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Disease

Colorectal Neoplasms (7)
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Colon cancer, rectal cancer, esophageal cancer, liver metastases from colorectal cancer, pancreato-biliary cancer, peritoneal carcinomatosis from colorectal cancer, retroperitoneal sarcoma, abdominal aortic aneurysm, renal cancer, bladder cancer, supratentorial meningioma, hip arthrosis, knee or hip arthroplasty failure, osteosarcoma, pulmonary cancer, thoracic aortic aneurysm, head and neck cancer, mouth cancer, breast reconstruction, ovarian cancer, endometrial cancer, vulvar cancer (1)
Patients that undergo FA-guided (1) esophagectomy (2) ileal pouch-anal anastomosis (IPAA), or (3) a partial or total mesorectal excision for colorectal cancer with restoration of bowel continuity will be included (1)
Pancreatoduodenectomy (1)
Anal Cancer (1)
The study population will consist of adult patients undergoing elective left-sided colonic surgery. (1)
Gastric adenocarcinoma (1)
Colonic Neoplasms (1)
Colorectal cancer (1)
Stomach and colorectal cancer (1)
Rectal Neoplasms (1)
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Acute leukemia (1)
Atherosclerosis (1)
Bladder adenocarcinoma (1)
Central retinal vein occlusion (1)

Technology Type

Mass Spectrometry (125)
Shotgun proteomics (68)
Bottom-up proteomics (24)
Mass spectrometry (21)
Data-dependent acquisition (12)
Gel-based experiment (10)
Top-down proteomics (7)
Mass spectrometry assay (5)
Chemical cross-linking coupled with mass spectrometry proteomics (4)
Illumina HiSeq 2000, ILLUMINA (3)
Affinity purification coupled with mass spectrometry proteomics (3)
Data-independent acquisition (3)
HDMSE (3)
Metaproteomics (3)
ILLUMINA, Illumina HiSeq 2500 (2)
MSE (2)
ILLUMINA, Low Pass Whole Genome Sequencing (LP-WGS), Illumina NovaSeq 6000, Illumina Genome Analyzer II, SNP array (1)
ILLUMINA, NextSeq 500, Illumina HiSeq 2000 (1)
Illumina HiSeq 2500, ILLUMINA, NextSeq 500 (1)
Illumina HumanOmniExpress-FFPE-12 v1.0 BeadChip (1)
Affymetrix OncoScan FFPE Express (1)
Illumina HiSeq 4000, Illumina HiSeq 2500, ILLUMINA (1)
HiSeq X Ten (1)
ILLUMINA, Illumina HiSeq 2000 (1)
Illumina Genome Analyzer, Illumina HiSeq 2000, Illumina MiSeq, Affymetrix_U133plus2- (1)
Illumina HiSeq 2000, ILLUMINA, Illumina HiSeq 2500 (1)
Illumina HiSeq 2500 (1)
Illumina MiSeq, Illumina HiSeq 2000 (1)
Illumina Genome Analyzer II (1)
NMR spectroscopy (1)

Instrument Platform

Illumina NovaSeq 6000 (15)
Illumina HiSeq 2500 (13)
Illumina HiSeq 2000 (7)
Illumina HiSeq 4000 (6)
Illumina Genome Analyzer IIx (4)
Fluidigm C1 (2)
Illumina Genome Analyzer (2)
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TruSeq RNA Sample Preparation Kit (Illumina) (1)
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GenePix 4000A [Axon Instruments] (1)
Variable Atmosphere Incubator (1)
10x Genomics Chromium Controller (1)
HiSeq X Ten (1)
Illumina MiSeq (1)
Impact (1)
TripleTOF 6600 (1)

Publication Date

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2014 (107)
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2018 (42)
2013 (39)
2011 (28)
2017 (27)
2008 (19)
2009 (14)
2007 (8)
2006 (2)
2004 (1)
2003 (1)

UNIPROT ID/AC

P04075 (72)
P14618 (70)
P05062 (70)
P09972 (70)
P00338 (70)
P07195 (70)
P30613 (70)
P06744 (70)
Q9BQG2 (68)
B3KXN9 (68)
Q53HM1 (68)
Q86SK9 (68)
E9KL42 (68)
Q3I5F7 (68)
P33897 (68)
Q99884 (68)
A8MU28 (68)
P35219 (68)
Q5FC00 (68)
Q15274 (68)
Q9NX14 (68)
Q9Y345 (68)
Q86YT5 (68)
Q53H96 (68)
Q9NWU1 (68)
Q96C36 (68)
Q9NRX3 (68)
O75610 (68)
Q6UWQ5 (68)
Q96KJ9 (68)

