21 published papers over the last 14 years

Publications

Since Zakodium was created, we have helped define how scientific software is done. The publications listed below trace a continuous line of original work across NMR, mass spectrometry, infrared spectroscopy, cheminformatics, machine learning, and forensic science. For example, ChemCalc, NMRium, the spin-system simulation algorithm, the FAIR data repositories, and the recent transformer-based structure elucidation models are all conceived, validated, and published in the peer-reviewed literature.

That is the difference we bring: our software is not a data-management layer wrapped around a chemistry problem, it grows directly out of the science it serves. This record is why research groups, universities, and companies with R&D labs trust us. When you work with Zakodium, you work with a team that understands the underlying methods deeply enough to advance them - and that has been doing so for over a decade.

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NMRMass SpectrometryMachine LearningCheminformaticsWeb ApplicationData ProcessingFAIR DataForensic ScienceEducationChemistry

2025

October 10, 2025

NMRMind: A Transformer-Based Model Enabling the Elucidation from Multidimensional NMR to Structures.

Xue, X, Sun, H, Sun, J, Patiny, L, et al

Analytical Chemistry

NMRMachine LearningCheminformatics
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September 23, 2025

Consensus Prediction of Chemical Reactions with OCHEM-R Platform.

Tetko IV, Godin G,, Jablonka KM, Mirza A, Patiny L

International Conference on Artificial Neural Networks

Machine LearningCheminformaticsWeb Application
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February 26, 2025

Unlocking the Potential of Browser- Based Scientific Data Analysis: A 20-Year Journey of Expertise

Patiny, L

Chimia

Web ApplicationData Processing
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2024

October 28, 2024

MetaboScope: a statistical toolbox for analyzing 1H nuclear magnetic resonance spectra from human clinical studies

Loo, RL, Mosquera, JO, Zasso, M, et al

Bioinformatics Advances

NMRWeb ApplicationData Processing
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July 16, 2024

A Quasi Real-Time Evaluation of High-Resolution Mass Spectra of Complex Chlorinated Paraffin Mixtures and Their Transformation Products

Mendo Diaz, O, Patiny, L, Tell, A, Hutter, J, et al

Analytical chemistry

Mass SpectrometryData ProcessingChemistry
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January 05, 2024

NMRium: Teaching nuclear magnetic resonance spectra interpretation in an online platform

Patiny, L, Musallam, H, Bolaños, A, Zasso, M, et al

Beilstein journal of organic chemistry

NMRWeb ApplicationEducation
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2023

December 04, 2023

Automatic extraction of FAIR data from publications using LLM.

Patiny, L, Godin, G

ChemRxiv

Machine LearningFAIR DataCheminformatics
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October 25, 2023

Two Decades of Online Teaching: Trends, Challenges, and Future Directions

Turin, R, Patiny, L

Chimia - 77(10), pp. 683-687

Education
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2021

May 24, 2021

NMRium browser-based nuclear magnetic resonance data processing

Davies, AN, Patiny, L

Spectroscopy Europe

NMRWeb ApplicationData Processing
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2020

December 09, 2020

Seized Ecstasy Pills: Infrared Spectra and Image Datasets

Patiny, L, Zasso, M, Esseiva, P, Wist, J

Data

Forensic ScienceFAIR Data
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2019

November 12, 2019

MSPolyCalc: a web‐based App for polymer mass spectrometry data interpretation. The case study of a pharmaceutical excipient

Desport, JS, Frache, G, Patiny, L

Rapid Communications in Mass Spectrometry - 56(6), pp. 520–528

Mass SpectrometryWeb ApplicationData Processing
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2017

October 05, 2017

The C6H6 NMR repository: An integral solution to control the flow of your data from the magnet to the public

Patiny, L, Zasso, M, Kostro, D, et al

Magnetic Resonance in Chemistry - 56(6), pp. 520–528

NMRFAIR DataData Processing
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2016

May 05, 2016

“Ask Ernö”: a self-learning tool for assignment and prediction of nuclear magnetic resonance spectra

Castillo, AM, Bernal, A, Dieden, R, Patiny, L, Wist, J

Journal of cheminformatics. Springer International Publishing - 8(1), pp. 1–8

NMRMachine LearningCheminformatics
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March 01, 2016

Development of a systematic computer vision-based method to analyse and compare images of false identity documents for forensic intelligence purposes--Part I: Acquisition, calibration and validation issues

Auberson, M, Baechler, S, Zasso, M, et al

Forensic science international. Elsevier - 260, pp. 74–84

Forensic Science
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2015

March 22, 2015

Wikipedia Chemical Structure Explorer: substructure and similarity searching of molecules from Wikipedia

Ertl, P, Patiny, L, Sander, T, Rufener, C, Zasso, M

Journal of cheminformatics. Springer International Publishing - 7(1), p. 10

CheminformaticsWeb Application
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2014

December 9, 2014

How accurately can we predict the melting points of drug-like compounds?

Tetko, IV, Sushko, Y, Novotarskyi, S, Patiny, L, et al

Journal of chemical information and modeling. American Chemical Society - 54(12), pp. 3320–3329

Machine LearningCheminformaticsChemistry
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2013

March 12, 2013

ChemCalc: A Building Block for Tomorrow’s Chemical Infrastructure

Patiny, L, Borel, A

Journal of Chemical Information and Modeling - 53(5), pp. 1223–1228

Mass SpectrometryCheminformaticsWeb Application
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2012

November 30, 2012

Monitoring of illicit pill distribution networks using an image collection exploration framework

Camargo, J, Esseiva, P, González, F, Wist, J, Patiny, L

Forensic science international. Elsevier - 223(1), pp. 298–305

Forensic Science
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2011

June 10, 2011

Online chemical modeling environment (OCHEM): Web platform for data storage, model development and publishing of chemical information

Sushko, I, et al

Journal of Computer-Aided Molecular Design

Machine LearningCheminformaticsWeb ApplicationFAIR Data
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April 02, 2011

Fast and accurate algorithm for the simulation of NMR spectra of large spin systems

Castillo, AM, Patiny, L, Wist, J

Journal of Magnetic Resonance. Academic Press - 209(2), pp. 123–130

NMRData Processing
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2006

March 03, 2006

EcoScale, a semi-quantitative tool to select an organic preparation based on economical and ecological parameters

Van Aken, K, Strekowski, L, Patiny, L

Beilstein journal of organic chemistry - Beilstein-Institut, 2(1), p. 3

Web ApplicationChemistry
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