Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 1 to 50 of 100

1.

Corrigendum to: Biochemical and bioinformatic methods for elucidating the role of RNA-protein interactions in posttranscriptional regulation.

Kloetgen A, Münch PC, Borkhardt A, Hoell JI, McHardy AC.

Brief Funct Genomics. 2019 Jun 6. pii: elz014. doi: 10.1093/bfgp/elz014. [Epub ahead of print] No abstract available.

PMID:
31169895
2.

Consent insufficient for data release-Response.

Amann RI, Baichoo S, Blencowe BJ, Bork P, Borodovsky M, Brooksbank C, Chain PSG, Colwell RR, Daffonchio DG, Danchin A, de Lorenzo V, Dorrestein PC, Finn RD, Fraser CM, Gilbert JA, Hallam SJ, Hugenholtz P, Ioannidis JPA, Jansson JK, Kim JF, Klenk HP, Klotz MG, Knight R, Konstantinidis KT, Kyrpides NC, Mason CE, McHardy AC, Meyer F, Ouzounis CA, Patrinos AAN, Podar M, Pollard KS, Ravel J, Muñoz AR, Roberts RJ, Rosselló-Móra R, Sansone SA, Schloss PD, Schriml LM, Setubal JC, Sorek R, Stevens RL, Tiedje JM, Turjanski A, Tyson GW, Ussery DW, Weinstock GM, White O, Whitman WB, Xenarios I.

Science. 2019 May 3;364(6439):446. doi: 10.1126/science.aax7509. No abstract available.

PMID:
31048484
3.

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

Klingen TR, Loers J, Stanelle-Bertram S, Gabriel G, McHardy AC.

Sci Rep. 2019 Apr 18;9(1):6267. doi: 10.1038/s41598-019-42614-y.

4.
5.

Assessing taxonomic metagenome profilers with OPAL.

Meyer F, Bremges A, Belmann P, Janssen S, McHardy AC, Koslicki D.

Genome Biol. 2019 Mar 4;20(1):51. doi: 10.1186/s13059-019-1646-y.

6.

CAMISIM: simulating metagenomes and microbial communities.

Fritz A, Hofmann P, Majda S, Dahms E, Dröge J, Fiedler J, Lesker TR, Belmann P, DeMaere MZ, Darling AE, Sczyrba A, Bremges A, McHardy AC.

Microbiome. 2019 Feb 8;7(1):17. doi: 10.1186/s40168-019-0633-6.

7.

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

Vatanen T, Plichta DR, Somani J, Münch PC, Arthur TD, Hall AB, Rudolf S, Oakeley EJ, Ke X, Young RA, Haiser HJ, Kolde R, Yassour M, Luopajärvi K, Siljander H, Virtanen SM, Ilonen J, Uibo R, Tillmann V, Mokurov S, Dorshakova N, Porter JA, McHardy AC, Lähdesmäki H, Vlamakis H, Huttenhower C, Knip M, Xavier RJ.

Nat Microbiol. 2019 Mar;4(3):545. doi: 10.1038/s41564-019-0393-x.

PMID:
30723264
8.

Toward unrestricted use of public genomic data.

Amann RI, Baichoo S, Blencowe BJ, Bork P, Borodovsky M, Brooksbank C, Chain PSG, Colwell RR, Daffonchio DG, Danchin A, de Lorenzo V, Dorrestein PC, Finn RD, Fraser CM, Gilbert JA, Hallam SJ, Hugenholtz P, Ioannidis JPA, Jansson JK, Kim JF, Klenk HP, Klotz MG, Knight R, Konstantinidis KT, Kyrpides NC, Mason CE, McHardy AC, Meyer F, Ouzounis CA, Patrinos AAN, Podar M, Pollard KS, Ravel J, Muñoz AR, Roberts RJ, Rosselló-Móra R, Sansone SA, Schloss PD, Schriml LM, Setubal JC, Sorek R, Stevens RL, Tiedje JM, Turjanski A, Tyson GW, Ussery DW, Weinstock GM, White O, Whitman WB, Xenarios I.

Science. 2019 Jan 25;363(6425):350-352. doi: 10.1126/science.aaw1280. No abstract available.

9.

