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1

Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities

Martín, Héctor García, Ivanova, Natalia, Kunin, Victor, Warnecke, Falk, Barry, Kerrie W, McHardy, Alice C, Yeates, Christine, He, Shaomei, Salamov, Asaf A, Szeto, Ernest

Journal:

Nature Biotechnology

Year:

2006

Language:

english

File:

PDF, 260 KB

english, 2006

2

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible

McMurdie, Paul J., Holmes, Susan, McHardy, Alice Carolyn

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 1.92 MB

english, 2014

3

Inferring functional modules of protein families with probabilistic topic models

Sebastian GA Konietzny, Laura Dietz, Alice C McHardy

Journal:

BMC Bioinformatics

Year:

2011

Language:

english

File:

PDF, 1.01 MB

english, 2011

4

Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite

Richardson, Toby H., Stege, Justin T., Cayouette, Michelle, McHardy, Alice C., Djordjevic, Gordana, Aboushadi, Nahla, Warnecke, Falk, Luginbühl, Peter, Ivanova, Natalia, Ghassemian, Majid

Journal:

Year:

2007

Language:

english

File:

PDF, 420 KB

english, 2007

5

Building a BRIDGE for the integration of heterogeneous data from functional genomics into a platform for systems biology

Alexander Goesmann, Burkhard Linke, Oliver Rupp, Lutz Krause, Daniela Bartels, Michael Dondrup, Alice C McHardy, Andreas Wilke, Alfred Pühler, Folker Meyer

Journal:

Journal of Biotechnology

Year:

2003

Language:

english

File:

PDF, 453 KB

english, 2003

6

Defining seasonal marine microbial community dynamics

Gilbert, Jack A, Steele, Joshua A, Caporaso, J Gregory, Steinbrück, Lars, Reeder, Jens, Temperton, Ben, Huse, Susan, McHardy, Alice C, Knight, Rob, Joint, Ian, Somerfield, Paul, Fuhrman, Jed A, Field,

Journal:

The ISME Journal

Year:

2012

Language:

english

File:

PDF, 703 KB

english, 2012

7

Microbial genome-enabled insights into plant–microorganism interactions

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

Journal:

Nature Reviews Genetics

Year:

2014

Language:

english

File:

PDF, 1.07 MB

english, 2014

8

Microbiota and Host Nutrition across Plant and Animal Kingdoms

Hacquard, Stéphane, Garrido-Oter, Ruben, González, Antonio, Spaepen, Stijn, Ackermann, Gail, Lebeis, Sarah, McHardy, Alice C., Dangl, Jeffrey L., Knight, Rob, Ley, Ruth, Schulze-Lefert, Paul

Journal:

Cell Host & Microbe

Year:

2015

Language:

english

File:

PDF, 3.82 MB

english, 2015

9

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

Ibrahim, Bashar, Arkhipova, Ksenia, Andeweg, Arno, Posada-Céspedes, Susana, Enault, François, Gruber, Arthur, Koonin, Eugene, Kupczok, Anne, Lemey, Philippe, McHardy, Alice, McMahon, Dino, Pickett, Br

Journal:

Year:

2018

Language:

english

File:

PDF, 3.23 MB

english, 2018

10

Comparing expression level-dependent features in codon usage with protein abundance: An analysis of ‘predictive proteomics’

Alice C. McHardy, Alfred Pühler, Jörn Kalinowski, Folker Meyer

Journal:

Year:

2004

Language:

english

File:

PDF, 384 KB

english, 2004

11

Multiple syntrophic interactions in a terephthalate-degrading methanogenic consortium

Lykidis, Athanasios, Chen, Chia-Lung, Tringe, Susannah G, McHardy, Alice C, Copeland, Alex, Kyrpides, Nikos C, Hugenholtz, Philip, Macarie, Hervé, Olmos, Alejandro, Monroy, Oscar

Journal:

The ISME Journal

Year:

2010

Language:

english

File:

PDF, 947 KB

english, 2010

12

High-resolution metagenomics targets specific functional types in complex microbial communities

