A5078578121- Machine Learning in Bioinformatics
- Genomics and Phylogenetic Studies
- Renal cell carcinoma treatment
- Breast Cancer Treatment Studies
- Lung Cancer Treatments and Mutations
- Ferroptosis and cancer prognosis
- Cancer Genomics and Diagnostics
- Ion channel regulation and function
- RNA modifications and cancer
- Renin-Angiotensin System Studies
- Erythropoietin and Anemia Treatment
- Ubiquitin and proteasome pathways
- Colorectal Cancer Treatments and Studies
- AI in cancer detection
- Advanced Proteomics Techniques and Applications
- Immune cells in cancer
- HER2/EGFR in Cancer Research
- Protein Structure and Dynamics
- Inflammatory Biomarkers in Disease Prognosis
- Cancer, Lipids, and Metabolism
- Cancer Cells and Metastasis
- Ion Transport and Channel Regulation
- Cancer Treatment and Pharmacology
- Peptidase Inhibition and Analysis
- Chemokine receptors and signaling
Tianjin Medical University Cancer Institute and Hospital
2013-2025
Tianjin Medical University
2013-2023
National Clinical Research
2022
Tianjin Medical University General Hospital
2019
Moffitt Cancer Center
2018
Tianjin Municipal Science and Technology Commission
2012
China Agricultural University
2007-2008
University of Minnesota
2007-2008
Abstract Sequence-based analysis and prediction are fundamental bioinformatic tasks that facilitate understanding of the sequence(-structure)-function paradigm for DNAs, RNAs proteins. Rapid accumulation sequences requires equally pervasive development new predictive models, which depends on availability effective tools support these efforts. We introduce iLearnPlus, first machine-learning platform with graphical- web-based interfaces construction pipelines predictions using nucleic acid...
As one of the most important reversible protein post-translation modifications, ubiquitination has been reported to be involved in lots biological processes and closely implicated with various diseases. To fully decipher molecular mechanisms ubiquitination-related processes, an initial but crucial step is recognition ubiquitylated substrates corresponding sites. Here, a new bioinformatics tool named CKSAAP_UbSite was developed predict sites from sequences. With assistance Support Vector...
Abstract Background As one of the most common protein post-translational modifications, glycosylation is involved in a variety important biological processes. Computational identification sites sequences becomes increasingly post-genomic era. A new encoding scheme was employed to improve prediction mucin-type O-glycosylation mammalian proteins. Results bioinformatics tool, CKSAAP_OGlySite, developed predict serine/threonine (S/T) Using composition k -spaced amino acid pairs (CKSAAP) based...
HER2 breast cancer (BC) remains a significant problem in patients with locally advanced or metastatic BC. We investigated the relationship between T helper 1 (Th1) immune response and proteasomal degradation pathway (PDP), HER2-sensitive -resistant cells. overexpression is partially maintained because E3 ubiquitin ligase Cullin5 (CUL5), which degrades HER2, frequently mutated underexpressed, while client-protective co-chaperones cell division cycle 37 (Cdc37) heat shock protein 90 (Hsp90)...
Sumoylation is one of the most essential mechanisms reversible protein post-translational modifications and a crucial biochemical process in regulation variety important biological functions. also closely involved various human diseases. The accurate computational identification sumoylation sites sequences aids experimental design mechanistic research cellular biology. In this study, we introduced amino acid hydrophobicity as parameter into traditional binary encoding scheme developed novel...
Abstract Lysine crotonylation (Kcr) is a newly discovered type of protein post-translational modification and has been reported to be involved in various pathophysiological processes. High-resolution mass spectrometry the primary approach for identification Kcr sites. However, experimental approaches identifying sites are often time-consuming expensive when compared with computational approaches. To date, several predictors site prediction have developed, most which capable predicting on...
Abstract Background Metastasis of breast cancer grows from the local invasion to distant colonization. Blocking step would be promising for treatment. Our present study demonstrated AQP1 was a crucial target in invasion. Methods Mass spectrometry combined with bioinformatics analysis used identify associated proteins ANXA2 and Rab1b. Co-immunoprecipitation, immunofluorescence assays cell functional experiments were carried out define relationship among AQP1, Rab1b their re-localization...
To investigate the role of neurotensin (NTS) in hepatocellular carcinoma (HCC) sub- grouping and clinical pathological significance activation NTS/IL-8 pathway HCC.The genome-wide gene expression profiling were conducted 10 pairs cancer tissues corresponding normal adjacent samples using Affymetrix GeneChip® Human Genome U133 Plus 2.0 microarray to screen differentially expressing genes enrich dysfunctional activated pathways among different HCC subgroups. The levels NTS protein multiple...
