Výpis publikací

BACON, Wendi Anne; Berenice BATUT; Sanjay Kumar SRIKAKULAM; Paul ZIEREP; Anthony BRETAUDEAU; Bjorn GRUNING; Gildas LE CORGUILLE; Helge HECHT; John Y. DAVIS; Hans-Rudolf HOTZ a Beatriz SERRANO-SOLANO. Ten common misconceptions about Galaxy (and why they are wrong!). Plos Computational Biology. SAN FRANCISCO: PUBLIC LIBRARY SCIENCE, 2026, roč. 22, č. 2, s. 1-17. ISSN 1553-734X. Dostupné z: https://doi.org/10.1371/journal.pcbi.1013869.

ROJAS VERASTEGUI, Wudmir Yudy; Zargham AHMAD; Julia JAKIELA; Helge HECHT; Jana KLÁNOVÁ a Elliott James PRICE. Galaxy QCxMS for straightforward semi-empirical quantum mechanical EI-MS prediction. GIGABYTE. Shek Mun: GigaScience Press, 2025, roč. 2025, July 2025, s. 1-11. ISSN 2709-4715. Dostupné z: https://doi.org/10.46471/gigabyte.160.

VAN DEN BOSSCHE, Tim; Theodore ALEXANDROV; Aivett BILBAO; Wout BITTREMIEUX; Federico Ivan BRIGANTE; Matthew Chase CHAMBERS; Joshua CHARKOW; Eric DEUTSCH; Andrew W. DOWSEY; El Abiead YASIN; Ralf GABRIELS; Helge HECHT; Steffen HEUCKEROTH; Joshua A. KLEIN; Michael KNIERMAN; Lennart MARTENS; Robert L. MORITZ; Laura-Isobel MCCALL; Steffen NEUMANN; Yasset PEREZ-RIVEROL; Hannes L. ROST; Elliott James PRICE; Jim SHOFSTAHL; David L. TABB; Julian USZKOREIT; Juan Antonio VIZCAINO; Mingxun WANG; Sander WILLEMS; Dirk WINKELHARDT; Oliver KOHLBACHER a Samuel P. WEIN. mzPeak: Designing a Scalable, Interoperable, and Future-Ready Mass Spectrometry Data Format. Journal of Proteome Research. Washington: American Chemical Society, 2025, roč. 24, č. 11, s. 5329-5335. ISSN 1535-3893. Dostupné z: https://doi.org/10.1021/acs.jproteome.5c00435.

HÁJEK, Adam; Helge HECHT; Elliott James PRICE a Aleš KŘENEK. SpecTUS: Spectral Translator for Unknown Structures annotation from EI-MS spectra. 2025. Dostupné z: https://doi.org/10.48550/arXiv.2502.05114.

DELPORTE, Cedric; Marie TREMBLAY-FRANCO; Yann GUITTON; Cecile CANLET; Ralf J. M. WEBER; Helge HECHT; Elliott James PRICE; Jana KLÁNOVÁ; Charlotte JOLY; Celine DALLE; Julien ST-VANNE; Etienne THEVENOT; Isabelle SCHMITZ; Sylvain CHEREAU; Sylvain DECHAUMET; Binta DIEME; Franck GIACOMONI; Gildas LE CORGUILLE; Melanie PETERA a Florence SOUARD. Workflow4Metabolomics (W4M): A User-Friendly Metabolomics Platform for Analysis of Mass Spectrometry and Nuclear Magnetic Resonance Data. Current Protocols. HOBOKEN: Wiley, 2025, roč. 5, č. 2, s. 1-72. ISSN 2691-1299. Dostupné z: https://doi.org/10.1002/cpz1.70095.

