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Radhouane's Profile


Radhouane Aniba
Job Title: Bioinformatician at BC Cancer Agency

Bio :
- Bioinformatics Expert Systems Developments
- Knowledge-based system
- Data integration
- Sequence analaysis
- Data mining and Text Mining 
- Machine learning
- Genome Wide Association studies (GWAS)
- Comparative Genomics & Genome Annotation
- Epigenomics
- Next generation sequencing (NGS) data analysis, ChIP-seq, RNA-seq ...
- Personalized medicine
- Genetic diseases

Experience :
Postdoctoral Fellow – NIH/NLM/NCBI
February 2013 –Present
Epigenomic characterization of liver enhancer variations: Development of machine learning techniques for SNP prioritization and enhancers detection.

Postdoctoral Research Associate – University of Maryland, USA
November 2010 – February 2013
Bioinformatics Project Manager: Planning and Execution of collaborative projects between CBCB, University of Maryland School of Medicine and Research Scientists from Cell Biology and Molecular Genetics at University of Maryland

Bioinformatics PhD, IGBMC, CNRS, France
2007-2010
Sequence Alignment Expert System (AlexSys) development, for the construction, refinement, analysis and exploitation of multiple sequence alignments, combining diverse, complementary algorithms and incorporating additional information (structural, functional and evolutionary).

Bioinformatics Programmer, IGBMC, CNRS, France
2005-2007
New algorithm implementation to improve the quality and the performance of protein sequence alignment.

Bioinformatics User-Support, Expertise Bioinformatique, Tunisia
2004-2005
In-house developer at the Institut Pasteur de Tunis, within the Immunology, vaccinology and molecular biology Laboratory.

Bioinformatics Database Developer, Bioinformatics Unit, Sfax Biotechnology Center, Tunisia
2004
Single Exonic gene Database development.

Bioinformatics Engineer, Bioinformatics Unit, Sfax Biotechnology Center, Tunisia
2003-2004
Metabolic pathways comparison in Yeast: Saccharomyces cerevisiae and Schyzosaccharomyces pombe genomes.


Publications :
1: Rabhi I, Rabhi S, Ben-Othman R, Aniba MR, Trentin B, Piquemal D, Regnault B,
Guizani-Tabbane L. Comparative analysis of resistant and susceptible macrophage
gene expression response to Leishmania major parasite. BMC Genomics. 2013 Oct
22;14(1):723. [Epub ahead of print] PubMed PMID: 24148319.

2: Malin J, Aniba MR, Hannenhalli S. Enhancer networks revealed by correlated
DNAse hypersensitivity states of enhancers. Nucleic Acids Res. 2013 May 21. [Epub
ahead of print] PubMed PMID: 23700312.

3: Sahu AD, Aniba R, Chang YP, Hannenhalli S. Epigenomic model of cardiac
enhancers with application to genome wide association studies. Pac Symp
Biocomput. 2013:92-102. PubMed PMID: 23424115; PubMed Central PMCID: PMC3581590.

4: Aniba MR, Poch O, Thompson JD. Issues in bioinformatics benchmarking: the case
study of multiple sequence alignment. Nucleic Acids Res. 2010 Nov;38(21):7353-63.
doi: 10.1093/nar/gkq625. Epub 2010 Jul 17. Review. PubMed PMID: 20639539; PubMed 
Central PMCID: PMC2995051.

5: Aniba MR, Poch O, Marchler-Bauer A, Thompson JD. AlexSys: a knowledge-based
expert system for multiple sequence alignment construction and analysis. Nucleic 
Acids Res. 2010 Oct;38(19):6338-49. doi: 10.1093/nar/gkq526. Epub 2010 Jun 8.
PubMed PMID: 20530533; PubMed Central PMCID: PMC2965243.

6: Ellouze O, Fattouch S, Mestiri F, Aniba MR, Marzouki MN. Optimization of
extracellular xylanase production by Sclerotinia sclerotiorum S2 using factorial 
design. Indian J Biochem Biophys. 2008 Dec;45(6):404-9. PubMed PMID: 19239127.

7: Aniba MR, Siguenza S, Friedrich A, Plewniak F, Poch O, Marchler-Bauer A,
Thompson JD. Knowledge-based expert systems and a proof-of-concept case study for
multiple sequence alignment construction and analysis. Brief Bioinform. 2009
Jan;10(1):11-23. doi: 10.1093/bib/bbn045. Epub 2008 Oct 29. PubMed PMID:
18971242; PubMed Central PMCID: PMC2638625.

8: Aifa S, Miled N, Frikha F, Aniba MR, Svensson SP, Rebai A. Electrostatic
interactions of peptides flanking the tyrosine kinase domain in the epidermal
growth factor receptor provides a model for intracellular dimerization and
autophosphorylation. Proteins. 2006 Mar 1;62(4):1036-43. PubMed PMID: 16380971.

