Molecular Omics

Article	Citations
Data-independent acquisition mass spectrometry (DIA-MS) for proteomic applications in oncology	123
Multi-omics data integration considerations and study design for biological systems and disease	104
Metabolomics: small molecules that matter more	85
Metabolomics in infectious diseases and drug discovery	76
Context contribution to the intermolecular recognition of human ACE2-derived peptides by SARS-CoV-2 spike protein: implications for improving the peptide affinity but not altering the peptide specific	43
Data-independent acquisition-based proteome and phosphoproteome profiling across six melanoma cell lines reveals determinants of proteotypes	28
The robust NMR toolbox for metabolomics	24
Mechanistic models of microbial community metabolism	22
Cerebrospinal fluid lipidomics for biomarkers of Alzheimer's disease	22
Plant proteomic research for improvement of food crops under stresses: a review	22
A novel multi-omics-based highly accurate prediction of symptoms, comorbid conditions, and possible long-term complications of COVID-19	21
Determination of hypoxia signature to predict prognosis and the tumor immune microenvironment in melanoma	21
Glycomics & Glycoproteomics: From Analytics to Function	21
The state of the art in plant lipidomics	21
Applications of lipidomics in marine organisms: progress, challenges and future perspectives	19
Extensive heterogeneity of glycopeptides in plasma revealed by deep glycoproteomic analysis using size-exclusion chromatography	19
Tissue metabolic profiling reveals major metabolic alteration in colorectal cancer	17
The pan-cancer analysis of the two types of uterine cancer uncovered clinical and prognostic associations with m6A RNA methylation regulators	16
Integrated multi-omics analyses of microbial communities: a review of the current state and future directions	15
Transcriptomic sequencing reveals the response of Dunaliella salina to copper stress via the increased photosynthesis and carbon mechanism	15
Advances in stable isotope labeling: dynamic labeling for spatial and temporal proteomic analysis	14
4D-quantitative proteomics signature of asthenozoospermia and identification of extracellular matrix protein 1 as a novel biomarker for sperm motility	14
Food authentication: truffle species classification by non-targeted lipidomics analyses using mass spectrometry assisted by ion mobility separation	14
Laser capture microdissection-capillary zone electrophoresis-tandem mass spectrometry (LCM-CZE-MS/MS) for spatially resolved top-down proteomics: a pilot study of zebrafish brain	14
Proximity-dependent biotin identification (BioID) reveals a dynamic LSD1–CoREST interactome during embryonic stem cell differentiation	14

Focus on the molecular mechanisms of cisplatin resistance based on multi-omics approaches	13
A proteomic view on lysosomes	13
N-Linked glycosylation profiles of therapeutic induced senescent (TIS) triple negative breast cancer cells (TNBC) and their extracellular vesicle (EV) progeny	13
Iron-meditated fungal starvation by lupine rhizosphere-associated and extremotolerant Streptomyces sp. S29 desferrioxamine production	13
Deciphering O-glycoprotease substrate preferences with O-Pair Search	13
BGMSDDA: a bipartite graph diffusion algorithm with multiple similarity integration for drug–disease association prediction	13
Proteomics in idiopathic pulmonary fibrosis: the quest for biomarkers	13
Targeting coenzyme Q10 synthesis overcomes bortezomib resistance in multiple myeloma	12
A 9-gene biomarker panel identifies bacterial coinfections in culture-negative COVID-19 cases	12
Cleavable linkers and their application in MS-based target identification	12
Enhanced detection and annotation of small molecules in metabolomics using molecular-network-oriented parameter optimization	11
Macrophages secrete murinoglobulin-1 and galectin-3 to regulate neutrophil degranulation after myocardial infarction	11
Multi-omics data integration reveals correlated regulatory features of triple negative breast cancer	11
NMR metabolomic and microarray-based transcriptomic data integration identifies unique molecular signatures of hypersensitivity pneumonitis	11
Computational approaches leveraging integrated connections of multi-omic data toward clinical applications	11
Omics technologies for high-throughput-screening of cell–biomaterial interactions	10
Metabolomics study reveals the alteration of fatty acid oxidation in the hearts of diabetic mice by empagliflozin	10
NMR-based plasma metabolomics of adult B-cell acute lymphoblastic leukemia	10
Comprehensive comparison of sample preparation workflows for proteomics	9
Metabolomics reveals the impact of the saturation of dietary lipids on the aging and longevity of C. elegans	9
Transcriptome features of striated muscle aging and predictability of protein level changes	9
