Bioinformatik der Infektionsforschung

• Sczyrba, A.*, Hofmann, P.*, Belmann, P.*, Koslicki, D., Janssen, S., Droge, J., Gregor, I., Majda, S., Fiedler, J., Dahms, E., Bremges, A., Fritz, A., Garrido-Oter, R., Jorgensen, T. S., Shapiro, N., Blood, P. D., Gurevich, A., Bai, Y., Turaev, D., DeMaere, M. Z., Chikhi, R., Nagarajan, N., Quince, C., Meyer, F., Balvociute, M., Hansen, L. H., Sorensen, S. J., Chia, B. K. H., Denis, B., Froula, J. L., Wang, Z., Egan, R., Don Kang, D., Cook, J. J., Deltel, C., Beckstette, M., Lemaitre, C., Peterlongo, P., Rizk, G., Lavenier, D., Wu, Y. W., Singer, S. W., Jain, C., Strous, M., Klingenberg, H., Meinicke, P., Barton, M. D., Lingner, T., Lin, H. H., Liao, Y. C., Silva, G. G. Z., Cuevas, D. A., Edwards, R. A., Saha, S., Piro, V. C., Renard, B. Y., Pop, M., Klenk, H. P., Goker, M., Kyrpides, N. C., Woyke, T., Vorholt, J. A., Schulze-Lefert, P., Rubin, E. M., Darling, A. E., Rattei, T. & McHardy, A. C. (*shared first authors) Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software. Nature Methods (2017) 14, 1063, doi:10.1038/nmeth.4458.
• Asgari, E., Münch, P. C., Lesker, T. R., McHardy, A. C.* & Mofrad, M. R. K.* (*shared last authors) DiTaxa: nucleotide-pair encoding of 16S rRNA for host phenotype and biomarker detection. Bioinformatics (2019) 35, 2498, doi:10.1093/bioinformatics/bty954.
• Meyer, F., Bremges, A., Belmann, P., Janssen, S., McHardy, A. C.* & Koslicki, D.* (*shared last authors) Assessing taxonomic metagenome profilers with OPAL. Genome Biol (2019) 20, 51, doi:10.1186/s13059-019-1646-y.
• Fritz, A.*, Hofmann, P.*, Majda, S., Dahms, E., Dröge, J., Fiedler, J., Lesker, T. R., Belmann, P., DeMaere, M. Z., Darling, A. E., Sczyrba, A., Bremges, A. & McHardy, A. C. (*shared first authors) CAMISIM: simulating metagenomes and microbial communities. Microbiome (2019) 7, 17, doi:10.1186/s40168-019-0633-6

2021

• Goeser, F., Münch, P., Lesker, T. R., Lutz, P. L., Krämer, B., Kaczmarek, D. J., Finnemann, C., Nischalke, H. D., Geffers, R., Parcina, M., McHardy, A., Strassburg, C., Hoerauf, A., Nattermann, J., Bekeredjian-Ding, I. & Spengler, U. Neither black nor white: do altered intestinal microbiota reflect chronic liver disease severity? Gut (2021) 70, 438, doi:10.1136/gutjnl-2020-321424.
• Münch, P. C., Franzosa, E. A., Stecher, B., McHardy, A. C.* & Huttenhower, C.* (*shared last authors) Identification of Natural CRISPR Systems and Targets in the Human Microbiome. Cell Host Microbe (2021) 29, 94, doi:10.1016/j.chom.2020.10.010.
• Rivas, M. A., Meydan, C., Chin, C. R., Challman, M. F., Kim, D., Bhinder, B., Kloetgen, A., Viny, A. D., Teater, M. R., McNally, D. R., Doane, A. S., Béguelin, W., Fernández, M. T. C., Shen, H., Wang, X., Levine, R. L., Chen, Z., Tsirigos, A., Elemento, O., Mason, C. E. & Melnick, A. M. Smc3 dosage regulates B cell transit through germinal centers and restricts their malignant transformation. Nat Immunol (2021), 22, 240, doi:10.1038/s41590-020-00827-8.
• Wang, E., Zhou, H., Nadorp, B., Cayanan, G., Chen, X., Yeaton, A. H., Nomikou, S., Witkowski, M. T., Narang, S., Kloetgen, A., Thandapani, P., Ravn-Boess, N., Tsirigos, A. & Aifantis, I. Surface antigen-guided CRISPR screens identify regulators of myeloid leukemia differentiation. Cell Stem Cell (2021) in press, doi:10.1016/j.stem.2020.12.005.
• Yusufova, N., Kloetgen, A., Teater, M., Osunsade, A., Camarillo, J. M., Chin, C. R., Doane, A. S., Venters, B. J., Portillo-Ledesma, S., Conway, J., Phillip, J. M., Elemento, O., Scott, D. W., Béguelin, W., Licht, J. D., Kelleher, N. L., Staudt, L. M., Skoultchi, A. I., Keogh, M. C., Apostolou, E., Mason, C. E., Imielinski, M., Schlick, T., David, Y., Tsirigos, A., Allis, C. D., Soshnev, A. A., Cesarman, E. & Melnick, A. M. Histone H1 loss drives lymphoma by disrupting 3D chromatin architecture. Nature (2021) 589, 299, doi:10.1038/s41586-020-3017-y.

