List of works - Alice Carolyn McHardy - Paulina

List of works by Alice Carolyn McHardy

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A Practical Approach to Using the Genomic Standards Consortium MIxS Reporting Standard for Comparative Genomics and Metagenomics

A platform for deep learning on (meta)genomic sequences

A self-supervised deep learning method for data-efficient training in genomics

Assessing computational predictions of antimicrobial resistance phenotypes from microbial genomes

Critical Assessment of Metagenome Interpretation - the second round of challenges

DeepPrime2Sec: Deep Learning for Protein Secondary Structure Prediction from the Primary Sequences

EpitopeVec: Linear Epitope Prediction Using Deep Protein Sequence Embeddings

Evaluating assembly and variant calling software for strain-resolved analysis of large DNA-viruses

GO Bench: Shared-hub for Universal Benchmarking of Machine Learning-Based Protein Functional Annotations

Haploflow: Strain-resolvedde novoassembly of viral genomes

Importations of SARS-CoV-2 lineages decline after nonpharmaceutical interventions in phylogeographic analyses

MicroPheno: Predicting environments and host phenotypes from 16S rRNA gene sequencing using a k-mer based representation of shallow sub-samples

Nucleotide-pair encoding of 16S rRNA sequences for host phenotype and biomarker detection

Optimized model architectures for deep learning on genomic data

ProSolo: Accurate Variant Calling from Single Cell DNA Sequencing Data

Probabilistic variable-length segmentation of protein sequences for discriminative motif discovery (DiMotif) and sequence embedding (ProtVecX)

TripletProt: Deep Representation Learning of Proteins based on Siamese Networks

Tutorial: Assessing metagenomics software with the CAMI benchmarking toolkit

WITHDRAWN: ToxVec: Deep Language Model-Based Representation Learning for Venom Peptide Classification