Using Comparative Proteomics to Identify Protein Signatures in Clear Cell Renal Cell Carcinoma
CONCLUSION: Comparative proteomics analysis of ccRCC tissues provided new evidence of SERPINA3 association with ccRCC progression.PMID:37889066 | DOI:10.21873/cgp.20408 (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - October 27, 2023 Category: Genetics & Stem Cells Authors: Juhee Park Eun Hye Lee Hyunchae Sim Ann-Yae Na So Young Choi Jae-Wook Chung Yun-Sok Ha Tae Gyun Kwon Sangkyu Lee Jun Nyung Lee Source Type: research
Filter and Wrapper Stacking Ensemble (FWSE): a robust approach for reliable biomarker discovery in high-dimensional omics data
Brief Bioinform. 2023 Sep 22;24(6):bbad382. doi: 10.1093/bib/bbad382.ABSTRACTSelecting informative features, such as accurate biomarkers for disease diagnosis, prognosis and response to treatment, is an essential task in the field of bioinformatics. Medical data often contain thousands of features and identifying potential biomarkers is challenging due to small number of samples in the data, method dependence and non-reproducibility. This paper proposes a novel ensemble feature selection method, named Filter and Wrapper Stacking Ensemble (FWSE), to identify reproducible biomarkers from high-dimensional omics data. In FWSE,...
Source: Genomics Proteomics ... - October 27, 2023 Category: Genetics & Stem Cells Authors: Sugam Budhraja Maryam Doborjeh Balkaran Singh Samuel Tan Zohreh Doborjeh Edmund Lai Alexander Merkin Jimmy Lee Wilson Goh Nikola Kasabov Source Type: research
Toward Inclusiveness and Thoroughness: A Paradigm Shift from More-ever-omics to Holovivology
Genomics Proteomics Bioinformatics. 2023 Oct 24:S1672-0229(23)00115-8. doi: 10.1016/j.gpb.2023.10.003. Online ahead of print.NO ABSTRACTPMID:37884224 | DOI:10.1016/j.gpb.2023.10.003 (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - October 26, 2023 Category: Genetics & Stem Cells Authors: Jun Yu Source Type: research
Systematic investigation of allelic regulatory activity of schizophrenia-associated common variants
Cell Genom. 2023 Sep 15;3(10):100404. doi: 10.1016/j.xgen.2023.100404. eCollection 2023 Oct 11.ABSTRACTGenome-wide association studies (GWASs) have successfully identified 145 genomic regions that contribute to schizophrenia risk, but linkage disequilibrium makes it challenging to discern causal variants. We performed a massively parallel reporter assay (MPRA) on 5,173 fine-mapped schizophrenia GWAS variants in primary human neural progenitors and identified 439 variants with allelic regulatory effects (MPRA-positive variants). Transcription factor binding had modest predictive power, while fine-map posterior probability, ...
Source: Genomics Proteomics ... - October 23, 2023 Category: Genetics & Stem Cells Authors: Jessica C McAfee Sool Lee Jiseok Lee Jessica L Bell Oleh Krupa Jessica Davis Kimberly Insigne Marielle L Bond Nanxiang Zhao Alan P Boyle Douglas H Phanstiel Michael I Love Jason L Stein W Brad Ruzicka Jose Davila-Velderrain Sriram Kosuri Hyejung Won Source Type: research
Systematic investigation of allelic regulatory activity of schizophrenia-associated common variants
Cell Genom. 2023 Sep 15;3(10):100404. doi: 10.1016/j.xgen.2023.100404. eCollection 2023 Oct 11.ABSTRACTGenome-wide association studies (GWASs) have successfully identified 145 genomic regions that contribute to schizophrenia risk, but linkage disequilibrium makes it challenging to discern causal variants. We performed a massively parallel reporter assay (MPRA) on 5,173 fine-mapped schizophrenia GWAS variants in primary human neural progenitors and identified 439 variants with allelic regulatory effects (MPRA-positive variants). Transcription factor binding had modest predictive power, while fine-map posterior probability, ...
