Enrique M. Muro

I am a Senior Scientist (tenured) working at the CBDM group at the Johannes Gutenberg University of Mainz in Germany.
My research interest focuses on Computational Biology and Bioinformatics.

Contact information:
Dr. Enrique M. Muro
Johannes Gutenberg University of Mainz
iomE - Faculty of Biology
Biozentrum I
Hans-Dieter-Huesch-Weg 15
55128 Mainz. Germany

E-mail: ed.zniam-inu@orum (not a palindrome, please read it backwards)

Research

Computational Biologist expert with additional training in Artificial Intelligence, Computational Neuroscience and Computational Physics. My research focuses in discovering and understanding what rules life and its products, the biological processes.
Science is full of rules that simplify the way nature works. Simplifications that, many times, stand on our incomplete knowledge of the domain and can mislead posterior research. It is not always the most efficient way to learn but, for practical reasons, is a good strategy. This has been previously approached in the concept of Falsifiability by Karl Popper. Biology, in particular, is specially prone to this problem due to its intrinsic complexity.
The state of the art is the best we have. Nevertheless, exceptions can be relevant, causal of functionality and even have implications in human diseases. Therefore, scientists supported by evidence and swimming against the tide, have big chances to make a difference if they are strong enough. In summary, there is no such unique way to develop science, but creativity, critical thinking and new perspectives lead straight to the conquest of new results, and if for any reason it is a must to ferret out where the mainstream is, trying alternative solutions that follow the parsimony principle will be my way to go.
Taking this into account, I am quite interested in discovering mechanisms, strategies and properties that lead to biological functionality, in special those that arise through evolution with consecuences for gene functionality and human diseases.

Keywords

Nowadays: proteome and genome evolution, evolution, genomics, non-coding genes, pseudogenes, transcription.

Still interested on: mobile DNA, systems biology, three-dimensional chromatin structure, stem cells, astrobiology, artificial intelligence, neural networks, models for the development of the central visual system.

Science outreach:

News

• 28th October 2024:
  Emilia Körner starts her pre-Master work under my supervision (in collaboration with Pablo Mier; Universidad Pablo Olavide of Seville). Working title: "The length of intrinsically disordered proteins across the whole tree of life".


• 9th October 2024:
  David Baker, Demis Hassabis and John Jumper have been awarded with the Nobel price of chemistry for the development of AI for predicting proteins’ complex structures. Again a Nobel prize where neural networks are one of the main players (press release). AlphaFold is a huge advance that will help us to understand how a protein folds, paving the way to solve the protein folding problem.


• 8th October 2024:
  John Hopfield and Geoffrey Hinton have been awarded with the Nobel price in physics for their pioneering work on artificial neural networks. Definitely, a clever movement from the physics' community at the Swedish Academy of Science. Today is the right time to remember the seminal work of colossus like Warren S. McCulloch (informal interview), Walter Pitts, and Donald O. Hebb. They were so influential!
  


• 1-8th July 2024:
  Prof. Ignacio Rojas visit.
  


• 5th June 2024:
  Anika du Plessis presents today in the general assembly of the European Astrobiology Institute (EAI). The title of her talk: "Design of a Computational model to simulate the possible evolution of protometabolic pathways".


• May 2024:
  Anika du Plessis' poster: Anna C. du Plessis, Hugh G. Patterton, and Enrique M. Muro. Design of a computational model to simulate the evolution of protometabolic networks. Women in Evolutionary Biology Conference (WEB) at the Max Planck Institute for Evolutionary Biology. 14th-16th May, 2024.
  


• Januar 2024:
  Anika du Plessis joins the lab. Anika is a South African Master Student from the Stellenbosch University that obtained a DAAD scholarship to perform research under my supervision together with Prof Hugh -G. Patterton from January 1st till June 30th 2024. She will be working on "protometabolic networks during the origin of life using genetic algorithms". Moreover, Anika is quite good in chess, actually she was Africa Junior Champion and planning to win some extra-money teaching here. So, in the case you want some chess lessons from her do not hesitate to contact.
  