Integrated proteomic and metabolomic analyses of the mitochondrial neurodegenerative disease MELAS	9
Metabolomic analysis of honey bee (Apis mellifera L.) response to glyphosate exposure	9
Plasma extracellular vesicles microRNA-208b-3p and microRNA-143-3p as novel biomarkers for sudden cardiac death prediction in acute coronary syndrome	8
Comparative evaluation of long non-coding RNA-based biomarkers in the urinary sediment and urinary exosomes for non-invasive diagnosis of bladder cancer	8
Long-read 16S-seq reveals nasopharynx microbial dysbiosis and enrichment of Mycobacterium and Mycoplasma in COVID-19 patients: a potential source of co-infection	8
Integrative miRNA–mRNA functional analysis identifies miR-182 as a potential prognostic biomarker in breast cancer	8
Metabolomics analysis provides new insights into the medicinal value of flavonoids in tobacco leaves	8
Graphene oxide links alterations of anti-viral signaling pathways with lipid metabolism via suppressing TLR3 in vascular smooth muscle cells	8
Interrogating the transcriptome with metabolically incorporated ribonucleosides	8
Differential N-glycosylation profiling of formalin-fixed paraffin-embedded (FFPE) invasive ductal carcinoma tissues using MALDI-TOF-MS	8
Quantitative proteomic analysis of MDCK cell adhesion	8
Multi-omics data integration approaches for precision oncology	7
Integrated proteomics and phosphoproteomics reveal perturbed regulative pathways in pancreatic ductal adenocarcinoma	7
Delineating toxicity mechanisms associated with MRI contrast enhancement through a multidimensional toxicogenomic profiling of gadolinium	7
Cleaning the molecular machinery of cells via proteostasis, proteolysis and endocytosis selectively, effectively, and precisely: intracellular self-defense and cellular perturbations	7
Butyrate promotes C2C12 myoblast proliferation by activating ERK/MAPK pathway	7
The miR-4732-5p/XPR1 axis suppresses the invasion, metastasis, and epithelial–mesenchymal transition of lung adenocarcinoma via the PI3K/Akt/GSK3β/Snail pathway	7
iDHS-DASTS: identifying DNase I hypersensitive sites based on LASSO and stacking learning	7
A drug discovery approach based on comparative transcriptomics between two toxin-secreting marine annelids:Glycera albaandHediste diversicolor	7
MS-based proteomics for comprehensive investigation of proteinO-GlcNAcylation	7
Nuciferine attenuates acute ischemic stroke in a rat model: a metabolomic approach for the mechanistic study	7
An NMR-based metabolomics study on sea anemones Exaiptasia diaphana (Rapp, 1829) with atrazine exposure	7
Phosphoproteomic analysis reveals the effects of sleep deprivation on the hippocampus in mice	7
Advancements in automation for plasma proteomics sample preparation	7
The application of omics techniques to evaluate the effects of Tanshinone IIA on dextran sodium sulfate induced ulcerative colitis	6
Differential profiles of HDAC1 substrates and associated proteins in breast cancer cells revealed by trapping	6
Identification of stem cells from large cell populations with topological scoring	6
Lnc-TMEM132D-AS1 as a potential therapeutic target for acquired resistance to osimertinib in non-small-cell lung cancer	6
Microarray investigation of glycan remodeling during macrophage polarization reveals α2,6 sialic acid as an anti-inflammatory indicator	6

Investigation of cattle plasma proteome in response to pain and inflammation using next generation proteomics technique, SWATH-MS	6
β-Adrenoceptor regulation of metabolism in U937 derived macrophages	6
Time-dependent re-organization of biological processes by the analysis of the dynamic transcriptional response of yeast cells to doxorubicin	6
Early-stage responses toPlasmodiophora brassicaeat the transcriptome and metabolome levels in clubroot resistant and susceptible oilseedBrassica napus	6
Identification of novel biomarkers for intracerebral hemorrhagevialong noncoding RNA-associated competing endogenous RNA network	6
Candidate kinases for adipogenesis and osteoblastogenesis from human bone marrow mesenchymal stem cells	6
Development of computational models using omics data for the identification of effective cancer metabolic biomarkers	6
Proteomic and metabolomic profiling of acute and chronic stress events associated with military exercises	6
Defining atherosclerotic plaque biology by mass spectrometry-based omics approaches	5
Systematic investigation of mouse models of Parkinson's disease by transcriptome mapping on a brain-specific genome-scale metabolic network	5
Analysis of pancreatic extracellular matrix protein post-translational modifications via electrostatic repulsion-hydrophilic interaction chromatography coupled with mass spectrometry	5
Prediction of cancer dependencies from expression data using deep learning	5
N-Glycosylation in isolated rat nerve terminals	5
Rbm20 ablation is associated with changes in the expression of titin-interacting and metabolic proteins	5
