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SysFate - Systems Biology of cell Fate decisions

Publications




Published on 11 December 2018

n° Citations: 754; h-index: 10; i10-index: 12 (November 2018)

2018

  1. 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.
  2. 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.
  3. 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.
  4. 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

  1. 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.

2016

  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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

  1. 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.
  2. 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.

2014

  1. 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.
  2. 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.
  3. 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

  1. 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. (PATENTED)
  2. 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.
  3. 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.