Prof. Dr. Alice McHardy

Goliaei S., Foroughmand-Araabi M.H., Roddy A., Weber A., Översti S., ... , Kühnert D., McHardy A.C. (2024)

Importations of SARS-CoV-2 lineages decline after nonpharmaceutical interventions in phylogeographic analyses

Nat.Commun., 15 (1)

DOI: 10.1038/s41467-024-48641-2 HZI-Repositorium PubMed

Eloe-Fadrosh E.A., Mungall C.J., Miller M.A., Smith M., Patil S.S., Kelliher J.M., Johnson L.Y.D., Rodriguez F.E., Chain P.S.G., Hu B., Thornton M.B., McCue L.A., McHardy A.C., Harris N.L., Reddy T.B.K., Mukherjee S., Hunter C.I., ... , Walls R., Schriml L.M. (2024)

A Practical Approach to Using the Genomic Standards Consortium MIxS Reporting Standard for Comparative Genomics and Metagenomics

Methods Mol Biol, 2. edition (20)

DOI: 10.1007/978-1-0716-3838-5_20 HZI-Repositorium PubMed

Gündüz H.A., Mreches R., Moosbauer J., Robertson G., To X.Y., Franzosa E.A., Huttenhower C., Rezaei M., McHardy A.C., Bischl B., ... , Münch P.C., Binder M. (2024)

Erratum: Author Correction: Optimized model architectures for deep learning on genomic data (Communications biology (2024) 7 1 (516))

Communications biology, 7 (1)

DOI: 10.1038/s42003-024-06318-y PubMed

Gündüz H.A., Mreches R., Moosbauer J., Robertson G., To X.Y., Franzosa E.A., Huttenhower C., Rezaei M., McHardy A.C., Bischl B., ... , Münch P.C., Binder M. (2024)

Optimized model architectures for deep learning on genomic data

Communications biology, 7 (1)

DOI: 10.1038/s42003-024-06161-1 HZI-Repositorium PubMed

Hu K., Meyer F., Deng Z.L., Asgari E., Kuo T.H., ... , Münch P.C., McHardy A.C. (2024)

Assessing computational predictions of antimicrobial resistance phenotypes from microbial genomes

Briefings in Bioinformatics, 25 (3)

DOI: 10.1093/bib/bbae206 HZI-Repositorium PubMed

Scheppach A., Gunduz H.A., Dorigatti E., Munch P.C., McHardy A.C., Bischl B., ... , Rezaei M., Binder M. (2023)

Neural Architecture Search for Genomic Sequence Data

DOI: 10.1109/CIBCB56990.2023.10264875 HZI-Repositorium

Huttenhower C., Finn R.D., McHardy A.C. (2023)

Challenges and opportunities in sharing microbiome data and analyses

Nat.Microbiol., 8 (11)

DOI: 10.1038/s41564-023-01484-x PubMed

Gündüz H.A., Binder M., To X.Y., Mreches R., Bischl B., McHardy A.C., ... , Münch P.C., Rezaei M. (2023)

A self-supervised deep learning method for data-efficient training in genomics

Commun.Biolog., 6 (1)

DOI: 10.1038/s42003-023-05310-2 HZI-Repositorium PubMed

Stanelle-Bertram S., Beck S., Mounogou N.K., Schaumburg B., Stoll F., Al Jawazneh A., Schmal Z., Bai T., Zickler M., Beythien G., Becker K., de la Roi M., Heinrich F., Schulz C., Sauter M., Krasemann S., Lange P., Heinemann A., Van Riel D., Leijten L., Bauer L., van den Bosch T.P.P., Lopuhaäa B., Busche T., Wibberg D., Schaudien D., Goldmann T., Lüttjohann A., Ruschinski J., Jania H., Müller Z., Pinho dos Reis V., Krupp-Buzimkic V., Wolff M., Fallerini C., Baldassarri M., Furini S., Norwood K., Käufer C., Schützenmeister N., Von Köckritz-Blickwede M., Schroeder M., Jarczak D., Nierhaus A., Welte T., Kluge S., McHardy A.C., Sommer F., Kalinowski J., Krauss-Etschmann S., Richter F., von der Thüsen J., Baumgärtner W., Klingel K., Ondruschka B., ... , Renieri A., Gabriel G. (2023)

CYP19A1 mediates severe SARS-CoV-2 disease outcome in males

Cell Rep.Med.