Proteomic changes associated with racial background and sepsis survival outcomes	5
Activation of KLF6 by titanate nanofibers and regulatory roles of KLF6 on ATF3 in the endothelial monolayer and mouse aortas	5
Propionate as the preferred carbon source to produce 3-indoleacetic acid inB. subtilis: comparative flux analysis using five carbon sources	5
A comparative lipidomic study of the human placenta from women with or without gestational diabetes mellitus	5
Spatial proteomic alterations detected via MALDI-MS imaging implicate neuronal loss in a Huntington's disease mouse (YAC128) brain	5
The phosphoproteome of rice leaves responds to water and nitrogen supply	5
Dauricine inhibits human pancreatic carcinoma cell proliferation through regulating miRNAs	5
Comprehensive expression profiles of CircRNAs, LncRNAs, and mRNAs in PBMCs from patients with the ossification of the posterior longitudinal ligament	5
In silico characterisation of the complete Ly6 protein family in Fasciola gigantica supported through transcriptomics of the newly-excysted juveniles	5
LC-MS-based metabolomics reveals the in vivo effect of Shegan Mahuang Decoction in an OVA-induced rat model of airway hyperresponsiveness	5
Multi-omic characterisation ofStreptomyces hygroscopicusNRRL 30439: detailed assessment of its secondary metabolic potential	5
Multi-omics insights into the interplay between gut microbiota and colorectal cancer in the “microworld” age	4
Multi-omic analysis of host-microbial interactions central to the gut-brain axis	4
Pre-analytical aspects in metabolomics of human biofluids – sample collection, handling, transport, and storage	4
Circular RNA profiles of osteoarthritic synovium	4
A transcriptome based approach to predict candidate drug targets and drugs for Parkinson's disease using an in vitro 6-OHDA model	4
Single cell proteomics analysis of drug response shows its potential as a drug discovery platform	4
Deciphering the architecture and interactome of hnRNP proteins and enigmRBPs	4
Proteome-wide analysis of protein alterations in response to aristolochic acids in rat kidney and liver tissues	4
Biomarker identification by reversing the learning mechanism of an autoencoder and recursive feature elimination	4
Screening and identification of key microRNAs and regulatory pathways associated with the renal fibrosis process	4
The complete change in bile acids and steroids in systematic metabolomics applied to the intrahepatic cholestasis of pregnancy	4
Multi-omic profiling of histone variant H3.3 lysine 27 methylation reveals a distinct role from canonical H3 in stem cell differentiation	4
Profiling protein targets of cellular toxicant exposure	4
The effect of krill oil on longevity and locomotion: a pilot study	4
Targeted metabolomics reveals dynamic portrayal of amino acids and derivatives in triple-negative breast cancer cells and culture media	4
Mass spectrometry-based proteomics in neurodegenerative lysosomal storage disorders	4
A comparative performance evaluation of imputation methods in spatially resolved transcriptomics data	4
Serum metabolic profiles of septic shock patients based upon co-morbidities and other underlying conditions	4
Identification of prognostic factors in classic Hodgkin lymphoma by integrating whole slide imaging and next generation sequencing	4
The effect of key DNA methylation in different regions on gene expression in hepatocellular carcinoma	4
KDM4B, a potential prognostic biomarker revealed by large-scale public databases and clinical samples in uterine corpus endometrial carcinoma	4
Characterization of methionine dependence in melanoma cells	3
Comparison between instrumental variable and mediation-based methods for reconstructing causal gene networks in yeast	3
Models for measuring metabolic chemical changes in the metastasis of high grade serous ovarian cancer: fallopian tube, ovary, and omentum	3
Meta-analyses of host metagenomes from colorectal cancer patients reveal strong relationship between colorectal cancer-associated species	3
A knowledge graph representation learning approach to predict novel kinase–substrate interactions	3
Maternal serum lipidomics identifies lysophosphatidic acid as a predictor of small for gestational age neonates	3
Proteomic analysis reveals mechanisms underlying increased efficacy of bleomycin by photochemical internalization in bladder cancer cells	3
Application of fluorescent turn-on aptamers in RNA studies	3
Gender-specific association of oxidative stress and immune response in septic shock mortality using NMR-based metabolomics	3
Integrated proteomic and metabolomic analysis of plasma reveals regulatory pathways and key elements in thyroid cancer	3
Intestinal microbiome and metabolome analyses reveal metabolic disorders in the early stage of renal transplantation	3
