Christopher Sifuentes Email and Phone Number

• Performed customized bioinformatic analyses with a variety of model organisms and experimental paradigms• Worked closely with clients and the DNA sequencing core to design experiments• Created NGS pipelines – using Snakemake, Python, R, Bash and open-source/third-party softwares• Developed essential project management skills while consistently working on multiple projects simultaneously• Experience ino Single-cell RNA-sequencing analysis (multiple platforms)o Single-cell pseudotiming analysiso PacBio and High-Throughput Sanger sequencing analysiso CRISPR/CAS libraryv mutation screeningo SNP/INDEL calling (CNV analysis, clonal population structure inference)o ATAC-seq analysis

• MethylCap-seq, ChIP-seq, RNA-seq, and microarray analysis, some gene expression network analysis• Multi-level integration of genomic and epigenomic sequencing data to answer the biological questions presented

Ph.D. Dissertation Research: Pamela Raymond Lab, MCDBWe use the zebrafish model to study retinal stem cells and regeneration. I am particularly interested in the regulation of the stem-like properties of Muller glia, which dedifferentiate and asymmetrically divide to produce one Muller glia and one neuronal progenitor. The neuronal progenitor will rapidly divide and migrate along the processes of the Muller glia to replace any lost neurons. Work has resulted in a co-second author on a publication entitled "Retinal regeneration in adult zebrafish requires regulation of TGFβ signaling", linked below. A first author publication entitled "Rapid, Dynamic Activation of Müller Glial Stem Cell Responses in Zebrafish" is also linked below, and a third in being written.Skills or experience gained:Bioinformatics - Technical proficiency in analysis of high-throughput sequencing data including ChIP-seq analysis, microarray analysis, Reduced Representation Bisulfite Sequencing analysis, and RNA-seq analysis including de novo transcriptome assembly, gene set clustering and enrichment analysis (gene ontology, disease ontology, and pathway) and SNP linkage analysis utilizing RNA-seq data. Familiarity with statistical/scripting languages such as R, Python, Unix, awk, and sed. Wet lab-RNA isolation and clean-up, library preparation, molecular cloning techniques, qRT-PCR, western blot, cell culture and transfections, flow cytometry, retinal dissection and dissociation, ChIP, DNA isolation, immunohistochemistry, fixation and cryosectioning, and microscopy.

Genetics Laboratory (MCDB306) instructor, largely juniors and senior science majors.Skills or experience gained:Communicating complex scientific concepts to students. Managing the progress of several, concurrent, semester-long projects.

Introductory Biology Laboratory (BIO173) instructor, largely freshmen and sophomore science major students or junior and senior non-science majors.Skills or experience gained:Communicating a breadth of scientific information to students.

Graduate rotation in the laboratory of Dr. Andrej Wierzbicki, in the field of epigenetics. The Wierzbicki lab uses the model organism Arabidopsis thaliana to study the role of non-coding RNA in RNA-directed DNA methylation (RdDM). My initial project was to investigate the step in which the double-stranded RNA-binding protein INVOLVED IN DE NOVO 2 (IDN2) was necessary for RdDM. For this project, I was able to clone IDN2 and create a fusion protein that I used to purify an antibody to IDN2 that we had generated. During this time I was moved to another project that the lab needed to finish quickly. This project resulted in coauthorship on a paper showing that ARGONAUTE4 and SUPPRESSOR OF TY INSERTION 5-LIKE (SPT5L) mediate RdDM independently, linked below.Skills or experience gained:Working with DNA, RNA, and transcription-level analysis techniques such as RT-PCR, qRT-PCR, ChIP-qPCR, methylation-specific-PCR, and Gateway cloning. Gained exposure to methods and concepts used to study epigenetic regulation of genome activity, which are important because transcriptional and epigenetic regulation work hand in hand to regulate many biological processes.

The Morrison lab studies the mechanisms regulating neural and hematopoietic stem cell (HSC) function and how cancer cells take advantage of these functions. My work with Dr. Daisuke Nakada examined the role of the tumor suppressor, liver kinase B1 (Lkb1) as a regulator of energy metabolism and cell-cycle in HSCs. I provided technical assistance for a publication "Lkb1 regulates cell cycle and energy metabolism in haematopoietic stem cells.", linked below. My primary focus was on the cloning of a family of 12 kinases controlled by Lkb1; I was successful in cloning 8 of the 12 kinases. Skills or experience acquired:Experience using a mouse model, tail bleeds, dissections, intraperitoneal injections, flow-cytometry and haematopoietic stem cell (HSC) isolation, western blotting, multiplex genotyping, competitive repopulation assays, metaphase chromosome counts, and molecular cloning techniques.While my work in the Morrison lab was primarily technical, I gained valuable knowledge about stem cell regulation and function by attending and taking part in weekly lab meetings, weekly journal clubs, and monthly stem cell club presentations. Working in the Morrison lab was a great experience that reinforced my interests in stem cell regulation.

Performed an Honors Undergraduate Research Thesis entitled "Partial Cloning of the Hamster Anthrax Toxin Tumor Endothelial Marker 8 (TEM8)", aimed at cloning the hamster homolog of the human TEM8, which acts as an anthrax receptor to mediate binding of Protective Antigen (PA), a component of the of the lethal anthrax toxin that is crucial for internalization of the other components of the lethal anthrax toxin, Lethal Factor (LF) and Edema Factor (EF). Cloning of the unknown hamster TEM8 cDNA sequence would allow for further characterization of the possible roles of TEM8 in anthrax toxicity.Skills or experience acquired: Cell culture, RNA isolation, cDNA synthesis, primer design, PCR and gel electrophoresis, familiarity with alignment tools, presentation and speaking skills