Pesquisa | BVS Violência e Saúde

1.

Assessing computational predictions of antimicrobial resistance phenotypes from microbial genomes.

Hu, Kaixin; Meyer, Fernando; Deng, Zhi-Luo; Asgari, Ehsaneddin; Kuo, Tzu-Hao; Münch, Philipp C; McHardy, Alice C.

Brief Bioinform ; 25(3)2024 Mar 27.

Artigo em Inglês | MEDLINE | ID: mdl-38706320

2.

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

Dickson, Andrew; Asgari, Ehsaneddin; McHardy, Alice C; Mofrad, Mohammad R K.

Bioinformatics ; 39(2)2023 02 03.

Artigo em Inglês | MEDLINE | ID: mdl-36786404

3.

Rapid and accurate identification of ribosomal RNA sequences via deep learning.

Deng, Zhi-Luo; Münch, Philipp C; Mreches, René; McHardy, Alice C.

Nucleic Acids Res ; 50(10): e60, 2022 06 10.

Artigo em Inglês | MEDLINE | ID: mdl-35188571

4.

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

Deng, Zhi-Luo; Dhingra, Akshay; Fritz, Adrian; Götting, Jasper; Münch, Philipp C; Steinbrück, Lars; Schulz, Thomas F; Ganzenmüller, Tina; McHardy, Alice C.

Brief Bioinform ; 22(3)2021 05 20.

Artigo em Inglês | MEDLINE | ID: mdl-34020538

5.

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

Hufsky, Franziska; Lamkiewicz, Kevin; Almeida, Alexandre; Aouacheria, Abdel; Arighi, Cecilia; Bateman, Alex; Baumbach, Jan; Beerenwinkel, Niko; Brandt, Christian; Cacciabue, Marco; Chuguransky, Sara; Drechsel, Oliver; Finn, Robert D; Fritz, Adrian; Fuchs, Stephan; Hattab, Georges; Hauschild, Anne-Christin; Heider, Dominik; Hoffmann, Marie; Hölzer, Martin; Hoops, Stefan; Kaderali, Lars; Kalvari, Ioanna; von Kleist, Max; Kmiecinski, Renó; Kühnert, Denise; Lasso, Gorka; Libin, Pieter; List, Markus; Löchel, Hannah F; Martin, Maria J; Martin, Roman; Matschinske, Julian; McHardy, Alice C; Mendes, Pedro; Mistry, Jaina; Navratil, Vincent; Nawrocki, Eric P; O'Toole, Áine Niamh; Ontiveros-Palacios, Nancy; Petrov, Anton I; Rangel-Pineros, Guillermo; Redaschi, Nicole; Reimering, Susanne; Reinert, Knut; Reyes, Alejandro; Richardson, Lorna; Robertson, David L; Sadegh, Sepideh; Singer, Joshua B.

Brief Bioinform ; 22(2): 642-663, 2021 03 22.

Artigo em Inglês | MEDLINE | ID: mdl-33147627

6.

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

Foroughmand-Araabi, Mohammad-Hadi; Goliaei, Sama; McHardy, Alice C.

PLoS Comput Biol ; 18(8): e1009100, 2022 08.

Artigo em Inglês | MEDLINE | ID: mdl-35951662

7.

Nobel nominators - which women will you suggest?

McHardy, Alice C.

Nature ; 601(7894): 508, 2022 01.

Artigo em Inglês | MEDLINE | ID: mdl-35042983

8.

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

Poussin, Carine; Khachatryan, Lusine; Sierro, Nicolas; Narsapuram, Vijay Kumar; Meyer, Fernando; Kaikala, Vinay; Chawla, Vandna; Muppirala, Usha; Kumar, Sunil; Belcastro, Vincenzo; Battey, James N D; Scotti, Elena; Boué, Stéphanie; McHardy, Alice C; Peitsch, Manuel C; Ivanov, Nikolai V; Hoeng, Julia.

BMC Genomics ; 23(1): 624, 2022 Aug 30.

Artigo em Inglês | MEDLINE | ID: mdl-36042406

9.

EpitopeVec: linear epitope prediction using deep protein sequence embeddings.

Bahai, Akash; Asgari, Ehsaneddin; Mofrad, Mohammad R K; Kloetgen, Andreas; McHardy, Alice C.

Bioinformatics ; 37(23): 4517-4525, 2021 12 07.

