SYSFATE

n° Citations: 2616; h-index: 19; i10-index: 26 (August. 2024)

2024

• Maria B. Goncalves, Yue Wu, Earl Clarke, John Grist, Julien Moehlin, Marco Antonio Mendoza-Parra, Carl Hobbs, Barret Kalindjian, Henry Fok, Adrian P. Mander, Hana Hassanin, Daryl Bendel, J¨org T¨aubel, Tim Mant, Thomas Carlstedt, Julian Jack and Jonathan P. T. Corcoran. C286, an orally available retinoic acid receptor β agonist drug, regulates multiple pathways to achieve spinal cord injury repair. Frontiers Molecular NeuroScience. 2024; 20th August 2024; doi: 10.3389/fnmol.2024.1411384

 

2023

• Koshy AM, Mendoza-Parra MA. Retinoids: Mechanisms of Action in Neuronal Cell Fate Acquisition. Life. 2023; 13(12):2279. https://doi.org/10.3390/life13122279

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• Antoine Aubert, Maria Grazia Mendoza-Ferri, Aude Bramoulle, François Stüder, Bruno Maria Colombo, Marco Antonio Mendoza-Parra; PSEN1-M146V and PSEN1-A246E mutations associated with Alzheimer’s disease impair proper microglia differentiation; October 10, 2023; BioRxv.

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• Gwendoline Lozachmeur, Aude Bramoulle, Antoine Aubert, François Stüder, Julien Moehlin, Lucie Madrange, Frank Yates, Jean-Philippe Deslys, Marco Antonio Mendoza-Parra; Three-dimensional molecular cartography of human cerebral organoids revealed by double-barcoded spatial transcriptomics; Cell Reports Methods; 1st Sept. 2023. 

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• Xian-Yang Qin, Marco Antonio Mendoza-Parra and Yohei Shirakami; Editorial: Cancer and nutrients: new chemicals, signals, and biomarker-based therapy; Frontiers in Oncology; April 11, 2023.

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​2022

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• Aysis Koshy, Elodie Mathieux, François Stüder, Aude Bramoulle, Michele Lieb, Bruno Maria Colombo, Hinrich Gronemeyer,  Marco Antonio Mendoza-Parra; Synergistic activation of RARb and RARg nuclear receptors restores cell specialization during stem cell differentiation by hijacking RARa-controlled programs; Life Science Alliance; November 29th 2022

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• A. Huyghe, G. Furlan, J. Schroeder, E. Cascales,  A. Trajkova, M. Ruel, F. Stüder, M. Larcombe, Y. Bo Yang Sun, F. Mugnier, L. De Matteo, A. Baygin,  J. Wang, Y Yu, N. Rama, B. Gibert, J. Kielbassa, L. Tonon, P. Wajda, N. Gadot, M. Brevet, M. Siouda, P. Mulligan, R. Dante, P. Liu, H. Gronemeyer, M. Mendoza-Parra, J.M. Polo and F. Lavial; Comparative roadmaps of reprogramming and oncogenic transformation identify Bcl11b and Atoh8 as broad regulators of cellular plasticity; Nature Cell Biology; September 8th 2022.

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2021

•  Akinchan Kumar, Yasenya Kasikci, Alaa Badredine, Karim Azzag, Marie L Quintyn Ranty, Falek Zaidi, Nathalie Aragou, Catherine Mazerolles, Bernard Malavaud, Marco A Mendoza-Parra, Laurence Vandel, Hinrich Gronemeyer; Patient-matched analysis identifies deregulated networks in prostate cancer to guide personalized therapeutic intervention; Am J Cancer Res; 2021 Nov 15;11(11):5299-5318. eCollection 2021

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• Aubert, Antoine, François Stüder, Bruno M. Colombo, and Marco A. Mendoza-Parra ; A Core Transcription Regulatory Circuitry Defining Microglia Cell Identity Inferred from the Reanalysis of Multiple Human Microglia Differentiation Protocols;  Brain Sciences 11, no. 10: 1338 ; 2021.

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• Julien Moehlin, Aysis Koshy, François Stüder and Marco Antonio Mendoza-Parra; Protocol for using MULTILAYER to reveal molecular tissue substructures from digitized spatial transcriptomes; STAR Protocols; September 17, 2021.

