In this seminar open to all students at the University of Jena (subject to subscribing via Fridolin) we are discussing current topics in Cheminformatics, which might involve discussing older papers if they are relevant. This is a seminar where active involvement by all participants at all occasions is assumed. Everyone will need to have read the paper *before* the seminar.

“Current Topics in Cheminformatics”  takes place at Lessingstraße 8, Seminar Room 113, every Tuesday from 10.04.2018 – 13.07.2018 from 10:15 to 11:45 o’ clock.

Please contact the organiser, christoph.steinbeck [at] uni [minus] jena [dot] de, if you are interested in participating.


Papers to be discussed are selected from the paper pile listed below. Please contact the organiser if you wish add a paper to the pile.

Paper Pile


Sivakumar, Tadi Venkata; Bhaduri, Anirban; Muni, Rajasekhara Reddy Duvvuru; Park, Jin Hwan; Kim, Tae Yong

SimCAL: a flexible tool to compute biochemical reaction similarity Journal Article

BMC Bioinformatics, 19 (1), pp. 254, 2018, ISSN: 1471-2105.

Abstract | Links | BibTeX

Boiteau, Rene; Hoyt, David; Nicora, Carrie; Kinmonth-Schultz, Hannah; Ward, Joy; Bingol, Kerem

Structure Elucidation of Unknown Metabolites in Metabolomics by Combined NMR and MS/MS Prediction Journal Article

Metabolites, 8 (1), pp. 8, 2018.

Abstract | Links | BibTeX

Blazenovic, Ivana; Kind, Tobias; Ji, Jian; Fiehn, Oliver

Software Tools and Approaches for Compound Identification of LC-MS/MS Data in Metabolomics Journal Article

Metabolites, 8 (2), pp. 31, 2018.

Abstract | Links | BibTeX

Chong, Jasmine; Soufan, Othman; Li, Carin; Caraus, Iurie; Li, Shuzhao; Bourque, Guillaume; Wishart, David S; Xia, Jianguo

MetaboAnalyst 4.0: towards more transparent and integrative metabolomics analysis Journal Article

Nucleic Acids Research, 37 , pp. W652, 2018.

Abstract | Links | BibTeX

KG, Georg Thieme Verlag; Scossa, Federico; Benina, Maria; Alseekh, Saleh; Zhang, Youjun; Fernie, Alisdair R

The Integration of Metabolomics and Next-Generation Sequencing Data to Elucidate the Pathways of Natural Product Metabolism in Medicinal Plants Journal Article

Planta Medica, (EFirst), 2018.

Abstract | Links | BibTeX

Tanaka, Wataru; Arita, Masanori

Physicochemical Prediction of Metabolite Fragmentation in Tandem Mass Spectrometry Journal Article

Mass Spectrometry, 7 (1), pp. A0066-A0066, 2018.

Links | BibTeX


Lai, Zijuan; Tsugawa, Hiroshi; Wohlgemuth, Gert; Mehta, Sajjan; Mueller, Matthew; Zheng, Yuxuan; Ogiwara, Atsushi; Meissen, John; Showalter, Megan; Takeuchi, Kohei; Kind, Tobias; Beal, Peter; Arita, Masanori; Fiehn, Oliver

Identifying metabolites by integrating metabolome databases with mass spectrometry cheminformatics Journal Article

Nature Methods, 122 (1), pp. 769–56, 2017.

Abstract | Links | BibTeX

Patiny, Luc; "e, Micha; Kostro, Daniel; Bernal, Andrés; Castillo, Andrés M; ~n, Alejandro Bola; Asencio, Miguel A; Pellet, Norman; Todd, Matthew; Schloerer, Nils; Kuhn, Stefan; Holmes, Elaine; Javor, Sacha; Wist, Julien

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

Magnetic Resonance in Chemistry, 3 (D1), pp. 160018, 2017.

Abstract | Links | BibTeX

Alden, Nicholas; Krishnan, Smitha; Porokhin, Vladimir; Raju, Ravali; McElearney, Kyle; Gilbert, Alan; Lee, Kyongbum

Biologically Consistent Annotation of Metabolomics Data Journal Article

Analytical Chemistry, 89 (24), pp. acs.analchem.7b02162–13104, 2017.

Abstract | Links | BibTeX

Naake, Thomas; Gaquerel, Emmanuel

MetCirc: navigating mass spectral similarity in high-resolution MS/MS metabolomics data Journal Article

Bioinformatics, 33 (15), pp. 2419–2420, 2017.

Abstract | Links | BibTeX


Heller, Stephen R; McNaught, Alan; Pletnev, Igor; Stein, Stephen; Tchekhovskoi, Dmitrii

InChI, the IUPAC International Chemical Identifier Journal Article

Journal of Cheminformatics, 7 (1), pp. 23, 2015, ISSN: 1758-2946.

Abstract | Links | BibTeX


Willoughby, Patrick H; Jansma, Matthew J; Hoye, Thomas R

A guide to small-molecule structure assignment through computation of (1H and 13C) NMR chemical shifts Journal Article

Nature protocols, 9 (3), pp. 643–660, 2014.

Abstract | Links | BibTeX