Kamil Cygan

About Kamil Cygan

Programming: C, C++, Perl, SQL, PL/SQL, R/Bioconductor, Unix/Linux, Bash, Java…

Experience

1. Staff Scientist - Bioinformatics

   Regeneron

   Dec 2021 — Present

   Developed, evaluated, and operated a clinical whole exome (WES) analysis pipeline for four clinical trials. • Identified multiple useful biomarkers for patient stratification based on clinical endpoints. • Provided neoantigen detection/analysis for multiple oncology studies. • Created proteogenomic workflow that combines detection of antigens from mutations, alternative splicing, gene fusions, expressed retrotransposons, reactivated cancer-testis genes, and noncoding regions of mouse and human genomes with immunopeptidomics data sets. • Performed proteogenomic analyses on over 800 samples. • Designed an algorithm to find sources of peptides identified by de novo peptide sequencing. • Carried out HLA phenotyping based on both RNA-seq and WES data. • Predicted antigen binding for samples without mass spectrometry data. • Built a machine learning tool that predicts splice-switching oligonucleotides’ influence on splicing. • Supervised a direct report, multiple co-ops, and intern research projects.

Skills

• Edc
• Data Analysis
• Laboratory
• Science
• Sql
• Whole-Exome Sequencing
• Polymerase Chain Reaction (Pcr)
• Clinical Data Management
• Biotechnology
• Clinical Trials
• Powerpoint
• Cancer
• Cell Biology
• Pl/Sql
• Microsoft Excel
• Dna Extraction
• R
• Perl
• C++
• Whole-Genome Sequencing
• Rnaseq
• Bedtools
• Clipseq
• Programming
• Pcr
• Bioconductor
• Software
• Unix
• Eclipse
• Oracle
• Bash
• Tophat
• Microsoft Office
• Iwork
• Life Sciences
• Samtools
• Bioinformatics
• Star
• Public Speaking
• Cell