Computational Biology of Infection Research

The Department of “Computational Biology for Infection Research” studies the human microbiome, viral and bacterial pathogens, and human cell lineages within individual patients by analysis of large-scale biological and epidemiological data sets with computational techniques. Focusing on high throughput meta’omics, population genomic and single cell sequencing data, we produce testable hypotheses, such as sets of key sites or relevant genes associated with the presence of a disease, of antibiotic resistance or pathogenic evasion of immune defense. We interact with experimental collaborators to verify our findings and to promote their translation into medical treatment or diagnosis procedures. To achieve its research goals, the department also develops novel algorithms and software.

Leader

Selected Publications

  • Meyer, F., Fritz, A., Deng, Z. L., Koslicki, D., Lesker, T. R., Gurevich, A., Robertson, G., Alser, M., Antipov, D., Beghini, F., Bertrand, D., Brito, J. J., Brown, C. T., Buchmann, J., Buluç, A., Chen, B., Chikhi, R., Clausen, P., Cristian, A., Dabrowski, P. W., Darling, A. E., Egan, R., Eskin, E., Georganas, E., Goltsman, E., Gray, M. A., Hansen, L. H., Hofmeyr, S., Huang, P., Irber, L., Jia, H., Jørgensen, T. S., Kieser, S. D., Klemetsen, T., Kola, A., Kolmogorov, M., Korobeynikov, A., Kwan, J., LaPierre, N., Lemaitre, C., Li, C., Limasset, A., Malcher-Miranda, F., Mangul, S., Marcelino, V. R., Marchet, C., Marijon, P., Meleshko, D., Mende, D. R., Milanese, A., Nagarajan, N., Nissen, J., Nurk, S., Oliker, L., Paoli, L., Peterlongo, P., Piro, V. C., Porter, J. S., Rasmussen, S., Rees, E. R., Reinert, K., Renard, B., Robertsen, E. M., Rosen, G. L., Ruscheweyh, H. J., Sarwal, V., Segata, N., Seiler, E., Shi, L., Sun, F., Sunagawa, S., Sørensen, S. J., Thomas, A., Tong, C., Trajkovski, M., Tremblay, J., Uritskiy, G., Vicedomini, R., Wang, Z., Wang, Z., Wang, Z., Warren, A., Willassen, N. P., Yelick, K., You, R., Zeller, G., Zhao, Z., Zhu, S., Zhu, J., Garrido-Oter, R., Gastmeier, P., Hacquard, S., Häußler, S., Khaledi, A., Maechler, F., Mesny, F., Radutoiu, S., Schulze-Lefert, P., Smit, N., Strowig, T., Bremges, A., Sczyrba, A. & McHardy, A. C. Critical Assessment of Metagenome Interpretation: the second round of challenges. Nat Methods (2022) 19, 429, doi:10.1038/s41592-022-01431-4.
  • 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.
  • 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 and last authors) Hepatitis C reference viruses highlight potent antibody responses and diverse viral functional interactions with neutralising antibodies.Gut (2021) 70, 1734, doi:10.1136/gutjnl-2020-321190.
  • 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.