2020

• Bankwitz, D.*, Bahai, A.*, Labuhn, M., Doepke, M., Ginkel, C., Khera, T., Todt, D., Ströh, L. J., Dold, L., Klein, F., Klawonn, F., Krey, T., Behrendt, P., Cornberg, M., McHardy, A. C.* & Pietschmann, T.* (*shared first & last authors) Hepatitis C reference viruses highlight potent antibody responses and diverse viral functional interactions with neutralising antibodies. Gut (2020) in press, gutjnl-2020-321190, doi:10.1136/gutjnl-2020-321190.
• Bremges, A., Fritz, A. & McHardy, A. C. CAMITAX: Taxon labels for microbial genomes.Gigascience (2020) 9, giz154, doi:10.1093/gigascience/giz154.
• Deng, Z.-L., Dhingra, A., Fritz, A., Götting, J., Münch, P. C., Steinbrück, L., Schulz, T. F., Ganzenmüller, T. & McHardy, A. C. Evaluating assembly and variant calling software for strain-resolved analysis of large DNA viruses. Briefings in Bioinformatics (2020) in press, bbaa123, doi:10.1093/bib/bbaa123.
• Eberl C., Ring D., Münch P.C., Beutler M., Basic M., Slack E.C., Schwarzer M., Srutkova D., Lange A., Frick J.S., Bleich A., Stecher B. , Reproducible Colonization of Germ-Free Mice With the Oligo-Mouse-Microbiota in Different Animal Facilities. Frontiers in Microbiology (2020) 10, 2999, doi:10.3389/fmicb.2019.02999.
• Hanniford, D., Ulloa-Morales, A., Karz, A., Berzoti-Coelho, M. G., Moubarak, R. S., Sánchez-Sendra, B., Kloetgen, A., Davalos, V., Imig, J., Wu, P., Vasudevaraja, V., Argibay, D., Lilja, K., Tabaglio, T., Monteagudo, C., Guccione, E., Tsirigos, A., Osman, I., Aifantis, I. & Hernando, E. Epigenetic Silencing of CDR1as Drives IGF2BP3-Mediated Melanoma Invasion and Metastasis. Cancer Cell (2020) 37, 55, doi:10.1016/j.ccell.2019.12.007.
• Hufsky, F., Lamkiewicz, K., Almeida, A., Aouacheria, A., Arighi, C., Bateman, A., Baumbach, J., Beerenwinkel, N., Brandt, C., Cacciabue, M., Chuguransky, S., Drechsel, O., Finn, R. D., Fritz, A., Fuchs, S., Hattab, G., Hauschild, A. C., Heider, D., Hoffmann, M., Hölzer, M., Hoops, S., Kaderali, L., Kalvari, I., von Kleist, M., Kmiecinski, R., Kühnert, D., Lasso, G., Libin, P., List, M., Löchel, H. F., Martin, M. J., Martin, R., Matschinske, J., McHardy, A. C., Mendes, P., Mistry, J., Navratil, V., Nawrocki, E. P., O'Toole Á, N., Ontiveros-Palacios, N., Petrov, A. I., Rangel-Pineros, G., Redaschi, N., Reimering, S., Reinert, K., Reyes, A., Richardson, L., Robertson, D. L., Sadegh, S., Singer, J. B., Theys, K., Upton, C., Welzel, M., Williams, L. & Marz, M. Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research. Brief Bioinform (2020) in press, bbaa232, doi:10.1093/bib/bbaa232.
• Khaledi, A.*, Weimann, A.*, Schniederjans, M., Asgari, E., Kuo, T. H., Oliver, A., Cabot, G., Kola, A., Gastmeier, P., Hogardt, M., Jonas, D., Mofrad, M. R., Bremges, A., McHardy, A. C.* & Häussler, S.* (*shared first & last authors) Predicting antimicrobial resistance in Pseudomonas aeruginosa with machine learning-enabled molecular diagnostics. EMBO Mol Med (2020) 12, e10264, doi:10.15252/emmm.201910264.
• Kloetgen, A., Duggimpudi, S., Schuschel, K., Hezaveh, K., Picard, D., Schaal, H., Remke, M., Klusmann, J. H., Borkhardt, A., McHardy, A. C. & Hoell, J. I. YBX1 Indirectly Targets Heterochromatin-Repressed Inflammatory Response-Related Apoptosis Genes through Regulating CBX5 mRNA. Int J Mol Sci (2020) 21, 4453, doi:10.3390/ijms21124453.
• Kloetgen, A.*, Thandapani, P.*, Ntziachristos, P.*, Ghebrechristos, Y., Nomikou, S., Lazaris, C., Chen, X., Hu, H., Bakogianni, S., Wang, J., Fu, Y., Boccalatte, F., Zhong, H., Paietta, E., Trimarchi, T., Zhu, Y., Van Vlierberghe, P., Inghirami, G. G., Lionnet, T., Aifantis, I. & Tsirigos, A. (*shared first authors) Three-dimensional chromatin landscapes in T cell acute lymphoblastic leukemia. Nat Genet (2020) 52, 388, doi:10.1038/s41588-020-0602-9.
• Lähnemann, D., Köster, J., Szczurek, E., McCarthy, D. J., Hicks, S. C., Robinson, M. D., Vallejos, C. A., Campbell, K. R., Beerenwinkel, N., Mahfouz, A., Pinello, L., Skums, P., Stamatakis, A., Attolini, C. S., Aparicio, S., Baaijens, J., Balvert, M., Barbanson, B., Cappuccio, A., Corleone, G., Dutilh, B. E., Florescu, M., Guryev, V., Holmer, R., Jahn, K., Lobo, T. J., Keizer, E. M., Khatri, I., Kielbasa, S. M., Korbel, J. O., Kozlov, A. M., Kuo, T. H., Lelieveldt, B. P. F., Mandoiu, II, Marioni, J. C., Marschall, T., Mölder, F., Niknejad, A., Raczkowski, L., Reinders, M., Ridder, J., Saliba, A. E., Somarakis, A., Stegle, O., Theis, F. J., Yang, H., Zelikovsky, A., McHardy, A. C., Raphael, B. J., Shah, S. P. & Schönhuth, A. Eleven grand challenges in single-cell data science. Genome Biol (2020) 21, 31, doi:10.1186/s13059-020-1926-6.
• Lesker, T. R., Durairaj, A. C., Gálvez, E. J. C., Lagkouvardos, I., Baines, J. F., Clavel, T., Sczyrba, A., McHardy, A. C. & Strowig, T. An Integrated Metagenome Catalog Reveals New Insights into the Murine Gut Microbiome. Cell Rep (2020) 30, 2909, doi:10.1016/j.celrep.2020.02.036.
• Nishana, M., Ha, C., Rodriguez-Hernaez, J., Ranjbaran, A., Chio, E., Nora, E. P., Badri, S. B., Kloetgen, A., Bruneau, B. G., Tsirigos, A. & Skok, J. A. Defining the relative and combined contribution of CTCF and CTCFL to genomic regulation. Genome Biol (2020) 21, 108, doi:10.1186/s13059-020-02024-0.
• Reimering, S., Muñoz, S. & McHardy, A. C. Phylogeographic reconstruction using air transportation data and its application to the 2009 H1N1 influenza A pandemic. PLoS Comput Biol (2020) 16, e1007101, doi:10.1371/journal.pcbi.1007101.
• Rodriguez, S., Abundis, C., Boccalatte, F., Mehrotra, P., Chiang, M. Y., Yui, M. A., Wang, L., Zhang, H., Zollman, A., Bonfim-Silva, R., Kloetgen, A., Palmer, J., Sandusky, G., Wunderlich, M., Kaplan, M. H., Mulloy, J. C., Marcucci, G., Aifantis, I., Cardoso, A. A. & Carlesso, N. Therapeutic targeting of the E3 ubiquitin ligase SKP2 in T-ALL. Leukemia (2020) 34, 1241, doi:10.1038/s41375-019-0653-z.
• Schira-Heinen, J., Czapla, A., Hendricks, M., Kloetgen, A., Wruck, W., Adjaye, J., Kögler, G., Werner Müller, H., Stühler, K. & Trompeter, H. I. Functional omics analyses reveal only minor effects of microRNAs on human somatic stem cell differentiation. Sci Rep (2020) 10, 3284, doi:10.1038/s41598-020-60065-8.
• Spriewald, S., Stadler, E., Hense, B. A., Münch, P. C., McHardy, A. C., Weiss, A. S., Obeng, N., Müller, J. & Stecher, B. Evolutionary Stabilization of Cooperative Toxin Production through a Bacterium-Plasmid-Phage Interplay. mBio (2020) 11, e00912-20, doi:10.1128/mBio.00912-20.
• Thiele, S., Stanelle-Bertram, S., Beck, S., Kouassi, N. M., Zickler, M., Müller, M., Tuku, B., Resa-Infante, P., van Riel, D., Alawi, M., Günther, T., Rother, F., Hügel, S., Reimering, S., McHardy, A., Grundhoff, A., Brune, W., Osterhaus, A., Bader, M., Hartmann, E. & Gabriel, G. Cellular Importin-α3 Expression Dynamics in the Lung Regulate Antiviral Response Pathways against Influenza A Virus Infection. Cell Reports (2020) 31, 107549, doi:https://doi.org/10.1016/j.celrep.2020.107549.

