Skip to Main Content

Author Details

Alice C McHardy
Computational Biology of Infection Research, Helmholtz Centre for Infection Research
2003
136
53
PMIDPaper TitleJournal TitlePublished Year
36786404GO Bench: shared hub for universal benchmarking of machine learning-based protein functional annotations.Bioinformatics2023
37572667CYP19A1 mediates severe SARS-CoV-2 disease outcome in males.Cell Rep Med2023
37783751Challenges and opportunities in sharing microbiome data and analyses.Nat Microbiol2023
37696966A self-supervised deep learning method for data-efficient training in genomics.Commun Biol2023
37279755Pulsed antibiotic treatments of gnotobiotic mice manifest in complex bacterial community dynamics and resistance effects.Cell Host Microbe2023
36697862Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies.Nature2023
36786404GO Bench: shared hub for universal benchmarking of machine learning-based protein functional annotations.Bioinformatics2023
37696966A self-supervised deep learning method for data-efficient training in genomics.Commun Biol2023
37783751Challenges and opportunities in sharing microbiome data and analyses.Nat Microbiol2023
37572667CYP19A1 mediates severe SARS-CoV-2 disease outcome in males.Cell Rep Med2023
37279755Pulsed antibiotic treatments of gnotobiotic mice manifest in complex bacterial community dynamics and resistance effects.Cell Host Microbe2023
36697862Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies.Nature2023
34460382TripletProt: Deep Representation Learning of Proteins Based On Siamese Networks.IEEE/ACM Trans Comput Biol Bioinform2022
36042406Crowdsourced benchmarking of taxonomic metagenome profilers: lessons learned from the sbv IMPROVER Microbiomics challenge.BMC Genomics2022
35951662Scelestial: Fast and accurate single-cell lineage tree inference based on a Steiner tree approximation algorithm.PLoS Comput Biol2022
35320064Peptide microarrays coupled to machine learning reveal individual epitopes from human antibody responses with neutralizing capabilities against SARS-CoV-2.Emerg Microbes Infect2022
34460382TripletProt: Deep Representation Learning of Proteins Based On Siamese Networks.IEEE/ACM Trans Comput Biol Bioinform2022
35188571Rapid and accurate identification of ribosomal RNA sequences via deep learning.Nucleic Acids Res2022
36042406Crowdsourced benchmarking of taxonomic metagenome profilers: lessons learned from the sbv IMPROVER Microbiomics challenge.BMC Genomics2022
35951662Scelestial: Fast and accurate single-cell lineage tree inference based on a Steiner tree approximation algorithm.PLoS Comput Biol2022
35320064Peptide microarrays coupled to machine learning reveal individual epitopes from human antibody responses with neutralizing capabilities against SARS-CoV-2.Emerg Microbes Infect2022
35188571Rapid and accurate identification of ribosomal RNA sequences via deep learning.Nucleic Acids Res2022
32503844Neither black nor white: do altered intestinal microbiota reflect chronic liver disease severity?Gut2021
34180989EpitopeVec: linear epitope prediction using deep protein sequence embeddings.Bioinformatics2021
34020538Evaluating assembly and variant calling software for strain-resolved analysis of large DNA viruses.Brief Bioinform2021
34281604Haploflow: strain-resolved de novo assembly of viral genomes.Genome Biol2021
33532769Haploflow: Strain-resolved <i>de novo</i> assembly of viral genomes.bioRxiv2021
34042900Needs for an Integration of Specific Data Sources and Items - First Insights of a National Survey Within the German Center for Infection Research.Stud Health Technol Inform2021
33649565Tutorial: assessing metagenomics software with the CAMI benchmarking toolkit.Nat Protoc2021
33147627Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research.Brief Bioinform2021
32503844Neither black nor white: do altered intestinal microbiota reflect chronic liver disease severity?Gut2021
33217332Identification of Natural CRISPR Systems and Targets in the Human Microbiome.Cell Host Microbe2021
33323394Hepatitis C reference viruses highlight potent antibody responses and diverse viral functional interactions with neutralising antibodies.Gut2021
34795237Accurate and scalable variant calling from single cell DNA sequencing data with ProSolo.Nat Commun2021
34789871Reporting guidelines for human microbiome research: the STORMS checklist.Nat Med2021
33649565Tutorial: assessing metagenomics software with the CAMI benchmarking toolkit.Nat Protoc2021
33532769Haploflow: Strain-resolved <i>de novo</i> assembly of viral genomes.bioRxiv2021
34789871Reporting guidelines for human microbiome research: the STORMS checklist.Nat Med2021
34795237Accurate and scalable variant calling from single cell DNA sequencing data with ProSolo.Nat Commun2021
34020538Evaluating assembly and variant calling software for strain-resolved analysis of large DNA viruses.Brief Bioinform2021
34042900Needs for an Integration of Specific Data Sources and Items - First Insights of a National Survey Within the German Center for Infection Research.Stud Health Technol Inform2021
34180989EpitopeVec: linear epitope prediction using deep protein sequence embeddings.Bioinformatics2021
34281604Haploflow: strain-resolved de novo assembly of viral genomes.Genome Biol2021
33217332Identification of Natural CRISPR Systems and Targets in the Human Microbiome.Cell Host Microbe2021
33323394Hepatitis C reference viruses highlight potent antibody responses and diverse viral functional interactions with neutralising antibodies.Gut2021
33147627Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research.Brief Bioinform2021
32130896An Integrated Metagenome Catalog Reveals New Insights into the Murine Gut Microbiome.Cell Rep2020
31909794CAMITAX: Taxon labels for microbial genomes.Gigascience2020
32320654Cellular Importin-α3 Expression Dynamics in the Lung Regulate Antiviral Response Pathways against Influenza A Virus Infection.Cell Rep2020
32130896An Integrated Metagenome Catalog Reveals New Insights into the Murine Gut Microbiome.Cell Rep2020
  • 1 - 50 of 272

