List of works - Alice Carolyn McHardy

"Candidatus Paraporphyromonas polyenzymogenes" encodes multi-modular cellulases linked to the type IX secretion system

scientific article published in March 2018

'Candidatus Adiutrix intracellularis', an endosymbiont of termite gut flagellates, is the first representative of a deep-branching clade of Deltaproteobacteria and a putative homoacetogen.

scientific article

A Fréchet tree distance measure to compare phylogeographic spread paths across trees

scientific article published in Scientific Reports

A probabilistic model to recover individual genomes from metagenomes

scientific article

AMBER: Assessment of Metagenome BinnERs.

scientific article published in June 2018

Accurate and scalable variant calling from single cell DNA sequencing data with ProSolo

scientific article published on 18 November 2021

Accurate phylogenetic classification of variable-length DNA fragments

scientific article

Adaptation to herbivory by the Tammar wallaby includes bacterial and glycoside hydrolase profiles different from other herbivores

scientific article

Adaptive Mutations That Occurred during Circulation in Humans of H1N1 Influenza Virus in the 2009 Pandemic Enhance Virulence in Mice.

scientific article

Alignment-free genome tree inference by learning group-specific distance metrics

scientific article published on January 2013

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

scientific article

Alterations of microRNA and microRNA-regulated messenger RNA expression in germinal center B-cell lymphomas determined by integrative sequencing analysis

scientific article

An Integrated Metagenome Catalog Reveals New Insights into the Murine Gut Microbiome

scientific article published on 01 March 2020

Assessing taxonomic metagenome profilers with OPAL

scientific article published on 04 March 2019

Bioboxes: standardised containers for interchangeable bioinformatics software

scientific article

Biochemical and bioinformatic methods for elucidating the role of RNA-protein interactions in posttranscriptional regulation

scientific article

Bioinformatics Meets Virology: The European Virus Bioinformatics Center's Second Annual Meeting.

scientific article

Bioinformatics support for high-throughput proteomics

scientific article published on December 2003

Building a BRIDGE for the integration of heterogeneous data from functional genomics into a platform for systems biology

scientific article

CAMISIM: simulating metagenomes and microbial communities

scientific article published on 08 February 2019

CAMITAX: Taxon labels for microbial genomes

scientific article published on 01 January 2020

Cellular Importin-α3 Expression Dynamics in the Lung Regulate Antiviral Response Pathways against Influenza A Virus Infection

scientific article published on 01 April 2020

Characterisation of a stable laboratory co-culture of acidophilic nanoorganisms

scientific article

Comparative whole-genome analysis reveals artificial selection effects on Ustilago esculenta genome

scientific article published on 19 July 2017

Comparing expression level-dependent features in codon usage with protein abundance: an analysis of 'predictive proteomics'.

scientific article published in January 2004

Complete genome of the mutualistic, N2-fixing grass endophyte Azoarcus sp. strain BH72.

scientific article

Complete genome sequence of the myxobacterium Sorangium cellulosum

scientific article

Computational Strategies to Combat COVID-19: Useful Tools to Accelerate SARS-CoV-2 and Coronavirus Research

scientific article published on 23 May 2020

Computational prediction of vaccine strains for human influenza A (H3N2) viruses

scientific article

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

scientific article published on 04 November 2020

Consent insufficient for data release-Response

scientific article published on 01 May 2019

Corrigendum to: Biochemical and bioinformatic methods for elucidating the role of RNA-protein interactions in posttranscriptional regulation

scientific article published on 01 November 2019

Coupling of diversification and pH adaptation during the evolution of terrestrial Thaumarchaeota

scientific article

Critical Assessment of Metagenome Interpretation Enters the Second Round.

scientific article published on 10 July 2018

Critical Assessment of Metagenome Interpretation − a benchmark of computational metagenomics software

article

Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software.

scientific article published on 2 October 2017

Critical Assessment of Metagenome Interpretation: the second round of challenges

scientific article published in April 2022

De novo prediction of the genomic components and capabilities for microbial plant biomass degradation from (meta-)genomes

scientific article published on 15 February 2013

Defining seasonal marine microbial community dynamics

scientific article

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

scientific article

Detecting patches of protein sites of influenza A viruses under positive selection

scientific article published on 16 March 2012

Determination of antigenicity-altering patches on the major surface protein of human influenza A/H3N2 viruses

scientific article

Development of joint application strategies for two microbial gene finders

scientific article published on 26 February 2004

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

scientific article published on 01 July 2019

EDEN: Evolutionary Dynamics within Environments.

