1. Molecular markers of hepatocellular carcinoma and their applications.

Pub. No.: WO/2007/039550 International Application No.: PCT/EP2006/066863Publication Date: 12.04.2007 International Filing Date: 28.09.2006IPC: G01N 33/574 (2006.01)


Together with Professor Heck, I am currently supervising two PhD students in our group and two Master students. Furthermore, I have participated in several courses organized by different depertments in the University of Utrecht:

  • Master in Regenerative Medicine-UMCU. Lecture entitled "Proteomic Analysis of Stem Cells". Utrecht (The Netherlands) September 2010
  • Master in Cancer Genomics & Developmental Biology. Lecture entitled "Analysis of protein phosphorylation with mass spectrometry". Utrecht (The Netherlands) April 2009.
  • Biomolecular Mass Spectrometry Course. Lecture entitled "Stem Cell Proteomics". Utrecht (The Netherlands) September 2009.
  • Biomolecular Mass Spectrometry Course. Lecture entitled "Stem Cell Proteomics". Utrecht (The Netherlands) September 2008.


"Young Gun" Early Career Investigator Award. HUPO 2010. Sydney (Australia)


Due to the clinical orientation of my former institution, my PhD dealt with the study of human pathologies such as Parkinson’s disease and hepatocellular carcinoma amongothers. There, I gained an important background in molecular biology techniques and developed experimental animal models which I finally complemented with proteomic analyses. During this time I noticed an important gap, in terms of knowledge communication, when working in multidisciplinary projects that involve classic biology and new high-throughput technologies like proteomics. Therefore, for my postdoctoral period I decided to specialize on MS-based proteomics as a tool to answer biological questions, becoming a bridge between both fields. Since I moved to Utrecht three years ago, I’ve been involved in several projects related to developmental biology, most importantly stem cells. These studies span from large-scale proteome and phosphoproteome analyses to understand global signaling events (i.e. during stem cell differentiation) to more targeted studies to reveal protein-protein interactions or functional characterization. I am actively working with relevant biology groups in the Netherlands such as Hans Clevers (Hubrecht Institute), Christine Mummery (Leiden University Medical Center) and Sander van den Heuvel (Utrecht University) and abroad like Andree Choo (BTI, Singapore) and Andras Nagy (Mount Sinai, Toronto). My research topic is mainly focused on quantitative mass spectrometry-based proteomics to unravel proteome dynamics in signaling networks involved in the differentiation and reprogramming processes of stem cells.Throughout this period I have acquired broad teamwork skills but at the same time I am becoming more independent by starting to lead projects: tpgether with Proffesor Heck, I am co-supervising two PhD students in our group and two Master students. I also participate in the continuous development of proteomic platforms in our group with special interests in bioinformatic approaches.


The average impact factor (IF) for the “Biochemical Research Methods” in 2009 is 2.347 (67 journals belong to this category). The average IF for the “Biochemistry & Molecular Biology” in 2009 is 2.582 (283 journals belong to this category). I have published 12 articles in peer-reviewed journals since 2005 with an absolute IF of 96.554 and an average IF of 8.777

Articles published in peer reviewed journals (Impact factors for the year of publication are shown):

RockerBox: analysis and filtering of massive proteomics search results.

van den Toorn HW, Muñoz J, Mohammed S, Raijmakers R, Heck AJ, van Breukelen B.

J Proteome Res. 2010 Dec 26. [Epub ahead of print].  PMID: 21184612 (IF=5.132)

Snapshots of kinase activities.

Muñoz J, Heck AJ.

Nat Biotechnol. 2009 Oct;27(10):912-3. PMID: 1981644 (IF=29.495)

Regulation of stathmin phosphorylation in mouse liver progenitor-29 cells during proteasome inhibition.

Santamaría E, Mora MI, Muñoz J, Sánchez-Quiles V, Fernández-Irigoyen J, Prieto J, Corrales FJ.

Proteomics. 2009 Oct;9(19):4495-506. PMID: 19688729 (IF=4.426)

Phosphorylation dynamics during early differentiation of human embryonic stem cells.

Van Hoof D, Muñoz J*, Braam SR, Pinkse MW, Linding R, Heck AJ, Mummery CL, Krijgsveld J.

Cell Stem Cell. 2009 Aug 7;5(2):214-26. PMID: 19664995 * Equally contribution. (IF=23.563)

Perspectives in stem cell proteomics.

Muñoz J, Heck AJ.