2019

• Amann, R. I., Baichoo, S., Blencowe, B. J., Bork, P., Borodovsky, M., Brooksbank, C., Chain, P. S. G., Colwell, R. R., Daffonchio, D. G., Danchin, A., de Lorenzo, V., Dorrestein, P. C., Finn, R. D., Fraser, C. M., Gilbert, J. A., Hallam, S. J., Hugenholtz, P., Ioannidis, J. P. A., Jansson, J. K., Kim, J. F., Klenk, H. P., Klotz, M. G., Knight, R., Konstantinidis, K. T., Kyrpides, N. C., Mason, C. E., McHardy, A. C., Meyer, F., Ouzounis, C. A., Patrinos, A. A. N., Podar, M., Pollard, K. S., Ravel, J., Muñoz, A. R., Roberts, R. J., Rosselló-Móra, R., Sansone, S. A., Schloss, P. D., Schriml, L. M., Setubal, J. C., Sorek, R., Stevens, R. L., Tiedje, J. M., Turjanski, A., Tyson, G. W., Ussery, D. W., Weinstock, G. M., White, O., Whitman, W. B. & Xenarios, I. Consent insufficient for data release-Response. Science (2019) 364, 446, doi:10.1126/science.aax7509.
• Amann, R. I., Baichoo, S., Blencowe, B. J., Bork, P., Borodovsky, M., Brooksbank, C., Chain, P. S. G., Colwell, R. R., Daffonchio, D. G., Danchin, A., de Lorenzo, V., Dorrestein, P. C., Finn, R. D., Fraser, C. M., Gilbert, J. A., Hallam, S. J., Hugenholtz, P., Ioannidis, J. P. A., Jansson, J. K., Kim, J. F., Klenk, H. P., Klotz, M. G., Knight, R., Konstantinidis, K. T., Kyrpides, N. C., Mason, C. E., McHardy, A. C., Meyer, F., Ouzounis, C. A., Patrinos, A. A. N., Podar, M., Pollard, K. S., Ravel, J., Muñoz, A. R., Roberts, R. J., Rosselló-Móra, R., Sansone, S. A., Schloss, P. D., Schriml, L. M., Setubal, J. C., Sorek, R., Stevens, R. L., Tiedje, J. M., Turjanski, A., Tyson, G. W., Ussery, D. W., Weinstock, G. M., White, O., Whitman, W. B. & Xenarios, I. Toward unrestricted use of public genomic data. Science (2019) 363, 350, doi:10.1126/science.aaw1280.
• Asgari, E., Garakani, K., McHardy, A. C. & Mofrad, M. R. K. MicroPheno: predicting environments and host phenotypes from 16S rRNA gene sequencing using a k-mer based representation of shallow sub-samples. Bioinformatics (2019) 35, 1082, doi:10.1093/bioinformatics/bty652.
• Asgari, E., McHardy, A. C. & Mofrad, M. R. K. Probabilistic variable-length segmentation of protein sequences for discriminative motif discovery (DiMotif) and sequence embedding (ProtVecX). Sci Rep (2019) 9, 3577, doi:10.1038/s41598-019-38746-w.
• Asgari, E., Münch, P. C., Lesker, T. R., McHardy, A. C. & Mofrad, M. R. K. DiTaxa: nucleotide-pair encoding of 16S rRNA for host phenotype and biomarker detection. Bioinformatics (2019) 35, 2498, doi:10.1093/bioinformatics/bty954.
• Bledea, R., Vasudevaraja, V., Patel, S., Stafford, J., Serrano, J., Esposito, G., Tredwin, L. M., Goodman, N., Kloetgen, A., Golfinos, J. G., Zagzag, D., Weigelt, B., Iafrate, A. J., Sulman, E. P., Chi, A. S., Dogan, S., Reis-Filho, J. S., Chiang, S., Placantonakis, D., Tsirigos, A. & Snuderl, M. Functional and topographic effects on DNA methylation in IDH1/2 mutant cancers. Sci Rep (2019) 9, 16830, doi:10.1038/s41598-019-53262-7.
• Chen, X., Glytsou, C., Zhou, H., Narang, S., Reyna, D. E., Lopez, A., Sakellaropoulos, T., Gong, Y., Kloetgen, A., Yap, Y. S., Wang, E., Gavathiotis, E., Tsirigos, A., Tibes, R. & Aifantis, I. Targeting Mitochondrial Structure Sensitizes Acute Myeloid Leukemia to Venetoclax Treatment. Cancer Discov (2019) 9, 890, doi:10.1158/2159-8290.Cd-19-0117.
• Di Giammartino, D. C.*, Kloetgen, A.*, Polyzos, A., Liu, Y., Kim, D., Murphy, D., Abuhashem, A., Cavaliere, P., Aronson, B., Shah, V., Dephoure, N., Stadtfeld, M., Tsirigos, A. & Apostolou, E. (*shared first authors) KLF4 is involved in the organization and regulation of pluripotency-associated three-dimensional enhancer networks. Nat Cell Biol (2019) 21, 1179, doi:10.1038/s41556-019-0390-6.
• Fritz, A., Hofmann, P., Majda, S., Dahms, E., Dröge, J., Fiedler, J., Lesker, T. R., Belmann, P., DeMaere, M. Z., Darling, A. E., Sczyrba, A., Bremges, A. & McHardy, A. C. CAMISIM: simulating metagenomes and microbial communities. Microbiome (2019) 7, 17, doi:10.1186/s40168-019-0633-6.
• Halaby, M. J., Hezaveh, K., Lamorte, S., Ciudad, M. T., Kloetgen, A., MacLeod, B. L., Guo, M., Chakravarthy, A., Medina, T. D. S., Ugel, S., Tsirigos, A., Bronte, V., Munn, D. H., Pugh, T. J., De Carvalho, D. D., Butler, M. O., Ohashi, P. S., Brooks, D. G. & McGaha, T. L. GCN2 drives macrophage and MDSC function and immunosuppression in the tumor microenvironment. Sci Immunol (2019) 4, eaax8189, doi:10.1126/sciimmunol.aax8189.
• Hoell, J. I., Ginzel, S., Kuhlen, M., Kloetgen, A., Gombert, M., Fischer, U., Hein, D., Demir, S., Stanulla, M., Schrappe, M., Zur Stadt, U., Bader, P., Babor, F., Schuster, F., Strahm, B., Alten, J., Moericke, A., Escherich, G., von Stackelberg, A., Thiele, R., McHardy, A. C., Peters, C., Bornhauser, B., Bourquin, J. P., Krause, S., Enczmann, J., Meyer, L. H., Eckert, C., Borkhardt, A. & Meisel, R. Pediatric ALL relapses after allo-SCT show high individuality, clonal dynamics, selective pressure, and druggable targets. Blood Adv (2019) 3, 3143, doi:10.1182/bloodadvances.2019000051.
• Ingenhag, D., Reister, S., Auer, F., Bhatia, S., Wildenhain, S., Picard, D., Remke, M., Hoell, J. I., Kloetgen, A., Sohn, D., Jänicke, R. U., Koegler, G., Borkhardt, A. & Hauer, J. The homeobox transcription factor HB9 induces senescence and blocks differentiation in hematopoietic stem and progenitor cells. Haematologica (2019) 104, 35, doi:10.3324/haematol.2018.189407.
• Klingen, T. R., Loers, J., Stanelle-Bertram, S., Gabriel, G. & McHardy, A. C. Structures and functions linked to genome-wide adaptation of human influenza A viruses. Sci Rep (2019) 9, 6267, doi:10.1038/s41598-019-42614-y.
• Kloetgen, A., Münch, P. C., Borkhardt, A., Hoell, J. I. & McHardy, A. C. Corrigendum to: Biochemical and bioinformatic methods for elucidating the role of RNA-protein interactions in posttranscriptional regulation. Brief Funct Genomics (2019) 18, 433, doi:10.1093/bfgp/elz014.
• Kloetgen, A.*, Thandapani, P.*, Tsirigos, A.* & Aifantis, I.* (*shared first authors) 3D Chromosomal Landscapes in Hematopoiesis and Immunity. Trends Immunol (2019) 40, 809, doi:10.1016/j.it.2019.07.003.
• Lhoumaud, P., Badri, S., Rodriguez-Hernaez, J., Sakellaropoulos, T., Sethia, G., Kloetgen, A., Cornwell, M., Bhattacharyya, S., Ay, F., Bonneau, R., Tsirigos, A. & Skok, J. A. NSD2 overexpression drives clustered chromatin and transcriptional changes in a subset of insulated domains. Nat Commun (2019) 10, 4843, doi:10.1038/s41467-019-12811-4.
• Meyer, F., Bremges, A., Belmann, P., Janssen, S., McHardy, A. C.* & Koslicki, D.* (*shared last authors) Assessing taxonomic metagenome profilers with OPAL. Genome Biol (2019) 20, 51, doi:10.1186/s13059-019-1646-y.
• Vatanen, T., Plichta, D. R., Somani, J., Münch, P. C., Arthur, T. D., Hall, A. B., Rudolf, S., Oakeley, E. J., Ke, X., Young, R. A., Haiser, H. J., Kolde, R., Yassour, M., Luopajärvi, K., Siljander, H., Virtanen, S. M., Ilonen, J., Uibo, R., Tillmann, V., Mokurov, S., Dorshakova, N., Porter, J. A., McHardy, A. C., Lähdesmäki, H., Vlamakis, H., Huttenhower, C., Knip, M. & Xavier, R. J. Genomic variation and strain-specific functional adaptation in the human gut microbiome during early life. Nat Microbiol (2019) 4, 470, doi:10.1038/s41564-018-0321-5.
• Vatanen, T., Plichta, D. R., Somani, J., Münch, P. C., Arthur, T. D., Hall, A. B., Rudolf, S., Oakeley, E. J., Ke, X., Young, R. A., Haiser, H. J., Kolde, R., Yassour, M., Luopajärvi, K., Siljander, H., Virtanen, S. M., Ilonen, J., Uibo, R., Tillmann, V., Mokurov, S., Dorshakova, N., Porter, J. A., McHardy, A. C., Lähdesmäki, H., Vlamakis, H., Huttenhower, C., Knip, M. & Xavier, R. J. Publisher Correction: Genomic variation and strain-specific functional adaptation in the human gut microbiome during early life. Nat Microbiol (2019) 4, 545, doi:10.1038/s41564-019-0393-x.
• Wang, E., Lu, S. X., Pastore, A., Chen, X., Imig, J., Chun-Wei Lee, S., Hockemeyer, K., Ghebrechristos, Y. E., Yoshimi, A., Inoue, D., Ki, M., Cho, H., Bitner, L., Kloetgen, A., Lin, K. T., Uehara, T., Owa, T., Tibes, R., Krainer, A. R., Abdel-Wahab, O. & Aifantis, I. Targeting an RNA-Binding Protein Network in Acute Myeloid Leukemia. Cancer Cell (2019) 35, 369, doi:10.1016/j.ccell.2019.01.010.
• Zhou, N., Jiang, Y., Bergquist, T. R., Lee, A. J., Kacsoh, B. Z., Crocker, A. W., Lewis, K. A., Georghiou, G., Nguyen, H. N., Hamid, M. N., Davis, L., Dogan, T., Atalay, V., Rifaioglu, A. S., Dalkıran, A., Cetin Atalay, R., Zhang, C., Hurto, R. L., Freddolino, P. L., Zhang, Y., Bhat, P., Supek, F., Fernández, J. M., Gemovic, B., Perovic, V. R., Davidović, R. S., Sumonja, N., Veljkovic, N., Asgari, E., Mofrad, M. R. K., Profiti, G., Savojardo, C., Martelli, P. L., Casadio, R., Boecker, F., Schoof, H., Kahanda, I., Thurlby, N., McHardy, A. C., Renaux, A., Saidi, R., Gough, J., Freitas, A. A., Antczak, M., Fabris, F., Wass, M. N., Hou, J., Cheng, J., Wang, Z., Romero, A. E., Paccanaro, A., Yang, H., Goldberg, T., Zhao, C., Holm, L., Törönen, P., Medlar, A. J., Zosa, E., Borukhov, I., Novikov, I., Wilkins, A., Lichtarge, O., Chi, P. H., Tseng, W. C., Linial, M., Rose, P. W., Dessimoz, C., Vidulin, V., Dzeroski, S., Sillitoe, I., Das, S., Lees, J. G., Jones, D. T., Wan, C., Cozzetto, D., Fa, R., Torres, M., Warwick Vesztrocy, A., Rodriguez, J. M., Tress, M. L., Frasca, M., Notaro, M., Grossi, G., Petrini, A., Re, M., Valentini, G., Mesiti, M., Roche, D. B., Reeb, J., Ritchie, D. W., Aridhi, S., Alborzi, S. Z., Devignes, M. D., Koo, D. C. E., Bonneau, R., Gligorijević, V., Barot, M., Fang, H., Toppo, S., Lavezzo, E., Falda, M., Berselli, M., Tosatto, S. C. E., Carraro, M., Piovesan, D., Ur Rehman, H., Mao, Q., Zhang, S., Vucetic, S., Black, G. S., Jo, D., Suh, E., Dayton, J. B., Larsen, D. J., Omdahl, A. R., McGuffin, L. J., Brackenridge, D. A., Babbitt, P. C., Yunes, J. M., Fontana, P., Zhang, F., Zhu, S., You, R., Zhang, Z., Dai, S., Yao, S., Tian, W., Cao, R., Chandler, C., Amezola, M., Johnson, D., Chang, J. M., Liao, W. H., Liu, Y. W., Pascarelli, S., Frank, Y., Hoehndorf, R., Kulmanov, M., Boudellioua, I., Politano, G., Di Carlo, S., Benso, A., Hakala, K., Ginter, F., Mehryary, F., Kaewphan, S., Björne, J., Moen, H., Tolvanen, M. E. E., Salakoski, T., Kihara, D., Jain, A., Šmuc, T., Altenhoff, A., Ben-Hur, A., Rost, B., Brenner, S. E., Orengo, C. A., Jeffery, C. J., Bosco, G., Hogan, D. A., Martin, M. J., O'Donovan, C., Mooney, S. D., Greene, C. S., Radivojac, P.* & Friedberg, I.* (*shared last authors) The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens. Genome Biol (2019) 20, 244, doi:10.1186/s13059-019-1835-8.

