailund, Gerth S Brodal, Rolf Fagerberg, Christian N S Pedersen, Derek Phillips

BMC Bioinformatics· January 2006

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