Bioinformatik der Infektionsforschung
Die Arbeitsgruppe “Bioinformatik der Infektionsforschung” erforscht mit computergestützten Techniken das menschliche Mikrobiom, virale und bakterielle Pathogene sowie menschliche Zelllinien anhand von großen biologischen und epidemiologischen Datensätzen. Durch die Analyse von Metaom-, Populationsgenom- und Einzelzellgenomdaten erzeugen wir experimentell überprüfbare Hypothesen, wie z.b. welche Veränderungen an Proteinen oder welche Gene assoziiert sind mit dem Auftreten einer Krankheit, von Antibiotikaresistenzen oder dem Ausweichen des Immunschutzes durch Pathogene. Wir arbeiten mit experimentellen Kollaborationspartnern zusammen, um unsere Erkenntnisse zu verifizieren und deren Translation in die medizinische Diagnostik und Behandlung zu fördern. Um die Forschungsziele zu erreichen, entwickelt die Arbeitsgruppe auch neue Algorithmen und Bioinformatik-Software.
Leitung
Ausgewählte Publikationen
- A. Sczyrba*, P. Hofmann*, P. Belmann*, D. Koslicki, S. Janssen, J. Droge, I. Gregor, S. Majda, J. Fiedler, E. Dahms, A. Bremges, A. Fritz, R. Garrido-Oter, T. Sparholt Jorgensen, N. Shapiro, P. D. Blood, A. Gurevich, Y. Bai, D. Turaev, M. Z. DeMaere, R. Chikhi, N. Nagarajan, C. Quince, F. Meyer, Monika Balvočiūtė, L. H. Hansen, S. J. Sorensen, B. K. H. Chia, B. Denis, J. L. Froula, Z. Wang, R. Egan, D. D. Kang, J. J. Cook, C. Deltel, M. Beckstette, C. Lemaitre, P. Peterlongo, G. Rizk, D. Lavenier, Y.-W. Wu, S. W. Singer, C. Jain, M. Strous, H. Klingenberg, P. Meinicke, M. Barton, T. Lingner, H.-H. Lin, Y.-C. Liao, G. Gueiros Z. Silva, D. A. Cuevas, R. A. Edwards, S. Saha, V. C. Piro, B. Y. Renard, M. Pop, H.-P. Klenk, M. Goker, N. Kyrpides, T. Woyke, J. A. Vorholt, P. Schulze-Lefert, E. M. Rubin, A. E. Darling, T. Rattei, A. C. McHardy (*shared first authors)
Critical Assessment of Metagenome Interpretation − a benchmark of metagenomics software.
Nat Methods 2017, 14: 1063 - E. Asgari, P. C. Munch, T. R. Lesker, A. C. McHardy*, M. R. K. Mofrad* (*shared last authors)
DiTaxa: Nucleotide-pair encoding of 16S rRNA for host phenotype and biomarker detection.
Bioinformatics 2018, Epub: bty954 - F. Meyer, A. Bremges, P. Belmann, S. Janssen, A. C. McHardy*, D. Koslicki* (*shared last authors)
Assessing taxonomic metagenome profilers with OPAL.
Genome Biol 2019, 20:51 - A. Fritz, P. Hofmann, S. Majda, E. Dahms, J. Droge, J. Fiedler, T. R. Lesker, P. Belmann, M. Z. DeMaere, A. E. Darling, A. Sczyrba, A. Bremges, A. C. McHardy
CAMISIM: simulating metagenomes and microbial communities.
Microbiome 2019, 7:17
Publikationen
2019
- T.R. Klingen, J. Loers, S. Stanelle-Bertram, G. Gabriel, A. C. McHardy
Structures and functions linked to genome-wide adaptation of human influenza A viruses.
Sci Rep 2019, 9:6267 - R. I. Amann, S. Baichoo, B. J. Blencowe, P. Bork, M. Borodovsky, C. Brooksbank, P. S. G. Chain, R. R. Colwell, D. G. Daffonchio, A. Danchin, V. de Lorenzo, P. C. Dorrestein, R. D. Finn, C. M. Fraser, J. A. Gilbert, S. J. Hallam, P. Hugenholtz, J. P. A. Ioannidis, J. K. Jansson, J. F. Kim, H.-P. Klenk, M. G. Klotz, R. Knight, K. T. Konstantinidis, N. C. Kyrpides, C. E. Mason, A. C. McHardy, F. Meyer, C. A. Ouzounis, A. A. N. Patrinos, M. Podar, K. S. Pollard, J. Ravel, A. R. Munoz, R. J. Roberts, R. Rossello-Mora, S.-A. Sansone, P. D. Schloss, L. M. Schriml, J. C. Setubal, R. Sorek, R. L. Stevens, J. M. Tiedje, A. Turjanski, G. W. Tyson, D. W. Ussery, G. M. Weinstock, O. White, W. B. Whitman, I. Xenarios
Toward unrestricted use of public genomic data.
Science 2019, 363:350 - T. Vatanen, D. R. Plichta, J. Somani, P. C. Munch, T. D. Arthur, A. B. Hall, S. Rudolf, E. J. Oakeley, X. Ke, R. A. Young, H. J. Haiser, R. Kolde, M. Yassour, K. Luopajarvi, H. Siljander, S. M. Virtanen, J. Ilonen, R. Uibo, V. Tillmann, S. Mokurov, N. Dorshakova, J. A. Porter, A. C. McHardy, H. Lahdesmaki, H. Vlamakis, C. Huttenhower, M. Knip, R. J. Xavier
Genomic variation and strain-specific functional adaptation in the human gut microbiome during early life.
