Phylogeny - OmicsDI

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Unknown (14182)
Genomics (2941)
Transcriptomics (126)
Models (105)
Proteomics (29)
Metabolomics (24)
Other (7)
Methylation profiling (2)
Genomic (1)

Organisms

Cryptococcus neoformans (2)
Clavispora lusitaniae (2)
Sporobolomyces roseus (2)
Aspergillus terreus (2)
Aspergillus niger (2)
Fusarium oxysporum (2)
Sclerotinia sclerotiorum (2)
Histoplasma capsulatum (2)
Nakaseomyces glabratus (2)
Chaetomium globosum (2)
Lodderomyces elongisporus (2)
Pyricularia grisea (2)
5306 (2)
Aspergillus clavatus (2)
Schizosaccharomyces japonicus (2)
Botrytis cinerea (2)
Aspergillus oryzae (2)
Aspergillus fumigatus (2)
140110 (2)
Coccidioides immitis (2)
Kluyveromyces lactis (2)
Fusarium graminearum (2)
Candida tropicalis (2)
Fusarium verticillioides (2)
Rhodonia placenta (2)
Debaryomyces hansenii (2)
Trichoderma reesei (2)
Candida albicans (2)
Parastagonospora nodorum (2)
Zymoseptoria tritici (2)

Organisms

Pasteurella multocida (48)
Homo sapiens (25)
Escherichia coli (19)
Taeniopygia guttata (9)
Rhizobium leguminosarum (6)
soil metagenome (5)
Eumops nanus (4)
Carassius gibelio (4)
Lasiurus ega (4)
Centurio senex (4)
gut metagenome (4)
Staphylococcus aureus (4)
Araneae (3)
Rhynochetos jubatus (3)
Nonomuraea sp. SYSU D8015 (3)
Clostridium thermarum (3)
Brucella melitensis (3)
Cucumis melo (3)
Salmonella enterica subsp. enterica serovar Typhimurium (3)
algae metagenome (3)
Drosophila melanogaster (3)
Camellia sinensis (3)
marine metagenome (3)
Mycobacterium tuberculosis (3)
Mus musculus (3)
Aquiflexum gelatinilyticum (2)
Sinocyclocheilus (2)
Peribacillus tepidiphilus (2)
Microbacterium sp. KCTC 39802 (2)
Azohydromonas sediminis (2)

Repository

ENA (2840)
BioModels (105)
biostudies-arrayexpress (83)
EGA (82)
geo (70)
pride (23)
MetaboLights (15)
GNPS (9)
MassIVE (5)
iProX (2)
dbGaP (1)

Tissue

Bone (2)
Tooth enamel (2)
Blood serum (1)
Brain (1)
Cell culture (1)
Cell suspension culture (1)
Dentin (1)
Gametophore (1)
Leaf (1)
Permanent cell line cell (1)
Photosynthetic cell (1)
Plant cell (1)
Protonema (1)
Tooth (1)
Venom (1)
Venom apparatus (1)
Whole body (1)

Disease

Raji Burkitt's lymphoma (1)

Technology Type

Mass Spectrometry (23)
Shotgun proteomics (15)
Mass spectrometry (12)
Bottom-up proteomics (5)
Mass spectrometry assay (3)
Data-dependent acquisition (3)
Gel-based experiment (3)
ILLUMINA, Illumina HiSeq 2500 (2)
Illumina HiSeq 2000, ILLUMINA (2)
ILLUMINA, Low Pass Whole Genome Sequencing (LP-WGS), Illumina NovaSeq 6000, Illumina Genome Analyzer II, SNP array (1)
Illumina HiSeq 2500, ILLUMINA, NextSeq 500 (1)
Illumina HumanOmniExpress-FFPE-12 v1.0 BeadChip (1)
Illumina HiSeq 4000, Illumina HiSeq 2500, ILLUMINA (1)
HiSeq X Ten (1)
ILLUMINA, Illumina HiSeq 2000 (1)
Illumina MiSeq, Illumina HiSeq 2000 (1)
Illumina Genome Analyzer II (1)
Data-independent acquisition (1)
Top-down proteomics (1)

