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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
, Bernd Bischl, Mina Rezaei, Martin Binder:
Neural Architecture Search for Genomic Sequence Data. CIBCB 2023: 1-10 - 2022
- [j22]Mohammad-Hadi Foroughmand-Araabi
, Sama Goliaei
, Alice C. McHardy
:
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
, Ehsaneddin Asgari, Alice C. McHardy
, Mohammad R. K. Mofrad
:
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
, Abdel Aouacheria, Cecilia N. Arighi, Alex Bateman
, Jan Baumbach
, Niko Beerenwinkel, Christian Brandt
, Marco Cacciabue, Sara Chuguransky
, Oliver Drechsel, Robert D. Finn
, Adrian Fritz, Stephan Fuchs, Georges Hattab
, Anne-Christin Hauschild, Dominik Heider, Marie Hoffmann, Martin Hölzer, Stefan Hoops, Lars Kaderali, Ioanna Kalvari
, Max von Kleist
, Renó Kmiecinski, Denise Kühnert
, Gorka Lasso, Pieter Libin
, Markus List
, Hannah F. Löchel
, Maria Jesus Martin
, Roman Martin
, Julian O. Matschinske, Alice C. McHardy
, Pedro Mendes
, Jaina Mistry
, Vincent Navratil
, Eric P. Nawrocki, Áine Niamh O'toole, Nancy Ontiveros-Palacios
, Anton I. Petrov
, Guillermo Rangel-Pineros
, Nicole Redaschi
, Susanne Reimering, Knut Reinert
, Alejandro Reyes
, Lorna J. Richardson
, David L. Robertson
, Sepideh Sadegh
, Joshua B. Singer, Kristof Theys, Chris Upton, Marius Welzel, Lowri Williams
, Manja Marz
:
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
, Akshay Dhingra, Adrian Fritz, Jasper Götting
, Philipp C. Münch, Lars Steinbrück, Thomas F. Schulz, Tina Ganzenmüller
, Alice C. McHardy
:
Evaluating assembly and variant calling software for strain-resolved analysis of large DNA viruses. Briefings Bioinform. 22(3) (2021) - [j18]Akash Bahai
, Ehsaneddin Asgari
, Mohammad R. K. Mofrad, Andreas Kloetgen, Alice C. McHardy
:
EpitopeVec: linear epitope prediction using deep protein sequence embeddings. Bioinform. 37(23): 4517-4525 (2021) - 2020
- [j17]Susanne Reimering
, Sebastian Muñoz, Alice C. McHardy
:
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
, Mohammad R. K. Mofrad:
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
, Mohammad R. K. Mofrad:
DiTaxa: nucleotide-pair encoding of 16S rRNA for host phenotype and biomarker detection. Bioinform. 35(14): 2498-2500 (2019) - [i2]David Laehnemann
, Johannes Köster
, Ewa Szczurek, Davis J. McCarthy
, Stephanie C. Hicks
, Mark D. Robinson
, Catalina A. Vallejos
, Niko Beerenwinkel, Kieran R. Campbell, Ahmed Mahfouz
, Luca Pinello, Pavel Skums, Alexandros Stamatakis
, Camille Stephan-Otto Attolini, Samuel Aparicio, Jasmijn A. Baaijens
, Marleen Balvert, Buys de Barbanson, Antonio Cappuccio, Giacomo Corleone, Bas E. Dutilh
, Maria Florescu
, Victor Guryev, Rens Holmer
, Katharina Jahn, Thamar Jessurun Lobo
, Emma M. Keizer, Indu Khatri
, Szymon M. Kielbasa
, Jan O. Korbel, Alexey M. Kozlov
, Tzu-Hao Kuo, Boudewijn P. F. Lelieveldt, Ion I. Mandoiu
, John C. Marioni
, Tobias Marschall
, Felix Mölder
, Amir Niknejad, Lukasz Raczkowski, Marcel J. T. Reinders, Jeroen de Ridder
, Antoine-Emmanuel Saliba
, Antonios Somarakis, Oliver Stegle, Fabian J. Theis, Huan Yang, Alex Zelikovsky, Alice C. McHardy, Benjamin J. Raphael, Sohrab P. Shah, Alexander Schönhuth:
12 Grand Challenges in Single-Cell Data Science. PeerJ Prepr. 7: e27885 (2019) - 2018
- [j14]Ehsaneddin Asgari, Kiavash Garakani
, Alice C. McHardy
, Mohammad R. K. Mofrad:
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
, Alice C. McHardy
:
EDEN: evolutionary dynamics within environments. Bioinform. 33(20): 3292-3295 (2017) - [j12]Johannes Dröge
, Alexander Schönhuth
, Alice C. McHardy
:
A probabilistic model to recover individual genomes from metagenomes. PeerJ Comput. Sci. 3: e117 (2017) - 2016
- [j11]David Laehnemann
, Arndt Borkhardt, Alice Carolyn McHardy
:
Denoising DNA deep sequencing data - high-throughput sequencing errors and their correction. Briefings Bioinform. 17(1): 154-179 (2016) - [j10]I. Gregor, Alexander Schönhuth
, Alice Carolyn McHardy
:
Snowball: strain aware gene assembly of metagenomes. Bioinform. 32(17): 649-657 (2016) - [i1]Johannes Dröge
, Alexander Schönhuth, Alice Carolyn McHardy:
A probabilistic model to recover individual genomes from metagenomes. PeerJ Prepr. 4: e2626 (2016) - 2015
- [j9]Johannes Dröge
, I. Gregor, Alice Carolyn McHardy
:
Taxator-tk: precise taxonomic assignment of metagenomes by fast approximation of evolutionary neighborhoods. Bioinform. 31(6): 817-824 (2015) - [j8]Yang Bai
, Daniel B. Müller, Girish Srinivas, Ruben Garrido-Oter, Eva Potthoff, Matthias Rott, Nina Dombrowski
, Philipp C. Münch, Stijn Spaepen
, Mitja Remus-Emsermann
, Bruno Hüttel, Alice C. McHardy
, Julia A. Vorholt
, Paul Schulze-Lefert:
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
, Alice Carolyn McHardy
:
RidgeRace: ridge regression for continuous ancestral character estimation on phylogenetic trees. Bioinform. 30(17): 527-533 (2014) - 2012
- [j5]Johannes Dröge
, Alice Carolyn McHardy
:
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
, Laura Dietz, Alice Carolyn McHardy
:
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
, Alexander Goesmann
, Alfred Pühler
, Folker Meyer
:
Development of joint application strategies for two microbial gene finders. Bioinform. 20(10): 1622-1631 (2004)
Coauthor Index
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last updated on 2024-08-05 20:24 CEST by the dblp team
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