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Alice C. McHardy
Person information
- affiliation: Helmholtz Centre for Infection Research, Braunschweig, Germany
- affiliation (former): Heinrich Heine University Düsseldorf, Department of Computer Science, Germany
- affiliation (former): Max Planck Institute for Informatics (MPII), Saarbrücken, Germany
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2020 – today
- 2024
- [i3]MohammadAli SadraeiJavaeri, Ehsaneddin Asgari, Alice Carolyn McHardy, Hamid Reza Rabiee:
SuperPos-Prompt: Enhancing Soft Prompt Tuning of Language Models with Superposition of Multi Token Embeddings. CoRR abs/2406.05279 (2024) - 2023
- [j23]Andrew Dickson, Ehsaneddin Asgari, Alice C. McHardy
, Mohammad R. K. Mofrad
GO Bench: shared hub for universal benchmarking of machine learning-based protein functional annotations. Bioinform. 39(2) (2023) - [c1]Amadeu Scheppach, Hüseyin Anil Gündüz, Emilio Dorigatti, Philipp C. Münch, Alice C. McHardy
Neural Architecture Search for Genomic Sequence Data. CIBCB 2023: 1-10 - 2022
- [j22]Mohammad-Hadi Foroughmand-Araabi
Scelestial: Fast and accurate single-cell lineage tree inference based on a Steiner tree approximation algorithm. PLoS Comput. Biol. 18(8) (2022) - [j21]Esmaeil Nourani
TripletProt: Deep Representation Learning of Proteins Based On Siamese Networks. IEEE ACM Trans. Comput. Biol. Bioinform. 19(6): 3744-3753 (2022) - 2021
- [j20]Franziska Hufsky, Kevin Lamkiewicz, Alexandre Almeida
Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research. Briefings Bioinform. 22(2): 642-663 (2021) - [j19]Zhi-Luo Deng
Evaluating assembly and variant calling software for strain-resolved analysis of large DNA viruses. Briefings Bioinform. 22(3) (2021) - [j18]Akash Bahai
EpitopeVec: linear epitope prediction using deep protein sequence embeddings. Bioinform. 37(23): 4517-4525 (2021) - 2020
- [j17]Susanne Reimering
Phylogeographic reconstruction using air transportation data and its application to the 2009 H1N1 influenza A pandemic. PLoS Comput. Biol. 16(2) (2020)
2010 – 2019
- 2019
- [j16]Ehsaneddin Asgari, Kiavash Garakani, Alice C. McHardy
MicroPheno: predicting environments and host phenotypes from 16S rRNA gene sequencing using a k-mer based representation of shallow sub-samples. Bioinform. 35(6): 1082 (2019) - [j15]Ehsaneddin Asgari, Philipp C. Münch, Till R. Lesker, Alice C. McHardy
DiTaxa: nucleotide-pair encoding of 16S rRNA for host phenotype and biomarker detection. Bioinform. 35(14): 2498-2500 (2019) - [i2]David Laehnemann
12 Grand Challenges in Single-Cell Data Science. PeerJ Prepr. 7: e27885 (2019) - 2018
- [j14]Ehsaneddin Asgari, Kiavash Garakani
MicroPheno: predicting environments and host phenotypes from 16S rRNA gene sequencing using a k-mer based representation of shallow sub-samples. Bioinform. 34(13): i32-i42 (2018) - 2017
- [j13]Philipp C. Münch, Bärbel Stecher
EDEN: evolutionary dynamics within environments. Bioinform. 33(20): 3292-3295 (2017) - [j12]Johannes Dröge
A probabilistic model to recover individual genomes from metagenomes. PeerJ Comput. Sci. 3: e117 (2017) - 2016
- [j11]David Laehnemann
Denoising DNA deep sequencing data - high-throughput sequencing errors and their correction. Briefings Bioinform. 17(1): 154-179 (2016) - [j10]I. Gregor, Alexander Schönhuth
Snowball: strain aware gene assembly of metagenomes. Bioinform. 32(17): 649-657 (2016) - [i1]Johannes Dröge
A probabilistic model to recover individual genomes from metagenomes. PeerJ Prepr. 4: e2626 (2016) - 2015
- [j9]Johannes Dröge
Taxator-tk: precise taxonomic assignment of metagenomes by fast approximation of evolutionary neighborhoods. Bioinform. 31(6): 817-824 (2015) - [j8]Yang Bai
Functional overlap of the Arabidopsis leaf and root microbiota. Nat. 528(7582): 364-369 (2015) - [j7]Alice Carolyn McHardy
How to Grow a Computational Biology Lab. PLoS Comput. Biol. 11(9) (2015) - 2014
- [j6]Christina Kratsch
RidgeRace: ridge regression for continuous ancestral character estimation on phylogenetic trees. Bioinform. 30(17): 527-533 (2014) - 2012
- [j5]Johannes Dröge
Taxonomic binning of metagenome samples generated by next-generation sequencing technologies. Briefings Bioinform. 13(6): 646-655 (2012) - [j4]Lars Steinbrück, Alice Carolyn McHardy
Inference of Genotype-Phenotype Relationships in the Antigenic Evolution of Human Influenza A (H3N2) Viruses. PLoS Comput. Biol. 8(4) (2012) - 2011
- [j3]Sebastian G. A. Konietzny
Inferring functional modules of protein families with probabilistic topic models. BMC Bioinform. 12: 141 (2011) - [j2]Lars Steinbrück, Alice Carolyn McHardy
Allele dynamics plots for the study of evolutionary dynamics in viral populations. Nucleic Acids Res. 39(1): 4 (2011)
2000 – 2009
- 2004
- [j1]Alice Carolyn McHardy
Development of joint application strategies for two microbial gene finders. Bioinform. 20(10): 1622-1631 (2004)
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