Nikolas Pontikos

Killer Immunoglobulin-like Receptors (KIR) play an important role in the innate immune system. Present on the surface of Natural Killer cells, KIRs mediate the fate of target cells based on the composite inhibiting/activating signal generated by binding to their HLA Class I ligands. Type 1 Diabetes (T1D) is an autoimmune disease known to be strongly associated with the HLA region, primarily with HLA Class II genes, but also with HLA Class I loci, such as HLA-Bw4/Bw6 epitope (P=6.57E-6… Show more

Killer Immunoglobulin-like Receptors (KIR) play an important role in the innate immune system. Present on the surface of Natural Killer cells, KIRs mediate the fate of target cells based on the composite inhibiting/activating signal generated by binding to their HLA Class I ligands. Type 1 Diabetes (T1D) is an autoimmune disease known to be strongly associated with the HLA region, primarily with HLA Class II genes, but also with HLA Class I loci, such as HLA-Bw4/Bw6 epitope (P=6.57E-6 conditional on HLA Class II). Of the 17 known KIR genes, KIR3DL1 is the only one known to interact biologically with HLA-Bw4, which makes it a suitable candidate gene for T1D. Furthermore, its activating counterpart, KIR3DS1, may also putatively interact with HLA-Bw4. We conducted a case-control study (816 cases: 813 controls) to assess whether there is evidence that copy number variation in KIR3DL1/3DS1 is associated with T1D. Show less

My PhD research is primarily on the development of data analysis techniques in high-throughput flow cytometry for characterising the immune profile associated with type 1 diabetes, and more generally on unsupervised and supervised clustering methods.

A software package I wrote as part of my PhD to automate the analysis of bead data used for the purpose of normalisation in flow cytometry.

I started off my PhD by reanalysing, using computational methods (k-means, mixtures of univariate distributions), previous published data to test the correlation between CD25 expression on naive and memory T cells with regulating SNPs in the IL2RA gene. I found that automatic methods were able to outdo manual methods by improving the reproducibility of the results and the strength of the correlation but did poorly when the data did not fit the prior assumptions (e.g. number of clusters larger… Show more

I started off my PhD by reanalysing, using computational methods (k-means, mixtures of univariate distributions), previous published data to test the correlation between CD25 expression on naive and memory T cells with regulating SNPs in the IL2RA gene. I found that automatic methods were able to outdo manual methods by improving the reproducibility of the results and the strength of the correlation but did poorly when the data did not fit the prior assumptions (e.g. number of clusters larger than expected). But this seeming weakness of the automatic method is in fact one of its strength as it makes for an excellent outlier detection tool, capabale of spotting cases were the data does not fit the expected model. I summarised and presented some of my findings as a poster (18-06-2012) at the Cyto 2012 Conference in Leipzig. Show less

Processing 3D nuclei images obtained from a Confocal Laser Scanning Microscopy (CLSM). In particular fine-tuning the Stable Count Thresholding algorithm for identifying fluorescently stained promyelotic (PML) nuclear bodies in cells which have undergone heat-shock treatment.
- Technologies: R, various Bioconductor packages, C and Python

Data analysis project involving DNA Copy Number Variations (CNV) profiling in genome-wide data obtained from BAC32K and Illumina HumanCNV370 BeadChip array-comparative genomic hybridisation experiments performed on 26 breast cancer cell lines. Different CNV calling methods such as a heuristic threshold and a hidden Markov model approach were compared.
- Technologies: Python, R and various R packages in Bioconductor

Group project in a team of four during which we created a database with a front-end website for kinases, phosphatases, the corresponding substrates as well as the reactions and pathways in which they are involved. We also gathered evolutionary information about kinase and phosphatase protein families. We successfully integrated and unified many data sources such as Uniprot, PhosphoELM, NetworKIN, Phosida, PhosphoPOINT, Reactome, Panther, KEGG, dbPTM and Treefam.
- Technologies: Python… Show more

Group project in a team of four during which we created a database with a front-end website for kinases, phosphatases, the corresponding substrates as well as the reactions and pathways in which they are involved. We also gathered evolutionary information about kinase and phosphatase protein families. We successfully integrated and unified many data sources such as Uniprot, PhosphoELM, NetworKIN, Phosida, PhosphoPOINT, Reactome, Panther, KEGG, dbPTM and Treefam.
- Technologies: Python, MySQL, Ajax, Django-Python Show less

Final year project on loss-aware forwarding in Greedy Perimeter Stateless Routing (GPSR) for wireless sensor networks. Gathered loss measurement data over long periods of time on a 40-node wireless sensor network and derived statistical properties of loss. Have improved performance of GPSR for certain topologies in terms of end-to-end delay and power usage by reducing retransmission count.
- Technologies: NesC, TinyOS, TOSSIM, Msp430 toolchain, C, Perl, Python,
Gnuplot

Group project involving the design and implementation of a test specification
language to generate unit tests, as well as a graphical interface to assist in the creation and execution of these tests. The specification language was parsed into an XML abstract syntax tree from which, an XSLT processor was used to generate either TestNG code or JUnit code. Our project won the first prize at the Goldman Sachs group presentation.
- Technologies: Java, Ant, JavaCUP, TestNG, XML and XSLT

Three-tier Hospital System coursework featuring a client, a login server and a patient record server. System needed to support many users, allowing them to concurrently read/write the same patient record.
- Technologies: Java, Ant, threads, non-blocking sockets, RMI, XML, JAXB

Side-scrolling spaceship game implemented in Java. Main features include parallax scrolling, rule-based enemy AI and collision detection.