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

Vatanen T, Plichta DR, Somani J, Münch PC, Arthur TD, Hall AB, Rudolf S, Oakeley EJ, Ke X, Young RA, Haiser HJ, Kolde R, Yassour M, Luopajärvi K, Siljander H, Virtanen SM, Ilonen J, Uibo R, Tillmann V, Mokurov S, Dorshakova N, Porter JA, McHardy AC, Lähdesmäki H, Vlamakis H, Huttenhower C, Knip M, Xavier RJ.

Nat Microbiol. 2019 Mar;4(3):470-479. doi: 10.1038/s41564-018-0321-5. Epub 2018 Dec 17. Erratum in: Nat Microbiol. 2019 Feb 5;:.

PMID:
30559407
10.

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

Asgari E, Münch PC, Lesker TR, McHardy AC, Mofrad MRK.

Bioinformatics. 2018 Nov 30. doi: 10.1093/bioinformatics/bty954. [Epub ahead of print]

PMID:
30500871
11.

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

Reimering S, Muñoz S, McHardy AC.

Sci Rep. 2018 Nov 19;8(1):17000. doi: 10.1038/s41598-018-35421-4.

12.

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

Reimering S, McHardy AC.

Methods Mol Biol. 2018;1836:551-565. doi: 10.1007/978-1-4939-8678-1_26.

PMID:
30151591
13.

Transcriptome-wide analysis uncovers the targets of the RNA-binding protein MSI2 and effects of MSI2's RNA-binding activity on IL-6 signaling.

Duggimpudi S, Kloetgen A, Maney SK, Münch PC, Hezaveh K, Shaykhalishahi H, Hoyer W, McHardy AC, Lang PA, Borkhardt A, Hoell JI.

J Biol Chem. 2018 Oct 5;293(40):15359-15369. doi: 10.1074/jbc.RA118.002243. Epub 2018 Aug 20.

PMID:
30126842
14.

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

Asgari E, Garakani K, McHardy AC, Mofrad MRK.

Bioinformatics. 2019 Mar 15;35(6):1082. doi: 10.1093/bioinformatics/bty652. No abstract available.

15.

Critical Assessment of Metagenome Interpretation Enters the Second Round.

Bremges A, McHardy AC.

mSystems. 2018 Jul 10;3(4). pii: e00103-18. doi: 10.1128/mSystems.00103-18. eCollection 2018 Jul-Aug. No abstract available.

16.

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

Garrido-Oter R, Nakano RT, Dombrowski N, Ma KW; AgBiome Team, McHardy AC, Schulze-Lefert P.

Cell Host Microbe. 2018 Jul 11;24(1):155-167.e5. doi: 10.1016/j.chom.2018.06.006.

17.

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

Asgari E, Garakani K, McHardy AC, Mofrad MRK.

Bioinformatics. 2018 Jul 1;34(13):i32-i42. doi: 10.1093/bioinformatics/bty296. Erratum in: Bioinformatics. 2019 Mar 15;35(6):1082.

18.

AMBER: Assessment of Metagenome BinnERs.

Meyer F, Hofmann P, Belmann P, Garrido-Oter R, Fritz A, Sczyrba A, McHardy AC.

Gigascience. 2018 Jun 1;7(6). doi: 10.1093/gigascience/giy069.

19.

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

Ibrahim B, Arkhipova K, Andeweg AC, Posada-Céspedes S, Enault F, Gruber A, Koonin EV, Kupczok A, Lemey P, McHardy AC, McMahon DP, Pickett BE, Robertson DL, Scheuermann RH, Zhernakova A, Zwart MP, Schönhuth A, Dutilh BE, Marz M.

Viruses. 2018 May 14;10(5). pii: E256. doi: 10.3390/v10050256.

20.

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

Naas AE, Solden LM, Norbeck AD, Brewer H, Hagen LH, Heggenes IM, McHardy AC, Mackie RI, Paša-Tolić L, Arntzen MØ, Eijsink VGH, Koropatkin NM, Hess M, Wrighton KC, Pope PB.

Microbiome. 2018 Mar 1;6(1):44. doi: 10.1186/s40168-018-0421-8.

21.