2018

• Asgari, E., Garakani, K., McHardy, A. C.* & Mofrad, M. R. K.* (*shared last authors) 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, doi:10.1093/bioinformatics/bty296.
• Bremges, A. & McHardy, A. C. Critical Assessment of Metagenome Interpretation Enters the Second Round. mSystems (2018) 3, e00103-18, doi:10.1128/mSystems.00103-18.
• Duggimpudi, S., Kloetgen, A., Maney, S. K., Münch, P. C., Hezaveh, K., Shaykhalishahi, H., Hoyer, W., McHardy, A. C., Lang, P. A., Borkhardt, A. & Hoell, J. I. 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, doi:10.1074/jbc.RA118.002243.
• Garrido-Oter, R., Nakano, R. T., Dombrowski, N., Ma, K. W., McHardy, A. C. & Schulze-Lefert, P. Modular Traits of the Rhizobiales Root Microbiota and Their Evolutionary Relationship with Symbiotic Rhizobia. Cell Host Microbe (2018) 24, 155, doi:10.1016/j.chom.2018.06.006.
• Hoell, J. I., Ginzel, S., Kuhlen, M., Klötgen, A., Gombert, M., Fischer, U., Schäfer, D., Stanulla, M., Schrappe, M., Stadt, U. z., Bader, P., Babor, F., Schuster, F., Strahm, B., Alten, J., Moericke, A., Escherich, G., von Stackelberg, A., Thiele, R., McHardy, A. C., Peters, C., Eckert, C., Borkhardt, A. & Meisel, R. Whole-Exome-Sequencing identifiziert hohe Plastizität, Selektionsdruck und „druggable targets“ in Leukämiezellen pädiatrischer ALL Rezidive nach allogener Stammzelltransplantation. Monatsschrift Kinderheilkunde (2018) 166, 648.
• Ibrahim, B., Arkhipova, K., Andeweg, A. C., Posada-Céspedes, S., Enault, F., Gruber, A., Koonin, E. V., Kupczok, A., Lemey, P., McHardy, A. C., McMahon, D. P., Pickett, B. E., Robertson, D. L., Scheuermann, R. H., Zhernakova, A., Zwart, M. P., Schönhuth, A., Dutilh, B. E. & Marz, M. Bioinformatics Meets Virology: The European Virus Bioinformatics Center's Second Annual Meeting. Viruses (2018) 10, 256, doi:10.3390/v10050256.
• Klingen, T. R.*, Reimering, S.*, Guzmán, C. A. & McHardy, A. C. (*shared first authors) In Silico Vaccine Strain Prediction for Human Influenza Viruses. Trends Microbiol (2018) 26, 119, doi:10.1016/j.tim.2017.09.001.
• Klingen, T. R.*, Reimering, S.*, Loers, J., Mooren, K., Klawonn, F., Krey, T., Gabriel, G. & McHardy, A. C. (*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, doi:10.1038/s41598-017-18791-z.
• Meyer, F., Hofmann, P., Belmann, P., Garrido-Oter, R., Fritz, A., Sczyrba, A. & McHardy, A. C. AMBER: Assessment of Metagenome BinnERs. Gigascience (2018) 7, giy069, doi:10.1093/gigascience/giy069.
• Naas, A. E., Solden, L. M., Norbeck, A. D., Brewer, H., Hagen, L. H., Heggenes, I. M., McHardy, A. C., Mackie, R. I., Paša-Tolić, L., Arntzen, M., Eijsink, V. G. H., Koropatkin, N. M., Hess, M., Wrighton, K. C. & Pope, P. B. "Candidatus Paraporphyromonas polyenzymogenes" encodes multi-modular cellulases linked to the type IX secretion system. Microbiome (2018) 6, 44, doi:10.1186/s40168-018-0421-8.
• Reimering, S. & McHardy, A. C. Software for Characterizing the Antigenic and Genetic Evolution of Human Influenza Viruses. Methods Mol Biol (2018) 1836, 551, doi:10.1007/978-1-4939-8678-1_26.
• Reimering, S., Muñoz, S. & McHardy, A. C. A Fréchet tree distance measure to compare phylogeographic spread paths across trees. Sci Rep (2018) 8, 17000, doi:10.1038/s41598-018-35421-4.

