Serena Lotreck

Using transcriptomics and proteomics to study photorespiration

Project examining the evolution fo thermotolerance in the photorespiratory pathway

No description provided.

Cis-element enrichment in domesticated and wild potato

Code to clip chaotic curves

Code to analyze genomic variation bewteen evolved strains of Nannochloropsis

Github profile README

Code for calculating linear regressions on stream data

Utility code for input data formatting for the DeuteRater tool

Code exploring the creation of knowledge graphs from plant science papers

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

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

LLM-based ontological extraction tools, including SPIRES

STHN: Simplifying Temporal Heterogeneous Network for Continuous-Time Link Prediction [CIKM 2023]

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

Code for multi-omic deep learning integration project

Collection of tutorials I've made or adapted

No description provided.

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

TaxoNERD : recognizing taxonomic entities using deep models

A framework for few-shot evaluation of autoregressive language models.

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

Code to run simulations of 13-C labelling data using INCA (MATLAB)

Lesson 6 for Foundations in Computational Plant Science (NRT-IMPACTS)

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

MSU team's code for the QSIDE Datathon4Justice

Python library to handle Gene Ontology (GO) terms

Inter-annotator agreement for Brat annotation projects

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

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