Alice C. McHardy

17 papers C 1Journal 15Unranked 1
YearRankTypeTitle / Venue / Authors
2024 J jnl
Assessing computational predictions of antimicrobial resistance phenotypes from microbial genomes.
Briefings Bioinform.
Kaixin Hu, Fernando Meyer, Zhi-Luo Deng, Ehsaneddin Asgari, Tzu-Hao Kuo, Philipp C. Münch, Alice C. McHardy
2024 — conf
SuperPos-Prompt: Enhancing Soft Prompt Tuning of Language Models with Superposition of Multi Token Embeddings.
ENLSP
Mohammad Ali Sadraei Javaheri, Ehsaneddin Asgari, Alice C. McHardy, Hamid R. Rabiee
2023 J jnl
GO Bench: shared hub for universal benchmarking of machine learning-based protein functional annotations.
Bioinform.
Andrew Dickson, Ehsaneddin Asgari, Alice C. McHardy, Mohammad R. K. Mofrad
2023 C conf
Neural Architecture Search for Genomic Sequence Data.
CIBCB
Amadeu Scheppach, Hüseyin Anil Gündüz, Emilio Dorigatti, Philipp C. Münch, Alice C. McHardy, Bernd Bischl, Mina Rezaei, Martin Binder
2022 J jnl
Scelestial: Fast and accurate single-cell lineage tree inference based on a Steiner tree approximation algorithm.
PLoS Comput. Biol.
Mohammad-Hadi Foroughmand-Araabi, Sama Goliaei, Alice C. McHardy
2022 J jnl
TripletProt: Deep Representation Learning of Proteins Based On Siamese Networks.
IEEE ACM Trans. Comput. Biol. Bioinform.
Esmaeil Nourani, Ehsaneddin Asgari, Alice C. McHardy, Mohammad R. K. Mofrad
2021 J jnl
Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research.
Briefings Bioinform.
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
2021 J jnl
EpitopeVec: linear epitope prediction using deep protein sequence embeddings.
Bioinform.
Akash Bahai, Ehsaneddin Asgari, Mohammad R. K. Mofrad, Andreas Kloetgen, Alice C. McHardy
2021 J jnl
Evaluating assembly and variant calling software for strain-resolved analysis of large DNA viruses.
Briefings Bioinform.
Zhi-Luo Deng, Akshay Dhingra, Adrian Fritz, Jasper Götting, Philipp C. Münch, Lars Steinbrück, Thomas Friedrich Schulz, Tina Ganzenmüller, Alice C. McHardy
2020 J jnl
Phylogeographic reconstruction using air transportation data and its application to the 2009 H1N1 influenza A pandemic.
PLoS Comput. Biol.
Susanne Reimering, Sebastian Muñoz, Alice C. McHardy
2019 J jnl
12 Grand Challenges in Single-Cell Data Science.
PeerJ Prepr.
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
2019 J jnl
DiTaxa: nucleotide-pair encoding of 16S rRNA for host phenotype and biomarker detection.
Bioinform.
Ehsaneddin Asgari, Philipp C. Münch, Till R. Lesker, Alice C. McHardy, Mohammad R. K. Mofrad
2019 J jnl
MicroPheno: predicting environments and host phenotypes from 16S rRNA gene sequencing using a k-mer based representation of shallow sub-samples.
Bioinform.
Ehsaneddin Asgari, Kiavash Garakani, Alice C. McHardy, Mohammad R. K. Mofrad
2018 J jnl
MicroPheno: predicting environments and host phenotypes from 16S rRNA gene sequencing using a k-mer based representation of shallow sub-samples.
Bioinform.
Ehsaneddin Asgari, Kiavash Garakani, Alice C. McHardy, Mohammad R. K. Mofrad
2017 J jnl
A probabilistic model to recover individual genomes from metagenomes.
PeerJ Comput. Sci.
Johannes Dröge, Alexander Schönhuth, Alice C. McHardy
2017 J jnl
EDEN: evolutionary dynamics within environments.
Bioinform.
Philipp C. Münch, Bärbel Stecher, Alice C. McHardy
2015 J jnl
Functional overlap of the
Nat.
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