scientific article published on 16 June 2017

Eleven grand challenges in single-cell data science

scientific article published on 07 February 2020

Erratum: Corrigendum: Complete genome of the mutualistic, N2-fixing grass endophyte Azoarcus sp. strain BH72

scientific article published on 09 April 2007

Erratum: Survival trade-offs in plant roots during colonization by closely related beneficial and pathogenic fungi

scientific article published on 29 September 2016

Evolution of 2009 H1N1 influenza viruses during the pandemic correlates with increased viral pathogenicity and transmissibility in the ferret model

scientific article

Evolutionary Stabilization of Cooperative Toxin Production through a Bacterium-Plasmid-Phage Interplay

scientific article published on 21 July 2020

Finding Genes in Genome Sequence

scientific article published on January 2017

Finding genes in genome sequence

scientific article published on January 2008

From Genomes to Phenotypes: Traitar, the Microbial Trait Analyzer

scientific article

Functional overlap of the Arabidopsis leaf and root microbiota

scientific article published on 2 December 2015

GISMO--gene identification using a support vector machine for ORF classification

scientific article published on 14 December 2006

GenDB--an open source genome annotation system for prokaryote genomes

scientific article

Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis

scientific article

Genome-based analysis of biosynthetic aminotransferase genes of Corynebacterium glutamicum

scientific article published in September 2003

Genome-guided design of a defined mouse microbiota that confers colonization resistance against Salmonella enterica serovar Typhimurium

scientific article

Genomic variation and strain-specific functional adaptation in the human gut microbiome during early life.

scientific article published on 17 December 2018

Genomics and drug profiling of fatal TCF3-HLF-positive acute lymphoblastic leukemia identifies recurrent mutation patterns and therapeutic options

scientific article

Genomics and prevalence of bacterial and archaeal isolates from biogas-producing microbiomes

scientific article published on 13 November 2017

Hepatitis C reference viruses highlight potent antibody responses and diverse viral functional interactions with neutralising antibodies

scientific article published on 15 December 2020

High-resolution metagenomics targets specific functional types in complex microbial communities

scientific article published in September 2008

High-throughput miRNA and mRNA sequencing of paired colorectal normal, tumor and metastasis tissues and bioinformatic modeling of miRNA-1 therapeutic applications

scientific article (publication date: 2013)

How to Grow a Computational Biology Lab

scientific article published on 24 September 2015

Identification of Natural CRISPR Systems and Targets in the Human Microbiome

scientific article published on 16 November 2020

Improved metagenome assemblies and taxonomic binning using long-read circular consensus sequence data

scientific article

In Silico Vaccine Strain Prediction for Human Influenza Viruses

scientific article

Inference of genotype-phenotype relationships in the antigenic evolution of human influenza A (H3N2) viruses.

scientific article

Inference of phenotype-defining functional modules of protein families for microbial plant biomass degraders

scientific article

Inferring functional modules of protein families with probabilistic topic models. ⬇️

scientific article

Insights into Genome Plasticity and Pathogenicity of the Plant Pathogenic Bacterium Xanthomonas campestris pv. vesicatoria Revealed by the Complete Genome Sequence

scientific article

Investigation of different nitrogen reduction routes and their key microbial players in wood chip-driven denitrification beds.

scientific article

Isolation of Succinivibrionaceae implicated in low methane emissions from Tammar wallabies

scientific article

Meeting report: the terabase metagenomics workshop and the vision of an Earth microbiome project

scientific article

Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities

scientific article

Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite

scientific article (publication date: 22 November 2007)

Metagenomics and CAZyme Discovery

scientific article published on January 2017

Metagenomics of the Svalbard reindeer rumen microbiome reveals abundance of polysaccharide utilization loci

scientific article (publication date: 2012)

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

scientific article published on 01 March 2019

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

scientific article

Microbial genome-enabled insights into plant-microorganism interactions

scientific article published on 30 September 2014

Modular Traits of the Rhizobiales Root Microbiota and Their Evolutionary Relationship with Symbiotic Rhizobia

scholarly article published by Ryohei Thomas Nakano in 2018

Multiple syntrophic interactions in a terephthalate-degrading methanogenic consortium

scientific article

NFDI4Microbiota – national research data infrastructure for microbiota research

Neither black nor white: do altered intestinal microbiota reflect chronic liver disease severity?

scientific article published on 05 June 2020

Nobel nominators — which women will you suggest?

scientific article published on 18 January 2022

Novel Syntrophic Populations Dominate an Ammonia-Tolerant Methanogenic Microbiome.

