Ph D, Universitat Autònoma de Barcelona (2002)
BS, Universitat Autònoma de Barcelona (1996)
Life is information. Information is processed both during an organism life-time and across generations by natural selection. In fact, life is probably the most complex information processing system ever created. As Robert Robbins fittingly put it, the DNA sequence of an organism is “the result of literally millions of maintenance revisions performed by the worst possible set of kludge–using, spaghetti–coding, opportunistic hackers (i.e. evolution) who delight in clever tricks like writing self–modifying code and relying upon undocumented system quirks”. As a result, deciphering molecular biology is the ultimate dream of a computer scientist.
My research interests lie primarily in the evolution of transcriptional regulatory networks in Bacteria, specifically on the co-evolution of transcription factors, their cognate binding sites and the regulatory networks they spawn to fulfill complex regulatory programs involved in key pathogenic processes, such as the transfer of antiobiotic resistance determinants or the creation of biofilms. My lab uses evolutionary simulations, biophysical and dynamic models, systems biology and comparative genomics approaches to probe into the evolution of transcriptional regulatory networks. My lab also works on the creation of community-oriented services for the annotation of scientific data, such as the CollecTF database (www.collectf.org) dedicated to compiling data on transcription factor-binding sites across the Bacteria domain. This work involves the design and development of biological databases, working in close collaboration with ontology development groups and core development teams at large biomedical data repositories, such as the NCBI and the EMBL-EBI.
Bioinformatics, computational biology, evolutionary biology, microbiology, biocuration, societal impacts of computers and biology
|Summer 2018||BIOL 316 – Phage Genome Analysis|
|Spring 2018||BIOL 313 – Bioinformatics Intro|
|BIOL 316 – Phage Genome Analysis|
(2019) A Novel Genus of Actinobacterial Tectiviridae Basel Viruses
(2019) Origin of the Mobile Di-Hydro-Pteroate Synthase Gene Determining Sulfonamide Resistance in Clinical Isolates. Frontiers in microbiology
(2019) ECO, the Evidence & Conclusion Ontology: community standard for evidence information. Nucleic acids research
(2018) Complete Genome Sequences of Six BI Cluster Streptomyces Bacteriophages, HotFries, Moozy, Rainydai, RavenPuff, Scap1, and SenditCS Washington, DC Microbiology Resource Announcements Download.
(2018) Complete Genome Sequences of HonestAbe, Anthony, and Taffo16, Three Cluster C Bacillus cereus Group Bacteriophages Washington, DC Genome Announcements Download.
(2018) Biocuration: Distilling data into knowledge. PLoS biology
(2018) Complete Genome Sequence of Streptomyces Bacteriophage Abt2graduatex2 Washington, DC Genome Announcements Download.
(2018) Gamifying critical reading through a genome annotation intercollegiate competition Tested Studies for Laboratory Teaching
(2017) An inclusive Research Education Community (iREC): Impact of the SEA-PHAGES program on research outcomes and student learning Washington, DC Proceedings of the National Academy of Sciences Download.
(2017) Comparative genomics of the DNA damage-inducible network in the Patescibacteria. Environmental microbiology
(2017) Bacillus cereus Group Bacteriophage Flapjack Genome Sequence Washington, DC Genome Announcements Download.
(2017) Complete Genome Sequences of Three phi29-Like Bacillus cereus Group Podoviridae Washington, DC Genome Announcements Download.
(2017) Comparative Analysis of Ralstonia solanacearum Methylomes. Frontiers in plant science
(2016) Parametric bootstrapping for biological sequence motifs. BMC bioinformatics
(2016) Complete Genome Sequence of the Streptomyces Phage Nanodon. Washington, DC Genome announcements Download.
(2016) Genome Sequence of Bacillus cereus Group Phage SalinJah Washington, DC Genome Announcements Download.
(2016) Assessment of transfer methods for comparative genomics of regulatory networks in Bacteria BMC Bioinformatics
(2016) The Verrucomicrobia LexA-Binding Motif: Insights into the Evolutionary Dynamics of the SOS Response. Frontiers in molecular biosciences
(2016) A Bayesian inference method for the analysis of transcriptional regulatory networks in metagenomic data. Algorithms for molecular biology : AMB
(2015) Genome Sequences of Two Bacillus cereus Group Bacteriophages, Eyuki and AvesoBmore Washington, DC Genome Announcements Download.
(2015) Complete Genome Sequence of Bacillus cereus Group Phage TsarBomba Washington, DC Genome Announcements Download.