DOI: 10.1016/j.xcrm.2023.101152 HZI-Repositorium PubMed

Münch P.C., Eberl C., Woelfel S., Ring D., Fritz A., Herp S., Lade I., Geffers R., Franzosa E.A., Huttenhower C., ... , McHardy A.C., Stecher B. (2023)

Pulsed antibiotic treatments of gnotobiotic mice manifest in complex bacterial community dynamics and resistance effects

Cell Host.Microbe, 31 (6)

DOI: 10.1016/j.chom.2023.05.013 PubMed

Dickson A., Asgari E., McHardy A.C., Mofrad M.R.K. (2023)

GO Bench: shared hub for universal benchmarking of machine learning-based protein functional annotations

Bioinformatics., 39 (2)

DOI: 10.1093/bioinformatics/btad081 HZI-Repositorium PubMed

Nourani E., Asgari E., McHardy A.C., Mofrad M.R.K. (2022)

TripletProt: Deep Representation Learning of Proteins Based On Siamese Networks

IEEE/ACM Trans.Comput.BioL.Bioinf., 19 (6)

DOI: 10.1109/TCBB.2021.3108718 HZI-Repositorium PubMed

Kennedy K.M., de Goffau M.C., Perez-Munoz M.E., Arrieta M.C., Bäckhed F., Bork P., Braun T., Bushman F.D., Dore J., de Vos W.M., Earl A.M., Eisen J.A., Elovitz M.A., Ganal-Vonarburg S.C., Gänzle M.G., Garrett W.S., Hall L.J., Hornef M.W., Huttenhower C., Konnikova L., Lebeer S., Macpherson A.J., Massey R.C., McHardy A.C., Koren O., Lawley T.D., Ley R.E., O'Mahony L., O'Toole P.W., Pamer E.G., Parkhill J., Raes J., Rattei T., Salonen A., Segal E., Segata N., Shanahan F., Sloboda D.M., Smith G.C.S., Sokol H., Spector T.D., Surette M.G., Tannock G.W., Walker A.W., ... , Yassour M., Walter J. (2023)

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

Nature, 613 (7945)

DOI: 10.1038/s41586-022-05546-8 HZI-Repositorium PubMed

Petrillo M., Fabbri M., Kagkli D.M., Querci M., Van den Eede G., Alm E., Aytan-Aktug D., Capella-Gutierrez S., Carrillo C., Cestaro A., Chan K.G., Coque T., Endrullat C., Gut I., Hammer P., Kay G.L., Madec J.Y., Mather A.E., McHardy A.C., Naas T., Paracchini V., Peter S., Pightling A., Raffael B., Rossen J., Ruppé E., Schlaberg R., Vanneste K., Weber L.M., ... , Westh H., Angers-Loustau A. (2022)

A roadmap for the generation of benchmarking resources for antimicrobial resistance detection using next generation sequencing

F1000 Res., 10

DOI: 10.12688/f1000research.39214.2 HZI-Repositorium PubMed

Poussin C., Khachatryan L., Sierro N., Narsapuram V.K., Meyer F., Kaikala V., Chawla V., Muppirala U., Kumar S., Belcastro V., Battey J.N.D., Scotti E., Boué S., McHardy A.C., Peitsch M.C., ... , Ivanov N.V., Hoeng J. (2022)

Crowdsourced benchmarking of taxonomic metagenome profilers: lessons learned from the sbv IMPROVER Microbiomics challenge

BMC.Genomics, 23 (1)

DOI: 10.1186/s12864-022-08803-2 HZI-Repositorium PubMed

Foroughmand-Araabi M.H., Goliaei S., McHardy A.C. (2022)

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

PLoS.Comput.Biol., 18 (8)

DOI: 10.1371/journal.pcbi.1009100 HZI-Repositorium PubMed

Cernava T., Rybakova D., Buscot F., Clavel T., McHardy A.C., Meyer F., Meyer F., Overmann J., Stecher B., Sessitsch A., ... , Schloter M., Berg G. (2022)

Metadata harmonization-Standards are the key for a better usage of omics data for integrative microbiome analysis

Environ.Microbiome., 17 (1)

DOI: 10.1186/s40793-022-00425-1 HZI-Repositorium PubMed

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., Buluc A., Chen B., Chikhi R., Clausen P.T.L.C., 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., Jorgensen 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., Sorensen S.J., Thomas A., Tong C., Trajkovski M., Tremblay J., Uritskiy G., Vicedomini R., 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. (2022)

Critical Assessment of Metagenome Interpretation: the second round of challenges

Nature Methods, 19 (4)

DOI: 10.1038/s41592-022-01431-4 HZI-Repositorium PubMed

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. (2022)

Peptide microarrays coupled to machine learning reveal individual epitopes from human antibody responses with neutralizing capabilities against SARS-CoV-2

Emerg.Microbes Infect, 11 (1)

DOI: 10.1080/22221751.2022.2057874 HZI-Repositorium PubMed

Deng Z.L., Münch P.C., Mreches R., McHardy A.C. (2022)

Rapid and accurate identification of ribosomal RNA sequences via deep learning

Nucleic Acids Res.

