Complexity, completeness, and quality of regulatory networks: Lessons from Abasy Atlas
What is the true structural nature of regulatory networks? Are these scale-free or is it a consequence of incompleteness? What is the size of these networks? How complex are? Using data from Abasy Atlas, we answer all these questions and others by finding and leveraging constrained global network properties. First, we use state-of-the-art statistical techniques to settle a previous controversy on the structural nature of biological networks by proving that regulatory networks truly are scale-free and that it is not a consequence of incompleteness. Next, we found that regulatory networks complexity seems to be constrained by dynamical stability. We then leverage this constraint to propose a model allowing to quantify the total numbers of interactions in a regulatory network. Finally, we provide evidence showing that regulatory network reconstructions based solely on high-throughput technologies, such as ChIP-seq, are biased and show how the clustering coefficient could be used to assess the quality of the network reconstruction.
Campos, A.I. and Freyre-González, J.A.* Evolutionary constraints on the complexity of genetic regulatory networks allow predictions of the total number of genetic interactions. Scientific Reports 9(1):3618 (2019) doi:10.1038/s41598-019-39866-z arXiv:1812.01252v2 bioRxiv:10.1101/486647
Open graduate and undergraduate positions in our lab
We invite enthusiastic undergraduate students in the areas of biology, computation, mathematics, or physics to join our lab and working on a thesis in systems and network biology. The database Abasy Atlas is actively developed by our group and is one of the main sources of data for our research. From January 2019, two positions will become available. These positions are related to research in funded projects on the large-scale massive inference of regulatory networks to study their organization and evolution. Undergrads will have access to a fellowship. Besides, they will have the opportunity to learn basic and advanced computer programming attending classes at the Undergraduate Program in Genomic Sciences, UNAM (in Spanish) as our lab is responsible for curricula in this area. We also will provide support if the candidate is interested in applying to our Ph.D. program (in Spanish). Candidates require being highly motivated for challenges in the frontier of the science. If interested please send your CV and motivation letter.
Our group moved into a new building!
From September 24 to 27, our research group moved offices, servers, and equipment into the new building hosting the Program of Systems Biology and Synthetic Biology at the Center for Genomic Sciences, UNAM.
Distinction for 15 years teaching at the Undergraduate Program in Genomic Sciences!
Prof. Freyre was distinguished for 15 years of outstanding work teaching and coordinating the curriculum of the Computing Science area in the Undergraduate Program in Genomic Sciences (UPGS), UNAM campus Morelos. Prof. Freyre turned the UPGS into a life project since inception: From the beginning participating in the development of the UPGS designing syllabi and teaching to supervising research thesis, most of which have derived into published research papers.
Conference at the Chemistry Faculty, UNAM
Prof. Freyre delivered the conference "Towards a large-scale comparative systems biology across bacteria: Abasy Atlas and massive prediction of regulatory networks" to colleagues and students of the Chemistry Faculty, UNAM. Thanks to Prof. Herminia Loza-Tavera for the invitation to give this talk!
Abasy Atlas v2.0 goes online!
The second version of our comprehensive atlas of meta-curated regulatory networks, systems, global network properties, and system-level elements shaping regulatory networks across bacteria, Abasy Atlas v2.0, goes online today with an important increase in content regarding the previous version 1.0:
Abasy (Across-bacteria systems) Atlas contains systems and system-level elements, and global properties for 71 (42% more) reconstructed and meta-curated regulatory networks (178,942 regulatory interactions [128% more]) covering 42 bacteria (64% Gram-positive and 36% Gram-negative) distributed in 9 species, containing 7,558 (104% more) regulons and 3,886 systems (modules [119% more]).
Carlos Cruz is a Ph.D. candidate!
After presenting the main results of his research project titled "Evolutionary rewiring and organizational landscape of prokaryotic regulatory networks: Towards a comparative systems biology" in a three-and-a-half-hour oral examination, Carlos was awarded the degree of Ph.D. candidate. Congratulations Carlos!