ENSEMBL ID

ENSDARG00000063559 (1)
ENSDARG00000090714 (1)
ENSDARG00000051873 (1)
ENSDARG00000061100 (1)
ENSDARG00000035506 (1)
ENSDARG00000024112 (1)
ENSDARG00000057714 (1)
ENSDARG00000010347 (1)
ENSDARG00000059411 (1)
ENSDARG00000036809 (1)
ENSDARG00000035565 (1)
ENSDARG00000029952 (1)
ENSDARG00000045414 (1)
ENSDARG00000020270 (1)
ENSDARG00000070844 (1)
ENSDARG00000077782 (1)
ENSDARG00000052942 (1)
ENSDARG00000075754 (1)
ENSDARG00000051853 (1)
ENSDARG00000077244 (1)
ENSDARG00000032218 (1)
ENSDARG00000063167 (1)
ENSDARG00000069937 (1)
ENSDARG00000063433 (1)
ENSDARG00000044642 (1)
ENSDARG00000016048 (1)
ENSDARG00000004115 (1)
ENSDARG00000006577 (1)
ENSDARG00000019236 (1)
ENSDARG00000059123 (1)

CHEBI ID

CHEBI:29033 (139)
CHEBI:16480 (138)
CHEBI:27931 (133)
CHEBI:17411 (133)
CHEBI:29034 (129)
CHEBI:27402 (123)
CHEBI:37671 (114)
CHEBI:17137 (111)
CHEBI:15428 (107)
CHEBI:17895 (105)
CHEBI:17115 (104)
CHEBI:61540 (102)
CHEBI:18191 (102)
CHEBI:16828 (102)
CHEBI:15971 (102)
CHEBI:17203 (102)
CHEBI:17191 (102)
CHEBI:16526 (102)
CHEBI:16977 (102)
CHEBI:16414 (102)
CHEBI:17268 (102)
CHEBI:16240 (101)
CHEBI:15343 (100)
CHEBI:17196 (99)
CHEBI:17561 (99)
CHEBI:15603 (99)
CHEBI:16349 (99)
CHEBI:16643 (99)
CHEBI:17295 (99)
CHEBI:16680 (99)

Metabolite Name

Spermidine (5)
Guanosine (4)
Xanthine (4)
Adenosine (4)
Uracil (4)
Putrescine (4)
Beta-alanine (4)
2'-deoxyadenosine (3)
Ergothioneine (3)
Tyramine (3)
Ribose (3)
Tryptophan (3)
Serine (3)
Proline (3)
Inosine (3)
Hypoxanthine (3)
Hypotaurine (3)
Guanine (3)
Cysteine (3)
Citrulline (3)
Arginine (3)
Adenine (3)
Phenylalanine (3)
Tyrosine (3)
Fructose (3)
Methionine (3)
Choline (3)
Creatinine (3)
Glutamine (3)
Ornithine (3)

First Public Date

2026 (287)
2025 (202)
2024 (161)
2021 (150)
2023 (147)
2022 (127)
2020 (103)
2019 (101)
2018 (82)
2014 (69)
2017 (60)
2013 (58)
2016 (52)
2015 (45)
2012 (8)
2011 (1)

Modelling Approach

Constraint-based model (169)
Ordinary differential equation model (29)
Metabolic network (7)
Other (2)

Study status

Completed (9)
Not provided (7)
Recruiting (5)
Not yet recruiting (2)
Terminated (1)