DOI: 10.1093/nar/gkac112 HZI-Repositorium PubMed

Mirzayi C., Renson A., Furlanello C., Sansone S.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., ... , Genomic Standards Consortium, Massive Analysis and Quality Control Society (2021)

Reporting guidelines for human microbiome research: the STORMS checklist

Nat.Med., 27 (11)

DOI: 10.1038/s41591-021-01552-x HZI-Repositorium PubMed

Lähnemann D., Köster J., Fischer U., Borkhardt A., McHardy A.C., Schönhuth A. (2021)

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

Nat.Commun., 12 (1)

DOI: 10.1038/s41467-021-26938-w HZI-Repositorium PubMed

Fritz A., Bremges A., Deng Z.L., Lesker T.R., Götting J., Ganzenmueller T., Sczyrba A., Dilthey A., ... , Klawonn F., McHardy A.C. (2021)

Haploflow: strain-resolved de novo assembly of viral genomes

Genome Biol., 22 (1)

DOI: 10.1186/s13059-021-02426-8 HZI-Repositorium PubMed

Bahai A., Asgari E., Mofrad M.R.K., Kloetgen A., McHardy A.C. (2021)

EpitopeVec: Linear Epitope Prediction Using Deep Protein Sequence Embeddings

Bioinformatics.

DOI: 10.1093/bioinformatics/btab467 HZI-Repositorium PubMed

Jakob C.E.M., Stecher M., Fuhrmann S., Wingen-Heimann S., Heinen S., Anton G., Behnke M., Behrends U., Boeker M., Castell S., Demski H., Diefenbach M., Falgenhauer J.C., Fritzenwanker M., Gastmeier P., Gerhard M., Glöckner S., Golubovic M., Gunsenheimer Bartmeyer B., Ingenerf J., Kaiser R., Körner M.L., Loag W., McHardy A., Molitor E., Nübel U., Pritsch M., Ramharter M., Rieg S.R., Rupp J., Schindler D., Schwudke D., Spinner C., Stottmeier B., Vehreschild M., ... , Willmann M., Vehreschild J.J. (2021)

Needs for an Integration of Specific Data Sources and Items - First Insights of a National Survey Within the German Center for Infection Research

Stud.Health Technol.Inform., 278 ([4] Medical Informatics, 29. chapter)

DOI: 10.3233/SHTI210075 HZI-Repositorium PubMed

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., Balfanz P., Eggermann T., Boor P., Hausmann R., Kuhn H., Isfort S., Stingl J.C., Schmalzing G., Kuhl C.K., Röhrig R., Marx G., Uhlig S., Dahl E., Müller-Wieland D., Dreher M., Marx N., 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., Angelov A., Bartholomäus A., Becker A., Bezdan D., Blumert C., Bonifacio E., Bork P., Boyke B., Blum H., Clavel T., Colome-Tatche M., Cornberg M., De La Rosa Velazquez I.A., Diefenbach A., Dilthey A., Fischer N., Förstner K., Franzenburg S., Frick J.S., Gabernet G., Gagneur J., Ganzenmueller T., Gauder M., Geißert J., Goesmann A., Göpel S., Grundhoff A., Grundmann H., Hain T., Hanses F., Hehr U., Heimbach A., Hoeper M., Horn F., Hübschmann D., Hummel M., Iftner T., Iftner A., Illig T., Janssen S., Kalinowski J., Kallies R., Kehr B., Keppler O.T., Klein C., Knop M., Kohlbacher O., Köhrer K., Korbel J., Kremsner P.G., Kühnert D., Landthaler M., Li Y., Ludwig K.U., Makarewicz O., Marz M., McHardy A.C., Mertes C., Münchhoff M., Nahnsen S., Nöthen M., Ntoumi F., Overmann J., Peter S., Pfeffer K., Pink I., Poetsch A.R., Protzer U., Pühler A., Rajewsky N., Ralser M., Reiche K., Ripke S., da Rocha U.N., Saliba A.E., Sander L.E., Sawitzki B., Scheithauer S., Schiffer P., Schmid-Burgk J., Schneider W., Schulte E.C., Sczyrba A., Sharaf M.L., Singh Y., Sonnabend M., Stegle O., Stoye J., Vehreschild J., Velavan T.P., Vogel J., Volland S., von Kleist M., Walker A., Walter J., Wieczorek D., Winkler S., Ziebuhr J., Breteler M.M.B., Giamarellos-Bourboulis E.J., Kox M., Becker M., Cheran S., Woodacre M.S., Goh E.L., Schultze J.L., ... , COVID-19 Aachen Study (COVAS), Deutsche COVID-19 Omics Initiative (DeCOI) (2021)

Swarm Learning for decentralized and confidential clinical machine learning

Nature, 594 (7862)