Start of the intensive course "Programming Principles" teached at the International Laboratory on Human Genome Research, UNAM
From August 13 to 17, Prof. Freyre taught the first of two parts of the course "Programming Principles" to the students of the recently established Undergraduate Program on Genomic Sciences ENES Juriquilla, UNAM. This effort condensed into two weeks the equivalent semestral course that has been successfully taught since 2003 as a fundamental part of the homologous undergraduate program based in the Center for Genomic Sciences, UNAM campus Morelos.
Successful thesis defense by Marco Tello, congratulations!
Marco Tello defended his B.Sc. thesis titled "Construction of Neurospora crassa transcriptional regulatory network and analysis focusing on circadian genes", carried out in our lab, to be awarded a B.Sc. in Genomic Sciences, Magna cum laude. Congratulations Marco!
Abasy Atlas is back online
Due to a catastrophic failure of the hard disk of the server hosting Abasy Atlas on Saturday 29 at 6:09 am, our database is down. We are working hard to put it back online as soon as possible. Sorry for the inconvenience.
We have moved Abasy to a new server and it is back online!
Seminar at the International Laboratory on Human Genome Research, UNAM
Prof. Freyre shared his research advances in an excellent and highly enthusiastic seminar with colleagues and past students now members of the Laboratorio Internacional de Investigación sobre el Genoma Humano [International Laboratory on Human Genome Research] at Juriquilla, Querétaro. Big thanks to Dr. Rafael Palacios and Dr. Guillermo Dávila for the invitation and all your deferences! It was a very enriching experience!
Successful thesis defense by Juan Escorcia, congratulations!
Juan Escorcia defended his B.Sc. thesis titled "Effect of the incompleteness and the abstraction level of the models on the quality of bacterial regulatory networks and their system-level component predictions", carried out in our lab, to be awarded a B.Sc. in Biotechnology Engineering, Magna cum laude. Congratulations Juan!
Abasy Atlas has been indexed by OMICtools
OMICtools is a community-based and manually curated metadatabase. Its authors define OMICtools as "a manually curated metadatabase that provides an overview of more than 4400 web-accessible tools related to genomics, transcriptomics, proteomics, and metabolomics". Now, Abasy Atlas is indexed by this metadatabase at https://omictools.com/across-bacteria-systems-atlas-tool. More information can be found in OMICtools website and the corresponding paper.
BIRS-CMO Talk - Towards a large-scale comparative systems biology across bacteria
Talk delivered by Prof. Freyre as part of the BIRS-CMO Workshop 17w5143 - Principles of Gene Circuit Design at Casa Matemática Oaxaca. Thanks to Prof. Pablo Meyer from the IBM Thomas J. Watson Research Center for the invitation to this meeting!
Paper on the functional architecture and global properties of the Corynebacterium glutamicum regulatory network
Journal of Biotechnology publishes as part of special issue Dedicated to Prof. Dr. Alfred Pühler on the occasion of his 75th birthday our study on the functional architecture and global properties of the Corynebacterium glutamicum regulatory network carried out in collaboration with Andreas Tauch from Bielefeld University, Germany:
Freyre-González, J.A.* and Tauch, A. Functional architecture and global properties of the Corynebacterium glutamicum regulatory network: novel insights from a dataset with a high genomic coverage. Journal of Biotechnology 257C:199-210 (2017) doi:10.1016/j.jbiotec.2016.10.025 arXiv:1610.08552
Paper on Abasy Atlas v1.0, published!
Database (Oxford) has published the paper reporting the use and construction of Abasy Atlas v1.0:
Ibarra-Arellano, M.A., Campos-González, A.I., Treviño-Quintanilla, L.G., Tauch, A., Freyre-González, J.A.* Abasy Atlas: a comprehensive inventory of systems, global network properties and systems-level elements across bacteria. Database 2016:baw089 (2016) doi:10.1093/database/baw089
First public release of Abasy Atlas!
The first version of our comprehensive atlas of systems, global network properties, and system-level elements shaping regulatory networks across bacteria goes online today.
Abasy (Across-bacteria systems) Atlas contains systems and systems-level elements, and global properties for 50 reconstructed and meta-curated regulatory networks (78,649 regulatory interactions) covering 42 bacteria (64% Gram-positive and 36% Gram-negative) distributed in 9 taxa, containing 3,708 regulons and 1,776 systems (modules).