Bioinformatik der Infektionsforschung

• 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, M. 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

2020

• A. Bremges, A. Fritz, A.C. McHardy
  CAMITAX: Taxon labels for microbial genomes.
  Gigascience 2020 9: pii
• J. Schira-Heinen, A. Czapla, M. Hendricks, A. Kloetgen, W. Wruck, J. Adjaye, G. Kögler, H. Werner Müller, K. Stühler, H. I. Trompeter
  Functional omics analyses reveal only minor effects of microRNAs on human somatic stem cell differentiation.
  Sci Rep. 2020 10: 3284
• A. Khaledi, A. Weimann, M. Schniederjans, E. Asgari, T. H. Kuo, A. Oliver, G. Cabot, A. Kola, P. Gastmeier, M. Hogardt, D. Jonas, M. R. Mofrad, A. Bremges, A. C. McHardy, S. Häussler
  Predicting antimicrobial resistance in Pseudomonas aeruginosa with machine learning-enabled molecular diagnostics.
  EMBO Mol Med. 2020 3: 10264
• D. Lähnemann, J. Köster, E. Szczurek, D. J. McCarthy, S. C. Hicks, M. D. Robinson, C. A. Vallejos, K. R. Campbell, N. Beerenwinkel, A. Mahfouz, L. Pinello, P. Skums, A. Stamatakis, C. S. Attolini, S. Aparicio, J. Baaijens, M. Balvert, B. Barbanson, A. Cappuccio, G. Corleone, B. E. Dutilh, M. Florescu, V. Guryev, R. Holmer, K. Jahn, T. J. Lobo, E. M. Keizer, I. Khatri, S. M. Kielbasa, J. O. Korbel, A. M. Kozlov, T. H. Kuo, B. P. F. Lelieveldt, I. I. Mandoiu, J. C. Marioni, T. Marschall, F. Mölder, A. Niknejad, L. Raczkowski, M. Reinders, J. Ridder, A. E. Saliba, A. Somarakis, O. Stegle, F. J. Theis, H. Yang, A. Zelikovsky, A. C. McHardy, B. J. Raphael, S. P. Shah, A. Schönhuth.
  Eleven grand challenges in single-cell data science.
  Genome Biol. 2020 1: 31

2019

• N. Zhou, Y. Jiang, T. R. Bergquist, A. J. Lee, B.Z. Kacsoh, A. W. Crocker, K. A. Lewis, G. Georghiou, H. N. Nguyen, M. N. Hamid, L. Davis, T. Dogan, V. Atalay, A. S. Rifaioglu, A. Dalkıran, R. Cetin Atalay, C. Zhang, R. L. Hurto, P. L. Freddolino, Y. Zhang, P. Bhat, F. Supek, J. M. Fernández, B. Gemovic, V. R. Perovic, R. S. Davidović, N. Sumonja, N. Veljkovic, E. Asgari, M. R. K. Mofrad, G. Profiti, C. Savojardo, P. L. Martelli, R. Casadio, F. Boecker, H. Schoof, I. Kahanda , N. Thurlby, A. C. McHardy, A. Renaux, R. Saidi, J. Gough, A. A. Freitas, M. Antczak, F. Fabris, M. N. Wass, J. Hou, J. Cheng, Z. Wang, A. E. Romero, A. Paccanaro, H. Yang, T. Goldberg, C. Zhao, L. Holm, P. Törönen, A. J. Medlar, E. Zosa, I. Borukhov, I. Novikov, A. Wilkins, O. Lichtarge, P. H. Chi, W. C. Tseng, M. Linial, P. W. Rose, C. Dessimoz, V. Vidulin, S. Dzeroski, I. Sillitoe, S. Das, J. G. Lees, D. T. Jones, C. Wan, D. Cozzetto, R. Fa, M.Torres, A. Warwick Vesztrocy, J. M. Rodriguez, M. L.Tress, M. Frasca, M. Notaro, G. Grossi, A. Petrini, M. Re, G. Valentini, M. Mesiti, D. B. Roche, J. Reeb, D.W. Ritchie, S. Aridhi, S. Z. Alborzi, M. D. Devignes, D. C. E. Koo, R. Bonneau, V. Gligorijević, M. Barot, H. Fang, S. Toppo, E. Lavezzo, M. Falda, M. Berselli, S. C. E. Tosatto, M. Carraro, D. Piovesan, H. Ur Rehman, Q. Mao, S. Zhang, S. Vucetic, G. S. Black, D. Jo, E. Suh, J. B.  Dayton, D. J. Larsen, A. R. Omdahl, L. J. McGuffin, D. A. Brackenridge, P. C. Babbitt, J. M. Yunes, P. Fontana, F. Zhang, S. Zhu, R. You, Z. Zhang, S. Dai, S. Yao, W. Tian, R. Car, C. Chandler, M. Amezola, D. Johnson, J. M. Chang, W. H. Liao, Y. W. Liu, S. Pascarelli, Y. Frank, R. Hoehndorf, M. Kulmanov, I. Boudellioua, G. Politano, S. Di Carlo, A. Benso, K. Hakala, F. Ginter, F. Mehryary, S. Kaewphan, J. Björne, H. Moen, M. E. E. Tolvanen,  T. Salakoski, D. Kihara, A. Jain, T. Šmuc, A. Altenhoff, A. Ben-Hur, B. Rost, S. E. Brenner, C. A. Orengo, C. J. Jeffery, G. Bosco, D. A. Hogan, M. J. Martin, C. O'Donovan, S. D. Mooney, C. S. Greene, P. Radivojac, I. Friedberg.
  The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens.
  Genome Biol 2019 20: 244
• J.I. Hoell, S. Ginzel, M. Kuhlen, A. Kloetgen, M. Gombert, U. Fischer, D. Hein, S. Demir, M. Stanulla, M. Schrappe, U. Zur Stadt, P. Bader, F. Babor, F. Schuster, B. Strahm, J. Alten, A. Moericke, G. Escherich, A. von Stackelberg, R. Thiele, A. C. McHardy, C. Peters, B. Bornhauser, J. P. Bourquin, S. Krause, J. Enczmann, L. H. Meyer, C. Eckert, A. Borkhardt, R. Meisel.
  Pediatric ALL relapses after allo-SCT show high individuality, clonal dynamics, selective pressure, and druggable targets.
  Blood Adv 2019, 3: 20
• A. Kloetgen, P. C. Münch, A. Borckhardt, J. I. Hoell, A. C. McHardy. Corrigendum to:
  Biochemical and bioinformatics methods for elucidating the role of RNA-protein interactions in posttranscriptional regulation.
  Brief Funct Genomics 2019, 18: 6
• 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