DOI: 10.1038/s41586-021-03583-3 PubMed

Bernardes J.P., Mishra N., Tran F., Bahmer T., Best L., Blase J.I., Bordoni D., Franzenburg J., Geisen U., Josephs-Spaulding J., Köhler P., Künstner A., Rosati E., Aschenbrenner A.C., Bacher P., Baran N., Boysen T., Brandt B., Bruse N., Dörr J., Dräger A., Elke G., Ellinghaus D., Fischer J., Forster M., Franke A., Franzenburg S., Frey N., Friedrichs A., Fuß J., Glück A., Hamm J., Hinrichsen F., Hoeppner M.P., Imm S., Junker R., Kaiser S., Kan Y.H., Knoll R., Lange C., Laue G., Lier C., Lindner M., Marinos G., Markewitz R., Nattermann J., Noth R., Pickkers P., Rabe K.F., Renz A., Röcken C., Rupp J., Schaffarzyk A., Scheffold A., Schulte-Schrepping J., Schunk D., Skowasch D., Ulas T., Wandinger K.P., Wittig M., Zimmermann J., Busch H., Hoyer B.F., Kaleta C., Heyckendorf J., Kox M., Rybniker J., Schreiber S., Schultze J.L., Rosenstiel P., Banovich N.E., Desai T., Eickelberg O., Haniffa M., Horvath P., Kropski J.A., Lafyatis R., Lundeberg J., Meyer K., Nawijn M.C., Nikolic M., Ordovas Montanes J., Pe'er D., Tata P.R., Rawlins E., Regev A., Reyfman P., Samakovlis C., Schultze J., Shalek A., Shepherd D., Spence J., Teichmann S., Theis F., Tsankov A., van den Berge M., von Papen M., Whitsett J., Zaragosi L.E., Angelov A., Bals R., Bartholomäus A., Becker A., Bezdan D., Bonifacio E., Bork P., Clavel T., Colme-Tatche M., Diefenbach A., Dilthey A., Fischer N., Förstner K., Frick J.S., Gagneur J., Goesmann A., Hain T., Hummel M., Janssen S., Kalinowski J., Kallies R., Kehr B., Keller A., Kim-Hellmuth S., Klein C., Kohlbacher O., Korbel J.O., Kurth I., Landthaler M., Li Y., Ludwig K., Makarewicz O., Marz M., McHardy A., Mertes C., Nöthen M., Nürnberg P., Ohler U., Ossowski S., Overmann J., Peter S., Pfeffer K., Poetsch A.R., Pühler A., Rajewsky N., Ralser M., Rieß O., Ripke S., Nunes da Rocha U., Saliba A.E., Sander L.E., Sawitzki B., Schiffer P., Schulte E.C., Sczyrba A., Stegle O., Stoye J., Vehreschild J., Vogel J., von Kleist M., Walker A., Walter J., Wieczorek D., Ziebuhr J., ... , HCA Lung Biological Network, the Deutsche C.O.V.I. (2020)

Longitudinal Multi-omics Analyses Identify Responses of Megakaryocytes, Erythroid Cells, and Plasmablasts as Hallmarks of Severe COVID-19

Immunity, 53 (6)

DOI: 10.1016/j.immuni.2020.11.017 HZI-Repositorium PubMed

Meyer F., Lesker T.R., Koslicki D., Fritz A., Gurevich A., Darling A.E., Sczyrba A., ... , Bremges A., McHardy A.C. (2021)

Tutorial: assessing metagenomics software with the CAMI benchmarking toolkit

Nat.Protoc., 16 (4)

DOI: 10.1038/s41596-020-00480-3 HZI-Repositorium PubMed

Deng Z.L., Dhingra A., Fritz A., Götting J., Münch P.C., Steinbrück L., Schulz T.F., ... , Ganzenmüller T., McHardy A. (2021)

Evaluating assembly and variant calling software for strain-resolved analysis of large DNA viruses

Briefings in Bioinformatics, 22 (3)

DOI: 10.1093/bib/bbaa123 HZI-Repositorium PubMed

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. (2021)

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

GUT

DOI: 10.1136/gutjnl-2020-321190 HZI-Repositorium PubMed

Münch P.C., Franzosa E.A., Stecher B., McHardy A.C., Huttenhower C. (2020)

Identification of Natural CRISPR Systems and Targets in the Human Microbiome

Cell Host.Microbe, 29 (1)

DOI: 10.1016/j.chom.2020.10.010 PubMed

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 ÁN, 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. (2021)

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

Brief.Bioinform., 22 (2)