Source: Genomics Proteomics ... - October 23, 2023 Category: Genetics & Stem Cells Authors: Jessica C McAfee Sool Lee Jiseok Lee Jessica L Bell Oleh Krupa Jessica Davis Kimberly Insigne Marielle L Bond Nanxiang Zhao Alan P Boyle Douglas H Phanstiel Michael I Love Jason L Stein W Brad Ruzicka Jose Davila-Velderrain Sriram Kosuri Hyejung Won Source Type: research
Systematic investigation of allelic regulatory activity of schizophrenia-associated common variants
Cell Genom. 2023 Sep 15;3(10):100404. doi: 10.1016/j.xgen.2023.100404. eCollection 2023 Oct 11.ABSTRACTGenome-wide association studies (GWASs) have successfully identified 145 genomic regions that contribute to schizophrenia risk, but linkage disequilibrium makes it challenging to discern causal variants. We performed a massively parallel reporter assay (MPRA) on 5,173 fine-mapped schizophrenia GWAS variants in primary human neural progenitors and identified 439 variants with allelic regulatory effects (MPRA-positive variants). Transcription factor binding had modest predictive power, while fine-map posterior probability, ...
Source: Genomics Proteomics ... - October 23, 2023 Category: Genetics & Stem Cells Authors: Jessica C McAfee Sool Lee Jiseok Lee Jessica L Bell Oleh Krupa Jessica Davis Kimberly Insigne Marielle L Bond Nanxiang Zhao Alan P Boyle Douglas H Phanstiel Michael I Love Jason L Stein W Brad Ruzicka Jose Davila-Velderrain Sriram Kosuri Hyejung Won Source Type: research
Systematic investigation of allelic regulatory activity of schizophrenia-associated common variants
Cell Genom. 2023 Sep 15;3(10):100404. doi: 10.1016/j.xgen.2023.100404. eCollection 2023 Oct 11.ABSTRACTGenome-wide association studies (GWASs) have successfully identified 145 genomic regions that contribute to schizophrenia risk, but linkage disequilibrium makes it challenging to discern causal variants. We performed a massively parallel reporter assay (MPRA) on 5,173 fine-mapped schizophrenia GWAS variants in primary human neural progenitors and identified 439 variants with allelic regulatory effects (MPRA-positive variants). Transcription factor binding had modest predictive power, while fine-map posterior probability, ...
Source: Genomics Proteomics ... - October 23, 2023 Category: Genetics & Stem Cells Authors: Jessica C McAfee Sool Lee Jiseok Lee Jessica L Bell Oleh Krupa Jessica Davis Kimberly Insigne Marielle L Bond Nanxiang Zhao Alan P Boyle Douglas H Phanstiel Michael I Love Jason L Stein W Brad Ruzicka Jose Davila-Velderrain Sriram Kosuri Hyejung Won Source Type: research
A Review of Machine Learning and Algorithmic Methods for Protein Phosphorylation Sites Prediction
Genomics Proteomics Bioinformatics. 2023 Oct 18:S1672-0229(23)00110-9. doi: 10.1016/j.gpb.2023.03.007. Online ahead of print.ABSTRACTPost-translational modifications (PTMs) have key roles in extending the functional diversity of proteins and as a result, regulating diverse cellular processes in prokaryotic and eukaryotic organisms. Phosphorylation modification is a vital PTM that occurs in most proteins and plays a significant role in many biological processes. Disorders in the phosphorylation process lead to multiple diseases including neurological disorders and cancers. The purpose of this review paper is to organize thi...
Source: Genomics Proteomics ... - October 20, 2023 Category: Genetics & Stem Cells Authors: Farzaneh Esmaili Mahdi Pourmirzaei Shahin Ramazi Seyedehsamaneh Shojaeilangari Elham Yavari Source Type: research
RNA Modification and Epitranscriptomics
Genomics Proteomics Bioinformatics. 2023 Oct 18:S1672-0229(23)00111-0. doi: 10.1016/j.gpb.2023.10.002. Online ahead of print.NO ABSTRACTPMID:37863386 | DOI:10.1016/j.gpb.2023.10.002 (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - October 20, 2023 Category: Genetics & Stem Cells Authors: Chengqi Yi Jianhua Yang Source Type: research
A Review of Machine Learning and Algorithmic Methods for Protein Phosphorylation Sites Prediction
Genomics Proteomics Bioinformatics. 2023 Oct 18:S1672-0229(23)00110-9. doi: 10.1016/j.gpb.2023.03.007. Online ahead of print.ABSTRACTPost-translational modifications (PTMs) have key roles in extending the functional diversity of proteins and as a result, regulating diverse cellular processes in prokaryotic and eukaryotic organisms. Phosphorylation modification is a vital PTM that occurs in most proteins and plays a significant role in many biological processes. Disorders in the phosphorylation process lead to multiple diseases including neurological disorders and cancers. The purpose of this review paper is to organize thi...