Nat Microbiol 2019, 4:470 - F. Meyer, A. Bremges, P. Belmann, S. Janssen, A. C. McHardy*, D. Koslicki* (*shared last authors)
Assessing taxonomic metagenome profilers with OPAL.
Genome Biol 2019, 20:51 - E. Asgari, A. C. McHardy, M. R. K. Mofrad
Probabilistic variable-length segmentation of protein sequences for discriminative motif discovery (DiMotif) and sequence embedding (ProtVecX).
Sci Rep 2019, 9:3577 - A. Fritz, P. Hofmann, S. Majda, E. Dahms, J. Droge, J. Fiedler, T. R. Lesker, P. Belmann, M. Z. DeMaere, A. E. Darling, A. Sczyrba, A. Bremges, A. C. McHardy
CAMISIM: simulating metagenomes and microbial communities.
Microbiome 2019, 7:17
2018
- E. Asgari, P. C. Munch, T. R. Lesker, A. C. McHardy*, M. R. K. Mofrad* (*shared last authors)
DiTaxa: Nucleotide-pair encoding of 16S rRNA for host phenotype and biomarker detection.
Bioinformatics 2018, Epub: bty954 - S. Duggimpudi, A. Kloetgen, S. K. Maney, P. C. Munch, K. Hezaveh, H. Shaykhalishahi, W. Hoyer, A. C. McHardy, P. A. Lang, A. Borkhardt, J. I. Hoell
Transcriptome-wide analysis uncovers the targets of the RNA-binding protein MSI2 and effects of MSI2's RNA-binding activity on IL-6 signaling.
J Biol Chem 2018, 293: 15359 - S. Reimering, A. C. McHardy
Software for Characterizing the Antigenic and Genetic Evolution of Human Influenza Viruses.
Methods Mol Biol 2018, 1836: 551 - S. Reimering, S. Muñoz, A. C. McHardy
A Fréchet tree distance measure to compare phylogeographic spread paths across trees.
Sci Rep 2018, 8: 17000 - J. I. Hoell, S. Ginzel, M. Kuhlen, A. Klötgen, M. Gombert, U. Fischer, D. Schäfer, M. Stanulla, M. Schrappe, U. z. Stadt, P. Bader, F. Babor, F. Schuster, B. Strahm, J. Alten, A. Moericke, G. Escherich, A. v. Stackelberg, R. Thiele, A. C. McHardy, C. Peters, C. Eckert, A. Borkhardt, R. Meisel
Whole-Exome-Sequencing identifiziert hohe Plastizität, Selektionsdruck und „druggable targets“ in Leukämiezellen pädiatrischer ALL Rezidive nach allogener Stammzelltransplantation.
Monatsschr Kinderheilkd. 2018, 166: 648 - A. E. Naas, L. M. Solden, A. D. Norbeck, H. Brewer, L. H. Hagen, I. M. Heggenes, A. C. McHardy, R. I. Mackie, L. Paša-Tolić, M. Ø. Arntzen, V. G. H. Eijsink, N. M. Koropatkin, M. Hess, K. C. Wrighton, P. B. Pope
"Candidatus Paraporphyromonas polyenzymogenes" encodes multi-modular cellulases linked to the type IX secretion system.
Microbiome 2018, 6: 44 - E. Asgari, K. Garakani, A. C. McHardy, M. R. K. Mofrad
MicroPheno: predicting environments and host phenotypes from 16S rRNA gene sequencing using a k-mer based representation of shallow sub-samples.
Bioinformatics 2018, 34: i32 - A. Bremges, A. C. McHardy
Critical Assessment of Metagenome Interpretation Enters the Second Round.
mSystems 2018, 3: e00103 - R. Garrido-Oter, R. T. Nakano, N. Dombrowski, K. W. Ma, A. C. McHardy, P. Schulze-Lefert
Modular Traits of the Rhizobiales Root Microbiota and Their Evolutionary Relationship with Symbiotic Rhizobia.
Cell Host Microbe 2018, 24: 155 - B. Ibrahim, K. Arkhipova, A. C. Andeweg, S. Posada-Cespedes, F. Enault, A. Gruber, E. V. Koonin, A. Kupczok, P. Lemey, A. C. McHardy, D. P. McMahon, B. E. Pickett, D. L. Robertson, R. H. Scheuermann, A. Zhernakova, M. P. Zwart, A. Schonhuth, B. E. Dutilh, M. Marz
Bioinformatics Meets Virology: The European Virus Bioinformatics Center's Second Annual Meeting.
Viruses 2018, 10: E256 - F. Meyer, P. Hofmann, P. Belmann, R. Garrido-Oter, A. Fritz, A. Sczyrba, A. C. McHardy
AMBER: Assessment of Metagenome BinnERs.
GigaScience 2018, 7 - T. R. Klingen*, S. Reimering*, J. Loers, K. Mooren, F. Klawonn, T. Krey, G. Gabriel, A. C. McHardy (*shared first authors)
Sweep Dynamics (SD) plots: Computational identification of selective sweeps to monitor the adaptation of influenza A viruses.
Sci Rep 2018, 8: 373
2017
- X. Dong, J. Dröge, C. von Toerne, S. Marozava, A.C. McHardy, R.U. Meckenstock
Reconstructing metabolic pathways of a member of the genus Pelotomaculum suggesting its potential to oxidize benzene to carbon dioxide with direct reduction of sulfate.