Abstract Background Non-small cell cancer (NSCLC) patients with concomitant epidermal growth factor receptor (EGFR) and TP53 mutations have a poor prognosis the treatment of tyrosine kinase inhibitors (TKIs), may benefit from combination regimen preferentially. The present study aims to compare benefits EGFR-TKIs its antiangiogenic drugs or chemotherapy in NSCLC harboring EGFR co-mutation real-life setting. Methods This retrospective analysis included 124 advanced having mutations, who...
With the advance of modern molecular biology it has become increasingly clear that few cellular processes are unaffected by protein phosphorylation. Therefore, computational identification phosphorylation sites is very helpful to accelerate functional understanding huge available sequences obtained from genomic and proteomic studies. Using a genetic algorithm integrated neural network (GANN), new bioinformatics method named GANNPhos been developed predict in proteins. Aided optimize weight...
The protein databases contain a huge number of function unknown proteins, including many proteins with newly determined 3D structures resulted from the Structural Genomics Projects. To accelerate experiment-based assignment function, de novo prediction functional sites, like active sites in enzymes, becomes increasingly important. Here, we attempted to improve catalytic residues enzyme by seeking and refining different encodings (i.e. residue properties) as well employing new machine...
Abstract Background Concomitant TP53 mutation results in poor prognosis patients with epidermal growth factor receptor (EGFR)-mutated non-small-cell lung cancer (NSCLC) treated tyrosine kinase inhibitors (TKIs) and may preferentially benefit from a combination regimen. The present study aims to compare the benefits of EGFR-TKIs its antiangiogenic drugs or chemotherapy NSCLC harboring EGFR co-mutation real-life setting. Methods This retrospective analysis included 124 advanced having...
Gastric adenocarcinoma with enteroblastic differentiation (GAED) is a rare subset of alpha-fetoprotein (AFP)-producing carcinomas poor prognosis. However, the molecular features associated malignant potential GEAD remain partially elucidated.In this study, relationship between clinicopathological parameters and aggressive biological behaviour was analysed in 37 patients GAED. The results showed that GAED tended to infiltrate deep layer gastric wall possessed more frequent vascular invasion...
Upstream stimulatory factors (USFs) are members of the basic helix-loop-helix leucine zipper transcription factor family, including USF1, USF2, and USF3. The first two have been well studied compared to third member, USF3, which has received scarce attention in cancer research date. Despite a recently reported association its alteration with thyroid carcinoma, expression not previously analyzed.We comprehensively analyzed differential levels USFs expression, genomic alteration, DNA...
Objective: The main reasons for the poor prognoses of pancreatic adenocarcinoma (PA) patients are rapid early-stage progression, advanced stage metastasis, and chemotherapy resistance. Identification novel diagnostic prognostic biomarkers PA is therefore urgently needed. Methods: Three mRNA microarray datasets were obtained from Gene Expression Omnibus database to select differentially expressed genes (DEGs). Ontology (GO) Kyoto Encyclopedia Genes Genomes pathway enrichment analyses hub...
Objective: To identify CT imaging biomarkers based on radiomic features for predicting brain metastases (BM) in patients with ALK-rearranged non-small cell lung cancer (NSCLC). Methods: NSCLC pathologically confirmed ALK rearrangement from January 2014 to December 2020 our hospital were enrolled retrospectively this study. Finally, 77 included according the inclusion and exclusion criteria. Patients divided into two groups: BM+ those who diagnosed BM at baseline examination (n = 16) or...
Background Cytokines are involved in many inflammatory diseases and thus play an important role tumor immune regulation. In recent years, researchers have found that breast cancer is not only related to genetic environmental factors, but also the chronic inflammation immunity. However, correlation between serum cytokines blood tests indicators remain unclear. Methods A total of 84 samples clinicopathological data patients from Tianjin Cancer Institute & Hospital, Medical University,...
ER-negative breast cancer includes most aggressive subtypes of such as triple negative (TN) cancer. Excluded from hormonal and targeted therapies effectively used for other cancer, standard chemotherapy is one the primary treatment options these patients. However, ER− patients have shown highly heterogeneous responses to different chemotherapies, it has been difficult select beneficial treatments them. In this study, we simultaneously developed single drug biomarker models four agents:...