scientific article published on 13 September 2016

Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins

scientific article

PTree: pattern-based, stochastic search for maximum parsimony phylogenies

scientific article published on 25 June 2013

Pediatric ALL relapses after allo-SCT show high individuality, clonal dynamics, selective pressure, and druggable targets

scientific article published on 01 October 2019

PhyloPythiaS+: a self-training method for the rapid reconstruction of low-ranking taxonomic bins from metagenomes

scientific article

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

scientific article published on 07 February 2020

Predicting antimicrobial resistance in Pseudomonas aeruginosa with machine learning-enabled molecular diagnostics

scientific article published on 12 February 2020

Probabilistic variable-length segmentation of protein sequences for discriminative motif discovery (DiMotif) and sequence embedding (ProtVecX)

scientific article published on 05 March 2019

Publisher Correction: Genomic variation and strain-specific functional adaptation in the human gut microbiome during early life

scientific article published on 01 March 2019

Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies

scientific article published in 2023

REGANOR

scientific article published on 01 January 2006

Rapid and accurate identification of ribosomal RNA sequences via deep learning

scientific article published on 01 June 2022

Reconstructing metabolic pathways of a member of the genus Pelotomaculum suggesting its potential to oxidize benzene to carbon dioxide with direct reduction of sulfate

scientific article published on 22 December 2016

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

scientific article

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

scientific article published in 2022

Short blocks from the noncoding parts of the human genome have instances within nearly all known genes and relate to biological processes

scholarly article

Snowball: strain aware gene assembly of metagenomes

scientific article

Software for Characterizing the Antigenic and Genetic Evolution of Human Influenza Viruses

scientific article published on 01 January 2018

Structure and function of the bacterial root microbiota in wild and domesticated barley.

scientific article

Structures and functions linked to genome-wide adaptation of human influenza A viruses

scientific article published on 18 April 2019

Survival trade-offs in plant roots during colonization by closely related beneficial and pathogenic fungi.

scientific article

Sweep Dynamics (SD) plots: Computational identification of selective sweeps to monitor the adaptation of influenza A viruses

scientific article published on 10 January 2018

T-cell acute lymphoblastic leukemia in infants has distinct genetic and epigenetic features compared to childhood cases

scientific article

Taxator-tk: precise taxonomic assignment of metagenomes by fast approximation of evolutionary neighborhoods.

scientific article

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

scientific article published on 31 July 2012

Taxonomic metagenome sequence assignment with structured output models

scientific article published on March 2011

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

scientific article published on 19 November 2019

The PARA-suite: PAR-CLIP specific sequence read simulation and processing

scientific article

The PhyloPythiaS web server for taxonomic assignment of metagenome sequences

scientific article

The amphioxus genome illuminates vertebrate origins and cephalochordate biology

scientific article

The complete Corynebacterium glutamicum ATCC 13032 genome sequence and its impact on the production of L-aspartate-derived amino acids and vitamins

scientific article

The genome sequence of the tomato-pathogenic actinomycete Clavibacter michiganensis subsp. michiganensis NCPPB382 reveals a large island involved in pathogenicity

scientific article (publication date: March 2008)

The impact of seasonal and year-round transmission regimes on the evolution of influenza A virus

scientific article published on 22 December 2010

The role of genomics in tracking the evolution of influenza A virus

scientific article

The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes

scientific article

Toward unrestricted use of public genomic data:

scientific article

Transcriptome-wide analysis uncovers the targets of the RNA-binding protein MSI2 and effects of MSI2's RNA-binding activity on IL-6 signaling

scientific article published in Journal of Biological Chemistry

Use of simulated data sets to evaluate the fidelity of metagenomic processing methods

scientific article

Viral bioinformatics

What's in the mix: phylogenetic classification of metagenome sequence samples

scientific article

YBX1 Indirectly Targets Heterochromatin-Repressed Inflammatory Response-Related Apoptosis Genes through Regulating CBX5 mRNA

scientific article published on 23 June 2020

List of works by Alice Carolyn McHardy

"Candidatus Paraporphyromonas polyenzymogenes" encodes multi-modular cellulases linked to the type IX secretion system

'Candidatus Adiutrix intracellularis', an endosymbiont of termite gut flagellates, is the first representative of a deep-branching clade of Deltaproteobacteria and a putative homoacetogen.

A Fréchet tree distance measure to compare phylogeographic spread paths across trees

A probabilistic model to recover individual genomes from metagenomes

AMBER: Assessment of Metagenome BinnERs.

Accurate and scalable variant calling from single cell DNA sequencing data with ProSolo

Accurate phylogenetic classification of variable-length DNA fragments

Adaptation to herbivory by the Tammar wallaby includes bacterial and glycoside hydrolase profiles different from other herbivores

Adaptive Mutations That Occurred during Circulation in Humans of H1N1 Influenza Virus in the 2009 Pandemic Enhance Virulence in Mice.

Alignment-free genome tree inference by learning group-specific distance metrics

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

Alterations of microRNA and microRNA-regulated messenger RNA expression in germinal center B-cell lymphomas determined by integrative sequencing analysis

An Integrated Metagenome Catalog Reveals New Insights into the Murine Gut Microbiome

Assessing taxonomic metagenome profilers with OPAL

Assessing taxonomic metagenome profilers with OPAL

Bioboxes: standardised containers for interchangeable bioinformatics software

Biochemical and bioinformatic methods for elucidating the role of RNA-protein interactions in posttranscriptional regulation

Bioinformatics Meets Virology: The European Virus Bioinformatics Center's Second Annual Meeting.

