Pedro Julio Collado Vides

Pedro Julio Collado VidesPedro Julio Collado Vides

Bioinformatics and Genomics

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Bioinformatics and Genomics Programme
Senior Visiting Scientist
Pedro Julio Collado Vides

Bioinformatics and Genomics

Staff Scientist
Pedro Julio Collado Vides

1989               Ph.D. in biomedical research, National Autonomous University of Mexico (UNAM), Mexico
1989-1992      Posdoctoral fellow, Department of Biology, Laboratory of Dr. Boris Magasanik, Massachusetts Institute of Technology, Cambridge, USA
1992-1997      Assistant Professor, Center for Nitrogen Fixation, UNAM, Mexico
1997-2000      Associate Professor, Center for Nitrogen Fixation, UNAM, Mexico
1998-1999      Sabbatical leave, Laboratory of Prof. Fred Blattner, Department of Genetics, University of Wsiconsin, Madison, USA
2000-2020      Professor, Center for Nitrogen Fixation transformed in 2004 into Center for Genomic Sciences, UNAM, Mexico
2018 to date   Adjunct Professor, Department of Biomedical Engineering, Boston University, Massachusetts, USA
2020               Emeritus Professor, Center for Genomic Sciences, UNAM, Mexico
2021               Visiting Researcher, Center for Genomic Regulation (CRG), Barcelona, Spain

See also: https://www.ccg.unam.mx/pedro-julio-collado-vides/

News

2020   
Mejía-Almonte C., Busby S.J.W., Wade J.T., Arkin A.P., Eilbeck K., Stormo G.D., van Helden J., Palsson B.O., Galagan J.E. and Collado-Vides J. “Redefining fundamental concepts of transcription initiation in bacteria”  Nature Reviews Genetics  (2020). July 14, doi: 10.1038/s41576-020-0254-8. PMID: 32665585
An study published in the expert recommendation category in Nature Reviews Genetics where fundamental concepts are revised and updated.

2019
Ledezma-Tejeida D., Altamirano-Pacheco L., Fajardo V., Collado-Vides J. (2019) Limits to a classic paradigm: most transcription factors in E.coli regulate genes involved in multiple biological processes.  Nucleic Acids Res. 2019 Jun 13. pii: gkz525. doi: 10.1093/nar/gkz525
A paper showing that regulons are not regulating groups of genes that work in a single functional category contrary to the classic paradigm.

2018 
Julio Collado-Vides becomes Adjunct Professor in the Department of Bioengineering at Boston University

2015
Julio Collado-Vides is recognized as “ISCB Distinguised Fellow” Class 2015, of the International Society for Computational Biology (http://www.iscb.org/iscb-fellows). Currently, the only one from Latin America.

2011
Julio Collado-Vides receives the National Award in Sciences and the Arts, within the physico-mathematics and natural sciences. Dec, 19 2011. The highest recognition in Mexico.

Funding acknowledgements

Research in the lab has been supported by UNAM, by the Mexican Conacyt and by NIH-NIGMS grants through the years.

List of Publications


SELECTED PUBLICATIONS: 20

 

Collado-Vides J.
"The Search for a Grammatical Theory of Gene Regulation is Formally Justified by Showing the Inadequacy of Context-free Grammars.", 1991, Comput. Applic. Biosci. (CABIOS) 7:321-326
 
Collado-Vides J., Magasanik B. and Gralla J.D.
"Control site location and transcriptional regulation in Escherichia coli",1991, Microbiol. Reviews. 55:371-394
 
Collado-Vides J.
"Grammatical model of the regulation of gene expression", 1992, Proc.Natl.Acad.Sci.USA 89:9405-9409
 
Rosenblueth D.A., Thieffry D., Huerta A.M., Salgado H., and Collado-Vides J.
"Syntactic recognition of regulatory regions in Escherichia coli", 1996, CABIOS 12: 415-422.
 
Blattner F.R.; Plunkett III G.; Bloch C.A.; Perna N.T.; Burland V.; Riley M.; Collado-Vides J.; Glasner J.D.; Rode C.K.; Mayhew G.; Gregor J.; Davis N.W.; Kirkpatrick H.A.; Goeden M.A.; Rose D.J.; Mau B.; Shao Y.
“The complete genome sequence of Escherichia coli K-12”, 1997, Science 277: 1453-1462
 
Huerta A.M.; Salgado H.; Thieffry D., and Collado-Vides J.
“RegulonDB: A Database on Transcription Regulation in Escherichia coli”, 1998, Nucleic Acids Res. 26: 55-60
 
Thieffry D.; Salgado H.; Huerta A.M., and Collado-Vides J.
“Prediction of transcription regulatory sites in the complete genome of Escherichia coli”, 1998, Bioinformatics 14: 391-400
 
Thieffry D., Huerta A.M., Pérez-Rueda E. and Collado-Vides J.
“From specific gene regulation to genomic networks: a global analysis of transcriptional regulation in Escherichia coli.”, 1998, BioEssays 20: 433-440
 
van Helden J., André B., and Collado-Vides J.
“Extracting Regulatory Sites from the Upstream Region of Yeast Genes by Computational Analysis of Oligonucleotide Frequencies",1998, J.Mol.Biol. 281 (5): 827-842.
 
