Gregorio Alanis-Lobato
Scientist, Programmer, Readaholic, Traveller, Gamer

Hola!

I'm a Mexican scientist who is currently working as a postdoctoral fellow at the Computational Biology and Data Mining Research Group of the Johannes Gutenberg Universität in Mainz, Germany.

Here you will find details about me, my work, my research and personal interests.

Education
2011-2014
PhD in Computational Biology
King Abdullah University of Science and Technology, KSA

GPA: 4.00/4.00

Dissertation title: Exploitation of complex network topology for link prediction in biological interactomes

Advisor: Prof. Timothy Ravasi

2009-2010
MSc in Computer Science
King Abdullah University of Science and Technology, KSA

GPA: 3.37/4.00

Research focus: Computational Biosciences

2005-2009
Computer Systems Engineering
Instituto Politécnico Nacional, Mexico City

GPA: 9.55/10.00

Dissertation title: Application of self-organising maps to the protein folding problem

Advisor: Prof. Jorge Rosas-Trigueros

Professional experience
Since Feb '15
Postdoctoral fellow
Computational Biology and Data Mining Lab, Johannes Gutenberg Universität
Mainz, Germany

Integration of protein interaction data, analysis of the latent geometry of the human protein interaction network, bias reduction in protein network datasets, development of bioinformatic web tools and teaching of the Network Biology section for the course Proteinbiochemie und Bioinformatik.

Jul '14-Dec '14
Research consultant
Environmental Epigenetics Program, King Abdullah University of Science and Technology
Thuwal, KSA

Systems-based analysis of RNASeq and hCAGE time series data from human skeletal muscle cell differentiation.

Summer '13
Intern
Center for Complex Network Research, Northeastern Univesity
Boston, USA

Explored different data integration approaches for the construction of a reliable human genetic interaction network.

Summer '10
Intern
Department of Chemistry, Wayne State University
Detroit, USA

Studied the role of low-complexity regions in the correct folding of P. falciparum’s proteins by means of molecular dynamics tools such as VMD. These analyses are important for drug design against malaria.

Jul '08-Jul '09
Intern
Service Management Automation, IBM
Mexico City, Mexico

- Administered the Server Resource Manager tool in the servers of >5 IBM clients, which allowed IBM to comply with the service level agreement contracted by these clients.

- Administered the Virtual Server Administration tool in the servers of a couple of IBM clients, which allowed for remote server administration of IBM software in client machines.

Sep '05-Jul '08
Software developer
Information Systems Department, National Paediatric Hospital
Mexico City, Mexico

- Developed the Patient Classification System and trained medical staff in its use. This improved the attention of the >30,000 patients that visit the hospital annually.

- Provided training to >20 administrative employees in Office tools, making them more updated and competent staff.

- Started the development of the current Surgery Scheduling System that serves the >9,000 patients that undergo surgery in the hospital annually.

Skills
Technical
  • Programming and scripting (R, C/C++, Java, Maxima, shell)
  • Web development
  • Data wrangling, analysis and interpretation
  • Text editing (Word, LaTeX, vi)
  • Databases (SQL, NoSQL)
Personal
  • Communication
  • Team work and leadership
  • Creativity
  • Teaching
  • Languages (Spanish: native, English: fluent, German: A2)
Portfolio
HIPPIE v2.0
LaBNE+HM
Network medicine
ncMCE
HIPPIE
Web tools
HIPPIE v2.1

The Human Integrated Protein-Protein Interaction rEference v2.1, a web tool to...

GAPI
Web tools
GAPI

Geometric analysis of the protein interactome

NetHypGeom
Code
NetHypGeom

Tools for the generation, analysis and visualisation of complex networks...

FunEnrich
Code
FunEnrich

Gene Ontology and REACTOME Pathway enrichment analyses for genes...

DisparityFilter
Code
DisparityFilter

Tools for the analysis, visualisation and filtering of complex undirected...

LinkPrediction
Code
LinkPrediction

Implementation of different classes of link predictors...

Interests
Network science

Network growth models; complex network geometry; network structure, formation and evolution; multilayer networks.

Genomics and systems biology

Network medicine; complex diseases; bias in biology; functional and disease ontologies; genetic and epigenetic regulation of gene expression.

Machine learning

Data mining; non-linear dimensionality reduction; manifold learning; parameter-free classification and clustering.

Data analytics and reproducibility

R; R Markdown; tidyverse; LaTeX; Overleaf; git; GitHub; caret; igraph; statistics; MapReduce.

Reading

I'm readaholic... Every night, before going to bed, I read some chapters of the book in turn. Every morning, before starting the work of the day, I read the news and check my Twitter feed.

Sports

I love sports! Especially the field events in Track & Field, like Discus Throw and Shot Put. In fact, I was part of an athletics club and represented my state as a Discus Thrower in the National Olympic Games in Mexico, where I won the silver medal.

Travelling

Travelling to other countries and having the opportunity to experience and learn from other cultures is one of the most enriching things there are. I've been to 38 different countries, and I'm eager to visit the next one.

Video games

I don't have much time to play video games anymore, but I always try to invest those weekend, spare hours in a good and challenging video game.

Whisky- and gin-based cocktails

Whisky sour, Old-fashioned, Manhattan, John Collins, Mint Julep, Pickleback, Lynchburg Lemonade; Martini, Gin and Tonic, Gimlet, Negroni, New Orleans Fizz, Singapore Sling, Floradora...

Coordinates
  • Address: Institute of Molecular Biology, Ackermannweg 4, 55128 Mainz, Germany
  • Phone: +49-6131-39-21584
  • E-mail: galanisl@uni-mainz.de