DOI: 10.1093/bib/bbaa232 HZI-Repositorium PubMed

Schulte-Schrepping J., Reusch N., Paclik D., Baßler K., Schlickeiser S., Zhang B., Krämer B., Krammer T., Brumhard S., Bonaguro L., De Domenico E., Wendisch D., Grasshoff M., Kapellos T.S., Beckstette M., Pecht T., Saglam A., Dietrich O., Mei H.E., Schulz A.R., Conrad C., Kunkel D., Vafadarnejad E., Xu C.J., Horne A., Herbert M., Drews A., Thibeault C., Pfeiffer M., Hippenstiel S., Hocke A., Müller-Redetzky H., Heim K.M., Machleidt F., Uhrig A., Bosquillon de Jarcy L., Jürgens L., Stegemann M., Glösenkamp C.R., Volk H.D., Goffinet C., Landthaler M., Wyler E., Georg P., Schneider M., Dang-Heine C., Neuwinger N., Kappert K., Tauber R., Corman V., Raabe J., Kaiser K.M., Vinh M.T., Rieke G., Meisel C., Ulas T., Becker M., Geffers R., Witzenrath M., Drosten C., Suttorp N., von Kalle C., Kurth F., Händler K., Schultze J.L., Aschenbrenner A.C., Li Y., Nattermann J., Sawitzki B., Saliba A.E., Sander L.E., Angelov A., Bals R., Bartholomäus A., Becker A., Bezdan D., Bonifacio E., Bork P., Clavel T., Colome-Tatche M., Diefenbach A., Dilthey A., Fischer N., Förstner K., Frick J.S., Gagneur J., Goesmann A., Hain T., Hummel M., Janssen S., Kalinowski J., Kallies R., Kehr B., Keller A., Kim-Hellmuth S., Klein C., Kohlbacher O., Korbel J.O., Kurth I., Ludwig K., Makarewicz O., Marz M., McHardy A., Mertes C., Nöthen M., Nürnberg P., Ohler U., Ossowski S., Overmann J., Peter S., Pfeffer K., Poetsch A.R., Pühler A., Rajewsky N., Ralser M., Rieß O., Ripke S., Nunes da Rocha U., Rosenstiel P., Schiffer P., Schulte E.C., Sczyrba A., Stegle O., Stoye J., Theis F., Vehreschild J., Vogel J., von Kleist M., Walker A., Walter J., Wieczorek D., ... , Ziebuhr J., Deutsche C.O.V.I. (2020)

Severe COVID-19 Is Marked by a Dysregulated Myeloid Cell Compartment

Cell, 182 (6)

DOI: 10.1016/j.cell.2020.08.001 HZI-Repositorium PubMed

Spriewald S., Stadler E., Hense B.A., Münch P.C., McHardy A.C., Weiss A.S., Obeng N., ... , Müller J., Stecher B. (2020)

Evolutionary stabilization of cooperative toxin production through a bacterium-plasmid-phage interplay

MBio, 11 (4)

DOI: 10.1128/mBio.00912-20 HZI-Repositorium PubMed

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. (2020)

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

Int.J.Mol.Sci., 21 (12)

DOI: 10.3390/ijms21124453 HZI-Repositorium PubMed

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. (2021)

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

GUT, 70 (2)

DOI: 10.1136/gutjnl-2020-321424 HZI-Repositorium PubMed

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. (2020)

Cellular Importin-a3 Expression Dynamics in the Lung Regulate Antiviral Response Pathways against Influenza A Virus Infection

Cell Rep., 31 (3)

DOI: 10.1016/j.celrep.2020.107549 HZI-Repositorium PubMed

Lesker T.R., Durairaj A.C., Gálvez E.J.C., Lagkouvardos I., Baines J.F., Clavel T., Sczyrba A., ... , McHardy A.C., Strowig T. (2020)

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

Cell Rep., 30 (9)

DOI: 10.1016/j.celrep.2020.02.036 HZI-Repositorium PubMed

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., Munoz A.R., Roberts R.J., Rossello-Mora 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. (2019)

Toward unrestricted use of public genomic data

Science, 363 (6425)

DOI: 10.1126/science.aaw1280 HZI-Repositorium PubMed

Reimering S., Munoz S., McHardy A.C. (2020)

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

PLoS.Comput.Biol., 16 (2)

DOI: 10.1371/journal.pcbi.1007101 HZI-Repositorium PubMed

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. (2020)

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

EMBO Mol.Med., 12 (3)

DOI: 10.15252/emmm.201910264 HZI-Repositorium PubMed

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.-O., 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 I.I., 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. (2020)

Eleven grand challenges in single-cell data science

Genome Biol., 21 (1)

DOI: 10.1186/s13059-020-1926-6 HZI-Repositorium PubMed

Bremges A., Fritz A., McHardy A.C. (2020)

CAMITAX: Taxon labels for microbial genomes

Gigascience., 9 (1)

DOI: 10.1093/gigascience/giz154 HZI-Repositorium PubMed

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., Dalkiran A., Cetin Atalay R., Zhang C., Hurto R.L., Freddolino P.L., Zhang Y., Bhat P., Supek F., Gemovic B., Perovic V.R., Davidovic 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., Gligorijevic 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. (2019)

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

Genome Biol., 20 (1)