Genome Med. 2009 Apr 28;1(4):45. (IF=NA)

Mass spectrometric characterization of mitochondrial complex I NDUFA10 variants.

Muñoz J, Fernández-Irigoyen J, Santamaría E, Parbel A, Obeso J, Corrales FJ.

Proteomics. 2008 May;8(9):1898-908. PMID: 18442173 (IF=4.586)

Redox regulation of methylthioadenosine phosphorylase in liver cells: molecular mechanism and functional implications.

Fernández-Irigoyen J, Santamaría M, Sánchez-Quiles V, Latasa MU, Santamaría E, Muñoz J, Sánchez Del Pino MM, Valero ML, Prieto J, Avila MA, Corrales FJ.

Biochem J. 2008 Apr 15;411(2):457-65. PMID: 18237276 (IF=4.371)

Proteomic analysis of liver diseases: molecular mechanisms and biomarker discovery.

Santamaría E, Muñoz J, Fernández-Irigoyen J, Sesma L, Odriozola L, Corrales FJ.

Mini Rev Med Chem. 2008 Jan;8(1):1-9. Review. PMID: 18220980 (IF=3.132)

Toward the discovery of new biomarkers of hepatocellular carcinoma by proteomics.

Santamaría E, Muñoz J, Fernández-Irigoyen J, Prìeto J, Corrales FJ.

Liver Int. 2007 Mar;27(2):163-73. Review. PMID: 17311610 (IF=2.559)

Methylthioadenosine reverses brain autoimmune disease.

Moreno B, Hevia H, Santamaria M, Sepulcre J, Muñoz J, García-Trevijano ER, Berasain C, Corrales FJ, Avila MA, Villoslada P.

Ann Neurol. 2006 Sep;60(3):323-34. PMID: 16786535 (IF=8.051)

Molecular profiling of hepatocellular carcinoma in mice with a chronic deficiency of hepatic s-adenosylmethionine: relevance in human liver diseases.

Santamaría E, Muñoz J*, Fernandez-Irigoyen J, Sesma L, Mora MI, Berasain C, Lu SC, Mato JM, Prieto J, Avila MA, Corrales FJ.

J Proteome Res. 2006 Apr;5(4):944-53. PMID: 16602702 * Equally contribution (IF=5.151)

Oxidation of specific methionine and tryptophan residues of apolipoprotein A-I in hepatocarcinogenesis.

Fernández-Irigoyen J, Santamaría E, Sesma L, Muñoz J, Riezu JI, Caballería J, Lu SC, Prieto J, Mato JM, Avila MA, Corrales FJ.

Proteomics. 2005 Dec;5(18):4964-72. PMID: 16252306 (IF=6.088)

Contributions to books:

Quantitative proteome and phosphoproteome analysis of human embryonic stem cells.

Muñoz J, Heck AJ.

Methods Mol Biol. 2009 In press. (IF=NA)

Conferences (only most relevant are shown)

  • HUPO 2010. September 2010, Sydney (Australia). Selected for Oral Presentation.
  • ISSCR 2009 Annual Meeting. July 2009, Barcelona (Spain). Poster presentation.
  • Perspectives in Stem Cell Proteomics Conference. March 2009, Hinxton (UK). Poster presentation.
  • NWO-CW studiegroepen. December 2008, Veldhoven (The Netherlands). Selected for Oral Presentation.
  • HUPO 2008. August 2008, Amsterdam (The Netherlands). Selected for Oral Presentation and Presented Poster.
  • First Congress for Spanish Proteomics Society. February 2008, Sitges (Spain). Selected for Oral Presentation.
  • 2nd Congress of the Spanish Proteomics Society, Firts Congress of the European Proteomics Association. February 2007, Valencia (Spain). Selected for Oral Presentation.

Work History

Work History
Sep 2002 - Jul 2007

PhD degree - University of Navarra

I obtained my PhD degree at the University of Navarra under the supervision of Dr. Fernando Corrales in the Genomics, Proteomics and Bioinformatics Group.





Molecular Biology

I am familiarized with the most common techniques used in Molecular Biology such as Western Blot, Immunoprecipitation, Immunocytochemistry....


I have been working with the main vendors for MS software, Mascot, Sequest...

Mass Spectrometry

Broad experience in MS analysis. Large scale analysis and targeted proteomics.



Jeroen Krijgsveld

Supervisor (2007-2008)

Albert Heck

Supervisor (2008-Present)

Fernando Corrales

Thesis Director