Instrument Platform

Q Exactive (6)
Liquid Chromatography MS - positive - reverse phase (6)
Liquid Chromatography MS - negative - reverse phase (4)
Illumina HiSeq 2000 (3)
Illumina Genome Analyzer (2)
Illumina Genome Analyzer II (2)
Illumina HiSeq 2500 (2)
Bruker ImpactII ultra-high-resolution Qq-TOF mass spectrometer (2)
LTQ Orbitrap Elite (2)
Liquid Chromatography MS - Negative (LC-MS (Negative)) (2)
Gas Chromatography MS - positive (2)
Liquid Chromatography MS - negative - hilic (2)
Liquid Chromatography MS - positive - hilic (2)
GeneQuant DNA/RNA caluculator (1)
Variable Atmosphere Incubator (1)
Illumina NovaSeq 6000 (1)
NextSeq 500 (1)
GC/MS Agilent MSD5977B (1)
Thermo Scientific instrument model|1000494 (1)
TripleTOF 5600 (1)
UHPLC-ESI-MS qTof (1)
LCMS-IT-TOF (1)
TSQ Vantage (Thermo Scientific) (1)
Exactive (Thermo Scientific) (1)
Liquid Chromatography MS - negative (1)
Liquid Chromatography MS - positive (1)
Liquid Chromatography MS - alternating - reverse phase (1)
Liquid Chromatography MS - positive - reverse-phase (1)
Liquid Chromatography MS - negative - reverse-phase (1)

Publication Date

2014 (60)
2016 (58)
2012 (25)
2010 (20)
2020 (19)
2023 (16)
2024 (16)
2026 (12)
2018 (9)
2015 (9)
2011 (9)
2025 (9)
2021 (8)
2022 (7)
2008 (7)
2007 (7)
2019 (6)
2013 (5)
2009 (4)
2017 (4)
2003 (1)

CHEBI ID

CHEBI:37671 (104)
CHEBI:18246 (56)
HSO3 (56)
CPD-7033 (56)
FE+2 (56)
CHEBI:17810 (56)
CHEBI52386 (56)
CHEBI52389 (56)
CHEBI52615 (56)
CHEBI52388 (56)
CPD-7000 (56)
CHEBI:58608 (56)
CHEBI:28573 (56)
CHEBI:74474 (56)
CHEBI:52329 (56)
CHEBI:52327 (56)
CHEBI:52325 (56)
CHEBI:52328 (56)
CHEBI:48943 (56)
CHEBI:17909 (56)
CHEBI:17029 (56)
CHEBI:49183 (56)
CHEBI:62098 (55)
CHEBI:52897 (55)
CHEBI:29121 (55)
CHEBI:71626 (55)
CHEBI:71627 (55)
CHEBI:35759 (55)
CHEBI:57560 (55)
CHEBI:75061 (55)

Metabolite Name

Spermidine (3)
Thiocolchicoside (2)
Ala-Met (2)
Coronaric acid (2)
Agmatine (2)
D-Ornithine (2)
2,4,5-tricaffeoylaltraric acid (2)
2,3,5-tricaffeoylaltraric acid (2)
Protocatechuic acid (2)
Biflavonoid (2)
1,5-dicaffeoylquinic acid (2)
Altraric acid (2)
3-O-methylquercetin (2)
Tryptamine (2)
Caffeine (2)
Ergothioneine (2)
Quinic acid (2)
L-Cystine (2)
Bergaptol (2)
Fagomine (2)
Tryptophan (2)
Serine (2)
Proline (2)
Kynurenine (2)
Guanosine (2)
Guanine (2)
Cytosine (2)
Cysteine (2)
Citrulline (2)
Arginine (2)

First Public Date

2024 (319)
2022 (308)
2019 (284)
2020 (271)
2025 (263)
2021 (243)
2026 (240)
2023 (232)
2018 (174)
2015 (118)
2017 (116)
2013 (96)
2014 (85)
2016 (73)
2012 (12)
2011 (4)
2010 (2)

Modelling Approach

Constraint-based model (56)

Lab affiliation

Analytics Core Facility Essen (ACE), Chemische Biologie, Universität Duisburg-Essen, ZMB, Germany (1)
Associate Professor and Head of Discovery Proteomics Facility (1)
CSIC (1)
Center for Reproductive Evolution, Biology Department, Syracuse University, Syracuse, NY, 13244, USA (1)
Crop Genetics John Innes Centre Norfolk United Kingdom (1)
Department of Computer Science, University of Antwerp, 2020 Antwerpen, Belgium (1)
Department of Food Safety and Environmental Health, University of Helsinki, Finland (1)
Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany (1)
Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany 2NNF Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark (1)
Evolutionary and translational venomics Lab, Instituto de Biomedicina de Valencia, CSIC (1)
Extremophiles metabolism laboratory, Winogradsky Institute of Microbiology, FRC Biotechnology, RAS, Russia (1)
Faculty of Chemistry, Biotechnology and Food Science Norwegian University of Life Sciences Post Office Box 5003 1432, Ås Norway (1)
Group Leader, Institute for Molecular Biosciences, The University of Queensland, Australia (1)
Laboratoire d’Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Université de Toulouse, CNRS, UPS, Toulouse, France (1)
Laboratory of Evolutionary Genetics, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia. (1)
Lundbeck Foundation GeoGenetics Centre, Natural History Museum of Denmark, University of Copenhagen, Denmark (1)
Max Planck Institute for Terrestrial Microbiology Karl-von-Frisch Str. 10 35043 Marburg Germany (1)
Oded Beja, Ph.D., Professor, The Louis and Lyra Richmond Chair in Life Sciences, Faculty of Biology, Technion - Israel Institute of Technology, Haifa 3200003, Israel (1)
Prof. Dr. Martin von Bergen Helmholtz Centre for Environmental Research - UFZ Head of Department for Molecular Systems Biology http://www.ufz.de/index.php?de=17634 Professor of Functional Proteomics Faculty of Life Sciences, Pharmacy and Psychology University of Leipzig Permoserstr. 15 04318 Leipzig GERMANY (1)
Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark (1)
Thomas and Margaret Pyle Chair at the Morgridge Institute for Research Professor, Biomolecular Chemistry and Chemistry University of Wisconsin, Madison Director, NIH National Center for Quantitative Biology of Complex Systems (1)
Univ of Washington Dept of Genome Sciences (1)
University of Calgary (1)