FOREMAN, Amy L.; Benedikt WARTH; Ellen V. S. HESSEL; Elliott James PRICE; Emma L. SCHYMANSKI; Gaia CANTELLI; Helen PARKINSON; Helge HECHT; Jana KLÁNOVÁ; Jelle VLAANDEREN; Klára HILSCHEROVÁ; Martine VRIJHEID; Paolo VINEIS; Rita ARAUJO; Robert BAROUKI; Roel VERMEULEN; Sophie LANONE; Soren BRUNAK; Sylvain SEBERT a Tuomo KARJALAINEN. Adopting Mechanistic Molecular Biology Approaches in Exposome Research for Causal Understanding. ENVIRONMENTAL SCIENCE & TECHNOLOGY. WASHINGTON: AMER CHEMICAL SOC, 2024, roč. 58, č. 17, s. 7256-7269. ISSN 0013-936X. Dostupné z: https://doi.org/10.1021/acs.est.3c07961.

GALVIS, Johanna; Joris GUYON; Benjamin DARTIGUES; Helge HECHT; Bjorn GRUENING; Florian SPECQUE; Hayssam SOUEIDAN; Slim KARKAR; Thomas DAUBON a Macha NIKOLSKI. DIMet: an open-source tool for differential analysis of targeted isotope-labeled metabolomics data. Bioinformatics. Oxford: Oxford University Press, 2024, roč. 40, č. 5, s. 1-5. ISSN 1367-4803. Dostupné z: https://doi.org/10.1093/bioinformatics/btae282.

LAI, Yunjia; Jeremy P. KOELMEL; Douglas I. WALKER; Elliott James PRICE; Stefano PAPAZIAN; Katherine E. MANZ; Delia CASTILLA-FERNANDEZ; John A. BOWDEN; Vladimir NIKIFOROV; Arthur DAVID; Vincent BESSONNEAU; Bashar AMER; Suresh SEETHAPATHY; Xin HU; Elizabeth Z. LIN; Akrem JBEBLI; Brooklynn R. MCNEIL; Dinesh BARUPAL; Marina CERASA; Hongyu XIE; Vrinda KALIA; Renu NANDAKUMAR; Randolph SINGH; Zhenyu TIAN; Peng GAO; Yujia ZHAO; Jean FROMENT; Pawel ROSTKOWSKI; Saurabh DUBEY; Kateřina COUFALÍKOVÁ; Hana SELIČOVÁ; Helge HECHT; Sheng LIU; Hanisha H. UDHANI; Sophie RESTITUITO; Kam-Meng TCHOU-WONG; Lu KUN; Jonathan W. MARTIN; Benedikt WARTH; Krystal J. Godri POLLITT; Jana KLÁNOVÁ; Oliver FIEHN; Thomas O. METZ; Kurt D. PENNELL; Dean P. JONES a Gary W. MILLER. High-Resolution Mass Spectrometry for Human Exposomics: Expanding Chemical Space Coverage. ENVIRONMENTAL SCIENCE & TECHNOLOGY. WASHINGTON: AMER CHEMICAL SOC, 2024, roč. 58, č. 29, s. 12784-12822. ISSN 0013-936X. Dostupné z: https://doi.org/10.1021/acs.est.4c01156.

TKALEC, Žiga; Jean-Philippe ANTIGNAC; Nicole BANDOW; Frederic M. BEEN; Lidia BELOVA; Jos BESSEMS; Bruno LE BIZEC; Werner BRACK; German CANO-SANCHO; Jade CHAKER; Adrian COVACI; Nicolas CREUSOT; Arthur DAVID; Laurent DEBRAUWER; Gaud DERVILLY; Radu Corneliu DUCA; Valerie FESSARD; Joan O. GRIMALT; Thierry GUERIN; Baninia HABCHI; Helge HECHT; Juliane HOLLENDER; Emilien L. JAMIN; Jana KLÁNOVÁ; Tina KOSJEK; Martin KRAUSS; Marja LAMOREE; Gwenaelle LAVISON-BOMPARD; Jeroen MEIJER; Ruth MOELLER; Hans MOL; Sophie MOMPELAT; An VAN NIEUWENHUYSE; Herbert OBERACHER; Julien PARINET; Christof VAN POUCKE; Robert ROSKAR; Anne TOGOLA; Jurij TRONTELJ a Elliott James PRICE. Innovative analytical methodologies for characterizing chemical exposure with a view to next-generation risk assessment. Environment International. OXFORD (ENGLAND): Pergamon Press, 2024, roč. 186, April 2024, s. 1-16. ISSN 0160-4120. Dostupné z: https://doi.org/10.1016/j.envint.2024.108585.