2017

• Doerrenberg, M., Kloetgen, A., Hezaveh, K., Wossmann, W., Bleckmann, K., Stanulla, M., Schrappe, M., McHardy, A. C., Borkhardt, A. & Hoell, J. I. T-cell acute lymphoblastic leukemia in infants has distinct genetic and epigenetic features compared to childhood cases. Genes Chromosomes Cancer (2017) 56, 159, doi:10.1002/gcc.22423.
• Dröge, J., Schonhuth, A. & McHardy, A. C. A probabilistic model to recover individual genomes from metagenomes. PeerJ Computer Science (2017) 3, e117.
• Grießmeier, V., Bremges, A., McHardy, A. C. & Gescher, J. Investigation of different nitrogen reduction routes and their key microbial players in wood chip-driven denitrification beds. Scientific Reports (2017) 7, 17028, doi:10.1038/s41598-017-17312-2.
• Krause, S., Bremges, A., Munch, P. C., McHardy, A. C. & Gescher, J. Characterisation of a stable laboratory co-culture of acidophilic nanoorganisms. Sci Rep (2017) 7, 3289, doi:10.1038/s41598-017-03315-6.
• Kunath, B. J., Bremges, A., Weimann, A., McHardy, A. C. & Pope, P. B. Metagenomics and CAZyme Discovery. Methods Mol Biol (2017) 1588, 255, doi:10.1007/978-1-4939-6899-2_20.
• Maus, I.*, Bremges, A.*, Stolze, Y., Hahnke, S., Cibis, K. G., Koeck, D. E., Kim, Y. S., Kreubel, J., Hassa, J., Wibberg, D., Weimann, A., Off, S., Stantscheff, R., Zverlov, V. V., Schwarz, W. H., König, H., Liebl, W., Scherer, P., McHardy, A. C., Sczyrba, A., Klocke, M., Pühler, A. & Schlüter, A. (*shared first authors) Genomics and prevalence of bacterial and archaeal isolates from biogas-producing microbiomes. Biotechnology for Biofuels (2017) 10, 264, doi:10.1186/s13068-017-0947-1.
• McHardy, A. C. & Kloetgen, A. Finding Genes in Genome Sequence. Methods Mol Biol (2017) 1525, 271, doi:10.1007/978-1-4939-6622-6_11.
• Münch, P. C., Stecher, B. & McHardy, A. C. EDEN: Evolutionary Dynamics within Environments. Bioinformatics (2017), 33, 3292 doi:10.1093/bioinformatics/btx394.
• Sczyrba, A.*, Hofmann, P.*, Belmann, P.*, Koslicki, D., Janssen, S., Dröge, J., Gregor, I., Majda, S., Fiedler, J., Dahms, E., Bremges, A., Fritz, A., Garrido-Oter, R., Jørgensen, T. S., Shapiro, N., Blood, P. D., Gurevich, A., Bai, Y., Turaev, D., DeMaere, M. Z., Chikhi, R., Nagarajan, N., Quince, C., Meyer, F., Balvočiūtė, M., Hansen, L. H., Sørensen, S. J., Chia, B. K. H., Denis, B., Froula, J. L., Wang, Z., Egan, R., Don Kang, D., Cook, J. J., Deltel, C., Beckstette, M., Lemaitre, C., Peterlongo, P., Rizk, G., Lavenier, D., Wu, Y.-W., Singer, S. W., Jain, C., Strous, M., Klingenberg, H., Meinicke, P., Barton, M. D., Lingner, T., Lin, H.-H., Liao, Y.-C., Silva, G. G. Z., Cuevas, D. A., Edwards, R. A., Saha, S., Piro, V. C., Renard, B. Y., Pop, M., Klenk, H.-P., Göker, M., Kyrpides, N. C., Woyke, T., Vorholt, J. A., Schulze-Lefert, P., Rubin, E. M., Darling, A. E., Rattei, T. & McHardy, A. C. (*shared first authors) Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software. Nature Methods (2017) 14, 1063, doi:10.1038/nmeth.4458
• Ye, Z., Pan, Y., Zhang, Y., Cui, H., Jin, G., McHardy, A. C., Fan, L. & Yu, X. Comparative whole-genome analysis reveals artificial selection effects on Ustilago esculenta genome. DNA Research (2017), 24, 635, doi:10.1093/dnares/dsx031.

2016

• Brugiroux, S., Beutler, M., Pfann, C., Garzetti, D., Ruscheweyh, H. J., Ring, D., Diehl, M., Herp, S., Lotscher, Y., Hussain, S., Bunk, B., Pukall, R., Huson, D. H., Munch, P. C., McHardy, A. C., McCoy, K. D., Macpherson, A. J., Loy, A., Clavel, T., Berry, D. & Stecher, B. Genome-guided design of a defined mouse microbiota that confers colonization resistance against Salmonella enterica serovar Typhimurium. Nat Microbiol (2016) 2, 16215, doi:10.1038/nmicrobiol.2016.215.
• Dong, X., Droge, J., von Toerne, C., Marozava, S., McHardy, A. C. & Meckenstock, R. U. 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 (2016), 93, doi:10.1093/femsec/fiw254.
• Frank, J. A., Arntzen, M. O., Sun, L., Hagen, L. H., McHardy, A. C., Horn, S. J., Eijsink, V. G., Schnurer, A. & Pope, P. B. Novel Syntrophic Populations Dominate an Ammonia-Tolerant Methanogenic Microbiome. mSystems (2016) 1, doi:10.1128/mSystems.00092-16.
• Frank, J. A., Pan, Y., Tooming-Klunderud, A., Eijsink, V. G., McHardy, A. C., Nederbragt, A. J. & Pope, P. B. Improved metagenome assemblies and taxonomic binning using long-read circular consensus sequence data. Sci Rep (2016) 6, 25373, doi:10.1038/srep25373.
• Gregor, I., Droge, J., Schirmer, M., Quince, C. & McHardy, A. C. PhyloPythiaS+: a self-training method for the rapid reconstruction of low-ranking taxonomic bins from metagenomes. PeerJ (2016) 4, e1603, doi:10.7717/peerj.1603.
• Gregor, I., Schonhuth, A. & McHardy, A. C. Snowball: strain aware gene assembly of metagenomes. Bioinformatics (2016) 32, i649, doi:10.1093/bioinformatics/btw426.
• Hacquard, S., Kracher, B., Hiruma, K., Munch, P. C., Garrido-Oter, R., Thon, M. R., Weimann, A., Damm, U., Dallery, J. F., Hainaut, M., Henrissat, B., Lespinet, O., Sacristan, S., Ver Loren van Themaat, E., Kemen, E., McHardy, A. C., Schulze-Lefert, P. & O'Connell, R. J. Survival trade-offs in plant roots during colonization by closely related beneficial and pathogenic fungi. Nat Commun (2016) 7, 11362, doi:10.1038/ncomms11362.
• Hezaveh, K., Kloetgen, A., Bernhart, S. H., Mahapatra, K. D., Lenze, D., Richter, J., Haake, A., Bergmann, A. K., Brors, B., Burkhardt, B., Claviez, A., Drexler, H. G., Eils, R., Haas, S., Hoffmann, S., Karsch, D., Klapper, W., Kleinheinz, K., Korbel, J., Kretzmer, H., Kreuz, M., Kuppers, R., Lawerenz, C., Leich, E., Loeffler, M., Mantovani-Loeffler, L., Lopez, C., McHardy, A. C., Moller, P., Rohde, M., Rosenstiel, P., Rosenwald, A., Schilhabel, M., Schlesner, M., Scholz, I., Stadler, P. F., Stilgenbauer, S., Sungalee, S., Szczepanowski, M., Trumper, L., Weniger, M. A., Siebert, R., Borkhardt, A., Hummel, M. & Hoell, J. I. Alterations of miRNAs and miRNA-regulated mRNA expression in GC B cell lymphomas determined by integrative sequencing analysis. Haematologica (2016), doi:10.3324/haematol.2016.143891.
• Ikeda-Ohtsubo, W., Strassert, J. F., Kohler, T., Mikaelyan, A., Gregor, I., McHardy, A. C., Tringe, S. G., Hugenholtz, P., Radek, R. & Brune, A. '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, doi:10.1111/1462-2920.13234.
• Kloetgen, A., Borkhardt, A., Hoell, J. I. & McHardy, A. C. The PARA-suite: PAR-CLIP specific sequence read simulation and processing. PeerJ (2016) 4, e2619, doi:10.7717/peerj.2619.
• Kratsch, C.*, Klingen, T. R.*, Mumken, L., Steinbruck, L. & McHardy, A. C. (*shared first authors) Determination of antigenicity-altering patches on the major surface protein of human influenza A/H3N2 viruses. Virus Evol (2016) 2, vev025, doi:10.1093/ve/vev025.
• Laehnemann, D., Borkhardt, A. & McHardy, A. C. Denoising DNA deep sequencing data-high-throughput sequencing errors and their correction. Brief Bioinform (2016) 17, 154, doi:10.1093/bib/bbv029.
• Otte, A., Marriott, A. C., Dreier, C., Dove, B., Mooren, K., Klingen, T. R., Sauter, M., Thompson, K. A., Bennett, A., Klingel, K., van Riel, D., McHardy, A. C., Carroll, M. W. & Gabriel, G. 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, doi:10.1038/srep28583.
• Weimann, A., Mooren, K., Frank, J., Pope, P. B., Bremges, A. & McHardy, A. C. From Genomes to Phenotypes: Traitar, the Microbial Trait Analyzer. mSystems (2016) 1, doi:10.1128/mSystems.00101-16.

