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Hi there! I'm Serena.

Serena at Pictured Rocks in the Upper Peninsula of Michigan

I'm a computational plant biologist with a background in biochemistry, pursuing my PhD at Michigan State University (MSU) co-advised by Drs. Bob VanBuren and Mohammad Ghassemi. I work on applying natural language processing techniques to answer biological questions in the plant science domain. For more details on active projects, feel free to browse my repositories or view my website.

I care about writing reproducible, well-documented code for biology, and am always looking for feedback on my code and documentation. If you're using code from one of my repositories and have any questions or feedback, please open an issue or email me at [email protected]!

I love science communication, and have written a guest blog for MSU SciComm and have been interviewed for their podcast. I also enjoy giving talks on topics like applications of machine learning in plant biology and my own research.

I'm also a founding member and past president of QT-Grad, an organization for queer and trans graduate students at MSU, and helped found & run the peer mentorship program in my home department.

Fun fact: In my undergrad, I was a rock climbing instructor at the Lindseth Climbing Center, where I taught people how to top rope and lead climb!

Serena Lotreck's Projects

bratiaa icon bratiaa

Inter-annotator agreement for Brat annotation projects

desiccation-network icon desiccation-network

Code for the project Drying to Connect: A bibliometric analysis of desiccation tolerance research across the kingdoms of life.

dygiepp icon dygiepp

Span-based system for named entity, relation, and event extraction.

goatools icon goatools

Python library to handle Gene Ontology (GO) terms

handson-ml2 icon handson-ml2

A series of Jupyter notebooks that walk you through the fundamentals of Machine Learning and Deep Learning in Python using Scikit-Learn, Keras and TensorFlow 2.

knowledge-graph icon knowledge-graph

Code exploring the creation of knowledge graphs from plant science papers

literature-genes icon literature-genes

Code to identify gene candidates involved in desiccation tolerance from the literature

ml-pipeline icon ml-pipeline

Shiu Lab code base for Machine Learning implemented in SciKit-Learn

multi-omics icon multi-omics

Code for multi-omic deep learning integration project

obie-wan icon obie-wan

Improved entity and relation extraction in the plant sciences through ontology-based information extraction

ontogpt icon ontogpt

LLM-based ontological extraction tools, including SPIRES

pickle-corpus-code icon pickle-corpus-code

Code for the manuscript "In a PICKLE: Entity and relation annotation guidelines for the molecular plant sciences"

plant-history icon plant-history

Using NLP techniques to explore the prevalance of topics of study in the plant sciences over the last 100 years

pure icon pure

NAACL'2021: A Frustratingly Easy Approach for Entity and Relation Extraction

taxonerd icon taxonerd

TaxoNERD : recognizing taxonomic entities using deep models

tutorials icon tutorials

Collection of tutorials I've made or adapted

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