As the sole Bioinformatics Scientist in the Histocompatibility Lab I work with Lab Directors and Technologists to monitor clinical NGS genotyping ensuring proper QC and QM plans are in place following CLIA, ASHI, CAP, and NY guidelines. I oversee the labs bioinformatic analyses and work with the IT team to achieve our data storage and automation needs. In addition, I develop software with the goal of automating and improving transplant donor and recipient matching and enabling the application of precision medicine in clinical decision making.

As the Arndt Labs Bioinformatics Consultant I help students and staff at all levels with their bioinformatics needs. I write bioinformatics pipelines and perform analysis of my own while also advising students on their own data analysis protocols and mentoring them on bioinformatics and data science in general. We work with data from a verity of NGS based assays (ChIP-seq, MNase-seq, RNA-seq, 4tU-seq, WGS) and mass spectrometry (cross-linking and mass spectrometry and quantitative mass spectrometry).

While performing my PhD thesis research with Dr. Karen Arndt, a leader in the field of transcription and epigenetics, I am involved in analyzing the effects of deletion of PAF1 (a key component of the Paf1 complex: an important epigenetic factor) on the Saccharomyces cerevisiae transcriptome using tiling microarrays, northern blots and RT-qPCR. My task is to identify and characterize a novel recruitment pathway for Paf1C at actively transcribed regions. I wrote and published scientific papers while receiving funding from NIH. I am responsible for implementing yeast genetics techniques including genetic crosses, one-step gene disruption, two-step gene disruption, and plasmid shuffle to perform effective research. I perform molecular cloning using both traditional methods and Gibson assembly to manipulate plasmid DNA. My task is to use affinity chromatography, ion exchange chromatography, and size exclusion chromatography to purify recombinant proteins. I conduct in-vitro biochemistry experiments including gel-shift, FRET, and fluorescence anisotropy binding assays. My main function is to perform protein crosslinking and analyzed mass spectrometry data to build structural models. I use R statistical computing software for data manipulation, generation of genome browser tracks, differential expression analysis, and data plotting of tiling microarray, RNAseq, 4tUseq, MNaseseq, ChIPseq, and DNAseq datasets. My main function is to prepare sequencing libraries and analyze next generation sequencing data.

Taught a Biochemistry lab with Dr. Andrew Van Demark focused on cloning, purification and biochemical characterization of viral proteins.

I am currently working in Dr. Karen Arndt’s Lab. I am working to identify and characterize the recruitment pathways for Paf1C to actively transcribed regions. I am also investigating the effects of deletion of PAF1 (a key component of the Paf1 complex: an important elongation factor) on the Saccharomyces cerevisiae transcriptome. I employ genomics, bioinformatics, genetics, molecular biology, and biochemistry approaches in my work.Research Rotation 3 February 2016 – April 2016 University of Pittsburgh (Dr. Miler Lee’s Lab)Investigated zygotic genome activation in Danio rerio by identifying putative enhancer binding sites, sequence motifs associated with those sites, and proteins associated with the identified motifs. Research Rotation 2 November 2015 – February 2016 University of Pittsburgh (Dr. Andrew VanDemark’s Lab)Investigated the interaction between Cdc73 (a component of the Paf1 complex: an important elongation factor) and the C-terminal domain (CTD) repeats of the Rpb1 subunit of RNA polymerase II. Research Rotation 1 August 2015 – November 2015 University of Pittsburgh (Dr. Karen Arndt’s Lab)Investigated global changes to the Saccharomyces cerevisiae transcriptome when PAF1 gene is lost.

My task is to identify genetic variants with a high degree of co-occurrence conducting analysis of a cohort of pancreatitis patients. I perform variant calling writing a pipeline capable of calling variants from both targeted next generation sequencing data and WGS using various tools. I am responsinsible for annotate variants with information from various databases utilizing OpenCRAVAT for ClinEff and SnpSIFT. I use bioinformatics programs such as VCFtools, BCFtools, PLINK1.9, GATK4, Beagle4.1. to call haplotypes on patient data and 1000 genomes data with custom shell scripts. One of my additional tasks is to conduct transcription factor binding motif analysis with HOMER on genes expressed in the pancreas and its different cell types.• Contributed in identifying putative disease haplotypes in disease populations using both custom scripts and established tools such as PLINK1.9.• Worked in close collaboration with the Medical and Programming team members to discuss written reports, grant application and manuscripts.

I am working as an independent contractor for the Ariel team to help solve bioinformatic problems and offer input into the development of software.

My duty was to create, improve, and implement a qPCR assay using SYBR green chemistry and an in-situ hybridization assay for detection of the pathogenic fungi Puccinia horiana in plant tissue. I was involved in using Bowtie and SAMtools and IGV to analyze transcriptomics data from Puccinia horiana generating genome browser tracks. I developed and executed an experimental plan to test for the systemic spread of Puccinia horiana in plant tissue under the mentorship of Dr. Douglas Luster. My task was to develop buffers, solutions, fungal culture media, and DNA, RNA, and protein extracts on daily basis. I was responsible for managing an undergraduate intern mentoring her through her project and supervising her research.

Performed routine laboratory and greenhouse tasks under the supervision of Dr. Nina Shishkoff.• Learned Botany and Mycology concepts and key skills including: plant care, sample collection, weeding, parasite scouting, media preparation, aseptic technique, autoclave safety, and proper lab note-bookkeeping under the supervision of Dr. Nina Shishkoff.• Learned molecular techniques: Sample preparation, Homogenization, RNA and DNA extraction, RNA and DNA quantification, qPCR with Taqman probe assay.

Studied differential Hsp70 expression in response to salinity change in the sea anemone Aiptasia pallida and it's intracellular symbiont Symbiodinium sp. using qPCR under the supervision of Dr. Susan Carney.• Designed and conducted experiments to investigate heat shock (Hsp70) expression in response to salinity change in the sea anemone Aiptasia pallida and its intracellular symbiont Symbiodinium sp. • Learned and independently performed molecular biology techniques, including: RNA extraction, purification, and quantification, cDNA synthesis, primer design and testing for PCR applications, and agarose gel electrophoresis, qPCR with SYBR Green assay.• Cared for and propagated research animals.• Reviewed primary literature and prepared scientific reports.