Ibrahim Tanyalçin

It’s becoming increasingly challenging to efficiently visualize and extract useful insight from complex and big data sets. JavaScript stands out as a suitable programming choice that offers mature libraries, easy implementation, and extensive customization, all of which stay in the shadow of new and rapid developments in the language. To illustrate...

One of the main goals of proteomics is to understand how point mutations impact on the protein structure. Visualization and clustering of point mutations on user-defined 3 dimensional space can allow researchers to have new insights and hypothesis about the mutation’s mechanism of action. Availability and Implementation We have developed an intera...

Abstract Background Collagens are one of the major constituents of the pial membrane, which plays a crucial role in neuronal migration and cortical lamination during brain development. Type III procollagen, the chains of which are encoded by COL3A1, is the ligand of the G protein-coupled receptor 56 (GPR56), also known as adhesion G protein-coupled...

High-throughput sequencing methods are generating enormous amounts of genomic data, giving unprecedented insights into human genetic variation and its relation to disease. An individual human genome contains millions of Single Nucleotide Variants: to discriminate the deleterious from the benign ones, a variety of methods have been developed that pr...

Background Collagens are one of the major constituents of the pial membrane, which plays a crucial role in neuronal migration and cortical lamination during brain development. Type III procollagen, the chains of which are encoded by COL3A1, is the ligand of the G protein-coupled receptor 56 (GPR56), also known as adhesion G protein-coupled receptor...

Background Predict whether a mutation is deleterious based on the custom 3D model of a protein. ResultsWe have developed modict, a mutation prediction tool which is based on per residue rmsd (root mean square deviation) values of superimposed 3D protein models. Our mathematical algorithm was tested for 42 described mutations in multiple genes inclu...

Today’s genome browsers and protein databanks supply vast amounts of information about proteins. The challenge is to concisely bring together this information in an interactive and easy to generate format. Availability and implementation: We have developed an interactive CIRCOS module called i-PV to visualize user supplied protein sequence, conser...

Background / Purpose: Derivation of a formula that utilizes the information from user-generated wild type and mutated protein model (.pdb) files and generating a probability score (the mutation being deleterious) based on functional impact. Main conclusion: Information in user-generated pdb files can be processed to yield a score proportional...

Background: The BIG2 protein, coded by ARFGEF2 indirectly assists neuronal proliferation and migration during cortical development. Mutations in ARFGEF2 have been reported as a rare cause of periventricular heterotopia. Methods: The presence of periventricular heterotopia, acquired microcephaly and suspected recessive inheritance led to mutation...

BACKGROUND: Dominant mutations in TUBB2B have been reported in patients with polymicrogyria. We further explore the phenotype associated with mutations in TUBB2B. METHODS: Twenty patients with polymicrogyria (5 unilateral) were tested for mutations in TUBB2B by Sanger sequencing. RESULTS: We identified two novel de novo mutations, c.743C>T (p.Ala24...

The FOXG1 syndrome is emerging as a relative new entity in paediatric neurology. We report a boy with acquired microcephaly, mental retardation and a thin genu of the corpus callosum. The combination of these findings led to mutation analysis of FOXG1. The patient was found to be heterozygous for a novel mutation in FOXG1, c.506dup (p.Lys170GInfsX2...

Congress poster presented at ICIEM 2013 with poster number P-798