• November 2023:
  "Fundamentals of programming for molecular biologists with Python" is ready to go. Online for mod1-a student.
  


• July 2023:
  See our new preprint: "The emergence of eukaryotes as an evolutionary algorithmic phase transition" .
  


• July 2023:
  The nine chapters of my e-book have been completely reviewed.
  


• September 2022:
  New presential and online courses. Prepare your computer for the course. Now, it is online!
  


• March 2022:
  My book on Bioinformatics has been translated to Italian and Romanian. Since the first publication in Spanish, I know it has been sold in South America: Argentina, Colombia, etc. These days it has been re-edited in Mallorca (Spain).
  
  

  Jan 2022: Preparing a course on "Fundamentals of programming in biomedicine with Python". I will use a part of it to teach @ the Modul 4.2. Biostatistik und Bioinformatik. Sept 2021: Working on the emergence of eukaryotes. My collaborators and me are quite excited, lets see what comes out of this. July 2021: A Methodology to Study Pseudogenized lincRNAs. Talyan S, Andrade-Navarro MA, Muro EM. Methods Mol Biol. 2021;2324:49-63. doi: 10.1007/978-1-0716-1503-4_4. PMID: 34165708 DOI: 10.1007/978-1-0716-1503-4_4 PubMed Some publications that represent my work As a principal investigator: The distributions of protein coding genes within chromatin domains in relation to human disease. Muro, E.M., Ibn-Salem, J. & Andrade-Navarro, M.A. Epigenetics & Chromatin 12, 72 (2019) doi:10.1186/s13072-019-0317-2. PMID: 31805995. The interest of Editor-in-Chief Steven Henikoff (BLOSUM matrices for sequence alignmnent) motivated us to send our paper there. Identification of transcribed protein coding sequence remnants within lincRNAs. Talyan S, Andrade-Navarro MA, Muro EM. Nucleic Acids Res. 2018 Jul 9. doi: 10.1093/nar/gky608. PMID: 29986053 As a post-doc: Functional evidence of post-transcriptional regulation by pseudogenes. Muro EM, Mah N, Andrade-Navarro MA. Biochimie. 2011 Nov;93(11):1916-21. doi: 10.1016/j.biochi.2011.07.024. Epub 2011 Jul 27. Review. PMID: 21816204 The pseudogenes of Mycobacterium leprae reveal the functional relevance of gene order within operons. Muro EM, Mah N, Moreno-Hagelsieb G, Andrade-Navarro MA. Nucleic Acids Res. 2011 Mar;39(5):1732-8. doi: 10.1093/nar/gkq1067. PMID: 21051341 Identification of gene 3' ends by automated EST cluster analysis. Muro EM, Herrington R, Janmohamed S, Frelin C, Andrade-Navarro MA, Iscove NN. Proc Natl Acad Sci U S A. 2008 Dec 23;105(51):20286-90. doi: 10.1073/pnas.0807813105. Epub 2008 Dec 18. PMID: 19095794 Complete list of publications:   Included in Pubmed      Not included in Pubmed Teaching I have been teaching at undergraduate/master/phD level since long ago. Here, at the Johannes Gutenberg University of Mainz, I devote part of my time to teach since 2014. Masterstudiengang Biomedizin. Modul: Proteinbiochemie und Bioinformatik, Winter 20[15,16,17,18,19,20,21,22,22-23,23, 24] BSc. Modul: Biostatistik und Bioinformatik, Fall 2017, 20[22,23,24] BSc. Modul: Bioinformatics techniques and databases, Winter-Fall 2024 What I did recently to improve my teaching at my university?: For I long time I realized that, due to the advance of technology in biology, it was necessary to fill-in an important gap in the CV of many graduated biologists. As soon as I had the opportunity, during the covid19-lockdown, I worked to cover that gap. The result of that effort is "Fundamentals of programming in biology with Python". Enjoy it! Open positions Students interested in Master's or PhD thesis are welcome to contact me