Lab affiliation

Globe Institute, University of Copenhagen, Denmark (3)
Natural History Museum of Denmark University of Copenhagen, Øster Voldgade 5–7, 1350 Copenhagen, Denmark (2)
Plant Biology (2)
University of Hohenheim, Institute of Animal Science, Stuttgart, Germany (2)
1 Department of Haematology, University of Cambridge, Hills Road, Cambridge, CB2 0XY, UK 2 Cambridge Institute for Medical Research, Keith Peters Building, Hills Road, Cambridge, CB2 0XY, UK 3 Wellcome Trust–Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK (1)
1 Max Planck Fellow Group Molecular Physiology of Microbes, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany 2 Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany 3 Department of Chemistry, University of Marburg, Marburg, Germany (1)
1. Division of Radiation Health, 2. Department of Pharmaceutical Sciences, 3. Neurobiology & Developmental Sciences, University of Arkansas for Medical Sciences, Little Rock, AR (1)
1. Institute of Genomics, University of Tartu, Tartu, 51010, Estonia 2. St John’s College, University of Cambridge, CB2 1TP, United Kingdom 3. Department of Zoology, University of Cambridge, CB2 3EJ, United Kingdom (1)
A.N. Bach Institute of Biochemistry, Federal Research Centre ‘Fundamentals of Biotechnology’ of the Russian Academy of Sciences, Leninsky pr., 33, 119071, Moscow, Russia (1)
Analytics Core Facility Essen (ACE), Chemische Biologie, Universität Duisburg-Essen, ZMB, Germany (1)
Andreas Otto, Institute for Microbiology, Ernst-Moritz-Arndt-University of Greifswald, F.-L. Jahnstrasse 15, 17489 Greifswald, Germany (1)
BMC, Zellbiologie, Anatomie III Großhaderener Strasse 9 D-82152 Planegg Germany (1)
Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China (1)
Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht 3584 CH, the Netherlands and Netherlands Proteomics Center, Padualaan 8, Utrecht 3584 CH, the Netherlands (1)
CEA-Marcoule, ProGénoMIX platform, DRF-Li2D, 30207 Bagnols-sur-Cèze, France (1)
CNC-Center for Neuroscience and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal; Biocant, Biotechnology Innovation Center, 3060-197 Cantanhede, Portugal; (1)
CSIR - Centre for Cellular and Molecular Biology, Hyderabad, India (1)
Caltech Division of Chemistry and Chemical Engineering (1)
Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO Box 1066 Blindern, 0316 Oslo, Norway (1)
Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Catalonia, Spain (1)
Centre for Inflammatory Diseases, Department of Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, 3168, Australia. (1)
Centro Nacional de Biotecnología (CNB-CSIC) (1)
Chongqing Medical University, Chonqqing, China (1)
Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Milton S. Hershey Medical Center, Hershey, PA 17033 (1)
Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, United States (1)
Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA; Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA (1)
Department of Biology, Faculty of Sciences-I, Lebanese University, Beirut, Lebanon (1)
Department of Biotechnology, TU Delft, The Netherlands (1)
Department of Chemical Sciences - University of Catania (1)
Department of Ecogenomics and Systems Biology, Division Molecular Systems Biology, University of Vienna, Austria (1)

Keyword

Restorative proctocolectomy (2)
Ileal pouch-anal anastomosis (2)
Near-infrared fluorescence (2)
Anastomotic leak (2)
Pouchitis (2)
Indocyanine green (2)
Side-to-end anastomosis (1)
Colon J pouch (1)
Anorectal function (1)
Are there differences between side-to-end anastomosis and colon J pouch in (1)
Bowel function (fecal incontinence, frequency of bowel movements, rectal urgency, incomplete evacuation) (1)
Operation time/ institutional costs (1)
Postoperative complications (1)
Cancer Colon (1)
Fascin-1 (1)
Actin assembly (1)
Ultrasound (1)
Abdomen (1)
Pelvis (1)
3D (1)
Guided written disclosure protocol (1)
Emotional disclosure (1)
Meaning (1)
Post-Traumatic Growth (1)
Objective perfusion rate (1)
Subjective perfusion rate (1)
Image guided surgery (1)
Fecal incontinence (1)
Bowel Function (1)
Sphincter Preservation Surgery (1)

IsPrivate

False (374)

Model Flag

Non Kinetic (267)

Submitter Keywords

FROG (44)
Not Peer Reviewed (9)
Manuscript Accepted (1)
Immuno-oncology (1)

Classification

bacteria (48)
viruses (8)
fungi (3)

Modification

Not available (2)
4-tetrahydrothiazine-3-carboxylic acid (1)
57.021464 (1)

Study type

Transcription profiling by array (138)
RNA-seq of coding RNA (73)
RNA-seq of coding RNA from single cells (19)
Interventional (18)
Comparative genomic hybridization by array (17)
ChIP-seq (13)
RNA-seq of non coding RNA (13)
Methylation profiling by array (11)
DNA-seq (7)
Unknown experiment type (6)
Other (5)
Observational (5)
ChIP-chip by tiling array (4)
Genotyping by array (4)
ChIP-chip by array (3)
Transcription profiling by SAGE (2)
Transcription profiling by tiling array (2)
Methylation profiling by high throughput sequencing (2)
Cell line - Methylation microarray (1)
Baseline (1)
Human - Single-cell sequencing (1)
Human - High-throughput sequencing (1)
Human - One-color microarray (1)
Animal - High-throughput sequencing (1)
Cell line - High-throughput sequencing (1)
Spatial transcriptomics by high-throughput sequencing (1)
Proteomic profiling by array (1)
Genotyping by high throughput sequencing (1)
RNA-seq of total RNA (1)
Observational patient registry (1)