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• François Stüder, Jean-Louis Petit, Stefan Engelen, Marco Antonio Mendoza-Parra; Real-time SARS-CoV-2 diagnostic and variants tracking over multiple candidates using nanopore DNA sequencing; Scientific Reports; 11; 15869; 5 August 2021. 

 

• Julien Moehlin, Bastien Mollet, Bruno Maria Colombo, Marco A. Mendoza-Parra, Inferring biologically relevant molecular tissue substructures by agglomerative clustering of digitized spatial transcriptomes with multilayer; Cell Systems; 07 May 2021. 

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• Florent Colin, Kristine Schauer, Ali Hamiche,  Pierre Martineau,  Jean‐Paul Borg, Jan Bednar, Guilia Bertolin, Luc Camoin, Yves Collette, Stephan Dimitrov, Isabelle Fournier, Vincent Hyenne , Marco A. Mendoza‐Parra, Xavier Morelli, Philippe Rondé, Izabela Sumara, Marc Tramier, Patrick Schultz, Jacky G. Goetz, The NANOTUMOR consortium ‐ towards the Tumor Cell Atlas; Biology of the Cell; 07 February 2021.

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​2020

•  Maha Siouda, Audrey D. Dujardin, Laetitia Barbollat-Boutrand, Marco A. Mendoza-Parra, Benjamin Gibert, Maria Ouzounova, Jebrane Bouaoud, Laurie Tonon, Marie Robert, Jean-Philippe Foy, Vincent Lavergne, Serge N. Manie, Alain Viari, Alain Puisieux, Gabriel Ichim, Hinrich Gronemeyer, Pierre Saintigny, Peter Mulligan. CDYL2 epigenetically regulates MIR124 to control NF-κB/STAT3-dependent breast cancer cell plasticity, iScience. 2020 May 6.

 

2019​

• Blum M, Cholley PE, Malysheva V, Nicaise S, Moehlin J, Gronemeyer H, Mendoza-Parra MA. A comprehensive resource for retrieving, visualizing, and integrating functional genomics data. Life Sci Alliance. 2019 Dec 9;3(1).

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• Goncalves, M.B., Moehlin, J., Clarke, E., Grist, J., Hobbs, C., Carr, A.M., Jack,J., Mendoza-Parra, M.A., Corcoran, J.P.T, RARβ agonist drug (C286) demonstrates efficacy in a pre-clinical neuropathic pain model restoring multiple pathways via DNA repair mechanisms, iScience. 2019 Nov 22;21:562-563.

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• Elodie Mathieux and Marco Antonio Mendoza-Parra; Systems Biology Perspectives for Studying Neurodevelopmental Events [Online First], IntechOpen; April 26th 2019; DOI: 10.5772/intechopen.85072. Available from: https://www.intechopen.com/online-first/systems-biology-perspectives-for-studying-neurodevelopmental-events

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2018

• Lucas Fauquier, Karim Azzag, Marco Antonio Mendoza Parra, Aurélie Quillien, Manon Boulet, Sarah Diouf, Gilles Carnac, Lucas Waltzer, Hinrich Gronemeyer & Laurence Vandel; CBP and P300 regulate distinct gene networks required for human primary myoblast differentiation and muscle integrity; Scientific Reports; 2018 August 22.

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• Pierre-Etienne Cholley, Julien Moehlin, Alexia Rohmer, Vincent Zilliox, Samuel Nicaise, Hinrich Gronemeyer and Marco Antonio Mendoza-Parra; Modeling gene-regulatory networks to describe cell fate transitions and predict master regulators; Nature Systems Biology & Applications; 2018 August 2.

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• Shinya Fujii, Shuichi Mori, Hiroyuki Kagechika, Marco Antonio Mendoza Parra and Hinrich Gronemeyer; Development of biotin-retinoid conjugates as chemical probes for analysis of retinoid function; Bioorganic & Medicinal Chemistry Letters; 2018 June 6,

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• Maja Milanovic, Dorothy N.Y. Fan, Dimitri Belenki, J. Henry M. Däbritz, Zhen Zhao, Yong Yu, Jan R. Dörr, Lora Dimitrova, Dido Lenze, Ines A. Monteiro Barbosa, Marco A. Mendoza-Parra, Tamara Kanashova, Marlen Metzner, Katharina Pardon, Maurice Reimann, Andreas Trumpp, Bernd Dörken, Johannes Zuber, Hinrich Gronemeyer, Michael Hummel, Gunnar Dittmar, Soyoung Lee and Clemens A. Schmitt; Senescence-associated reprogramming promotes cancer stemness; Nature; 2018 Jan 4;553 (7686):96-100.