2015

• Bai, Y., Muller, D. B., Srinivas, G., Garrido-Oter, R., Potthoff, E., Rott, M., Dombrowski, N., Munch, P. C., Spaepen, S., Remus-Emsermann, M., Huttel, B., McHardy, A. C., Vorholt, J. A. & Schulze-Lefert, P. Functional overlap of the Arabidopsis leaf and root microbiota. Nature (2015) 528, 364, doi:10.1038/nature16192.
• Belmann, P., Droge, J., Bremges, A., McHardy, A. C., Sczyrba, A. & Barton, M. D. Bioboxes: standardised containers for interchangeable bioinformatics software. Gigascience (2015) 4, 47, doi:10.1186/s13742-015-0087-0.
• Bulgarelli, D.*, Garrido-Oter, R.*, Munch, P. C., Weiman, A., Droge, J., Pan, Y., McHardy, A. C.* & Schulze-Lefert, P.* (*shared first & last authors) Structure and function of the bacterial root microbiota in wild and domesticated barley. Cell Host Microbe (2015) 17, 392, doi:10.1016/j.chom.2015.01.011.
• Droge, J., Gregor, I. & McHardy, A. C. Taxator-tk: precise taxonomic assignment of metagenomes by fast approximation of evolutionary neighborhoods. Bioinformatics (2015) 31, 817, doi:10.1093/bioinformatics/btu745.
• Fischer, U., Forster, M., Rinaldi, A., Risch, T., Sungalee, S., Warnatz, H. J., Bornhauser, B., Gombert, M., Kratsch, C., Stutz, A. M., Sultan, M., Tchinda, J., Worth, C. L., Amstislavskiy, V., Badarinarayan, N., Baruchel, A., Bartram, T., Basso, G., Canpolat, C., Cario, G., Cave, H., Dakaj, D., Delorenzi, M., Dobay, M. P., Eckert, C., Ellinghaus, E., Eugster, S., Frismantas, V., Ginzel, S., Haas, O. A., Heidenreich, O., Hemmrich-Stanisak, G., Hezaveh, K., Holl, J. I., Hornhardt, S., Husemann, P., Kachroo, P., Kratz, C. P., Kronnie, G. T., Marovca, B., Niggli, F., McHardy, A. C., Moorman, A. V., Panzer-Grumayer, R., Petersen, B. S., Raeder, B., Ralser, M., Rosenstiel, P., Schafer, D., Schrappe, M., Schreiber, S., Schutte, M., Stade, B., Thiele, R., Weid, N., Vora, A., Zaliova, M., Zhang, L., Zichner, T., Zimmermann, M., Lehrach, H., Borkhardt, A., Bourquin, J. P., Franke, A., Korbel, J. O., Stanulla, M. & Yaspo, M. L. Genomics and drug profiling of fatal TCF3-HLF-positive acute lymphoblastic leukemia identifies recurrent mutation patterns and therapeutic options. Nat Genet (2015) 47, 1020, doi:10.1038/ng.3362.
• Gubry-Rangin, C., Kratsch, C., Williams, T. A., McHardy, A. C., Embley, T. M., Prosser, J. I. & Macqueen, D. J. Coupling of diversification and pH adaptation during the evolution of terrestrial Thaumarchaeota. Proc Natl Acad Sci U S A (2015) 112, 9370, doi:10.1073/pnas.1419329112.
• Hacquard, S., Garrido-Oter, R., Gonzalez, A., Spaepen, S., Ackermann, G., Lebeis, S., McHardy, A. C., Dangl, J. L., Knight, R., Ley, R. & Schulze-Lefert, P. Microbiota and Host Nutrition across Plant and Animal Kingdoms. Cell Host Microbe (2015) 17, 603, doi:10.1016/j.chom.2015.04.009.
• Kloetgen, A., Munch, P. C., Borkhardt, A., Hoell, J. I. & McHardy, A. C. Biochemical and bioinformatic methods for elucidating the role of RNA-protein interactions in posttranscriptional regulation. Brief Funct Genomics (2015) 14, 102, doi:10.1093/bfgp/elu020.
• McHardy, A. C. How to Grow a Computational Biology Lab. PLoS Comput Biol (2015) 11, e1004397, doi:10.1371/journal.pcbi.1004397.
• McHardy, A. C. PhyloPythia(S). In: Encyclopedia of Metagenomics - Genes, Genomes and Metagenomes. Basics, Methods, Databases and Tools, Karen E. Nelson (Editor), Springer US, 2015, 582.
• Otte, A., Sauter, M., Daxer, M. A., McHardy, A. C., Klingel, K. & Gabriel, G. Adaptive Mutations That Occurred during Circulation in Humans of H1N1 Influenza Virus in the 2009 Pandemic Enhance Virulence in Mice. J Virol (2015) 89, 7329, doi:10.1128/JVI.00665-15.

2014

• Guttman, D. S.*, McHardy, A. C.* & Schulze-Lefert, P.* (*all authors contributed equally) Microbial genome-enabled insights into plant-microorganism interactions. Nature reviews. Genetics (2014) 15, 797, doi:10.1038/nrg3748.
• Konietzny, S. G., Pope, P. B., Weimann, A. & McHardy, A. C. Inference of phenotype-defining functional modules of protein families for microbial plant biomass degraders. Biotechnol Biofuels (2014) 7, 124, doi:10.1186/s13068-014-0124-8.
• Kratsch, C. & McHardy, A. C. RidgeRace: ridge regression for continuous ancestral character estimation on phylogenetic trees. Bioinformatics (2014) 30, i527, doi:10.1093/bioinformatics/btu477.
• Steinbruck, L., Klingen, T. R. & McHardy, A. C. Computational prediction of vaccine strains for human Influenza A (H3N2) viruses. J Virol (2014) 88, 12123, doi:10.1128/JVI.01861-14.

2013

• Gregor, I., Steinbruck, L. & McHardy, A. C. PTree: pattern-based, stochastic search for maximum parsimony phylogenies. PeerJ (2013) 1, e89, doi:10.7717/peerj.89.
• Patil, K. R. & McHardy, A. C. Alignment-free genome tree inference by learning group-specific distance metrics. Genome Biol Evol (2013) 5, 1470, doi:10.1093/gbe/evt105.
• Rohr, C., Kerick, M., Fischer, A., Kuhn, A., Kashofer, K., Timmermann, B., Daskalaki, A., Meinel, T., Drichel, D., Borno, S. T., Nowka, A., Krobitsch, S., McHardy, A. C., Kratsch, C., Becker, T., Wunderlich, A., Barmeyer, C., Viertler, C., Zatloukal, K., Wierling, C., Lehrach, H. & Schweiger, M. R. 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, doi:10.1371/journal.pone.0067461.
• Steinbrück, L. & Mchardy, A. C. Evaluating the Evolutionary Dynamics of Viral Populations. In: Dynamic Models of Infectious Diseases, V. Sree, Hari Rao (Editors), Springer, 2013, 205, doi:10.1007/978-1-4614-9224-5_8.
• Weimann, A.*, Trukhina, Y.*, Pope, P. B., Konietzny, S. G. & McHardy, A. C. (*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, doi:10.1186/1754-6834-6-24.

2012

• Droge, J. & McHardy, A. C. Taxonomic binning of metagenome samples generated by next-generation sequencing technologies. Brief Bioinform (2012) 13, 646, doi:10.1093/bib/bbs031.
• Gilbert, J. A., Steele, J. A., Caporaso, J. G., Steinbruck, L., Reeder, J., Temperton, B., Huse, S., McHardy, A. C., Knight, R., Joint, I., Somerfield, P., Fuhrman, J. A. & Field, D. Defining seasonal marine microbial community dynamics. Isme J (2012) 6, 298, doi:10.1038/ismej.2011.107.
• Patil, K. R., Roune, L. & McHardy, A. C. The PhyloPythiaS web server for taxonomic assignment of metagenome sequences. PLoS One (2012) 7, e38581, doi:10.1371/journal.pone.0038581.
• Pope, P. B., Mackenzie, A. K., Gregor, I., Smith, W., Sundset, M. A., McHardy, A. C., Morrison, M. & Eijsink, V. G. Metagenomics of the Svalbard reindeer rumen microbiome reveals abundance of polysaccharide utilization loci. PLoS One (2012) 7, e38571, doi:10.1371/journal.pone.0038571.
• Steinbruck, L. & McHardy, A. C. Inference of genotype-phenotype relationships in the antigenic evolution of human influenza A (H3N2) viruses. PLoS Comput Biol (2012) 8, e1002492, doi:10.1371/journal.pcbi.1002492.
• Tusche, C., Steinbruck, L. & McHardy, A. C. Detecting patches of protein sites of influenza A viruses under positive selection. Mol Biol Evol (2012) 29, 2063, doi:10.1093/molbev/mss095.

