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Ivan Erill Sagales

Associate Professor

Biological Sciences
Computer Science and Electrical Engineering
Biological Sciences Bldg, Room BS-117
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.

Research Interests

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 ( 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.

Teaching Interests

Bioinformatics, computational biology, evolutionary biology, microbiology, biocuration, societal impacts of computers and biology

Selected Classes
Spring 2015 BIOL 313 – Bioinformatics Intro
BIOL 316L – Phage Genome Analysis
BIOL 495 – Seminar Bioinformatics
Fall 2014 BIOL 737 – Bioinformatics Res. Sem
Spring 2014 BIOL 313 – Bioinformatics Intro
BIOL 316L – Phage Genome Analysis
BIOL 495 – Seminar Bioinformatics
Intellectual Contributions

Complete Genome Sequence of the Streptomyces Phage Nanodon. 5 vol. 4 Genome announcements

5 vol. 4 e00953–16 Genome Announcements

February 2016 vol. 489 243-251 Virology

5 vol. 3 e01178–15 Washington, DC Genome Announcements .

5 vol. 3 e01199–15 Washington, DC Genome Announcements .

Diagnostic yield of targeted next generation sequencing in various cancer types: an information-theoretic approach. 9 vol. 208 441-7 Cancer genetics

Every Site Counts: Submitting Transcription Factor-Binding Site Information through the CollecTF Portal. 15 vol. 197 2454-7 Journal of bacteriology

An SOS Regulon under Control of a Noncanonical LexA-Binding Motif in the Betaproteobacteria. 16 vol. 197 2622-30 Journal of bacteriology

7 vol. 197 1221-35 Journal of bacteriology

5 vol. 21 373-384 Journal of Computational Biology

3 vol. 196 660-71 Journal of bacteriology

Bioinformatics (Oxford, England)

Database issue vol. 42 D156-60 Nucleic acids research

scnRCA: a novel method to detect consistent patterns of translational selection in mutationally-biased genomes. 10 vol. 8 e76177 PloS one

vol. 8 449-461 Evolutionary Bioinformatics

Information Theory: New Research 1-28 Hauppauge, NY Nova Science Publishers .

vol. 13 124 BMC Bioinformatics

58 vol. 13 BMC Genomics

1 vol. 2 6 Mobile DNA

2 vol. 5 49-51 Bioinformation

3 vol. 17 185-196 DNA Research

5930 vol. 324 1034 Science

57 vol. 10 BMC Bioinformatics

5 vol. 88 716–22 Transplantation

6 vol. 31 637-56 FEMS microbiology reviews

24 vol. 189 8855–62 J Bacteriol

3 vol. 81 483–6 Transplantation

Pt 4 vol. 152 1109–18 Microbiology

1 vol. 34 66–77 Nucleic Acids Res

1 vol. 8 43–9 Biomed Microdevices

15 vol. 187 5367–75 J Bacteriol

1 vol. 54 212–22 Mol Microbiol

Pt 11 vol. 150 3783–95 Microbiology

22 vol. 32 6617–26 Nucleic Acids Res

11 vol. 14 1558–1568 Journal of Micromechanics and Microengineering

17 vol. 19 2225–36 Bioinformatics

3 vol. 96 685–692 Sensors and Actuators B-Chemical

21 vol. 184 6073–80 J Bacteriol

4-5 vol. 40 787–789 Microelectronics Reliability

Assessment of transfer methods for comparative genomics of regulatory networks in Bacteria BMC Bioinformatics

From data repositories to submission portals: rethinking the role of domain-specific databases in CollecTF Database (Oxford)


(Author & Presenter) (Author & Presenter) 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

(Author & Presenter) (Author) (Author) (Author) (Author) 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

(Author) (Author) (Author) (Author) (Author & Presenter) 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

(Author & Presenter) (Author) (Author) (Author) 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)

(Author & Presenter) (Author) 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)

(Author & Presenter) (Author) 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)