Kalyuzhnaya, Marina G, Lapidus, Alla, Ivanova, Natalia, Copeland, Alex C, McHardy, Alice C, Szeto, Ernest, Salamov, Asaf, Grigoriev, Igor V, Suciu, Dominic, Levine, Samuel R

Journal:

Nature Biotechnology

Year:

2008

Language:

english

File:

PDF, 347 KB

english, 2008

13

Taxonomic metagenome sequence assignment with structured output models

Patil, Kaustubh R, Haider, Peter, Pope, Phillip B, Turnbaugh, Peter J, Morrison, Mark, Scheffer, Tobias, McHardy, Alice C

Journal:

Year:

2011

Language:

english

File:

PDF, 315 KB

english, 2011

14

Use of simulated data sets to evaluate the fidelity of metagenomic processing methods

Mavromatis, Konstantinos, Ivanova, Natalia, Barry, Kerrie, Shapiro, Harris, Goltsman, Eugene, McHardy, Alice C, Rigoutsos, Isidore, Salamov, Asaf, Korzeniewski, Frank, Land, Miriam

Journal:

Year:

2007

Language:

english

File:

PDF, 332 KB

english, 2007

15

Accurate phylogenetic classification of variable-length DNA fragments

McHardy, Alice Carolyn, Martín, Héctor García, Tsirigos, Aristotelis, Hugenholtz, Philip, Rigoutsos, Isidore

Journal:

Year:

2006

Language:

english

File:

PDF, 324 KB

english, 2006

16

What's in the mix: phylogenetic classification of metagenome sequence samples

Alice C. McHardy, Isidore Rigoutsos

Journal:

Current Opinion in Microbiology

Year:

2007

Language:

english

File:

PDF, 121 KB

english, 2007

17

Bioinformatics support for high-throughput proteomics

Andreas Wilke, Christian Rückert, Daniela Bartels, Michael Dondrup, Alexander Goesmann, Andrea T. Hüser, Sebastian Kespohl, Burkhard Linke, Martina Mahne, Alice McHardy, Alfred Pühler, Folker Meyer

Journal:

Journal of Biotechnology

Year:

2003

Language:

english

File:

PDF, 687 KB

english, 2003

18

Genome-based analysis of biosynthetic aminotransferase genes of Corynebacterium glutamicum

Alice C McHardy, Andreas Tauch, Christian Rückert, Alfred Pühler, Jörn Kalinowski

Journal:

Journal of Biotechnology

Year:

2003

Language:

english

File:

PDF, 254 KB

english, 2003

19

REGANOR

Burkhard Linke, Alice C. McHardy, Heiko Neuweger, Lutz Krause…

Journal:

Applied Bioinformatics

Year:

2006

Language:

english

File:

PDF, 406 KB

english, 2006

20

Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins

Peter J. Turnbaugh, Christopher Quince, Jeremiah J. Faith, Alice C. McHardy, Tanya Yatsunenko, Faheem Niazi, Jason Affourtit, Michael Egholm, Bernard Henrissat, Rob Knight and Jeffrey I. Gordon

Journal:

Proceedings of the National Academy of Sciences

Year:

2010

Language:

english

File:

PDF, 1.54 MB

english, 2010

21

Inference of phenotype-defining functional modules of protein families for microbial plant biomass degraders

Konietzny, Sebastian, Pope, Phillip B, Weimann, Aaron, McHardy, Alice C

Journal:

Biotechnology for Biofuels

Year:

2014

Language:

english

File:

PDF, 3.31 MB

english, 2014

22

Structure and Function of the Bacterial Root Microbiota in Wild and Domesticated Barley

Bulgarelli, Davide, Garrido-Oter, Ruben, Münch, Philipp C., Weiman, Aaron, Dröge, Johannes, Pan, Yao, McHardy, Alice C., Schulze-Lefert, Paul

Journal:

Cell Host & Microbe

Year:

2015

Language:

english

File:

PDF, 1.60 MB

english, 2015

23

PRIMAL: Fast and Accurate Pedigree-based Imputation from Sequence Data in a Founder Population

Livne, Oren E., Han, Lide, Alkorta-Aranburu, Gorka, Wentworth-Sheilds, William, Abney, Mark, Ober, Carole, Nicolae, Dan L., McHardy, Alice Carolyn

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 660 KB

english, 2015

24

Mining Host-Pathogen Protein Interactions to Characterize Burkholderia mallei Infectivity Mechanisms

Memišević, Vesna, Zavaljevski, Nela, Rajagopala, Seesandra V., Kwon, Keehwan, Pieper, Rembert, DeShazer, David, Reifman, Jaques, Wallqvist, Anders, McHardy, Alice Carolyn

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 1.58 MB

english, 2015

25

BiomeNet: A Bayesian Model for Inference of Metabolic Divergence among Microbial Communities

Shafiei, Mahdi, Dunn, Katherine A., Chipman, Hugh, Gu, Hong, Bielawski, Joseph P., McHardy, Alice Carolyn

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 1.08 MB

english, 2014

26

A Scalable and Accurate Targeted Gene Assembly Tool (SAT-Assembler) for Next-Generation Sequencing Data

Zhang, Yuan, Sun, Yanni, Cole, James R., McHardy, Alice Carolyn

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 1.20 MB

english, 2014

27

Viral Quasispecies Assembly via Maximal Clique Enumeration

Töpfer, Armin, Marschall, Tobias, Bull, Rowena A., Luciani, Fabio, Schönhuth, Alexander, Beerenwinkel, Niko, Carolyn McHardy, Alice

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 503 KB

english, 2014

28

Inference of Genotype–Phenotype Relationships in the Antigenic Evolution of Human Influenza A (H3N2) Viruses

Steinbrück, Lars, McHardy, Alice Carolyn, Ferguson, Neil

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 329 KB

english, 2012

29

Universal Count Correction for High-Throughput Sequencing

Hashimoto, Tatsunori B., Edwards, Matthew D., Gifford, David K., McHardy, Alice Carolyn

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 787 KB

english, 2014

30

The Role of Genomics in Tracking the Evolution of Influenza A Virus

McHardy, Alice Carolyn, Adams, Ben, Manchester, Marianne

Journal:

Year:

2009

Language:

english

File:

PDF, 880 KB

english, 2009

31

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.

Journal:

Proceedings of the National Academy of Sciences

Year:

2015

Language:

english

File:

PDF, 968 KB

english, 2015

32

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

Kratsch, Christina, Klingen, Thorsten R., Mümken, Linda, Steinbrück, Lars, McHardy, Alice C.

Journal:

Virus Evolution

Year:

2016

Language:

english

File:

PDF, 1.02 MB

english, 2016

33

Bioboxes: standardised containers for interchangeable bioinformatics software

Belmann, Peter, Dröge, Johannes, Bremges, Andreas, McHardy, Alice C., Sczyrba, Alexander, Barton, Michael D.

Journal:

Year:

2015

Language:

english

File:

PDF, 720 KB

english, 2015

34

The impact of seasonal and year-round transmission regimes on the evolution of influenza A virus

Ben Adams and Alice Carolyn McHardy

Journal:

Proceedings Biological Sciences

Year:

2011

Language:

english

File:

PDF, 1.49 MB

english, 2011

35

‘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, Wakako, Strassert, Jürgen F. H., Köhler, Tim, Mikaelyan, Aram, Gregor, Ivan, McHardy, Alice C., Tringe, Susannah Green, Hugenholtz, Phil, Radek, Renate, Brune, Andreas

Journal:

Environmental Microbiology

Year:

2016

Language:

english

File:

PDF, 845 KB

english, 2016

36

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

Journal:

Genes, Chromosomes and Cancer

Year:

2016

Language:

english

File:

PDF, 1.49 MB

english, 2016

37

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

Otte, Anna, Marriott, Anthony C., Dreier, Carola, Dove, Brian, Mooren, Kyra, Klingen, Thorsten R., Sauter, Martina, Thompson, Katy-Anne, Bennett, Allan, Klingel, Karin, van Riel, Debby, McHardy, Alice

Journal:

Scientific Reports

Year:

2016

Language:

english

File:

PDF, 1.81 MB

english, 2016

38

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, Xiyang, Dröge, Johannes, von Toerne, Christine, Marozava, Sviatlana, McHardy, Alice C., Meckenstock, Rainer U.