Recommended Authors

Migun Shakya
Los Alamos National Laboratory
Career Start Year 2012
Number of shared co-authors 2
James J Davis
University of Chicago
Career Start Year 2010
Number of shared co-authors 9
Chien-Chi Lo
Los Alamos National Laboratory
Career Start Year 2009
Number of shared co-authors 1
Salvador Capella-Gutierrez
Spanish National Bioinformatics Institute (INB/ELIXIR-ES)
Career Start Year 2009
Number of shared co-authors 15
Fangfang Xia
University of Chicago
Career Start Year 2007
Number of shared co-authors 12
Davide Albanese
Fondazione Edmund Mach
Career Start Year 2006
Number of shared co-authors 14
Wataru Iwasaki
the University of Tokyo
Career Start Year 2006
Number of shared co-authors 7
Gail L Rosen
Drexel University
Career Start Year 2006
Number of shared co-authors 6
Bonnie L Hurwitz
The University of Arizona
Career Start Year 2006
Number of shared co-authors 8
Paolo Ribeca
The James Hutton Institute
Career Start Year 2006
Number of shared co-authors 7
Christopher J Fields
University of Illinois Urbana-Champaign
Career Start Year 2005
Number of shared co-authors 0
Maulik Shukla
University of Chicago
Career Start Year 2003
Number of shared co-authors 12
Adam M Phillippy
National Human Genome Research Institute, National Institutes of Health
Career Start Year 2002
Number of shared co-authors 6
Paramvir S Dehal
Lawrence Berkeley National Laboratory
Career Start Year 2001
Number of shared co-authors 13
Samuel V Angiuoli
Personal Genome Diagnostics Inc.
Career Start Year 2001
Number of shared co-authors 7
Weizhong Li
J. Craig Venter Institute
Career Start Year 2000
Number of shared co-authors 8
Haixu Tang
Indiana University
Career Start Year 2000
Number of shared co-authors 7
Jonathan Crabtree
Institute for Genome Sciences, University of Maryland School of Medicine
Career Start Year 1998
Number of shared co-authors 8
Eric J Alm
Massachusetts Institute of Technology 21 Ames St. Cambridge
Career Start Year 1998
Number of shared co-authors 19
Shibu Yooseph
University of Central Florida
Career Start Year 1998
Number of shared co-authors 15
Nicholas J Loman
University of Birmingham
Career Start Year 1998
Number of shared co-authors 5
Thomas Junier
Institute of Biology, University of Neuchatel
Career Start Year 1998
Number of shared co-authors 5
Ana Tereza Ribeiro de Vasconcelos
The National Laboratory for Scientific Computing (LNCC)
Career Start Year 1997
Number of shared co-authors 4
Thomas Brettin
University of Chicago
Career Start Year 1996
Number of shared co-authors 19
James A Foster
University of Idaho
Career Start Year 1996
Number of shared co-authors 3
Evgeny M Zdobnov
University of Geneva Medical School
Career Start Year 1995
Number of shared co-authors 13
Fiona S L Brinkman
Simon Fraser University
Career Start Year 1995
Number of shared co-authors 6
Granger Sutton
J. Craig Venter Institute
Career Start Year 1993
Number of shared co-authors 10
Steven L Salzberg
Center for Computational Biology, Johns Hopkins University
Career Start Year 1992
Number of shared co-authors 27
Pavel A Pevzner
University of California
Career Start Year 1987
Number of shared co-authors 20

