Homology model - OmicsDI

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Unknown (4549)
Transcriptomics (816)
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Methylation profiling (5)
Metabolomics (2)

Organisms

Mus musculus (275)
Homo sapiens (262)
Danio rerio (44)
Arabidopsis thaliana (20)
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Drosophila melanogaster (18)
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Ovis aries (6)
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Callithrix jacchus (2)
Dictyostelium discoideum (2)
Bacillus subtilis subsp. subtilis str. 168 (2)

Organisms

Mus musculus (38)
Homo sapiens (31)
Drosophila melanogaster (5)
Saccharomyces cerevisiae (4)
Macaca fascicularis (3)
Papio anubis (3)
Barbodes semifasciolatus (3)
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Brassica fruticulosa (2)
Mus (2)
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Caenorhabditis elegans (2)
Glycine max (2)
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Didelphis virginiana (1)
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Steinernema carpocapsae (1)
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Lytechinus variegatus (1)
Enchytraeus albidus (1)
Mustela putorius furo (1)
Cryptococcus neoformans H99 (1)
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Lateolabrax japonicus (1)

Repository

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pride (89)
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Tissue

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Disease

N/A (culture-derived) (1)
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Pancreatic ductal adenocarcinoma (1)
Parkinson's disease (1)
Giardiasis (1)
Malaria (1)
Crohn's disease (1)
Cystic fibrosis (1)
Disease free (1)
Acute leukemia (1)

Technology Type

Mass Spectrometry (89)
Shotgun proteomics (47)
Gel-based experiment (14)
Bottom-up proteomics (14)
Affinity purification coupled with mass spectrometry proteomics (9)
Chemical cross-linking coupled with mass spectrometry proteomics (8)
Data-independent acquisition (7)
HDMSE (6)
MSE (4)
Data-dependent acquisition (3)
Mass spectrometry (2)
Top-down proteomics (2)
All-ion fragmentation (1)
SWATH MS (1)

Instrument Platform

Illumina NovaSeq 6000 (159)
Illumina HiSeq 2500 (94)
NextSeq 500 (89)
Illumina HiSeq 4000 (79)
Illumina HiSeq 2000 (66)
NextSeq 550 (28)
NextSeq 2000 (17)
Illumina NovaSeq X (14)
Illumina MiSeq (12)
Illumina Genome Analyzer IIx (9)
Illumina HiSeq 1500 (8)
Fluidigm C1 (5)
Agilent 2100 Bioanalyzer (4)
DNBSEQ-G400 (4)
Illumina HiSeq 1000 (4)
BGISEQ-500 (4)
Illumina HiSeq 3000 (4)
Illumina HiScanSQ (3)
AB SOLiD 4 System (3)
HiSeq X Ten (3)
AB 5500xl Genetic Analyzer (3)
Qubit 4.0 Fluorometer/ Agilen 5300 Fragment Analyzer (2)
Element AVITI (2)
Chromium 10x (2)
PromethION (2)
BD FACS Aria III (2)
Sony SH800 (2)
Not applicable (2)
Usegalaxy.org (2)
Illumina Genome Analyzer (2)

Publication Date

2024 (93)
2021 (93)
2026 (87)
2025 (85)
2022 (85)
2023 (79)
2020 (71)
2019 (68)
2018 (48)
2015 (46)
2010 (45)
2016 (43)
2014 (39)
2017 (35)
2013 (32)
2011 (27)
2012 (26)
2008 (20)
2005 (14)
2009 (8)
2007 (6)
2006 (1)

UNIPROT ID/AC

CSEC_STRCO (3)
Q9RD03_STRCO (3)
Q9S2B3_STRCO (3)
Q9EX14_STRCO (3)
O86590_STRCO (3)
Q93JE5_STRCO (3)
O86748_STRCO (3)
Q9S280_STRCO (3)
Q9K3Q8_STRCO (3)
O69961_STRCO (3)
Q9FBZ3_STRCO (3)
Q9RK21_STRCO (3)
Q93IZ2_STRCO (3)
O86689_STRCO (3)
Q9L1D1_STRCO (3)
Q9RDK2_STRCO (3)
Q9KYR1_STRCO (3)
Q9KZ31_STRCO (3)
Q9S2V9_STRCO (3)
Q9RKF7_STRCO (3)
Q9FCE6_STRCO (3)
Q9ADJ5_STRCO (3)
Q93RW6_STRCO (3)
Q9XA23_STRCO (3)
Q9ZBT4_STRCO (3)
Q9K4C2_STRCO (3)
Q9L2J1_STRCO (3)
Q9RKW3_STRCO (3)
Q9KYA5_STRCO (3)
Q8K4S1 (1)

CHEBI ID

CHEBI:18035 (14)
CHEBI:11812 (13)
CHEBI:11596 (13)
CHEBI:77740 (13)
CHEBI:17594 (13)
CHEBI:17164 (13)
CHEBI:74393 (13)
CHEBI:77802 (13)
CHEBI:35621 (13)
CHEBI:58680 (13)
CHEBI:74631 (13)
CHEBI:15593 (13)
CHEBI:132957 (13)
CHEBI:74604 (13)
CHEBI:32528 (13)
CHEBI:58675 (13)
CHEBI:58083 (13)
CHEBI:73784 (13)
CHEBI:73898 (13)
CHEBI:320061 (13)
CHEBI:73888 (13)
CHEBI:74363 (13)
CHEBI:73771 (13)
CHEBI:231935 (13)
CHEBI:61904 (13)
CHEBI:15245 (13)
CHEBI:77843 (13)
CHEBI:15226 (13)
CHEBI:78236 (13)
CHEBI:73762 (13)

Metabolite Name

DAG 44:1 (1)
DAG 42:2 (1)
DAG 42:1 (1)
DAG 42:0 (1)
DAG 41:1 (1)
DAG 40:1 (1)
DAG 40:0 (1)
DAG 39:0 (1)
DAG 38:2 (1)
DAG 38:1 (1)
DAG 38:0 (1)
DAG 37:1 (1)
DAG 36:3 (1)
DAG 36:2 (1)
DAG 36:1 (1)
DAG 36:0 (1)
DAG 35:2 (1)
DAG 35:1 (1)
DAG 34:3 (1)
DAG 34:2 (1)
DAG 34:1 (1)
DAG 34:0 (1)
DAG 33:2 (1)
DAG 33:1 (1)
DAG 32:3 (1)
DAG 32:2 (1)
DAG 32:1 (1)
DAG 32:0 (1)
DAG 31:1 (1)
DAG 30:2 (1)

First Public Date

2024 (28)
2026 (27)
2023 (24)
2014 (24)
2025 (16)
2013 (14)
2022 (13)
2019 (13)
2017 (13)
2021 (11)
2015 (9)
2020 (8)
2018 (8)
2016 (5)
2010 (2)
2012 (1)

Modelling Approach

Constraint-based model (15)
Ordinary differential equation model (1)

Lab affiliation

Neuroproteomics Group Department of Molecular Neurobiology Max Planck Institute for Multidisciplinary Sciences Hermann-Rein-Str. 3 37075 Goettingen Germany (3)
University of Missouri-Columbia (2)
Chair of Biochemistry II, Theodor Boveri-Institute, Biocenter, University of Würzburg, Würzburg, Germany (2)
Faculty of Chemistry, Biotechnology and Food Science Norwegian University of Life Sciences Post Office Box 5003 1432, Ås Norway (2)
NHMRC Principal Research Fellow Editor-in-Chief, Toxicon & Toxicon:X Theme Leader, Australian Research Council Centre of Excellence for Innovations in Peptide & Protein Science Deputy Head, Division of Chemistry & Structural Biology Institute for Molecular Bioscience The University of Queensland (1)
Centre for Proteome Research, Department of Biochemistry, University of Liverpool, UK (1)
Assistant Professor of Microbiology, Immunology, and Cancer Biology Associate Director for Diversity, Equity, and Inclusio at the Carter Immunology Center University of Virginia Charlottesville, VA (1)
Charles University in Prague, Faculty of Science Department of Parasitology Biocev, Průmyslová 595, Vestec 252 42 (1)
Crop Research Institute, Prague, Czechia (1)
Department of Chemistry, Southern University of Science and Technology, Shenzhen, China (1)
Department of Infection Biology Institute of Infection & Global Health University of Liverpool Liverpool Science Park IC2 146 Brownlow Hill Liverpool L3 5RF UK (1)
Department of Electrical Engineering and Electronics University of Liverpool Liverpool (1)
Department of intracellular signalling and transport, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia (1)
Discovery Proteomics, Genentech (1)
National Heart & Lung Institute, Imperial College London, London, UK (1)
Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal (1)
Proteomics Service, CIC bioGUNE. Bizkaia Tech Park Build. 800 Detio 48160 Spain (1)
Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool. Liverpool, UK. (1)
1 Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia (1)
Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Allianz, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany (1)
Deputy Head (Research), Department of Biochemistry and Molecular Biology Head Immunoproteomics Laboratory Infection and Immunity Program Room 214, level 2, 15 Innovation Walk Monash Biomedicine Discovery Institute Monash University, Clayton Campus Clayton 3800 Victoria Australia (1)
Department of Oral Biology and Pathology, Faculty of Odontology, Malmo University, Malmo, Sweden (1)
Dept of Chemistry, Umeå University, Umeå, Sweden. (1)
Chair in Infection and Global Health, Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, UK (1)
University of North Carolina at Chapel Hill Department of Chemistry Chapel Hill, NC, USA (1)
Department of Ecology and Genetics, Uppsala University (1)
Professor at Section for Computational and RNA Biology, Copenhagen University (1)
Department of Chemistry Washington University in St. Louis (1)
Department of Entomology and Plant Pathology, 127 Noble Research Center, Oklahoma State University, Stillwater, Oklahoma, USA, 74078 (1)
College of Pharmacy, Research Institute of Pharmaceutical Sciences, Kyungpook National University, South Korea (1)