Artigo em Inglês | MEDLINE | ID: mdl-34180989

10.

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

Bankwitz, Dorothea; Bahai, Akash; Labuhn, Maurice; Doepke, Mandy; Ginkel, Corinne; Khera, Tanvi; Todt, Daniel; Ströh, Luisa J; Dold, Leona; Klein, Florian; Klawonn, Frank; Krey, Thomas; Behrendt, Patrick; Cornberg, Markus; McHardy, Alice C; Pietschmann, Thomas.

Gut ; 70(9): 1734-1745, 2021 09.

Artigo em Inglês | MEDLINE | ID: mdl-33323394

11.

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

Reimering, Susanne; Muñoz, Sebastian; McHardy, Alice C.

PLoS Comput Biol ; 16(2): e1007101, 2020 02.

Artigo em Inglês | MEDLINE | ID: mdl-32032362

12.

Functional overlap of the Arabidopsis leaf and root microbiota.

Bai, Yang; Müller, Daniel B; Srinivas, Girish; Garrido-Oter, Ruben; Potthoff, Eva; Rott, Matthias; Dombrowski, Nina; Münch, Philipp C; Spaepen, Stijn; Remus-Emsermann, Mitja; Hüttel, Bruno; McHardy, Alice C; Vorholt, Julia A; Schulze-Lefert, Paul.

Nature ; 528(7582): 364-9, 2015 Dec 17.

Artigo em Inglês | MEDLINE | ID: mdl-26633631

13.

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

Asgari, Ehsaneddin; Münch, Philipp C; Lesker, Till R; McHardy, Alice C; Mofrad, Mohammad R K.

Bioinformatics ; 35(14): 2498-2500, 2019 07 15.

Artigo em Inglês | MEDLINE | ID: mdl-30500871

14.

Microbial genome-enabled insights into plant-microorganism interactions.

Guttman, David S; McHardy, Alice C; Schulze-Lefert, Paul.

Nat Rev Genet ; 15(12): 797-813, 2014 Dec.

Artigo em Inglês | MEDLINE | ID: mdl-25266034

15.

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

Kloetgen, Andreas; Duggimpudi, Sujitha; Schuschel, Konstantin; Hezaveh, Kebria; Picard, Daniel; Schaal, Heiner; Remke, Marc; Klusmann, Jan-Henning; Borkhardt, Arndt; McHardy, Alice C; Hoell, Jessica I.

Int J Mol Sci ; 21(12)2020 Jun 23.

Artigo em Inglês | MEDLINE | ID: mdl-32585856

16.

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, Sujitha; Kloetgen, Andreas; Maney, Sathish Kumar; Münch, Philipp C; Hezaveh, Kebria; Shaykhalishahi, Hamed; Hoyer, Wolfgang; McHardy, Alice C; Lang, Philipp A; Borkhardt, Arndt; Hoell, Jessica I.

J Biol Chem ; 293(40): 15359-15369, 2018 10 05.

Artigo em Inglês | MEDLINE | ID: mdl-30126842

17.

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

Asgari, Ehsaneddin; Garakani, Kiavash; McHardy, Alice C; Mofrad, Mohammad R K.

Bioinformatics ; 34(13): i32-i42, 2018 07 01.

Artigo em Inglês | MEDLINE | ID: mdl-29950008

18.

EDEN: evolutionary dynamics within environments.

Münch, Philipp C; Stecher, Bärbel; McHardy, Alice C.

Bioinformatics ; 33(20): 3292-3295, 2017 Oct 15.

Artigo em Inglês | MEDLINE | ID: mdl-28637301

19.

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

Gubry-Rangin, Cécile; Kratsch, Christina; Williams, Tom A; McHardy, Alice C; Embley, T Martin; Prosser, James I; Macqueen, Daniel J.

Proc Natl Acad Sci U S A ; 112(30): 9370-5, 2015 07 28.

Artigo em Inglês | MEDLINE | ID: mdl-26170282

20.

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

Doerrenberg, Mareike; Kloetgen, Andreas; Hezaveh, Kebria; Wössmann, Wilhelm; Bleckmann, Kirsten; Stanulla, Martin; Schrappe, Martin; McHardy, Alice C; Borkhardt, Arndt; Hoell, Jessica I.

Genes Chromosomes Cancer ; 56(2): 159-167, 2017 02.

Artigo em Inglês | MEDLINE | ID: mdl-27717083

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