FEMS Microbiol Ecol 2017, 93: fiw254 - V. Griessmeier, A. Bremges, A. C. McHardy, J. Gescher
Investigation of different nitrogen reduction routes and their key microbial players in wood chip-driven denitrification beds.
Sci Rep 2017, 7: 17028 - I. Maus*, A. Bremges*, Y. Stolze, S. Hahnke, K. G. Cibis, D. E. Koeck, Y. S. Kim, J. Kreubel, J. Hassa, D. Wibberg, A. Weimann, S. Off, R. Stantscheff, V. V. Zverlov, W. H. Schwarz, H. König, W. Liebl, P. Scherer, A. C. McHardy, A. Sczyrba, M. Klocke, A. Pühler, A. Schlüter (*shared first authors)
Genomics and prevalence of bacterial and archaeal isolates from biogas-producing microbiomes.
Biotechnol Biofuels 2017, 10: 264 - A. Sczyrba*, P. Hofmann*, P. Belmann*, D. Koslicki, S. Janssen, J. Droge, I. Gregor, S. Majda, J. Fiedler, E. Dahms, A. Bremges, A. Fritz, R. Garrido-Oter, T. Sparholt Jorgensen, N. Shapiro, P. D. Blood, A. Gurevich, Y. Bai, D. Turaev, M. Z. DeMaere, R. Chikhi, N. Nagarajan, C. Quince, F. Meyer, Monika Balvočiūtė, L. H. Hansen, S. J. Sorensen, B. K. H. Chia, B. Denis, J. L. Froula, Z. Wang, R. Egan, D. D. Kang, J. J. Cook, C. Deltel, M. Beckstette, C. Lemaitre, P. Peterlongo, G. Rizk, D. Lavenier, Y.-W. Wu, S. W. Singer, C. Jain, M. Strous, H. Klingenberg, P. Meinicke, M. Barton, T. Lingner, H.-H. Lin, Y.-C. Liao, G. Gueiros Z. Silva, D. A. Cuevas, R. A. Edwards, S. Saha, V. C. Piro, B. Y. Renard, M. Pop, H.-P. Klenk, M. Goker, N. Kyrpides, T. Woyke, J. A. Vorholt, P. Schulze-Lefert, E. M. Rubin, A. E. Darling, T. Rattei, A. C. McHardy (*shared first authors)
Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software.
Nat Methods 2017, 14: 1063 - T. R. Klingen*, S. Reimering*, C. A. Guzman, A. C. McHardy (*shared first authors)
In Silico Vaccine Strain Prediction for Human Influenza Viruses.
Trends Microbiol 2017, 26: 119 - Z. Ye, Y. Pan, Y. Zhang, H. Cui, G. Jin, A. C. McHardy, L. Fan, X. Yu
Comparative whole-genome analysis reveals artificial selection effects on Ustilago esculenta genome.
DNA Res 2017, 24: 635 - P.C. Münch, B. Stecher, A.C. McHardy
EDEN: evolutionary dynamics within environments.
Bioinformatics 2017, 33: 3292J. - J. Dröge, A. Schönhut, A.C. McHardy
A probabilistic model to recover individual genomes from metagenomes.
PeerJ Computer Science 2017, 3: 117 - A.C. McHardy, A. Klötgen
Finding Genes in Genome Sequence.
Methods Mol Biol 2017, 1525: 271 - S. Krause, A. Bremges, P. C. Münch, A. C. McHardy, J. Gescher.
Characterisation of a stable laboratory co-culture of acidophilic nanoorganisms.
Sci Rep 2017, 7: 3289 - M. Doerrenberg, A. Kloetgen, K. Hezaveh, W. Wössmann, K. Bleckmann, M. Stanulla, M. Schrappe, A.C. McHardy, A. Borkhardt, I. Hoell Jessica
T-cell acute lymphoblastic leukemia in infants has distinct genetic and epigenetic features compared to childhood cases.
Genes Chromosomes Cancer 2017, 56: 159 - B.J. Kunath, A. Bremges, A. Weimann, A.C. McHardy, P.B. Pope
Metagenomics and CAZyme Discovery.
Methods Mol Biol 2017, 1588: 255
2016
- A. Weimann, K. Mooren, J. Frank, P.B. Pope, A. Bremges, A.C. McHardy
From Genomes to Phenotypes: Traitar, the Microbial Trait Analyzer.
mSystems 2016, 1: e00101 - A. Otte, A.C. Marriott, C. Dreier, B. Dove, K. Mooren, T.R. Klingen, M. Sauter, K.A. Thompson, A. Bennett, K. Klingel, D. van Riel, A.C. McHardy, M.W. Carroll, G. Gabriel
Evolution of 2009 H1N1 influenza viruses during the pandemic correlates with increased viral pathogenicity and transmissibility in the ferret model.
Sci Rep 2016, 6: 28583 - A. Klötgen, A. Borkhardt, J.I. Hoell, A.C. McHardy
The PARA-suite: PAR-CLIP specific sequence read simulation and processing.
