Grimm Lab - Bioinformatics and Machine Learning

MicrobiomeBestPracticeReview

Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing

BookChapter-RNA-Seq-Analyses

Best practice RNA-Seq analysis pipeline for reference-based RNA-Seq analysis

permGWAS

Efficient Permutation-based GWAS for Normal and Skewed Phenotypic Distributions

UAVWeedSegmentation

Deep Learning-based Early Weed Segmentation using Motion Blurred UAV Images of Sorghum Fields

GerminationPrediction

Accurate Machine Learning Based Germination Detection, Prediction and Quality Assessment of Different Seed Cultivars

easyPheno

easyPheno: a model agnostic phenotype prediction framework

HorticulturalSalesPredictions

Machine Learning Outperforms Classical Forecasting on Horticultural Sales Predictions

ForeTiS

Time Series Forecasting in Python

gumbeldore

Self-Improvement for Neural Combinatorial Optimization: Sample Without Replacement, but Improvement

MFWD

Code repository for the manuscript "Manually annotated and curated dataset of diverse weed species in maize and sorghum for computer vision"

evars-gpr

EVARS-GPR: EVent-triggered Augmented Refitting of Gaussian Process Regression for Seasonal Data

policy-based-self-competition

Official implementation of the ICLR 2023 paper "Policy-Based Self-Competition for Planning Problems"

SynGameZero

SynGameZero – Flowsheet Synthesis in a Game environment with Zero Knowledge

HeliantHome

HeliantHOME: a public and centralized database Home of a comprehensive collection of phenotypes for different Sunflower species

phenotype_prediction

A comparison of classical and machine learning-based phenotype prediction methods on simulated data and three plant species

ProLaTherm

Protein Language Model-based Protein Thermophilicity Prediction

AraGWAS

The AraGWAS Catalog - Togninalli*, Seren*, ..., Grimm, 2018, Nucleic Acid Research (https://bit.ly/2DaVj2r)

AraPheno

AraPheno: A public database for Arabidopsis thaliana phenotypes. Seren*, Grimm*, et. al. 2017, Nucleic Acid Research (https://bit.ly/2AwpTRF)

cem

Convex Envelope Method for determining liquid multi-phase equilibria in systems with arbitrary number of components

DeBlurWeedSeg

Improved weed segmentation in UAV imagery of sorghum fields with a combined deblurring segmentation model

drl4procsyn

Deep reinforcement learning uncovers processes for separating azeotropic mixtures without prior knowledge

ForeTiS-HortiCo

Lecture_ML4Genomics

Introduction into machine learning and its applications in genomics and genetics

easyGWASCore

Computational Framework for Genome-Wide Association Studies and Meta-Studies in C/C++ with Python Interfaces – Grimm et. al. 2017, Plant Cell (https://bit.ly/2Jqgr5e)

Genetic-Heterogeneity-Detection-FAIS

Genome-wide detection of intervals of genetic heterogeneity (Llinares-Lopez et al., ISMB/Bioinformatics 2015) http://goo.gl/h9gl6K

Multi-SConES

Multi-task feature selection coupled with multiple network regularizers (Sugiyama et al, SDM 2014) http://goo.gl/4q78Yp

Pathogenicity-Prediction

The evaluation of tools used to predict the impact of missense mutations is hindered by two types of circularity – Grimm et. al. 2015, Human Mutation (https://bit.ly/2ERhf4q)

SConES

A network-guided multi-locus association mapping method (Azencott et al., ISMB/Bioinformatics 2013) http://goo.gl/a8f6az

Structural-Variant-Prediction-SV-M

Structural Variant Machine (SV-M) to accurately predict InDels from NGS paired-end short reads – Grimm*, Hagmann*, et. al. 2013, BMC Genomics (https://bit.ly/2EQOu7X)

transcriptional-translational-coupling

Systematic analysis of the underlying genomic architecture for transcriptional-translational coupling in prokaryotes