Publications

2022

  • Deng, Z. L., Münch, P. C., Mreches, R. & McHardy, A. C. Rapid and accurate identification of ribosomal RNA sequences via deep learning.Nucleic Acids Res (2022), doi:10.1093/nar/gkac112.
  • Hotop, S. K., Reimering, S., Shekhar, A., Asgari, E., Beutling, U., Dahlke, C., Fathi, A., Khan, F., Lütgehetmann, M., Ballmann, R., Gerstner, A., Tegge, W., Cicin-Sain, L., Bilitewski, U., McHardy, A. C. & Brönstrup, M. Peptide microarrays coupled to machine learning reveal individual epitopes from human antibody responses with neutralizing capabilities against SARS-CoV-2.Emerg Microbes Infect (2022) 11, 1037, doi:10.1080/22221751.2022.2057874.
  • McHardy, A. C. Nobel nominators - which women will you suggest?Nature (2022) 601, 508, doi:10.1038/d41586-022-00133-3.
  • Meyer, F., Fritz, A., Deng, Z. L., Koslicki, D., Lesker, T. R., Gurevich, A., Robertson, G., Alser, M., Antipov, D., Beghini, F., Bertrand, D., Brito, J. J., Brown, C. T., Buchmann, J., Buluç, A., Chen, B., Chikhi, R., Clausen, P., Cristian, A., Dabrowski, P. W., Darling, A. E., Egan, R., Eskin, E., Georganas, E., Goltsman, E., Gray, M. A., Hansen, L. H., Hofmeyr, S., Huang, P., Irber, L., Jia, H., Jørgensen, T. S., Kieser, S. D., Klemetsen, T., Kola, A., Kolmogorov, M., Korobeynikov, A., Kwan, J., LaPierre, N., Lemaitre, C., Li, C., Limasset, A., Malcher-Miranda, F., Mangul, S., Marcelino, V. R., Marchet, C., Marijon, P., Meleshko, D., Mende, D. R., Milanese, A., Nagarajan, N., Nissen, J., Nurk, S., Oliker, L., Paoli, L., Peterlongo, P., Piro, V. C., Porter, J. S., Rasmussen, S., Rees, E. R., Reinert, K., Renard, B., Robertsen, E. M., Rosen, G. L., Ruscheweyh, H. J., Sarwal, V., Segata, N., Seiler, E., Shi, L., Sun, F., Sunagawa, S., Sørensen, S. J., Thomas, A., Tong, C., Trajkovski, M., Tremblay, J., Uritskiy, G., Vicedomini, R., Wang, Z., Wang, Z., Wang, Z., Warren, A., Willassen, N. P., Yelick, K., You, R., Zeller, G., Zhao, Z., Zhu, S., Zhu, J., Garrido-Oter, R., Gastmeier, P., Hacquard, S., Häußler, S., Khaledi, A., Maechler, F., Mesny, F., Radutoiu, S., Schulze-Lefert, P., Smit, N., Strowig, T., Bremges, A., Sczyrba, A. & McHardy, A. C. Critical Assessment of Metagenome Interpretation: the second round of challenges. Nat Methods (2022) 19, 429, doi:10.1038/s41592-022-01431-4.