Bioinformatics support for high-throughput proteomics

Building a BRIDGE for the integration of heterogeneous data from functional genomics into a platform for systems biology

CAMISIM: simulating metagenomes and microbial communities

CAMITAX: Taxon labels for microbial genomes

Cellular Importin-α3 Expression Dynamics in the Lung Regulate Antiviral Response Pathways against Influenza A Virus Infection

Characterisation of a stable laboratory co-culture of acidophilic nanoorganisms

Comparative whole-genome analysis reveals artificial selection effects on Ustilago esculenta genome

Comparing expression level-dependent features in codon usage with protein abundance: an analysis of 'predictive proteomics'.

Complete genome of the mutualistic, N2-fixing grass endophyte Azoarcus sp. strain BH72.

Complete genome sequence of the myxobacterium Sorangium cellulosum

Computational Strategies to Combat COVID-19: Useful Tools to Accelerate SARS-CoV-2 and Coronavirus Research

Computational prediction of vaccine strains for human influenza A (H3N2) viruses

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

Consent insufficient for data release-Response

Corrigendum to: Biochemical and bioinformatic methods for elucidating the role of RNA-protein interactions in posttranscriptional regulation

Coupling of diversification and pH adaptation during the evolution of terrestrial Thaumarchaeota

Critical Assessment of Metagenome Interpretation Enters the Second Round.

Critical Assessment of Metagenome Interpretation − a benchmark of computational metagenomics software

Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software.

Critical Assessment of Metagenome Interpretation: the second round of challenges

De novo prediction of the genomic components and capabilities for microbial plant biomass degradation from (meta-)genomes

Defining seasonal marine microbial community dynamics

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

Detecting patches of protein sites of influenza A viruses under positive selection

Determination of antigenicity-altering patches on the major surface protein of human influenza A/H3N2 viruses

Development of joint application strategies for two microbial gene finders

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

EDEN: Evolutionary Dynamics within Environments.

Eleven grand challenges in single-cell data science

Erratum: Corrigendum: Complete genome of the mutualistic, N2-fixing grass endophyte Azoarcus sp. strain BH72

Erratum: Survival trade-offs in plant roots during colonization by closely related beneficial and pathogenic fungi

Evolution of 2009 H1N1 influenza viruses during the pandemic correlates with increased viral pathogenicity and transmissibility in the ferret model

Evolutionary Stabilization of Cooperative Toxin Production through a Bacterium-Plasmid-Phage Interplay

Finding Genes in Genome Sequence

Finding genes in genome sequence

From Genomes to Phenotypes: Traitar, the Microbial Trait Analyzer

Functional overlap of the Arabidopsis leaf and root microbiota

GISMO--gene identification using a support vector machine for ORF classification

GenDB--an open source genome annotation system for prokaryote genomes

Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis

Genome-based analysis of biosynthetic aminotransferase genes of Corynebacterium glutamicum

Genome-guided design of a defined mouse microbiota that confers colonization resistance against Salmonella enterica serovar Typhimurium

Genomic variation and strain-specific functional adaptation in the human gut microbiome during early life.

Genomics and drug profiling of fatal TCF3-HLF-positive acute lymphoblastic leukemia identifies recurrent mutation patterns and therapeutic options

Genomics and prevalence of bacterial and archaeal isolates from biogas-producing microbiomes

Hepatitis C reference viruses highlight potent antibody responses and diverse viral functional interactions with neutralising antibodies

High-resolution metagenomics targets specific functional types in complex microbial communities

High-throughput miRNA and mRNA sequencing of paired colorectal normal, tumor and metastasis tissues and bioinformatic modeling of miRNA-1 therapeutic applications

How to Grow a Computational Biology Lab

Identification of Natural CRISPR Systems and Targets in the Human Microbiome

Improved metagenome assemblies and taxonomic binning using long-read circular consensus sequence data

In Silico Vaccine Strain Prediction for Human Influenza Viruses

Inference of genotype-phenotype relationships in the antigenic evolution of human influenza A (H3N2) viruses.

Inference of phenotype-defining functional modules of protein families for microbial plant biomass degraders

Inferring functional modules of protein families with probabilistic topic models. ⬇️

Insights into Genome Plasticity and Pathogenicity of the Plant Pathogenic Bacterium Xanthomonas campestris pv. vesicatoria Revealed by the Complete Genome Sequence

Investigation of different nitrogen reduction routes and their key microbial players in wood chip-driven denitrification beds.

Isolation of Succinivibrionaceae implicated in low methane emissions from Tammar wallabies

Meeting report: the terabase metagenomics workshop and the vision of an Earth microbiome project

Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities

Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite