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Nov 2021

Hall NA,Carlyle BC,Haerty W,Tunbridge EM

Roadblock: improved annotations do not necessarily translate into new functional insights

Genome Biology

Publishers version: doi:10.1186/s13059-021-02542-5

Oct 2021

Csabai L,Fazekas D,Kadlecsik T,Szalay-Beko M,Bohár B,Madgwick M,Módos D,Olbei M,Gul L,Sudhakar P,Kubisch J,Oyeyemi OJ,Liska O,Ari E,Hotzi B,Billes VA,Molnár E,Földvári-Nagy L,Csályi K,Demeter A,Pápai N,Koltai M,Varga M,Lenti K,Farkas IJ,Türei D,Csermely P,Vellai T,Korcsmáros T

SignaLink3: a multi-layered resource to uncover tissue-specific signaling networks.

Nucleic acids research

Publishers version: doi:10.1093/nar/gkab909

Sep 2021

Mckee A,Kirkup B,Madgwick M,Fowler W,Price C,Dreger S,Ansorge R,Makin K,Caim S,Le Gall G,Pavely J,Leclaire C,Dalby M,Alcon-Giner C,Andrusaite A,Feng TY,Di Modica M,Triulzi T,Tagliabue E,Milling S,Weilbaecher K,Rutkowski M,Korcsmaros T,Hall L,Robinson S

Antibiotic-induced disturbances of the gut microbiota result in accelerated breast tumour growth

iScience

Publishers version: doi:10.1016/J.ISCI.2021.103012

Sep 2021

Dudley QM,Cai Y,Kallam K,Debreyne H,Carrasco Lopez J,Patron NJ

Biofoundry-Assisted Expression and Characterisation of Plant Proteins

Synthetic Biology

Publishers version: doi:10.1093/synbio/ysab029

Sep 2021

Martin K,Schmidt K,Toseland A,Boulton CA,Barry K,Beszteri B,Brussaard CPD,Clum A,Daum CG,Eloe-Fadrosh E,Fong A,Foster B,Foster B,Ginzburg M,Huntemann M,Ivanova NN,Kyrpides NC,Lindquist E,Mukherjee S,Palaniappan K,Reddy TBK,Rizkallah MR,Roux S,Timmermans K,Tringe SG,van de,Varghese N,Valentin KU,Lenton TM,Grigoriev IV,Leggett RM,Moulton V,Mock T

The biogeographic differentiation of algal microbiomes in the upper ocean from pole to pole.

Nature communications

Publishers version: doi:10.1038/s41467-021-25646-9

Aug 2021

Dudley QM,Jo J,Serna Guerrero DA,O'Connor S,Caputi L,Patron NJ

Reconstitution of monoterpene indole alkaloid biosynthesis inNicotiana benthamiana

bioRxiv

Publishers version: doi:10.1101/2021.08.12.456143

Aug 2021

Higgins J.,Santos B.,Khanh T.D.,Trung K.H.,Duong T.D.,Doai N.T.P.,Hall A.,Dyer S.,Caccamo M.,De Vega J

Identifying genomic regions and candidate genes selected during the breeding of rice in Vietnam

bioRxiv

Publishers version: doi:0.1101/2021.08.04.455072

Aug 2021

Olbei M,Thomas JP,Hautefort I,Treveil A,Bohar B,Madgwick M,Gul L,Csabai L,Modos D,Korcsmaros T

CytokineLink: A Cytokine Communication Map to Analyse Immune Responses-Case Studies in Inflammatory Bowel Disease and COVID-19.

Cells

Publishers version: doi:10.3390/cells10092242

Aug 2021

Hildebrand F

Ultra-resolution Metagenomics: When Enough Is Not Enough.

mSystems

Publishers version: doi:10.1128/mSystems.00881-21

Jul 2021

Martin S,Ayling M,Patrono L,Caccamo M,Murcia P,Leggett R

Capturing variation in metagenomic assembly graphs with MetaCortex

bioRxiv

Publishers version: doi:10.1101/2021.07.23.453484

Jul 2021

Higgins J.,Tomaszewska P.,Pellny T.,Castiblanco V.,Arango J.,Tohme J.,Schwarzacher T.,Mitchell R.,Heslop-Harrison J.,De Vega J

The five Urochloa spp. used in development of tropical forage cultivars originate from defined subpopulations with differentiated gene pools

bioRxiv

Publishers version: doi:10.1101/2021.07.21.453213

Jul 2021

Quince C,Nurk S,Raguideau S,James R,Soyer OS,Summers JK,Limasset A,Eren AM,Chikhi R,Darling AE

STRONG: metagenomics strain resolution on assembly graphs.

Genome biology

Publishers version: doi:10.1186/s13059-021-02419-7

Jul 2021

Hall N

Inter-kingdom relationships in Crohn's disease explored using a multi-omics approach

Gut Microbes

Publishers version: doi:10.1080/19490976.2021.1930871

Jul 2021

Salazar G,Ruscheweyh HJ,Hildebrand F,Acinas SG,Sunagawa S

mTAGs: taxonomic profiling using degenerate consensus reference sequences of ribosomal RNA genes.

Bioinformatics (Oxford, England)

Publishers version: doi:10.1093/bioinformatics/btab465

Jun 2021

Huws SA,Edwards JE,Lin W,Rubino F,Alston M,Swarbreck D,Caim S,Stevens PR,Pachebat J,Won MY,Oyama LB,Creevey CJ,Kingston-Smith AH

Microbiomes attached to fresh perennial ryegrass are temporally resilient and adapt to changing ecological niches.

Microbiome

Publishers version: doi:10.1186/s40168-021-01087-w