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. C., 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) 438,  440. doi.org/10.1136/gutjnl-2020-321424
  • 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.
  • Weiss, A. S., Burrichter, A. G., Durai Raj, A. C., von Strempel, A., Meng, C., Kleigrewe, K., Münch, P. C., Rössler, L., Huber, C., Eisenreich, W., Jochum, L. M., Göing, S., Jung, K., Lincetto, C., Hübner, J., Marinos, G., Zimmermann, J., Kaleta, C., Sanchez, A. & Stecher, B. In vitro interaction network of a synthetic gut bacterial community.Isme j (2021) in press, doi:10.1038/s41396-021-01153-z.
  • 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) 28, 718, doi:10.1016/j.stem.2020.12.005.
  • Warnat-Herresthal, S., Schultze, H., Shastry, K. L., Manamohan, S., Mukherjee, S., Garg, V., Sarveswara, R., Händler, K., Pickkers, P., Aziz, N. A., Ktena, S., Tran, F., Bitzer, M., Ossowski, S., Casadei, N., Herr, C., Petersheim, D., Behrends, U., Kern, F., Fehlmann, T., Schommers, P., Lehmann, C., Augustin, M., Rybniker, J., Altmüller, J., Mishra, N., Bernardes, J. P., Krämer, B., Bonaguro, L., Schulte-Schrepping, J., De Domenico, E., Siever, C., Kraut, M., Desai, M., Monnet, B., Saridaki, M., Siegel, C. M., Drews, A., Nuesch-Germano, M., Theis, H., Heyckendorf, J., Schreiber, S., Kim-Hellmuth, S., Nattermann, J., Skowasch, D., Kurth, I., Keller, A., Bals, R., Nürnberg, P., Rieß, O., Rosenstiel, P., Netea, M. G., Theis, F., Mukherjee, S., Backes, M., Aschenbrenner, A. C., Ulas, T., Breteler, M. M. B., Giamarellos-Bourboulis, E. J., Kox, M., Becker, M., Cheran, S., Woodacre, M. S., Goh, E. L. & Schultze, J. L. Swarm Learning for decentralized and confidential clinical machine learning.Nature (2021) 594, 265, doi:10.1038/s41586-021-03583-3.
  • 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.
  • Rivas, M. A., Durmaz, C., Kloetgen, A., Chin, C. R., Chen, Z., Bhinder, B., Koren, A., Viny, A. D., Scharer, C. D., Boss, J. M., Elemento, O., Mason, C. E. & Melnick, A. M. Cohesin Core Complex Gene Dosage Contributes to Germinal Center Derived Lymphoma Phenotypes and Outcomes. Front Immunol (2021) 12, 688493, doi:10.3389/fimmu.2021.688493.
  • Pelham-Webb, B., Polyzos, A., Wojenski, L., Kloetgen, A., Li, J., Di Giammartino, D. C., Sakellaropoulos, T., Tsirigos, A., Core, L. & Apostolou, E. H3K27ac bookmarking promotes rapid post-mitotic activation of the pluripotent stem cell program without impacting 3D chromatin reorganization. Mol Cell (2021) 81, 1732, doi:10.1016/j.molcel.2021.02.032.
  • 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.
  • Mirzayi, C., Renson, A., Zohra, F., Elsafoury, S., Geistlinger, L., Kasselman, L. J., Eckenrode, K., van de Wijgert, J., Loughman, A., Marques, F. Z., MacIntyre, D. A., Arumugam, M., Azhar, R., Beghini, F., Bergstrom, K., Bhatt, A., Bisanz, J. E., Braun, J., Bravo, H. C., Buck, G. A., Bushman, F., Casero, D., Clarke, G., Collado, M. C., Cotter, P. D., Cryan, J. F., Demmer, R. T., Devkota, S., Elinav, E., Escobar, J. S., Fettweis, J., Finn, R. D., Fodor, A. A., Forslund, S., Franke, A., Furlanello, C., Gilbert, J., Grice, E., Haibe-Kains, B., Handley, S., Herd, P., Holmes, S., Jacobs, J. P., Karstens, L., Knight, R., Knights, D., Koren, O., Kwon, D. S., Langille, M., Lindsay, B., McGovern, D., McHardy, A. C., McWeeney, S., Mueller, N. T., Nezi, L., Olm, M., Palm, N., Pasolli, E., Raes, J., Redinbo, M. R., Rühlemann, M., Balfour Sartor, R., Schloss, P. D., Schriml, L., Segal, E., Shardell, M., Sharpton, T., Smirnova, E., Sokol, H., Sonnenburg, J. L., Srinivasan, S., Thingholm, L. B., Turnbaugh, P. J., Upadhyay, V., Walls, R. L., Wilmes, P., Yamada, T., Zeller, G., Zhang, M., Zhao, N., Zhao, L., Bao, W., Culhane, A., Devanarayan, V., Dopazo, J., Fan, X., Fischer, M., Jones, W., Kusko, R., Mason, C. E., Mercer, T. R., Sansone, S. A., Scherer, A., Shi, L., Thakkar, S., Tong, W., Wolfinger, R., Hunter, C., Segata, N., Huttenhower, C., Dowd, J. B., Jones, H. E. & Waldron, L. Reporting guidelines for human microbiome research: the STORMS checklist.Nat Med (2021) 27, 1885, doi:10.1038/s41591-021-01552-x.