Journal:

FEMS Microbiology Ecology

Year:

2016

Language:

english

File:

PDF, 339 KB

english, 2016

39

From Genomes to Phenotypes: Traitar, the Microbial Trait Analyzer

Weimann, Aaron, Mooren, Kyra, Frank, Jeremy, Pope, Phillip B., Bremges, Andreas, McHardy, Alice C., Segata, Nicola

Journal:

Year:

2016

Language:

english

File:

PDF, 1.62 MB

english, 2016

40

EDEN: Evolutionary Dynamics within Environments

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

Journal:

Year:

2017

Language:

english

File:

PDF, 377 KB

english, 2017

41

Characterisation of a stable laboratory co-culture of acidophilic nanoorganisms

Krause, Susanne, Bremges, Andreas, Münch, Philipp C., McHardy, Alice C., Gescher, Johannes

Journal:

Scientific Reports

Year:

2017

Language:

english

File:

PDF, 8.56 MB

english, 2017

42

In Silico Vaccine Strain Prediction for Human Influenza Viruses

Klingen, Thorsten R., Reimering, Susanne, Guzmán, Carlos A., McHardy, Alice C.

Journal:

Trends in Microbiology

Year:

2017

Language:

english

File:

PDF, 2.88 MB

english, 2017

43

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

Grießmeier, Victoria, Bremges, Andreas, McHardy, Alice C., Gescher, Johannes

Journal:

Scientific Reports

Year:

2017

Language:

english

File:

PDF, 3.59 MB

english, 2017

44

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

Ye, Zihong, Pan, Yao, Zhang, Yafen, Cui, Haifeng, Jin, Gulei, McHardy, Alice C, Fan, Longjiang, Yu, Xiaoping

Journal:

Year:

2017

Language:

english

File:

PDF, 1.02 MB

english, 2017

45

DISK–JET CONNECTION IN THE RADIO GALAXY 3C 120

Chatterjee, Ritaban, Marscher, Alan P., Jorstad, Svetlana G., Olmstead, Alice R., McHardy, Ian M., Aller, Margo F., Aller, Hugh D., Lähteenmäki, Anne, Tornikoski, Merja, Hovatta, Talvikki, Marshall, K

Journal:

The Astrophysical Journal

Year:

2009

Language:

english

File:

PDF, 2.09 MB

english, 2009

46

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

Klingen, Thorsten R., Reimering, Susanne, Loers, Jens, Mooren, Kyra, Klawonn, Frank, Krey, Thomas, Gabriel, Gülsah, McHardy, Alice C.

Journal:

Scientific Reports

Year:

2018

Language:

english

File:

PDF, 3.68 MB

english, 2018

47

AMBER: Assessment of Metagenome BinnERs

Meyer, Fernando, Hofmann, Peter, Belmann, Peter, Garrido-Oter, Ruben, Fritz, Adrian, Sczyrba, Alexander, McHardy, Alice C

Journal:

Year:

2018

Language:

english

File:

PDF, 1.28 MB

english, 2018

48

A phylogenetic method to perform genome-wide association studies in microbes that accounts for population structure and recombination

Collins, Caitlin, Didelot, Xavier, McHardy, Alice Carolyn

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 3.13 MB

english, 2018

49

The PhyloPythiaS Web Server for Taxonomic Assignment of Metagenome Sequences

Patil, Kaustubh Raosaheb, Roune, Linus, McHardy, Alice Carolyn, Highlander, Sarah K.

Journal:

Year:

2012

Language:

english

File:

PDF, 389 KB

english, 2012

50

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

Garrido-Oter, Ruben, Nakano, Ryohei Thomas, Dombrowski, Nina, Ma, Ka-Wai, McHardy, Alice C., Schulze-Lefert, Paul

Journal:

Cell Host & Microbe

Year:

2018

Language:

english

File:

PDF, 4.34 MB

english, 2018

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