HECHT, Helge; Wudmir Yudy ROJAS VERASTEGUI; Zargham AHMAD; Aleš KŘENEK; Jana KLÁNOVÁ a Elliott James PRICE. Quantum Chemistry-Based Prediction of Electron Ionization Mass Spectra for Environmental Chemicals. Analytical chemistry. WASHINGTON: American Chemical Society, 2024, roč. 96, č. 33, s. 13652-13662. ISSN 0003-2700. Dostupné z: https://doi.org/10.1021/acs.analchem.4c02589.

DE JONGE, Niek F.; Helge HECHT; Michael STROBEL; Mingxun WANG; Justin J. J. VAN DER HOOFT a Florian HUBER. Reproducible MS/MS library cleaning pipeline in matchms. Journal of Cheminformatics. London: BIOMED CENTRAL LTD, 2024, roč. 16, č. 1, s. 1-9. ISSN 1758-2946. Dostupné z: https://doi.org/10.1186/s13321-024-00878-1.

ABUEG, Linelle Ann L.; Enis AFGAN; Olivier ALLART; Ahmed H. A. WAN; W. Endi A. BACON; Dannon BAKER; Madeline BASSETTI; Berenice BATUT; Matthias BERNT; Daniel BLANKENBERG; Aureliano BOMBARELY; Anthony BRETAUDEAU; Catherine J. BROMHEAD; Melissa L. BURKE; Patrick K. CAPON; Martin CECH; Maria CHAVERO-DIEZ; John M. CHILTON; Tyler J. COLLINS; Frederik COPPENS; Nate CORAOR; Gianmauro CUCCURU; Fabio CUMBO; John DAVIS; F. Paul DE GEEST; Willem DE KONING; Martin DEMKO; Assunta DESANTO; Jose Manuel Dominguez BEGINES; Maria A. DOYLE; Bert DROESBEKE; Anika ERXLEBEN-EGGENHOFER; Melanie C. FOLL; Giulio FORMENTI; Anne FOUILLOUX; Rendani GANGAZHE; Tanguy GENTHON; Jeremy GOECKS; Alejandra N. Gonzalez BELTRAN; Nuwan A. GOONASEKERA; Nadia GOUE; Timothy J. GRIFFIN; Bjorn A. GRUNING; Aysam GUERLER; Sveinung GUNDERSEN; Ove Johan Ragnar GUSTAFSSON; Christina HALL; Thomas W. HARROP; Helge HECHT; Alireza HEIDARI; Tillman HEISNER; Florian HEYL; Saskia HILTEMANN; Hans-Rudolf HOTZ; Cameron J. HYDE; Pratik D. JAGTAP; Julia JAKIELA; James E. JOHNSON; Jayadev JOSHI; Marie JOSSE; Khaled JUM'AH; Matus KALAS; Katarzyna KAMIENIECKA; Tunc KAYIKCIOGLU; Markus KONKOL; Leonid KOSTRYKIN; Natalie KUCHER; Anup KUMAR; Mira KUNTZ; Delphine LARIVIERE; Ross LAZARUS; Yvan LE BRAS; Gildas LE CORGUILLE; Justin LEE; Simone LEO; Leandro LIBORIO; Romane LIBOUBAN; David Lopez TABERNERO; Lucille LOPEZ-DELISLE; Laila S. LOS; Alexandru MAHMOUD; Igor MAKUNIN; Pierre MARIN; Subina MEHTA; Winnie MOK; Pablo A. MORENO; Francois MORIER-GENOUD; Stephen MOSHER; Teresa MUELLER; Engy NASR; Anton NEKRUTENKO; Tiffanie M. NELSON; Asime J. OBA; Alexander OSTROVSKY; Polina V. POLUNINA; Krzysztof POTERLOWICZ; Elliott James PRICE; Gareth R. PRICE; Helena RASCHE; Bryan RAUBENOLT; Coline ROYAUX; Luke SARGENT; Michelle T. SAVAGE; Volodymyr SAVCHENKO; Denys SAVCHENKO; Michael C. SCHATZ; Pauline SEGUINEAU; Beatriz SERRANO-SOLANO; Nicola SORANZO; Sanjay Kumar SRIKAKULAM; Keith SUDERMAN; Anna E. SYME; Marco Antonio TANGARO; Jonathan A. T. EDDS; Mehmet T. EKMAN; Wai Cheng THANG; Anil S. THANKI; Michael UHL; Marius VAN DEN BEEK; Deepti VARSHNEY; Jenn VESSIO; Pavankumar VIDEM; Von Kuster GREG; Gregory R. WATSON; Natalie WHITAKER-ALLEN; Uwe WINTER; Martin WOLSTENCROFT; Federico ZAMBELLI; Paul ZIEREP a Rand ZOABI. The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update. Nucleic acids research. Oxford: Oxford University Press, 2024, roč. 52, W1, s. "W83"-"W94", 12 s. ISSN 0305-1048. Dostupné z: https://doi.org/10.1093/nar/gkae410.