Th1, Th2 and Th17 inflammatory pathways synergistically predict cardiometabolic protein expression in serum of COVID-19 patients	3
Transcriptional profiling of the chick retina identifies down-regulation of VIP and UTS2B genes during early lens-induced myopia	3
Integration of fluxome and transcriptome data in Saccharomyces cerevisiae offers unique features of doxorubicin and imatinib	3
DeepSIBA: chemical structure-based inference of biological alterations using deep learning	3
Comprehensive expression profiles of mRNAs, lncRNAs and miRNAs in Kashin-Beck disease identified by RNA-sequencing	3
The relationship between bacterial outer membrane vesicles and halophilic adaptation	3
The alteration of urinary metabolomics profiles in Kashin–Beck disease in a three consecutive year study	3
Lamiophlomis rotata attenuates rheumatoid arthritis by regulating sphingolipid and steroid hormone metabolism	3
Transcriptomic landscape of sodium butyrate-induced growth inhibition of human colorectal cancer organoids	3
A multi-omics study of the anti-cancer effect of a ferulic acid derivative FA-30	3
Role of identified proteins in the proteome profiles of CDK4/6 inhibitor-resistant breast cancer cell lines	3
An integrative chemometric approach and correlative metabolite networking of LC-MS and 1H NMR based urine metabolomics for radiation signatures	3
IVS I-5 (G > C) is associated with changes to the RBC membrane lipidome in response to hydroxyurea treatment in β-thalassemia patients	3
Analysis of the transcriptome and metabolome of pancreatic spheroids derived from human induced pluripotent stem cells and matured in an organ-on-a-chip	3
Genome-scale mutant fitness reveals versatilec-type cytochromes inShewanella oneidensisMR-1	2
Crosslinking mass spectrometry unveils novel interactions and structural distinctions in the model green alga Chlamydomonas reinhardtii	2
Label-free serum proteomics for the identification of the putative biomarkers of postoperative pain in patients with gastric cancer	2
Integrative analysis of cancer dependency data and comprehensive phosphoproteomics data revealed the EPHA2-PARD3 axis as a cancer vulnerability in KRAS-mutant colorectal cancer	2
Serum proteomic analysis of differentially expressed proteins and pathways involved in the mechanism of endemic osteoarthritis	2
FGF-2 induces a failure of cell cycle progression in cells harboring amplified K-Ras, revealing new insights into oncogene-induced senescence	2
An experimental design to extract more information from MS-based histone studies	2
Genome scale metabolic model driven strategy to delineate host response to Mycobacterium tuberculosis infection	2
Label-free quantitation of the changes in salivary proteome associated with the chronic consumption of the betel nut (Areca catechu)	2

Analyses of pseudoexfoliation aqueous humor lipidome	2
Biochemical and metabolic signatures are fundamental to drought adaptation in PGPR Enterobacter bugandensis WRS7	2
Geographical origin traceability of rice using a FTIR-based metabolomics approach	2
Network modeling suggests HIV infection phenocopies PI3K-AKT pathway mutations to enhance HPV-associated cervical cancer	2
Proteomic analysis of Listeria monocytogenes exposed to free and nanostructured antimicrobial lipopeptides	2
Functional response of microbial communities in lab-controlled oil-contaminated marine sediment	2
Production of mannosylerythritol lipids: biosynthesis, multi-omics approaches, and commercial exploitation	2
Metabolite variations in the sera of HIV+ patients after an oral administration of effervescent glutamine and in comparison to non-HIV individuals by NMR	2
Systems-level analysis of transcriptome reorganization during liver regeneration	2
Pancreatic cancer environment: from patient-derived models to single-cell omics	2
Pre-illness data reveals differences in multiple metabolites and metabolic pathways in those who do and do not recover from infectious mononucleosis	2
Integrative analysis of small non-coding RNAs predicts a piRNA/miRNA-CCND1/BRAF/HRH1/ATXN3 regulatory circuit that drives oncogenesis in glioblastoma	2
Plasma metabolomic signatures from patients following high-dose total body irradiation	2
Acute exercise dynamically modulates the hepatic mitochondrial proteome	2
Nontargeted metabolomics reveals differences in the metabolite profiling among methicillin-resistant and methicillin-susceptible Staphylococcus aureus in response to antibiotics	2
Lipid profile variability in children at different ages measured in dried blood spots	2
TALKIEN: crossTALK IntEraction Network. A web-based tool for deciphering molecular communication through ligand–receptor interactions	2
Genetic variant effect prediction by supervised nonnegative matrix tri-factorization	2
Antibiotic-induced gut microbiota dysbiosis altered host metabolism	2
