Alice C. McHardy

According to our database, Alice C. McHardy authored at least 25 papers between 2004 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2024

SuperPos-Prompt: Enhancing Soft Prompt Tuning of Language Models with Superposition of Multi Token Embeddings.

MohammadAli SadraeiJavaeri, Ehsaneddin Asgari, Alice Carolyn McHardy, Hamid Reza Rabiee

CoRR, 2024

2023

GO Bench: shared hub for universal benchmarking of machine learning-based protein functional annotations.

Andrew Dickson, Ehsaneddin Asgari, Alice C. McHardy, Mohammad R. K. Mofrad

Bioinform., February, 2023

Neural Architecture Search for Genomic Sequence Data.

Amadeu Scheppach, Hüseyin Anil Gündüz, Emilio Dorigatti, Philipp C. Münch, Alice C. McHardy, Bernd Bischl, Mina Rezaei, Martin Binder

Proceedings of the IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, 2023

2022

TripletProt: Deep Representation Learning of Proteins Based On Siamese Networks.

Esmaeil Nourani, Ehsaneddin Asgari, Alice C. McHardy, Mohammad R. K. Mofrad

IEEE ACM Trans. Comput. Biol. Bioinform., 2022

Scelestial: Fast and accurate single-cell lineage tree inference based on a Steiner tree approximation algorithm.

Mohammad-Hadi Foroughmand-Araabi, Sama Goliaei, Alice C. McHardy

PLoS Comput. Biol., 2022

2021

EpitopeVec: linear epitope prediction using deep protein sequence embeddings.

Akash Bahai, Ehsaneddin Asgari, Mohammad R. K. Mofrad, Andreas Kloetgen, Alice C. McHardy

Bioinform., 2021

Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research.

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

Briefings Bioinform., 2021

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

Zhi-Luo Deng, Akshay Dhingra, Adrian Fritz, Jasper Götting, Philipp C. Münch, Lars Steinbrück, Thomas F. Schulz, Tina Ganzenmüller, Alice C. McHardy

Briefings Bioinform., 2021

2020

Phylogeographic reconstruction using air transportation data and its application to the 2009 H1N1 influenza A pandemic.

Susanne Reimering, Sebastian Muñoz, Alice C. McHardy

PLoS Comput. Biol., 2020

2019

12 Grand Challenges in Single-Cell Data Science.

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

PeerJ Prepr., 2019

DiTaxa: nucleotide-pair encoding of 16S rRNA for host phenotype and biomarker detection.

Ehsaneddin Asgari, Philipp C. Münch, Till R. Lesker, Alice C. McHardy, Mohammad R. K. Mofrad

Bioinform., 2019

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

Ehsaneddin Asgari, Kiavash Garakani, Alice C. McHardy, Mohammad R. K. Mofrad

Bioinform., 2019

2017

EDEN: evolutionary dynamics within environments.

Philipp C. Münch, Bärbel Stecher, Alice C. McHardy

Bioinform., 2017

2016

A probabilistic model to recover individual genomes from metagenomes.

Johannes Dröge, Alexander Schönhuth, Alice Carolyn McHardy

PeerJ Prepr., 2016

<i>Snowball</i>: strain aware gene assembly of metagenomes.

I. Gregor, Alexander Schönhuth, Alice Carolyn McHardy

Bioinform., 2016

Denoising DNA deep sequencing data - high-throughput sequencing errors and their correction.

David Laehnemann, Arndt Borkhardt, Alice Carolyn McHardy

Briefings Bioinform., 2016

2015

How to Grow a Computational Biology Lab.

Alice Carolyn McHardy

PLoS Comput. Biol., 2015

Functional overlap of the <i>Arabidopsis</i> leaf and root microbiota.

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

Nat., 2015

<i>Taxator-tk</i>: precise taxonomic assignment of metagenomes by fast approximation of evolutionary neighborhoods.

Johannes Dröge, I. Gregor, Alice Carolyn McHardy

Bioinform., 2015

2014

RidgeRace: ridge regression for continuous ancestral character estimation on phylogenetic trees.

Christina Kratsch, Alice Carolyn McHardy

Bioinform., 2014

2012

Inference of Genotype-Phenotype Relationships in the Antigenic Evolution of Human Influenza A (H3N2) Viruses.

Lars Steinbrück, Alice Carolyn McHardy

PLoS Comput. Biol., 2012

Taxonomic binning of metagenome samples generated by next-generation sequencing technologies.

Johannes Dröge, Alice Carolyn McHardy

Briefings Bioinform., 2012

2011

Allele dynamics plots for the study of evolutionary dynamics in viral populations.

Lars Steinbrück, Alice Carolyn McHardy

Nucleic Acids Res., 2011

Inferring functional modules of protein families with probabilistic topic models.

Sebastian G. A. Konietzny, Laura Dietz, Alice Carolyn McHardy

BMC Bioinform., 2011

2004

Development of joint application strategies for two microbial gene finders.

Alice Carolyn McHardy, Alexander Goesmann, Alfred Pühler, Folker Meyer

Bioinform., 2004