(2015) An SOS Regulon under Control of a Noncanonical LexA-Binding Motif in the Betaproteobacteria. Journal of bacteriology
(2015) Every Site Counts: Submitting Transcription Factor-Binding Site Information through the CollecTF Portal. Journal of bacteriology
(2015) Identification and Characterization of VpsR and VpsT Binding Sites in Vibrio cholerae. Journal of bacteriology
(2014) Informational requirements for transcriptional regulation Journal of Computational Biology
(2014) Characterization of the SOS meta-regulon in the human gut microbiome. Bioinformatics (Oxford, England)
(2014) CollecTF: a database of experimentally validated transcription factor-binding sites in Bacteria. Nucleic acids research
(2012) Inference of self-regulated transcriptional networks by comparative genomics Evolutionary Bioinformatics
(2012) Information theory and biological sequences: insights from an evolutionary perspective Information Theory: New Research Hauppauge, NY Nova Science Publishers Download.
(2012) BioWord: a sequence manipulation suite for Microsoft Word BMC Bioinformatics
(2010) xFITOM: a generic GUI tool to search for transcription factor binding sites Bioinformation
(2009) The SOS Response Controls Integron Recombination Science
(2009) A reexamination of information theory-based methods for DNA-binding site identification BMC Bioinformatics
(2007) Aeons of distress: an evolutionary perspective on the bacterial SOS response. FEMS microbiology reviews
(2007) Cohabitation of two different lexA regulons in Pseudomonas putida J Bacteriol
(2006) A SiC microdevice for the minimally invasive monitoring of ischemia in living tissues Biomed Microdevices
(2006) Dispersal and regulation of an adaptive mutagenesis cassette in the bacteria domain Nucleic Acids Res
(2004) Development of a CMOS-compatible PCR chip: comparison of design and system strategies Journal of Micromechanics and Microengineering
(2004) Reconstruction of the evolutionary history of the LexA-binding sequence Microbiology
(2003) Biochemical analysis and optimization of inhibition and adsorption phenomena in glass-silicon PCR-chips Sensors and Actuators B-Chemical
(2000) Silicon microsystem passivation for high-voltage applications in DNA chips Microelectronics Reliability
Research in Progress
Intracellular Signaling in Alteromonas Scholarly (On-Going) Nov 1, 2017
Molecular Genetics of Bacteria and Phages Meeting Oral Presentation Origin of the mobile di-hydro-pteroate synthase genes conferring sulfonamide resistance University of Wisconsin Madison, WI (Aug 7, 2018)
Tenth Annual NGRI SEA-Phages Symposium Poster GOing forward: developing critical reading skills through an inter-campus GO annotation competition Howard Hughes Medical Institute Janelia Farms, Ashburn, VA (Jun 9, 2018)
6th International Bacterial Wilt Symposium Oral Presentation Comparative analysis of Ralstonia solanacearum methylomes Toulouse, France (Jul 4, 2016)
BioCuration 2016 Oral Presentation From data repositories to submission portals: rethinking the role of domain-specific databases in CollecTF International Society for BioCuration Geneva, Switzerland (Apr 11, 2016)
Applied Bioinformatics in the Life Sciences 2016 Poster Comparative analysis of stress response systems in the human gut microbiome Vlaams Instituut voor Biotechnologie Leuven, Belgium (Mar 17, 2016)
Seventh Annual NGRI SEA-Phages Symposium Poster Giving it a GO - enhancing bacteriophage genome annotation and student learning with the Gene Ontology Seventh Annual SEA-Phages Symposium Howard Hughes Medical Institute Janelia Farms, Ashburn, VA (Jun 14, 2015)
Seventh Annual NGRI SEA-Phages Symposium Poster Host range of Bacillus phages. Seventh Annual SEA-Phages Symposium Howard Hughes Medical Institute Janelia Farms, Ashburn, VA (Jun 14, 2015)
Molecular Genetics of Bacteria and Phages Meeting Poster A SOS regulon under control of a non-canonical LexA-binding motif in the Betaproteobacteria Madison, WI (Aug 5, 2014)
South Eastern Population Ecology & Evolutionary Genetics (SEPEEG) meeting Oral Presentation Computational Model of the Environmental Selection of the Feed Forward Loop Network Motif American Society of Naturalists (ASN) Mountain Lake Biological Station, Pembroke, VA (USA) (Sep 28, 2013)
Seventh q-bio Conference Oral Presentation Exact Chemical Potentials for Prokaryotic Transcription Factors National Institute of General Medical Sciences of the National Institutes of Health St. John's College, Santa Fe, NM (USA) (Aug 8, 2013)
Great Lakes Bioinformatics Conference Poster A graph-based optimization system for comparative genomics of bacterial regulatory networks International Society for Computational Biology Pittsburgh, PA (USA) (May 15, 2013)