PeerJ 2016, 4: e2619 - K. Hezaveh, A. Kloetgen, S.H. Bernhart, K.D. Mahapatra, D. Lenze, J. Richter, A. Haake, A.K. Bergmann, B. Brors, B. Burkhardt, A. Claviez, H.G. Drexler, R. Eils, S. Haas, S. Hoffmann, D. Karsch, W. Klapper, K. Kleinheinz, J. Korbel, H. Kretzmer, M. Kreuz, R. Kuppers, C. Lawerenz, E. Leich, M. Loeffler, L. Mantovani-Loeffler, C. Lopez, A.C. McHardy, P. Moller, M. Rohde, P. Rosenstiel, A. Rosenwald, M. Schilhabel, M. Schlesner, I. Scholz, P.F. Stadler, S. Stilgenbauer, S. Sungalee, M. Szczepanowski, L. Trumper, M.A. Weniger, R. Siebert, A. Borkhardt, M. Hummel, J.I. Hoell
Alterations of miRNAs and miRNA-regulated mRNA expression in GC B cell lymphomas determined by integrative sequencing analysis.
Haematologica 2016, 101: 1380 - J.A. Frank, M.O. Arntzen, L. Sun, L.H. Hagen, A.C. McHardy, S.J. Horn, V.G. Eijsink, A. Schnürer, P.B. Pope
Novel Syntrophic Populations Dominate an Ammonia-Tolerant Methanogenic Microbiome.
mSystems 2016, 1: e00092 - S. Brugiroux, M. Beutler, C. Pfann, D. Garzetti, H.J. Ruscheweyh, D. Ring, M. Diehl, S. Herp, Y. Lotscher, S. Hussain, B. Bunk, R. Pukall, D.H. Huson, P.C. Münch, A.C. McHardy, K.D. McCoy, A.J. Macpherson, A. Loy, T. Clavel, D. Berry, B. Stecher
Genome-guided design of a defined mouse microbiota that confers colonization resistance against Salmonella enterica serovar Typhimurium.
Nat Microbiol 2016, 2: 16215 - I. Gregor, A. Schönhuth, A.C. McHardy
Snowball: strain aware gene assembly of metagenomes.
Bioinformatics 2016, 32: i649 - C. Kratsch*, T.R. Klingen*, L. Mümken, L. Steinbrück, A.C. McHardy (*shared first authors)
Determination of antigenicity-altering patches on the major surface protein of human influenza A/H3N2 viruses.
Virus Evolution 2016, 2: vev025 - J.A. Frank, Y. Pan, A. Tooming-Klunderud, V.G. Eijsink, A.C. McHardy, A.J. Nederbragt, P.B. Pope
Improved metagenome assemblies and taxonomic binning using long-read circular consensus sequence data.
Sci Rep. 2016, 6: 25373 - S. Hacquard, B. Kracher, K. Hiruma,P.C. Münch, R. Garrido-Oter, M.R. Thon, A. Weimann, U. Damm, J.F. Dallery, M. Hainaut, B. Henrissat, O. Lespinet, S. Sacristán, E. Ver Loren van Themaat, E. Kemen,A.C. McHardy, P. Schulze-Lefert, R.J. O'Connell
Survival trade-offs in plant roots during colonization by closely related beneficial and pathogenic fungi.
Nat Commun. 2016, 7: 11362 - W. Ikeda-Ohtsubo, J.F. Strassert, T. Köhler, A. Mikaelyan, I. Gregor, A.C. McHardy, S.G. Tringe, P. Hugenholtz, R. Radek, A. Brune
'Candidatus Adiutrix intracellularis', an endosymbiont of termite gut flagellates, is the first representative of a deep-branching clade of Deltaproteobacteria and a putative homoacetogen.
Environ Microbiol. 2016, 18: 2548 - I. Gregor, J. Dröge, M. Schirmer, C. Quince, A.C. McHardy
PhyloPythiaS+: a self-training method for the rapid reconstruction of low-ranking taxonomic bins from metagenomes.
PeerJ 2016, 4: e1603 - D. Laehnemann, A. Borkhardt, A.C. McHardy
Denoising DNA deep sequencing data-high-throughput sequencing errors and their correction
Brief Bioinform. 2016, 17: 154
2015
- Y. Bai, D.B. Müller, G. Srinivas, R. Garrido-Oter, E. Potthoff, M. Rott, N. Dombrowski, P.C. Münch, S. Spaepen, M. Remus-Emsermann, B. Hüttel, A.C. McHardy, J.A. Vorholt, P. Schulze-Lefert
Functional overlap of the Arabidopsis leaf and root microbiota.
Nature 2015, 528: 364 - A.C. McHardy
How to Grow a Computational Biology Lab.
PLoS Comput Biol. 2015, 11: e1004397 - A. Klötgen, P.C. Münch, A. Borkhardt, J.I. Hoell, A.C. McHardy
Biochemical and bioinformatic methods for elucidating the role of RNA-protein interactions in posttranscriptional regulation.
Brief Funct Genomics 2015, 14: 102 - P. Belmann, J. Dröge, A. Bremges, A.C. McHardy, A. Sczyrba, M.D. Barton
Bioboxes: standardised containers for interchangeable bioinformatics software.