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

Klingen TR, Reimering S, Loers J, Mooren K, Klawonn F, Krey T, Gabriel G, McHardy AC.

Sci Rep. 2018 Jan 10;8(1):373. doi: 10.1038/s41598-017-18791-z.

22.

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

Grießmeier V, Bremges A, McHardy AC, Gescher J.

Sci Rep. 2017 Dec 5;7(1):17028. doi: 10.1038/s41598-017-17312-2.

23.

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

Maus I, Bremges A, Stolze Y, Hahnke S, Cibis KG, Koeck DE, Kim YS, Kreubel J, Hassa J, Wibberg D, Weimann A, Off S, Stantscheff R, Zverlov VV, Schwarz WH, König H, Liebl W, Scherer P, McHardy AC, Sczyrba A, Klocke M, Pühler A, Schlüter A.

Biotechnol Biofuels. 2017 Nov 13;10:264. doi: 10.1186/s13068-017-0947-1. eCollection 2017.

24.

In Silico Vaccine Strain Prediction for Human Influenza Viruses.

Klingen TR, Reimering S, Guzmán CA, McHardy AC.

Trends Microbiol. 2018 Feb;26(2):119-131. doi: 10.1016/j.tim.2017.09.001. Epub 2017 Oct 9. Review.

PMID:
29032900
25.

Comparative whole-genome analysis reveals artificial selection effects on Ustilago esculenta genome.

Ye Z, Pan Y, Zhang Y, Cui H, Jin G, McHardy AC, Fan L, Yu X.

DNA Res. 2017 Dec 1;24(6):635-648. doi: 10.1093/dnares/dsx031.

26.

Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software.

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 TS, Shapiro N, Blood PD, Gurevich A, Bai Y, Turaev D, DeMaere MZ, Chikhi R, Nagarajan N, Quince C, Meyer F, Balvočiūtė M, Hansen LH, Sørensen SJ, Chia BKH, Denis B, Froula JL, Wang Z, Egan R, Don Kang D, Cook JJ, Deltel C, Beckstette M, Lemaitre C, Peterlongo P, Rizk G, Lavenier D, Wu YW, Singer SW, Jain C, Strous M, Klingenberg H, Meinicke P, Barton MD, Lingner T, Lin HH, Liao YC, Silva GGZ, Cuevas DA, Edwards RA, Saha S, Piro VC, Renard BY, Pop M, Klenk HP, Göker M, Kyrpides NC, Woyke T, Vorholt JA, Schulze-Lefert P, Rubin EM, Darling AE, Rattei T, McHardy AC.

Nat Methods. 2017 Nov;14(11):1063-1071. doi: 10.1038/nmeth.4458. Epub 2017 Oct 2.

27.

EDEN: evolutionary dynamics within environments.

Münch PC, Stecher B, McHardy AC.

Bioinformatics. 2017 Oct 15;33(20):3292-3295. doi: 10.1093/bioinformatics/btx394.

28.

Characterisation of a stable laboratory co-culture of acidophilic nanoorganisms.

Krause S, Bremges A, Münch PC, McHardy AC, Gescher J.

Sci Rep. 2017 Jun 12;7(1):3289. doi: 10.1038/s41598-017-03315-6.

29.

Metagenomics and CAZyme Discovery.

Kunath BJ, Bremges A, Weimann A, McHardy AC, Pope PB.

Methods Mol Biol. 2017;1588:255-277. doi: 10.1007/978-1-4939-6899-2_20.

PMID:
28417375
30.

From Genomes to Phenotypes: Traitar, the Microbial Trait Analyzer.

Weimann A, Mooren K, Frank J, Pope PB, Bremges A, McHardy AC.

mSystems. 2016 Dec 27;1(6). pii: e00101-16. doi: 10.1128/mSystems.00101-16. eCollection 2016 Nov-Dec.

31.

Reconstructing metabolic pathways of a member of the genus Pelotomaculum suggesting its potential to oxidize benzene to carbon dioxide with direct reduction of sulfate.

Dong X, Dröge J, von Toerne C, Marozava S, McHardy AC, Meckenstock RU.

FEMS Microbiol Ecol. 2017 Mar 1;93(3). doi: 10.1093/femsec/fiw254.