  • Meyer, F., Lesker, T. R., Koslicki, D., Fritz, A., Gurevich, A., Darling, A. E., Sczyrba, A., Bremges, A. & McHardy, A. C. Tutorial: assessing metagenomics software with the CAMI benchmarking toolkit.Nat Protoc (2021) 16, 1785, doi:10.1038/s41596-020-00480-3.
  • Lähnemann, D., Köster, J., Fischer, U., Borkhardt, A., McHardy, A. C.* & Schönhuth, A.* (*shared last authors) Accurate and scalable variant calling from single cell DNA sequencing data with ProSolo.Nat Commun (2021) 12, 6744, doi:10.1038/s41467-021-26938-w.
  • Krämer, B., Knoll, R., Bonaguro, L., ToVinh, M., Raabe, J., Astaburuaga-García, R., Schulte-Schrepping, J., Kaiser, K. M., Rieke, G. J., Bischoff, J., Monin, M. B., Hoffmeister, C., Schlabe, S., De Domenico, E., Reusch, N., Händler, K., Reynolds, G., Blüthgen, N., Hack, G., Finnemann, C., Nischalke, H. D., Strassburg, C. P., Stephenson, E., Su, Y., Gardner, L., Yuan, D., Chen, D., Goldman, J., Rosenstiel, P., Schmidt, S. V., Latz, E., Hrusovsky, K., Ball, A. J., Johnson, J. M., Koenig, P. A., Schmidt, F. I., Haniffa, M., Heath, J. R., Kümmerer, B. M., Keitel, V., Jensen, B., Stubbemann, P., Kurth, F., Sander, L. E., Sawitzki, B., Aschenbrenner, A. C., Schultze, J. L. & Nattermann, J. Early IFN-α signatures and persistent dysfunction are distinguishing features of NK cells in severe COVID-19.Immunity (2021) 54, 2650, doi:10.1016/j.immuni.2021.09.002.
  • Jacobsen, H., Walendy-Gnirß, K., Tekin-Bubenheim, N., Kouassi, N. M., Ben-Batalla, I., Berenbrok, N., Wolff, M., Dos Reis, V. P., Zickler, M., Scholl, L., Gries, A., Jania, H., Kloetgen, A., Düsedau, A., Pilnitz-Stolze, G., Jeridi, A., Yildirim, A., Fuchs, H., Gailus-Durner, V., Stoeger, C., de Angelis, M. H., Manuylova, T., Klingel, K., Culley, F. J., Behrends, J., Loges, S., Schneider, B., Krauss-Etschmann, S., Openshaw, P. & Gabriel, G. Offspring born to influenza A virus infected pregnant mice have increased susceptibility to viral and bacterial infections in early life. Nat Commun (2021) 12, 4957, doi:10.1038/s41467-021-25220-3.
  • 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 (2021) 22, 642, doi:10.1093/bib/bbaa232.
  • Grigoriou, M., Banos, A., Hatzioannou, A., Kloetgen, A., Kouzis, P., Aggouraki, D., Zakopoulou, R., Bamias, G., Kassi, E., Mavroudis, D., Bamias, A., Boumpas, D. T., Tsirigos, A., Gogas, H., Alissafi, T. & Verginis, P.  Regulatory T-cell Transcriptomic Reprogramming Characterizes Adverse Events by Checkpoint Inhibitors in Solid Tumors. Cancer Immunol Res (2021) 9, 726, doi:10.1158/2326-6066.Cir-20-0969.
  • Fritz, A., Bremges, A., Deng, Z. L., Lesker, T. R., Götting, J., Ganzenmueller, T., Sczyrba, A., Dilthey, A., Klawonn, F. & McHardy, A. C.Haploflow: strain-resolved de novo assembly of viral genomes.Genome Biol (2021) 22, 212, doi:10.1186/s13059-021-02426-8.
  • 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.Brief Bioinform (2021) 22, doi:10.1093/bib/bbaa123.
  • 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 and last authors) Hepatitis C reference viruses highlight potent antibody responses and diverse viral functional interactions with neutralising antibodies.Gut (2021) 70, 1734, doi:10.1136/gutjnl-2020-321190.
  • Bahai, A., Asgari, E., Mofrad, M. R. K., Kloetgen, A. & McHardy, A. C. EpitopeVec: Linear Epitope Prediction Using Deep Protein Sequence Embeddings.Bioinformatics (2021) 37, 23, doi:10.1093/bioinformatics/btab467.
  • Aronson, B. E., Scourzic, L., Shah, V., Swanzey, E., Kloetgen, A., Polyzos, A., Sinha, A., Azziz, A., Caspi, I., Li, J., Pelham-Webb, B., Glenn, R. A., Vierbuchen, T., Wichterle, H., Tsirigos, A., Dawlaty, M. M., Stadtfeld, M. & Apostolou, E. A bipartite element with allele-specific functions safeguards DNA methylation imprints at the Dlk1-Dio3 locus.Dev Cell (2021) 56, 3052, doi:10.1016/j.devcel.2021.10.004.

2020

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

2017

2016

2015

2014

2013

2012

2011

2010

2009

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

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

2003

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