Daniel Moakley
New York,NY
Summary
Expert in systems biology and neuroscience with a broad knowledge base. Skills include computational and experimental techniques, data presentation, and manuscript preparation. My track record shows my dedication to biological research and consistent contributions to innovative projects.
Overview
12
12
years of professional experience
Work History
Graduate Research Assistant, Postdoctoral Researcher
Zhang Laboratory, Columbia University
New York, NY
09.2017 - Current
- Reverse engineered neuron type-specific alternative RNA splicing regulation by pioneering a new approach analyzing single-cell RNA-seq data.
- Experimentally confirmed computational predictions using CRISPR/Cas9 genome editing and embryonic stem cell (ESC)-derived neurons.
- Successfully defended Ph.D thesis in November 2023.
Research Assistant/Lab Manager
Wainger Laboratory, Massachusetts General Hospital
Boston, MA
09.2014 - 08.2017
- Conducted research focusing on the electrophysiology of motor neurons in ALS.
- Developed experimental and analytical protocols for ESC-derived motor neuron microelectrode array recordings.
- Started up the Wainger Lab as the lab’s first employee.
- Rotated with collaborators to learn techniques, then personally identified, procured, and implemented all equipment and supplies needed for experiments.
- Oversaw lab compliance and maintenance as manager.
Undergraduate Student, Master’s Student
Grabel Laboratory, Wesleyan University
Middletown, CT
06.2012 - 08.2014
- Optimized long-term culture of human ESC-derived GABAergic interneurons.
- Assessed the neurons' molecular and electrophysiological maturation as part of a three-lab initiative investigating an ESC-based treatment for temporal lobe epilepsy.
Education
Doctor of Philosophy - Systems Biology
Columbia University
11.2023
Master of Arts - Neuroscience and Behavior
Wesleyan University
01.2015
Bachelor of Arts - Double major: Neuroscience and Behavior, Science in Society
Wesleyan University
05.2013
Skills
Computational
● Languages: R (advanced), Python (advanced), shell/bash scripting (intermediate), MATLAB (basic)
● Statistics: R, Python, Excel
● Bioinformatics: NGS data analysis (integrated bulk and single cell -omics), electrophysiological data analysis, image analysis automation with ImageJ
● Advanced network biology algorithms: biological network reverse engineering and protein activity estimation (ARACNe/VIPER), gene set enrichment analysis (GSEA), gene ontology (GO) analysis
● Data visualization: complex graphs and animations (R/Python), integrated genome browser
Experimental
● Genome engineering: CRISPR/Cas9 gene editing, Gibson assembly
● Molecular biology: bulk and single-cell RNA-seq, RT-qPCR, Sanger sequencing analysis, genotyping,
● Cell and tissue culture: neuronal differentiation and long-term culture (mouse and human embryonic stem cell), primary mouse CNS dissections and neural culture (cortical cell, cortical glia, spinal motor neuron)
● Other: immunostaining, fluorescence and confocal microscopy, microelectrode arrays, in vitro optogenetics, tissue sectioning
Publications
- Moakley, D.F. et al. Reverse engineering neuron type-specific splicing-regulatory networks from single-cell transcriptomes. In submission.
- Moakley, D.F. et al. Nova1 mediates abnormal splicing in BRCA tumor samples. In submission.
- Feng, H.F. Moakley, D.F., et al. Complexity and graded regulation of neuronal cell-type-specific alternative splicing revealed by single-cell RNA sequencing. PNAS 118 (2021). PMID: 33674385.
- Bao, S., Moakley, D. F. & Zhang, C. The Splicing Code Goes Deep. Cell 176, 414–416 (2019).PMID:30682368
- Moakley, D. et al. Pharmacological Profiling of Purified Human Stem Cell-Derived and Primary Mouse Motor Neurons. Sci. Rep. 9, 1–10 (2019). PMCID: PMC6658502
- Chen, C. Y. ... Moakley, D. et al. Transcriptome and in Vitro Differentiation Profile of Human Embryonic Stem Cell Derived NKX2.1-Positive Neural Progenitors. Stem Cell Rev. Reports 12 (2016). PMID: 27539622
Timeline
Graduate Research Assistant, Postdoctoral Researcher
Zhang Laboratory, Columbia University
09.2017 - Current
Research Assistant/Lab Manager
Wainger Laboratory, Massachusetts General Hospital
09.2014 - 08.2017
Undergraduate Student, Master’s Student
Grabel Laboratory, Wesleyan University
06.2012 - 08.2014
Doctor of Philosophy - Systems Biology
Columbia University
Master of Arts - Neuroscience and Behavior
Wesleyan University
Bachelor of Arts - Double major: Neuroscience and Behavior, Science in Society
Wesleyan University