Alice C. McHardy

Publication Activity (10 Years)

Years Active: 2015-2023
Publications (10 Years): 15

Top Topics

Protein Function

Grand Challenges

Top Venues

Briefings Bioinform.

PLoS Comput. Biol.

Publications

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)
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)
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) (2022)
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)
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)
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) (2021)
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) (2021)
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)
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) (2019)
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 (2019)
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) (2019)
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) (2018)
Philipp C. Münch, Bärbel Stecher, Alice C. McHardy
EDEN: evolutionary dynamics within environments. Bioinform. 33 (20) (2017)
Johannes Dröge, Alexander Schönhuth, Alice C. McHardy
A probabilistic model to recover individual genomes from metagenomes. PeerJ Comput. Sci. 3 (2017)
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
leaf and root microbiota. Nat. 528 (7582) (2015)