Maria Sirenko

Postdoctoral Fellow

2023

Graduate Teaching Assistant

2019 - 2023

Developed curriculum and taught Quantitative and Computational Biology course for 1st year PhD students at GSK. Course Summary: Students in this course will learn to apply quantitative exploratory data analysis techniques to different forms of experimental data. The course will begin with an introduction for students to computing via the UNIX shell, and to computing in the R programming language. The course will then cover visualization of TCGA data, analysis of RNA-sequencing data - including single cell RNA-seq, and conclude with epigenomic and integrative analysis. Students will become comfortable performing exploratory data analysis, and will understand how concepts from statistics underlie the tools they use. Overall the goal of this course is to serve as a practical primer for various bioinformatic analyses, and should provide students with the foundation for future self-guided learning and skill acquisition in this discipline. These skills will enable them both to collaborate effectively with computational biologists, as well as begin to carry out their own computational experiments.

PhD Candidate

2016 - 2023

Integrative single cell profiling and population genomic studies to characterize the role of somatic mutations in hematologic malignancies

Undergraduate Researcher

2012 - 2016

Single molecule imaging techniques to study protein oligomerization: At Cornell University, I worked in the lab of Prof. Warren Zipfel. Most studies of proteins forming higher order structures has been done using bulk assays which average across protein populations and obscure heterogeneity relevant to protein function. Our aim was to develop a method to resolve protein oligomerization at the single molecule (SM) level. The main challenge to SM studies is the high in vivo protein concentrations and therefore, the diffraction limit. We developed a SM imaging technique to assemble protein complexes at physiological conditions and then dilute them using cellular fusion between expressing and non-expressing cells. Upon dilution, fluorescently tagged SM complexes can be resolved and stepwise photobleaching can be used to determine the stoichiometry.

Summer Undergraduate Researcher

2015 - 2015

Carbon nanotube sensor for cancer biomarker detection: In Dan Heller Lab at MSKCC, I worked on a project to address the unmet need in medicine of non-invasively monitoring biomarker levels to inform treatment. We developed a carbon nanotube-based sensor platform. Nanotubes make good sensors because their emission wavelength and intensity 1) changes predictably as a result of their local electron density and environment and 2) is not absorbed by water, enabling deep tissue imaging. We implemented our sensor in ovarian cancer because regular blood biomarker measurements are used to inform treatment. To enable in vivo biomarker detection, we synthesized a polymer-encapsulated nanotube conjugated to an antibody which responds optically to the ovarian cancer biomarker human epididymis protein (HE4). We are able to detect HE4 concentrations using near-infrared spectroscopy and microscopy. An implantable sensor prototype was developed to detect HE4 in ovarian cancer mouse models. The ultimate goal is to develop an implantable prototype that can be used to monitor HE4 levels in patients with or at high risk for ovarian cancer to better track cancer progression and adjust treatment accordingly. We published this work in 2018.

Science Undergraduate Laboratory Internships

2014 - 2014

I interned in the Lisa Miller Group at BNL during Summers 2013, 2014 in the US Department of Energy-funded SULI program and worked independently on a project quantifying metal accumulation in amyloid beta plaques in Alzheimer’s disease mouse models. We used X-Ray Fluorescence Microscopy (XFM) at NSLS to quantify copper and iron concentrations and FTIRM to investigate the beta sheet character of the plaques.

Summer Research Intern

2011 - 2013

Lisa Miller Research Group - National Synchrotron Light Source Summer 2013-Summer Research Intern Summer 2011, 2012-High School Research Program In the High School Research Program in Summers 2011 and 2012 I used synchrotron radiation to investigate the effects of a genetic modification (GM) intended to create a better biofuel source, in the lab of Dr. Lisa Miller at BNL-NSLS. Our collaborators modified a plant to express a putative acetyl esterase and predicted its biomass would be more easily degraded in the biofuel production process. We used Fourier Transform Infrared Microspectroscopy (FTIRM) at NSLS to determine the chemical composition of the plant’s pollen tubes to evaluate the effects of the modification. I grew samples, performed spectroscopic mapping, and quantified data by generating maps of certain vibrational modes and comparing them in GM and wildtype samples. We found that the plant tissue indeed contained reduced levels of acetyl esters, compounds that contribute to plant recalcitrance, enabling optimization of biomass yield and acetyl esterase expression.