IsPrivate

False (18)

Model Flag

Non Kinetic (4)

Submitter Keywords

FROG (1)

Classification

bacteria (6)
fungi (3)
protozoa (1)

Study type

RNA-seq of coding RNA (363)
Transcription profiling by array (109)
RNA-seq of coding RNA from single cells (86)
ChIP-seq (44)
RNA-seq of total RNA (25)
Animal - High-throughput sequencing (20)
DNA-seq (18)
RNA-seq of non coding RNA (18)
Cell line - High-throughput sequencing (15)
Unknown experiment type (14)
Comparative genomic hybridization by array (10)
ATAC-seq (10)
ChIP-chip by tiling array (8)
CUT&RUN (8)
MicroRNA profiling by high throughput sequencing (7)
Single nucleus RNA sequencing (5)
Methylation profiling by high throughput sequencing (5)
Plant - High-throughput sequencing (4)
RIP-seq (4)
Transcription profiling by SAGE (3)
Human - High-throughput sequencing (3)
High-throughput sequencing (3)
Other (3)
Genotyping by high throughput sequencing (3)
Baseline (2)
CLIP-seq (2)
Spatial transcriptomics by high-throughput sequencing (2)
Bisulfite-seq (2)
Ribo-seq (2)
ScATAC-seq (2)

Release Date

2021 (373)
2022 (372)
2020 (329)
2023 (315)
2019 (314)
2014 (286)
2025 (281)
2024 (281)
2015 (277)
2018 (259)
2017 (253)
2016 (251)
2013 (247)
2012 (230)
2010 (223)
2011 (210)
2008 (143)
2009 (142)
2007 (96)
2026 (95)
2005 (82)
2006 (72)
2004 (57)
2003 (42)
2002 (37)
2001 (24)
1999 (20)
2000 (19)
1998 (17)
1997 (3)

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Model-guided development of evolutionarily stable yeast chassis for dicarboxylic acids production

Chassis strain suitable for producing multiple compounds is a central concept in synthetic biology. Design of a chassis using computational, first-principle, models is particularly attractive due to the predictability and control it offers, including against phenotype reversal due to adaptive mut...

2021-07-19 | MTBLS2007 | MetaboLights

Sustained Correction of a Murine Model of Phenylketonuria following a Single Intravenous Administration of AAVHSC15-PAH.

Not available

S-EPMC7118282 | biostudies-literature

LNA blockers for improved amplification selectivity.

Not available

S-EPMC10038989 | biostudies-literature

Expression profiling of thymic lymphomas from p53 mutant (R270H) mice with varying HIF levels

Expression profiling of thymic lymphomas derived from HIF1a+/+, p53R270H/R270H; HIF1a+/-, p53R270H/R270H; and HIF1aKI/+, p53R270H/R270H mice. HIF1a and HIF2a share a high degree of sequence homology, but recent work has shown that the two a subunits can have contrasting and tissue-specific effects ...

ORGANISM(S): Mus musculus

2009-01-12 | E-GEOD-14336 | biostudies-arrayexpress

SWISS-MODEL: homology modelling of protein structures and complexes.

Not available

S-EPMC6030848 | biostudies-literature

Prefiltering Model for Homology Detection Algorithms on GPU.

Not available

S-EPMC5170890 | biostudies-literature

Homology model of the GABAA receptor examined using Brownian dynamics.

Not available

S-EPMC1305477 | biostudies-literature

ABT-737 treatment induces regulation and activation of pathways implicated in cell survival, proliferation and stem cells in treated AML mice survival, proliferation and stem cells in treated AML mice

Myelodysplastic syndrome (MDS) transforms into an acute myelogenous leukemia (AML) with associated increased bone marrow blast infiltration. Using a transgenic mouse model, MRP8[NRASD12/hBCL-2], in which the NRAS:BCL-2 complex at the mitochondria induces MDS progressing to AML with dysplastic featur...

ORGANISM(S): Mus musculus

2013-11-06 | E-GEOD-48601 | biostudies-arrayexpress

Protein homology model refinement by large-scale energy optimization.

Not available

S-EPMC5866580 | biostudies-literature

Model comparison via simplicial complexes and persistent homology.

Not available

S-EPMC8511761 | biostudies-literature

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