PMID:
28011598
32.

Finding Genes in Genome Sequence.

McHardy AC, Kloetgen A.

Methods Mol Biol. 2017;1525:271-291.

PMID:
27896725
33.

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

Brugiroux S, Beutler M, Pfann C, Garzetti D, Ruscheweyh HJ, Ring D, Diehl M, Herp S, Lötscher Y, Hussain S, Bunk B, Pukall R, Huson DH, Münch PC, McHardy AC, McCoy KD, Macpherson AJ, Loy A, Clavel T, Berry D, Stecher B.

Nat Microbiol. 2016 Nov 21;2:16215. doi: 10.1038/nmicrobiol.2016.215.

PMID:
27869789
34.

Novel Syntrophic Populations Dominate an Ammonia-Tolerant Methanogenic Microbiome.

Frank JA, Arntzen MØ, Sun L, Hagen LH, McHardy AC, Horn SJ, Eijsink VG, Schnürer A, Pope PB.

mSystems. 2016 Sep 13;1(5). pii: e00092-16. eCollection 2016 Sep-Oct.

35.

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

Kloetgen A, Borkhardt A, Hoell JI, McHardy AC.

PeerJ. 2016 Oct 27;4:e2619. eCollection 2016.

36.

Alterations of microRNA and microRNA-regulated messenger RNA expression in germinal center B-cell lymphomas determined by integrative sequencing analysis.

Hezaveh K, Kloetgen A, Bernhart SH, Mahapatra KD, Lenze D, Richter J, Haake A, Bergmann AK, Brors B, Burkhardt B, Claviez A, Drexler HG, Eils R, Haas S, Hoffmann S, Karsch D, Klapper W, Kleinheinz K, Korbel J, Kretzmer H, Kreuz M, Küppers R, Lawerenz C, Leich E, Loeffler M, Mantovani-Loeffler L, López C, McHardy AC, Möller P, Rohde M, Rosenstiel P, Rosenwald A, Schilhabel M, Schlesner M, Scholz I, Stadler PF, Stilgenbauer S, Sungalee S, Szczepanowski M, Trümper L, Weniger MA, Siebert R, Borkhardt A, Hummel M, Hoell JI; ICGC MMML-Seq Project.

Haematologica. 2016 Nov;101(11):1380-1389. Epub 2016 Jul 6.

37.

T-cell acute lymphoblastic leukemia in infants has distinct genetic and epigenetic features compared to childhood cases.

Doerrenberg M, Kloetgen A, Hezaveh K, Wössmann W, Bleckmann K, Stanulla M, Schrappe M, McHardy AC, Borkhardt A, Hoell JI.

Genes Chromosomes Cancer. 2017 Feb;56(2):159-167. doi: 10.1002/gcc.22423. Epub 2016 Oct 26.

PMID:
27717083
38.

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

Kratsch C, Klingen TR, Mümken L, Steinbrück L, McHardy AC.

Virus Evol. 2016 Feb 14;2(1):vev025. eCollection 2016 Jan.

39.

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

Hacquard S, Kracher B, Hiruma K, Münch PC, Garrido-Oter R, Thon MR, Weimann A, Damm U, Dallery JF, Hainaut M, Henrissat B, Lespinet O, Sacristán S, van Themaat EV, Kemen E, McHardy AC, Schulze-Lefert P, O'Connell RJ.

Nat Commun. 2016 Sep 29;7:13072. doi: 10.1038/ncomms13072. No abstract available.

40.

Snowball: strain aware gene assembly of metagenomes.

Gregor I, Schönhuth A, McHardy AC.

Bioinformatics. 2016 Sep 1;32(17):i649-i657. doi: 10.1093/bioinformatics/btw426.

PMID:
27587685
41.

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

Otte A, Marriott AC, Dreier C, Dove B, Mooren K, Klingen TR, Sauter M, Thompson KA, Bennett A, Klingel K, van Riel D, McHardy AC, Carroll MW, Gabriel G.

Sci Rep. 2016 Jun 24;6:28583. doi: 10.1038/srep28583.

42.

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

Frank JA, Pan Y, Tooming-Klunderud A, Eijsink VG, McHardy AC, Nederbragt AJ, Pope PB.