Tags

pathogen (144)
pathogen:bacterium (133)
xref:PubMed:23045667 (15)
xref:PubMed:33911273 (11)
xref:PubMed:29166127 (9)
xref:PubMed:32948272 (8)
pathogen:virus (6)
xref:PubMed:24606129 (5)
xref:PubMed:27476034 (5)
covid19 (5)
pathogen:fungus (5)
xref:PubMed:37729611 (4)
xref:PubMed:24034719 (4)
xref:PubMed:40220298 (3)
xref:PubMed:25726302 (2)
xref:PubMed:21984240 (2)
xref:PubMed:42184164 (2)
xref:PubMed:40832330 (2)
xref:PubMed:39568153 (2)
xref:PubMed:40653200 (2)
xref:PubMed:40401952 (2)
xref:PubMed:34685951 (2)
xref:PubMed:22840345 (2)
xref:PubMed:17848203 (2)
xref:PubMed:25378574 (1)
xref:PubMed:32226006 (1)
xref:PubMed:30557299 (1)
xref:PubMed:39798088 (1)
xref:PubMed:9563170 (1)
xref:PubMed:33950183 (1)

IsPrivate

False (105)

Model Flag

Non Kinetic (105)

Classification

bacteria (133)
viruses (6)
fungi (5)

Study type

Transcription profiling by array (39)
RNA-seq of coding RNA (17)
Comparative genomic hybridization by array (11)
Unknown experiment type (3)
RNA-seq of non coding RNA (3)
ChIP-chip by tiling array (2)
Genotyping by array (2)
ChIP-chip by array (1)
Spatial transcriptomics by high-throughput sequencing (1)
Other (1)
Proteomic profiling by array (1)
Methylation profiling by high throughput sequencing (1)
RNA-seq of total RNA (1)

Release Date

2022 (1447)
2021 (1356)
2023 (1254)
2020 (1127)
2019 (966)
2024 (960)
2025 (953)
2018 (870)
2017 (838)
2016 (685)
2015 (586)
2014 (563)
2013 (483)
2012 (422)
2011 (338)
2010 (252)
2009 (222)
2008 (186)
2007 (165)
2026 (120)
2006 (108)
2005 (99)
2004 (68)
2002 (39)
2003 (37)
2001 (34)
2000 (30)
1999 (29)
1998 (19)
1997 (8)

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Phylogeny of Lygaeoidea

Phylogeny of Lygaeoidea

PRJEB26674 | ENA

Phylogeny of snowfinches

Phylogeny of snowfinches

PRJEB61937 | ENA

The phylogeny of Aliivibrio

Revised phylogeny of genus Aliivibrio

PRJEB34882 | ENA

Phylogeny of Stachytarpheta group Lycnhantha

Phylogeny of Stachytarpheta group Lycnhantha

PRJEB57092 | ENA

The phylogeny of Apodemus

The phylogeny of Apodemus from China Genome sequencing

PRJNA1222099 | ENA

Y phylogeny haplogroupDE

High-coverage whole genome sequences using Hiseq X for 4 individuals to investigate their Y chrosmosmes' relationship to the known phylogeny. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (incl...

EGAS00001002674 | EGA

Crambidae Phylogeny

The first Crambidae phylogeny including all 15 subfamilies

PRJEB34477 | ENA

Coryphoideae Subfamily phylogeny

In this study, the phylogeny of the palm subfamily Coryphoideae is produced based on targeted sequence capture.

PRJEB48475 | ENA

Australian marsupial phylogeny

Australian marsupial phylogeny with denovo assembly of target exons captured sequences.

PRJEB39788 | ENA

Whole Chloroplast Phylogeny of Saccharum officinarum

Whole chloroplast phylogeny of Saccharum officinarum, Saccharum cultum and allies

PRJEB32212 | ENA

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