Source: Genomics Proteomics ... - October 20, 2023 Category: Genetics & Stem Cells Authors: Farzaneh Esmaili Mahdi Pourmirzaei Shahin Ramazi Seyedehsamaneh Shojaeilangari Elham Yavari Source Type: research
RNA Modification and Epitranscriptomics
Genomics Proteomics Bioinformatics. 2023 Oct 18:S1672-0229(23)00111-0. doi: 10.1016/j.gpb.2023.10.002. Online ahead of print.NO ABSTRACTPMID:37863386 | DOI:10.1016/j.gpb.2023.10.002 (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - October 20, 2023 Category: Genetics & Stem Cells Authors: Chengqi Yi Jianhua Yang Source Type: research
High-Throughput Prediction and Design of Novel Conopeptides for Biomedical Research and Development
Biodes Res. 2022 Nov 7;2022:9895270. doi: 10.34133/2022/9895270. eCollection 2022.ABSTRACTCone snail venoms have been considered a valuable treasure for international scientists and businessmen, mainly due to their pharmacological applications in development of marine drugs for treatment of various human diseases. To date, around 800 Conus species are recorded, and each of them produces over 1,000 venom peptides (termed as conopeptides or conotoxins). This reflects the high diversity and complexity of cone snails, although most of their venoms are still uncharacterized. Advanced multiomics (such as genomics, transcriptomic...
Source: Genomics Proteomics ... - October 18, 2023 Category: Genetics & Stem Cells Authors: Bingmiao Gao Yu Huang Chao Peng Bo Lin Yanling Liao Chao Bian Jiaan Yang Qiong Shi Source Type: research
High-Throughput Prediction and Design of Novel Conopeptides for Biomedical Research and Development
Biodes Res. 2022 Nov 7;2022:9895270. doi: 10.34133/2022/9895270. eCollection 2022.ABSTRACTCone snail venoms have been considered a valuable treasure for international scientists and businessmen, mainly due to their pharmacological applications in development of marine drugs for treatment of various human diseases. To date, around 800 Conus species are recorded, and each of them produces over 1,000 venom peptides (termed as conopeptides or conotoxins). This reflects the high diversity and complexity of cone snails, although most of their venoms are still uncharacterized. Advanced multiomics (such as genomics, transcriptomic...
Source: Genomics Proteomics ... - October 18, 2023 Category: Genetics & Stem Cells Authors: Bingmiao Gao Yu Huang Chao Peng Bo Lin Yanling Liao Chao Bian Jiaan Yang Qiong Shi Source Type: research
High-Throughput Prediction and Design of Novel Conopeptides for Biomedical Research and Development
Biodes Res. 2022 Nov 7;2022:9895270. doi: 10.34133/2022/9895270. eCollection 2022.ABSTRACTCone snail venoms have been considered a valuable treasure for international scientists and businessmen, mainly due to their pharmacological applications in development of marine drugs for treatment of various human diseases. To date, around 800 Conus species are recorded, and each of them produces over 1,000 venom peptides (termed as conopeptides or conotoxins). This reflects the high diversity and complexity of cone snails, although most of their venoms are still uncharacterized. Advanced multiomics (such as genomics, transcriptomic...
Source: Genomics Proteomics ... - October 18, 2023 Category: Genetics & Stem Cells Authors: Bingmiao Gao Yu Huang Chao Peng Bo Lin Yanling Liao Chao Bian Jiaan Yang Qiong Shi Source Type: research
GERONIMO: A tool for systematic retrieval of structural RNAs in a broad evolutionary context
CONCLUSION: GERONIMO, built using Snakemake, has undergone extensive testing on hundreds of genomes, establishing itself as a valuable tool in the identification of ncRNA homologs across diverse taxonomic groups. Consequently, GERONIMO facilitates the investigation of the evolutionary patterns of functionally significant ncRNA players, whose understanding has previously been limited to individual organisms and close relatives.PMID:37848616 | PMC:PMC10580375 | DOI:10.1093/gigascience/giad080 (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - October 17, 2023 Category: Genetics & Stem Cells Authors: Agata M Kilar Petr Fajkus Ji ří Fajkus Source Type: research