Gigascience 2015, 4: 47 - U. Fischer, M. Forster, A. Rinaldi, T. Risch, S. Sungalee, H.J. Warnatz, B. Bornhauser, M. Gombert, C. Kratsch, A.M. Stütz, M. Sultan, J. Tchinda, C.L. Worth, V. Amstislavskiy, N. Badarinarayan, A. Baruchel, T. Bartram, G. Basso, C. Canpolat, G. Cario, H. Cavé, D. Dakaj, M. Delorenzi, M.P. Dobay, C. Eckert, E. Ellinghaus, S. Eugster, V. Frismantas, S. Ginzel, O.A. Haas, O. Heidenreich, G. Hemmrich-Stanisak, K. Hezaveh, J.I. Höll, S. Hornhardt, P. Husemann, P. Kachroo, C.P. Kratz, G.T. Kronnie, B. Marovca, F. Niggli, A.C. McHardy, A.V. Moorman, R. Panzer-Grümayer, B.S. Petersen, B. Raeder, M. Ralser, P. Rosenstiel, D. Schäfer, M. Schrappe, S. Schreiber, M. Schütte, B. Stade, R. Thiele, N.v. Weid, A. Vora, M. Zaliova, L. Zhang, T. Zichner, M. Zimmermann, H. Lehrach, A. Borkhardt, J.P. Bourquin, A. Franke, J.O. Korbel, M. Stanulla, M.L. Yaspo
Genomics and drug profiling of fatal TCF3-HLF-positive acute lymphoblastic leukemia identifies recurrent mutation patterns and therapeutic options
Nat Genet. 2015, 47: 1020 - C. Gubry-Rangin, C. Kratsch, T.A. Williams, A.C. McHardy, T.M. Embley, J.I. Prosser, D.J. Macqueen
Coupling of diversification and pH ada ptation during the evolution of terrestrial Thaumarchaeota
Proc Natl Acad Sci U S A 2015, 112: 9370 - A. Otte, M. Sauter, M.A. Daxer, A.C. McHardy, K. Klingel, G. Gabriel
Adaptive mutations that occurred during 2009 H1N1 influenza virus pandemic circulation in humans enhance virulence in mice
J Virol 2015, 89: 7329 - S. Hacquard, R. Garrido-Oter, A. González, S. Spaepen, G. Ackermann, S. Lebeis, A.C. McHardy, J.L. Dangl, R. Knight, R. Ley, P. Schulze-Lefert
Microbiota and Host Nutrition across Plant and Animal Kingdoms
Cell Host Microbe 2015, 17: 603 - J. Dröge, I.Gregor, A.C. McHardy
Taxator-tk: Precise Taxonomic Assignment of Metagenomes by Fast Approximation of Evolutionary Neighborhoods
Bioinformatics 2015, 31: 817 - D. Bulgarelli*, R. Garrido-Oter*, P.C. Münch, A. Weiman, J. Dröge, Y. Pan, A.C. McHardy*, P. Schulze-Lefert* (*shared first & last authors)
Structure and Function of the Bacterial Root Microbiota in Wild and Domesticated Barley
Cell Host Microbe 2015, 17: 392 - A.C. McHardy
PhyloPythia(S)
in Encyclopedia of Metagenomics - Genes, Genomes and Metagenomes. Basics, Methods, Databases and Tools, Karen E. Nelson (Editor) Springer US, 2015: 582
2014
- L. Steinbrück, T.R. Klingen, A.C. McHardy
Computational prediction of vaccine strains for human influenza A(H3N2) viruses
J Virol 2014, 88: 12123 - S.G.A. Konietzny, P.B. Pope, A. Weimann, A.C. McHardy
Inference of phenotype-defining functional modules of protein families for microbial plant biomass degraders
Biotechnol Biofuels 2014, 7: 124 - D. Guttman*, A.C. McHardy*, P. Schulze-Lefert* (*all authors contributed equally)
Microbial genome-enabled insights into plant-microbe interactions
Nat Rev Genet 2014, 15: 797 - C. Kratsch, A.C. McHardy
RidgeRace: ridge regression for continous ancestral character estimation on phylogenetic trees
Bioinformatics 2014, 30: i527
2013
- L. Steinbrück, A.C. McHardy
Evaluating the Evolutionary Dynamics of Viral Populations
in Dynamic Models of Infectious Diseases, V. Sree Hari Rao, Ravi Durvasula (Editors), Springer Verlag, 2013: 205 - K.R. Patil, A.C. McHardy
Alignment-free genome tree inference by learning group-specific distance metrics
Genome Biology and Evolution 2013, 5: 1470 - C. Röhr, M. Kerick, A. Fischer, A. Kühn, K. Kashofer, B. Timmermann, A. Daskalaki, S.T. Börno, A. Nowka, S. Krobitsch, A.C. McHardy, C. Kratsch, T. Becker, A. Wunderlich, C. Barmeyer, C. Viertler, K. Zatloukal, C. Wierling, H. Lehrach, M.R. Schweiger
High-Throughput miRNA and mRNA Sequencing of Paired Colorectal Normal, Tumor and Metastasis Tissues and Bioinformatic Modeling of miRNA-1 Therapeutic Applications
PLoS One 2013, 8: e67461 - I. Gregor, L. Steinbrück, A.C. McHardy
PTree: pattern-based, stochastic search for maximum parsimony phylogenies
PeerJ 2013, 1: e89 - A. Weimann*, Y. Trukhina*, P.B. Pope, S.G.A. Konietzny, A.C. McHardy (*shared first authors)
De novo prediction of the genomic components and capabilities for microbial plant biomass degradation from (meta-)genomes