Pérez-Rueda E., and Collado-Vides J.
"The Repertoire of DNA-Binding Transcriptional Regulators in Escherichia coli", 2000, Nucleic Acids Research 28: 1838-1847
 
Salgado H., Moreno-Hagelsieb G., Smith T.F., and Collado-Vides J.
"Operons in Escherichia coli: Genomic Analyses and Predictions", 2000, Proc.Natl.Acad.Sci.USA 97:6652-6657
 
Martínez-Antonio A., and Collado-Vides J.
“Identifying Global Regulators in Transcriptional Regulatory Networks in Bacteria”, 2003, Current Opininon in Microbiol. 6:482-489
 
Huerta A.M. and Collado-Vides J.
“Sigma 70 Promoters in Escherichia coli: Specific Transcription in Dense Regions of Promoter-like Signals”, 2003, J.Mol.Biol.333:261-278
 
Gutiérrez-Ríos R.M., Rosenblueth D.A., Lozada J.A., Huerta A.M., Glasner J.D., Blattner F.R. and Collado-Vides J.
Regulatory Network of Escherichia coli:Congruence between Literature Knowledge and Microarray Profiles”, 2003, Genome Res.13: 2435-2443
 
Le Novere, N., Finney, A., hucka, M., Bhalla U.S., Campagne, F., Collado-Vides J., Crampin, E.J., Halstead, M., Klipp, E., mendes, P., Nielsen, P., Sauro, H., Shapiro, B., Snoep, J.L., Spence, H.D., and Wanner, B.C.
“Minimum information requested in the annotation of biochemical models (MIRIAM)”, 2005, Nature Biotechnology 23 (12): 1509-1515.
 
González V, Santamaría RI, Bustos P, Hernández-González I, Medrano-Soto A, Moreno-Hagelsieb G, Janga SC, Ramírez MA, Jiménez-Jacinto V, Collado-Vides J., Davila G.
“The partitioned Rhizobium etli genome: Genetic and metabolic redundancy in seven interacting replicons”, 2006, Proc Natl Acad Sci U S A. 103: 3834-3839
 
Karp P., Keseler I., Shearer A. ; Latendresse M.; Krummenacker M.; Paley S.M.; Paulsen I.; Collado-Vides J.; Gama-Castro S.; Peralta-Gil M.; Santos-Zavaleta A.; Penaloza-Spinola M.;Bonavides-Martinez C.;Ingraham J.
“Multidimensional annotation of the E.coli K-12 genome”, 2007, Nucleic Acids Res. doi:10.1093/nar/gkm740
 
Medina-Rivera A, Abreu-Goodger C, Thomas-Chollier M, Salgado H, Collado-Vides J., van Helden J.
“Theoretical and empirical quality assessment of transcription factor-binding motifs”, 2011, Nucleic Acids Res. Feb;39(3):808-24.PMID:20923783
 
Gama-Castro S., Rinaldi F., López-Fuentes A., Balderas-Martínez YI., Clematide S., Ellendorff TR., Santos-Zavaleta A., Marques-Madeira H. and Collado-Vides J.
“Assisted curation of regulatory interactions and growth conditions of OxyR in E. coli K-12”. Database (Oxford). 2014 Jun 4;2014. pii: bau049. Doi. 10. 1093/ database/ bau049. Volume:2014.
 
Ledezma-Tejeida D., Altamirano-Pacheco L., Fajardo V. and Collado-Vides J.
Limits to a classic paradigm: most transcription factors in E.coli regulate genes involved in multiple biological processes., Nucleic Acids Res., 2019 Jun 13. pii: gkz525. doi: 10.1093/nar/gkz525
 
Mejía-Almonte C., Busby S.J.W., Wade J.T., Arkin A.P., Eilbeck K., Stormo G.D., van Helden J., Palsson B.O., Galagan J.E. and Collado-Vides J.
“Redefining fundamental concepts of transcription initiation in bacteria”, Nature Reviews Genetics (2020). July 14, doi: 10.1038/s41576-020-0254-8. PMID: 32665585