Skills

C#1 Perl5 Python41 R10 Ruby1 Shell7 Text1

Trending

Analysis package with multiple programs1 Analysis Tools7 Gene set enrichment2 Generalities24 Information retrieval6 Machine Learning1 Maths and Algorithm implementation1 Next Generation Sequencing11 RNA-seq2 Similarity and Homology3 Statistics2 ToolKits/Programming3 Visualization tools3
Codes I Posted
66
Solutions I posted
44
Points I earned
1092
Coders I helped
16

Activity Details

LanguageCode Name
Python Detailed traceback information (text format)
Python Checking if modules exist before importing them in Python
R Running gganimate on a rocker image
Limited Access Code
Unlocked Upon Validation
R Rendering R plots from ggplot2 and extracting the base64 image from a Docker container
Python ggplot style in matplotlib
Python Testing Sckit-Learn in a container
Python Dictionary with duplicate keys in python
Python File size conversion into human readable format
R Error reading a table
Limited Access Code
Unlocked Upon Validation
Python Serving proxy logging to ruffus tasks
Python Using python super() effectively
Limited Access Code
Unlocked Upon Validation
Shell Display git log tree in terminal
Python Disk Usage alert utiliy in python
Python What Are The Twitter Haps ?
Python 'du -h' command in python
Python Running jobs in parallel in ruffus
Python Progress bar in python made easy
Python Printing nice tables in python
Shell Nearest Flanking genes
Python Handy dataframe
Python Obfuscating "Hello world!"
Limited Access Code
Unlocked Upon Validation
Python Runnable learnxinyminutes where x=python
Python When exit code is not enough
Ruby Ruby Tutorial
Limited Access Code
Unlocked Upon Validation
Python Decorator to check if a module is imported before running a bloc
Python Plot genome coverage
Limited Access Code
Unlocked Upon Validation
Python Testing schematics module
Python Get coverage from a Bam file at regions from a file
Python Ruffus jumping some tasks
Limited Access Code
Unlocked Upon Validation
Python Extract average sequence length from a fastq file
Python How to shortcut a Ruffus pipeline
Python Extract mapped and unmapped reads from a bamfile
R Fastest way to intersect dataframes in R ?
Python Easily spot information from a large output in python
Python Testing Ruffus pipelines
Python Timing a code in python
R Extract ggplot2 color information in a vector
Text Most used file formats in Bioinformatics
Shell Using bedtools to get difference in features between overlapping positions
Python Another Smith Waterman implementation
R Order a dataframe according to a target vector
Python How to create a Bioinformatics pipeline using Spotify !
R RangedData object : changing chromosome names
Shell Extract columns from a list of files
Python Cut adaptors, trim sequence from fastq files
Shell Extract the last 25 bp from each read in fastq and output fasta
Python Running bedtools from python
Python Alignment in Python
R FastQ quality report using ShortRead package
R Gene list KEGG enrichment using GOstats
Python Calculating gene expression for RNA-Seq data
Shell [one-line : part III] Useful one-line sed commands
Perl [one-line : part II] Useful one-line perl commands
Shell [one-line : part I] Useful one-line awk commands
Python RNA-seq python pipeline
Perl Extract bigWig data for a bed file in Bulk
Python Command Line access to UCSC [Exercice]
Limited Access Code
Unlocked Upon Validation
Python Parse Bowtie output
Python Extract sequence by ID
Python Parse phylogenetic tree in python using ETE package
C# Multifasta Parser in C#
Python Convert HTML report tables to excel spreadsheet using BeautifulSoup (Python)
R Analyzing Human Genome sequences with R
Perl Parsing Genbank report using regexp.
Perl Computing Pearson Correlation
Perl Parse Blast Output in Perl
LanguageCode Name
Python Heat map from DataFrame pandas
Python Testing python import : hello_world
Python Testing Sckit-Learn in a container
Python calculate primer temperature
Python Python Project
Python Shuffling multiple NumPy arrays in unison
Python What Are The Twitter Haps ?
Python 'du -h' command in python
Python Plotting Decision Regions of Machine Learning Classifiers
Python wish list
Python Comparing values
Python String usage in python
Python Unable to read from file
Python Generalizing First and Last Names
Python python poetry
Python When exit code is not enough
Python Decorator to check if a module is imported before running a bloc
Python Visualize Flagstat Files
Python Get coverage from a Bam file at regions from a file
Python Ruffus jumping some tasks
Python Read count within a genomic window
Perl How to filter a large blast result
Python A simple Python decorator for timing functions
Python Timing a code in python
R Extract ggplot2 color information in a vector
Text Most used file formats in Bioinformatics
Shell Using bedtools to get difference in features between overlapping positions
Python Testing some python features
R RangedData object : changing chromosome names
Python Cut adaptors, trim sequence from fastq files
Python Retrieve Fasta from Genbank by ID
Python Alignment in Python
Python Calculating gene expression for RNA-Seq data
R Extract SNP flanking region
Shell [one-line : part I] Useful one-line awk commands
Shell Using sed to remove newline from file
Python Convert HTML report tables to excel spreadsheet using BeautifulSoup (Python)