Biotechnol Biofuels 2013, 6: 24
2012
- J. Dröge, A.C. McHardy
Taxonomic binning of metagenome samples generated by next-generation sequencing technologies
Brief Bioinform. 2012, 13: 646 - K.R. Patil, L. Roune, A.C. McHardy
The PhyloPythiaS web server for taxonomic assignment of metagenome sequence
PLoS One 2012, 7: e38581 - L. Steinbrück, A.C. McHardy
Inference of Genotype-Phenotype Relationships in the Antigenic Evolution of Human Influenza A (H3N2) Viruses
PLoS Comput Biol. 2012, 8: e1002492 - C. Tusche, L. Steinbrück, A.C. McHardy
Detecting patches of protein sites of influenza A viruses under positive selection
Mol Biol Evol. 2012, 29: 2063 - J.A. Gilbert, J.A. Steele, J.G. Caporaso, L. Steinbrück, J. Reeder, B. Temperton, S. Huse, A.C. McHardy, R. Knight, I. Joint, P. Somerfield, J.A. Fuhrman, D. Field
Defining seasonal marine microbial community dynamics
ISME J 2012, 6: 298 - P.B. Pope, A.K. Mackenzie, I. Gregor, W. Smith, M.A. Sundset, A.C. McHardy, M. Morrison, V.G. Eijsink
Metagenomics of the Svalbard reindeer rumen microbiome reveals abundance of polysaccharide utilization loci
PLoS One 2012, 7: e38571
2011
- P. B. Pope, W. Smith, S. E. Denman, S. G. Tringe, K. Barry, P. Hugenholtz, C. S. McSweeney, A. C. McHardy, M. Morrison
Isolation of Succinivibrionaceae Implicated in Low Methane Emissions from Tammar Wallabies
Science 2011, 333: 646 - S.G.A. Konietzny, L. Dietz, A.C. McHardy
Inferring functional modules of protein families with probabilistic topic models
BMC Bioinformatics 2011, 12: 141 - A.C. McHardy, K. Patil
Phylogenetic Binning of Metagenome Sequence Samples
in Handbook of Molecular, Microbial Ecology I: Metagenomics and Complementary Approaches, F. De Bruijn (Editor), Wiley/Blackwell, 2011: 353 - K. Patil, P. Haider, P.B. Pope, P.J. Turnbaugh, M. Morrison, T. Scheffer, A.C. McHardy
Taxonomic metagenome sequence assignment with structured output models
Nat Methods 2011, 8: 191 - B. Adams, A.C. McHardy
The impact of seasonal and year-round transmission regimes on the evolution of influenza A virus
Proceedings of the Royal Society B 2011, 278: 2249 - L. Steinbrück, A.C. McHardy
Allele dynamics plots for the study of evolutionary dynamics in viral populations
Nucleic Acids Res 2011, 39: 1 - A. Lykidis, C.L. Chen, S.G. Tringe, A.C. McHardy, A. Copeland, N.C. Kyrpides, P. Hugenholtz, W.T. Liu
Multiple syntrophic interactions in a terephthalate-degrading methanogenic consortium
ISME J. 2011, 5: 122
2010
- J.A. Gilbert, F. Meyer, D. Antonopoulos, P. Balaji, C.T. Brown, C.T. Brown, N. Desai, J.A. Eisen, D. Evers, D. Field, W. Feng, D. Huson, J. Jansson, R. Knight, J. Knight, E. Kolker, K. Konstantindis, J. Kostka, N. Kyrpides, R. Mackelprang, A.C. McHardy, C. Quince, J. Raes, A. Sczyrba, A. Shade, R. Stevens
Meeting report: the terabase metagenomics workshop and the vision of an Earth microbiome project
Genomic Sci. 2010, 3: 243 - P.B. Pope, S.E. Denman, M. Jones, S.G. Tringe, K. Barry, S.A. Malfatti, A.C. McHardy, J.F. Cheng, P. Hugenholtz, C.S. McSweeney, M. Morrison
Adaptation to herbivory by the Tammar Wallaby includes bacterial and glycoside hydrolases profiles different to other herbivores
Proc Natl Acad Sci U S A 2010, 107: 14793 - P.J. Turnbaugh, C. Quince, J.J. Faith, A.C. McHardy, T. Yatsunenko, F. Niazi, J. Affourtit, M. Egholm, B. Henrissat, R. Knight, J.I. Gordon
Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins
Proc Natl Acad Sci U S A 2010, 107: 7503
2009
- A.C. McHardy, B. Adams
The role of genomics in tracking the evolution of influenza A virus
PLoS Pathogens 2009, 5(10): e1000566
2008
- M.G. Kalyuzhnaya, A. Lapidus, N. Ivanova, A.C. Copeland, A.C. McHardy, E. Szeto, A. Salamov, I.V. Grigoriev, D. Suciu, S.R. Levine, V.M. Markowitz, I. Rigoutsos, S.G. Tringe, D.C. Bruce, P.M. Richardson, M.E. Lidstrom, L. Chistoserdova
High-resolution metagenomics targets specific functional types in complex microbial communities
Nat Biotechnol 2008, 26: 1029 - A.C. McHardy
Finding genes in genome sequence
