Stephanie J. Spielman

Assistant Professor of Biological Sciences

Rowan University

About

Welcome to the Spielman Lab! We conduct research broadly within the fields of computational molecular evolution and evolutionary genomics. We use scientific computing, bioinformatics techniques, and biostatistics to study how DNA and protein sequences evolve. In particular, we are interested in the phylogenetic modeling frameworks used to describe sequence evolution.

Interests

Models of sequence evolution
Phylogenetic methods
Data science and bioinformatics
Open science and education

Education

Research Assistant Professor and Bioinformatics Consultant, 2016-2018

Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA
PhD in Ecology, Evolution, and Behavior, 2016

The University of Texas at Austin, Austin, TX
BSc in Biology, with Honors, 2010

Brown University, Providence, RI

Lab Members

Introduction to Evolution and Scientific Inquiry

Materials for Spring 2020 BIOL01104 Section 4.

Data Science for Biologists

Materials for Spring 2020 BIOL01301.

A collection of materials to learn bioinformatics at home

An Introduction to Programming for Bioscientists: A Python-Based Primer

Learn concepts in programming through the lens of Python with this primer from PLOS Computational Biology.

Biostatistics

Materials for BIO5312, taught Fall 2017 at Temple University.

Data Visualization: A practical introduction

Master ggplot2 with this excellent book by Kieran Healy.

Functional Genomics Workshop

Materials for 2017 Workshop at Lacawac Sanctuary, focusing on basic UNIX skills and regular expressions.

Fundamentals of Data Visualization

Learn how to design compelling figures with this book by Claus Wilke.

Interactive UNIX Bootcamp

Free interactive guide for getting started with UNIX (command line).

Introduction to Github

Interactive lesson to introduce fundamental concepts in version control with git (requires a free account with https://github.com).

Introduction to LaTeX

Learn about this powerful markup language with free lessons from Overleaf.

Introduction to Markdown

Learn about this more-enjoyable-than-LaTeX markup language.

Introduction to Python

Materials for UT Austin’s Big Data in Biology 2018 python short course.

learnlatex.org

A website of short lessons that comprise a fantastic free introduction to LaTeX.

Modern Statistics for Modern Biology

An online book for hands-on application of statistical analyses to modern biological data by Susan Holmes and Wolfgang Huber.

Practical Computing for Biologists

Highly-recommended book for basic computing skills by Casey Dunn and Steve Haddock.

R Cheatsheets

Free cheatsheets for R/tidyverse courtesy of RStudio.

R for Data Science

Learn the ‘tidyverse’ with this excellent book by Garrett Grolemund and Hadley Wickham.

R for Data Science

Learn R with free resoures from RStudio Education.

RStudio Primers

Free interactive lessons in R/tidyverse created by RStudio (requires a free account on rstudio.cloud.

Software Carpentry Homepage

Free lessons from the awesome folks at Software Carpentry on topics including command line, Python, R, and version control with github.

UNIX Tutorial for Beginners

Free lessons online for getting started with UNIX (command line).

Chante Bethell (2018 - 2019)

Chante is a former undergraduate research student who graduated in May 2019 with her BSc in Bioinformatics from the department of …

Francis K. Picone (2019 - Present)

Frankie is an undergraduate student majoring in Biology in the department of Biological Sciences at Rowan University. He is researching …

Molly Miraglia (2019 - Present)

Molly is an undergraduate student majoring in Bioinformatics in the department of Molecular and Cellular Biosciences at Rowan …

Naman Srivastava (2019 - Present)

Naman is an undergraduate student majoring in Biological Sciences Rowan University. He is researching the deep-time geological dynamics …

dragon

Shiny application for interactive analysis of the mineral-chemistry network in deep time.

evolfoRces

Shiny application for teaching simple population genetics using simulations.

phyphy

Python library for facilitating and parsing standard HyPhy analyses.

pyvolve

Python library for simulating sequences along phylogenies using continuous time Markov models.

Publications and Preprints

Relative Model Fit Does Not Predict Topological Accuracy in Single-Gene Protein Phylogenetics

Stephanie J. Spielman

PDF Repository Link to publisher

The evolving redox chemistry and bioavailability of vanadium in deep time

Eli K. Moore, Jihua Hao, Stephanie J. Spielman, Nathan Yee

PDF Link to publisher

HyPhy 2.5 – a customizable platform for evolutionary hypothesis testing using phylogenies

Sergei L. Kosakovsky Pond, Art F. Y. Poon, Ryan Velazquez, Steven Weaver, N. Lance Hepler, Ben Murrell, Stephen D. Shank, Brittany Rife Magalis, Dave Bouvier, Anton Nekrutenko, Sadie Wisotsky, Stephanie J. Spielman, Simon D. W. Frost, Spencer V. Muse

PDF Repository Link to publisher

Evolution of Viral Genomes: Interplay Between Selection, Recombination, and Other Forces

Stephanie J. Spielman, Steven Weaver, Stephen D. Shank, Brittany Rife Magalis, Michael Li, Sergei L. Kosakovsky Pond

PDF Repository Link to publisher

Relative Evolutionary Rates in Proteins Are Largely Insensitive to the Substitution Model

Stephanie J. Spielman, Sergei L. Kosakovsky Pond

PDF Repository Link to publisher

See all publications