CycloBranch
Publications

Publication to Cite

Jiri Novak, Anton Skriba and Vladimir Havlicek.
CycloBranch 2: Molecular Formula Annotations Applied to imzML Data Sets in Bimodal Fusion and LC-MS Data Files.
Anal. Chem., vol. 92, no. 10, pp. 6844-6849, 2020. DOI: 10.1021/acs.analchem.0c00170.
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Other Publications to Cite

Jiri Novak, Karel Lemr, Kevin A. Schug and Vladimir Havlicek.
CycloBranch: De Novo Sequencing of Nonribosomal Peptides from Accurate Product Ion Mass Spectra.
J. Am. Soc. Mass Spectrom., vol. 26, no. 10, pp. 1780-1786, 2015. DOI: 10.1007/s13361-015-1211-1.
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Jiri Novak, Lucie Sokolova, Karel Lemr, Tomas Pluhacek, Andrea Palyzova and Vladimir Havlicek.
Batch-processing of Imaging or Liquid-chromatography Mass Spectrometry Datasets and De Novo Sequencing of Polyketide Siderophores.
BBA - Proteins Proteom., vol. 1865, no. 7, pp. 768-775, 2017. DOI: 10.1016/j.bbapap.2016.12.003.
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Jiri Novak, Anton Skriba, Jakub Zapal, Marek Kuzma and Vladimir Havlicek.
CycloBranch: An open tool for fine isotope structures in conventional and product ion mass spectra.
J. Mass Spectrom., vol. 53, no. 11, pp. 1097-1103, 2018. DOI: 10.1002/jms.4285.
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Jiri Novak, Kevin A. Schug and Vladimir Havlicek.
Quantitation of Small Molecules from Liquid Chromatography-Mass Spectrometric Accurate Mass Datasets using CycloBranch.
Eur. J. Mass Spectrom., vol. 29, no. 2, pp. 102-110, 2023. DOI: 10.1177/14690667231164766.
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MassSpecBlocks

Jan Privratsky and Jiri Novak.
MassSpecBlocks: a web-based tool to create building blocks and sequences of nonribosomal peptides and polyketides for tandem mass spectra analysis.
J. Cheminformatics, vol. 13, no. 1, pp. 51, 2021. DOI: 10.1186/s13321-021-00530-2.

Other Related Publications

Jiri Novak and Vladimir Havlicek.
Compound Dereplication and De Novo Characterization of Small Molecules by Mass Spectrometry / Dereplikace latek a de novo charakterizace malych molekul z hmotnostnich spekter.
Chem. Listy, vol. 116, no. 1, pp. 11-19, 2022. DOI: 10.54779/chl20220011 (in Czech only).

Radim Dobias, Anton Skriba, Tomas Pluhacek, Milos Petrik, Andrea Palyzova, Marcela Kanova, Eva Cubova, Jiri Houst, Jiri Novak, David A. Stevens, Goran Mitulovic, Eva Krejci, Petr Hubacek and Vladimir Havlicek.
Noninvasive Combined Diagnosis and Monitoring of Aspergillus and Pseudomonas Infections: Proof of Concept
J. Fungi, vol. 7, no. 9, pp. 730, 2021. DOI: 10.3390/jof7090730.

Tereza Jurikova, Dominika Luptakova, Olga Kofronova, Anton Skriba, Jiri Novak, Helena Maresova, Andrea Palyzova, Milos Petrik, Vladimir Havlicek and Oldrich Benada.
Bringing SEM and MSI Closer Than Ever Before: Visualizing Aspergillus and Pseudomonas Infection in the Rat Lungs
J. Fungi, vol. 6, no. 4, pp. 257, 2020. DOI: 10.3390/jof6040257.

Andrea Palyzova, Helena Maresova, Jiri Novak, Jiri Zahradnik and Tomas Rezanka.
Effect of the anti-inflammatory drug diclofenac on lipid composition of bacterial strain Raoultella sp. KDF8.
Folia Microbiol., vol. 65, no. 4, pp. 763-773, 2020. DOI: 10.1007/s12223-020-00790-9.

Jiri Novak and Vladimir Havlicek.
Interpretation of peptide product ion mass spectra: Examples / Resene priklady interpretace produktovych spekter peptidu.
Chem. Listy, vol. 114, no. 3, pp. 200-208, 2020. Link (in Czech only).

Ludovit Skultety, Jiri Novak and Vladimir Havlicek.
Fundamentals of the mass spectra interpretation / Zaklady interpretace hmotnostnich spekter.
Chem. Listy, vol. 114, no. 2, pp. 145-154, 2020. Link (in Czech only).

Tomas Pluhacek, Anton Skriba, Jiri Novak, Dominika Luptakova and Vladimir Havlicek.
Analysis of Microbial Siderophores by Mass Spectrometry.
In: Sanjoy K. Bhattacharya (ed.), Metabolomics: Methods and Protocols, Methods in Molecular Biology, vol. 1996, pp. 131-153, Springer, 2019. DOI: 10.1007/978-1-4939-9488-5_12.

Andrea Palyzova, Katerina Svobodova, Lucie Sokolova, Jiri Novak and Cenek Novotny.
Metabolic profiling of Fusarium oxysporum f. sp. conglutinans race 2 in dual cultures with biocontrol agents Bacillus amyloliquefaciens, Pseudomonas aeruginosa, and Trichoderma harzianum.
Folia Microbiol., vol. 64, no. 6, pp. 779-787, 2019. DOI: 10.1007/s12223-019-00690-7.

Dominika Luptakova, Tomas Pluhacek, Milos Petrik, Jiri Novak, Andrea Palyzova, Lucie Sokolova, Anton Skriba, Blanka Sediva, Karel Lemr and Vladimir Havlicek.
Non-invasive and Invasive Diagnoses of Aspergillosis in a Rat Model by Mass Spectrometry.
Sci. Rep., vol. 7, pp. 16523, 2017. DOI: 10.1038/s41598-017-16648-z.

Jiri Novak and Vladimir Havlicek.
Dereplication and Visualization of Fungal Siderophores by CycloBranch.
Mycoses, vol. 60, no. S2, pp. 200, 2017. DOI: 10.1111/myc.12674.

Tomas Pluhacek, Karel Lemr, Dipankar Ghosh, David Milde, Jiri Novak and Vladimir Havlicek.
Characterization of Microbial Siderophores by Mass Spectrometry.
Mass Spectrom. Rev., vol. 35, no. 1, pp. 35-47, 2016. DOI: 10.1002/mas.21461.

Jakub Prichystal, Kevin A. Schug, Karel Lemr, Jiri Novak and Vladimir Havlicek.
Structural Analysis of Natural Products.
Anal. Chem., vol. 88, no. 21, pp. 10338-10346, 2016. DOI: 10.1021/acs.analchem.6b02386.