Methods in Molecular Biology 2008, 452: 163 - L.Z. Holland, R. Albalat, K. Azumi, E. Benito-Gutiérrez, M.J. Blow, M. Bronner-Fraser, F. Brunet, T. Butts, S. Candiani, L.J. Dishaw, D.E. Ferrier, J. Garcia-Fernàndez, J.J. Gibson-Brown, C. Gissi, A. Godzik, F. Hallböök, D. Hirose, K. Hosomichi, T. Ikuta, H. Inoko, M. Kasahara, J. Kasamatsu, T. Kawashima, A. Kimura, M. Kobayashi, Z. Kozmik, K. Kubokawa, V. Laudet, G.W. Litman, A.C. McHardy, D. Meulemans, M. Nonaka, R.P. Olinski, Z. Pancer, L.A. Pennacchio, M. Pestarino, J.P. Rast, I. Rigoutsos, M. Robinson-Rechavi, G. Roch, H. Saiga, Y. Sasakura, M. Satake, Y. Satou, M. Schubert, N. Sherwood, T. Shiina, N. Takatori, J. Tello, P. Vopalensky, S. Wada, A. Xu, Y. Ye, K. Yoshida, F. Yoshizaki, J.K. Yu, Q. Zhang, C.M. Zmasek, P.J. de Jong, K. Osoegawa, N.H. Putnam, D.S. Rokhsar, N. Satoh, P.W. Holland
The amphioxus genome illuminates vertebrate origins and cephalochordate biology
Genome Res 2008, 18: 1100 - K.H. Gartemann, B. Abt, T. Bekel, A. Burger, J. Engemann, M. Flügel, L. Gaigalat, A. Goesmann, I. Gräfen, J. Kalinowski, O. Kaup, O. Kirchner, L. Krause, B. Linke, A.C. McHardy, F. Meyer, S. Pohle, C. Rückert, S. Schneiker, E.M. Zellermann, A. Pühler, R. Eichenlaub, O. Kaiser, D. Bartels
The genome sequence of the tomato-pathogenic actinomycete Clavibacter michiganensis subsp. michiganensis NCPPB382 reveals a large island involved in pathogenicity
Journal of Bacteriology 2008, 190: 2138 - B. Adams, A.C. McHardy, C. Lundegaard, T. Lengauer
Viral Bioinformatics
in Modern Genome Annotation, D. Frishman, A. Valencia (Editors) Springer Verlag, 2009: 429
2007
- F. Warnecke, P. Luginbühl, N. Ivanova, M. Ghassemian, T.H. Richardson, J.T. Stege, M. Cayouette, A.C. McHardy, G. Djordjevic, N. Aboushadi, R. Sorek, S.G. Tringe, M. Podar, H.G. Martin, V. Kunin, D. Dalevi, J. Madejska, E. Kirton, D. Platt, E. Szeto, A. Salamov, K. Barry, N. Mikhailova, N.C. Kyrpides, E.G. Matson, E.A. Ottesen, X. Zhang, M. Hernández, C. Murillo, L.G. Acosta, I. Rigoutsos, G. Tamayo, B.D. Green, C. Chang, E.M. Rubin, E.J. Mathur, D.E. Robertson, P. Hugenholtz, J.R. Leadbetter
Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite
Nature 2007, 450: 560 - S. Schneiker, O. Perlova, O. Kaiser, K. Gerth, A. Alici, M.O. Altmeyer, D. Bartels, T. Bekel, S. Beyer, E. Bode, H.B. Bode, C.J. Bolten, J.V. Choudhuri, S. Doss, Y.A. Elnakady, B. Frank, L. Gaigalat, A. Goesmann, C. Groeger, F. Gross, L. Jelsbak, J. Kalinowski, C. Kegler, T. Knauber, S. Konietzny, M. Kopp, L. Krause, D. Krug, B. Linke, T. Mahmud, R. Martinez-Arias, A.C. McHardy, M. Merai, F. Meyer, S. Mormann, J. Muñoz-Dorado, J. Perez, S. Pradella, S. Rachid, G. Raddatz, F. Rosenau, C. Rückert, F. Sasse, M. Scharfe, S.C. Schuster, G. Suen, A. Treuner-Lange, G.J. Velicer, F.J. Vorhölter, K.J. Weissman, R.D. Welch, S.C. Wenzel, D.E. Whitworth, S. Wilhelm, C. Wittmann, H. Blöcker, A. Pühler,R. Müller
Complete genome sequence of the myxobacterium Sorangium cellulosum
Nat Biotechnol 2007, 25: 1281 - A.C. McHardy, I. Rigoutsos
What's in the mix: phylogenetic classification of metagenome sequence samples
Curr Opin Microbiol 2007, 10: 499 - K. Mavromatis, N. Ivanova, K. Barry, H. Shapiro, E. Goltsman, A.C. McHardy, I. Rigoutsos, A. Salamov, F. Korzeniewski, M. Land, A. Lapidus, I. Grigoriev, P. Richardson, P. Hugenholtz, N.C. Kyrpides
Use of simulated data sets to evaluate the fidelity of metagenomic processing methods
Nat Methods 2007, 4: 495 - A.C. McHardy, H. Garcia Martin, A. Tsirigos, P. Hugenholtz, I. Rigoutsos
Accurate phylogenetic classification of variable-length DNA fragments
Nat Methods 2007, 4: 63 - A.C. McHardy*, L. Krause*, J. Stoye, T. Nattkemper, A. Pühler, F. Meyer (*joint first authors)
GISMO - gene identification using a support vector machine for ORF classification
Nucleic Acids Res 2007, 35: 540
2006
- A. Krause, A. Ramakumar, D. Bartels, F. Battistoni, T. Bekel, J. Boch, M. Bohm, F. Friedrich, T. Hurek, L. Krause, B. Linke, A.C. McHardy, A. Sarkar, S. Schneiker, A.A. Syed, R. Thauer, F. Vorholter, S. Weidner, Alfred Pühler, B. Reinhold-Hurek, O. Kaiser, A. Goesmann
Complete genome of the mutualistic, N2-fixing grass endophyte Azoarcus sp. strain BH72
