Genomic Analysis

Genomic data may include inputs such as DNA sequences, (e.g. Hiseq output files), regulatory data or structural information. Typical genomic analysis may include sequence alignments, phylogenetic tree constructions or special mutation traits. RNA-Seq analysis including Single-Cell (SC) experiments. Alignment to the Genome or directly to the Transcriptome. Clustering tests including dendrograms, correlation matrics , PCA and tSNE. Differential gene (DE) exploration, followed by molecular pathway examination. Database searches may be part of the services including re-analysis of published data and investigating patient data based (GDC/TCGA, ICGC).

Database Searches

Next Generation Sequencing (NGS) technologies result in rapidly growing volumes of biological data. Biological and Medical progress depends on exploiting this rich and diverse data in comprehensive databases such as NCBI and in theme-based data sources such as TCGA. Bioinformatics services offers searches, data mining and data processing across various databases. The goal is to assist the users in achieving an integrated view of their project.

• Remote programming access, format conversions and data restructuring.
• On-line tools (e.g. BLAST and CLUSTAL) combined with and off-line computational data processing.
• Review and analysis of project-related abstracts and of full-text biomedical published literature.

Software Tools

Our main tools are Python and R programming languages, together with their extensive biological software libraries (Biopython, Bioconductor). Remote web-based utilities are deployed (eg. NCBI BLAST tools) per need.

Background

The field of genomic analysis is growing rapidly. Sequencing technologies are improving and costs are decreasing. Huge quantities of sequenced data are nurturing the need for bioinformatics-based analysis in diverse application fields:

• Research Centers
• Medical treatment, analysis, Molecular medicine and drug design
• Agriculture, plant genomics and engineering
• Environmental studies, microbial genomics, metagenomics
• Outsourcing from overloaded bioinformatics centers

About

Bioinformatics-services is led by Jonathan Monin, M.Sc. Physics, B.Sc. Mathematics, MBA and experience in multi-disciplinary technological and scientific projects. Bioinformatics expertise drawn from courses: Methods (I and II), Introduction to Genomic Technologies, Algorithms I (Finding Hidden Messages in DNA), Algorithms II (Genome Sequencing), Algorithms III (Comparing Genes, Proteins and Genomes), Algorithms IV (Molecular Evolution).