Release Date

2025 (3508)
2022 (2891)
2023 (2753)
2024 (2590)
2021 (2496)
2020 (1914)
2019 (1493)
2018 (1337)
2017 (1149)
2016 (974)
2015 (861)
2014 (644)
2026 (578)
2013 (549)
2012 (409)
2011 (284)
2010 (260)
2009 (213)
2008 (181)
2007 (132)
2006 (79)
2005 (53)
2004 (35)
2003 (29)
2002 (22)
2001 (18)
2000 (10)
1998 (7)
1999 (6)
1996 (1)

Location

Germany (5)
China (3)
Netherlands (3)
Australia (3)
Spain (2)
Egypt (1)
India (1)
Colombia (1)
Sweden (1)
Italy (1)
Brazil (1)
United States (1)
Switzerland (1)
Japan (1)

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Evaluation of the Efficacy and Mechanism of FMT in Treating Malnutrition Following Gastroduodenal Reconstruction Surgery

Objective: To investigate the clinical efficacy of FMT in treating malnutrition following gastroduodenal reconstruction surgery, alongside changes in the metagenome and metabolome before and after transplantation.

Methods: A total of 20 patients underwent FMT (10 cases each in the...

2026-08-02 | MTBLS13415 | MetaboLights

Phenotypes and Multi—omics Reveal Changes and Molecular Mechanism of Suspension Adaptation of HEK293 Cells Structural Remodelling, Metabolic Reconstruction and Stress Resistance

Human embryonic kidney 293 (HEK293) cells have been successfully adapted from adherent to suspension culture and have been widely applied in both scientific research and the pharmaceutical industry. However, the alterations in cells during the adaptation have not been well described, which raise ...

2025-12-16 | MTBLS13517 | MetaboLights

Reconstruction of signaling networks regulating fungal morphogenesis by transcriptomics

Reconstruction of signaling networks regulating fungal morphogenesis by the expression profiling of wild-type and the temperature sensitive morphological ramosa-1 mutant. Aspergillus niger wildtype versus Ramosa mutant for 1h at 37 under controlled growth condition in 5L bioreactor

ORGANISM(S): Aspergillus niger

2010-05-05 | E-GEOD-17641 | biostudies-arrayexpress

Whole-genome Haplotype Reconstruction using Proximity-ligation and Shotgun Sequencing

Rapid advances in high-throughput DNA sequencing technologies are accelerating the pace of research into personalized medicine. While methods for variant discovery and genotyping from whole genome sequencing (WGS) datasets have been well established, linking variants together into a single haplotype...

ORGANISM(S): Homo sapiens

2013-11-03 | E-GEOD-48592 | biostudies-arrayexpress

Dianthus ancestral sequence reconstruction

Ancestral sequence reconstruction in Dianthus

PRJEB54098 | ENA

Use of Proteomics for Dietary Reconstruction: a Case Study using Animal Teeth from Ancient Mesopotamia

This research examines animal teeth from Early Dynastic (2900-2350 BC) Mesopotamia (Southern Iraq) to assess animal management practices and identify consumption patterns in animal diets. The objective to answer larger questions about food management and environmental resilience in ancient early com...

ORGANISM(S): environmental samples <mammals>

2025-03-24 | PXD050140 | Pride

RNA sequencing of mouse DCs

RNA-Seq data were targeted for de novo assembly and reconstruction of full-length mouse transcripts. Sequencing of RNA taken from unstimulated DCs.

ORGANISM(S): Mus musculus

2011-05-12 | E-GEOD-29209 | biostudies-arrayexpress

Smallbone2013 - Yeast metabolic model with linlog rate law

Kieran Smallbone & Pedro Mendes. Large-Scale Metabolic Models: From Reconstruction to Differential Equations. Industrial Biotechnology 9, 4 (2013). Genome-scale kinetic models of metabolism are important for rational design of the metabolic engineering required for industrial biotechnology applicat...

2024-09-02 | BIOMD0000000471 | BioModels

Smallbone2013 - Yeast metabolic model with modular rate law

2024-09-02 | BIOMD0000000472 | BioModels

Smallbone2013 - Yeast metabolic model with modular rate law, merged with Pritchard 2002

2024-09-02 | BIOMD0000000473 | BioModels