Nat Biotechnol 2006, 24: 1385 - H. Garcia Martin, N. Ivanova, V. Kunin, F. Warnecke, K. Barry, A.C. McHardy, C. Yeates, S. He, A. Salamov, E. Szeto, E. Dalin, N. Putnam, I. Rigoutsos, N.C. Kyrpides, L.L. Blackall, K.D. McMahon, P. Hugenholtz
Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities
Nat Biotechnol 2006, 24: 1263 - A.C. McHardy*, B. Linke*, H. Neuwege, L. Krause, F. Meyer (*joint first authors)
REGANOR: a gene prediction server for prokaryotic genomes and a database of high quality gene predictions for prokaryotes
Appl Bioinformatics 2006, 5: 193 - S. Schneiker, A.P. dos Santos, D. Bartels, T. Bekel, M. Brecht, J. Buhrmester, T.N. Chernikova, M. Ferrer, C. Gertler, A. Goesmann, O.V. Golyshina, F. Kaminski, A.N. Khachane, S. Lang, B. Linke, A.C. McHardy, F. Meyer, T. Nechitaylo, A. Pühler, D. Regenhardt, O. Rupp, J.S. Sabirova, W. Selbitschka, M.M. Yakimov, K.N. Timmis, F. Vorholter, S. Weidner, O. Kaiser, P.N. Golyshin
Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis
Nat Biotechnol 2006, 24: 997 - I. Rigoutsos, T. Huynh, K. Miranda, A. Tsirigos, A.C. McHardy, D. Platt
Short blocks from the noncoding parts of the human genome have instances within nearly all known genes and relate to biological processes
Proc Natl Acad Sci U S A 2006, 103: 6605
2005
- F. Thieme, R. Koebnik, T. Bekel, C. Berger, J. Boch, D. Buttner, C. Caldana, L. Gaigalat, A. Goesmann, S. Kay, O. Kirchner, C. Lanz, B. Linke, A.C. McHardy, F. Meyer, G. Mittenhuber, D.H. Nies, U. Niesbach-Klosgen, T. Patschkowski, C. Rückert, O. Rupp, S. Schneiker, S.C. Schuster, F.J. Vorholter, E. Weber, A. Pühler, U. Bonas, D. Bartels, O. Kaiser
Insights into genome plasticity and pathogenicity of the plant pathogenic bacterium Xanthomonas campestris pv. vesicatoria revealed by the complete genome sequence
J Bacteriol 2005, 187: 7254 - R. Overbeek, T. Begley, R.M. Butler, J.V. Choudhuri, H.Y. Chuang, M. Cohoon, V. de Crecy-Lagard, N. Diaz, T. Disz, R. Edwards, M. Fonstein, E.D. Frank, S. Gerdes, E.M. Glass, A. Goesmann, A. Hanson, D. Iwata-Reuyl, R. Jensen, N. Jamshidi, L. Krause, M.Kubal, N. Larsen, B. Linke, A.C. McHardy, F. Meyer, H. Neuweger, G. Olsen, R. Olson, A. Osterman,V. Portnoy, G.D. Pusch, D.A. Rodionov, C. Rückert, J. Steiner, R. Stevens, I. Thiele, O. Vassieva, Y. Ye, O. Zagnitko, V. Vonstein
The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes
Nucleic Acids Res 2005, 33: 5691
2004
- A.C. McHardy, A. Goesmann, A. Pühler, F. Meyer
Development of joint application strategies for two microbial gene finders
Bioinformatics 2004, 20: 1622 - A.C. McHardy, J. Kalinowski, A. Pühler, F. Meyer
Comparing expression level-dependent features in codon usage with protein abundance: an analysis of 'predictive proteomics'
Proteomics 2004, 4: 46
2003
- A. Wilke, C. Rückert, D. Bartels, M. Dondrup, A. Goesmann, A. Huser, S. Kespohl, B. Linke, M. Mahne, A.C. McHardy, A. Pühler, F. Meyer
Bioinformatics support for high-throughput proteomics
J Biotechnol 2003, 106: 147 - A. Goesmann, B. Linke, O. Rupp, L. Krause, D. Bartels, M. Dondrup, A.C. McHardy, A. Wilke, A. Pühler, F. Meyer
Building a BRIDGE for the integration of heterogeneous data from functional genomics into a platform for systems biology
J Biotechnol 2003, 106: 157 - A.C. McHardy, A. Tauch, C. Ruckert, A. Pühler, J. Kalinowski
Genome-based analysis of biosynthetic aminotransferase genes of Corynebacterium glutamicum
J Biotechnol 2003, 104: 229 - J. Kalinowski, B. Bathe, D. Bartels, N. Bischoff, M. Bott, A. Burkovski, N. Dusch, L. Eggeling, B.J. Eikmanns, L. Gaigalat, A. Goesmann, M. Hartmann, K. Huthmacher, R. Kramer, B. Linke, A.C. McHardy, F. Meyer, B. Mockel, W. Pfefferle, A. Pühler, D.A. Rey, C. Rückert, O. Rupp, H. Sahm, V.F. Wendisch, I. Wiegrabe, A. Tauch
The complete Corynebacterium glutamicum ATCC 13032 genome sequence and its impact on the production of L-aspartate-derived amino acids and vitamins
J Biotechnol 2003, 104: 5 - F. Meyer, A. Goesmann, A.C. McHardy, D. Bartels, T. Bekel, J. Clausen, J. Kalinowski, B. Linke, O. Rupp, R. Giegerich, A. Pühler
GenDB - an open source genome annotation system for prokaryote genomes
Nucleic Acids Res 2003, 31: 2187
