Co-evolution - OmicsDI

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Unknown (7048)
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Organisms

Homo sapiens (108)
Mus musculus (87)
Arabidopsis thaliana (18)
Saccharomyces cerevisiae (12)
Drosophila melanogaster (10)
Taeniopygia guttata (9)
Plasmodium falciparum (8)
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Formica selysi (3)
Branchiostoma lanceolatum (3)
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Nomascus leucogenys (3)
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Escherichia coli K-12 (3)
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Elymnias hypermnestra (2)
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Caenorhabditis briggsae (2)
Monodelphis domestica (2)
Ureaplasma sp. (2)
human vaginal metagenome (2)
Nitratidesulfovibrio vulgaris str. Hildenborough (2)
viral metagenome (2)

Repository

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Instrument Platform

Illumina NovaSeq 6000 (5)
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Liquid Chromatography MS - positive (1)
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Publication Date

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2011 (19)
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2016 (16)
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2009 (4)
2005 (1)
2006 (1)

UNIPROT ID/AC

14331_ORYSJ (1)
14331_SOLLC (1)
14334_ORYSJ (1)
14335_SOLLC (1)
14337_ORYSJ (1)
14337_SOLLC (1)
14338_SOLLC (1)
1433B_SOYBN (1)
2A5K_ORYSJ (1)
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3055.EDP02272 (1)
3055.EDP03640 (1)
3055.EDP03813 (1)
3055.EDP04366 (1)
3847.GLYMA06G11530.1 (1)
3847.GLYMA07G36560.3 (1)
3847.GLYMA08G02375.1 (1)
3847.GLYMA08G11940.1 (1)
3847.GLYMA08G19320.1 (1)
3847.GLYMA09G19800.2 (1)
3847.GLYMA11G00590.2 (1)
3847.GLYMA11G15650.4 (1)
3847.GLYMA11G15700.1 (1)
3847.GLYMA11G15820.1 (1)
3847.GLYMA11G15850.4 (1)
3847.GLYMA11G15890.2 (1)
3847.GLYMA11G16040.1 (1)
3847.GLYMA11G16090.1 (1)
3847.GLYMA11G16190.1 (1)

CHEBI ID

CHEBI:15741 (3)
CHEBI:18012 (3)
CHEBI:30769 (3)
CHEBI:6650 (3)
CHEBI:15428 (2)
CHEBI:16449 (2)
CHEBI:16811 (2)
CHEBI:16865 (2)
CHEBI:17268 (2)
CHEBI:17822 (2)
CHEBI:18186 (2)
CHEBI:18237 (2)
CHEBI:22660 (2)
CHEBI:24898 (2)
CHEBI:25017 (2)
CHEBI:25094 (2)
CHEBI:26986 (2)
CHEBI:27266 (2)
CHEBI:27570 (2)
CHEBI:27897 (2)
CHEBI:28044 (2)
CHEBI:28300 (2)
CHEBI:28757 (2)
CHEBI:30915 (2)
CHEBI:32816 (2)
CHEBI:1148 (1)
CHEBI:11805 (1)
CHEBI:139369 (1)
CHEBI:139373 (1)
CHEBI:139374 (1)

Metabolite Name

Glycerol (2)
((4-(4-Amidinophenoxy)butanoyl)aspartyl)valine (1)
(+)-Neomenthol (1)
(+/-)-6-Chlorotryptophan (1)
(+/-)-Tryptophan (1)
(-)-Slaframine (1)
(1S,2S,4R,8R)-p-Menthane-1,2,8,9-tetrol (1)
(1r,3r)-1-Aminocyclopentane-1,3-dicarboxylic acid (1)
(2-Mercaptomethyl-3-phenyl-propionyl)-glycine (1)
(2R,3S,5R)-5-(4,5-Dihydroimidazo[2,1-f]purin-3-yl)-2-(hydroxymethyl)oxolan-3-ol (1)
(2S)-2-(2-Benzamidoethylamino)-5-(diaminomethylideneamino)pentanoic acid (1)
(2S,2'S)-Pyrosaccharopine (1)
(2Z,4'Z)-2-(5-Methylthio-4-penten-2-ynylidene)-1,6-dioxaspiro[4.4]non-3-ene (1)
(3S,5S)-3,5-Diaminohexanoate (1)
(3beta,5alpha,9alpha,22E,24R)-3,5,9-Trihydroxy-23-methylergosta-7,22-dien-6-one (1)
(4E)-3-Hydroxyhex-4-enoylcarnitine (1)
(4R,5R)-1-Aminooxy-2,4,5,6-tetrahydroxyhexan-3-one (1)
(4S,8R)-8,9-Dihydroxy-p-menth-1(6)-en-2-one (1)
(4Z,7Z,10Z,13Z,15E,19Z)-17-Hydroxydocosa-4,7,10,13,15,19-hexaenoylcarnitine (1)
(5E)-7-[3,5-Dihydroxy-2-(3-hydroxyoctyl)cyclopentyl]hept-5-enoylcarnitine (1)
(5S,6R)-Methyl 5,6,7-trihydroxyheptanoate (1)
(E)-10-Hydroxy-8-decenoic acid (1)
(R)-2,3-Dihydroxy-isovalerate (1)
(R)-2-Hydroxy-2H-1,4-benzoxazin-3(4H)-one (1)
(S)-(-)-Perillyl alcohol (1)
(S)-10,16-Dihydroxyhexadecanoic acid (1)
(S)-5-Amino-3-oxohexanoate (1)
(S)-9-Hydroxy-10-undecenoic acid (1)
(S)-Isowillardiine (1)
(Z)-2-Decene-4,6,8-triyn-1-ol (1)

First Public Date

2026 (133)
2024 (119)
2023 (93)
2020 (83)
2025 (79)
2021 (71)
2022 (69)
2014 (69)
2019 (48)
2017 (44)
2018 (37)
2015 (32)
2016 (21)
2013 (21)
2012 (1)

Modelling Approach

Agent-based model (1)
Ordinary differential equation model (1)

Study status

Recruiting (1)

Lab affiliation

Australian Institute for Bioengineering and Nanotechnology, The University of Queensland (2)
CCBIO, Department of Clinical Medicine, Faculty of Medicine, University of Bergen, Bergen, Norway (2)
IMB, Ackermannweg 4, 55128 Mainz (2)
Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic (2)
A*STAR-SRIS (1)
Associate Professor Department of Biological Sciences University of Denver (1)
Basic Immune System of Plants / Protein Mass Spectrometry Max Planck Institute for Plant Breeding Research Carl-von-Linne-Weg 10, 50829 Cologne, Germany (1)
Biochemistry (1)
Biomedical Informatics, The Ohio State University, United States (1)
Biozentrum der LMU München Pflanzenwissenschaften Großhaderner Str. 2-4 82152 Planegg-Martinsried (1)
Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Old Road, University of Oxford, Oxford OX3 7LD, UK (1)
Centre for Advanced Imaging, the University of Queensland (1)
Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO Box 1066 Blindern, 0316 Oslo, Norway (1)
Charité Universitätsmedizin Berlin, Germany (1)
Consultant Medical oncology (1)
Department of Biological Engineering, Massachusetts Institute of Technology (1)
Department of Biotechnology, Yonsei University, Seoul 03722, South Korea (1)
Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel (1)
Department of Microbiology and Immunology, Department of Biochemistry and Biophysics, and Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill (1)
Department of Pharmacology, Yale University School of Medicine (1)
Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried, 82152 Munich, Germany. (1)
Director, Structural Biology Initiative, CUNY Advanced Science Research Center Distinguished and Einstein Professor of Chemistry & Biochemistry, City College of New York Biochemistry, Chemistry and Biology Ph.D. Programs, CUNY Graduate Center (1)
Div. Cell Biology, Biocenter, Medical University Innsbruck, Austria (1)
EMBL (1)
ETH Zurich, D-HEST, Lab of Systems Neuroscience (1)
Faculty of Life Sciences & Medicine, King’s College London, 150 Stamford Street, London SE1 9NH, United Kingdom. (1)
Functional Genomics Center Zurich (University of Zurich / ETHZ Zurich) (1)
Gregor Mendel Institute of Molecular Plant Biology GmbH Dr. Bohr-Gasse 3, 1030 Vienna, Austria Phone: +43 1 79044 9850 http://www.gmi.oeaw.ac.at (1)
Head of the Curie Institute Mass Spectrometry Platform (1)
Head of the Necker Proteomics Faculty of Medecine, University Paris Cité SFR Necker INSERM US24 160 rue de Vaugirard | 75015 Paris Tél. 01 40 61 54 67 (1)

IsPrivate

False (3)

Model Flag

Non Kinetic (1)

Submitter Keywords

Manuscript Accepted (1)

Classification

bacteria (36)
viruses (12)
protozoa (11)
fungi (3)

Modification

-17.026549 (1)
15.994915 (1)
2x(15)N labeled L-lysine (1)
42.010565 (1)
45.029395 (1)
4x(15)N labeled L-arginine (1)
57.021464 (1)

Study type

Transcription profiling by array (175)
RNA-seq of coding RNA (28)
ChIP-seq (12)
RNA-seq of non coding RNA (10)
Comparative genomic hybridization by array (6)
RNA-seq of coding RNA from single cells (5)
Unknown experiment type (4)
ChIP-chip by tiling array (3)
Other (3)
Genotyping by array (2)
DNA-seq (2)
Methylation profiling by array (2)
ChIP-chip by array (1)
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Observational (1)

Release Date

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2004 (83)
2008 (80)
2007 (60)
2006 (25)
2005 (20)
2003 (8)
2002 (6)
2000 (3)
2001 (1)

Location

Italy (1)

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Adaptive laboratory evolution of microbial co-cultures for improved metabolite secretion

Adaptive laboratory evolution has proven highly effective for obtaining microorganisms with enhanced capabilities. Yet, this method is inherently restricted to the traits that are positively linked to cell fitness, such as nutrient utilization. Here, we introduce coevolution of obligatory mutuali...

2021-07-02 | MTBLS2217 | MetaboLights

Adaptive Laboratory Evolution of microbial co-cultures for improved metabolite secretion

Small microbial mutualistic communities consisting of lactic acid bateria and S. cerevisiae evolved together for increased vitamin secretion from the lactic acid bacteria. Proteomics analysis of the parental and evolved bacteria to identify differences that occured during the prolonged co-evolution.

ORGANISM(S): Lactobacillus plantarum

2021-08-05 | PXD022250 | Pride

Dynamic co-evolution of transposable elements and the piRNA pathway in East African cichlid fishes

East African cichlid fishes have radiated in an explosive fashion. The (epi)genetic basis for the abundant phenotypic diversity of these fishes remains largely unknown. As transposable elements (TEs) contribute extensively to genome evolution, we reasoned that TEs may have fuelled cichlid radiations...

ORGANISM(S): Cichlidae sp.

2024-04-02 | PXD047439 | Pride

Lc-ms/ms

Protein co-evolution, co-adaptation and interactions.

Not available

S-EPMC2556093 | biostudies-literature

Dynamic co-evolution of transposable elements and the piRNA pathway in East African cichlid fishes

PRJNA1062739 | ENA

Co-mapping Clonal and Transcriptional Heterogeneity in Somatic Evolution via GoT-Multi.

PRJNA1247954 | ENA

Co-evolution of Neisseria species

PRJNA1207413 | ENA

Transcriptomic and phylogenetic analysis of a bacterial cell cycle reveals strong associations between gene co-expression and evolution

We used deep RNA sequencing to obtain high coverage RNA-Seq data of five C. crescentus cell cycle stages, each with three biological replicates. We found that 1,586 genes (over a third of the genome) display significant differential expression between stages. This gene list, which contains many gene...

ORGANISM(S): Caulobacter vibrioides

2013-05-15 | E-GEOD-46915 | biostudies-arrayexpress

PolyQ length co-evolution in neural proteins.

Not available

S-EPMC8121095 | biostudies-literature

Dynamic co-evolution of transposable elements and the piRNA pathway in East African cichlid fishes [smallRNA-seq]

PRJNA1062736 | ENA

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