2011

• Adams, B. & McHardy, A. C. The impact of seasonal and year-round transmission regimes on the evolution of influenza A virus. Proc Biol Sci (2011) 278, 2249, doi:10.1098/rspb.2010.2191.
• Konietzny, S. G., Dietz, L. & McHardy, A. C. Inferring functional modules of protein families with probabilistic topic models. BMC Bioinformatics (2011) 12, 141, doi:10.1186/1471-2105-12-141.
• Lykidis, A., Chen, C. L., Tringe, S. G., McHardy, A. C., Copeland, A., Kyrpides, N. C., Hugenholtz, P., Macarie, H., Olmos, A., Monroy, O. & Liu, W. T. Multiple syntrophic interactions in a terephthalate-degrading methanogenic consortium. Isme J (2011) 5, 122, doi:10.1038/ismej.2010.125.
• McHardy, A. C. & Patil, K. R. Phylogenetic Binning of Metagenome Sequence Samples. In: Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary, Frans J. de Bruijn (Editor), John Wiley & Sons, 2011, 353.
• Patil, K. R., Haider, P., Pope, P. B., Turnbaugh, P. J., Morrison, M., Scheffer, T. & McHardy, A. C. Taxonomic metagenome sequence assignment with structured output models. Nat Methods (2011) 8, 191, doi:10.1038/nmeth0311-191.
• Pope, P. B., Smith, W., Denman, S. E., Tringe, S. G., Barry, K., Hugenholtz, P., McSweeney, C. S., McHardy, A. C. & Morrison, M. Isolation of Succinivibrionaceae implicated in low methane emissions from Tammar wallabies. Science (2011) 333, 646, doi:10.1126/science.1205760.
• Steinbruck, L. & McHardy, A. C. Allele dynamics plots for the study of evolutionary dynamics in viral populations. Nucleic Acids Res (2011) 39, e4, doi:10.1093/nar/gkq909.

2010

• Gilbert, J. A., Meyer, F., Antonopoulos, D., Balaji, P., Brown, C. T., Brown, C. T., Desai, N., Eisen, J. A., Evers, D., Field, D., Feng, W., Huson, D., Jansson, J., Knight, R., Knight, J., Kolker, E., Konstantindis, K., Kostka, J., Kyrpides, N., Mackelprang, R., McHardy, A., Quince, C., Raes, J., Sczyrba, A., Shade, A. & Stevens, R. Meeting report: the terabase metagenomics workshop and the vision of an Earth microbiome project. Standards in genomic sciences (2010) 3, 243, doi:10.4056/sigs.1433550.
• Pope, P. B., Denman, S. E., Jones, M., Tringe, S. G., Barry, K., Malfatti, S. A., McHardy, A. C., Cheng, J.-F., Hugenholtz, P., McSweeney, C. S. & Morrison, M. Adaptation to herbivory by the Tammar wallaby includes bacterial and glycoside hydrolase profiles different from other herbivores. Proceedings of the National Academy of Sciences (2010) 107, 14793, doi:10.1073/pnas.1005297107.
• Turnbaugh, P. J., Quince, C., Faith, J. J., McHardy, A. C., Yatsunenko, T., Niazi, F., Affourtit, J., Egholm, M., Henrissat, B., Knight, R. & Gordon, J. I. Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins. Proceedings of the National Academy of Sciences (2010) 107, 7503, doi:10.1073/pnas.1002355107.

2009

• McHardy, A. C. & Adams, B. The role of genomics in tracking the evolution of influenza A virus. PLoS Pathog (2009) 5, e1000566, doi:10.1371/journal.ppat.1000566.

2008

• Adams, B., McHardy, A. C., Lundegard, C. & Lengauer, T. Viral Bioinformatics. In: Modern Genome Annotation, A. Valencia, D. Frishman (Editors), Springer, 2008, 429.
• Gartemann, K. H., Abt, B., Bekel, T., Burger, A., Engemann, J., Flugel, M., Gaigalat, L., Goesmann, A., Grafen, I., Kalinowski, J., Kaup, O., Kirchner, O., Krause, L., Linke, B., McHardy, A. C., Meyer, F., Pohle, S., Ruckert, C., Schneiker, S., Zellermann, E. M., Puhler, A., Eichenlaub, R., Kaiser, O. & Bartels, D. The genome sequence of the tomato-pathogenic actinomycete Clavibacter michiganensis subsp. michiganensis NCPPB382 reveals a large island involved in pathogenicity. J Bacteriol (2008) 190, 2138, doi:10.1128/JB.01595-07.
• Holland, L. Z., Albalat, R., Azumi, K., Benito-Gutierrez, E., Blow, M. J., Bronner-Fraser, M., Brunet, F., Butts, T., Candiani, S., Dishaw, L. J., Ferrier, D. E., Garcia-Fernandez, J., Gibson-Brown, J. J., Gissi, C., Godzik, A., Hallbook, F., Hirose, D., Hosomichi, K., Ikuta, T., Inoko, H., Kasahara, M., Kasamatsu, J., Kawashima, T., Kimura, A., Kobayashi, M., Kozmik, Z., Kubokawa, K., Laudet, V., Litman, G. W., McHardy, A. C., Meulemans, D., Nonaka, M., Olinski, R. P., Pancer, Z., Pennacchio, L. A., Pestarino, M., Rast, J. P., Rigoutsos, I., Robinson-Rechavi, M., Roch, G., Saiga, H., Sasakura, Y., Satake, M., Satou, Y., Schubert, M., Sherwood, N., Shiina, T., Takatori, N., Tello, J., Vopalensky, P., Wada, S., Xu, A., Ye, Y., Yoshida, K., Yoshizaki, F., Yu, J. K., Zhang, Q., Zmasek, C. M., de Jong, P. J., Osoegawa, K., Putnam, N. H., Rokhsar, D. S., Satoh, N. & Holland, P. W. The amphioxus genome illuminates vertebrate origins and cephalochordate biology. Genome Res (2008) 18, 1100, doi:10.1101/gr.073676.107.
• Kalyuzhnaya, M. G., Lapidus, A., Ivanova, N., Copeland, A. C., McHardy, A. C., Szeto, E., Salamov, A., Grigoriev, I. V., Suciu, D., Levine, S. R., Markowitz, V. M., Rigoutsos, I., Tringe, S. G., Bruce, D. C., Richardson, P. M., Lidstrom, M. E. & Chistoserdova, L. High-resolution metagenomics targets specific functional types in complex microbial communities. Nat Biotechnol (2008) 26, 1029, doi:10.1038/nbt.1488.
• McHardy, A. C. Finding genes in genome sequence. Methods Mol Biol (2008) 452, 163, doi:10.1007/978-1-60327-159-2_8.