DOI: 10.1186/s13059-019-1835-8 HZI-Repositorium PubMed

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. (2019)

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

Blood Adv., 3 (20)

DOI: 10.1182/bloodadvances.2019000051 HZI-Repositorium PubMed

Asgari E., Garakani K., McHardy A.C., Mofrad M.R.K. (2019)

Corrigendum: MicroPheno: Predicting environments and host phenotypes from 16S rRNA gene sequencing using a k-mer based representation of shallow sub-samples (Bioinformatics (2019) 35:6 (1082) DOI: 10.1093/bioinformatics/bty296)

Bioinformatics, 35 (6)

DOI: 10.1093/bioinformatics/bty652 HZI-Repositorium PubMed

Klingen T.R., Loers J., Stanelle-Bertram S., Gabriel G., McHardy A.C. (2019)

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

Sci.Rep., 9 (1)

DOI: 10.1038/s41598-019-42614-y HZI-Repositorium PubMed

Meyer F., Bremges A., Belmann P., Janssen S., McHardy A.C., Koslicki D. (2019)

Assessing taxonomic metagenome profilers with OPAL

Genome Biol., 20 (1)

DOI: 10.1186/s13059-019-1646-y HZI-Repositorium PubMed

Asgari E., McHardy A.C., Mofrad M.R.K. (2019)

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

Sci.Rep., 9 (1)

DOI: 10.1038/s41598-019-38746-w HZI-Repositorium PubMed

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. (2018)

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., 293 (40)

DOI: 10.1074/jbc.RA118.002243 HZI-Repositorium PubMed

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. (2019)

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

Nat.Microbiol., 4 (3)

DOI: 10.1038/s41564-018-0321-5 HZI-Repositorium PubMed

Fritz A., Hofmann P., Majda S., Dahms E., Droge J., Fiedler J., Lesker T.R., Belmann P., DeMaere M.Z., Darling A.E., Sczyrba A., ... , Bremges A., McHardy A.C. (2019)

CAMISIM: simulating metagenomes and microbial communities

Microbiome., 7 (1)

DOI: 10.1186/s40168-019-0633-6 HZI-Repositorium PubMed

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. (2019)

Correction to: Genomic variation and strain-specific functional adaptation in the human gut microbiome during early life (Nature Microbiology, (2019), 4, 3, (470-479), 10.1038/s41564-018-0321-5)

Nat.Microbiol., 4 (3)

DOI: 10.1038/s41564-019-0393-x HZI-Repositorium PubMed

Asgari E., Münch P.C., Lesker T.R., McHardy A.C., Mofrad M.R.K. (2019)

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

Bioinformatics., 35 (14)

DOI: 10.1093/bioinformatics/bty954 PubMed

Reimering S., Munoz S., McHardy A.C. (2018)

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

Sci.Rep., 8 (1)

DOI: 10.1038/s41598-018-35421-4 HZI-Repositorium PubMed

Reimering S., McHardy A.C. (2018)

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

Methods Mol.Biol., 1836 (chapter 26)

DOI: 10.1007/978-1-4939-8678-1_26 PubMed

Bremges A., McHardy A.C. (2018)

Critical Assessment of Metagenome Interpretation Enters the Second Round

mSystems., 3 (4)

DOI: 10.1128/mSystems.00103-18

Asgari E., Garakani K., McHardy A.C., Mofrad M.R.K. (2018)

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

Bioinformatics., 34 (13)

DOI: 10.1093/bioinformatics/bty296 HZI-Repositorium PubMed

Garrido-Oter R., Nakano R.T., Dombrowski N., Ma K.W., McHardy A.C., ... , Schulze-Lefert P., The AgBiome Team (2018)

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

Cell Host and Microbe, 24 (1)

DOI: 10.1016/j.chom.2018.06.006 HZI-Repositorium PubMed

Meyer F., Hofmann P., Belmann P., Garrido-Oter R., Fritz A., ... , Sczyrba A., McHardy A.C. (2018)

AMBER: Assessment of Metagenome BinnERs

Gigascience., 7 (6)

DOI: 10.1093/gigascience/giy069 HZI-Repositorium

Ibrahim B., Arkhipova K., Andeweg A.C., Posada-Cespedes 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., Schonhuth A., ... , Dutilh B.E., Marz M. (2018)

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

Viruses., 10 (5)

DOI: 10.3390/v10050256 HZI-Repositorium PubMed

Naas A.E., Solden L.M., Norbeck A.D., Brewer H., Hagen L.H., Heggenes I.M., McHardy A.C., Mackie R.I., Pasa-Tolic L., Arntzen M.Ï., Eijsink V.G.H., Koropatkin N.M., Hess M., ... , Wrighton K.C., Pope P.B. (2018)

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

Microbiome, 6 (1)