 

2017

• MAM Saleem, Marco Antonio Mendoza-Parra, PE Cholley, M Blum and Hinrich Gronemeyer; Epimetheus: a multi-profile normalizer for epigenomic sequencing data; BMC Bioinformatics; 12 May 2017, 18 (1), 259;. [IF 2.435]

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​2016

• Marco Antonio Mendoza-Parra, Valeriya Malysheva, Mohamed Ashick Mohamed Saleem, Michele Lieb, Aurelie Godel and Hinrich Gronemeyer; Reconstructed cell fate-regulatory programs in stem cells reveal hierarchies and key factors of neurogenesis; Genome Research; 20 September 2016, 26 (11), 1505-1519. [IF 14.630]

 

• Valeriya Malysheva, Marco Antonio Mendoza-Parra, Mohamed Ashick Mohamed Saleem and Hinrich Gronemeyer; Reconstructing gene regulatory networks of tumorigenesis; Genome Medicine; 19 May 2016, 8 (1), 57. [IF 5.338]

 

• Marco Antonio Mendoza-Parra, Matthias Blum, Valeriya Malysheva, Pierre-Etienne Cholley and Hinrich Gronemeyer; LOGIQA: A database dedicated to Long-range Genome Interactions Quality Assessment; BMC Genomics; 16 May 2016, 17 (1), 355. [IF 3.986]

 

• Marco A. Mendoza-Parra, Mohamed Saleem MA, Matthias Blum, Pierre-Etienne Cholley and Hinrich Gronemeyer; NGS-QC Generator: A Quality control system for ChIP-seq and related deep sequencing-generated datasets; Statistical Genomics : Methods and Protocols; Springer Book Series; 24 March 2016; Volume 1418; pp 243-65.

 

• Marco Antonio Mendoza-Parra, Vincent Saravaki, Pierre-Etienne Cholley, Matthias Blum, Benjamin Billoré and Hinrich Gronemeyer; Antibody performance in ChIP-sequencing assays: From quality scores of public data sets to quantitative certification; F1000Research; 12 January 2016; 5:14; doi: 10.12688/f1000research.7637.2

 

​2015

• Marco Antonio Mendoza-Parra, and Hinrich Gronemeyer, Systems biology approaches to uncover the function of RAR and RXR subtypes and of selective ligands in gene regulation during cell lineage specification, The Retinoids: Biology, Biochemistry and Disease" (Wiley-Blackwell publisher Book Series); May 2015. pp 165-192.

 

• Ronan Chaligné, Tatiana Popova, Marco Antonio Mendoza Parra, Mohamed Ashick Mohamed Saleem‎‎, David Gentien, Kristen Ban, Tristan Piolot, Olivier Leroy, Odette Mariani, Hinrich Gronemeyer, Anne Vincent-Salomon, Marc-Henri Stern and Edith Heard ; The inactive X chromosome is epigenetically unstable and transcriptionally labile in breast cancer; Genome Research; 2015 Apr, 25(4): 488-503. [IF 14.630]

 

​2014

• Marco A. Mendoza-Parra and Hinrich Gronemeyer; Assessing quality standards for ChIP-seq and related massive parallel sequencing-generated datasets: When rating goes beyond avoiding the crisis; Genomics Data; Dec. 2014; vol. 2, pages 268-273.

 

• Jelena Vjetrovic, Pattabhiraman Shankaranarayanan, Marco A. Mendoza-Parra and Hinrich Gronemeyer; Senescence-secreted factors activate Myc and sensitize pretrasformed cells to TRAIL-induced apoptosis; Aging Cell; 2014 June; 13(3):487-96; doi: 10.1111/acel.12197 [IF. 6.340]

 

• Marco Antonio Mendoza-Parra, and Hinrich Gronemeyer, Integrative genomics to dissect retinoids functions, The Biochemistry of Retinoic Acid Receptors I: Structure, Activation and Function at the Molecular Level; Subceullar Biochemistry; Springer Book Series; 25th June 2014; Volume 70, pp 181-202.

