ToDonePy
A command-line task manager written in Python using Click
Posts by Collection
portfolio
covid-epitope-prediction
Developing reproducible pipelines using Data Version Control
dash-covid19
A Dash app for viewing and exploring up-to-date information on the Covid19 pandemic
LipidTA
Lipid Traffic Analysis - a python commandline interface for analysing lipidomics data
publications
Vision loss shifts the balance of feedforward and intracortical circuits in opposite directions in mouse primary auditory and visual cortices
Published in Journal of Neuroscience, 2015
Our results suggest that loss of vision produces distinct circuit changes in the spared and deprived sensory cortices to shift between feedforward and intracortical processing to allow adaptation.
Recommended citation: Petrus E, Rodriguez G, Patterson R, Connor B, Kanold PO, Lee HK. (2015). "Vision loss shifts the balance of feedforward and intracortical circuits in opposite directions in mouse primary auditory and visual cortices." J Neurosci. 35(23).
Selecting single cell clustering parameter values using subsampling-based clustering metrics
Published in BMC Bioinformatics, 2021
Here, we illustrate a subsampling-based approach (chooseR) that simultaneously guides parameter selection and characterizes cluster robustness.
Recommended citation: Patterson-Cross RB, Levine AJ, Menon V. Selecting single cell clustering parameter values using subsampling-based robustness metrics. BMC Bioinformatics. 2021 Feb 1;22(1):39.
A Harmonized Atlas of Spinal Cord Cell Types and Their Spatial Organization
Published in Nature Communications, 2021
This work provides an unprecedented view of spinal cell types, their specific gene expression signatures, and the general molecular organization.
Recommended citation: Russ DE, Cross RBP, Li L, Koch SC, Matson KJE, Yadav A, Alkaslasi MR, Lee DI, Le Pichon CE, Menon V, Levine AJ. A harmonized atlas of mouse spinal cord cell types and their spatial organization. Nat Commun. 2021 Sep 29;12(1):5722. doi: 10.1038/s41467-021-25125-1. Erratum in: Nat Commun. 2022 Feb 18;13(1):1033. Erratum in: Nat Commun. 2022 Oct 19;13(1):6184. PMID: 34588430; PMCID: PMC8481483.
A Comparison of the Cellular and Molecular Atlases of the Macaque and Mouse Dorsal Horns
Published in Neuron, In Press, 2021
The study thus provides an essential resource for the functional interrogation of neural circuits underlying somatosensory processing within the dorsal horn and across species as well as for the validation of therapeutic targets.
Recommended citation: Arokiaraj, Cynthia Mary and Kleyman, Michael and Chamessian, Alexander and Shiers, Stephanie and Kang, Byungsoo and Kennedy, Meaghan M. and Patterson, Ryan and Lewis, David A. and Qadri, Yawar and Levine, Ariel J. and Price, Theodore and Pfenning, Andreas R. and Seal, Rebecca P., A Comparison of the Cellular and Molecular Atlases of the Macaque and Mouse Dorsal Horns. Available at SSRN: https://ssrn.com/abstract=3924596 or http://dx.doi.org/10.2139/ssrn.3924596
A comparative transcriptomic analysis of glucagon-like peptide-1 receptor- and glucose-dependent insulinotropic polypeptide receptor-expressing cells in the hypothalamus
Published in Appetite, 2022
We have provided a detailed comparison of Glp1r and Gipr cells of the hypothalamus with single-cell resolution. This resource will provide mechanistic insight into how engaging Gipr- and Glp1r-expressing cells of the hypothalamus may result in changes in feeding behaviour and energy balance.
Recommended citation: Smith C, Patterson-Cross R, Woodward O, Lewis J, Chiarugi D, Merkle F, Gribble F, Reimann F, Adriaenssens A. A comparative transcriptomic analysis of glucagon-like peptide-1 receptor- and glucose-dependent insulinotropic polypeptide receptor-expressing cells in the hypothalamus. Appetite. 2022 Jul 1;174:106022. doi: 10.1016/j.appet.2022.106022. Epub 2022 Apr 14. PMID: 35430298; PMCID: PMC7614381.
talks
Talk 1 on Relevant Topic in Your Field
Published:
This is a description of your talk, which is a markdown files that can be all markdown-ified like any other post. Yay markdown!
Conference Proceeding talk 3 on Relevant Topic in Your Field
Published:
This is a description of your conference proceedings talk, note the different field in type. You can put anything in this field.
teaching
Introductory Chemistry Lab Teaching Assistant
Undergraduate course, Johns Hopkins University, Dept. of Chemistry, 2014
Lead a section of 20 students in experiments each week while helping students develop skills in lab safety, critical analysis, and chemical principles. Additionally, I assisted in grading worksheets, notebooks, lab reports, and exams for ~100 students.
Introduction to Python (BIOF309) Teaching Assistant
Graduate course, Fellowship for Advanced Education in the Sciences, 2019
Lectured on packaging projects and assisted in teaching and answering questions in a class of 75 students while helping students develop fundamental python skills, including Jupyter notebooks, data visualisation, and reading/writing files.
Bioinformatics Supervisor
Undergraduate Supervisor, Dept. of Computer Science and Technology, University of Cambridge, 2021
Led 2-3 person study groups in working through theoretical and practical applications of core bioinformatics topics, including dynamic programming, phylogeny (UPGMA, Neighbour Joining, Parsimony), clustering (hard/soft K-means, hierarchical, Markov), genome sequencing (Hamiltonian and De Bruijn graphs), genome alignment (suffix tries and the Burrows-Wheeler Transform), and Hidden Markov Models (Viterbi algorithm, Baum-Welch learning).