Sci Rep. 2016 May 9;6:25373. doi: 10.1038/srep25373.

43.

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

Hacquard S, Kracher B, Hiruma K, Münch PC, Garrido-Oter R, Thon MR, Weimann A, Damm U, Dallery JF, Hainaut M, Henrissat B, Lespinet O, Sacristán S, Ver Loren van Themaat E, Kemen E, McHardy AC, Schulze-Lefert P, O'Connell RJ.

Nat Commun. 2016 May 6;7:11362. doi: 10.1038/ncomms11362.

44.

'Candidatus Adiutrix intracellularis', an endosymbiont of termite gut flagellates, is the first representative of a deep-branching clade of Deltaproteobacteria and a putative homoacetogen.

Ikeda-Ohtsubo W, Strassert JF, Köhler T, Mikaelyan A, Gregor I, McHardy AC, Tringe SG, Hugenholtz P, Radek R, Brune A.

Environ Microbiol. 2016 Sep;18(8):2548-64. doi: 10.1111/1462-2920.13234. Epub 2016 Apr 21.

45.

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

Gregor I, Dröge J, Schirmer M, Quince C, McHardy AC.

PeerJ. 2016 Feb 8;4:e1603. doi: 10.7717/peerj.1603. eCollection 2016.

46.

Functional overlap of the Arabidopsis leaf and root microbiota.

Bai Y, Müller DB, Srinivas G, Garrido-Oter R, Potthoff E, Rott M, Dombrowski N, Münch PC, Spaepen S, Remus-Emsermann M, Hüttel B, McHardy AC, Vorholt JA, Schulze-Lefert P.

Nature. 2015 Dec 17;528(7582):364-9. doi: 10.1038/nature16192. Epub 2015 Dec 2.

PMID:
26633631
47.

Bioboxes: standardised containers for interchangeable bioinformatics software.

Belmann P, Dröge J, Bremges A, McHardy AC, Sczyrba A, Barton MD.

Gigascience. 2015 Oct 15;4:47. doi: 10.1186/s13742-015-0087-0. eCollection 2015.

48.

How to Grow a Computational Biology Lab.

McHardy AC.

PLoS Comput Biol. 2015 Sep 24;11(9):e1004397. doi: 10.1371/journal.pcbi.1004397. eCollection 2015 Sep. No abstract available.

49.

Genomics and drug profiling of fatal TCF3-HLF-positive acute lymphoblastic leukemia identifies recurrent mutation patterns and therapeutic options.

Fischer U, Forster M, Rinaldi A, Risch T, Sungalee S, Warnatz HJ, Bornhauser B, Gombert M, Kratsch C, Stütz AM, Sultan M, Tchinda J, Worth CL, Amstislavskiy V, Badarinarayan N, Baruchel A, Bartram T, Basso G, Canpolat C, Cario G, Cavé H, Dakaj D, Delorenzi M, Dobay MP, Eckert C, Ellinghaus E, Eugster S, Frismantas V, Ginzel S, Haas OA, Heidenreich O, Hemmrich-Stanisak G, Hezaveh K, Höll JI, Hornhardt S, Husemann P, Kachroo P, Kratz CP, Te Kronnie G, Marovca B, Niggli F, McHardy AC, Moorman AV, Panzer-Grümayer R, Petersen BS, Raeder B, Ralser M, Rosenstiel P, Schäfer D, Schrappe M, Schreiber S, Schütte M, Stade B, Thiele R, von der Weid N, Vora A, Zaliova M, Zhang L, Zichner T, Zimmermann M, Lehrach H, Borkhardt A, Bourquin JP, Franke A, Korbel JO, Stanulla M, Yaspo ML.

Nat Genet. 2015 Sep;47(9):1020-1029. doi: 10.1038/ng.3362. Epub 2015 Jul 27.

50.

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

Gubry-Rangin C, Kratsch C, Williams TA, McHardy AC, Embley TM, Prosser JI, Macqueen DJ.

Proc Natl Acad Sci U S A. 2015 Jul 28;112(30):9370-5. doi: 10.1073/pnas.1419329112. Epub 2015 Jul 13.

Supplemental Content

Loading ...
Support Center