2007

• Krause, L.*, McHardy, A. C.*, Nattkemper, T. W., Puhler, A., Stoye, J. & Meyer, F. (*shared first authors) GISMO--gene identification using a support vector machine for ORF classification. Nucleic Acids Res (2007) 35, 540, doi:10.1093/nar/gkl1083.
• Mavromatis, K., Ivanova, N., Barry, K., Shapiro, H., Goltsman, E., McHardy, A. C., Rigoutsos, I., Salamov, A., Korzeniewski, F., Land, M., Lapidus, A., Grigoriev, I., Richardson, P., Hugenholtz, P. & Kyrpides, N. C. Use of simulated data sets to evaluate the fidelity of metagenomic processing methods. Nat Methods (2007) 4, 495, doi:10.1038/nmeth1043.
• McHardy, A. C., Martin, H. G., Tsirigos, A., Hugenholtz, P. & Rigoutsos, I. Accurate phylogenetic classification of variable-length DNA fragments. Nat Methods (2007) 4, 63, doi:10.1038/nmeth976.
• McHardy, A. C. & Rigoutsos, I. What's in the mix: phylogenetic classification of metagenome sequence samples. Curr Opin Microbiol (2007) 10, 499, doi:10.1016/j.mib.2007.08.004.
• Schneiker, S., Perlova, O., Kaiser, O., Gerth, K., Alici, A., Altmeyer, M. O., Bartels, D., Bekel, T., Beyer, S., Bode, E., Bode, H. B., Bolten, C. J., Choudhuri, J. V., Doss, S., Elnakady, Y. A., Frank, B., Gaigalat, L., Goesmann, A., Groeger, C., Gross, F., Jelsbak, L., Jelsbak, L., Kalinowski, J., Kegler, C., Knauber, T., Konietzny, S., Kopp, M., Krause, L., Krug, D., Linke, B., Mahmud, T., Martinez-Arias, R., McHardy, A. C., Merai, M., Meyer, F., Mormann, S., Munoz-Dorado, J., Perez, J., Pradella, S., Rachid, S., Raddatz, G., Rosenau, F., Ruckert, C., Sasse, F., Scharfe, M., Schuster, S. C., Suen, G., Treuner-Lange, A., Velicer, G. J., Vorholter, F. J., Weissman, K. J., Welch, R. D., Wenzel, S. C., Whitworth, D. E., Wilhelm, S., Wittmann, C., Blocker, H., Puhler, A. & Muller, R. Complete genome sequence of the myxobacterium Sorangium cellulosum. Nat Biotechnol (2007) 25, 1281, doi:10.1038/nbt1354.
• Warnecke, F., Luginbuhl, P., Ivanova, N., Ghassemian, M., Richardson, T. H., Stege, J. T., Cayouette, M., McHardy, A. C., Djordjevic, G., Aboushadi, N., Sorek, R., Tringe, S. G., Podar, M., Martin, H. G., Kunin, V., Dalevi, D., Madejska, J., Kirton, E., Platt, D., Szeto, E., Salamov, A., Barry, K., Mikhailova, N., Kyrpides, N. C., Matson, E. G., Ottesen, E. A., Zhang, X., Hernandez, M., Murillo, C., Acosta, L. G., Rigoutsos, I., Tamayo, G., Green, B. D., Chang, C., Rubin, E. M., Mathur, E. J., Robertson, D. E., Hugenholtz, P. & Leadbetter, J. R. Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature (2007) 450, 560, doi:10.1038/nature06269.

2006

• Garcia Martin, H., Ivanova, N., Kunin, V., Warnecke, F., Barry, K. W., McHardy, A. C., Yeates, C., He, S., Salamov, A. A., Szeto, E., Dalin, E., Putnam, N. H., Shapiro, H. J., Pangilinan, J. L., Rigoutsos, I., Kyrpides, N. C., Blackall, L. L., McMahon, K. D. & Hugenholtz, P. Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities. Nat Biotechnol (2006) 24, 1263, doi:10.1038/nbt1247.
• Krause, A., Ramakumar, A., Bartels, D., Battistoni, F., Bekel, T., Boch, J., Bohm, M., Friedrich, F., Hurek, T., Krause, L., Linke, B., McHardy, A. C., Sarkar, A., Schneiker, S., Syed, A. A., Thauer, R., Vorholter, F. J., Weidner, S., Puhler, A., Reinhold-Hurek, B., Kaiser, O. & Goesmann, A. Complete genome of the mutualistic, N2-fixing grass endophyte Azoarcus sp. strain BH72. Nat Biotechnol (2006) 24, 1385, doi:10.1038/nbt1243.
• Linke, B.*, McHardy, A. C.*, Neuweger, H., Krause, L. & Meyer, F. (*shared 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, doi:10.2165/00822942-200605030-00008
• Rigoutsos, I., Huynh, T., Miranda, K., Tsirigos, A., McHardy, A. C. & Platt, D. 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, doi:10.1073/pnas.0601688103.
• Schneiker, S., Martins dos Santos, V. A., Bartels, D., Bekel, T., Brecht, M., Buhrmester, J., Chernikova, T. N., Denaro, R., Ferrer, M., Gertler, C., Goesmann, A., Golyshina, O. V., Kaminski, F., Khachane, A. N., Lang, S., Linke, B., McHardy, A. C., Meyer, F., Nechitaylo, T., Puhler, A., Regenhardt, D., Rupp, O., Sabirova, J. S., Selbitschka, W., Yakimov, M. M., Timmis, K. N., Vorholter, F. J., Weidner, S., Kaiser, O. & Golyshin, P. N. Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis. Nat Biotechnol (2006) 24, 997, doi:10.1038/nbt1232.

2005

• Overbeek, R., Begley, T., Butler, R. M., Choudhuri, J. V., Chuang, H. Y., Cohoon, M., de Crecy-Lagard, V., Diaz, N., Disz, T., Edwards, R., Fonstein, M., Frank, E. D., Gerdes, S., Glass, E. M., Goesmann, A., Hanson, A., Iwata-Reuyl, D., Jensen, R., Jamshidi, N., Krause, L., Kubal, M., Larsen, N., Linke, B., McHardy, A. C., Meyer, F., Neuweger, H., Olsen, G., Olson, R., Osterman, A., Portnoy, V., Pusch, G. D., Rodionov, D. A., Ruckert, C., Steiner, J., Stevens, R., Thiele, I., Vassieva, O., Ye, Y., Zagnitko, O. & Vonstein, V. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res (2005) 33, 5691, doi:10.1093/nar/gki866.
• Thieme, F., Koebnik, R., Bekel, T., Berger, C., Boch, J., Buttner, D., Caldana, C., Gaigalat, L., Goesmann, A., Kay, S., Kirchner, O., Lanz, C., Linke, B., McHardy, A. C., Meyer, F., Mittenhuber, G., Nies, D. H., Niesbach-Klosgen, U., Patschkowski, T., Ruckert, C., Rupp, O., Schneiker, S., Schuster, S. C., Vorholter, F. J., Weber, E., Puhler, A., Bonas, U., Bartels, D. & Kaiser, O. 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, doi:10.1128/JB.187.21.7254-7266.2005.

2004

• McHardy, A. C., Goesmann, A., Puhler, A. & Meyer, F. Development of joint application strategies for two microbial gene finders. Bioinformatics (2004) 20, 1622, doi:10.1093/bioinformatics/bth137.
• McHardy, A. C., Puhler, A., Kalinowski, J. & Meyer, F. Comparing expression level-dependent features in codon usage with protein abundance: an analysis of 'predictive proteomics'. Proteomics (2004) 4, 46, doi:10.1002/pmic.200300501.     

2003

• Goesmann, A., Linke, B., Rupp, O., Krause, L., Bartels, D., Dondrup, M., McHardy, A. C., Wilke, A., Puhler, A. & Meyer, F. Building a BRIDGE for the integration of heterogeneous data from functional genomics into a platform for systems biology. J Biotechnol (2003) 106, 157, doi:10.1016/j.jbiotec.2003.08.007.
• Kalinowski, J., Bathe, B., Bartels, D., Bischoff, N., Bott, M., Burkovski, A., Dusch, N., Eggeling, L., Eikmanns, B. J., Gaigalat, L., Goesmann, A., Hartmann, M., Huthmacher, K., Kramer, R., Linke, B., McHardy, A. C., Meyer, F., Mockel, B., Pfefferle, W., Puhler, A., Rey, D. A., Ruckert, C., Rupp, O., Sahm, H., Wendisch, V. F., Wiegrabe, I. & Tauch, A. 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, doi:10.1016/S0168-1656(03)00154-8.
• McHardy, A. C., Tauch, A., Ruckert, C., Puhler, A. & Kalinowski, J. Genome-based analysis of biosynthetic aminotransferase genes of Corynebacterium glutamicum. J Biotechnol (2003) 104, 229, doi:10.1016/S0168-1656(03)00161-5.
• Meyer, F., Goesmann, A., McHardy, A. C., Bartels, D., Bekel, T., Clausen, J., Kalinowski, J., Linke, B., Rupp, O., Giegerich, R. & Puhler, A. GenDB--an open source genome annotation system for prokaryote genomes. Nucleic Acids Res (2003) 31, 2187, doi: 10.1093/nar/gkg312.
• Wilke, A., Ruckert, C., Bartels, D., Dondrup, M., Goesmann, A., Huser, A. T., Kespohl, S., Linke, B., Mahne, M., McHardy, A. C., Puhler, A. & Meyer, F. Bioinformatics support for high-throughput proteomics. J Biotechnol (2003) 106, 147, doi: 10.1016/j.jbiotec.2003.08.009.