KLEIN, Joshua; Henry LAM; Tytus D. MAK; Wout BITTREMIEUX; Yasset PEREZ-RIVEROL; Ralf GABRIELS; Jim SHOFSTAHL; Helge HECHT; Pierre-Alain BINZ; Shin KAWANO; Tim VAN DEN BOSSCHE; Jeremy CARVER; Benjamin A. NEELY; Luis MENDOZA; Tomi SUOMI; Tine CLAEYS; Thomas PAYNE; Douwe SCHULTE; Zhi SUN; Nils HOFFMANN; Yunping ZHU; Steffen NEUMANN; Andrew R. JONES; Nuno BANDEIRA; Juan Antonio VIZCAINO a Eric W. DEUTSCH. The Proteomics Standards Initiative Standardized Formats for Spectral Libraries and Fragment Ion Peak Annotations: mzSpecLib and mzPAF. Analytical chemistry. WASHINGTON: AMER CHEMICAL SOC, 2024, roč. 96, č. 46, s. 18491-18501. ISSN 0003-2700. Dostupné z: https://doi.org/10.1021/acs.analchem.4c04091.

TROJÁK, Matej; Helge HECHT; Martin ČECH a Elliott James PRICE. MSMetaEnhancer: A Python package for mass spectra metadata annotation. Journal of Open Source Software. 2022, roč. 7, č. 79. Dostupné z: https://doi.org/10.21105/joss.04494.

HECHT, Helge; Maksym SKORYK; Martin ČECH a Elliott James PRICE. RIAssigner: A package for gas chromatographic retention index calculation. Journal of Open Source Software. Open Journals, 2022, roč. 7, č. 75, s. 1-4. ISSN 2475-9066. Dostupné z: https://doi.org/10.21105/joss.04337.

HECHT, Helge; Sarhan MHD HASAN a Vlad POPOVICI. Disentangled Autoencoder for Cross-Stain Feature Extraction in Pathology Image Analysis. Applied Sciences. Basel: MDPI, 2020, roč. 10, č. 18, s. 1-14. ISSN 2076-3417. Dostupné z: https://doi.org/10.3390/app10186427.