Software Engineer and Junior Computational Neuroscientist

• Aug 2023 - Present

Research Technologist

• Oct 2022 - May 2023

* Built a python package exploring how an estimated fMRI time-course generated from different hemodynamic models and an EEG spike train fits to an observed fMRI time-course (https://github.com/freesurfer/explore_hdr_model). * Examined optimal EEG pre-processing for Hidden Markov modeling on EEG data acquired during fMRI scans. * Collected, pre-processed, analyzed, and presented simultaneous EEG/fMRI data from participants aged 55-80, including hypertensive COVID survivors and patients… Show more * Built a python package exploring how an estimated fMRI time-course generated from different hemodynamic models and an EEG spike train fits to an observed fMRI time-course (https://github.com/freesurfer/explore_hdr_model). * Examined optimal EEG pre-processing for Hidden Markov modeling on EEG data acquired during fMRI scans. * Collected, pre-processed, analyzed, and presented simultaneous EEG/fMRI data from participants aged 55-80, including hypertensive COVID survivors and patients with mild cognitive impairment. * Collaborated with Dr. Tatiana Sitnikova to prepare an IRB protocol. Show less * Built a python package exploring how an estimated fMRI time-course generated from different hemodynamic models and an EEG spike train fits to an observed fMRI time-course (https://github.com/freesurfer/explore_hdr_model). * Examined optimal EEG pre-processing for Hidden Markov modeling on EEG data acquired during fMRI scans. * Collected, pre-processed, analyzed, and presented simultaneous EEG/fMRI data from participants aged 55-80, including hypertensive COVID survivors and patients… Show more * Built a python package exploring how an estimated fMRI time-course generated from different hemodynamic models and an EEG spike train fits to an observed fMRI time-course (https://github.com/freesurfer/explore_hdr_model). * Examined optimal EEG pre-processing for Hidden Markov modeling on EEG data acquired during fMRI scans. * Collected, pre-processed, analyzed, and presented simultaneous EEG/fMRI data from participants aged 55-80, including hypertensive COVID survivors and patients with mild cognitive impairment. * Collaborated with Dr. Tatiana Sitnikova to prepare an IRB protocol. Show less

Software Engineer

• Mar 2022 - Jul 2022

Technical Lead

• May 2021 - Mar 2022

Software Engineer

• Sep 2019 - May 2021

Software Engineer

• May 2019 - May 2021

Data Analyst

• Sep 2018 - May 2019

I maintained distributed pipelines gathering and analyzing over 6 TB of survey responses and timings, audio diaries, videotaped interviews, structural and functional MRI, medical history, actigraphy, and passive phone data. I also develop software to streamline these pipelines and clarify their output. I worked as part system administrator, part developer, part IT support.

Volunteer

• Oct 2017 - Aug 2018

I write and maintain computer programs used by members of the Pizzagalli lab, as well as process EEG and sMRI data.

Research Assistant and Customer Project Manager

• Jun 2014 - Jul 2016

Overall, I worked in open source bioinformatics. Specifically, this includes developing and experimenting with tiling, a form of encoding called genomes which can be compressed to 4 MB per genome, and can be analyzed, visualized, and queried without decompression. Tiled genomes may be annotated for precision medicine. Additionally, they are easily learned on: I ran principle component analysis and built a support vector machine to predict blood type. I presented the work Curoverse did on tiling… Show more Overall, I worked in open source bioinformatics. Specifically, this includes developing and experimenting with tiling, a form of encoding called genomes which can be compressed to 4 MB per genome, and can be analyzed, visualized, and queried without decompression. Tiled genomes may be annotated for precision medicine. Additionally, they are easily learned on: I ran principle component analysis and built a support vector machine to predict blood type. I presented the work Curoverse did on tiling to the Wellcome Trust Sanger Institute, the European Bioinformatics Institute, and the Global Alliance for Genomics and Health in 2015. The preprint we wrote describing tiling is shown in the link below. I led the porting and optimization of several customer pipeline projects focusing in RNA analysis and exome and whole genome alignment and calling as Customer Project Manager. Some of these projects were written in the Common Workflow Language (CWL), and some were written as custom Arvados pipelines. Finally, I led 8 Arvados training sessions for Curoverse customers, ranging from 2 hours to 3 days. Show less Overall, I worked in open source bioinformatics. Specifically, this includes developing and experimenting with tiling, a form of encoding called genomes which can be compressed to 4 MB per genome, and can be analyzed, visualized, and queried without decompression. Tiled genomes may be annotated for precision medicine. Additionally, they are easily learned on: I ran principle component analysis and built a support vector machine to predict blood type. I presented the work Curoverse did on tiling… Show more Overall, I worked in open source bioinformatics. Specifically, this includes developing and experimenting with tiling, a form of encoding called genomes which can be compressed to 4 MB per genome, and can be analyzed, visualized, and queried without decompression. Tiled genomes may be annotated for precision medicine. Additionally, they are easily learned on: I ran principle component analysis and built a support vector machine to predict blood type. I presented the work Curoverse did on tiling to the Wellcome Trust Sanger Institute, the European Bioinformatics Institute, and the Global Alliance for Genomics and Health in 2015. The preprint we wrote describing tiling is shown in the link below. I led the porting and optimization of several customer pipeline projects focusing in RNA analysis and exome and whole genome alignment and calling as Customer Project Manager. Some of these projects were written in the Common Workflow Language (CWL), and some were written as custom Arvados pipelines. Finally, I led 8 Arvados training sessions for Curoverse customers, ranging from 2 hours to 3 days. Show less