DOI: 10.1186/s40168-018-0421-8 HZI-Repositorium PubMed

Klingen T.R., Reimering S., Loers J., Mooren K., Klawonn F., Krey T., ... , Gabriel G., McHardy A.C. (2018)

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

Sci.Rep., 8 (1)

DOI: 10.1038/s41598-017-18791-z HZI-Repositorium PubMed

Grießmeier V., Bremges A., McHardy A.C., Gescher J. (2017)

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

Sci.Rep., 7 (1)

DOI: 10.1038/s41598-017-17312-2 HZI-Repositorium

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., Konig H., Liebl W., Scherer P., McHardy A.C., Sczyrba A., Klocke M., ... , Puhler A., Schluter A. (2017)

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

Biotechnol.Biofuels., 10 (1)

DOI: 10.1186/s13068-017-0947-1 HZI-Repositorium

Dröge J., Schönhuth A., McHardy A.C. (2017)

A probabilistic model to recover individual genomes from metagenomes

PeerJ Comput.Sci., 2017 (5)

DOI: 10.7717/peerj-cs.117 HZI-Repositorium

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. (2017)

Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software

Nat.Methods, 14 (11)

DOI: 10.1038/nmeth.4458

Klingen T.R., Reimering S., Guzmán C.A., McHardy A.C. (2017)

In Silico Vaccine Strain Prediction for Human Influenza Viruses

Trends Microbiol., 26 (2)

DOI: 10.1016/j.tim.2017.09.001 HZI-Repositorium PubMed

Krause S., Bremges A., Münch P.C., McHardy A.C., Gescher J. (2017)

Characterisation of a stable laboratory co-culture of acidophilic nanoorganisms

Sci.Rep., 7 (1)

DOI: 10.1038/s41598-017-03315-6 HZI-Repositorium PubMed

Münch P.C., Stecher B., McHardy A.C. (2017)

EDEN: Evolutionary Dynamics within Environments

Bioinformatics., 33 (20)

DOI: 10.1093/bioinformatics/btx394 HZI-Repositorium PubMed

Dong X., Droge J., von Toerne C., Marozava S., McHardy A.C., Meckenstock R.U. (2016)

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., 93 (3)

DOI: 10.1093/femsec/fiw254 HZI-Repositorium PubMed

Kunath B.J., Bremges A., Weimann A., McHardy A.C., Pope P.B. (2017)

Metagenomics and CAZyme Discovery

Methods Mol.Biol., 1588

DOI: 10.1007/978-1-4939-6899-2_20 PubMed

Weimann A., Mooren K., Frank J., Pope P.B., Bremges A., McHardy A.C. (2016)

From Genomes to Phenotypes: Traitar, the Microbial Trait Analyzer

mSystems, 1 (6)

DOI: 10.1128/mSystems.00101-16 HZI-Repositorium

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., Münch P.C., McHardy A.C., McCoy K.D., Macpherson A.J., Loy A., Clavel T., ... , Berry D., Stecher B. (2016)

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

Nat.Microbiol., 2

DOI: 10.1038/nmicrobiol.2016.215 HZI-Repositorium PubMed

McHardy A.C., Kloetgen A. (2017)

Finding Genes in Genome Sequence

Methods Mol.Biol., 1525 (11)

DOI: 10.1007/978-1-4939-6622-6_11 HZI-Repositorium PubMed

Kloetgen A., Borkhardt A., Hoell J.I., McHardy A.C. (2016)

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

PeerJ., 4

DOI: 10.7717/peerj.2619 HZI-Repositorium PubMed

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. (2016)

Novel Syntrophic Populations Dominate an Ammonia-Tolerant Methanogenic Microbiome

mSystems., 1 (5)

DOI: 10.1128/mSystems.00092-16 HZI-Repositorium

Kratsch C., Klingen T.R., Mumken L., Steinbruck L., McHardy A.C. (2016)

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

Virus Evol., 2 (1)

DOI: 10.1093/ve/vev025 HZI-Repositorium

Doerrenberg M., Kloetgen A., Hezaveh K., Wossmann W., Bleckmann K., Stanulla M., Schrappe M., McHardy A.C., ... , Borkhardt A., Hoell J.I. (2016)

T-Cell Acute Lymphoblastic Leukemia in Infants Has Distinct Genetic and Epigenetic Features Compared to Childhood Cases

Genes Chromosomes.Cancer, 56 (2)

DOI: 10.1002/gcc.22423 PubMed

Gregor I., Schonhuth A., McHardy A.C. (2016)

Snowball: strain aware gene assembly of metagenomes

Bioinformatics., 32 (17)

DOI: 10.1093/bioinformatics/btw426 HZI-Repositorium PubMed

Ikeda-Ohtsubo W., Strassert J.F., Kohler T., Mikaelyan A., Gregor I., McHardy A.C., Tringe S.G., Hugenholtz P., ... , Radek R., Brune A. (2016)