Collaborators

Andreas Bremges
Co-authored papers 15
Folker Meyer
Institute for Artificial Intelligence, University of Duisburg-Essen
Co-authored papers 15
Arndt Borkhardt
Hematology and Clinical Immunology, Heinrich Heine University Dusseldorf
Co-authored papers 11
Alexander Goesmann
Co-authored papers 11
Adrian Fritz
Co-authored papers 10
Ehsaneddin Asgari
University of California berkeley
Co-authored papers 10
Alexander Sczyrba
Center for Biotechnology (CeBiTec), Bielefeld University, Universitatsstrasse 27
Co-authored papers 10
Mohammad R K Mofrad
University of California Berkeley
Co-authored papers 9
Ruben Garrido-Oter
Co-authored papers 8
Paul Schulze-Lefert
Co-authored papers 8
Johannes Dröge
Co-authored papers 8
Ivan Gregor
Co-authored papers 7
Nikos C Kyrpides
Co-authored papers 7
Rob Knight
University of California
Co-authored papers 6
Curtis Huttenhower
Broad Institute of MIT and Harvard
Co-authored papers 6
Fernando Meyer
Co-authored papers 5
Peter Belmann
Co-authored papers 5
Asaf Salamov
US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory
Co-authored papers 4
Christopher Quince
Co-authored papers 4
Jeroen Raes
KU Leuven - University of Leuven
Co-authored papers 3
Robert D Finn
European Bioinformatics Institute
Co-authored papers 3
Aaron E Darling
Co-authored papers 3
Ute Fischer
Hematology and Clinical Immunology, Heinrich Heine University Dusseldorf
Co-authored papers 3
Peter Hofmann
Co-authored papers 3
Jan O Korbel
European Bioinformatics Institute (EMBL-EBI)
Co-authored papers 3
Moran Yassour
Co-authored papers 3
Hector Garcia Martin
Lawrence Berkeley National Laboratory
Co-authored papers 3
David Koslicki
and the Huck Institutes of the Life Sciences, Penn State University, University Park
Co-authored papers 3
Peter J Turnbaugh
University of California san francisco
Co-authored papers 3
Jack A Gilbert
Scripps Institution of Oceanography, University of California San Diego
Co-authored papers 3
Release 1.2