Undergraduate Researcher

• Jun 2012 - Jun 2014

I examined the mechanisms of antibiotic resistance in bacteria (A. baumanii). I focused on modeling the antibiotic breakdown of doripenem and imipenem by OXA-24 using umbrella sampling and transition path sampling. Doripenem and imipenem are chemically similar; however, doripenem is degraded by OXA-24 relatively slowly (kcat=0.074 /s), while imipenem is degraded relatively quickly (kcat=2.1 /s). I investigated the mechanistic reason for the difference in reaction rates for these two similar… Show more I examined the mechanisms of antibiotic resistance in bacteria (A. baumanii). I focused on modeling the antibiotic breakdown of doripenem and imipenem by OXA-24 using umbrella sampling and transition path sampling. Doripenem and imipenem are chemically similar; however, doripenem is degraded by OXA-24 relatively slowly (kcat=0.074 /s), while imipenem is degraded relatively quickly (kcat=2.1 /s). I investigated the mechanistic reason for the difference in reaction rates for these two similar antibiotics. Show less I examined the mechanisms of antibiotic resistance in bacteria (A. baumanii). I focused on modeling the antibiotic breakdown of doripenem and imipenem by OXA-24 using umbrella sampling and transition path sampling. Doripenem and imipenem are chemically similar; however, doripenem is degraded by OXA-24 relatively slowly (kcat=0.074 /s), while imipenem is degraded relatively quickly (kcat=2.1 /s). I investigated the mechanistic reason for the difference in reaction rates for these two similar… Show more I examined the mechanisms of antibiotic resistance in bacteria (A. baumanii). I focused on modeling the antibiotic breakdown of doripenem and imipenem by OXA-24 using umbrella sampling and transition path sampling. Doripenem and imipenem are chemically similar; however, doripenem is degraded by OXA-24 relatively slowly (kcat=0.074 /s), while imipenem is degraded relatively quickly (kcat=2.1 /s). I investigated the mechanistic reason for the difference in reaction rates for these two similar antibiotics. Show less

CS&T Intern

• Jun 2011 - Aug 2011

I designed and fabricated props for use in daily Current Science and Technology presentations to the public. Constructed an animal cell model three feet in diameter with removable organelles. Constructed a 3D model brain with removable brain stem and limbic system. I designed and fabricated props for use in daily Current Science and Technology presentations to the public. Constructed an animal cell model three feet in diameter with removable organelles. Constructed a 3D model brain with removable brain stem and limbic system.

Undergraduate Researcher

• Jun 2010 - Aug 2010

I assisted Nidhi Shrivastav in research examining the effect different DNA lesions have on the rate of repair in replicating bacterial cells. Alongside assisting Nidhi Shrivastav, I designed and implemented a Python script to automate predictions of transition state structures from kinetic isotope effects. I assisted Nidhi Shrivastav in research examining the effect different DNA lesions have on the rate of repair in replicating bacterial cells. Alongside assisting Nidhi Shrivastav, I designed and implemented a Python script to automate predictions of transition state structures from kinetic isotope effects.

Volunteer

• 2007 - 2009

I performed trail maintenance during three summers (from July to August): 2007, 2008, and 2009. I performed trail maintenance during three summers (from July to August): 2007, 2008, and 2009.