'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., 18 (8)

DOI: 10.1111/1462-2920.13234 HZI-Repositorium PubMed

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. (2016)

Alterations of miRNAs and miRNA-regulated mRNA expression in GC B cell lymphomas determined by integrative sequencing analysis

Haematologica, 101

DOI: 10.3324/haematol.2016.143891 HZI-Repositorium PubMed

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. (2016)

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

Sci.Rep., 6

DOI: 10.1038/srep28583 HZI-Repositorium PubMed

Hacquard S., Kracher B., Hiruma K., Münch 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. (2016)

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

Nat.Commun., 7

DOI: 10.1038/ncomms11362 HZI-Repositorium PubMed

Frank J.A., Pan Y., Tooming-Klunderud A., Eijsink V.G., McHardy A.C., ... , Nederbragt A.J., Pope P.B. (2016)

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

Sci Rep., 6

DOI: 10.1038/srep25373 HZI-Repositorium PubMed

Gregor I., Droge J., Schirmer M., Quince C., McHardy A.C. (2016)

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

PeerJ, 4

DOI: 10.7717/peerj.1603 HZI-Repositorium PubMed

Bulgarelli D., Garrido-Oter R., Münch P.C., Weiman A., Dröge J., Pan Y., ... , McHardy A.C., Schulze-Lefert P. (2015)

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

Cell Host.Microbe, 17 (3)

DOI: 10.1016/j.chom.2015.01.011 HZI-Repositorium PubMed

Bai Y., Muller D.B., Srinivas G., Garrido-Oter R., Potthoff E., Rott M., Dombrowski N., Münch P.C., Spaepen S., Remus-Emsermann M., Huttel B., McHardy A.C., ... , Vorholt J.A., Schulze-Lefert P. (2015)

Functional overlap of the Arabidopsis leaf and root microbiota

Nature, 528

DOI: 10.1038/nature16192 PubMed

Belmann P., Droge J., Bremges A., McHardy A.C., Sczyrba A., Barton M.D. (2015)

Bioboxes: standardised containers for interchangeable bioinformatics software

Gigascience., 4

McHardy A.C. (2015)

How to Grow a Computational Biology Lab

PLoS Comput.Biol., 11 (9)

Kloetgen A., Münch P.C., Borkhardt A., Hoell J.I., McHardy A.C. (2015)

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

Brief.Funct.Genomics, 14 (2)

Gubry-Rangin C., Kratsch C., Williams T.A., McHardy A.C., Embley T.M., ... , Prosser J.I., Macqueen D.J. (2015)

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

Proc.Natl.Acad.Sci U.S A, 112

DOI: 10.1073/pnas.1419329112 HZI-Repositorium PubMed

Otte A., Sauter M., Daxer M.A., McHardy A.C., Klingel K., Gabriel G. (2015)

Adaptive mutations that occurred during 2009 H1N1 influenza virus pandemic circulation in humans enhance virulence in mice

J Virol., 89

DOI: 10.1128/JVI.00665-15 HZI-Repositorium PubMed

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. (2015)

Microbiota and Host Nutrition across Plant and Animal Kingdoms

Cell Host.Microbe, 17 (5)

Dröge J., Gregor I., McHardy Alison C. (2014)

Taxator-tk: Precise Taxonomic Assignment of Metagenomes by Fast Approximation of Evolutionary Neighborhoods

Bioinformatics, 31

DOI: 10.1093/bioinformatics/btu745 HZI-Repositorium PubMed

Steinbruck L., Klingen T.R., McHardy Alison C. (2014)

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

Journal of Virology, 88 (20)

DOI: 10.1128/JVI.01861-14 HZI-Repositorium PubMed

Schneiker S., Perlova O., Kaiser O., Gerth Klaus*, 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., Muoz-Dorado J., Perez J., Pradella S., Rachid S., Raddatz G., Rosenau F., Rückert C., Sasse Florian*, Scharfe Maren*, Schuster S.C., Suen G., Treuner-Lange A., Velicer G.J., Vorhölter F.-J., Weissmann K.J., Welch R.D., Wenzel S.C., Whithworth D.E., Wilhelm S., Wittmann C., Blöcker Helmut*, ... , Pühler A., Müller Rolf* (2007)

Complete genome sequence of the myxobacterium Sorangium cellulosum

Nature Biotechnology, 25 (11)

Schneiker S., Martins dos Santos Vitor A.P.*, Bartels D., Bekel T., Brecht M., Buhrmester J., Chernikova T.N., Denaro R., Ferrer M., Gertler C., Goesmann A., Golyshina Olga 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 Kenneth N.*, Vorholter F.J., Weidner S., ... , Kaiser O., Golyshin Peter N.* (2006)

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

Nature Biotechnology, 24 (8)

Prof. Dr. Alice McHardy

Forschungsgruppe

Standort

Social Media