Unraveling the role of intra-cellular metabolites in the lactic acid production by novel Bacillus amyloliquefaciens using sugarcane molasses as a substratum	2
HOPMCLDA: predicting lncRNA–disease associations based on high-order proximity and matrix completion	2
An integrated network analysis approach to identify potential key genes, transcription factors, and microRNAs regulating human hematopoietic stem cell aging	2
PARP-1 inhibitor alleviates liver lipid accumulation of atherosclerosis via modulating bile acid metabolism and gut microbes	2
The dynamic inflammatory profile of pregnancy can be monitored using a novel lipid-based mass spectrometry technique	2
Genetic and structural analyses of ssRNA viruses pave the way for the discovery of novel antiviral pharmacological targets	2
A Q-marker screening strategy based on ADME studies and systems biology for Chinese herbal medicine, taking Qianghuo Shengshi decoction in treating rheumatoid arthritis as an example	1
ITIH5, as a predictor of prognosis and immunotherapy response for P53-like bladder cancer, is related to cell proliferation and invasion	1
The RNA cargo of Myxococcus outer membrane vesicles	1
Computational identification of human ubiquitination sites using convolutional and recurrent neural networks	1
Genome-scale metabolic models in translational medicine: the current status and potential of machine learning in improving the effectiveness of the models	1
Comprehensive analysis of epigenetic signatures of human transcription control	1
Metabolic responses in the cortex and hippocampus induced by Il-15rα mutation	1
Contents list	1
A metabolomic snapshot through NMR revealed differences in phase transition during the induction of reproduction in Ulva ohnoi (Chlorophyta)	1
Brain-wide transcriptome-based metabolic alterations in Parkinson's disease: human inter-region and human-experimental model correlations	1
Association of lipid metabolism-related metabolites with overweight/obesity based on the FTO rs1421085	1
Temporal gene expression profiling of maslinic acid-treated Raji cells	1
Open-tubular trap columns: towards simple and robust liquid chromatography separations for single-cell proteomics	1
Metabolomic approaches to dissect dysregulated metabolism in the progression of pre-diabetes to T2DM	1
What transcriptomics and proteomics can tell us about a high borate perturbed boron tolerant Bacilli strain	1
Metabolomics assessment of vitamin D impact in Pam3CSK4 stimulation	1
Lipopolysaccharide and statin-mediated immune-responsive protein networks revealed in macrophages through affinity purification spacer-arm controlled cross-linking (AP-SPACC) proteomics	1
Untargeted metabolomics reveals altered branch chain amino acids, glucose and fat metabolism contributing to coronary artery disease among Indian diabetic patients	1
Anti-inflammatory effects of myristic acid mediated by the NF-κB pathway in lipopolysaccharide-induced BV-2 microglial cells	1
Proteome- and metabolome-level changes during early stages of clubroot infection in Brassica napus canola	1
Correction: The pan-cancer analysis of the two types of uterine cancer uncovered clinical and prognostic associations with m6A RNA methylation regulators	1
The mechanism of chronic unpredictable mild stress induced high blood pressure in rats: a proteomic and targeted metabolomic analysis	1
Identification of core miRNAs and regulatory pathways in breast cancer by integrated bioinformatics analysis	1
Re-mining serum proteomics data reveals extensive post-translational modifications upon Zika and dengue infection	1
Metabolomic analysis reveals stress tolerance mechanisms in common bean (Phaseolus vulgaris L.) related to treatment with a biostimulant obtained from Corynebacterium glutamicum	1
TarpiD, a database of putative and validated targets of piRNAs	1
Effect of short-term use of FFP2 (N95) masks on the salivary metabolome of young healthy volunteers: a pilot study	1
Untargeted metabolomics and phenotype data indicate the therapeutic and prophylactic potential of Lysimachia candida Lindl. towards high-fat high-fructose-induced metabolic syndrome in rats	1
Examination of oestrus-dependent alterations of bovine cervico-vaginal mucus glycosylation for potential as optimum fertilisation indicators	1
The plasma phospholipidome of the bottlenose dolphin (Tursiops truncatus) is modulated by both sex and developmental stage	1
Critical assessment of genome-scale metabolic models of Arabidopsis thaliana	1
A blood-based multi-omic landscape for the molecular characterization of kidney stone disease	1
Generation of β-like cell subtypes from differentiated human induced pluripotent stem cells in 3D spheroids	1
Identification of epigenetic regulators in the estrogen signaling pathwayviasiRNA screening	1
Correction: Examination of oestrus-dependent alterations of bovine cervico-vaginal mucus glycosylation for potential as optimum fertilisation indicators	1