 

​2013

• Marco Antonio Mendoza-Parra, Wouter Van Gool, Mohamed Saleem MA, Danilo Guillermo Ceschin and Hinrich Gronemeyer; A quality control system for profiles obtained by massive parallel sequencing; Nucleic Acid Research; 2013 Nov 1; 41(21):e196. doi: 10.1093/nar/gkt829. [IF 9.112]  (PATENTED)

 

• Marco Antonio Mendoza-Parra, Malgorzata Nowicka, Wouter Van Gool and Hinrich Gronemeyer; Characterising ChIP-seq binding patterns by model-based peak shape deconvolution; BMC Genomics; 2013 Nov.26; 14(1): 834. doi: 10.1186/1471-2164-14-834 [IF 3.986]

 

•  Marco Antonio Mendoza-Parra, and Hinrich Gronemeyer, Genome-wide studies of nuclear receptors in cell fate decisions, Review journal “Seminars in Cell and Developmental Biology”, Thematic issue: Nuclear receptors and cell differentiation, pluripotency, development and stem cells; 2013 Dec; 24 (10-12): 706-15. [IF 6.265]

 

​2012

• Pattabhiraman Shankaranarayanan*, Marco Antonio Mendoza-Parra*, Wouter Van Gool, Luisa M. Trindade and Hinrich Gronemeyer, Single-tube linear DNA amplification (LinDA) for genome-wide studies using a few thousand cells, Nature Protocols. 2012 Jan 26;7(2):328-38. doi: 10.1038/nprot.2011.447. [IF 9.673]  (*equal first author’s contribution)

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• Marco Antonio Mendoza-Parra, Martial Sankar, Mannu Walia and Hinrich Gronemeyer ; POLYPHEMUS : R package for comparative analysis of RNA Polymerase II ChIP-seq profiles by non-linear normalization ; Nucleic Acid Research. 2012 Feb; 40(4):e30 doi: 10.1093/nar/gkr1205. [IF 9.112]

 

​2011

• Marco Antonio Mendoza-Parra, Mannu Walia, Martial Sankar and Hinrich Gronemeyer ; Dissecting the retinoic acid-induced differentiation of F9  mouse embryonal stem cells through integrative genomic analysis; Molecular Systems Biology; 2011 Oct 11; 7: 538 [IF 10.872]

 

• Marco Antonio Mendoza-Parra, Martial Sankar, Mannu Walia and Hinrich Gronemeyer ; POLYPHEMUS : R package for comparative analysis of RNA Polymerase II ChIP-seq profiles by non-linear normalization ; Nucleic Acid Research. 2011 Dec 7; doi: 10.1093/nar/gkr1205. [IF 9.112]

 

• Pattabhiraman Shankaranarayanan, Marco Antonio Mendoza-Parra, Mannu Walia, Li Wang, Ning Li, Luisa M. Trindade and Hinrich Gronemeyer, Single-tube linear DNA amplification (LinDA) for robust ChIP-seq, Nature Methods. 2011 Jun 5; 8(7):565-7. [IF 32.072]

 

• Silvia Panizza, Marco Antonio Mendoza, Marc Berlinger,Lingzhi Huang, Alain Nicolas, Katsuhiko Shirahige and Franz Klein, Spo11-accessory proteins link double-strand break sites to the chromosome axis in early meiotic recombination, Cell. 2011 Aug 5; 146 (3): 372-83. [IF 32.242]

 

​2009

• Marco Antonio Mendoza, Silvia Panizza and Franz Klein, Analysis of protein-DNA interactions during meiosis by quantitative chromatin-immunoprecipitation (qChIP), Methods in Molecular Biology Book Series, 2009 ; 557 : 267-83.

 

non-peer-reviewed articles

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• Marco Antonio Mendoza-Parra, Pattabhiraman Shankaranarayanan & Hinrich Gronemeyer. Sequential chromatin immunoprecipitation protocol for global analysis through massive parallel sequencing (reChIP-seq). Protocol Exchange, DOI 10.1038/protex.2011.1256 (2012).

 

• Marco Antonio Mendoza, 2001, Les Phytases : Structure, Caractérisation et Applications, www.123bio.net/revues/